NAMD-L: By Date

NAMD

NamdWiki

NAMD-L: By Date

By Date

2670 messages sorted by: [ author ] [ thread ] [ subject ] [ attachment ]
About this archive

Starting: Fri Jan 02 2015 - 23:19:01 CST
Ending: Tue Dec 27 2016 - 20:48:03 CST

Re: Query regarding colvar distanceZ Peter Mawanga (Tue Dec 27 2016 - 20:47:16 CST)
Re: Query regarding colvar distanceZ Vermaas, Joshua (Tue Dec 27 2016 - 19:14:06 CST)
Re: Query regarding colvar distanceZ Peter Mawanga (Tue Dec 27 2016 - 19:07:07 CST)
Re: Query regarding colvar distanceZ Giacomo Fiorin (Tue Dec 27 2016 - 13:20:42 CST)
NAMD parallelisation / patch grid P.-L. Chau (Tue Dec 27 2016 - 04:37:15 CST)
Modifying equilibrium distance for part of carbon nanotubes in parameter file jashnvareh 1395 (Tue Dec 27 2016 - 02:55:42 CST)
Re: NAMD 2.12 released Francesco Pietra (Tue Dec 27 2016 - 01:40:40 CST)
Re: Regarding Trajectory files Harish Srinivasan (Mon Dec 26 2016 - 23:44:52 CST)
Re: Regarding Trajectory files Harish Srinivasan (Mon Dec 26 2016 - 23:44:03 CST)
NAMD 2.12 released Angelo Rossi (Mon Dec 26 2016 - 15:53:42 CST)
Re: Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 11:39:48 CST)
Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file zeynab mohamad hoseyni (Sun Dec 25 2016 - 12:46:28 CST)
Re: Query regarding colvar distanceZ Vermaas, Joshua (Mon Dec 26 2016 - 10:49:38 CST)
Re: Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 09:17:34 CST)
Re: Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 09:07:18 CST)
Re: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file Abhishek TYAGI (Mon Dec 26 2016 - 08:59:58 CST)
Modifying equilibrium distance for a specific region of carbon nanotube in the parameter file jashnvareh 1395 (Mon Dec 26 2016 - 08:30:59 CST)
Re: Query regarding colvar distanceZ Vermaas, Joshua (Mon Dec 26 2016 - 08:12:23 CST)
Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 06:57:57 CST)
Fwd: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file zeynab hoseyni (Mon Dec 26 2016 - 06:45:28 CST)
Re: NAMD 2.12 released Francesco Pietra (Mon Dec 26 2016 - 04:17:27 CST)
Regarding Trajectory files Amit Kumar (Sun Dec 25 2016 - 23:18:26 CST)
Fwd: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file zeynab hoseyni (Sun Dec 25 2016 - 14:31:53 CST)
Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file zeynab hoseyni (Sun Dec 25 2016 - 12:51:46 CST)
NAMD 2.12 released Jim Phillips (Fri Dec 23 2016 - 12:57:34 CST)
Re: Constraint bonds that does not include hydrogrens Jeff Comer (Thu Dec 22 2016 - 13:24:30 CST)
Re: Constraint bonds that does not include hydrogrens Karteek Bejagam (Thu Dec 22 2016 - 10:00:08 CST)
Re: Constraint bonds that does not include hydrogrens Jeff Comer (Thu Dec 22 2016 - 09:38:50 CST)
RMSD based PMF calculation with umbrella sampling Wang, X. Y. (Thu Dec 22 2016 - 04:26:21 CST)
Constraint bonds that does not include hydrogrens Karteek Bejagam (Wed Dec 21 2016 - 23:00:55 CST)
Re: NAMD_CUDA Jim Phillips (Tue Dec 20 2016 - 23:30:12 CST)
Re: 2.11 how to remove charmrun remote-shell options Jim Phillips (Tue Dec 20 2016 - 23:29:12 CST)
Re: 2.11 how to remove charmrun remote-shell options Scott Brozell (Tue Dec 20 2016 - 19:05:08 CST)
Automate QwikMD set up for a large number of NAMD jobs? Danny Xu (Tue Dec 20 2016 - 15:24:36 CST)
Fw (5): zmhoseyni zmhoseyni (Mon Dec 19 2016 - 13:47:30 CST)
Re: Studying Folding of 870 Small Peptides. Computationally Feasible? Brian Radak (Mon Dec 19 2016 - 09:32:10 CST)
Re: Studying Folding of 870 Small Peptides. Computationally Feasible? Nicholas M. Glykos (Mon Dec 19 2016 - 03:36:15 CST)
Re: Studying Folding of 870 Small Peptides. Computationally Feasible? Peter Freddolino (Sat Dec 17 2016 - 22:04:38 CST)
Re: Studying Folding of 870 Small Peptides. Computationally Feasible? JC Gumbart (Sat Dec 17 2016 - 19:18:46 CST)
Re: Studying Folding of 870 Small Peptides. Computationally Feasible? Eric A Brenner (Sat Dec 17 2016 - 19:02:39 CST)
Re: Studying Folding of 870 Small Peptides. Computationally Feasible? JC Gumbart (Sat Dec 17 2016 - 18:48:50 CST)
Studying Folding of 870 Small Peptides. Computationally Feasible? Eric A Brenner (Sat Dec 17 2016 - 12:35:59 CST)
Re: Writing number of atoms in a specific group to a file Vermaas, Joshua (Fri Dec 16 2016 - 13:12:22 CST)
Re: Writing number of atoms in a specific group to a file Hamed Fadaei (Fri Dec 16 2016 - 12:52:06 CST)
Re: Writing number of atoms in a specific group to a file Brian Radak (Fri Dec 16 2016 - 12:11:04 CST)
Writing number of atoms in a specific group to a file Hamed Fadaei (Fri Dec 16 2016 - 11:35:24 CST)
Re: Problem with using autoPSF on TMCL lipid Giacomo Fiorin (Fri Dec 16 2016 - 11:18:21 CST)
Re: Problem with using autoPSF on TMCL lipid Jeff Comer (Fri Dec 16 2016 - 10:40:17 CST)
Problem with using autoPSF on TMCL lipid salehesam101 . (Fri Dec 16 2016 - 10:11:47 CST)
GBIS intrinsic radii set from aber parm7 Norman Geist (Fri Dec 16 2016 - 02:04:15 CST)
NAMD_CUDA Sana Saeed (Thu Dec 15 2016 - 20:23:18 CST)
Re: psfgen - pdbalias when using readpsf Peter Freddolino (Thu Dec 15 2016 - 15:37:40 CST)
Re: psfgen - pdbalias when using readpsf Vermaas, Joshua (Thu Dec 15 2016 - 15:26:11 CST)
Re: psfgen - pdbalias when using readpsf Peter Freddolino (Thu Dec 15 2016 - 15:03:23 CST)
Re: psfgen - pdbalias when using readpsf Brian Radak (Thu Dec 15 2016 - 14:48:01 CST)
Re: psfgen - pdbalias when using readpsf Peter Freddolino (Thu Dec 15 2016 - 14:40:40 CST)
Re: NVT and NPT simulationd faride badalkhani (Thu Dec 15 2016 - 14:38:24 CST)
psfgen - pdbalias when using readpsf Brian Radak (Thu Dec 15 2016 - 14:28:56 CST)
AW: NVT and NPT simulationd Norman Geist (Thu Dec 15 2016 - 02:20:28 CST)
Re: NAMD Energies Peter Freddolino (Wed Dec 14 2016 - 13:54:52 CST)
Re: NAMD Energies Giacomo Fiorin (Wed Dec 14 2016 - 13:53:02 CST)
RE: NAMD Energies Radak, Brian K (Wed Dec 14 2016 - 13:42:36 CST)
Re: NAMD Energies Giacomo Fiorin (Wed Dec 14 2016 - 13:47:16 CST)
NAMD Energies Chris Goedde (Wed Dec 14 2016 - 13:13:01 CST)
Re: NVT and NPT simulationd faride badalkhani (Wed Dec 14 2016 - 12:14:08 CST)
Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 11:11:00 CST)
Re: NVT and NPT simulationd faride badalkhani (Wed Dec 14 2016 - 11:09:40 CST)
Re: using colvars to constrain two atoms in a direction Hamed Fadaei (Wed Dec 14 2016 - 11:02:37 CST)
Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 10:49:31 CST)
Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 10:40:57 CST)
Re: using colvars to constrain two atoms in a direction Hamed Fadaei (Wed Dec 14 2016 - 10:34:08 CST)
Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 10:22:39 CST)
using colvars to constrain two atoms in a direction Hamed Fadaei (Wed Dec 14 2016 - 10:15:20 CST)
AW: NVT and NPT simulationd Norman Geist (Wed Dec 14 2016 - 01:33:16 CST)
NVT and NPT simulationd faride badalkhani (Tue Dec 13 2016 - 23:50:53 CST)
water permeability calculation using NAMD trajectories Pragya Priyadarshini (Tue Dec 13 2016 - 22:39:41 CST)
Re: protonating ASP and GLU Brian Radak (Tue Dec 13 2016 - 13:20:27 CST)
Re: protonating ASP and GLU Giacomo Fiorin (Tue Dec 13 2016 - 13:06:05 CST)
Re: protonating ASP and GLU Nehad Elsalamouny (Tue Dec 13 2016 - 12:48:35 CST)
Re: protonating ASP and GLU Brian Radak (Tue Dec 13 2016 - 08:27:28 CST)
protonating ASP and GLU Nehad Elsalamouny (Tue Dec 13 2016 - 05:58:51 CST)
Re: Setting up symmetry restraints in a homo-dimer with non-equal number of residues Mark Hilge (Mon Dec 12 2016 - 16:55:07 CST)
NAMD_2.12b1 build on Cray XC40 is failing Ianni, James C CTR USARMY RDECOM ARL (US) (Mon Dec 12 2016 - 14:35:32 CST)
RE: FATAL ERROR: Duplicate bond when going from nvt to npt Radak, Brian K (Mon Dec 12 2016 - 09:33:46 CST)
FATAL ERROR: Duplicate bond when going from nvt to npt Marlon Sidore (Mon Dec 12 2016 - 04:02:17 CST)
Re: Problem with alpha colvar in NAMD 2.12b1 JC Gumbart (Fri Dec 09 2016 - 16:58:23 CST)
Re: Problem with alpha colvar in NAMD 2.12b1 Giacomo Fiorin (Fri Dec 09 2016 - 17:14:34 CST)
(no subject) Tom King (Fri Dec 09 2016 - 16:43:07 CST)
Re: Setting up symmetry restraints in a homo-dimer with non-equal number of residues Ryan McGreevy (Fri Dec 09 2016 - 12:46:04 CST)
Re: Setting up symmetry restraints in a homo-dimer with non-equal number of residues Giacomo Fiorin (Fri Dec 09 2016 - 12:34:43 CST)
Setting up symmetry restraints in a homo-dimer with non-equal number of residues Mark Hilge (Fri Dec 09 2016 - 00:17:19 CST)
Re: Problem with alpha colvar in NAMD 2.12b1 Giacomo Fiorin (Thu Dec 08 2016 - 16:04:41 CST)
Problem with alpha colvar in NAMD 2.12b1 Amy Rice (Thu Dec 08 2016 - 15:23:16 CST)
Re: Vermaas, Joshua (Thu Dec 08 2016 - 10:17:25 CST)
Re: Returning energy values from .log file. Ajasja LjubetiÄ (Thu Dec 08 2016 - 02:30:28 CST)
Re: NAMD How to calculate ns/day Abhishek TYAGI (Thu Dec 08 2016 - 01:38:04 CST)
(no subject) Nehir NALINCI (Thu Dec 08 2016 - 01:06:44 CST)
Re: NAMD How to calculate ns/day Shikha Sharma (Wed Dec 07 2016 - 23:01:44 CST)
Re: NAMD How to calculate ns/day Ajasja LjubetiÄ (Wed Dec 07 2016 - 16:59:45 CST)
NAMD How to calculate ns/day Jan Fredin (Wed Dec 07 2016 - 16:02:16 CST)
RE: Returning energy values from .log file. Radak, Brian K (Wed Dec 07 2016 - 15:19:49 CST)
Re: Returning energy values from .log file. Ajasja LjubetiÄ (Wed Dec 07 2016 - 14:41:54 CST)
Re: Returning energy values from .log file. Chitrak Gupta (Wed Dec 07 2016 - 14:36:57 CST)
Returning energy values from .log file. matthew reeves (Wed Dec 07 2016 - 14:16:44 CST)
Re: Minimization error Vermaas, Joshua (Wed Dec 07 2016 - 11:36:44 CST)
Minimization error Santanu Santra (Tue Dec 06 2016 - 23:00:04 CST)
Re: selectively assign HIE or HID for HIS residues Jim Phillips (Tue Dec 06 2016 - 16:08:47 CST)
Re: Low global exclusion count errors! Jim Phillips (Tue Dec 06 2016 - 15:59:34 CST)
Re: AW: NAMD 2.11 on CRAY XK with CPU+GPU Jim Phillips (Tue Dec 06 2016 - 15:54:31 CST)
Re: selectively assign HIE or HID for HIS residues Nehad Elsalamouny (Tue Dec 06 2016 - 15:03:47 CST)
Re: Energy output values Brian Radak (Tue Dec 06 2016 - 13:35:47 CST)
Energy output values matthew reeves (Tue Dec 06 2016 - 13:16:00 CST)
Re: selectively assign HIE or HID for HIS residues Vermaas, Joshua (Tue Dec 06 2016 - 11:03:38 CST)
Re: selectively assign HIE or HID for HIS residues Brian Radak (Mon Dec 05 2016 - 22:13:09 CST)
selectively assign HIE or HID for HIS residues Nehad Elsalamouny (Mon Dec 05 2016 - 20:19:44 CST)
Re: Getting cluster with defined criteria Brian Radak (Sun Dec 04 2016 - 17:54:21 CST)
Getting cluster with defined criteria Peter Mawanga (Sun Dec 04 2016 - 07:05:35 CST)
AW: How to continue RMSD of previous production simulation Norman Geist (Sat Dec 03 2016 - 05:45:35 CST)
AW: How to continue RMSD of previous production simulation Norman Geist (Sat Dec 03 2016 - 05:51:18 CST)
Re: How to continue RMSD of previous production simulation Chitrak Gupta (Fri Dec 02 2016 - 12:43:05 CST)
How to continue RMSD of previous production simulation Farhad Jahanfar (Fri Dec 02 2016 - 12:21:36 CST)
Re: Low global exclusion count error Brian Radak (Fri Dec 02 2016 - 09:25:30 CST)
Re: Low global exclusion count error B.W.J. Irwin (Fri Dec 02 2016 - 04:43:49 CST)
Re: Amber forcefield in namd simulation in parallel version Teerapong Pirojsirikul (Fri Dec 02 2016 - 03:30:11 CST)
AW: Amber forcefield in namd simulation in parallel version Norman Geist (Fri Dec 02 2016 - 01:59:20 CST)
Re: Amber forcefield in namd simulation in parallel version Santanu Santra (Fri Dec 02 2016 - 00:05:35 CST)
Re: Amber forcefield in namd simulation in parallel version Santanu Santra (Thu Dec 01 2016 - 23:00:45 CST)
FATAL ERROR: cuda_check_progress polled 1000000 times over 101.178648 s on step 6418536 sunyeping (Thu Dec 01 2016 - 17:27:36 CST)
Low global exclusion count error faride badalkhani (Thu Dec 01 2016 - 15:21:03 CST)
Spawning too many gpu processes on the first node Robert Sawko (Thu Dec 01 2016 - 13:10:12 CST)
AW: Amber forcefield in namd simulation in parallel version Norman Geist (Thu Dec 01 2016 - 07:58:00 CST)
Amber forcefield in namd simulation in parallel version Santanu Santra (Thu Dec 01 2016 - 06:36:24 CST)
Re: Running gromacs in namd Subbarao Kanchi (Thu Dec 01 2016 - 01:42:24 CST)
AW: Running gromacs in namd Norman Geist (Thu Dec 01 2016 - 01:06:23 CST)
AW: NAMD 2.11 on CRAY XK with CPU+GPU Norman Geist (Thu Dec 01 2016 - 01:04:38 CST)
Re: Running gromacs in namd Subbarao Kanchi (Thu Dec 01 2016 - 00:27:37 CST)
DNA not translocating under electric field Athreya, Nagendra Bala Murali (Wed Nov 30 2016 - 21:20:55 CST)
NAMD 2.11 on CRAY XK with CPU+GPU P.-L. Chau (Wed Nov 30 2016 - 17:47:07 CST)
Re: query on OuputTotalforce Vs OnesiteTotal force ? Bala subramanian (Wed Nov 30 2016 - 07:39:14 CST)
AW: Running gromacs in namd Norman Geist (Wed Nov 30 2016 - 02:45:09 CST)
Re: NVE simulations in NAMD - the right choice of timesteps and parameters Brian Radak (Tue Nov 29 2016 - 12:52:15 CST)
Re: A problem in ABF simulation Karteek Bejagam (Tue Nov 29 2016 - 12:14:44 CST)
Re: NVE simulations in NAMD - the right choice of timesteps and parameters Vlad Cojocaru (Tue Nov 29 2016 - 11:09:40 CST)
Re: query on OuputTotalforce Vs OnesiteTotal force ? Giacomo Fiorin (Tue Nov 29 2016 - 10:20:36 CST)
Re: NVE simulations in NAMD - the right choice of timesteps and parameters Axel Kohlmeyer (Tue Nov 29 2016 - 10:16:11 CST)
Re: query on OuputTotalforce Vs OnesiteTotal force ? Giacomo Fiorin (Tue Nov 29 2016 - 10:14:34 CST)
Re: NVE simulations in NAMD - the right choice of timesteps and parameters Brian Radak (Tue Nov 29 2016 - 10:04:53 CST)
query on OuputTotalforce Vs OnesiteTotal force ? Bala subramanian (Tue Nov 29 2016 - 09:39:39 CST)
How to create 3'-3' phosphodiester linkage for a DNA. Susmita Ghosh (Mon Nov 28 2016 - 23:50:26 CST)
Re: NVE simulations in NAMD - the right choice of timesteps and parameters Felipe Merino (Tue Nov 29 2016 - 07:03:45 CST)
NVE simulations in NAMD - the right choice of timesteps and parameters Harish Srinivasan (Tue Nov 29 2016 - 04:54:32 CST)
Re: Running gromacs in namd Subbarao Kanchi (Tue Nov 29 2016 - 04:25:06 CST)
AW: Running gromacs in namd Norman Geist (Tue Nov 29 2016 - 01:36:48 CST)
Running gromacs in namd Subbarao Kanchi (Tue Nov 29 2016 - 00:30:37 CST)
Re: tclBC during SMD and ABF simulations Olya Kravchenko (Mon Nov 28 2016 - 19:44:01 CST)
tclBC during SMD and ABF simulations Olya Kravchenko (Mon Nov 28 2016 - 12:36:47 CST)
Re: A common tool to read the output of NAMD run Ajasja LjubetiÄ (Mon Nov 28 2016 - 08:34:47 CST)
Re: A common tool to read the output of NAMD run Richard Overstreet (Mon Nov 28 2016 - 08:08:03 CST)
A common tool to read the output of NAMD run Harish Srinivasan (Mon Nov 28 2016 - 06:28:00 CST)
NAMD installation Puneet (Sat Nov 26 2016 - 01:41:14 CST)
Re: Simulation of metalo-binding proteins luca belmonte (Fri Nov 25 2016 - 06:47:10 CST)
Ligand jump out of the protein through NPT ensemle runs mahdi K (Fri Nov 25 2016 - 06:40:31 CST)
Re: Simulation of metalo-binding proteins James Starlight (Thu Nov 24 2016 - 14:44:03 CST)
Re: Simulation of metalo-binding proteins Francesco Pietra (Thu Nov 24 2016 - 14:41:58 CST)
Re: Simulation of metalo-binding proteins James Starlight (Thu Nov 24 2016 - 14:01:08 CST)
Re: REMD Vermaas, Joshua (Thu Nov 24 2016 - 11:07:06 CST)
Low global exclusion count errors! faride badalkhani (Thu Nov 24 2016 - 10:28:53 CST)
AW: Simulation of metalo-binding proteins Daniel MÃ¶ller (Wed Nov 23 2016 - 15:52:53 CST)
REMD kaushik chakraborty (Wed Nov 23 2016 - 13:58:51 CST)
Simulation of metalo-binding proteins James Starlight (Wed Nov 23 2016 - 13:52:38 CST)
Re: Query on colvar distanceZ Giacomo Fiorin (Mon Nov 21 2016 - 11:10:57 CST)
Re: Separate switchdist for electrostatic interactions Fotis Baltoumas (Mon Nov 21 2016 - 09:54:33 CST)
Separate switchdist for electrostatic interactions Peter Mawanga (Mon Nov 21 2016 - 06:17:18 CST)
Re: Charmm++ error Sourav Ray (Sun Nov 20 2016 - 17:12:02 CST)
Re: Charmm++ error Sourav Ray (Sun Nov 20 2016 - 17:10:44 CST)
â€œCannot compile C++ programs with mpicxx" error when compiling charm-6.7 sunyeping (Sun Nov 20 2016 - 13:22:02 CST)
Charmm++ error matthew reeves (Sun Nov 20 2016 - 11:29:25 CST)
Re: Query on colvar distanceZ Karteek Bejagam (Sat Nov 19 2016 - 10:12:36 CST)
Query on colvar distanceZ Bala subramanian (Sat Nov 19 2016 - 08:18:57 CST)
Re: Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 19:04:06 CST)
Re: Generate psf file in x-plor format Vermaas, Joshua (Thu Nov 17 2016 - 18:56:55 CST)
Re: Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 16:59:53 CST)
Re: Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 14:44:40 CST)
Re: Generate psf file in x-plor format Vermaas, Joshua (Thu Nov 17 2016 - 14:56:01 CST)
Pressure Profile. msa5 (Thu Nov 17 2016 - 11:06:48 CST)
Re: Generate psf file in x-plor format Vermaas, Joshua (Thu Nov 17 2016 - 09:47:42 CST)
Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 06:07:39 CST)
NAMD GPU+ibverbs on multiple nodes: timeout problems Robert Sawko (Thu Nov 17 2016 - 05:51:21 CST)
Re: K40 benchmark problem in NAMD sonia ziada (Thu Nov 17 2016 - 01:54:59 CST)
K40 benchmark problem in NAMD Atanu Maity (Thu Nov 17 2016 - 01:27:04 CST)
Hands-On Workshop on Integrative Modeling and Simulations Jodi Ann Hadden (Wed Nov 16 2016 - 11:28:03 CST)
Re: Crashes with dihedral PC Giacomo Fiorin (Tue Nov 15 2016 - 22:40:17 CST)
Crashes with dihedral PC Jiyong Park (Tue Nov 15 2016 - 20:28:32 CST)
Re: About pbc Jeff Comer (Tue Nov 15 2016 - 17:40:12 CST)
RE: SMD restraints Allen, Caley R (Tue Nov 15 2016 - 13:30:17 CST)
Re: SMD restraints Giacomo Fiorin (Tue Nov 15 2016 - 13:17:17 CST)
Re: Queries regarding metadynamics and .pmf visualization Giacomo Fiorin (Tue Nov 15 2016 - 10:40:15 CST)
Re: NPT with graphene Jeff Comer (Tue Nov 15 2016 - 08:10:57 CST)
AW: NPT with graphene Norman Geist (Tue Nov 15 2016 - 03:04:09 CST)
Re: Are there features NOT or POORLY supported on GPU ? sonia ziada (Tue Nov 15 2016 - 01:34:34 CST)
Re: SMD restraints Vermaas, Joshua (Mon Nov 14 2016 - 16:26:01 CST)
Re: SMD restraints Giacomo Fiorin (Mon Nov 14 2016 - 15:59:07 CST)
Re: SMD restraints Giacomo Fiorin (Mon Nov 14 2016 - 15:17:59 CST)
SMD restraints Allen, Caley R (Mon Nov 14 2016 - 15:14:09 CST)
Re: NPT with graphene Richard Overstreet (Mon Nov 14 2016 - 15:03:43 CST)
Re: Are there features NOT or POORLY supported on GPU ? Brian Radak (Mon Nov 14 2016 - 14:46:40 CST)
Re: Are there features NOT or POORLY supported on GPU ? Chris Goedde (Mon Nov 14 2016 - 14:30:16 CST)
Re: Are there features NOT or POORLY supported on GPU ? Brian Radak (Mon Nov 14 2016 - 14:24:13 CST)
Re: Need help with TCL script Vermaas, Joshua (Mon Nov 14 2016 - 14:17:08 CST)
Need help with TCL script Nicholus Bhattacharjee (Mon Nov 14 2016 - 13:10:13 CST)
NPT with graphene Richard Overstreet (Mon Nov 14 2016 - 11:29:27 CST)
Are there features NOT or POORLY supported on GPU ? sonia ziada (Mon Nov 14 2016 - 04:11:43 CST)
Re: NAMD2.12b1 and CUDA Jeff Comer (Thu Nov 10 2016 - 17:23:04 CST)
Re: NAMD2.12b1 and CUDA Jim Phillips (Thu Nov 10 2016 - 16:20:31 CST)
Re: NAMD2.12b1 and CUDA Giacomo Fiorin (Thu Nov 10 2016 - 11:09:04 CST)
NAMD2.12b1 and CUDA Jeff Comer (Thu Nov 10 2016 - 09:09:50 CST)
AW: AW: Trigger DCD frame from TCL? Norman Geist (Thu Nov 10 2016 - 02:09:22 CST)
Re: AW: Trigger DCD frame from TCL? Jim Phillips (Wed Nov 09 2016 - 16:48:00 CST)
restraint backbone to keep secondary structure in coarse grain MD Deng, Jinxia (Nancy) (Wed Nov 09 2016 - 10:42:46 CST)
Re: AW: Trigger DCD frame from TCL? Brian Radak (Wed Nov 09 2016 - 07:34:48 CST)
AW: Trigger DCD frame from TCL? Norman Geist (Wed Nov 09 2016 - 02:48:33 CST)
AW: Trigger DCD frame from TCL? Norman Geist (Wed Nov 09 2016 - 02:05:50 CST)
Re: Parameters for determining run time Oscar Bastidas (Tue Nov 08 2016 - 15:33:00 CST)
About pbc Francesco Pietra (Tue Nov 08 2016 - 15:10:56 CST)
Re: Parameters for determining run time Peter Freddolino (Tue Nov 08 2016 - 15:10:04 CST)
Re: Trigger DCD frame from TCL? Brian Radak (Tue Nov 08 2016 - 09:22:24 CST)
Re: Parameters for determining run time Brian Radak (Tue Nov 08 2016 - 09:18:15 CST)
Trigger DCD frame from TCL? Norman Geist (Tue Nov 08 2016 - 09:12:04 CST)
steepest descent Ma'Mon Hatmal (Tue Nov 08 2016 - 08:58:30 CST)
problem in minimization Ma'Mon Hatmal (Tue Nov 08 2016 - 00:01:28 CST)
Re: Parameters for determining run time Vermaas, Joshua (Mon Nov 07 2016 - 18:43:03 CST)
Re: Parameters for determining run time Peter Freddolino (Mon Nov 07 2016 - 21:21:51 CST)
Re: Parameters for determining run time Richard Overstreet (Mon Nov 07 2016 - 19:12:59 CST)
Parameters for determining run time Oscar Bastidas (Mon Nov 07 2016 - 16:10:34 CST)
performance of GPU calculations Hao Dong (Sun Nov 06 2016 - 21:11:40 CST)
Dear NAMD users msa5 (Thu Nov 03 2016 - 17:18:00 CDT)
NAMD 2.12b1 released Jim Phillips (Thu Nov 03 2016 - 17:06:48 CDT)
multiple run commands freeze when using MTS? Brian Radak (Thu Nov 03 2016 - 15:45:40 CDT)
Hi All msa5 (Tue Nov 01 2016 - 22:06:01 CDT)
Re: CHARMM22-STAR force field for NAMD JC Gumbart (Tue Nov 01 2016 - 21:28:04 CDT)
CHARMM22-STAR force field for NAMD Nicholas M. Glykos (Tue Nov 01 2016 - 13:15:48 CDT)
CHARMM22-STAR force field for NAMD Nicholas M. Glykos (Tue Nov 01 2016 - 13:07:39 CDT)
Re: Re: no response from mail list Giacomo Fiorin (Tue Nov 01 2016 - 09:36:49 CDT)
Remembering Klaus Schulten Thomas C. Bishop (Tue Nov 01 2016 - 09:33:31 CDT)
(no subject) Santanu Santra (Mon Oct 31 2016 - 23:22:58 CDT)
Re: no response from mail list Peter Freddolino (Mon Oct 31 2016 - 20:36:12 CDT)
Re: no response from mail list sunyeping (Mon Oct 31 2016 - 20:32:18 CDT)
Re: no response from mail list Oscar Bastidas (Mon Oct 31 2016 - 20:16:50 CDT)
no response from mail list sunyeping (Mon Oct 31 2016 - 19:23:09 CDT)
Re: is it possible to restrict the access of ions to certain volume? Olya Kravchenko (Mon Oct 31 2016 - 15:55:28 CDT)
Re: is it possible to restrict the access of ions to certain volume? Giacomo Fiorin (Mon Oct 31 2016 - 15:43:34 CDT)
is it possible to restrict the access of ions to certain volume? Olya Kravchenko (Mon Oct 31 2016 - 15:28:40 CDT)
Re: NAMD Execution Error Vermaas, Joshua (Mon Oct 31 2016 - 14:09:02 CDT)
Re: Diagnosing CUDA (non)performance Brian Radak (Mon Oct 31 2016 - 13:37:13 CDT)
Diagnosing CUDA (non)performance Chris Goedde (Mon Oct 31 2016 - 07:48:31 CDT)
NAMD Execution Error Oscar Bastidas (Sun Oct 30 2016 - 18:46:19 CDT)
Re: AW: Turning off and back on fixed atoms Brian Radak (Sat Oct 29 2016 - 12:04:57 CDT)
AW: Turning off and back on fixed atoms Norman Geist (Fri Oct 28 2016 - 04:40:22 CDT)
RE: Turning off and back on fixed atoms Radak, Brian K (Thu Oct 27 2016 - 12:05:27 CDT)
AW: vmd-l: Error connecting to localhost on port 3000 and IMD connection ended unexpectedly; connection terminated. Norman Geist (Thu Oct 27 2016 - 07:50:19 CDT)
Re: Problem with minimization Abhishek TYAGI (Thu Oct 27 2016 - 06:13:10 CDT)
Problem with minimization Ma'Mon Hatmal (Thu Oct 27 2016 - 05:22:52 CDT)
Turning off and back on fixed atoms Norman Geist (Thu Oct 27 2016 - 05:14:28 CDT)
NAMD Question: NAMD Message "364"-What does it mean? Oscar Bastidas (Thu Oct 27 2016 - 03:34:17 CDT)
NAMD Question: How to run on 2-chain system Oscar Bastidas (Wed Oct 26 2016 - 20:08:18 CDT)
RE: Switch off rescale temperature after some number of timesteps Radak, Brian K (Wed Oct 26 2016 - 11:12:36 CDT)
Switch off rescale temperature after some number of timesteps Harish Srinivasan (Wed Oct 26 2016 - 01:05:50 CDT)
Re: mail reg compilation of mdenergy Vidhya Sankar (Tue Oct 25 2016 - 20:20:07 CDT)
Re: Using NAMD with NMR structure Pardis Tabaee (Mon Oct 24 2016 - 16:02:48 CDT)
Re: Using NAMD with NMR structure Steve Chou (Mon Oct 24 2016 - 13:18:34 CDT)
fix disulfide bond in coarse grain(CG) model for NAMD Deng, Jinxia (Nancy) (Mon Oct 24 2016 - 11:46:11 CDT)
Re: Using NAMD with NMR structure Pardis Tabaee (Mon Oct 24 2016 - 11:26:09 CDT)
Re: Using NAMD with NMR structure Pardis Tabaee (Mon Oct 24 2016 - 11:20:26 CDT)
Re: Using NAMD with NMR structure Brian Radak (Mon Oct 24 2016 - 09:02:02 CDT)
Re: Using NAMD with NMR structure Pardis Tabaee (Mon Oct 24 2016 - 06:13:04 CDT)
Re: Using NAMD with NMR structure Peter Freddolino (Sun Oct 23 2016 - 05:55:08 CDT)
Using NAMD with NMR structure Oscar Bastidas (Sun Oct 23 2016 - 02:00:14 CDT)
Re: NAMD breaks with wrong timestep GÃ¶tz, Alexander (Sat Oct 22 2016 - 10:19:42 CDT)
Re: NAMD breaks with wrong timestep Brian Radak (Fri Oct 21 2016 - 15:20:19 CDT)
Re: Minimization failing on one machine only David Hardy (Fri Oct 21 2016 - 15:16:47 CDT)
Re: Minimization failing on one machine only Chris Goedde (Fri Oct 21 2016 - 14:11:42 CDT)
Re: NAMD breaks with wrong timestep Axel Kohlmeyer (Fri Oct 21 2016 - 10:54:00 CDT)
Re: NAMD breaks with wrong timestep Vermaas, Joshua (Fri Oct 21 2016 - 10:49:22 CDT)
Re: NAMD breaks with wrong timestep Brian Radak (Fri Oct 21 2016 - 10:41:46 CDT)
NAMD breaks with wrong timestep Götz, Alexander (Fri Oct 21 2016 - 08:23:33 CDT)
Re: mail reg compilation of mdenergy Axel Kohlmeyer (Wed Oct 19 2016 - 14:27:04 CDT)
Re: mail reg compilation of mdenergy David Hardy (Wed Oct 19 2016 - 14:11:32 CDT)
Re: fix disulfide bridge in coarse grain MD Fotis Baltoumas (Wed Oct 19 2016 - 12:36:11 CDT)
mail reg compilation of mdenergy Vidhya Sankar (Wed Oct 19 2016 - 12:08:12 CDT)
fix disulfide bridge in coarse grain MD Deng, Jinxia (Nancy) (Wed Oct 19 2016 - 11:54:59 CDT)
Re: Minimization failing on one machine only Ajasja LjubetiÄ (Sat Oct 15 2016 - 01:50:29 CDT)
Minimization failing on one machine only Chris Goedde (Fri Oct 14 2016 - 15:34:10 CDT)
Re: Collecting average energies via Tcl callback? Subbarao Kanchi (Thu Oct 13 2016 - 19:20:39 CDT)
Collecting average energies via Tcl callback? Brian Radak (Thu Oct 13 2016 - 11:19:40 CDT)
AW: Re: AW: Reason: FATAL ERROR: Unknown command-line option ++local Norman Geist (Tue Oct 11 2016 - 00:33:25 CDT)
Re: AW: Reason: FATAL ERROR: Unknown command-line option ++local sunyeping (Mon Oct 10 2016 - 21:55:27 CDT)
RE: visualizing and analyzing long simulation Deng, Jinxia (Nancy) (Mon Oct 10 2016 - 10:51:42 CDT)
Re: visualizing and analyzing long simulation Richard Overstreet (Mon Oct 10 2016 - 11:48:28 CDT)
visualizing and analyzing long simulation Dhiraj Srivastava (Mon Oct 10 2016 - 10:41:53 CDT)
AW: NAMD running on a Cluster of Ubuntu Linux Norman Geist (Mon Oct 10 2016 - 01:27:59 CDT)
AW: Reason: FATAL ERROR: Unknown command-line option ++local Norman Geist (Mon Oct 10 2016 - 01:24:44 CDT)
NAMD running on a Cluster of Ubuntu Linux Marisol Oswald (Sun Oct 09 2016 - 18:37:55 CDT)
Reason: FATAL ERROR: Unknown command-line option ++local å™ä¸šå¹³ (Sun Oct 09 2016 - 14:09:47 CDT)
Re: question regarding rmsd dhirajks_at_gmail.com (Thu Oct 06 2016 - 17:37:23 CDT)
Re: question regarding rmsd Leandro MartÃnez (Wed Oct 05 2016 - 15:58:39 CDT)
RE: question regarding rmsd Radak, Brian K (Wed Oct 05 2016 - 15:39:01 CDT)
Re: question regarding rmsd Dhiraj Srivastava (Wed Oct 05 2016 - 14:02:32 CDT)
Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 13:34:41 CDT)
RE: question regarding rmsd Radak, Brian K (Wed Oct 05 2016 - 11:18:12 CDT)
Re: question regarding rmsd Roshan Shrestha (Wed Oct 05 2016 - 11:07:09 CDT)
Re: question regarding rmsd dhirajks_at_gmail.com (Wed Oct 05 2016 - 11:03:41 CDT)
Re: Tcl clock Giacomo Fiorin (Wed Oct 05 2016 - 10:58:47 CDT)
Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 10:55:01 CDT)
Re: Tcl clock Laura Joana (Wed Oct 05 2016 - 10:42:00 CDT)
Re: Tcl clock Mayne, Christopher G (Wed Oct 05 2016 - 09:51:15 CDT)
question regarding rmsd Dhiraj Srivastava (Tue Oct 04 2016 - 16:07:43 CDT)
Tcl clock Laura Joana (Tue Oct 04 2016 - 14:10:12 CDT)
Re: Switch function equation Brian Radak (Mon Oct 03 2016 - 21:16:58 CDT)
(no subject) Sourav Pal (Mon Oct 03 2016 - 02:44:00 CDT)
Switch function equation Faramarz Joodaki (Sun Oct 02 2016 - 23:57:40 CDT)
stripping off water from DCD file except structural water Dhiraj Srivastava (Sun Oct 02 2016 - 22:57:24 CDT)
Re: Oxidized cysteine parameters for CHARMM36 Brian Radak (Fri Sep 30 2016 - 09:35:08 CDT)
Oxidized cysteine parameters for CHARMM36 Gergely Gyimesi (Fri Sep 30 2016 - 08:40:04 CDT)
Re: Half of the structure goes out of the simulation box! Ana Celia Vila Verde (Fri Sep 30 2016 - 07:31:03 CDT)
Re: Half of the structure goes out of the simulation box! Richard Overstreet (Fri Sep 30 2016 - 06:25:19 CDT)
Half of the structure goes out of the simulation box! faride badalkhani (Fri Sep 30 2016 - 05:18:51 CDT)
dcd file frame number Dhiraj Srivastava (Thu Sep 29 2016 - 22:22:54 CDT)
Hands-On Workshop on Computational Biophysics: November 14-18 in Atlanta, GA Jodi Ann Hadden (Thu Sep 29 2016 - 00:27:31 CDT)
ACS COMP Division awards deadline this week Carlos Simmerling (Wed Sep 28 2016 - 11:34:52 CDT)
Shrinking a polymer to match its density using pbc Sonu Kumar (Wed Sep 28 2016 - 10:21:11 CDT)
RE: Martini CG models parameters errors Mahad Gatti (Wed Sep 28 2016 - 05:40:51 CDT)
RE: Wrapall on or off? Radak, Brian K (Tue Sep 27 2016 - 10:50:33 CDT)
Wrapall on or off? sunyeping (Tue Sep 27 2016 - 00:14:49 CDT)
Re: graphene with proteins Zeina Salman (Mon Sep 26 2016 - 16:02:36 CDT)
Re: graphene with proteins Jeff Comer (Mon Sep 26 2016 - 15:18:07 CDT)
Re: Martini CG models parameters errors Fotis Baltoumas (Mon Sep 26 2016 - 14:58:52 CDT)
Re: Martini CG models parameters errors Vermaas, Joshua (Mon Sep 26 2016 - 10:48:56 CDT)
RE: Martini CG models parameters errors Mahad Gatti (Mon Sep 26 2016 - 04:01:32 CDT)
graphene with proteins Zeina Salman (Sun Sep 25 2016 - 19:42:51 CDT)
FEP double annihilation Carlo Guardiani (Fri Sep 23 2016 - 13:28:30 CDT)
Re: Coordinate DCD file was not created during restart of adaptive biasing force simulation using colvars. JÃ©rÃ´me HÃ©nin (Thu Sep 22 2016 - 14:34:27 CDT)
Re: Martini CG models parameters errors Vermaas, Joshua (Thu Sep 22 2016 - 10:36:40 CDT)
Martini CG models parameters errors Mahad Gatti (Thu Sep 22 2016 - 10:07:34 CDT)
NAMD Equil Config Jackson Cavett (Thu Sep 22 2016 - 07:24:53 CDT)
Re: Coordinate DCD file was not created during restart of adaptive biasing force simulation using colvars. JÃ©rÃ´me HÃ©nin (Thu Sep 22 2016 - 05:04:25 CDT)
Coordinate DCD file was not created during restart of adaptive biasing force simulation using colvars. Zach Bonham (Wed Sep 21 2016 - 15:15:45 CDT)
Re: Running REMD Nicolas Martin (Wed Sep 21 2016 - 03:26:18 CDT)
Re: Running REMD Giacomo Fiorin (Mon Sep 19 2016 - 11:22:52 CDT)
Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL Jodi Ann Hadden (Fri Sep 16 2016 - 15:35:45 CDT)
COORDINATE DCD FILE WAS NOT CREATED Mihaela Drenscko (Thu Sep 15 2016 - 15:42:20 CDT)
AW: NAMD2.11 DCD HEADER PROBLEM Norman Geist (Thu Sep 15 2016 - 01:09:39 CDT)
Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Wed Sep 14 2016 - 08:32:43 CDT)
Re: NAMD2.11 DCD HEADER PROBLEM Marco Sant (Wed Sep 14 2016 - 06:37:02 CDT)
Re: NAMD2.11 DCD HEADER PROBLEM Sourav Ray (Wed Sep 14 2016 - 06:10:20 CDT)
NAMD2.11 DCD HEADER PROBLEM Marco Sant (Wed Sep 14 2016 - 05:35:31 CDT)
Running REMD Nicolas Martin (Wed Sep 14 2016 - 03:10:55 CDT)
GPU acceleration using K40 and k80 Atanu Maity (Wed Sep 14 2016 - 00:32:00 CDT)
Re: Umbrella sampling colvars DistanceZ deviates a lot Kevin C Chan (Tue Sep 13 2016 - 23:10:21 CDT)
Re: Gradual Heating Periodic Error Jackson Cavett (Tue Sep 13 2016 - 15:39:42 CDT)
Re: Umbrella sampling colvars DistanceZ deviates a lot Sourav Ray (Tue Sep 13 2016 - 15:22:47 CDT)
Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Tue Sep 13 2016 - 15:16:14 CDT)
Re: Gradual Heating Periodic Error Hardy, David Joseph (Tue Sep 13 2016 - 14:13:52 CDT)
Re: Umbrella sampling colvars DistanceZ deviates a lot Tabris Chun Chan (Tue Sep 13 2016 - 12:27:25 CDT)
Re: Gradual Heating Periodic Error david gae (Tue Sep 13 2016 - 12:03:07 CDT)
Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Tue Sep 13 2016 - 11:23:56 CDT)
Umbrella sampling colvars DistanceZ deviates a lot Kevin C Chan (Tue Sep 13 2016 - 11:19:08 CDT)
Re: REMD and sortreplicas program Horia Jalily Hasani (Tue Sep 13 2016 - 10:34:22 CDT)
Re: Gradual Heating Periodic Error Jackson Cavett (Tue Sep 13 2016 - 10:32:22 CDT)
Re: Gradual Heating Periodic Error david gae (Tue Sep 13 2016 - 09:27:25 CDT)
Re: Gradual Heating Periodic Error Ajasja LjubetiÄ (Tue Sep 13 2016 - 09:15:38 CDT)
Re: Gradual Heating Periodic Error Jackson Cavett (Tue Sep 13 2016 - 09:01:43 CDT)
Gradual Heating Periodic Error Jackson Cavett (Tue Sep 13 2016 - 08:34:30 CDT)
AW: REMD and sortreplicas program Norman Geist (Tue Sep 13 2016 - 01:19:34 CDT)
Re: PMF decompostion Azadeh Alavi (Mon Sep 12 2016 - 13:34:22 CDT)
RE: PMF decompostion Radak, Brian K (Mon Sep 12 2016 - 12:31:48 CDT)
Re: REMD and sortreplicas program Horia Jalily Hasani (Mon Sep 12 2016 - 11:21:55 CDT)
PMF decompostion Azadeh Alavi (Mon Sep 12 2016 - 06:49:50 CDT)
AW: REMD and sortreplicas program Norman Geist (Mon Sep 12 2016 - 01:38:01 CDT)
AW: REMD and sortreplicas program Norman Geist (Mon Sep 12 2016 - 01:05:39 CDT)
Shear Stress modelling in NAMD James Starlight (Sun Sep 11 2016 - 05:12:26 CDT)
Re: Simulated annealing, in solvent or in vacuum? Roshan Shrestha (Fri Sep 09 2016 - 03:17:37 CDT)
RE: convert .xyz file in .psf file for non-protein molecule grenier_at_cinam.univ-mrs.fr (Fri Sep 09 2016 - 02:51:25 CDT)
Simulated annealing, in solvent or in vacuum? faride badalkhani (Thu Sep 08 2016 - 14:21:26 CDT)
RE: convert .xyz file in .psf file for non-protein molecule Radak, Brian K (Thu Sep 08 2016 - 12:39:04 CDT)
Re: REMD and sortreplicas program Horia Jalily Hasani (Thu Sep 08 2016 - 12:22:39 CDT)
RE: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 11:22:31 CDT)
Re: Query regarding parameter file generation of non standard residue Vermaas, Joshua (Thu Sep 08 2016 - 11:19:05 CDT)
RE: Query regarding parameter file generation of non standard residue Bennion, Brian (Thu Sep 08 2016 - 11:07:13 CDT)
Re: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 11:01:22 CDT)
Re: convert .xyz file in .psf file for non-protein molecule Axel Kohlmeyer (Thu Sep 08 2016 - 10:41:07 CDT)
convert .xyz file in .psf file for non-protein molecule grenier_at_cinam.univ-mrs.fr (Thu Sep 08 2016 - 10:20:03 CDT)
query in the equilibration step d.ronika_at_iitg.ernet.in (Thu Sep 08 2016 - 07:32:32 CDT)
Re: Query regarding parameter file generation of non standard residue Abhishek TYAGI (Thu Sep 08 2016 - 06:37:37 CDT)
Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 04:54:35 CDT)
Re: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 02:36:31 CDT)
AW: REMD and sortreplicas program Norman Geist (Thu Sep 08 2016 - 01:41:21 CDT)
Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 00:12:37 CDT)
REMD and sortreplicas program Horia Jalily Hasani (Wed Sep 07 2016 - 19:10:49 CDT)
Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL Jodi Ann Hadden (Wed Sep 07 2016 - 18:06:53 CDT)
Re: Query regarding parameter file generation of a non standard residue Vermaas, Joshua (Wed Sep 07 2016 - 16:49:15 CDT)
Query regarding parameter file generation of a non standard residue Mahrukh Imtiaz (Wed Sep 07 2016 - 15:12:14 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Wed Sep 07 2016 - 09:17:03 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Wed Sep 07 2016 - 01:14:08 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Tue Sep 06 2016 - 16:43:30 CDT)
The needed time for a MD simulation faride badalkhani (Mon Sep 05 2016 - 10:11:08 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Mon Sep 05 2016 - 06:03:13 CDT)
ION CHANNEL gating mechanism Shambo Hore (Sat Sep 03 2016 - 05:42:46 CDT)
PDB File of Primary structure and Simulation Emerson Macedo (Fri Sep 02 2016 - 11:19:18 CDT)
Re: ion escapes the channel during US simulation Vermaas, Joshua (Thu Sep 01 2016 - 10:27:16 CDT)
Re: ion escapes the channel during US simulation Olya Kravchenko (Thu Sep 01 2016 - 10:17:08 CDT)
Re: ion escapes the channel during US simulation Vermaas, Joshua (Thu Sep 01 2016 - 09:44:22 CDT)
did anyone built NAMD with PLUMED on XSEDE Maksym Korablyov (Thu Sep 01 2016 - 09:36:07 CDT)
Re: ion escapes the channel during US simulation Olya Kravchenko (Thu Sep 01 2016 - 09:03:14 CDT)
Re: NAMD Question: Generating ensemble of structures Brian Radak (Thu Sep 01 2016 - 08:44:10 CDT)
AW: FATAL ERROR CUDA error during equilibration using NAMD Norman Geist (Thu Sep 01 2016 - 01:15:55 CDT)
FATAL ERROR CUDA error during equilibration using NAMD Abraham A. Gutierrez Hernandez (Tue Aug 30 2016 - 18:27:38 CDT)
Re: ion escapes the channel during US simulation Amy Rice (Wed Aug 31 2016 - 10:40:16 CDT)
AW: NAMD Question: Generating ensemble of structures Norman Geist (Wed Aug 31 2016 - 01:29:49 CDT)
NAMD Question: Generating ensemble of structures Oscar Bastidas (Wed Aug 31 2016 - 00:52:20 CDT)
Topology and parameter files for liquid methane Monika Madhavi (Wed Aug 31 2016 - 00:24:24 CDT)
ion escapes the channel during US simulation Olya Kravchenko (Tue Aug 30 2016 - 16:17:26 CDT)
(no subject) krishna (Mon Aug 29 2016 - 03:03:21 CDT)
Re: targetCenters in Umbrella Sampling Vermaas, Joshua (Wed Aug 24 2016 - 18:04:31 CDT)
targetCenters in Umbrella Sampling Olya Kravchenko (Wed Aug 24 2016 - 17:50:36 CDT)
Re: PMF calculation input files Olya Kravchenko (Wed Aug 24 2016 - 16:23:30 CDT)
Re: interpretation of eigenvec colvar? JC Gumbart (Tue Aug 23 2016 - 22:12:48 CDT)
Re: interpretation of eigenvec colvar? Giacomo Fiorin (Tue Aug 23 2016 - 20:29:37 CDT)
interpretation of eigenvec colvar? JC Gumbart (Tue Aug 23 2016 - 20:02:37 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Tue Aug 23 2016 - 14:28:36 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Tue Aug 23 2016 - 14:16:28 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Tue Aug 23 2016 - 13:59:31 CDT)
Re: NAMD equilibrium step Brian Radak (Tue Aug 23 2016 - 13:55:47 CDT)
Re: PMF calculation input files Vermaas, Joshua (Tue Aug 23 2016 - 11:02:01 CDT)
Re: PMF calculation input files Olya Kravchenko (Tue Aug 23 2016 - 10:01:05 CDT)
Re: PMF calculation input files Vermaas, Joshua (Mon Aug 22 2016 - 16:27:34 CDT)
Shrinking a molecule (Colvars and Constant Pressure not working) Sonu Kumar (Mon Aug 22 2016 - 15:21:48 CDT)
Re: PMF calculation input files Olya Kravchenko (Mon Aug 22 2016 - 15:10:57 CDT)
Re: PMF calculation input files Vermaas, Joshua (Mon Aug 22 2016 - 11:23:58 CDT)
PMF calculation input files Olya Kravchenko (Mon Aug 22 2016 - 10:30:28 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Mon Aug 22 2016 - 07:34:17 CDT)
NAMD equilibrium step d.ronika_at_iitg.ernet.in (Mon Aug 22 2016 - 00:34:01 CDT)
Re: Graphene Oxide Parameter File Jeff Comer (Sat Aug 20 2016 - 16:25:07 CDT)
Graphene Oxide Parameter File Marisol Oswald (Sat Aug 20 2016 - 14:25:38 CDT)
Re: how to rerun a namd trajectory in order to complement the missing snapshots? Brian Radak (Fri Aug 19 2016 - 07:54:54 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Fri Aug 19 2016 - 04:00:59 CDT)
RE: Autocorrelation function of Rg goes down without fluctuation around zero Lennart Nilsson (Fri Aug 19 2016 - 01:42:03 CDT)
how to rerun a namd trajectory in order to complement the missing snapshots? sunyeping (Thu Aug 18 2016 - 22:35:51 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 13:50:23 CDT)
RE: Autocorrelation function of Rg goes down without fluctuation around zero Lennart Nilsson (Thu Aug 18 2016 - 13:29:40 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 11:37:31 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 11:31:05 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 11:27:39 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 11:20:22 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 11:16:57 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 11:00:16 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 10:31:53 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 10:21:30 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 10:16:34 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 09:47:02 CDT)
Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 04:21:07 CDT)
Re: AW: Energy minimization Vermaas, Joshua (Wed Aug 17 2016 - 10:55:14 CDT)
Re: AW: Energy minimization d.ronika_at_iitg.ernet.in (Wed Aug 17 2016 - 05:09:01 CDT)
AW: Energy minimization Norman Geist (Tue Aug 16 2016 - 23:53:20 CDT)
Hands-On Workshop on Computational Biophysics: November 14-18 in Atlanta, GA Jodi Ann Hadden (Tue Aug 16 2016 - 15:41:22 CDT)
Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL Jodi Ann Hadden (Tue Aug 16 2016 - 15:21:32 CDT)
Re: Lipid Bilayer Shearing Vermaas, Joshua (Tue Aug 16 2016 - 13:06:52 CDT)
Re: Lipid Bilayer Shearing Sachin Natesh (Tue Aug 16 2016 - 13:01:45 CDT)
Re: Lipid Bilayer Shearing Vermaas, Joshua (Tue Aug 16 2016 - 12:25:06 CDT)
Lipid Bilayer Shearing Sachin Natesh (Tue Aug 16 2016 - 12:01:15 CDT)
Introducing PDBManip Ali Khanlarkhani (Tue Aug 16 2016 - 10:10:05 CDT)
Re: Energy minimization Aron Broom (Tue Aug 16 2016 - 09:57:04 CDT)
Energy minimization d.ronika_at_iitg.ernet.in (Mon Aug 15 2016 - 00:05:12 CDT)
Re: PMF Calculation Brian Radak (Sun Aug 14 2016 - 16:36:06 CDT)
Re: psfgen: creating segments without extra hydrogens? Brian Radak (Sun Aug 14 2016 - 16:39:59 CDT)
psfgen: creating segments without extra hydrogens? Emerson Macedo (Sat Aug 13 2016 - 13:58:49 CDT)
PMF Calculation Crystal Liu (Fri Aug 12 2016 - 19:15:46 CDT)
RE: Is it possible to perform NVT FEP on a fluid system? Radak, Brian K (Tue Aug 09 2016 - 10:22:59 CDT)
RE: Is it possible to perform NVT FEP on a fluid system? Jeffrey Potoff (Tue Aug 09 2016 - 12:10:10 CDT)
RE: Is it possible to perform NVT FEP on a fluid system? Radak, Brian K (Tue Aug 09 2016 - 11:51:05 CDT)
Re: Energy minimization in NAMD Ajasja LjubetiÄ (Tue Aug 09 2016 - 11:27:41 CDT)
RE: Is it possible to perform NVT FEP on a fluid system? B.W.J. Irwin (Tue Aug 09 2016 - 11:23:58 CDT)
Is it possible to perform NVT FEP on a fluid system? B.W.J. Irwin (Tue Aug 09 2016 - 05:22:08 CDT)
Re: Energy minimization in NAMD Ajasja LjubetiÄ (Tue Aug 09 2016 - 04:24:08 CDT)
Re: Energy minimization in NAMD Ajasja LjubetiÄ (Mon Aug 08 2016 - 15:54:58 CDT)
Energy minimization in NAMD Faramarz Joodaki (Mon Aug 08 2016 - 11:37:45 CDT)
how to not overwrite a modified file? (while producing coordinates for ABF/US windows) Olya Kravchenko (Sat Aug 06 2016 - 07:18:56 CDT)
Re: How to replace NAMD Eletrostatic Forces Emerson Macedo (Fri Aug 05 2016 - 10:45:12 CDT)
Re: How to replace NAMD Eletrostatic Forces Giacomo Fiorin (Fri Aug 05 2016 - 09:45:05 CDT)
Re: How to replace NAMD Eletrostatic Forces Ajasja LjubetiÄ (Fri Aug 05 2016 - 02:46:00 CDT)
AW: How to replace NAMD Eletrostatic Forces Norman Geist (Fri Aug 05 2016 - 02:33:51 CDT)
Re: How to replace NAMD Eletrostatic Forces Brian Radak (Thu Aug 04 2016 - 15:17:17 CDT)
How to replace NAMD Eletrostatic Forces Emerson Macedo (Thu Aug 04 2016 - 13:15:38 CDT)
Re: Fatal Error: vdw atom type CC3161 Allen, Caley R (Wed Aug 03 2016 - 13:46:17 CDT)
Re: Fatal Error: vdw atom type CC3161 Chitrak Gupta (Wed Aug 03 2016 - 10:11:51 CDT)
Fatal Error: vdw atom type CC3161 Allen, Caley R (Wed Aug 03 2016 - 09:53:37 CDT)
Re: Generalized Born solvation models supported by NAMD Chitrak Gupta (Tue Aug 02 2016 - 17:54:08 CDT)
Re: Generalized Born solvation models supported by NAMD Aron Broom (Tue Aug 02 2016 - 09:41:09 CDT)
Maximum dihedral angle Mahdi Tavakol (Sun Jul 31 2016 - 03:19:16 CDT)
Re: Generalized Born solvation models supported by NAMD Chitrak Gupta (Fri Jul 29 2016 - 16:05:02 CDT)
Re: Generalized Born solvation models supported by NAMD Aron Broom (Fri Jul 29 2016 - 14:24:21 CDT)
Re: Generalized Born solvation models supported by NAMD Thomas Evangelidis (Fri Jul 29 2016 - 13:18:08 CDT)
Re: Generalized Born solvation models supported by NAMD Aron Broom (Fri Jul 29 2016 - 12:25:49 CDT)
Re: Generalized Born solvation models supported by NAMD Thomas Evangelidis (Fri Jul 29 2016 - 11:20:46 CDT)
Re: Generalized Born solvation models supported by NAMD Aron Broom (Fri Jul 29 2016 - 10:55:51 CDT)
performance drop during run Chitrak Gupta (Fri Jul 29 2016 - 10:41:32 CDT)
Generalized Born solvation models supported by NAMD Thomas Evangelidis (Fri Jul 29 2016 - 10:26:13 CDT)
water permeation through nanotube in lipid bilayer Nikhil Maroli (Fri Jul 29 2016 - 07:18:45 CDT)
Re: SMD Constant velocity pulling jeevan gc (Wed Jul 27 2016 - 16:45:19 CDT)
Re: SMD Constant velocity pulling Allen, Caley R (Wed Jul 27 2016 - 13:38:19 CDT)
group selection in TCL script for use in NAMD Allen, Caley R (Wed Jul 27 2016 - 13:35:05 CDT)
SMD Constant velocity pulling Roshan Shrestha (Wed Jul 27 2016 - 12:59:49 CDT)
Re: Kenneth Huang (Tue Jul 26 2016 - 08:09:12 CDT)
(no subject) krishna (Tue Jul 26 2016 - 00:56:38 CDT)
RE: Msd Radak, Brian K (Mon Jul 25 2016 - 12:48:13 CDT)
Re: Equivalent of gromacs' "rdd" option Marlon Sidore (Mon Jul 25 2016 - 10:44:48 CDT)
Re: Equivalent of gromacs' "rdd" option Fotis Baltoumas (Mon Jul 25 2016 - 10:26:05 CDT)
Re: Equivalent of gromacs' "rdd" option Axel Kohlmeyer (Mon Jul 25 2016 - 10:16:08 CDT)
Re: Equivalent of gromacs' "rdd" option Fotis Baltoumas (Mon Jul 25 2016 - 10:08:18 CDT)
Msd Mahdiye Azadpour (Sat Jul 23 2016 - 23:21:09 CDT)
Re: Equivalent of gromacs' "rdd" option Marlon Sidore (Mon Jul 25 2016 - 02:56:06 CDT)
Re: Problems with wrapAll Sonu Kumar (Fri Jul 22 2016 - 13:08:33 CDT)
Re: Problems with wrapAll Vermaas, Joshua (Fri Jul 22 2016 - 11:55:30 CDT)
Re: Problems with wrapAll MEHRAN MB (Fri Jul 22 2016 - 11:35:12 CDT)
Re: Equivalent of gromacs' "rdd" option Fotis Baltoumas (Fri Jul 22 2016 - 11:05:50 CDT)
Re: Equivalent of gromacs' "rdd" option Marlon Sidore (Fri Jul 22 2016 - 10:16:57 CDT)
Equivalent of gromacs' "rdd" option Marlon Sidore (Fri Jul 22 2016 - 10:12:47 CDT)
Repulsion of lipid bilayer during equilibration Mahrukh Imtiaz (Fri Jul 22 2016 - 05:00:41 CDT)
Re: Problems with wrapAll Sonu Kumar (Fri Jul 22 2016 - 06:58:13 CDT)
System temperature check of specific atoms , sys temp of only coupled atoms? Karson Bader (Thu Jul 21 2016 - 15:36:13 CDT)
is there a way to prevent ions from entering the channel? Olya Kravchenko (Thu Jul 21 2016 - 12:56:57 CDT)
Re: Problems with wrapAll Vermaas, Joshua (Thu Jul 21 2016 - 11:14:48 CDT)
Problems with wrapAll Sonu Kumar (Thu Jul 21 2016 - 00:52:55 CDT)
NAMD related theoretical questions Kostas Malavazos (Wed Jul 20 2016 - 12:33:11 CDT)
Re: Boyang Wang (Tue Jul 19 2016 - 23:33:49 CDT)
(no subject) d.ronika_at_iitg.ernet.in (Tue Jul 19 2016 - 22:52:43 CDT)
aMD doesn't work when some atoms are fixed sunyeping (Mon Jul 18 2016 - 20:41:34 CDT)
Re: how to reassign dcdfreq?? Faramarz Joodaki (Wed Jul 13 2016 - 08:02:23 CDT)
Re: how to reassign dcdfreq?? Faramarz Joodaki (Wed Jul 13 2016 - 08:01:09 CDT)
Re: how to reassign dcdfreq?? Marlon Sidore (Wed Jul 13 2016 - 03:35:52 CDT)
namd2 seg fault NAMD_2.11_Source Linux-x86_64-g++ Doug Stetner (Tue Jul 12 2016 - 22:51:40 CDT)
RE: how to reassign dcdfreq?? Radak, Brian K (Tue Jul 12 2016 - 13:22:08 CDT)
how to reassign dcdfreq?? Faramarz Joodaki (Mon Jul 11 2016 - 22:17:54 CDT)
Intramolecular interaction energy of protein in vacuum from NAMD simualtions dayanidhi mohanta (Sat Jul 09 2016 - 08:26:13 CDT)
The adaptTemp and Temp in Adaptive tempering Chenyi L (Thu Jul 07 2016 - 19:51:03 CDT)
Possible bug in DCD writer, number of frames not in NSET but in 5-ZEROS Norman Geist (Wed Jul 06 2016 - 07:26:01 CDT)
Re: unbinding free energy using ABF JC Gumbart (Tue Jul 05 2016 - 18:28:59 CDT)
Re: metadynamics and pmf file Giacomo Fiorin (Tue Jul 05 2016 - 16:29:10 CDT)
Re: vmd-l: Inconsistent atom count John Stone (Tue Jul 05 2016 - 12:54:26 CDT)
Inconsistent atom count Laura Joana (Tue Jul 05 2016 - 12:04:44 CDT)
metadynamics and pmf file Stefano Guglielmo (Mon Jul 04 2016 - 19:43:23 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Fri Jul 01 2016 - 18:42:21 CDT)
Re: unbinding free energy using ABF Gabriel Jara (Fri Jul 01 2016 - 16:13:32 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Fri Jul 01 2016 - 15:50:15 CDT)
get seed Laura Joana (Fri Jul 01 2016 - 11:52:46 CDT)
Re: unbinding free energy using ABF JC Gumbart (Thu Jun 30 2016 - 15:51:09 CDT)
unbinding free energy using ABF Gabriel Jara (Thu Jun 30 2016 - 13:25:27 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Tue Jun 28 2016 - 16:37:49 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Tue Jun 28 2016 - 16:20:13 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Tue Jun 28 2016 - 15:57:14 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Tue Jun 28 2016 - 15:35:53 CDT)
Re: MDFF based on known EM maps Ryan McGreevy (Tue Jun 28 2016 - 12:20:46 CDT)
MDFF based on known EM maps giulia palermo (Tue Jun 28 2016 - 12:08:12 CDT)
Potential per TS looks wierd faride badalkhani (Mon Jun 27 2016 - 13:18:33 CDT)
Re: LJcorrection option in NAMD Grace Brannigan (Mon Jun 27 2016 - 06:41:33 CDT)
Re: PME vs. cutoff with switching function JC Gumbart (Mon Jun 27 2016 - 00:33:36 CDT)
Re: Tesla K80 vs 3 x GTX 980Ti JC Gumbart (Mon Jun 27 2016 - 00:26:31 CDT)
Re: LJcorrection option in NAMD JC Gumbart (Mon Jun 27 2016 - 00:23:12 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Sun Jun 26 2016 - 15:13:36 CDT)
Re: Tesla K80 vs 3 x GTX 980Ti Aron Broom (Sun Jun 26 2016 - 15:07:13 CDT)
Tesla K80 vs 3 x GTX 980Ti Nikhil Maroli (Sat Jun 25 2016 - 11:24:25 CDT)
Tesla K80 vs 3 x GTX 980ti Nikhil Maroli (Sat Jun 25 2016 - 08:02:25 CDT)
PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Fri Jun 24 2016 - 17:01:13 CDT)
Re: transition metal parameters luca belmonte (Fri Jun 24 2016 - 03:04:02 CDT)
transition metal parameters Francesca Lønstad Bleken (Fri Jun 24 2016 - 02:19:01 CDT)
Re: Exit Command Failure Jeff Comer (Thu Jun 23 2016 - 08:45:54 CDT)
Exit Command Failure Sarah Sweger (Thu Jun 23 2016 - 08:01:09 CDT)
The question about Network calculation ÀîÎÄ¾ê (Thu Jun 23 2016 - 03:28:47 CDT)
Re: Applying "selectionRule" in Multiple Walker ABF Souvik Sinha (Thu Jun 23 2016 - 03:07:13 CDT)
Re: LJcorrection option in NAMD Brian Radak (Wed Jun 22 2016 - 17:22:07 CDT)
Re: LJcorrection option in NAMD Brian Radak (Wed Jun 22 2016 - 17:04:02 CDT)
Re: Applying "selectionRule" in Multiple Walker ABF Marlon Sidore (Wed Jun 22 2016 - 11:00:32 CDT)
Re: Applying "selectionRule" in Multiple Walker ABF Jeff Comer (Wed Jun 22 2016 - 09:49:31 CDT)
Re: LJcorrection option in NAMD Grace Brannigan (Tue Jun 21 2016 - 13:03:24 CDT)
Re: LJcorrection option in NAMD Brian Radak (Tue Jun 21 2016 - 07:36:06 CDT)
LJcorrection option in NAMD Yue Qian (Mon Jun 20 2016 - 17:09:04 CDT)
Re: Coarse Grain Angle Parameter Issue Fotis Baltoumas (Sat Jun 18 2016 - 00:23:37 CDT)
Coarse Grain Angle Parameter Issue Nisler, Collin R. (Fri Jun 17 2016 - 22:37:42 CDT)
PME vs. cutoff with switching function Benjamin Brown (Fri Jun 17 2016 - 10:25:44 CDT)
Re: namd2 or charmrun ++local ? Giacomo Fiorin (Fri Jun 17 2016 - 13:18:48 CDT)
namd2 or charmrun ++local ? Laura Joana (Fri Jun 17 2016 - 11:35:05 CDT)
Re: RMSD faride badalkhani (Thu Jun 16 2016 - 14:13:40 CDT)
Re: RMSD Brian Radak (Thu Jun 16 2016 - 14:11:29 CDT)
Re: RMSD faride badalkhani (Thu Jun 16 2016 - 14:02:43 CDT)
Re: RMSD Brian Radak (Thu Jun 16 2016 - 13:51:46 CDT)
RMSD faride badalkhani (Thu Jun 16 2016 - 12:42:32 CDT)
Colvar orientation and CoG Nicolas Martin (Thu Jun 16 2016 - 09:02:28 CDT)
Regarding radial distribution function graph siddharth kamal (Thu Jun 16 2016 - 08:31:23 CDT)
Re: Free energy calculation using MM-GBSA with NAMD Jeff Comer (Wed Jun 15 2016 - 09:10:21 CDT)
Free energy calculation using MM-GBSA with NAMD Sneha Menon (Wed Jun 15 2016 - 05:50:41 CDT)
RE: Missing atom type for hydroperoxide Radak, Brian K (Tue Jun 14 2016 - 12:58:25 CDT)
Missing atom type for hydroperoxide Jean-FranÃ§ois Fabre (Tue Jun 14 2016 - 10:48:55 CDT)
Why does the water box collapse in an aMD sunyeping (Mon Jun 13 2016 - 21:11:00 CDT)
Re: Topology Command in VMD Josh Vermaas (Mon Jun 13 2016 - 08:22:33 CDT)
Drude Prepper error in genic Francesco Pietra (Mon Jun 13 2016 - 01:33:15 CDT)
Permeation of liquid through Silicon Dioxide Crystal Roshan Shrestha (Fri Jun 10 2016 - 07:30:00 CDT)
Topology Command in VMD Eric Weine (Thu Jun 09 2016 - 19:27:39 CDT)
The adaptTemp and Temp in Adaptive tempering §³henyi (Thu Jun 09 2016 - 15:17:25 CDT)
RE: Building PSF for the system prepared by Packmol Radak, Brian K (Thu Jun 09 2016 - 14:16:46 CDT)
Re: ATP - CGENFF JC Gumbart (Thu Jun 09 2016 - 09:36:37 CDT)
Building PSF for the system prepared by Packmol faride badalkhani (Thu Jun 09 2016 - 09:27:31 CDT)
NBFIX parameters for Calcium ion Azadeh Alavi (Thu Jun 09 2016 - 04:49:04 CDT)
ATP - CGENFF Benjamin Hill (Tue Jun 07 2016 - 19:34:15 CDT)
An script for ACF faride badalkhani (Tue Jun 07 2016 - 16:37:13 CDT)
Help about Drude Prepper Francesco Pietra (Tue Jun 07 2016 - 10:06:48 CDT)
Re: AW: Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Tue Jun 07 2016 - 11:21:09 CDT)
cgenff Benjamin Hill (Mon Jun 06 2016 - 14:48:30 CDT)
Re: Colvars order in the pmf file Marlon Sidore (Mon Jun 06 2016 - 10:49:01 CDT)
Re: Colvars order in the pmf file Giacomo Fiorin (Mon Jun 06 2016 - 09:57:38 CDT)
Re: How can I find the proper number of solvent molecules in the simulation? Brian Radak (Mon Jun 06 2016 - 09:49:42 CDT)
How can I find the proper number of solvent molecules in the simulation? faride badalkhani (Mon Jun 06 2016 - 09:25:50 CDT)
Colvars order in the pmf file Marlon Sidore (Mon Jun 06 2016 - 09:14:53 CDT)
much larger diameter of ssDNA, Aliasghar Alizadeh-Mojarad (Sat Jun 04 2016 - 04:22:41 CDT)
namdenergy and bigdcd Grant Schauer (Thu Jun 02 2016 - 23:58:23 CDT)
Re: Unable to compile Tachyon on Sun Grid Engine Sourav Ray (Sat Jun 04 2016 - 08:03:44 CDT)
Re: Unable to compile Tachyon on Sun Grid Engine Sourav Ray (Sat Jun 04 2016 - 05:59:00 CDT)
Unable to compile Tachyon on Sun Grid Engine Sourav Ray (Sat Jun 04 2016 - 04:20:29 CDT)
Re: Is GPU double-precision floating point performance important for NAMD? Mert GÃ¼r (Fri Jun 03 2016 - 09:20:42 CDT)
AW: Is GPU double-precision floating point performance important for NAMD? Norman Geist (Fri Jun 03 2016 - 01:49:06 CDT)
AW: AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Fri Jun 03 2016 - 01:39:54 CDT)
Is GPU double-precision floating point performance important for NAMD? Mert GÃ¼r (Thu Jun 02 2016 - 16:48:07 CDT)
Re: AW: Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Thu Jun 02 2016 - 10:59:56 CDT)
autocorrelation function faride badalkhani (Thu Jun 02 2016 - 09:06:04 CDT)
AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Thu Jun 02 2016 - 01:33:55 CDT)
download stmv files for benchmarking Bennion, Brian (Wed Jun 01 2016 - 14:29:22 CDT)
Re: Chitrak Gupta (Wed Jun 01 2016 - 13:03:34 CDT)
non-standard solvants faride badalkhani (Wed Jun 01 2016 - 11:55:28 CDT)
Re: Umbrella sampling of 2 CNT's taking distance as collective variable JÃ©rÃ´me HÃ©nin (Wed Jun 01 2016 - 10:26:27 CDT)
Re: Chitrak Gupta (Wed Jun 01 2016 - 08:57:57 CDT)
Re: Umbrella sampling of 2 CNT's taking distance as collective variable Giacomo Fiorin (Wed Jun 01 2016 - 05:07:50 CDT)
AW: Simulation runs only in background Daniel MÃ¶ller (Wed Jun 01 2016 - 04:44:55 CDT)
Re: Simulation runs only in background Marlon Sidore (Wed Jun 01 2016 - 04:09:16 CDT)
Simulation runs only in background Roshan Shrestha (Wed Jun 01 2016 - 03:44:15 CDT)
Umbrella sampling of 2 CNT's taking distance as collective variable Kashish Punjani (Wed Jun 01 2016 - 01:16:45 CDT)
(no subject) Srijita Paul (Tue May 31 2016 - 23:29:11 CDT)
Using Mergestructs Eric Weine (Tue May 31 2016 - 14:09:46 CDT)
namd "WARNING: ignoring command" problem Shambo Hore (Tue May 31 2016 - 12:11:35 CDT)
Re: Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Tue May 31 2016 - 11:18:08 CDT)
AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Tue May 31 2016 - 08:41:23 CDT)
(no subject) Srijita Paul (Tue May 31 2016 - 05:03:47 CDT)
AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Tue May 31 2016 - 04:24:52 CDT)
Re: Applying "selectionRule" in Multiple Walker ABF Souvik Sinha (Tue May 31 2016 - 01:27:08 CDT)
Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Mon May 30 2016 - 11:28:24 CDT)
Re: No parameter for ribose ring, Charmm 27 JC Gumbart (Mon May 30 2016 - 07:19:44 CDT)
Re: setting up simulation in vmd using charmm 36 forcefield JC Gumbart (Mon May 30 2016 - 07:29:44 CDT)
SMD simulation problem. Shambo Hore (Sun May 29 2016 - 20:15:57 CDT)
Re: No parameter for ribose ring, Charmm 27 Benjamin Hill (Sun May 29 2016 - 11:12:07 CDT)
RE: No parameter for ribose ring, Charmm 27 Lennart Nilsson (Fri May 27 2016 - 15:28:43 CDT)
Re: Conversion from GROMACS .top .itp to CHARMM .psf .par combo Roshan Shrestha (Sat May 28 2016 - 10:04:08 CDT)
Conversion from GROMACS .top .itp to CHARMM .psf .par combo Sourav Ray (Sat May 28 2016 - 10:00:54 CDT)
setting up simulation in vmd using charmm 36 forcefield Rabeta Yeasmin (Fri May 27 2016 - 16:28:38 CDT)
More FEP using separated topologies David Huggins (Fri May 27 2016 - 15:21:01 CDT)
Re: No parameter for ribose ring, Charmm 27 JC Gumbart (Fri May 27 2016 - 14:14:17 CDT)
Applying "selectionRule" in Multiple Walker ABF Souvik Sinha (Fri May 27 2016 - 09:43:28 CDT)
Re: No parameter for ribose ring, Charmm 27 Benjamin Hill (Fri May 27 2016 - 05:51:40 CDT)
No parameter for ribose ring, Charmm 27 Lennart Nilsson (Fri May 27 2016 - 05:42:02 CDT)
Re: truncated text RE: external computational power for NAMD Roshan Shrestha (Thu May 26 2016 - 21:35:39 CDT)
Re: No parameter for ribose ring, Charmm 27 JC Gumbart (Thu May 26 2016 - 18:42:52 CDT)
No parameter for ribose ring, Charmm 27 Benjamin Hill (Thu May 26 2016 - 17:18:43 CDT)
truncated text RE: external computational power for NAMD Deng, Jinxia (Nancy) (Thu May 26 2016 - 12:59:40 CDT)
external computational power for NAMD Deng, Jinxia (Nancy) (Thu May 26 2016 - 12:02:54 CDT)
Binding energy of organic molecules/small peptides on the surface of Silicon Dioxide Roshan Shrestha (Thu May 26 2016 - 10:29:01 CDT)
Re: AW: Re: AW: AW: AW: why does the transition seem to be irreversible in aMD sunyeping (Wed May 25 2016 - 00:48:18 CDT)
Re: FES analysis Giacomo Fiorin (Tue May 24 2016 - 16:00:51 CDT)
FES analysis Stefano Guglielmo (Tue May 24 2016 - 15:46:21 CDT)
hyper-branched polymers faride badalkhani (Tue May 24 2016 - 09:24:41 CDT)
Re: H-bonds in charmm36 with namd2.11 Francesco Pietra (Tue May 24 2016 - 04:30:13 CDT)
AW: Re: AW: AW: AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue May 24 2016 - 00:57:09 CDT)
Re: I cannot make MD simulation constant in pressure Peter Freddolino (Mon May 23 2016 - 22:56:48 CDT)
Re: I cannot make MD simulation constant in pressure Faramarz Joodaki (Mon May 23 2016 - 22:44:21 CDT)
Re: I cannot make MD simulation constant in pressure Peter Freddolino (Mon May 23 2016 - 21:01:23 CDT)
Re: Adsorption energy of protein in vacuum Abhishek TYAGI (Mon May 23 2016 - 19:52:56 CDT)
Re: I cannot make MD simulation constant in pressure Faramarz Joodaki (Mon May 23 2016 - 18:29:14 CDT)
Re: I cannot make MD simulation constant in pressure Jeff Comer (Mon May 23 2016 - 16:06:17 CDT)
I cannot make MD simulation constant in pressure Faramarz Joodaki (Mon May 23 2016 - 14:41:54 CDT)
Re: Adsorption energy of protein in vacuum Jeff Comer (Mon May 23 2016 - 12:02:17 CDT)
namd leaves zombie processes on nodes? JC Gumbart (Mon May 23 2016 - 10:01:45 CDT)
Re: H-bonds in charmm36 with namd2.11 JC Gumbart (Mon May 23 2016 - 08:59:24 CDT)
AW: Re: AW: AW: AW: why does the transition seem to be irreversible in aMD Norman Geist (Mon May 23 2016 - 08:42:04 CDT)
firstTimestep error message Laura Joana (Mon May 23 2016 - 05:55:51 CDT)
Re: AW: AW: AW: why does the transition seem to be irreversible in aMD sunyeping (Mon May 23 2016 - 03:53:37 CDT)
Re: Restart multiple walker ABF Atanu Maity (Mon May 23 2016 - 01:13:10 CDT)
Re: Restart multiple walker ABF Atanu Maity (Sun May 22 2016 - 23:55:32 CDT)
Re: Adsorption energy of protein in vacuum Abhishek TYAGI (Sun May 22 2016 - 22:46:38 CDT)
RE: Parameters for HS(CH2)11NH2 Deng, Jinxia (Nancy) (Sun May 22 2016 - 14:03:37 CDT)
Re: SMD simulation problem Madhulika Gupta (Sun May 22 2016 - 10:59:18 CDT)
SMD simulation problem Shambo Hore (Sun May 22 2016 - 10:37:52 CDT)
Fwd: H-bonds in charmm36 with namd2.11 Francesco Pietra (Sun May 22 2016 - 01:46:52 CDT)
Re: H-bonds in charmm36 with namd2.11 Francesco Pietra (Sun May 22 2016 - 01:43:55 CDT)
Re: H-bonds in charmm36 with namd2.11 JC Gumbart (Sat May 21 2016 - 18:44:09 CDT)
Re: Coarse-grained simulation with Polarizable Water crashing Fotis Baltoumas (Sat May 21 2016 - 17:14:36 CDT)
Re: Coarse-grained simulation with Polarizable Water crashing Sourav Ray (Sat May 21 2016 - 11:39:42 CDT)
Re: Adsorption energy of protein in vacuum Madhulika Gupta (Sat May 21 2016 - 10:20:34 CDT)
Re: Adsorption energy of protein in vacuum Ana Celia Vila Verde (Sat May 21 2016 - 04:17:54 CDT)
Parameters for HS(CH2)11NH2 Natnael Doilicho (Fri May 20 2016 - 19:06:55 CDT)
H-bonds in charmm36 with namd2.11 Francesco Pietra (Fri May 20 2016 - 16:18:22 CDT)
Have GPU-accelerated NAMD Questions? Join us for a Live Webinar MARK (Fri May 20 2016 - 13:07:08 CDT)
RE: Excessively high dE_avg values in FEP output (NAMD CVS) Radak, Brian K (Fri May 20 2016 - 11:58:43 CDT)
Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Pardis Tabaee (Fri May 20 2016 - 11:12:24 CDT)
Re: Some questions on the Deca-Alanine ABF tutorial Pardis Tabaee (Fri May 20 2016 - 09:52:09 CDT)
Re: Colvars: Unable to restrict rotation and translation along y and z axes Giacomo Fiorin (Fri May 20 2016 - 10:33:27 CDT)
Re: Some questions on the Deca-Alanine ABF tutorial Pardis Tabaee (Fri May 20 2016 - 10:01:13 CDT)
Re: Excessively high dE_avg values in FEP output (NAMD CVS) Brian Radak (Fri May 20 2016 - 07:47:33 CDT)
Adsorption energy of protein in vacuum Madhulika Gupta (Fri May 20 2016 - 06:01:05 CDT)
Re: Colvars: Unable to restrict rotation and translation along y and z axes Sourav Ray (Fri May 20 2016 - 01:31:38 CDT)
Re: Some questions on the Deca-Alanine ABF tutorial sunyeping (Thu May 19 2016 - 22:41:05 CDT)
Re: Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Thu May 19 2016 - 16:21:08 CDT)
Re: Restart multiple walker ABF Jeff Comer (Thu May 19 2016 - 15:58:22 CDT)
Re: Restart multiple walker ABF Atanu Maity (Thu May 19 2016 - 03:36:30 CDT)
Restart multiple walker ABF Atanu Maity (Thu May 19 2016 - 03:32:24 CDT)
Re: Some questions on the Deca-Alanine ABF tutorial sunyeping (Wed May 18 2016 - 20:29:46 CDT)
Re: TIP4P water with flexible bonds Jeff Comer (Wed May 18 2016 - 17:03:53 CDT)
TIP4P water with flexible bonds Hartling, Kathryn (Wed May 18 2016 - 14:32:24 CDT)
Re: Excessively high dE_avg values in FEP output (NAMD CVS) Brian Radak (Wed May 18 2016 - 13:25:44 CDT)
Re: Colvars: Unable to restrict rotation and translation along y and z axes Giacomo Fiorin (Wed May 18 2016 - 08:23:14 CDT)
Colvars: Unable to restrict rotation and translation along y and z axes Sourav Ray (Wed May 18 2016 - 07:22:00 CDT)
Re: Some questions on the Deca-Alanine ABF tutorial sunyeping (Wed May 18 2016 - 03:06:08 CDT)
MDFF with two symmetry groups Benjamin.Haberl_at_physik.uni-muenchen.de (Tue May 17 2016 - 14:48:19 CDT)
Re: Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Tue May 17 2016 - 14:20:32 CDT)
Error associated with protected variable initialization: Nightly Build version Sourav Ray (Tue May 17 2016 - 13:50:54 CDT)
Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Tue May 17 2016 - 11:43:05 CDT)
Ph.D. positions available Ivaylo Nikolaev Ivanov (Tue May 17 2016 - 10:10:41 CDT)
Postdoc position available Ivaylo Nikolaev Ivanov (Tue May 17 2016 - 10:05:18 CDT)
Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params JC Gumbart (Tue May 17 2016 - 09:29:52 CDT)
ffTK fitting dihedrals Seth Axen (Tue May 17 2016 - 01:36:02 CDT)
Re: Excessively high dE_avg values in FEP output (NAMD CVS) Giacomo Fiorin (Mon May 16 2016 - 18:51:55 CDT)
running simulations in successive steps faride badalkhani (Mon May 16 2016 - 17:31:31 CDT)
Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Mon May 16 2016 - 16:29:32 CDT)
Combining Drude structures Jeff Comer (Mon May 16 2016 - 16:25:32 CDT)
Re: Coarse-grained simulation with Polarizable Water crashing Sourav Ray (Mon May 16 2016 - 15:31:14 CDT)
Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Mon May 16 2016 - 12:42:27 CDT)
Re: Coarse-grained simulation with Polarizable Water crashing Jeff Comer (Mon May 16 2016 - 12:04:43 CDT)
Particle Mesh Ewald with Martini Sourav Ray (Mon May 16 2016 - 10:55:14 CDT)
Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 08:54:45 CDT)
Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 08:54:31 CDT)
Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Peter Freddolino (Mon May 16 2016 - 07:46:47 CDT)
Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 04:30:29 CDT)
Some questions on the Deca-Alanine ABF tutorial sunyeping (Mon May 16 2016 - 04:19:33 CDT)
Re: Equilibration and production run Ajasja LjubetiÄ (Mon May 16 2016 - 03:23:29 CDT)
CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 02:45:55 CDT)
Equilibration and production run dhirajks_at_gmail.com (Mon May 16 2016 - 01:25:32 CDT)
Re: Coarse-grained simulation with Polarizable Water crashing Sourav Ray (Sun May 15 2016 - 17:08:31 CDT)
Coarse-grained simulation with Polarizable Water crashing Sourav Ray (Sun May 15 2016 - 16:34:18 CDT)
Re: Conversion from c6 and c12 = 0 to sigma epsilon Brian Radak (Sat May 14 2016 - 15:39:48 CDT)
Conversion from c6 and c12 = 0 to sigma epsilon Sourav Ray (Sat May 14 2016 - 06:29:49 CDT)
Output temperature not agreeing with tcouple temperature Karson Bader (Fri May 13 2016 - 12:07:52 CDT)
Martini polarizable water topology and/or psf file Sourav Ray (Thu May 12 2016 - 17:30:57 CDT)
Re: Colvars crossing "upperboundary" limit Giacomo Fiorin (Tue May 10 2016 - 15:25:18 CDT)
Re: Chitrak Gupta (Tue May 10 2016 - 13:57:03 CDT)
PMF calculation using ABF Souvik Sinha (Tue May 10 2016 - 08:57:52 CDT)
Re: Srijita Paul (Tue May 10 2016 - 08:41:10 CDT)
Re: Chitrak Gupta (Mon May 09 2016 - 11:07:14 CDT)
RE: gradual heating problem Radak, Brian K (Mon May 09 2016 - 10:12:01 CDT)
Re: Maxim Belkin (Mon May 09 2016 - 09:38:23 CDT)
PMEProcessors setting on one node dhirajks_at_gmail.com (Sun May 08 2016 - 21:22:54 CDT)
Re: Jeff Comer (Sun May 08 2016 - 20:19:44 CDT)
Re: gradual heating problem dhirajks_at_gmail.com (Sun May 08 2016 - 11:21:13 CDT)
Re: gradual heating problem Brian Radak (Sun May 08 2016 - 11:04:31 CDT)
gradual heating problem Dhiraj Srivastava (Sun May 08 2016 - 10:27:39 CDT)
Re: Abhishek TYAGI (Sat May 07 2016 - 07:45:54 CDT)
(no subject) Srijita Paul (Sat May 07 2016 - 06:17:48 CDT)
RE: heating in NPT ensemble Radak, Brian K (Fri May 06 2016 - 10:04:07 CDT)
Re: LJ parameters for Pd surface Axel Kohlmeyer (Fri May 06 2016 - 08:36:59 CDT)
LJ parameters for Pd surface Madhulika Gupta (Fri May 06 2016 - 08:33:03 CDT)
Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Pardis Tabaee (Fri May 06 2016 - 08:05:10 CDT)
heating in NPT ensemble Dhiraj Srivastava (Thu May 05 2016 - 17:39:35 CDT)
NAMD Recipe for Success with GPUs! MARK (Thu May 05 2016 - 11:35:42 CDT)
Colvars crossing "upperboundary" limit Sourav Ray (Thu May 05 2016 - 05:33:26 CDT)
Recipe for Success - GPU accelerated NAMD Mark Berger (Wed May 04 2016 - 19:25:24 CDT)
Re: excluding non-bonded interactions between two proteins Peter Freddolino (Wed May 04 2016 - 19:14:34 CDT)
Re: excluding non-bonded interactions between two proteins JC Gumbart (Wed May 04 2016 - 19:04:43 CDT)
Re: excluding non-bonded interactions between two proteins Peter Freddolino (Wed May 04 2016 - 18:41:18 CDT)
excluding non-bonded interactions between two proteins JC Gumbart (Wed May 04 2016 - 18:16:26 CDT)
parameterization of cations faride badalkhani (Wed May 04 2016 - 11:28:59 CDT)
Re: WHY!!! num_runs should be divisible by runs_per_frame * frames_per_restart -->REMD Nicholus Bhattacharjee (Wed May 04 2016 - 10:07:53 CDT)
Re: WHY!!! num_runs should be divisible by runs_per_frame * frames_per_restart -->REMD Peter Freddolino (Tue May 03 2016 - 11:08:17 CDT)
parameterizing a new solvent faride badalkhani (Tue May 03 2016 - 08:54:06 CDT)
Re: TCL Scripting for Force Calculations Allen, Caley R (Mon May 02 2016 - 14:08:17 CDT)
Re: water box and padding Jeff Comer (Mon May 02 2016 - 11:10:45 CDT)
TCL Scripting for Force Calculations Allen, Caley R (Mon May 02 2016 - 10:48:56 CDT)
Re: water box and padding Brian Radak (Mon May 02 2016 - 09:54:43 CDT)
Re: unix path length limits for namd Shyam Saladi (Sun May 01 2016 - 19:21:27 CDT)
unix path length limits for namd Chris Goedde (Sun May 01 2016 - 17:10:34 CDT)
water box and padding Dhiraj Srivastava (Sat Apr 30 2016 - 11:40:53 CDT)
Compilation of NAMD for CUDA and replica exchange #YEO JINGJIE# (Fri Apr 29 2016 - 13:53:44 CDT)
Re: Re: accessing values of 'extendedLagrangian' fictious degree of freedom JÃ©rÃ´me HÃ©nin (Fri Apr 29 2016 - 04:37:36 CDT)
Dihedral missing faride badalkhani (Thu Apr 28 2016 - 17:54:15 CDT)
Re: restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 15:59:09 CDT)
Re: restart file - langevin options removed? Maxim Belkin (Thu Apr 28 2016 - 15:36:52 CDT)
Re: restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 15:28:57 CDT)
Re: restart file - langevin options removed? Maxim Belkin (Thu Apr 28 2016 - 15:17:35 CDT)
Re: restart file - langevin options removed? Josh Vermaas (Thu Apr 28 2016 - 15:16:41 CDT)
Re: restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 15:13:00 CDT)
Re: restart file - langevin options removed? Maxim Belkin (Thu Apr 28 2016 - 15:00:57 CDT)
restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 14:49:45 CDT)
Re: accessing values of 'extendedLagrangian' fictious degree of freedom Prabhakar Bhimalapuram (Thu Apr 28 2016 - 12:23:36 CDT)
Re: Running a test simulation using GPU only (without any CPU core) Axel Kohlmeyer (Thu Apr 28 2016 - 10:40:38 CDT)
Re: Running a test simulation using GPU only (without any CPU core) Josh Vermaas (Thu Apr 28 2016 - 10:09:28 CDT)
minimization, heating, equilibration and production run in one script Dhiraj Srivastava (Thu Apr 28 2016 - 10:05:55 CDT)
Re: Running a test simulation using GPU only (without any CPU core) Sourav Ray (Thu Apr 28 2016 - 10:04:29 CDT)
Re: Running a test simulation using GPU only (without any CPU core) Brian Radak (Thu Apr 28 2016 - 10:00:42 CDT)
Running a test simulation using GPU only (without any CPU core) Sourav Ray (Thu Apr 28 2016 - 09:40:00 CDT)
Re: Autoionize and topology Josh Vermaas (Wed Apr 27 2016 - 08:11:15 CDT)
Re: accessing values of 'extendedLagrangian' fictious degree of freedom JÃ©rÃ´me HÃ©nin (Wed Apr 27 2016 - 04:24:18 CDT)
Autoionize and topology Dhiraj Srivastava (Tue Apr 26 2016 - 22:07:04 CDT)
accessing values of 'extendedLagrangian' fictious degree of freedom Prabhakar Bhimalapuram (Tue Apr 26 2016 - 22:01:58 CDT)
Re: CHARMM36 and TIP3 Josh Vermaas (Tue Apr 26 2016 - 19:49:04 CDT)
Re: CHARMM36 and TIP3 Dhiraj Srivastava (Tue Apr 26 2016 - 17:01:10 CDT)
Re: Constraint failure in RATTLE algorithm for atom 6! faride badalkhani (Tue Apr 26 2016 - 16:47:59 CDT)
Re: Constraint failure in RATTLE algorithm for atom 6! faride badalkhani (Tue Apr 26 2016 - 16:46:40 CDT)
RE: Constraint failure in RATTLE algorithm for atom 6! Radak, Brian K (Tue Apr 26 2016 - 16:40:45 CDT)
RE: Constraint failure in RATTLE algorithm for atom 6! Bennion, Brian (Tue Apr 26 2016 - 16:29:09 CDT)
RE: Constraint failure in RATTLE algorithm for atom 6! Radak, Brian K (Tue Apr 26 2016 - 16:26:30 CDT)
Re: Constraint failure in RATTLE algorithm for atom 6! faride badalkhani (Tue Apr 26 2016 - 16:22:02 CDT)
Re: Constraint failure in RATTLE algorithm for atom 6! Jeff Comer (Tue Apr 26 2016 - 16:14:50 CDT)
Re: CHARMM36 and TIP3 Brian Radak (Tue Apr 26 2016 - 13:57:05 CDT)
CHARMM36 and TIP3 Dhiraj Srivastava (Tue Apr 26 2016 - 13:37:49 CDT)
Re: Alchemify Possibilities David Huggins (Tue Apr 26 2016 - 09:28:15 CDT)
Amino acid as ligand Dhiraj Srivastava (Mon Apr 25 2016 - 12:22:24 CDT)
Re: Alchemify Possibilities Brian Radak (Mon Apr 25 2016 - 11:15:19 CDT)
Alchemify Possibilities David Huggins (Mon Apr 25 2016 - 11:03:10 CDT)
Constraint failure in RATTLE algorithm for atom 6! faride badalkhani (Mon Apr 25 2016 - 10:42:52 CDT)
XPLOR format PSF file for small molecules Felix W.-H. Weng (Sun Apr 24 2016 - 11:21:45 CDT)
Re: Why wrapped and unwrapped trajectories show different energies over the time? Brian Radak (Sun Apr 24 2016 - 09:03:07 CDT)
Re: Why wrapped and unwrapped trajectories show different energies over the time? Jason Swails (Sun Apr 24 2016 - 00:23:50 CDT)
Re: Chitrak Gupta (Sat Apr 23 2016 - 23:19:09 CDT)
Why wrapped and unwrapped trajectories show different energies over the time? zeynab hoseyni (Sat Apr 23 2016 - 21:22:04 CDT)
Why wrapped and unwrapped trajectories show different energies over time? zeynab mohamad hoseyni (Sat Apr 23 2016 - 09:30:08 CDT)
SMD in NAMD Madhulika Gupta (Sat Apr 23 2016 - 05:15:34 CDT)
Re: Peter Freddolino (Fri Apr 22 2016 - 12:26:51 CDT)
WHY!!! num_runs should be divisible by runs_per_frame * frames_per_restart -->REMD Nicholus Bhattacharjee (Fri Apr 22 2016 - 08:21:46 CDT)
Re: Srijita Paul (Fri Apr 22 2016 - 05:39:12 CDT)
Re: Replica exchange arpita agarwal (Fri Apr 22 2016 - 02:54:50 CDT)
Re: Akshay Bhatnagar (Fri Apr 22 2016 - 02:30:13 CDT)
(no subject) Srijita Paul (Fri Apr 22 2016 - 01:19:21 CDT)
Replica exchange arpita agarwal (Thu Apr 21 2016 - 00:43:44 CDT)
RE: How to use a proper force constant to decrease computational cost while keeping calculation precision? Radak, Brian K (Wed Apr 20 2016 - 16:22:09 CDT)
cell basis vectors faride badalkhani (Wed Apr 20 2016 - 13:59:11 CDT)
Re: rotation angle Giacomo Fiorin (Wed Apr 20 2016 - 13:51:43 CDT)
rotation angle giulia palermo (Wed Apr 20 2016 - 12:25:16 CDT)
Re: How to use a proper force constant to decrease computational cost while keeping calculation precision? Ana Celia Vila Verde (Wed Apr 20 2016 - 03:03:08 CDT)
How to use a proper force constant to decrease computational cost while keeping calculation precision? wliu (Wed Apr 20 2016 - 02:18:01 CDT)
Re: Peter Freddolino (Tue Apr 19 2016 - 10:03:52 CDT)
simulation of hyperbranched polymers faride badalkhani (Tue Apr 19 2016 - 07:54:49 CDT)
clarification sem ciccioni (Mon Apr 18 2016 - 16:21:08 CDT)
Early bird extended! ISQBP2016 meeting - Bergen Norway Vlad Cojocaru (Mon Apr 18 2016 - 14:35:38 CDT)
initial structure faride badalkhani (Mon Apr 18 2016 - 10:17:30 CDT)
Re: ERROR: ofstream_namd::close() called when file is not open Giacomo Fiorin (Mon Apr 18 2016 - 07:36:01 CDT)
Re: ERROR: ofstream_namd::close() called when file is not open Souvik Sinha (Mon Apr 18 2016 - 06:54:37 CDT)
Re: ERROR: ofstream_namd::close() called when file is not open Giacomo Fiorin (Mon Apr 18 2016 - 06:40:09 CDT)
ERROR: ofstream_namd::close() called when file is not open Souvik Sinha (Mon Apr 18 2016 - 02:36:33 CDT)
Re: Peter Freddolino (Sat Apr 16 2016 - 20:14:41 CDT)
(no subject) Srijita Paul (Sat Apr 16 2016 - 00:06:47 CDT)
initial structure faride badalkhani (Fri Apr 15 2016 - 14:18:03 CDT)
NAMD Developer Workshop: May 26-27 in Chicago, IL Jodi Ann Hadden (Fri Apr 15 2016 - 13:14:22 CDT)
Re: Dynamics of an interface Water/Hexane Maxim Belkin (Fri Apr 15 2016 - 07:39:43 CDT)
Re: Corrfunc output not generated Giacomo Fiorin (Thu Apr 14 2016 - 17:41:44 CDT)
Bad initial structure? faride badalkhani (Thu Apr 14 2016 - 13:50:14 CDT)
Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Thu Apr 14 2016 - 09:56:07 CDT)
Sugar phosphate topology and parameter Dhiraj Srivastava (Thu Apr 14 2016 - 00:32:55 CDT)
Regarding Bionanotechnology tutorial arpita agarwal (Wed Apr 13 2016 - 20:07:26 CDT)
Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Wed Apr 13 2016 - 12:55:28 CDT)
Re: Dynamics of an interface Water/Hexane Amy Rice (Wed Apr 13 2016 - 11:32:09 CDT)
Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Wed Apr 13 2016 - 08:32:29 CDT)
Re: Jeff Comer (Wed Apr 13 2016 - 08:32:23 CDT)
Re: Polymer moves to the edge of water box during the simulation Josh Vermaas (Wed Apr 13 2016 - 08:02:36 CDT)
Dynamics of an interface Water/Hexane Jean-FranÃ§ois Fabre (Wed Apr 13 2016 - 07:54:17 CDT)
(no subject) Srijita Paul (Wed Apr 13 2016 - 07:08:28 CDT)
Re: Corrfunc output not generated Giacomo Fiorin (Tue Apr 12 2016 - 22:00:04 CDT)
Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Tue Apr 12 2016 - 17:02:19 CDT)
Re: Polymer moves to the edge of water box during the simulation Josh Vermaas (Tue Apr 12 2016 - 16:54:35 CDT)
Polymer moves to the edge of water box during the simulation faride badalkhani (Tue Apr 12 2016 - 16:49:21 CDT)
Re: Corrfunc output not generated Giacomo Fiorin (Tue Apr 12 2016 - 16:16:00 CDT)
Unexpected(?) callback behavior when minimizing before MD Radak, Brian K (Tue Apr 12 2016 - 16:02:34 CDT)
Re: Few doubt on the numbers implying in REMD simulation Chitrak Gupta (Tue Apr 12 2016 - 10:00:21 CDT)
Re: Jeff Comer (Tue Apr 12 2016 - 08:56:29 CDT)
(no subject) Srijita Paul (Tue Apr 12 2016 - 07:33:41 CDT)
Few doubt on the numbers implying in REMD simulation Nicholus Bhattacharjee (Tue Apr 12 2016 - 07:06:42 CDT)
Corrfunc output not generated Sourav Ray (Mon Apr 11 2016 - 12:38:39 CDT)
Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 2 Sourav Ray (Mon Apr 11 2016 - 11:10:57 CDT)
Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 2 Giacomo Fiorin (Mon Apr 11 2016 - 10:08:14 CDT)
Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 1 Giacomo Fiorin (Mon Apr 11 2016 - 10:02:45 CDT)
Ru surface potential Madhulika Gupta (Mon Apr 11 2016 - 03:52:26 CDT)
Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 2 Sourav Ray (Sat Apr 09 2016 - 14:53:15 CDT)
Metadynamics simulation with Radius of Gyration and RMSD variation - 2 Sourav Ray (Sat Apr 09 2016 - 12:11:53 CDT)
Metadynamics simulation with Radius of Gyration and RMSD variation - 1 Sourav Ray (Sat Apr 09 2016 - 12:03:36 CDT)
Running Charmm36 Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Fri Apr 08 2016 - 19:04:49 CDT)
Re: Chitrak Gupta (Fri Apr 08 2016 - 16:40:46 CDT)
Re: LJ Parameters for Au and S and harmonic constraints Jeff Comer (Fri Apr 08 2016 - 12:52:50 CDT)
Re: Chitrak Gupta (Fri Apr 08 2016 - 10:01:07 CDT)
(no subject) Srijita Paul (Fri Apr 08 2016 - 08:00:25 CDT)
Re: LJ Parameters for Au and S and harmonic constraints Madhulika Gupta (Fri Apr 08 2016 - 03:24:34 CDT)
Re: LJ Parameters for Au and S and harmonic constraints Ana Celia Vila Verde (Fri Apr 08 2016 - 02:55:45 CDT)
LJ Parameters for Au and S and harmonic constraints Madhulika Gupta (Fri Apr 08 2016 - 02:18:29 CDT)
Re: Simulated annealing error Brian Radak (Thu Apr 07 2016 - 15:34:51 CDT)
Simulated annealing error faride badalkhani (Thu Apr 07 2016 - 13:13:38 CDT)
Packing of different system Srijita Paul (Thu Apr 07 2016 - 10:51:32 CDT)
Re: simulated annealing Brian Radak (Thu Apr 07 2016 - 10:00:03 CDT)
simulated annealing faride badalkhani (Thu Apr 07 2016 - 08:14:10 CDT)
Few doubt on the numbers implying in REMD simulatio Nicholus Bhattacharjee (Thu Apr 07 2016 - 03:34:44 CDT)
Re: restart a job Ana Celia Vila Verde (Thu Apr 07 2016 - 02:43:32 CDT)
Re: water box has a weird shape Ana Celia Vila Verde (Thu Apr 07 2016 - 02:40:47 CDT)
FEP/REMD with NAMD2.11 - missing alchLambda? Nathan Lim (Wed Apr 06 2016 - 20:42:58 CDT)
Re: water box has a weird shape Aron Broom (Wed Apr 06 2016 - 13:41:04 CDT)
water box has a weird shape faride badalkhani (Wed Apr 06 2016 - 13:21:28 CDT)
Re: restart a job Life Sciences Inc (Wed Apr 06 2016 - 12:40:28 CDT)
restart a job Farideh Badalkhani Khamseh (Wed Apr 06 2016 - 11:57:49 CDT)
simulated annealing faride badalkhani (Wed Apr 06 2016 - 11:24:30 CDT)
Re: Lowe-Andersen, Langevin and velocity rescaling thermostats (lipid bilayers) Jeff Comer (Wed Apr 06 2016 - 08:49:16 CDT)
Post Doctoral Fellow Opening at IBM for Biomolecular Modeling Tien Huynh (Tue Apr 05 2016 - 18:30:43 CDT)
Re: AW: problem with +devices using nikolaev_at_spbau.ru (Tue Apr 05 2016 - 07:41:17 CDT)
Re: Constraint failure in RATTLE algorithm for atom 538 Chitrak Gupta (Tue Apr 05 2016 - 11:04:08 CDT)
Re: Constraint failure in RATTLE algorithm for atom 538 Olya Kravchenko (Tue Apr 05 2016 - 10:29:38 CDT)
Re: Constraint failure in RATTLE algorithm for atom 538 faride badalkhani (Tue Apr 05 2016 - 10:18:25 CDT)
Re: Constraint failure in RATTLE algorithm for atom 538 Chitrak Gupta (Tue Apr 05 2016 - 10:10:44 CDT)
Re: Constraint failure in RATTLE algorithm for atom 538 Brian Radak (Tue Apr 05 2016 - 10:04:40 CDT)
Few doubt on the numbers implying in REMD simulation Nicholus Bhattacharjee (Tue Apr 05 2016 - 10:00:50 CDT)
Constraint failure in RATTLE algorithm for atom 538 faride badalkhani (Tue Apr 05 2016 - 09:57:30 CDT)
Re: AW: AW: AW: why does the transition seem to be irreversible in aMD Brian Radak (Tue Apr 05 2016 - 09:42:27 CDT)
AW: AW: problem with +devices using Norman Geist (Tue Apr 05 2016 - 08:21:37 CDT)
AW: problem with +devices using Norman Geist (Tue Apr 05 2016 - 07:09:22 CDT)
problem with +devices using nikolaev_at_spbau.ru (Tue Apr 05 2016 - 06:35:23 CDT)
AW: AW: AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue Apr 05 2016 - 04:31:27 CDT)
Re: AW: AW: why does the transition seem to be irreversible in aMD sunyeping (Tue Apr 05 2016 - 04:10:59 CDT)
AW: AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue Apr 05 2016 - 03:06:43 CDT)
Re: AW: why does the transition seem to be irreversible in aMD sunyeping (Tue Apr 05 2016 - 02:47:39 CDT)
AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue Apr 05 2016 - 02:29:42 CDT)
Re: Running multi-node jobs on Sun Grid Engine Sourav Ray (Tue Apr 05 2016 - 00:19:23 CDT)
why does the transition seem to be irreversible in aMD sunyeping (Mon Apr 04 2016 - 22:21:00 CDT)
Re: Dihedral parameter missing Josh Vermaas (Mon Apr 04 2016 - 16:30:27 CDT)
Dihedral parameter missing faride badalkhani (Mon Apr 04 2016 - 16:26:03 CDT)
Re: Stray PME grid charges detected Sourav Ray (Mon Apr 04 2016 - 13:12:41 CDT)
Re: Stray PME grid charges detected faride badalkhani (Mon Apr 04 2016 - 13:02:51 CDT)
Re: Lowe-Andersen, Langevin and velocity rescaling thermostats (lipid bilayers) Brian Radak (Mon Apr 04 2016 - 09:44:37 CDT)
Wrapping molecules in a NAMD simulation Sourav Ray (Mon Apr 04 2016 - 08:23:02 CDT)
Lowe-Andersen, Langevin and velocity rescaling thermostats (lipid bilayers) Loison Claire (Mon Apr 04 2016 - 07:16:22 CDT)
AW: Running multi-node jobs on Sun Grid Engine Norman Geist (Mon Apr 04 2016 - 05:32:12 CDT)
Re: Stray PME grid charges detected Sourav Ray (Mon Apr 04 2016 - 05:26:56 CDT)
Re: Running multi-node jobs on Sun Grid Engine Sourav Ray (Mon Apr 04 2016 - 04:39:57 CDT)
AW: Running multi-node jobs on Sun Grid Engine Norman Geist (Mon Apr 04 2016 - 01:50:27 CDT)
AW: Occasional performance slow down using NAMD with Xeon Phi Norman Geist (Mon Apr 04 2016 - 01:47:27 CDT)
Stray PME grid charges detected faride badalkhani (Sun Apr 03 2016 - 12:49:18 CDT)
Re: Running multi-node jobs on Sun Grid Engine Ã‰ric Germaneau (Sun Apr 03 2016 - 20:34:20 CDT)
Running multi-node jobs on Sun Grid Engine Sourav Ray (Sun Apr 03 2016 - 10:49:30 CDT)
Re: Steered MD diminishing distances Giacomo Fiorin (Sat Apr 02 2016 - 20:56:34 CDT)
Steered MD diminishing distances giulia palermo (Sat Apr 02 2016 - 20:29:14 CDT)
Re: maximum coordinate is negative for z faride badalkhani (Fri Apr 01 2016 - 12:23:38 CDT)
Re: maximum coordinate is negative for z Maxim Belkin (Fri Apr 01 2016 - 12:21:05 CDT)
Re: maximum coordinate is negative for z Aron Broom (Fri Apr 01 2016 - 12:16:52 CDT)
maximum coordinate is negative for z faride badalkhani (Fri Apr 01 2016 - 12:14:17 CDT)
Re: "Jump" in Energy and Volume graphs of my MD David Hardy (Fri Apr 01 2016 - 12:09:44 CDT)
Occasional performance slow down using NAMD with Xeon Phi Mattia Felice Palermo (Fri Apr 01 2016 - 09:53:37 CDT)
Re: Making NAMD aware of Tcl packages? Brian Radak (Thu Mar 31 2016 - 16:12:20 CDT)
Re: Making NAMD aware of Tcl packages? Giacomo Fiorin (Thu Mar 31 2016 - 11:36:20 CDT)
Re: "Jump" in Energy and Volume graphs of my MD Daniela Rivas (Thu Mar 31 2016 - 11:21:03 CDT)
Re: Making NAMD aware of Tcl packages? Brian Radak (Thu Mar 31 2016 - 10:20:42 CDT)
Re: Making NAMD aware of Tcl packages? Giacomo Fiorin (Thu Mar 31 2016 - 10:17:30 CDT)
Making NAMD aware of Tcl packages? Brian Radak (Thu Mar 31 2016 - 10:11:07 CDT)
Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Thu Mar 31 2016 - 09:13:46 CDT)
Re: AW: "Jump" in Energy and Volume graphs of my MD Jeff Comer (Thu Mar 31 2016 - 08:44:50 CDT)
Re: AW: "Jump" in Energy and Volume graphs of my MD Brian Radak (Thu Mar 31 2016 - 07:56:32 CDT)
constant velocity pulling Jamal Zanjani (Thu Mar 31 2016 - 06:04:18 CDT)
AW: "Jump" in Energy and Volume graphs of my MD Norman Geist (Thu Mar 31 2016 - 01:00:46 CDT)
Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Wed Mar 30 2016 - 19:33:49 CDT)
segmentation fault (core dumped) faride badalkhani (Wed Mar 30 2016 - 16:24:26 CDT)
Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Wed Mar 30 2016 - 15:56:22 CDT)
Re: "Jump" in Energy and Volume graphs of my MD Daniela Rivas (Wed Mar 30 2016 - 15:49:01 CDT)
Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Wed Mar 30 2016 - 15:23:46 CDT)
"Jump" in Energy and Volume graphs of my MD Daniela Rivas (Wed Mar 30 2016 - 15:04:07 CDT)
RE: problem with angle parameters Radak, Brian K (Wed Mar 30 2016 - 11:09:12 CDT)
Fwd: problem with angle parameters faride badalkhani (Wed Mar 30 2016 - 10:01:22 CDT)
problem with angle parameters faride badalkhani (Wed Mar 30 2016 - 09:01:20 CDT)
Re: size of water box and cellbasisvectors Ajasja LjubetiÄ (Wed Mar 30 2016 - 08:08:14 CDT)
size of water box and cellbasisvectors faride badalkhani (Wed Mar 30 2016 - 07:51:14 CDT)
Re: Mixing all_36_cgenff with all_36_prot Tristan Croll (Mon Mar 28 2016 - 14:36:33 CDT)
Mixing all_36_cgenff with all_36_prot Francesco Pietra (Sat Mar 26 2016 - 13:02:27 CDT)
Re: varying two colvar distances simultaneously Giacomo Fiorin (Fri Mar 25 2016 - 17:22:37 CDT)
Re: varying two colvar distances simultaneously Chitrak Gupta (Fri Mar 25 2016 - 17:20:57 CDT)
Re: force units conversion Maxim Belkin (Fri Mar 25 2016 - 14:12:22 CDT)
Re: varying two colvar distances simultaneously Chitrak Gupta (Fri Mar 25 2016 - 10:58:08 CDT)
Re: force units conversion Maxim Belkin (Fri Mar 25 2016 - 10:42:40 CDT)
HBB2-pol R. Charbel MAROUN (Fri Mar 25 2016 - 09:01:46 CDT)
Re: Opinions on Haptic Feedback Devices with NAMD/VMD Axel Kohlmeyer (Fri Mar 25 2016 - 08:52:33 CDT)
Opinions on Haptic Feedback Devices with NAMD/VMD Ben Fritch (Fri Mar 25 2016 - 08:37:31 CDT)
Re: varying two colvar distances simultaneously Giacomo Fiorin (Thu Mar 24 2016 - 16:53:46 CDT)
varying two colvar distances simultaneously Chitrak Gupta (Thu Mar 24 2016 - 16:49:06 CDT)
Opinions on Haptic Feedback Devices with NAMD/VMD Ben Fritch (Thu Mar 24 2016 - 14:29:02 CDT)
force units conversion Olya Kravchenko (Thu Mar 24 2016 - 14:15:05 CDT)
Re: dynamic_cast & runtime type information Ã‰ric Germaneau (Wed Mar 23 2016 - 19:43:44 CDT)
Restarting ABF Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Tue Mar 22 2016 - 13:45:51 CDT)
instantaneous pressure and temp change for multiple run calls? Radak, Brian K (Tue Mar 22 2016 - 13:21:53 CDT)
Parameterizing residues of a polymer faride badalkhani (Tue Mar 22 2016 - 12:47:57 CDT)
Parameterizing residues of a polymer faride badalkhani (Tue Mar 22 2016 - 09:17:46 CDT)
Re: GPU configuration suggestions daniel aguayo (Tue Mar 22 2016 - 06:59:16 CDT)
AW: GPU configuration suggestions Norman Geist (Tue Mar 22 2016 - 05:20:52 CDT)
Re: GPU configuration suggestions Nikhil Maroli (Tue Mar 22 2016 - 04:31:33 CDT)
AW: GPU configuration suggestions Norman Geist (Tue Mar 22 2016 - 04:26:39 CDT)
AW: GPU configuration suggestions Norman Geist (Tue Mar 22 2016 - 03:44:44 CDT)
AW: GPU configuration suggestions Norman Geist (Tue Mar 22 2016 - 02:28:40 CDT)
GPU configuration suggestions Nikhil Maroli (Tue Mar 22 2016 - 00:52:25 CDT)
Re: AW: AW: Testing NAMD scalability Ã‰ric Germaneau (Mon Mar 21 2016 - 22:20:54 CDT)
Postdoctoral opening in biomolecular modeling at IBM Payel Das (Mon Mar 21 2016 - 16:38:19 CDT)
Re: Basic validation of CGenFF Peter Freddolino (Mon Mar 21 2016 - 08:19:53 CDT)
Basic validation of CGenFF faride badalkhani (Mon Mar 21 2016 - 07:31:05 CDT)
AW: AW: Testing NAMD scalability Norman Geist (Mon Mar 21 2016 - 03:31:30 CDT)
Re: AW: Testing NAMD scalability Eric Germaneau (Mon Mar 21 2016 - 03:15:06 CDT)
AW: Testing NAMD scalability Norman Geist (Mon Mar 21 2016 - 02:45:31 CDT)
Testing NAMD scalability Ã‰ric Germaneau (Fri Mar 18 2016 - 20:31:31 CDT)
CGENFF validation faride badalkhani (Fri Mar 18 2016 - 15:12:56 CDT)
Manganese force field Taejin Kim (Fri Mar 18 2016 - 14:07:35 CDT)
Re: charge group faride badalkhani (Fri Mar 18 2016 - 13:36:14 CDT)
dynamic_cast & runtime type information Ã‰ric Germaneau (Fri Mar 18 2016 - 11:46:10 CDT)
Re: charge group Josh Vermaas (Fri Mar 18 2016 - 11:36:21 CDT)
Re: charge group faride badalkhani (Fri Mar 18 2016 - 11:23:39 CDT)
Re: charge group Josh Vermaas (Fri Mar 18 2016 - 11:10:51 CDT)
charge group faride badalkhani (Fri Mar 18 2016 - 10:56:42 CDT)
Fwd: Appropriate FF for a specific solvent faride badalkhani (Fri Mar 18 2016 - 10:53:15 CDT)
Re: ------------- Processor 0 Exiting: Called CmiAbort ------------ Pardis Tabaee (Thu Mar 17 2016 - 12:09:43 CDT)
adaptive biasing force with RMSD colvar Haleh a (Thu Mar 17 2016 - 11:39:45 CDT)
Appropriate FF for a specific solvent faride badalkhani (Thu Mar 17 2016 - 10:48:57 CDT)
2016 ISQBP Meeting: early registration / abstract submission deadline approaching Vlad Cojocaru (Thu Mar 17 2016 - 03:49:47 CDT)
NAMD 2.11 CUDA freezes on windows 8 Ajasja LjubetiÄ (Wed Mar 16 2016 - 13:08:59 CDT)
RE: AW: Tcl script for simulated tempering? Radak, Brian K (Wed Mar 16 2016 - 10:17:07 CDT)
AW: AW: Tcl script for simulated tempering? Norman Geist (Wed Mar 16 2016 - 05:10:14 CDT)
Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Tue Mar 15 2016 - 15:50:18 CDT)
Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Tue Mar 15 2016 - 14:48:58 CDT)
NAMD survey starting Jim Phillips (Tue Mar 15 2016 - 13:34:00 CDT)
RE: AW: Tcl script for simulated tempering? Radak, Brian K (Tue Mar 15 2016 - 13:01:56 CDT)
AW: AW: Tcl script for simulated tempering? Norman Geist (Tue Mar 15 2016 - 10:21:11 CDT)
Re: AW: Tcl script for simulated tempering? Brian Radak (Tue Mar 15 2016 - 08:14:11 CDT)
AW: Tcl script for simulated tempering? Norman Geist (Tue Mar 15 2016 - 02:53:21 CDT)
Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Mon Mar 14 2016 - 11:24:35 CDT)
Re: Fwd: Urey-Bradley parameters Brian Radak (Mon Mar 14 2016 - 10:25:22 CDT)
restarting simulation Francesco Pietra (Mon Mar 14 2016 - 09:45:44 CDT)
Fwd: Urey-Bradley parameters faride badalkhani (Mon Mar 14 2016 - 07:20:08 CDT)
WG: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Greipel.Joachim_at_mh-hannover.de (Mon Mar 14 2016 - 04:47:28 CDT)
Fwd: ISQBP 2016 meeting - registration opened! Vlad Cojocaru (Mon Mar 14 2016 - 03:13:10 CDT)
Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Fri Mar 11 2016 - 21:42:23 CST)
Tcl script for simulated tempering? Radak, Brian K (Fri Mar 11 2016 - 16:12:21 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Fri Mar 11 2016 - 15:31:50 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Fri Mar 11 2016 - 14:57:55 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Fri Mar 11 2016 - 14:39:06 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Fri Mar 11 2016 - 14:34:35 CST)
Re: AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Jim Phillips (Fri Mar 11 2016 - 09:45:19 CST)
Re: Tutorial example of replica exchange Dr. Eddie (Fri Mar 11 2016 - 09:35:03 CST)
Re: AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Josh Vermaas (Fri Mar 11 2016 - 09:29:09 CST)
AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Greipel.Joachim_at_mh-hannover.de (Fri Mar 11 2016 - 01:47:27 CST)
Urey-Bradley parameters faride badalkhani (Fri Mar 11 2016 - 09:10:39 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Thu Mar 10 2016 - 20:01:12 CST)
Re: problem with bringing down the pressure Josh Vermaas (Thu Mar 10 2016 - 19:26:12 CST)
AW: Tutorial example of replica exchange Norman Geist (Thu Mar 10 2016 - 16:53:22 CST)
AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Norman Geist (Thu Mar 10 2016 - 16:43:55 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Thu Mar 10 2016 - 15:58:45 CST)
Re: Tutorial example of replica exchange Dr. Eddie (Thu Mar 10 2016 - 12:26:19 CST)
problem with bringing down the pressure faride badalkhani (Thu Mar 10 2016 - 11:31:36 CST)
Re: installing NAMD 2.11 Chitrak Gupta (Thu Mar 10 2016 - 11:30:44 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Thu Mar 10 2016 - 11:21:00 CST)
Re: Tutorial example of replica exchange Josh Vermaas (Thu Mar 10 2016 - 10:04:07 CST)
Re: Tutorial example of replica exchange Dr. Eddie (Thu Mar 10 2016 - 09:46:50 CST)
AW: Tutorial example of replica exchange Norman Geist (Thu Mar 10 2016 - 02:03:38 CST)
AW: periodic boundary condition in XY, hard wall in Z - errors Norman Geist (Thu Mar 10 2016 - 01:05:33 CST)
periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Wed Mar 09 2016 - 21:23:05 CST)
equilibration error faride badalkhani (Wed Mar 09 2016 - 15:22:25 CST)
Hands-On Workshop on Computational Biophysics: June 6-10 in Pittsburgh, PA Jodi Ann Hadden (Wed Mar 09 2016 - 14:34:10 CST)
NAMD Developer Workshop: May 26-27 in Chicago, IL Jodi Ann Hadden (Wed Mar 09 2016 - 14:31:56 CST)
cellBasisVectors faride badalkhani (Wed Mar 09 2016 - 10:27:53 CST)
Re: installing NAMD 2.11 faride badalkhani (Wed Mar 09 2016 - 07:54:23 CST)
Re: installing NAMD 2.11 Ajasja LjubetiÄ (Wed Mar 09 2016 - 07:38:39 CST)
installing NAMD 2.11 faride badalkhani (Wed Mar 09 2016 - 07:32:46 CST)
Tutorial example of replica exchange Dr. Eddie (Tue Mar 08 2016 - 16:55:34 CST)
AW: selection error in forces script Norman Geist (Tue Mar 08 2016 - 01:35:26 CST)
Re: selection error in forces script Olya Kravchenko (Tue Mar 08 2016 - 00:08:00 CST)
selection error in forces script Olya Kravchenko (Mon Mar 07 2016 - 23:02:34 CST)
Re: segmentation error Giacomo Fiorin (Fri Mar 04 2016 - 10:54:29 CST)
segmentation error Stefano Guglielmo (Fri Mar 04 2016 - 04:15:01 CST)
AW: applying constant force only within certain part of simulation cell? Norman Geist (Fri Mar 04 2016 - 02:27:49 CST)
Re: applying constant force only within certain part of simulation cell? Ajasja LjubetiÄ (Thu Mar 03 2016 - 15:27:35 CST)
applying constant force only within certain part of simulation cell? Olya Kravchenko (Thu Mar 03 2016 - 14:00:33 CST)
Re: æ¥è‡ª"ZOU Changling" <zoucl@ihep.ac.cn>çš„é‚®ä»¶ Jeff Comer (Thu Mar 03 2016 - 11:22:49 CST)
Constraint failure in RATTLE algorithm Stefano Guglielmo (Tue Mar 01 2016 - 19:18:05 CST)
Re: INTERNAL COORDINATES Josh Vermaas (Tue Mar 01 2016 - 08:28:33 CST)
INTERNAL COORDINATES faride badalkhani (Tue Mar 01 2016 - 07:52:09 CST)
Combination of top_all36_cgenff with top_all36_prot faride badalkhani (Mon Feb 29 2016 - 15:03:31 CST)
Re: Energy gradient in colvars.state file Giacomo Fiorin (Mon Feb 29 2016 - 14:25:35 CST)
Energy gradient in colvars.state file Carlo Guardiani (Mon Feb 29 2016 - 13:09:31 CST)
Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= ZOU Changling (Mon Feb 29 2016 - 02:43:31 CST)
AW: problem in running targeted MD Norman Geist (Mon Feb 29 2016 - 01:37:21 CST)
Re: AW: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ ZOU Changling (Sun Feb 28 2016 - 19:36:06 CST)
plumed Stefano Guglielmo (Sun Feb 28 2016 - 10:21:32 CST)
AW: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ Norman Geist (Fri Feb 26 2016 - 06:10:11 CST)
Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= ZOU Changling (Fri Feb 26 2016 - 05:20:03 CST)
AW: problem in running targeted MD Norman Geist (Fri Feb 26 2016 - 01:57:15 CST)
test area method to calculate surface tension Yan Shen (Thu Feb 25 2016 - 15:05:45 CST)
AW: problem in running targeted MD Norman Geist (Thu Feb 25 2016 - 01:38:33 CST)
problem in running targeted MD giulia palermo (Wed Feb 24 2016 - 19:56:11 CST)
AW: Energy increase with fixed atoms in POPC membrane Norman Geist (Mon Feb 22 2016 - 02:04:39 CST)
Re: Energy increase with fixed atoms in POPC membrane Tristan Croll (Fri Feb 19 2016 - 10:51:52 CST)
AW: Energy increase with fixed atoms in POPC membrane Norman Geist (Fri Feb 19 2016 - 01:47:51 CST)
Re: external HPC resource Mahya Hemmat (Thu Feb 18 2016 - 17:10:12 CST)
Re: Should you cap C and N termini? Gianluca Interlandi (Thu Feb 18 2016 - 12:57:24 CST)
external HPC resource Deng, Jinxia (Nancy) (Thu Feb 18 2016 - 10:23:36 CST)
Re: Should you cap C and N termini? Vlad Cojocaru (Thu Feb 18 2016 - 09:31:56 CST)
Should you cap C and N termini? ashika torikora (Thu Feb 18 2016 - 07:09:10 CST)
AW: Energy increase with fixed atoms in POPC membrane Norman Geist (Thu Feb 18 2016 - 02:03:09 CST)
Energy increase with fixed atoms in POPC membrane Mihaela Drenscko (Wed Feb 17 2016 - 16:27:15 CST)
Re: Replica Exchange US, Colvar suggestion Laurent Chaloin (Sat Feb 13 2016 - 02:02:24 CST)
Re: Replica Exchange US, Colvar suggestion Laurent Chaloin (Sat Feb 13 2016 - 01:53:46 CST)
AW: vmd-l: moving atoms and updating distances Norman Geist (Mon Feb 15 2016 - 00:11:47 CST)
Re: Replica Exchange US, Colvar suggestion Abhishek TYAGI (Sat Feb 13 2016 - 22:39:29 CST)
Re: Replica Exchange US, Colvar suggestion Giacomo Fiorin (Sat Feb 13 2016 - 13:21:00 CST)
Replica Exchange US, Colvar suggestion Abhishek TYAGI (Sat Feb 13 2016 - 01:07:38 CST)
Re: Non respect of sequence of commands in command file Josh Vermaas (Fri Feb 12 2016 - 11:04:28 CST)
Non respect of sequence of commands in command file R. Charbel MAROUN (Fri Feb 12 2016 - 05:11:39 CST)
Re: velocity computation Tristan Croll (Tue Feb 09 2016 - 03:04:40 CST)
AW: velocity computation Norman Geist (Tue Feb 09 2016 - 02:22:54 CST)
Re: velocity computation Tristan Croll (Mon Feb 08 2016 - 12:33:16 CST)
Re: velocity computation 'Patrick Welche' (Mon Feb 08 2016 - 08:34:19 CST)
AW: velocity computation Norman Geist (Mon Feb 08 2016 - 00:51:46 CST)
velocity computation Patrick Welche (Fri Feb 05 2016 - 13:05:25 CST)
Fwd: namd on Windows 10 Branko (Fri Feb 05 2016 - 08:13:51 CST)
Re: namd on Windows 10 Kostas Malavazos (Thu Feb 04 2016 - 14:14:09 CST)
namd on Windows 10 Branko (Thu Feb 04 2016 - 12:24:14 CST)
About parseFEP error Atsutoshi Okabe (Wed Feb 03 2016 - 08:01:21 CST)
bond energy high Ipsita Basu (Wed Feb 03 2016 - 05:15:35 CST)
NAMD Implicit GB Parameters Samuel Bowerman (Mon Feb 01 2016 - 12:41:03 CST)
Re: PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Mon Feb 01 2016 - 10:39:06 CST)
AW: Re: tclBC relective boundaries Norman Geist (Mon Feb 01 2016 - 00:10:45 CST)
Re: Lennard-Jones potential in coarse grained MD Yongcheng Zhou (Sun Jan 31 2016 - 00:16:37 CST)
Re: Problems in NAMD's code about real implementation of function named ComputeNonbondedUtil:calc_pair_energy Peter Freddolino (Sat Jan 30 2016 - 21:00:17 CST)
Re: Lennard-Jones potential in coarse grained MD bay__gulf618_at_sina.com (Sat Jan 30 2016 - 01:19:17 CST)
Lennard-Jones potential in coarse grained MD Yongcheng Zhou (Sat Jan 30 2016 - 00:36:20 CST)
Re: tclBC relective boundaries Art (Fri Jan 29 2016 - 17:27:02 CST)
Problems in NAMD's code about real implementation of function named ComputeNonbondedUtil:calc_pair_energy yeguoqiao (Fri Jan 29 2016 - 09:05:31 CST)
tclBC relective boundaries Art (Fri Jan 29 2016 - 13:51:17 CST)
MD trajectory analysis Deng, Jinxia (Nancy) (Thu Jan 28 2016 - 13:02:14 CST)
Re: PBC in lipid bilayer: receptor vs. ligand Jeff Comer (Thu Jan 28 2016 - 12:38:45 CST)
Re: PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Thu Jan 28 2016 - 11:59:14 CST)
Re: PBC in lipid bilayer: receptor vs. ligand Josh Vermaas (Thu Jan 28 2016 - 11:09:08 CST)
Re: PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Thu Jan 28 2016 - 11:03:17 CST)
Re: PBC in lipid bilayer: receptor vs. ligand Josh Vermaas (Thu Jan 28 2016 - 09:43:21 CST)
Re: PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Thu Jan 28 2016 - 05:26:33 CST)
AW: PBC in lipid bilayer: receptor vs. ligand Norman Geist (Wed Jan 27 2016 - 09:35:05 CST)
Re: PBC in lipid bilayer: receptor vs. ligand Josh Vermaas (Wed Jan 27 2016 - 09:22:40 CST)
Re: PBC in lipid bilayer: receptor vs. ligand Ajasja LjubetiÄ (Wed Jan 27 2016 - 09:21:11 CST)
PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Wed Jan 27 2016 - 07:54:34 CST)
Re: calculating replica exchange acceptance ratio Chitrak Gupta (Wed Jan 27 2016 - 04:18:38 CST)
Re: Ajasja LjubetiÄ (Wed Jan 27 2016 - 03:39:04 CST)
(no subject) Srijita Paul (Tue Jan 26 2016 - 23:06:12 CST)
(no subject) Srijita Paul (Tue Jan 26 2016 - 23:02:28 CST)
AW: calculating replica exchange acceptance ratio Norman Geist (Tue Jan 26 2016 - 08:03:40 CST)
Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 12:31:10 CST)
Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 12:11:58 CST)
Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 11:00:26 CST)
Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 09:58:31 CST)
Re: compute capability Josh Vermaas (Mon Jan 25 2016 - 09:52:37 CST)
Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 09:51:48 CST)
segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 07:58:49 CST)
AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 05:51:31 CST)
AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 04:37:56 CST)
Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 02:54:15 CST)
AW: PBC BUG in coorfile + pair interaction Norman Geist (Mon Jan 25 2016 - 02:33:18 CST)
Re: Enabling GPU for Replica exchange umbrella sampling Abhishek TYAGI (Mon Jan 25 2016 - 01:49:23 CST)
AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 01:13:51 CST)
AW: Enabling GPU for Replica exchange umbrella sampling Norman Geist (Mon Jan 25 2016 - 01:06:05 CST)
calculating replica exchange acceptance ratio Chitrak Gupta (Sun Jan 24 2016 - 23:16:09 CST)
compute capability Stefano Guglielmo (Sun Jan 24 2016 - 17:15:43 CST)
Re: Enabling GPU for Replica exchange umbrella sampling Abhishek TYAGI (Sat Jan 23 2016 - 13:05:26 CST)
AW: Enabling GPU for Replica exchange umbrella sampling Norman Geist (Fri Jan 22 2016 - 03:09:24 CST)
AW: Re: Enabling GPU for Replica exchange umbrella sampling Norman Geist (Fri Jan 22 2016 - 03:07:59 CST)
charmc rpath Scott Brozell (Thu Jan 21 2016 - 22:04:41 CST)
Re: Enabling GPU for Replica exchange umbrella sampling Abhishek TYAGI (Thu Jan 21 2016 - 22:02:59 CST)
Re: multipld .dcd analysis by VMD Zhao Qin (Thu Jan 21 2016 - 12:40:25 CST)
AW: PBC BUG in coorfile + pair interaction Norman Geist (Thu Jan 21 2016 - 04:32:33 CST)
PBC BUG in coorfile + pair interaction Norman Geist (Thu Jan 21 2016 - 03:50:59 CST)
Enabling GPU for REUS Abhishek TYAGI (Wed Jan 20 2016 - 21:12:50 CST)
multipld .dcd analysis by VMD Deng, Jinxia (Nancy) (Wed Jan 20 2016 - 13:53:21 CST)
Re: LSU SuperMIC Kenneth Huang (Tue Jan 19 2016 - 17:15:39 CST)
LSU SuperMIC Jeff Comer (Tue Jan 19 2016 - 16:21:39 CST)
Re: Replica Exchange Jason Swails (Tue Jan 19 2016 - 15:06:24 CST)
Re: Replica Exchange Chitrak Gupta (Tue Jan 19 2016 - 14:40:20 CST)
Replica Exchange Dr. Eddie (Tue Jan 19 2016 - 10:35:00 CST)
»Ø¸´: about User-Defined Forces bay__gulf618_at_sina.com (Mon Jan 18 2016 - 05:23:00 CST)
about User-Defined Forces ¸ß¾ü (Mon Jan 18 2016 - 03:28:31 CST)
RE: RE: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Tim.Ho_at_csiro.au (Thu Jan 14 2016 - 22:02:44 CST)
Recover the PMF along an unbiased CV Felipe Merino (Thu Jan 14 2016 - 16:11:37 CST)
RE: [Non-DoD Source] RE: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Tim.Ho_at_csiro.au (Thu Jan 14 2016 - 16:00:28 CST)
RE: [Non-DoD Source] RE: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Thu Jan 14 2016 - 09:24:50 CST)
RE: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) Tim.Ho_at_csiro.au (Wed Jan 13 2016 - 22:28:53 CST)
2.11 how to remove charmrun remote-shell options Scott Brozell (Wed Jan 13 2016 - 12:04:54 CST)
AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Norman Geist (Wed Jan 13 2016 - 02:17:01 CST)
restart namd calculations Bylund, Tatsiana (NIH/NIAID) [F] (Tue Jan 12 2016 - 16:55:09 CST)
Re: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Brunner, Robert Kraemer (Tue Jan 12 2016 - 14:31:36 CST)
RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 14:04:36 CST)
AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Norman Geist (Tue Jan 12 2016 - 13:23:21 CST)
RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 09:44:54 CST)
Re: Aoid protein to reach periodic boundary Jeff Comer (Tue Jan 12 2016 - 09:30:36 CST)
AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Norman Geist (Tue Jan 12 2016 - 08:31:52 CST)
RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 07:27:59 CST)
Re: Aoid protein to reach periodic boundary Felipe Merino (Tue Jan 12 2016 - 06:13:43 CST)
Re: Aoid protein to reach periodic boundary Branko (Tue Jan 12 2016 - 05:41:21 CST)
AW: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) Norman Geist (Tue Jan 12 2016 - 02:16:38 CST)
Aoid protein to reach periodic boundary Dharmeshkumar Patel (Mon Jan 11 2016 - 18:15:16 CST)
Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Mon Jan 11 2016 - 13:10:19 CST)
Re: Regarding system forces in NAMD sruthi c k (Fri Jan 08 2016 - 06:14:08 CST)
Fwd: Regarding system forces in NAMD sruthi c k (Fri Jan 08 2016 - 03:38:26 CST)
Re: TIP4P/2005 par file by Jordi Faraudo Monika Madhavi (Sat Jan 09 2016 - 14:38:50 CST)
Re: TIP4P/2005 par file by Jordi Faraudo Fotis Baltoumas (Sat Jan 09 2016 - 12:13:01 CST)
TIP4P/2005 par file by Jordi Faraudo Monika Madhavi (Sat Jan 09 2016 - 07:16:17 CST)
Re: Regarding system forces in NAMD Giacomo Fiorin (Fri Jan 08 2016 - 08:36:45 CST)
PhD and postdoctoral positions in biomolecular simulation Allison, Jane (Thu Jan 07 2016 - 19:01:29 CST)
Re: Regarding system forces in NAMD sruthi c k (Thu Jan 07 2016 - 11:43:49 CST)
Re: Regarding system forces in NAMD Giacomo Fiorin (Thu Jan 07 2016 - 09:18:35 CST)
Re: Regarding system forces in NAMD Giacomo Fiorin (Thu Jan 07 2016 - 09:14:45 CST)
Re: Regarding system forces in NAMD sruthi c k (Thu Jan 07 2016 - 09:13:57 CST)
Re: Regarding system forces in NAMD Giacomo Fiorin (Thu Jan 07 2016 - 09:10:39 CST)
Regarding system forces in NAMD sruthi c k (Thu Jan 07 2016 - 06:49:51 CST)
Re: Regarding merging of .grad files obtained from ABF simulations sruthi c k (Thu Jan 07 2016 - 04:31:11 CST)
Re: Regarding merging of .grad files obtained from ABF simulations JÃ©rÃ´me HÃ©nin (Thu Jan 07 2016 - 04:07:17 CST)
Regarding merging of .grad files obtained from ABF simulations sruthi c k (Thu Jan 07 2016 - 01:49:18 CST)
(no subject) Srijita Paul (Wed Jan 06 2016 - 22:25:56 CST)
Re: solvent other than water Jeff Comer (Wed Jan 06 2016 - 13:39:14 CST)
solvent other than water Deng, Jinxia (Nancy) (Wed Jan 06 2016 - 12:17:11 CST)
Re: NAMD 2.11 released Jeff Comer (Wed Jan 06 2016 - 08:35:12 CST)
Re: NAMD 2.11 released JC Gumbart (Tue Jan 05 2016 - 16:16:03 CST)
Equilibration fails for long time ,NPT Nikhil Maroli (Sun Jan 03 2016 - 11:42:32 CST)
GBIS error sunyeping (Sat Jan 02 2016 - 22:55:10 CST)
Re: Add ions/molecules different from Autoionize defaults Tristan Croll (Tue Dec 29 2015 - 07:12:10 CST)
Energy decomposition analyse in NAMD sunyzero (Mon Dec 28 2015 - 20:23:28 CST)
Re: Restraints on the outer solutes Vibhor Agrawal (Mon Dec 28 2015 - 03:50:57 CST)
Restraints on the outer solutes Diksha Dubey (Mon Dec 28 2015 - 03:39:00 CST)
Re: Add ions/molecules different from Autoionize defaults Peter Freddolino (Sun Dec 27 2015 - 22:04:00 CST)
Re: Add ions/molecules different from Autoionize defaults Josh Vermaas (Sun Dec 27 2015 - 06:25:50 CST)
Re: Add ions/molecules different from Autoionize defaults Peter Freddolino (Sat Dec 26 2015 - 21:12:23 CST)
Re: mail reg parameters sena (Fri Dec 25 2015 - 22:29:17 CST)
mail reg parameters Vidhya Sankar (Fri Dec 25 2015 - 20:51:57 CST)
Re: The script of Umbrella sampling JC Gumbart (Fri Dec 25 2015 - 12:49:51 CST)
Re: Add ions/molecules different from Autoionize defaults Ardavan Mehdizadeh (Fri Dec 25 2015 - 12:28:43 CST)
Re: Add ions/molecules different from Autoionize defaults amin_at_imtech.res.in (Fri Dec 25 2015 - 07:16:46 CST)
DIDN'T FIND vdW PARAMETER FOR ATOM TYPE SG3O1 Srijita Paul (Fri Dec 25 2015 - 00:41:47 CST)
SMD with PBC Mahdi Tavakol (Thu Dec 24 2015 - 00:22:36 CST)
Re: Add ions/molecules different from Autoionize defaults Peter Freddolino (Thu Dec 24 2015 - 08:45:43 CST)
Re: Add ions/molecules different from Autoionize defaults Ardavan Mehdizadeh (Thu Dec 24 2015 - 07:37:39 CST)
Add ions/molecules different from Autoionize defaults Ardavan Mehdizadeh (Thu Dec 24 2015 - 07:37:01 CST)
Re: NAMD 2.11 released Ajasja LjubetiÄ (Thu Dec 24 2015 - 02:35:34 CST)
Re: NAMD 2.11 released Francesco Pietra (Thu Dec 24 2015 - 01:22:37 CST)
Re: NAMD 2.11 released Jeff Comer (Wed Dec 23 2015 - 19:38:21 CST)
Add ions/molecules different from Autoionize defaults Ardavan Mehdizadeh (Wed Dec 23 2015 - 12:05:36 CST)
LangevinDamping Coefficient for MARTINI Mahdi Tavakol (Wed Dec 23 2015 - 05:33:48 CST)
Re: NAMD 2.11 released Jim Phillips (Tue Dec 22 2015 - 21:37:31 CST)
Re: NAMD 2.11 released Branko (Tue Dec 22 2015 - 16:19:37 CST)
NAMD 2.11 released Jim Phillips (Tue Dec 22 2015 - 10:38:50 CST)
The script of Umbrella sampling sunyzero (Tue Dec 22 2015 - 03:33:13 CST)
(no subject) Srijita Paul (Tue Dec 22 2015 - 00:06:49 CST)
Re: "implausibly old time stamp" for charm++ 6.7 in CVS Jim Phillips (Mon Dec 21 2015 - 10:04:11 CST)
Re: how to get the restart files from the dcd file? Azadeh Alavi (Mon Dec 21 2015 - 07:10:47 CST)
OpenGL Display Window, "Key 2", SMD with NAMD Zeinab Emami (Sun Dec 20 2015 - 11:57:52 CST)
Re: how to get the restart files from the dcd file? Azadeh Alavi (Sun Dec 20 2015 - 14:30:07 CST)
Re: how to get the restart files from the dcd file? Jeff Comer (Sun Dec 20 2015 - 12:46:16 CST)
Re: how to get the restart files from the dcd file? Jeff Comer (Sun Dec 20 2015 - 12:06:17 CST)
how to get the restart files from the dcd file? Azadeh Alavi (Sun Dec 20 2015 - 03:02:36 CST)
RE: SMP NAMD reports threads greater than physical cores, even when distributed to other nodes Jim Phillips (Sat Dec 19 2015 - 21:39:50 CST)
RE: SMP NAMD reports threads greater than physical cores, even when distributed to other nodes Tom Coles (Fri Dec 18 2015 - 15:16:01 CST)
RE: SMP NAMD reports threads greater than physical cores, even when distributed to other nodes Jim Phillips (Fri Dec 18 2015 - 09:38:15 CST)
Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer Chitrak Gupta (Fri Dec 18 2015 - 09:08:27 CST)
Re: ERROR in CUDA run Jim Phillips (Thu Dec 17 2015 - 19:50:54 CST)
Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer Jim Phillips (Thu Dec 17 2015 - 19:49:32 CST)
SMP NAMD reports threads greater than physical cores, even when distributed to other nodes Tom Coles (Thu Dec 17 2015 - 10:26:20 CST)
AW: ERROR in CUDA run Norman Geist (Thu Dec 17 2015 - 09:24:20 CST)
ERROR in CUDA run Lara rajam (Thu Dec 17 2015 - 08:50:49 CST)
Re: free energy changes via FEP method Haleh a (Thu Dec 17 2015 - 05:42:15 CST)
Re: free energy changes via FEP method Gianluca Interlandi (Wed Dec 16 2015 - 12:49:26 CST)
Re: vmd-l: Number of pdb and psf atoms are not the same! Ashar Malik (Wed Dec 16 2015 - 09:57:47 CST)
Re: free energy changes via FEP method Brian Radak (Wed Dec 16 2015 - 12:15:10 CST)
"implausibly old time stamp" for charm++ 6.7 in CVS Brian Radak (Wed Dec 16 2015 - 11:42:29 CST)
Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer Chitrak Gupta (Wed Dec 16 2015 - 11:23:39 CST)
Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer begÃ¼m alaybeyoÄŸlu (Wed Dec 16 2015 - 10:21:17 CST)
Re: vmd-l: Number of pdb and psf atoms are not the same! Francesco Pietra (Wed Dec 16 2015 - 10:14:12 CST)
Number of pdb and psf atoms are not the same! Francesco Pietra (Wed Dec 16 2015 - 09:23:41 CST)
Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer Chitrak Gupta (Wed Dec 16 2015 - 09:21:07 CST)
Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer begÃ¼m alaybeyoÄŸlu (Wed Dec 16 2015 - 03:46:10 CST)
Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer Chitrak Gupta (Tue Dec 15 2015 - 12:46:36 CST)
RATTLE Error During Minimization of Charmm Gui Generated Bilayer begÃ¼m alaybeyoÄŸlu (Tue Dec 15 2015 - 10:27:48 CST)
free energy changes via FEP method Haleh a (Tue Dec 15 2015 - 09:59:10 CST)
Re: vmd-l: Re: VMD-NAMD and PDB element column Victor Ovchinnikov (Mon Dec 14 2015 - 16:27:41 CST)
Re: vmd-l: Re: VMD-NAMD and PDB element column Francesco Pietra (Mon Dec 14 2015 - 14:52:18 CST)
Re: vmd-l: Re: VMD-NAMD and PDB element column Francesco Pietra (Mon Dec 14 2015 - 14:42:21 CST)
Re: OutputAccumulatedWork...where's the output? Giacomo Fiorin (Mon Dec 14 2015 - 13:32:17 CST)
Viscosity Calculation using EMD Gaurab Sarkar (Mon Dec 14 2015 - 13:22:02 CST)
Re: OutputAccumulatedWork...where's the output? Bryan Roessler (Mon Dec 14 2015 - 12:41:08 CST)
Re: OutputAccumulatedWork...where's the output? Giacomo Fiorin (Mon Dec 14 2015 - 10:55:36 CST)
Re: vmd-l: Re: VMD-NAMD and PDB element column Victor Ovchinnikov (Mon Dec 14 2015 - 09:47:54 CST)
Re: vmd-l: Re: VMD-NAMD and PDB element column Jim Phillips (Mon Dec 14 2015 - 09:04:21 CST)
Usage of velDCDfile and forceDCDfile keywords in viscosity calculations Debashis Kundu (Mon Dec 14 2015 - 00:34:56 CST)
OutputAccumulatedWork...where's the output? Bryan Roessler (Sun Dec 13 2015 - 19:36:26 CST)
Re: vmd-l: Re: VMD-NAMD and PDB element column Francesco Pietra (Sun Dec 13 2015 - 15:59:37 CST)
Re: vmd-l: Re: VMD-NAMD and PDB element column Jim Phillips (Sun Dec 13 2015 - 14:32:38 CST)
Re: vmd-l: Re: VMD-NAMD and PDB element column Francesco Pietra (Sun Dec 13 2015 - 13:39:11 CST)
Re: VMD-NAMD and PDB element column Jim Phillips (Sun Dec 13 2015 - 12:17:57 CST)
VMD-NAMD and PDB element column Francesco Pietra (Sat Dec 12 2015 - 09:09:55 CST)
Re: Problems with GLUP and ASPP with CHARMM36 Francesco Pietra (Fri Dec 11 2015 - 09:35:48 CST)
Re: Problems with GLUP and ASPP with CHARMM36 Josh Vermaas (Fri Dec 11 2015 - 09:25:11 CST)
Re: Problems with GLUP and ASPP with CHARMM36 Francesco Pietra (Fri Dec 11 2015 - 09:21:34 CST)
Re: Problems with GLUP and ASPP with CHARMM36 Josh Vermaas (Fri Dec 11 2015 - 08:45:00 CST)
Problems with GLUP and ASPP with CHARMM36 Francesco Pietra (Fri Dec 11 2015 - 05:07:03 CST)
Re: NAMD on TACC (Darter) Chitrak Gupta (Thu Dec 10 2015 - 17:35:15 CST)
Re: vmd-l: PRES and water-ions issues with charmm36 Brian Radak (Thu Dec 10 2015 - 15:58:49 CST)
PRES and water-ions issues with charmm36 Francesco Pietra (Thu Dec 10 2015 - 15:30:14 CST)
Re: extendedLagrangian for non-scalar colvar Jerome Karp (Thu Dec 10 2015 - 12:05:51 CST)
extendedLagrangian for non-scalar colvar Jerome Karp (Thu Dec 10 2015 - 10:45:27 CST)
Re: NAMD on TACC (Darter) Jim Phillips (Thu Dec 10 2015 - 10:03:56 CST)
Re: energy output Jeffrey Potoff (Wed Dec 09 2015 - 11:56:45 CST)
RE: energy output Deng, Jinxia (Nancy) (Wed Dec 09 2015 - 13:12:11 CST)
Re: energy output Branko (Wed Dec 09 2015 - 11:51:45 CST)
Re: energy output Chitrak Gupta (Wed Dec 09 2015 - 11:47:57 CST)
energy output Deng, Jinxia (Nancy) (Wed Dec 09 2015 - 11:39:14 CST)
Re: NAMD on TACC (Darter) Chitrak Gupta (Wed Dec 09 2015 - 07:49:53 CST)
Re: anionic cysteine Tristan Croll (Wed Dec 09 2015 - 04:23:03 CST)
Re: anionic cysteine Francesco Pietra (Wed Dec 09 2015 - 04:13:54 CST)
Re: NAMD on TACC (Darter) Jim Phillips (Tue Dec 08 2015 - 22:41:19 CST)
Re: NAMD on TACC (Darter) Chitrak Gupta (Tue Dec 08 2015 - 22:19:12 CST)
Re: NAMD on TACC (Darter) Jim Phillips (Tue Dec 08 2015 - 22:15:15 CST)
Re:Re: Determining the PMF with Adaptive Biasing Forces sunyzero (Tue Dec 08 2015 - 22:00:19 CST)
Re: anionic cysteine Tristan Croll (Tue Dec 08 2015 - 22:00:12 CST)
NAMD on TACC (Darter) Chitrak Gupta (Tue Dec 08 2015 - 18:16:29 CST)
Re: buffer overflow with long file paths in psfgen in NAMD 2.11b2? Jim Phillips (Tue Dec 08 2015 - 16:41:22 CST)
buffer overflow with long file paths in psfgen in NAMD 2.11b2? Brian Radak (Tue Dec 08 2015 - 15:54:28 CST)
anionic cysteine Francesco Pietra (Tue Dec 08 2015 - 08:50:19 CST)
RE: multiple output .dcd files?? Deng, Jinxia (Nancy) (Tue Dec 08 2015 - 08:43:02 CST)
Re: Determining the PMF with Adaptive Biasing Forces Souvik Sinha (Tue Dec 08 2015 - 01:42:34 CST)
Determining the PMF with Adaptive Biasing Forces sunyzero (Mon Dec 07 2015 - 23:48:55 CST)
Determining the PMF with Adaptive Biasing Forces sunyzero (Mon Dec 07 2015 - 20:02:35 CST)
Re: multiple output .dcd files?? Jim Phillips (Mon Dec 07 2015 - 16:43:12 CST)
Re: Overflow in LJcorrection? Jim Phillips (Mon Dec 07 2015 - 16:35:27 CST)
multiple output .dcd files?? Deng, Jinxia (Nancy) (Mon Dec 07 2015 - 14:56:53 CST)
NAMD 2.11b2 released Jim Phillips (Sun Dec 06 2015 - 22:01:09 CST)
Re: Overflow in LJcorrection? Peter Freddolino (Sat Dec 05 2015 - 21:15:12 CST)
Re: Overflow in LJcorrection? Peter Freddolino (Sat Dec 05 2015 - 17:57:22 CST)
Re: namd2.22b CUDA Phi Jim Phillips (Sat Dec 05 2015 - 08:50:57 CST)
Re: Overflow in LJcorrection? Jason Swails (Sat Dec 05 2015 - 07:54:57 CST)
namd2.22b CUDA Phi Francesco Pietra (Sat Dec 05 2015 - 01:06:49 CST)
Re: NAMD 2.11b1 multicore CUDA: Incorrect number of exclusions Jim Phillips (Fri Dec 04 2015 - 16:52:30 CST)
Re: modify input file for production phase MD Branko (Fri Dec 04 2015 - 11:50:53 CST)
modify input file for production phase MD Deng, Jinxia (Nancy) (Fri Dec 04 2015 - 11:31:26 CST)
Re: Overflow in LJcorrection? Brian Radak (Thu Dec 03 2015 - 16:26:19 CST)
Re: Overflow in LJcorrection? Jason Swails (Thu Dec 03 2015 - 16:18:40 CST)
Re: Overflow in LJcorrection? Brian Radak (Thu Dec 03 2015 - 16:15:59 CST)
Re: Overflow in LJcorrection? Jason Swails (Thu Dec 03 2015 - 16:15:15 CST)
Re: Overflow in LJcorrection? Brian Radak (Thu Dec 03 2015 - 16:10:59 CST)
Re: Overflow in LJcorrection? Jason Swails (Thu Dec 03 2015 - 16:04:28 CST)
Re: Overflow in LJcorrection? Brian Radak (Thu Dec 03 2015 - 15:59:27 CST)
Re: Overflow in LJcorrection? Peter Freddolino (Thu Dec 03 2015 - 15:55:49 CST)
Re: Overflow in LJcorrection? Jason Swails (Thu Dec 03 2015 - 15:55:30 CST)
Overflow in LJcorrection? Brian Radak (Thu Dec 03 2015 - 15:45:38 CST)
NAMD 2.11b1 multicore CUDA: Incorrect number of exclusions Jeff Comer (Thu Dec 03 2015 - 14:20:42 CST)
Re: concerning paratools Mayne, Christopher G (Thu Dec 03 2015 - 14:11:52 CST)
Re: Fwd: TIP4P and CHARMM27 Francesco Pietra (Thu Dec 03 2015 - 12:19:58 CST)
Re: error when use Charmm_Gui prepared *.inp for NAMD Jeffrey Potoff (Thu Dec 03 2015 - 08:44:53 CST)
RE: error when use Charmm_Gui prepared *.inp for NAMD Deng, Jinxia (Nancy) (Thu Dec 03 2015 - 09:52:20 CST)
Re: error when use Charmm_Gui prepared *.inp for NAMD Josh Vermaas (Thu Dec 03 2015 - 08:50:36 CST)
Re: error when use Charmm_Gui prepared *.inp for NAMD Chitrak Gupta (Thu Dec 03 2015 - 08:49:59 CST)
error when use Charmm_Gui prepared *.inp for NAMD Deng, Jinxia (Nancy) (Thu Dec 03 2015 - 08:37:14 CST)
concerning paratools luca belmonte (Thu Dec 03 2015 - 04:36:04 CST)
Re: Fwd: TIP4P and CHARMM27 Peter Freddolino (Wed Dec 02 2015 - 12:51:43 CST)
Re: Fwd: TIP4P and CHARMM27 Francesco Pietra (Wed Dec 02 2015 - 11:47:58 CST)
fructose 1,6 bisphosphate forcefield parameters. Dhiraj Srivastava (Wed Dec 02 2015 - 00:06:45 CST)
Re: DOF during alchemical simulations Brian Radak (Tue Dec 01 2015 - 10:08:08 CST)
Re: DOF during alchemical simulations Hannes Loeffler (Tue Dec 01 2015 - 08:19:00 CST)
Re: Fwd: TIP4P and CHARMM27 Francesco Pietra (Tue Dec 01 2015 - 03:22:31 CST)
Re: Fwd: TIP4P and CHARMM27 Jim Phillips (Mon Nov 30 2015 - 16:21:44 CST)
Re: DOF during alchemical simulations Grace Brannigan (Mon Nov 30 2015 - 14:45:55 CST)
Re: DOF during alchemical simulations Brian Radak (Mon Nov 30 2015 - 12:30:33 CST)
Re: DOF during alchemical simulations Grace Brannigan (Mon Nov 30 2015 - 12:05:36 CST)
Re: accelerated MD new variant Brian Radak (Mon Nov 30 2015 - 09:48:36 CST)
Re: DOF during alchemical simulations Brian Radak (Mon Nov 30 2015 - 09:36:55 CST)
Re: accelerated MD new variant Vlad Cojocaru (Mon Nov 30 2015 - 10:00:35 CST)
accelerated MD new variant Vlad Cojocaru (Sun Nov 29 2015 - 03:53:20 CST)
Re: Re: Re: Re: NAMD 2.11b1 released Jim Phillips (Fri Nov 27 2015 - 20:10:42 CST)
Re: Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 15:54:56 CST)
Re: Fwd: TIP4P and CHARMM27 Peter Freddolino (Fri Nov 27 2015 - 11:37:48 CST)
Re: Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 11:35:25 CST)
Re: Fwd: TIP4P and CHARMM27 Peter Freddolino (Fri Nov 27 2015 - 10:26:05 CST)
Re: Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 10:18:28 CST)
Re: Fwd: TIP4P and CHARMM27 Peter Freddolino (Fri Nov 27 2015 - 09:41:00 CST)
Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 09:17:35 CST)
AW: Re: Re: Re: NAMD 2.11b1 released Norman Geist (Fri Nov 27 2015 - 01:22:44 CST)
Re: Re: Re: NAMD 2.11b1 released sunyeping (Thu Nov 26 2015 - 23:26:33 CST)
Re: DOF during alchemical simulations Aron Broom (Thu Nov 26 2015 - 12:28:27 CST)
DOF during alchemical simulations Brian Radak (Wed Nov 25 2015 - 10:31:11 CST)
Re: how does NAMD calculate intramolecular electrostatic interactions between Drude pairs? Ana Celia Vila Verde (Thu Nov 26 2015 - 01:13:38 CST)
Re: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ Abhishek TYAGI (Wed Nov 25 2015 - 07:03:45 CST)
Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= ZOU Changling (Wed Nov 25 2015 - 06:39:26 CST)
recommendations for a fast multicore workstation Jeff Comer (Tue Nov 24 2015 - 11:56:54 CST)
Re: how does NAMD calculate intramolecular electrostatic interactions between Drude pairs? Ana Celia Vila Verde (Mon Nov 23 2015 - 09:27:00 CST)
Re: Which namd to use Jim Phillips (Fri Nov 20 2015 - 11:11:30 CST)
Re: query for system size in pmf calculation Giacomo Fiorin (Fri Nov 20 2015 - 08:52:35 CST)
Re: Which namd to use Maxime Boissonneault (Fri Nov 20 2015 - 08:13:58 CST)
Re: Which namd to use Jim Phillips (Fri Nov 20 2015 - 08:02:36 CST)
Which namd to use Maxime Boissonneault (Fri Nov 20 2015 - 07:29:45 CST)
query for system size in pmf calculation Atanu Maity (Fri Nov 20 2015 - 05:24:47 CST)
AW: Changing Boundary conditions from PBC to non-periodic Norman Geist (Fri Nov 20 2015 - 01:52:26 CST)
Re: NAMD2.11 source code not compiling Madhulika Gupta (Fri Nov 20 2015 - 01:20:05 CST)
Crazy rigid water molecules Brian Radak (Thu Nov 19 2015 - 15:40:55 CST)
Re: Changing Boundary conditions from PBC to non-periodic Gianluca Interlandi (Thu Nov 19 2015 - 14:30:16 CST)
Changing Boundary conditions from PBC to non-periodic Mahdi Tavakol (Thu Nov 19 2015 - 12:30:23 CST)
Re: Re: Fw: æ¥è‡ª"ZOU Changling" <zoucl@ihep.ac.cn>çš„é‚®ä»¶ Axel Kohlmeyer (Wed Nov 18 2015 - 20:15:49 CST)
Re: Re: Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ Abhishek TYAGI (Wed Nov 18 2015 - 20:12:47 CST)
Re: Re: Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ ZOU Changling (Wed Nov 18 2015 - 19:34:42 CST)
Re: NAMD2.11 source code not compiling Madhulika Gupta (Wed Nov 18 2015 - 10:31:55 CST)
Re: Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ Abhishek TYAGI (Wed Nov 18 2015 - 09:45:45 CST)
Re: NAMD2.11 source code not compiling Jim Phillips (Wed Nov 18 2015 - 09:21:13 CST)
Re: AW: time per step during GPU-accelerated Implicit Solvent calculations Thomas Albers (Wed Nov 18 2015 - 08:38:07 CST)
NAMD2.11 source code not compiling Madhulika Gupta (Wed Nov 18 2015 - 02:47:38 CST)
Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ ZOU Changling (Wed Nov 18 2015 - 02:43:26 CST)
Fw: Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ ZOU Changling (Wed Nov 18 2015 - 02:40:15 CST)
Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ ZOU Changling (Wed Nov 18 2015 - 00:26:54 CST)
Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= ZOU Changling (Wed Nov 18 2015 - 00:25:35 CST)
Re: Can't start SMP NAMD - Problem clearly is in front of the monitor Jim Phillips (Tue Nov 17 2015 - 12:45:51 CST)
Can't start SMP NAMD - Problem clearly is in front of the monitor Vogel, Alexander (Tue Nov 17 2015 - 03:18:05 CST)
Re: ABF calculations - reaction coordinate Giacomo Fiorin (Mon Nov 16 2015 - 20:30:56 CST)
ABF calculations - reaction coordinate Mohan maruthi sena (Mon Nov 16 2015 - 19:15:15 CST)
Re: Bubble in water during membrane simulations Kevin Chan (Mon Nov 16 2015 - 10:41:21 CST)
Re: Bubble in water during membrane simulations Giacomo Fiorin (Mon Nov 16 2015 - 09:48:42 CST)
Re: AW: time per step during GPU-accelerated Implicit Solvent calculations Jim Phillips (Mon Nov 16 2015 - 08:55:26 CST)
Re: error reading colvars.conf in REUS Chitrak Gupta (Mon Nov 16 2015 - 08:42:08 CST)
Re: Free energy profiles in ABF tutorial Giacomo Fiorin (Mon Nov 16 2015 - 07:52:31 CST)
Free energy profiles in ABF tutorial Haleh a (Mon Nov 16 2015 - 06:35:30 CST)
Bubble in water during membrane simulations Kevin C Chan (Mon Nov 16 2015 - 02:12:29 CST)
AW: time per step during GPU-accelerated Implicit Solvent calculations Norman Geist (Mon Nov 16 2015 - 01:52:00 CST)
time per step during GPU-accelerated Implicit Solvent calculations Thomas Albers (Sun Nov 15 2015 - 19:11:26 CST)
Re: vmd-l: Re: On-the-fly modification of tclforces script? John Stone (Fri Nov 13 2015 - 20:17:53 CST)
Re: vmd-l: Re: On-the-fly modification of tclforces script? Tristan Croll (Fri Nov 13 2015 - 19:28:39 CST)
Re: vmd-l: Re: On-the-fly modification of tclforces script? John Stone (Fri Nov 13 2015 - 19:05:34 CST)
Re: On-the-fly modification of tclforces script? Tristan Croll (Fri Nov 13 2015 - 18:14:28 CST)
Re: On-the-fly modification of tclforces script? Tristan Croll (Fri Nov 13 2015 - 16:48:21 CST)
Re: NAMD 2.11 CUDA forces IBverbs Jim Phillips (Fri Nov 13 2015 - 08:31:50 CST)
NAMD 2.11 CUDA forces IBverbs Norman Geist (Fri Nov 13 2015 - 06:00:18 CST)
Re: Re: Re: NAMD 2.11b1 released Jim Phillips (Thu Nov 12 2015 - 22:41:32 CST)
Re: FATAL ERROR: Unable to access config file ubq_ws_eq.log Jim Phillips (Thu Nov 12 2015 - 22:45:32 CST)
Re: Would it be possible to continue a simulation from any snapshot of a trajectory? sunyeping (Thu Nov 12 2015 - 20:57:20 CST)
Re: Re: NAMD 2.11b1 released sunyeping (Thu Nov 12 2015 - 20:29:18 CST)
FATAL ERROR: Unable to access config file ubq_ws_eq.log Hugo Siles (Thu Nov 12 2015 - 16:40:41 CST)
Re: NAMD 2.11b1 released Tien Huynh (Thu Nov 12 2015 - 11:24:00 CST)
Re: NAMD 2.11b1 released Jim Phillips (Thu Nov 12 2015 - 11:15:27 CST)
FEP using separated topologies David Huggins (Thu Nov 12 2015 - 07:46:54 CST)
Re: Re: NAMD 2.11b1 released Jim Phillips (Thu Nov 12 2015 - 06:55:42 CST)
Re: Would it be possible to continue a simulation from any snapshot of a trajectory? Felipe Merino (Thu Nov 12 2015 - 03:33:05 CST)
Would it be possible to continue a simulation from any snapshot of a trajectory? sunyeping (Thu Nov 12 2015 - 02:45:51 CST)
Re: NAMD 2.11b1 released sunyeping (Thu Nov 12 2015 - 02:39:43 CST)
Re: NAMD 2.11b1 released Tristan Croll (Wed Nov 11 2015 - 20:11:00 CST)
Re: error reading colvars.conf in REUS Giacomo Fiorin (Wed Nov 11 2015 - 11:00:21 CST)
Re: error reading colvars.conf in REUS Chitrak Gupta (Tue Nov 10 2015 - 20:18:11 CST)
Re: On-the-fly modification of tclforces script? Tristan Croll (Tue Nov 10 2015 - 16:03:38 CST)
Re: NAMD 2.11b1 released Jeff Comer (Tue Nov 10 2015 - 13:18:06 CST)
Van der Waals and Electrostatic Forces - CUDA Kostas Malavazos (Tue Nov 10 2015 - 11:11:37 CST)
Re: NAMD 2.11b1 released Tien Huynh (Tue Nov 10 2015 - 11:10:25 CST)
Re: On-the-fly modification of tclforces script? Jim Phillips (Tue Nov 10 2015 - 09:53:42 CST)
NAMD 2.11b1 released Jim Phillips (Tue Nov 10 2015 - 09:39:44 CST)
Re: On-the-fly modification of tclforces script? Tristan Croll (Tue Nov 10 2015 - 04:27:19 CST)
AW: On-the-fly modification of tclforces script? Norman Geist (Tue Nov 10 2015 - 04:18:02 CST)
On-the-fly modification of tclforces script? Tristan Croll (Tue Nov 10 2015 - 03:01:19 CST)
Fw: vmd-l: what is difference between "TOTAL", â€œTOTAL2" and "POTENTIAL" in the VMD plugin NAMD Plot? å™ä¸šå¹³ (Mon Nov 09 2015 - 06:49:42 CST)
Re: error reading colvars.conf in REUS Giacomo Fiorin (Fri Nov 06 2015 - 14:41:42 CST)
Re: OPLSAA to CHARMM Francesco Pietra (Fri Nov 06 2015 - 00:59:02 CST)
error reading colvars.conf in REUS Chitrak Gupta (Thu Nov 05 2015 - 16:45:48 CST)
OPLSAA to CHARMM Francesco Pietra (Thu Nov 05 2015 - 10:21:42 CST)
Re: Topology and parameters for Sodium dodecanoate Mayne, Christopher G (Wed Nov 04 2015 - 08:05:46 CST)
Re: pdb files to dcd Josh Vermaas (Tue Nov 03 2015 - 14:40:53 CST)
pdb files to dcd Amitkumar Majhi (Tue Nov 03 2015 - 14:33:21 CST)
Topology and parameters for Sodium dodecanoate Sadegh Faramarzi Ganjabad (Tue Nov 03 2015 - 11:21:45 CST)
Re: Problem with tcl intepreter Belkin, Maxim (Tue Nov 03 2015 - 10:53:53 CST)
AW: 16 total processes killed (some possibly by mpirun during cleanup) Norman Geist (Tue Nov 03 2015 - 00:25:15 CST)
Multiple NAMD calculations on windows Mai Aamer (Mon Nov 02 2015 - 16:40:06 CST)
Fwd: Re: about deca alanine tutorial setup Branko (Mon Nov 02 2015 - 16:26:57 CST)
Re: about deca alanine tutorial setup Ajasja LjubetiÄ (Mon Nov 02 2015 - 16:14:28 CST)
about deca alanine tutorial setup Jessen Lucas (Mon Nov 02 2015 - 15:22:16 CST)
16 total processes killed (some possibly by mpirun during cleanup) Shalton Evans (Mon Nov 02 2015 - 14:34:13 CST)
How occupancy relates to force in SMD daneshkaftroody_v_at_mech.sharif.ir (Mon Nov 02 2015 - 10:41:11 CST)
Re: ABF error on NAMD 2.10 Giacomo Fiorin (Mon Nov 02 2015 - 08:51:52 CST)
Re: ABF error on NAMD 2.10 Haleh a (Mon Nov 02 2015 - 08:45:29 CST)
substrate and membrane protein LucÃa DÃaz (Mon Nov 02 2015 - 08:03:28 CST)
Re: ABF error on NAMD 2.10 Giacomo Fiorin (Mon Nov 02 2015 - 07:49:46 CST)
ABF error on NAMD 2.10 Haleh a (Mon Nov 02 2015 - 05:55:59 CST)
Weird psfgen bug? Tristan Croll (Fri Oct 30 2015 - 03:22:06 CDT)
Re: Problem with tcl intepreter Bryan Roessler (Thu Oct 29 2015 - 20:06:58 CDT)
Re: Problem with tcl intepreter Bryan Roessler (Thu Oct 29 2015 - 20:00:31 CDT)
Re: Problem with tcl intepreter Axel Kohlmeyer (Thu Oct 29 2015 - 19:54:34 CDT)
Re: Problem with tcl intepreter Josh Vermaas (Thu Oct 29 2015 - 19:45:12 CDT)
Problem with tcl intepreter Bryan Roessler (Thu Oct 29 2015 - 19:24:53 CDT)
RE: Fwd: ANGLE PARAMETERS FOR NH3 HC NH3 Tristan Croll (Wed Oct 28 2015 - 20:36:08 CDT)
Re: vmd-l: Including two parameters for protein-ligand simulation Sourav Ray (Wed Oct 28 2015 - 02:20:04 CDT)
Re: vmd-l: Re: Including two parameters for protein-ligand simulation Payal Chatterjee (Wed Oct 28 2015 - 03:08:16 CDT)
Re: Including two parameters for protein-ligand simulation Abhishek TYAGI (Wed Oct 28 2015 - 01:59:21 CDT)
Including two parameters for protein-ligand simulation Nikhil Maroli (Wed Oct 28 2015 - 01:52:30 CDT)
namd 2.10 crashes when using more than 1 CPU for FEP simulation Tien Huynh (Tue Oct 27 2015 - 21:58:14 CDT)
Re: Biasing potential of a Metadynamics Simulation Giacomo Fiorin (Tue Oct 27 2015 - 15:55:13 CDT)
Re: Biasing potential of a Metadynamics Simulation Fidan Sumbul (Tue Oct 27 2015 - 14:38:16 CDT)
Re: Fwd: ANGLE PARAMETERS FOR NH3 HC NH3 Francesco Pietra (Tue Oct 27 2015 - 13:33:59 CDT)
Re: Biasing potential of a Metadynamics Simulation Giacomo Fiorin (Tue Oct 27 2015 - 13:14:06 CDT)
Biasing potential of a Metadynamics Simulation Fidan Sumbul (Tue Oct 27 2015 - 13:05:02 CDT)
Re: Fwd: ANGLE PARAMETERS FOR NH3 HC NH3 Josh Vermaas (Tue Oct 27 2015 - 11:24:47 CDT)
Fwd: ANGLE PARAMETERS FOR NH3 HC NH3 Francesco Pietra (Tue Oct 27 2015 - 11:19:48 CDT)
ANGLE PARAMETERS FOR NH3 HC NH3 Francesco Pietra (Tue Oct 27 2015 - 11:12:20 CDT)
Re: Lennard-Jones and Electrostatic Forces and Energies Brian Radak (Tue Oct 27 2015 - 08:50:27 CDT)
Re: replica exchange module Jessen Lucas (Tue Oct 27 2015 - 03:42:23 CDT)
AW: replica exchange module Norman Geist (Tue Oct 27 2015 - 03:08:42 CDT)
Re: replica exchange module Jessen Lucas (Mon Oct 26 2015 - 22:49:20 CDT)
Re: Dielectric constant of water from MSM and PME simulations Otello Maria Roscioni (Mon Oct 26 2015 - 12:29:02 CDT)
Lennard-Jones and Electrostatic Forces and Energies Kostas Malavazos (Mon Oct 26 2015 - 13:54:28 CDT)
Re: constraint failure in Rattle algorithm for atom 54134 Life Sciences Inc (Mon Oct 26 2015 - 13:37:42 CDT)
Re: constraint failure in Rattle algorithm for atom 54134 Chitrak Gupta (Mon Oct 26 2015 - 13:01:16 CDT)
Re: constraint failure in Rattle algorithm for atom 54134 Chitrak Gupta (Mon Oct 26 2015 - 09:10:59 CDT)
RE: constraint failure in Rattle algorithm for atom 54134 Tristan Croll (Mon Oct 26 2015 - 01:59:47 CDT)
Re: constraint failure in Rattle algorithm for atom 54134 Chitrak Gupta (Mon Oct 26 2015 - 08:31:44 CDT)
Re: replica exchange module Jessen Lucas (Mon Oct 26 2015 - 03:25:46 CDT)
AW: replica exchange module Norman Geist (Mon Oct 26 2015 - 03:21:01 CDT)
Re: replica exchange module Jessen Lucas (Mon Oct 26 2015 - 02:25:49 CDT)
AW: replica exchange module Norman Geist (Mon Oct 26 2015 - 02:11:47 CDT)
replica exchange module Jessen Lucas (Mon Oct 26 2015 - 01:29:43 CDT)
constraint failure in Rattle algorithm for atom 54134 Life Sciences Inc (Sun Oct 25 2015 - 19:42:57 CDT)
Re: Re: NH4+ params Mikhail Suyetin (Sat Oct 24 2015 - 11:56:15 CDT)
Re: NH4+ params Thomas Albers (Sat Oct 24 2015 - 09:26:17 CDT)
Re: global does not work in configuration and callback function jc guo (Sat Oct 24 2015 - 08:51:33 CDT)
AW: global does not work in configuration and callback function Norman Geist (Sat Oct 24 2015 - 08:30:48 CDT)
global does not work in configuration and callback function jc guo (Sat Oct 24 2015 - 01:46:21 CDT)
NH4+ params Mikhail Suyetin (Fri Oct 23 2015 - 16:38:55 CDT)
Re: Dielectric constant of water from MSM and PME simulations Zhe Wu (Fri Oct 23 2015 - 10:46:41 CDT)
Re: Dielectric constant of water from MSM and PME simulations Zhe Wu (Fri Oct 23 2015 - 10:31:04 CDT)
Re: Dielectric constant of water from MSM and PME simulations Axel Kohlmeyer (Fri Oct 23 2015 - 09:47:38 CDT)
Dielectric constant of water from MSM and PME simulations Mattia Felice Palermo (Fri Oct 23 2015 - 08:57:37 CDT)
Re: Error in Metadynamics Simulation Fidan Sumbul (Fri Oct 23 2015 - 06:08:40 CDT)
AW: GPU accelerated MD Norman Geist (Fri Oct 23 2015 - 05:00:05 CDT)
GPU accelerated MD Nikhil Maroli (Fri Oct 23 2015 - 04:12:24 CDT)
AW: Re: AW: Why the computational speed does not increase with the increase of GPUs? Norman Geist (Fri Oct 23 2015 - 03:49:49 CDT)
Re: vmd-l: gromacs to charmm conversion Ajasja LjubetiÄ (Fri Oct 23 2015 - 03:28:28 CDT)
Re: AW: Why the computational speed does not increase with the increase of GPUs? sunyeping (Fri Oct 23 2015 - 02:57:48 CDT)
gromacs to charmm conversion Francesco Pietra (Fri Oct 23 2015 - 02:34:15 CDT)
Re: Error in Metadynamics Simulation Giacomo Fiorin (Thu Oct 22 2015 - 15:41:57 CDT)
aMD and GPU acceleration Thomas Albers (Thu Oct 22 2015 - 13:53:09 CDT)
AW: Why the computational speed does not increase with the increase of GPUs? Norman Geist (Thu Oct 22 2015 - 02:27:54 CDT)
Why the computational speed does not increase with the increase of GPUs? sunyeping (Wed Oct 21 2015 - 22:18:17 CDT)
Error in Metadynamics Simulation Fidan Sumbul (Wed Oct 21 2015 - 16:31:30 CDT)
Re: Zhe Wu (Wed Oct 21 2015 - 14:16:02 CDT)
Re: vmd-l: Topology for drugs to do MD after docking Mayne, Christopher G (Wed Oct 21 2015 - 14:44:18 CDT)
Re: Topology for drugs to do MD after docking Evandro Semighini (Wed Oct 21 2015 - 11:48:21 CDT)
Topology for drugs to do MD after docking Nikhil Maroli (Wed Oct 21 2015 - 11:40:04 CDT)
Re: Reverse Coarse Graining using VMD CG Builder Peter Freddolino (Wed Oct 21 2015 - 11:25:44 CDT)
Re: Reverse Coarse Graining using VMD CG Builder Peter Freddolino (Wed Oct 21 2015 - 10:49:38 CDT)
Re: Reverse Coarse Graining using VMD CG Builder Ardavan Mehdizadeh (Wed Oct 21 2015 - 10:41:55 CDT)
Re: Rigid bonds and non-bonded energy Grzegorz Nawrocki (Wed Oct 21 2015 - 08:29:22 CDT)
Re: Reverse Coarse Graining using VMD CG Builder Peter Freddolino (Wed Oct 21 2015 - 07:29:13 CDT)
ApoA1 simulation Kostas Malavazos (Wed Oct 21 2015 - 05:21:28 CDT)
(no subject) Mattia Felice Palermo (Wed Oct 21 2015 - 04:07:03 CDT)
Reverse Coarse Graining using VMD CG Builder Ardavan Mehdizadeh (Wed Oct 21 2015 - 03:15:35 CDT)
AW: How to calculate the temperature for a subset of my simulation Norman Geist (Wed Oct 21 2015 - 02:24:09 CDT)
Re: about replica exchange example in lib of 2.10 NAMD Jeff Comer (Tue Oct 20 2015 - 20:10:00 CDT)
Re: How to calculate the temperature for a subset of my simulation Josh Vermaas (Tue Oct 20 2015 - 14:03:32 CDT)
Re: How to calculate the temperature for a subset of my simulation Jhonatam Cordeiro Rodrigues (Tue Oct 20 2015 - 13:47:53 CDT)
Re: Rigid bonds and non-bonded energy Grzegorz Nawrocki (Tue Oct 20 2015 - 11:09:20 CDT)
Re: Rigid bonds and non-bonded energy Brian Radak (Tue Oct 20 2015 - 12:52:34 CDT)
Re: How to calculate the temperature for a subset of my simulation Jhonatam Cordeiro Rodrigues (Tue Oct 20 2015 - 12:20:46 CDT)
About the TMDInitialRMSD parameter in targeted molecular dynamics sunyeping (Tue Oct 20 2015 - 12:06:22 CDT)
Re: Rigid bonds and non-bonded energy Grzegorz Nawrocki (Tue Oct 20 2015 - 10:11:42 CDT)
Re: Rigid bonds and non-bonded energy Brian Radak (Tue Oct 20 2015 - 10:33:51 CDT)
Re: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark Brian Radak (Tue Oct 20 2015 - 09:46:32 CDT)
Re: Regarding FFTW routines usage in NAMD Axel Kohlmeyer (Tue Oct 20 2015 - 08:10:09 CDT)
Regarding FFTW routines usage in NAMD Puneet Singh (Tue Oct 20 2015 - 07:39:50 CDT)
AW: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark Norman Geist (Tue Oct 20 2015 - 03:53:51 CDT)
Re: about re install sunyeping (Tue Oct 20 2015 - 02:09:33 CDT)
AW: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark Norman Geist (Tue Oct 20 2015 - 01:29:19 CDT)
AW: How to calculate the temperature for a subset of my simulation Norman Geist (Tue Oct 20 2015 - 01:23:57 CDT)
about re install jc guo (Tue Oct 20 2015 - 01:20:08 CDT)
Regarding significance of days per ns (days/ns) parameter in NAMD benchmark Puneet Singh (Tue Oct 20 2015 - 01:01:24 CDT)
How to calculate the temperature for a subset of my simulation Jhonatam Cordeiro Rodrigues (Mon Oct 19 2015 - 15:08:27 CDT)
Re: Rigid bonds and non-bonded energy Brian Radak (Mon Oct 19 2015 - 14:40:51 CDT)
Re: AW: stepspercycle Gianluca Interlandi (Mon Oct 19 2015 - 12:31:23 CDT)
Several questions about targeted molecular dynamics sunyeping (Mon Oct 19 2015 - 04:54:09 CDT)
AW: about command replicaRecv and replicaSend Norman Geist (Mon Oct 19 2015 - 02:43:43 CDT)
about command replicaRecv and replicaSend jc guo (Mon Oct 19 2015 - 02:09:43 CDT)
AW: stepspercycle Norman Geist (Mon Oct 19 2015 - 01:25:18 CDT)
stepspercycle Gianluca Interlandi (Sun Oct 18 2015 - 20:20:26 CDT)
Bias-exchange metadynamics Fidan Sumbul (Sun Oct 18 2015 - 18:16:34 CDT)
Problem on merging multi-psf files into one wliu (Sun Oct 18 2015 - 07:52:11 CDT)
Re: Performing MD simulations with protein and halide ions (iodide, bromide, chloride) Stojanoski, Vlatko (Sat Oct 17 2015 - 15:49:19 CDT)
Re: Performing MD simulations with protein and halide ions (iodide, bromide, chloride) Branko (Sat Oct 17 2015 - 15:42:11 CDT)
Re: Performing MD simulations with protein and halide ions (iodide, bromide, chloride) Stojanoski, Vlatko (Sat Oct 17 2015 - 15:31:43 CDT)
Re: Performing MD simulations with protein and halide ions (iodide, bromide, chloride) Branko (Sat Oct 17 2015 - 14:35:37 CDT)
Performing MD simulations with protein and halide ions (iodide, bromide, chloride) Stojanoski, Vlatko (Sat Oct 17 2015 - 14:05:29 CDT)
Re: Rigid bonds and non-bonded energy Brian Radak (Fri Oct 16 2015 - 17:42:34 CDT)
Rigid bonds and non-bonded energy Grzegorz Nawrocki (Fri Oct 16 2015 - 16:39:48 CDT)
Re: about replica exchange Jeff Comer (Fri Oct 16 2015 - 16:17:13 CDT)
Re: NAMD - wrap atoms, not center of mass Josh Vermaas (Fri Oct 16 2015 - 10:48:35 CDT)
about replica exchange jc guo (Fri Oct 16 2015 - 10:43:23 CDT)
Re: NAMD - wrap atoms, not center of mass Sourav Ray (Fri Oct 16 2015 - 10:27:09 CDT)
NAMD - wrap atoms, not center of mass Stanislav Q=A0imko?= (Fri Oct 16 2015 - 10:20:28 CDT)
Re: MD Simulation of accelerated MD using GPU jeevan gc (Fri Oct 16 2015 - 08:25:29 CDT)
about replica exchange example in lib of 2.10 NAMD jc guo (Fri Oct 16 2015 - 00:11:18 CDT)
SMD or moving contraints Kevin C Chan (Thu Oct 15 2015 - 21:50:20 CDT)
Re: Compile NAMD - Projections Stefan Richter (Thu Oct 15 2015 - 04:40:44 CDT)
Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Sridhar Kumar Kannam (Thu Oct 15 2015 - 02:24:52 CDT)
Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. JÃ©rÃ´me HÃ©nin (Thu Oct 15 2015 - 01:43:25 CDT)
Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Sridhar Kumar Kannam (Thu Oct 15 2015 - 00:54:00 CDT)
Re: MD Simulation of accelerated MD using GPU jeevan gc (Wed Oct 14 2015 - 16:21:36 CDT)
Compile NAMD - Projections Kostas Malavazos (Wed Oct 14 2015 - 11:45:04 CDT)
Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Giacomo Fiorin (Wed Oct 14 2015 - 06:33:28 CDT)
Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Sridhar Kumar Kannam (Wed Oct 14 2015 - 05:41:58 CDT)
Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. JÃ©rÃ´me HÃ©nin (Wed Oct 14 2015 - 05:14:41 CDT)
Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Marlon Sidore (Wed Oct 14 2015 - 05:12:16 CDT)
Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. JÃ©rÃ´me HÃ©nin (Wed Oct 14 2015 - 05:05:54 CDT)
Re: Compilation of NAMD from Source (Cray XC40) Stefan Richter (Wed Oct 14 2015 - 04:38:17 CDT)
keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Sridhar Kumar Kannam (Tue Oct 13 2015 - 23:39:14 CDT)
Re: AW: Compilation of NAMD from Source (Cray XC40) Jim Phillips (Tue Oct 13 2015 - 17:00:08 CDT)
Re: Compilation of NAMD from Source (Cray XC40) Vlad Cojocaru (Tue Oct 13 2015 - 15:04:02 CDT)
AW: Compilation of NAMD from Source (Cray XC40) Richter, Stefan (Tue Oct 13 2015 - 13:10:44 CDT)
Re: Compilation of NAMD from Source (Cray XC40) Jim Phillips (Tue Oct 13 2015 - 10:03:39 CDT)
Compilation of NAMD from Source (Cray XC40) Richter, Stefan (Tue Oct 13 2015 - 09:26:06 CDT)
Re: MD Simulation of accelerated MD using GPU Kenneth Huang (Mon Oct 12 2015 - 20:09:26 CDT)
Re: MD Simulation of accelerated MD using GPU Brian Radak (Mon Oct 12 2015 - 20:01:24 CDT)
MD Simulation of accelerated MD using GPU jeevan gc (Mon Oct 12 2015 - 17:19:15 CDT)
MD Simulation of accelerated MD using GPU jeevan gc (Mon Oct 12 2015 - 17:07:39 CDT)
Re: simulating TIP5P water Monika Madhavi (Mon Oct 12 2015 - 05:10:35 CDT)
Re: simulating TIP5P water Monika Madhavi (Mon Oct 12 2015 - 03:44:50 CDT)
Re: simulating TIP5P water Peter Freddolino (Sat Oct 10 2015 - 21:33:50 CDT)
Re: BONDS vs DOUBLE in topology file Gianluca Interlandi (Fri Oct 09 2015 - 12:42:43 CDT)
Re: BONDS vs DOUBLE in topology file Josh Vermaas (Fri Oct 09 2015 - 09:46:07 CDT)
simulating TIP5P water Monika Madhavi (Fri Oct 09 2015 - 05:29:35 CDT)
BONDS vs DOUBLE in topology file Gianluca Interlandi (Fri Oct 09 2015 - 00:42:05 CDT)
about "small molecules" in OPLS-AAM FF Francesco Pietra (Wed Oct 07 2015 - 16:14:12 CDT)
Triple-hybrid topology? Tristan Croll (Tue Oct 06 2015 - 19:26:07 CDT)
Re: Regarding problem in psfgen of heparin Tristan Croll (Tue Oct 06 2015 - 18:44:21 CDT)
Subscribe Vijay L. Roy (Tue Oct 06 2015 - 01:22:14 CDT)
Re: Regarding biasTemperature used in Well-tempered metadynamics Giacomo Fiorin (Tue Oct 06 2015 - 09:01:52 CDT)
Regarding biasTemperature used in Well-tempered metadynamics Vijay L. Roy (Tue Oct 06 2015 - 01:49:12 CDT)
RE: Regarding problem in psfgen of heparin Tristan Croll (Mon Oct 05 2015 - 23:00:32 CDT)
Coarse grained instability: atoms moving too fast Marlon Sidore (Mon Oct 05 2015 - 06:47:41 CDT)
Output to a file Mahdi Tavakol (Mon Oct 05 2015 - 01:31:55 CDT)
Segmentation Fault - Debug Kumar, Amit (Mon Oct 05 2015 - 09:13:14 CDT)
Re: Re: vmd-l: script error Nikhil Maroli (Sat Oct 03 2015 - 02:44:17 CDT)
Regarding problem in psfgen of heparin siddharth kamal (Fri Oct 02 2015 - 14:20:15 CDT)
Ispopetide bond Milica UtjeÅ¡anoviÄ‡ (Fri Oct 02 2015 - 14:30:04 CDT)
Re: vmd-l: script error John Stone (Fri Oct 02 2015 - 10:10:56 CDT)
Cyclic peptide Nanotube Nikhil Maroli (Fri Oct 02 2015 - 08:52:59 CDT)
script error Nikhil Maroli (Fri Oct 02 2015 - 08:44:13 CDT)
PSF for cyclic peptide nanotube Nikhil Maroli (Fri Oct 02 2015 - 08:36:47 CDT)
Re: namd simulation with TIP5P Monika Madhavi (Fri Oct 02 2015 - 01:16:41 CDT)
simulating tip5p water Monika Madhavi (Thu Oct 01 2015 - 23:36:51 CDT)
Outward tilting which colvar to use Nicolas Martin (Thu Oct 01 2015 - 05:13:01 CDT)
Re: LJ Parameters on hydrogen for TIP4P water models Shayon Bhattacharya (Wed Sep 30 2015 - 16:39:45 CDT)
Re: LJ Parameters on hydrogen for TIP4P water models Peter Freddolino (Wed Sep 30 2015 - 08:14:45 CDT)
Re: Atomselect within radial pair distribution function g(r) Chitrak Gupta (Wed Sep 30 2015 - 08:09:16 CDT)
Atomselect within radial pair distribution function g(r) Aditya Ranganathan (Wed Sep 30 2015 - 03:55:37 CDT)
Re: LJ Parameters on hydrogen for TIP4P water models Brian Radak (Tue Sep 29 2015 - 14:52:44 CDT)
Re: LJ Parameters on hydrogen for TIP4P water models Shayon Bhattacharya (Tue Sep 29 2015 - 14:04:44 CDT)
Re: LJ Parameters on hydrogen for TIP4P water models Peter Freddolino (Tue Sep 29 2015 - 13:25:07 CDT)
LJ Parameters on hydrogen for TIP4P water models Shayon Bhattacharya (Tue Sep 29 2015 - 10:20:36 CDT)
Hybrid coarse-grained/all-atom simulation Mahya Hemmat (Mon Sep 28 2015 - 14:25:24 CDT)
Re: PSF for CYCLIC PEPTIDE : bay__gulf618_at_sina.com (Sat Sep 26 2015 - 21:26:01 CDT)
psf for cyclic peptide nanotube:psf ready for one ring but required for 8 ring Nikhil Maroli (Sat Sep 26 2015 - 06:50:31 CDT)
PSF for CYCLIC PEPTIDE : Nikhil Maroli (Sat Sep 26 2015 - 05:45:17 CDT)
Q=B4=D7=D4"=C2=C0=D0=A1=D3=A8"_<lv-xy11@mail?= s.tsinghua.edu.cn>µÄÓÊ¼þ ÂÀÐ¡Ó¨ (Fri Sep 25 2015 - 09:19:53 CDT)
Re: Solvation free energy calculation with MM/GBSA Neelanjana Sengupta (Fri Sep 25 2015 - 07:36:50 CDT)
Re: Adaptive tempering implementation in NAMD differs Nicholas M Glykos (Fri Sep 25 2015 - 04:36:52 CDT)
Re: Adaptive tempering implementation in NAMD differs Sachin Natesh (Thu Sep 24 2015 - 20:28:36 CDT)
Re: Solvation free energy calculation with MM/GBSA Jeff Comer (Thu Sep 24 2015 - 08:27:26 CDT)
Re: Solvation free energy calculation with MM/GBSA Abhishek TYAGI (Thu Sep 24 2015 - 07:40:43 CDT)
Re: Solvation free energy calculation with MM/GBSA Neelanjana Sengupta (Thu Sep 24 2015 - 07:37:04 CDT)
Re: Solvation free energy calculation with MM/GBSA Abhishek TYAGI (Thu Sep 24 2015 - 07:13:20 CDT)
Re: Adaptive tempering implementation in NAMD differs Sachin Natesh (Wed Sep 23 2015 - 10:28:05 CDT)
Solvation free energy calculation with MM/GBSA Neelanjana Sengupta (Wed Sep 23 2015 - 06:51:28 CDT)
Re: Adaptive tempering implementation in NAMD differs Nicholas M. Glykos (Wed Sep 23 2015 - 05:45:40 CDT)
Adaptive tempering implementation in NAMD differs from original paper? Sachin Natesh (Tue Sep 22 2015 - 19:45:22 CDT)
Re: vmd-l: Which VMD AND NAMD should install John Stone (Tue Sep 22 2015 - 14:07:17 CDT)
Re: string method in NAMD 2.10 Jerome Karp (Tue Sep 22 2015 - 11:44:37 CDT)
Re: string method in NAMD 2.10 Chris Chipot (Tue Sep 22 2015 - 10:46:28 CDT)
Re: string method in NAMD 2.10 Jerome Karp (Tue Sep 22 2015 - 10:39:30 CDT)
Re: string method in NAMD 2.10 Chris Chipot (Tue Sep 22 2015 - 10:26:53 CDT)
Re: string method in NAMD 2.10 Jerome Karp (Tue Sep 22 2015 - 10:05:05 CDT)
Re: string method in NAMD 2.10 Thomas Evangelidis (Tue Sep 22 2015 - 05:31:34 CDT)
Re: string method in NAMD 2.10 Thomas Evangelidis (Tue Sep 22 2015 - 05:29:16 CDT)
string method in NAMD 2.10 Jerry Karp (Mon Sep 21 2015 - 10:46:45 CDT)
string method in NAMD 2.10 Jerome Karp (Mon Sep 21 2015 - 10:49:42 CDT)
Re: Atoms moving too fast; simulation has become unstable Peter Freddolino (Mon Sep 21 2015 - 07:53:14 CDT)
Re: Atoms moving too fast; simulation has become unstable Monika Madhavi (Mon Sep 21 2015 - 00:58:32 CDT)
Re: Automatic PSF builder for cyclic peptide Aditya Ranganathan (Sun Sep 20 2015 - 08:20:24 CDT)
Automatic PSF builder for cyclic peptide Nikhil Maroli (Sun Sep 20 2015 - 07:04:36 CDT)
Which VMD AND NAMD should install Nikhil Maroli (Sat Sep 19 2015 - 01:57:30 CDT)
Re: NAMD Anisotropic pressure control Mahdi Tavakol (Fri Sep 18 2015 - 11:51:29 CDT)
Re: NAMD Anisotropic pressure control Fotis Baltoumas (Fri Sep 18 2015 - 09:50:14 CDT)
NAMD Anisotropic pressure control Mahdi Tavakol (Fri Sep 18 2015 - 08:50:04 CDT)
Re: Atoms moving too fast; simulation has become unstable Peter Freddolino (Thu Sep 17 2015 - 23:01:32 CDT)
Re: Atoms moving too fast; simulation has become unstable Monika Madhavi (Thu Sep 17 2015 - 22:58:12 CDT)
Re: Atoms moving too fast; simulation has become unstable Peter Freddolino (Thu Sep 17 2015 - 21:44:09 CDT)
Re: Atoms moving too fast; simulation has become unstable Monika Madhavi (Thu Sep 17 2015 - 04:42:40 CDT)
Re: simulating graphene sheets (with bonds across boundaries) with water upayan baul (Wed Sep 16 2015 - 05:40:38 CDT)
Re: LJcorrection + switching? Peter Freddolino (Tue Sep 15 2015 - 20:11:32 CDT)
Re: simulating graphene sheets (with bonds across boundaries) with water Axel Kohlmeyer (Tue Sep 15 2015 - 19:22:27 CDT)
Re: simulating graphene sheets (with bonds across boundaries) with water Abhishek TYAGI (Tue Sep 15 2015 - 18:58:52 CDT)
Re: NAMD/VMD: generating psf for Abeta, ACE patch Tristan Croll (Tue Sep 15 2015 - 17:53:20 CDT)
NAMD/VMD: generating psf for Abeta, ACE patch Mona Habibi (Tue Sep 15 2015 - 15:31:37 CDT)
Re: Parameterizing a novel peptide Bryan Roessler (Tue Sep 15 2015 - 12:06:12 CDT)
RE: Parameterizing a novel peptide Bennion, Brian (Tue Sep 15 2015 - 11:15:56 CDT)
Re: simulating graphene sheets (with bonds across boundaries) with water upayan baul (Tue Sep 15 2015 - 06:57:20 CDT)
Can NAMD handle two different LJ cutoffs in a single simulation? Lewis Martin (Mon Sep 14 2015 - 23:17:36 CDT)
Re: Parameterizing a novel peptide Peter Freddolino (Mon Sep 14 2015 - 22:00:56 CDT)
Re: Parameterizing a novel peptide Mayne, Christopher G (Mon Sep 14 2015 - 21:38:04 CDT)
Re: Parameterizing a novel peptide Peter Freddolino (Mon Sep 14 2015 - 21:08:55 CDT)
Re: simulating graphene sheets (with bonds across boundaries) with water Abhishek TYAGI (Mon Sep 14 2015 - 19:28:04 CDT)
FEP utility for binding estimation HERBERT MAX VENTHUR PEÂ¥A (Mon Sep 14 2015 - 10:35:17 CDT)
Re: Parameterizing a novel peptide Mayne, Christopher G (Mon Sep 14 2015 - 08:48:57 CDT)
simulating graphene sheets (with bonds across boundaries) with water upayan baul (Mon Sep 14 2015 - 06:59:00 CDT)
Re: node file for NAMD Sourav Ray (Sat Sep 12 2015 - 01:13:32 CDT)
Re: node file for NAMD Sourav Ray (Sat Sep 12 2015 - 01:11:30 CDT)
Re: node file for NAMD Abhishek Tyagi (Fri Sep 11 2015 - 22:55:16 CDT)
Re: Parameterizing a novel peptide Tomek StÄ™pniewski (Fri Sep 11 2015 - 18:16:27 CDT)
Parameterizing a novel peptide Bryan Roessler (Fri Sep 11 2015 - 17:14:05 CDT)
Re: Re: vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech Sourav Ray (Fri Sep 11 2015 - 11:15:47 CDT)
Re: Re: vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech JC Gumbart (Fri Sep 11 2015 - 10:08:07 CDT)
node file for NAMD Parag Khuraswar (Fri Sep 11 2015 - 08:02:54 CDT)
Re: Error in NAMD Controller Class Reference- Adaptive Tempering Jeff Comer (Fri Sep 11 2015 - 08:12:15 CDT)
Re: Error in NAMD Controller Class Reference- Adaptive Tempering Jeff Comer (Fri Sep 11 2015 - 08:10:02 CDT)
Error in NAMD Controller Class Reference- Adaptive Tempering Sachin Natesh (Thu Sep 10 2015 - 19:13:41 CDT)
Re: vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech Sourav Ray (Wed Sep 09 2015 - 22:51:54 CDT)
Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech JC Gumbart (Wed Sep 09 2015 - 18:15:34 CDT)
Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech JC Gumbart (Wed Sep 09 2015 - 10:13:31 CDT)
Re: charm36 for ATP and MG Radhika Anoop (Wed Sep 09 2015 - 05:09:39 CDT)
Re: charm36 for ATP and MG Julian Gamboa (Tue Sep 08 2015 - 11:19:03 CDT)
Re: charm36 for ATP and MG Josh Vermaas (Tue Sep 08 2015 - 11:13:19 CDT)
charm36 for ATP and MG Radhika Anoop (Tue Sep 08 2015 - 00:55:48 CDT)
Thermodynamic integration question Randall Hall (Sat Sep 05 2015 - 23:28:57 CDT)
Re: "UNABLE TO FIND BOND PARAMETERS" but bond is defined in stream file Josh Vermaas (Fri Sep 04 2015 - 10:29:38 CDT)
"UNABLE TO FIND BOND PARAMETERS" but bond is defined in stream file Bryan Roessler (Fri Sep 04 2015 - 00:07:49 CDT)
Re: patching SO3 group to GAG Lara rajam (Thu Sep 03 2015 - 22:45:34 CDT)
Re: patching SO3 group to GAG Peter Freddolino (Thu Sep 03 2015 - 20:36:45 CDT)
patching SO3 group to GAG Lara rajam (Thu Sep 03 2015 - 19:13:21 CDT)
Re: parameters problem in sulfated molecules siddharth kamal (Wed Sep 02 2015 - 08:33:11 CDT)
node file for NAMD Parag Khuraswar (Tue Sep 01 2015 - 23:28:06 CDT)
AW: Reducing the amount of work being done on CPU Norman Geist (Tue Sep 01 2015 - 12:47:56 CDT)
RE: parameters problem in sulfated molecules Bennion, Brian (Tue Sep 01 2015 - 12:27:17 CDT)
Re: parameters problem in sulfated molecules Peter Freddolino (Tue Sep 01 2015 - 12:25:02 CDT)
parameters problem in sulfated molecules Lara rajam (Tue Sep 01 2015 - 12:12:42 CDT)
Reducing the amount of work being done on CPU Maxime Boissonneault (Tue Sep 01 2015 - 09:48:24 CDT)
LJcorrection + switching? Brian Radak (Tue Sep 01 2015 - 09:31:34 CDT)
Re: Sampling frequency Jeff Comer (Tue Sep 01 2015 - 08:40:14 CDT)
Sampling frequency Dr. Eddie (Mon Aug 31 2015 - 14:02:46 CDT)
Adaptive Tempering - Velocity Rescaling Sachin Natesh (Mon Aug 31 2015 - 09:45:16 CDT)
Re: Atoms moving too fast; simulation has become unstable Peter Freddolino (Mon Aug 31 2015 - 08:30:48 CDT)
Re: Atoms moving too fast; simulation has become unstable Sourav Ray (Mon Aug 31 2015 - 06:29:30 CDT)
Re: Atoms moving too fast; simulation has become unstable farzad kiani (Mon Aug 31 2015 - 06:17:38 CDT)
Atoms moving too fast; simulation has become unstable Monika Madhavi (Mon Aug 31 2015 - 05:42:48 CDT)
heparin Lara rajam (Sat Aug 29 2015 - 18:48:08 CDT)
running namd gpu version Sanjana Anil Kumar Nair (Sat Aug 29 2015 - 05:21:41 CDT)
AW: Problem running REMD simulation Norman Geist (Thu Aug 27 2015 - 03:42:10 CDT)
Re: Problem running REMD simulation Nicholus Bhattacharjee (Thu Aug 27 2015 - 03:00:31 CDT)
Re: Format of colvars.state Hossein Mohammadiarani (Wed Aug 26 2015 - 18:05:19 CDT)
Re: Problem running REMD simulation Peter Freddolino (Wed Aug 26 2015 - 08:28:57 CDT)
Re: Problem running REMD simulation Peter Freddolino (Tue Aug 25 2015 - 23:25:00 CDT)
Re: Problem running REMD simulation Nicholus Bhattacharjee (Tue Aug 25 2015 - 04:59:07 CDT)
Re: Problem running REMD simulation Douglas Houston (Tue Aug 25 2015 - 04:16:55 CDT)
Re: Problem with iron ion (FE2+) Tristan Croll (Tue Aug 25 2015 - 03:56:51 CDT)
AW: Problem running REMD simulation Norman Geist (Tue Aug 25 2015 - 03:50:15 CDT)
Problem running REMD simulation Nicholus Bhattacharjee (Tue Aug 25 2015 - 03:01:36 CDT)
Re: Problem with iron ion (FE2+) Josh Vermaas (Mon Aug 24 2015 - 14:17:20 CDT)
Re: Problem with iron ion (FE2+) Branko (Mon Aug 24 2015 - 13:40:17 CDT)
Re: Problem with iron ion (FE2+) Daniela Rivas (Mon Aug 24 2015 - 13:16:15 CDT)
Re: Problem with iron ion (FE2+) Branko (Mon Aug 24 2015 - 13:09:01 CDT)
Format of colvars.state Hossein Mohammadiarani (Mon Aug 24 2015 - 12:53:14 CDT)
Problem with iron ion (FE2+) Daniela Rivas (Mon Aug 24 2015 - 12:51:59 CDT)
Re: feature request: external initiated clean exit Peter Freddolino (Fri Aug 21 2015 - 20:04:42 CDT)
AW: feature request: external initiated clean exit Daniel MÃ¶ller (Fri Aug 21 2015 - 19:21:54 CDT)
Re: feature request: external initiated clean exit Peter Freddolino (Fri Aug 21 2015 - 17:09:40 CDT)
Re: feature request: external initiated clean exit Axel Kohlmeyer (Fri Aug 21 2015 - 17:03:32 CDT)
Re: feature request: external initiated clean exit Peter Freddolino (Fri Aug 21 2015 - 16:47:55 CDT)
Re: feature request: external initiated clean exit Peter Freddolino (Fri Aug 21 2015 - 16:44:27 CDT)
RE: feature request: external initiated clean exit Parag Khuraswar (Fri Aug 21 2015 - 07:58:53 CDT)
feature request: external initiated clean exit Daniel Möller (Fri Aug 21 2015 - 07:37:02 CDT)
Problem running REMD simulation Nicholus Bhattacharjee (Thu Aug 20 2015 - 03:47:33 CDT)
Charm++ warning> fences and atomic operations not available in native assembly Ern Seang Ong (Thu Aug 20 2015 - 02:56:40 CDT)
Lambda-exchange multiple-copy alchemical free energy calculations å²¡éƒ¨ç¯¤ä¿Š (Tue Aug 18 2015 - 09:54:40 CDT)
AW: AW: Regarding NAMD installation Norman Geist (Mon Aug 17 2015 - 05:22:11 CDT)
Re: AW: Regarding NAMD installation Pragya Priyadarshini (Mon Aug 17 2015 - 04:38:29 CDT)
AW: Regarding NAMD installation Norman Geist (Mon Aug 17 2015 - 04:32:19 CDT)
Re: Regarding NAMD installation Sourav Ray (Mon Aug 17 2015 - 02:53:00 CDT)
Regarding NAMD installation Pragya Priyadarshini (Mon Aug 17 2015 - 02:45:13 CDT)
Looking for benchmarks on k80's rswett_at_chem.wayne.edu (Thu Aug 13 2015 - 10:40:45 CDT)
Re: sausage plot for a namd trajectory in vmd Thomas C. Bishop (Tue Aug 11 2015 - 10:30:23 CDT)
Re: PME Seg Fault Vibhor Agrawal (Mon Aug 10 2015 - 11:31:56 CDT)
PME Seg Fault Richard Overstreet (Mon Aug 10 2015 - 09:11:27 CDT)
Verification of NAMD Results Kanzliersch, Lukas (Wed Aug 05 2015 - 15:32:38 CDT)
OPLS/AA force field oguz gurbulak (Wed Aug 05 2015 - 09:00:01 CDT)
eBiothon platform eBiothon Admin Team (Mon Aug 03 2015 - 10:07:36 CDT)
Re: namd-l digest V1 #1726 nader zabarjad (Sun Aug 02 2015 - 10:41:55 CDT)
how to create two namd jobs in a single script with 2 x dual cuda gpus? nam kim (Sat Aug 01 2015 - 16:36:15 CDT)
Re: how to create two namd jobs in a single script with 2 x dual cuda gpus? nam kim (Sat Aug 01 2015 - 16:33:04 CDT)
Re: sausage plot for a namd trajectory in vmd Aaron Larsen (Fri Jul 31 2015 - 05:44:17 CDT)
sausage plot for a namd trajectory in vmd luca belmonte (Fri Jul 31 2015 - 05:01:02 CDT)
Re: Metadynamics: writeHillsTrajectory Chola Regmi (Thu Jul 30 2015 - 16:48:15 CDT)
Metadynamics: writeHillsTrajectory Chola Regmi (Thu Jul 30 2015 - 16:37:53 CDT)
Re: Interrupted Molecular Dynamics Simulation Daniela Rivas (Wed Jul 29 2015 - 10:25:29 CDT)
run NAMD 2.10 on Xeon Phi machine Xiaoge Wang (Tue Jul 28 2015 - 12:50:23 CDT)
Re: Interrupted Molecular Dynamics Simulation Axel Kohlmeyer (Tue Jul 28 2015 - 10:53:28 CDT)
Re: Interrupted Molecular Dynamics Simulation Felipe Merino (Tue Jul 28 2015 - 10:34:17 CDT)
Re: Interrupted Molecular Dynamics Simulation Purushottam Dixit (Tue Jul 28 2015 - 09:51:22 CDT)
Re: Interrupted Molecular Dynamics Simulation Daniela Rivas (Tue Jul 28 2015 - 09:45:07 CDT)
Re: Interrupted Molecular Dynamics Simulation Chitrak Gupta (Tue Jul 28 2015 - 09:34:21 CDT)
Re: Interrupted Molecular Dynamics Simulation Felipe Merino (Tue Jul 28 2015 - 02:03:00 CDT)
RE: "missing operator at _@_ in expression" for if statement Norman Geist (Tue Jul 28 2015 - 01:33:01 CDT)
The 2 NAMD tests "Alanin" and "tclforces" fail to run with "Atoms moving too fast" error Sriram Adhyapak (Mon Jul 27 2015 - 20:36:14 CDT)
"missing operator at _@_ in expression" for if statement Simon Kit Sang Chu (Mon Jul 27 2015 - 19:39:51 CDT)
Re: Interrupted Molecular Dynamics Simulation Daniela Rivas (Mon Jul 27 2015 - 19:21:00 CDT)
Re: Interrupted Molecular Dynamics Simulation Chitrak Gupta (Mon Jul 27 2015 - 12:29:25 CDT)
Interrupted Molecular Dynamics Simulation Daniela Rivas (Mon Jul 27 2015 - 10:32:29 CDT)
NAMD hybrid configuration: Atoms moving too fast error Puneet Singh (Mon Jul 27 2015 - 06:41:38 CDT)
RE: Patch-size Error (not like the other ones) Norman Geist (Mon Jul 27 2015 - 02:32:33 CDT)
Instability in harmonic restraints when equilibrating large systems Tristan Croll (Fri Jul 24 2015 - 16:52:05 CDT)
Re: Patch-size Error (not like the other ones) Jeffrey Potoff (Fri Jul 24 2015 - 13:38:52 CDT)
Patch-size Error (not like the other ones) Merrill, Dante (Fri Jul 24 2015 - 13:14:28 CDT)
segmentation fault when running with mpirun Puneet Singh (Fri Jul 24 2015 - 08:05:23 CDT)
FATAL ERROR: Incorrect atom count in binary file min.coor Urszula Uciechowska (Fri Jul 24 2015 - 03:27:31 CDT)
Re: namd ibverbs Kevin C Chan (Thu Jul 23 2015 - 05:38:49 CDT)
Re: backbone constraint Josh Vermaas (Wed Jul 22 2015 - 08:59:48 CDT)
Tilt angle clockwise rotation Nicolas Martin (Wed Jul 22 2015 - 08:34:47 CDT)
RE: FEP method- Free energy of solvation of ligand hannes.loeffler_at_stfc.ac.uk (Wed Jul 22 2015 - 03:10:42 CDT)
Re: FEP method- Free energy of solvation of ligand Felipe Merino (Wed Jul 22 2015 - 03:07:32 CDT)
backbone constraint Urszula Uciechowska (Wed Jul 22 2015 - 02:59:37 CDT)
FEP method- Free energy of solvation of ligand Mohan maruthi sena (Wed Jul 22 2015 - 02:25:40 CDT)
Re: wrapping in NVT Abhishek TYAGI (Wed Jul 22 2015 - 00:27:02 CDT)
Re: wrapping in NVT Richard Overstreet (Wed Jul 22 2015 - 01:05:30 CDT)
wrapping in NVT Abhishek TYAGI (Tue Jul 21 2015 - 22:59:52 CDT)
Error in TI derivatives for staggered lambda scaling? Brian Radak (Tue Jul 21 2015 - 13:41:28 CDT)
Re: nvt run error Felipe Merino (Tue Jul 21 2015 - 03:28:40 CDT)
nvt run error Urszula Uciechowska (Tue Jul 21 2015 - 02:54:10 CDT)
restart error Lara rajam (Mon Jul 20 2015 - 10:15:23 CDT)
Debugging and Force Checking? Brian Radak (Mon Jul 20 2015 - 09:32:44 CDT)
Compilation with OpenMPI Kevin C Chan (Mon Jul 20 2015 - 05:02:10 CDT)
Re: Controlling water diffusion Evandro Semighini (Sun Jul 19 2015 - 21:42:17 CDT)
Re: Controlling water diffusion Peter Freddolino (Sun Jul 19 2015 - 21:13:15 CDT)
VDW energy diverged & VMD functions applied on cluster Simon Kit Sang Chu (Sat Jul 18 2015 - 16:37:54 CDT)
Re: what exactly is the form of the cosine angle potential? Fotis Baltoumas (Fri Jul 17 2015 - 08:47:55 CDT)
Re: nvt input file Branko (Fri Jul 17 2015 - 08:44:24 CDT)
nvt input file Urszula Uciechowska (Fri Jul 17 2015 - 08:25:21 CDT)
what exactly is the form of the cosine angle potential? Charlesworth, Henry (Fri Jul 17 2015 - 08:08:50 CDT)
Re: Controlling water diffusion Evandro Semighini (Fri Jul 17 2015 - 07:44:36 CDT)
Re: Controlling water diffusion Peter Freddolino (Thu Jul 16 2015 - 21:54:49 CDT)
Re: Minimization without MD Ajasja LjubetiÄ (Thu Jul 16 2015 - 17:18:20 CDT)
Re: namd ibverbs Gianluca Interlandi (Thu Jul 16 2015 - 17:09:40 CDT)
Minimization without MD Simon Kit Sang Chu (Thu Jul 16 2015 - 15:37:39 CDT)
Re: namd ibverbs Maxime Boissonneault (Thu Jul 16 2015 - 16:43:06 CDT)
Minimization without MD Simon Kit Sang Chu (Thu Jul 16 2015 - 16:21:40 CDT)
Re: namd ibverbs Gianluca Interlandi (Thu Jul 16 2015 - 16:20:34 CDT)
Re: namd ibverbs Gianluca Interlandi (Thu Jul 16 2015 - 16:06:37 CDT)
Re: namd ibverbs Maxime Boissonneault (Thu Jul 16 2015 - 15:59:19 CDT)
Re: namd ibverbs Gianluca Interlandi (Thu Jul 16 2015 - 15:56:14 CDT)
Re: namd ibverbs Maxime Boissonneault (Thu Jul 16 2015 - 15:50:36 CDT)
Re: namd ibverbs Gianluca Interlandi (Thu Jul 16 2015 - 15:31:34 CDT)
Controlling water diffusion Evandro Semighini (Thu Jul 16 2015 - 14:21:50 CDT)
namd ibverbs Maxime Boissonneault (Thu Jul 16 2015 - 12:59:50 CDT)
Re: protein-DNA complex Vlad Cojocaru (Thu Jul 16 2015 - 10:59:19 CDT)
protein-DNA complex Urszula Uciechowska (Thu Jul 16 2015 - 09:40:25 CDT)
Fwd: Regarding problem in generating psf file of heparin and heparan sulfate siddharth kamal (Thu Jul 16 2015 - 07:44:46 CDT)
Compilation with OpenMPI Kevin C Chan (Tue Jul 14 2015 - 00:11:38 CDT)
UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Anjela Manandhar (Mon Jul 13 2015 - 15:58:55 CDT)
Re: replica exchange and GPU acceleration Mitchell Gleed (Mon Jul 13 2015 - 01:32:14 CDT)
RE: replica exchange and GPU acceleration Norman Geist (Mon Jul 13 2015 - 00:51:11 CDT)
Re: replica exchange and GPU acceleration Mitchell Gleed (Sun Jul 12 2015 - 22:36:54 CDT)
Compilation with OpenMPI Kevin C Chan (Sun Jul 12 2015 - 01:13:30 CDT)
Re: call "NAMD" from another program bay__gulf618_at_sina.com (Sat Jul 11 2015 - 22:21:09 CDT)
Re: NAMD workflows <- : Re: call "NAMD" from another program Ajasja LjubetiÄ (Fri Jul 10 2015 - 02:50:31 CDT)
NAMD workflows <- : Re: call "NAMD" from another program Thomas C Bishop (Fri Jul 10 2015 - 02:38:00 CDT)
Re: Running constant pH molecular dynamics (CpHMD) Jason Swails (Thu Jul 09 2015 - 20:05:36 CDT)
Running constant pH molecular dynamics (CpHMD) Leonardo Herrera (Thu Jul 09 2015 - 19:00:02 CDT)
Re: call "NAMD" from another program Aron Broom (Thu Jul 09 2015 - 17:59:08 CDT)
call "NAMD" from another program Ma'Mon Hatmal (Thu Jul 09 2015 - 17:53:24 CDT)
model.conf Mai Aamer (Thu Jul 09 2015 - 17:09:01 CDT)
Re: NAMD 2.10 Building from Source Giacomo Fiorin (Thu Jul 09 2015 - 16:05:02 CDT)
RE: NAMD 2.10 Building from Source Kumar, Amit (Thu Jul 09 2015 - 16:02:07 CDT)
Re: polymerization simulations Giacomo Fiorin (Thu Jul 09 2015 - 15:51:38 CDT)
Re: NAMD 2.10 Building from Source Giacomo Fiorin (Thu Jul 09 2015 - 15:45:32 CDT)
NAMD 2.10 Building from Source Kumar, Amit (Thu Jul 09 2015 - 15:28:07 CDT)
polymerization simulations L. Signorile (Thu Jul 09 2015 - 13:06:51 CDT)
Re: does fixedAtoms modify velocities? Brian Radak (Tue Jul 07 2015 - 12:48:23 CDT)
does fixedAtoms modify velocities? Brian Radak (Tue Jul 07 2015 - 12:25:32 CDT)
-xHost Gianluca Interlandi (Mon Jul 06 2015 - 13:08:37 CDT)
Error: Constraint failure in RATTLE algorithm for atom 5380! in NAMD Mahya Hemmat (Mon Jul 06 2015 - 11:06:39 CDT)
RE: replica exchange and GPU acceleration Norman Geist (Mon Jul 06 2015 - 01:38:11 CDT)
Generating solvent models. VINAYAK BHAT (Sun Jul 05 2015 - 04:06:27 CDT)
running multicore version on a 2-CPU node Gianluca Interlandi (Sat Jul 04 2015 - 15:33:25 CDT)
multicore vs ibverbs Gianluca Interlandi (Sat Jul 04 2015 - 12:52:40 CDT)
Re: replica exchange and GPU acceleration Mitchell Gleed (Sat Jul 04 2015 - 10:49:22 CDT)
Re: extra bonds Josh Vermaas (Fri Jul 03 2015 - 09:08:25 CDT)
RE: replica exchange and GPU acceleration Norman Geist (Fri Jul 03 2015 - 03:16:17 CDT)
Re: extra bonds Lara rajam (Thu Jul 02 2015 - 12:35:14 CDT)
Re: extra bonds Josh Vermaas (Thu Jul 02 2015 - 09:48:22 CDT)
extra bonds Lara rajam (Thu Jul 02 2015 - 09:20:59 CDT)
Re: statistical error of mean force in (NAMD) ABF calculations Jeff Comer (Thu Jul 02 2015 - 09:09:38 CDT)
Re: replica exchange and GPU acceleration Mitchell Gleed (Wed Jul 01 2015 - 11:01:50 CDT)
statistical error of mean force in (NAMD) ABF calculations Branko (Wed Jul 01 2015 - 05:09:48 CDT)
RE: replica exchange and GPU acceleration Norman Geist (Wed Jul 01 2015 - 02:13:56 CDT)
replica exchange and GPU acceleration Mitchell Gleed (Tue Jun 30 2015 - 18:09:27 CDT)
Attempting modification to accumulate "Langevin heat" Brian Radak (Tue Jun 30 2015 - 10:43:40 CDT)
Re: Re: I can not run fixed protein in membrane with NAMD Chitrak Gupta (Mon Jun 29 2015 - 14:41:11 CDT)
Re: I can not run fixed protein in membrane with NAMD R.L. Ma (Sat Jun 27 2015 - 21:27:18 CDT)
Re: Pressure coupling options Chitrak Gupta (Sun Jun 28 2015 - 15:54:05 CDT)
Re: Pressure coupling options Josh Vermaas (Sat Jun 27 2015 - 19:36:17 CDT)
applying a force to some atoms jing liang (Sat Jun 27 2015 - 06:22:02 CDT)
Pressure coupling options Kevin C Chan (Fri Jun 26 2015 - 23:32:05 CDT)
Re: not able to view trajectory in VMD Axel Kohlmeyer (Fri Jun 26 2015 - 13:04:20 CDT)
not able to view trajectory in VMD Lara rajam (Fri Jun 26 2015 - 12:55:01 CDT)
Minimisation goes to several values Kevin C Chan (Thu Jun 25 2015 - 11:32:10 CDT)
NAMD 2.10 on IBM POWER(8) machines Baker D.J. (Thu Jun 25 2015 - 07:00:49 CDT)
Re: Re: run on sungle node Alexander Tzanov (Wed Jun 24 2015 - 13:37:01 CDT)
Re: Re: run on sungle node Axel Kohlmeyer (Wed Jun 24 2015 - 11:16:34 CDT)
Re: Re: run on sungle node Josh Vermaas (Wed Jun 24 2015 - 11:14:16 CDT)
Re: run on sungle node Alexander Tzanov (Wed Jun 24 2015 - 11:03:24 CDT)
run on sungle node Alexander Tzanov (Wed Jun 24 2015 - 09:56:18 CDT)
free energy calculation along image index in us ÂÀÐ¡Ó¨ (Wed Jun 24 2015 - 02:27:35 CDT)
Re: Create psf file Asma el-magboub (Mon Jun 22 2015 - 18:43:13 CDT)
bond lengths and angles constraints oguz gurbulak (Tue Jun 23 2015 - 10:04:53 CDT)
Getting Infinity in Calculation of Free Energy using SMD Ebru Ã‡etin (Tue Jun 23 2015 - 00:23:19 CDT)
Re: Create psf file Mayne, Christopher G (Mon Jun 22 2015 - 10:01:23 CDT)
RE: Create psf file Raed Ahmed Abdelsalam Shalaby (Mon Jun 22 2015 - 05:54:32 CDT)
Re: OPLS force field in NAMD Peter Freddolino (Sat Jun 20 2015 - 22:20:00 CDT)
Create psf file Fransiska Kurniawan (Sat Jun 20 2015 - 17:56:52 CDT)
Re: OPLS force field in NAMD AnkiReddy katha (Sat Jun 20 2015 - 16:17:31 CDT)
Re: OPLS force field in NAMD farzad kiani (Sat Jun 20 2015 - 15:28:39 CDT)
OPLS force field in NAMD oguz gurbulak (Sat Jun 20 2015 - 11:43:02 CDT)
Re: Remembering resid Kevin C Chan (Thu Jun 18 2015 - 11:48:50 CDT)
Re: Weird Bond In Non-Polar Tail Axel Kohlmeyer (Thu Jun 18 2015 - 10:45:06 CDT)
Weird Bond In Non-Polar Tail Danielle Grodi (Thu Jun 18 2015 - 10:15:53 CDT)
Re: Remembering resid Chitrak Gupta (Thu Jun 18 2015 - 08:52:08 CDT)
Re: Remembering resid Branko (Thu Jun 18 2015 - 08:54:40 CDT)
Remembering resid Kevin C Chan (Thu Jun 18 2015 - 08:42:34 CDT)
Second Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) Lela Vukovic (Tue Jun 16 2015 - 12:04:27 CDT)
Re: Combining parameter files from CHARMM Josh Vermaas (Mon Jun 15 2015 - 11:10:43 CDT)
Re: Combining parameter files from CHARMM Branko (Mon Jun 15 2015 - 07:39:49 CDT)
Re: Combining parameter files from CHARMM Kevin C Chan (Mon Jun 15 2015 - 07:29:36 CDT)
Re: Why the Lennardâˆ’Jones parameters E for anions are usually larger than cations? Axel Kohlmeyer (Mon Jun 15 2015 - 05:36:16 CDT)
Fwd: Re: Combining parameter files from CHARMM Branko (Mon Jun 15 2015 - 05:12:57 CDT)
Why the Lennardâˆ’Jones parameters E for anions are usually larger than cations? bay__gulf618_at_sina.com (Mon Jun 15 2015 - 04:02:44 CDT)
Re: Combining parameter files from CHARMM Kevin C Chan (Mon Jun 15 2015 - 03:08:06 CDT)
Announcement: Workshop on Simulation Based Drug Discovery (San Diego, CA, Sept 21-25, 2015) Lela Vukovic (Fri Jun 12 2015 - 21:06:22 CDT)
Re: Multiple-replicas metadynamics / Well-tempered metadynamics Giacomo Fiorin (Fri Jun 12 2015 - 14:21:15 CDT)
Multiple-replicas metadynamics / Well-tempered metadynamics Yerko Escalona (Fri Jun 12 2015 - 14:15:39 CDT)
Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CTL2 OC301 (ATOMS 25 45) Sourav Ray (Fri Jun 12 2015 - 13:49:00 CDT)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CTL2 OC301 (ATOMS 25 45) Danielle Grodi (Fri Jun 12 2015 - 13:39:30 CDT)
Re: Using a different potential with NAMD Axel Kohlmeyer (Fri Jun 12 2015 - 09:39:47 CDT)
Re: Using a different potential with NAMD Peter Freddolino (Fri Jun 12 2015 - 09:25:32 CDT)
non-bonded energy of individual atoms Bärwinkel, Tom (Fri Jun 12 2015 - 09:17:46 CDT)
Using a different potential with NAMD Wade, Alex (Fri Jun 12 2015 - 09:08:48 CDT)
Re: Recomposing the system splitted by periodicity Tristan Croll (Thu Jun 11 2015 - 23:22:50 CDT)
Recomposing the system splitted by periodicity Francesco Pietra (Thu Jun 11 2015 - 04:34:57 CDT)
Constant velocity SMD maral hassani (Tue Jun 09 2015 - 07:14:16 CDT)
FFTK - error Mayne, Christopher G (Mon Jun 08 2015 - 11:56:34 CDT)
Postdoc in Theoretical and Computational Biophysics Aksimentiev, Oleksii (Mon Jun 08 2015 - 11:51:11 CDT)
electrostatics cutoff parameters Z (Mon Jun 08 2015 - 09:06:00 CDT)
FFTK - error Mohan maruthi sena (Sat Jun 06 2015 - 18:35:44 CDT)
Re: Combining parameter files from CHARMM Branko (Fri Jun 05 2015 - 05:17:56 CDT)
Combining parameter files from CHARMM Kevin C Chan (Fri Jun 05 2015 - 04:51:13 CDT)
RE: error in writing colvars state file Bennion, Brian (Thu Jun 04 2015 - 16:30:07 CDT)
error in writing colvars state file Bennion, Brian (Thu Jun 04 2015 - 16:24:44 CDT)
Re: Colvars Boundary potentials do not look harmonic Panel Nicolas (M.) (Thu Jun 04 2015 - 08:08:49 CDT)
Re: Colvars Boundary potentials do not look harmonic Jeff Comer (Wed Jun 03 2015 - 11:54:28 CDT)
Colvars Boundary potentials do not look harmonic Panel Nicolas (M.) (Wed Jun 03 2015 - 10:00:53 CDT)
RE: Using the multi-copy version of NAMD on a linux workstation Avisek Das (Mon Jun 01 2015 - 12:22:46 CDT)
RE: Using the multi-copy version of NAMD on a linux workstation Norman Geist (Mon Jun 01 2015 - 02:43:36 CDT)
RE: atom types in PSF/PRM/RTF hannes.loeffler_at_stfc.ac.uk (Sun May 31 2015 - 07:43:34 CDT)
Using the multi-copy version of NAMD on a linux workstation Avisek Das (Fri May 29 2015 - 14:43:18 CDT)
Re: atom types in PSF/PRM/RTF Jason Swails (Thu May 28 2015 - 13:55:44 CDT)
Re: atom types in PSF/PRM/RTF Hannes Loeffler (Thu May 28 2015 - 13:19:14 CDT)
NAMD-Replica exchange ZOU Changling (Wed May 27 2015 - 04:31:28 CDT)
Can 'nonbonded interaction parameters' be ignored in the parameter file? ¶¡êÏ (Tue May 26 2015 - 20:43:52 CDT)
Re: where can I find the parameter file for chlorophenols? Jeff Comer (Mon May 25 2015 - 14:35:46 CDT)
the method to move freely in one direction like a rigid body Xiaokang Liu (Mon May 25 2015 - 05:46:40 CDT)
running with replica exchange on stampede Peter Freddolino (Sun May 24 2015 - 21:40:09 CDT)
where can I find the parameter file for chlorophenols? ¶¡êÏ (Sun May 24 2015 - 08:30:15 CDT)
Re: Force-field for DOPI lipid Josh Vermaas (Sun May 24 2015 - 08:27:46 CDT)
Force-field for DOPI lipid Kevin C Chan (Sat May 23 2015 - 13:58:30 CDT)
Re: atom types in PSF/PRM/RTF Josh Vermaas (Fri May 22 2015 - 09:55:44 CDT)
Re: atom types in PSF/PRM/RTF Aaron Larsen (Fri May 22 2015 - 07:34:37 CDT)
atom types in PSF/PRM/RTF Hannes Loeffler (Fri May 22 2015 - 04:42:45 CDT)
Re: Restarting trajectories Grzegorz Nawrocki (Thu May 21 2015 - 09:10:28 CDT)
Error during Opt. Charges while using FF Took Kit Aaron Larsen (Wed May 20 2015 - 16:38:19 CDT)
RE: Restarting trajectories Bennion, Brian (Wed May 20 2015 - 14:38:43 CDT)
Re: Restarting trajectories Grzegorz Nawrocki (Wed May 20 2015 - 14:24:08 CDT)
Re: Restarting trajectories Emad Tajkhorshid (Wed May 20 2015 - 12:32:12 CDT)
Re: optimising namd ibverb runs Jim Phillips (Wed May 20 2015 - 12:28:37 CDT)
Re: +p option on Windows 7 Jim Phillips (Wed May 20 2015 - 11:58:13 CDT)
RE: Restarting trajectories Michael Feig (Wed May 20 2015 - 11:18:12 CDT)
Re: Restarting trajectories Maxim Belkin (Wed May 20 2015 - 11:11:33 CDT)
Re: Restarting trajectories Josh Vermaas (Wed May 20 2015 - 11:07:42 CDT)
Re: Restarting trajectories Axel Kohlmeyer (Wed May 20 2015 - 11:07:56 CDT)
RE: Restarting trajectories Michael Feig (Wed May 20 2015 - 10:59:07 CDT)
Re: Restarting trajectories Axel Kohlmeyer (Wed May 20 2015 - 10:49:11 CDT)
RE: Restarting trajectories Bennion, Brian (Wed May 20 2015 - 10:42:46 CDT)
Restarting trajectories Michael Feig (Wed May 20 2015 - 02:47:08 CDT)
Best Practices for Nucleobase Parameterization Mayne, Christopher G (Wed May 20 2015 - 08:12:55 CDT)
Restarting trajectories Michael Feig (Wed May 20 2015 - 03:01:37 CDT)
Re: Announcement: 'Hands On' Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) Emad Tajkhorshid (Wed May 20 2015 - 00:43:55 CDT)
Re: Announcement: 'Hands On' Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) Sourav Ray (Wed May 20 2015 - 00:33:00 CDT)
Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) Lela Vukovic (Wed May 20 2015 - 00:06:46 CDT)
Re: Different trajectories with and without restarting Grzegorz Nawrocki (Mon May 18 2015 - 15:04:17 CDT)
Best Practices for Nucleobase Parameterization Aaron Larsen (Mon May 18 2015 - 11:30:22 CDT)
Re: optimising namd ibverb runs Aaron Larsen (Mon May 18 2015 - 08:48:18 CDT)
RE: optimising namd ibverb runs Norman Geist (Mon May 18 2015 - 08:16:11 CDT)
optimising namd ibverb runs Thanassis Silis (Mon May 18 2015 - 06:48:03 CDT)
RE: +p option on Windows 7 Norman Geist (Mon May 18 2015 - 02:39:30 CDT)
Re: Different trajectories with and without restarting Axel Kohlmeyer (Sat May 16 2015 - 00:06:27 CDT)
Re: Different trajectories with and without restarting Grzegorz Nawrocki (Fri May 15 2015 - 21:08:40 CDT)
Re: Different trajectories with and without restarting Axel Kohlmeyer (Fri May 15 2015 - 18:26:53 CDT)
Re: Different trajectories with and without restarting btreece_at_andrew.cmu.edu (Fri May 15 2015 - 18:26:09 CDT)
Different trajectories with and without restarting Grzegorz Nawrocki (Fri May 15 2015 - 18:09:57 CDT)
+p option on Windows 7 Kukol, Andreas (Fri May 15 2015 - 05:07:55 CDT)
Re: Calculation of PMF between protein domains NAMD Chola Regmi (Wed May 13 2015 - 18:14:49 CDT)
Re: Error applying PME to simulation set up Axel Kohlmeyer (Wed May 13 2015 - 08:00:00 CDT)
Re: Error applying PME to simulation set up Sourav Ray (Wed May 13 2015 - 06:02:51 CDT)
RE: Error applying PME to simulation set up Norman Geist (Wed May 13 2015 - 05:08:45 CDT)
Error applying PME to simulation set up Sourav Ray (Wed May 13 2015 - 04:24:41 CDT)
startup phase 1 for benchmark Branko (Tue May 12 2015 - 09:29:28 CDT)
NAMD Repeated failures launching tasks Kumar, Amit (Mon May 11 2015 - 13:47:40 CDT)
Re: Calculating the spin angle collective variable value Marlon SIDORE (Mon May 11 2015 - 09:06:46 CDT)
Re: Calculating the spin angle collective variable value Giacomo Fiorin (Mon May 11 2015 - 08:57:41 CDT)
Re: Calculating the spin angle collective variable value Marlon SIDORE (Mon May 11 2015 - 08:48:51 CDT)
Re: Calculating the spin angle collective variable value Giacomo Fiorin (Mon May 11 2015 - 08:40:34 CDT)
Calculating the spin angle collective variable value Marlon SIDORE (Mon May 11 2015 - 03:51:38 CDT)
Processing 64-window FEP Matthew Ralph Adendorff (Sun May 10 2015 - 08:44:08 CDT)
School on Molecular Dynamics and Enhanced Sampling Methods @ Temple University July 6-10, 2015 Axel Kohlmeyer (Fri May 08 2015 - 11:28:54 CDT)
RE: output files are not stored when running namd-2.10 ibverbs Thanassis Silis (Fri May 08 2015 - 05:07:50 CDT)
Re: NAMD nightly build compilation Vlad Cojocaru (Fri May 08 2015 - 04:11:52 CDT)
Re: NAMD nightly build compilation Vlad Cojocaru (Fri May 08 2015 - 03:12:16 CDT)
OPLS force-field in NAMD AnkiReddy katha (Thu May 07 2015 - 02:12:03 CDT)
output files are not stored when running namd-2.10 ibverbs Thanassis Silis (Thu May 07 2015 - 10:29:26 CDT)
Re: NAMD nightly build compilation Vlad Cojocaru (Thu May 07 2015 - 08:40:00 CDT)
atoms sequence in improper, OPLS, TOPOTOOLS, CHARMM AnkiReddy katha (Thu May 07 2015 - 06:17:27 CDT)
Re: OPLS in NAMD AnkiReddy katha (Thu May 07 2015 - 04:40:47 CDT)
OPLS in NAMD AnkiReddy katha (Thu May 07 2015 - 04:17:23 CDT)
PSFgen with RNA-like nucleotide monophosphates Aaron Larsen (Wed May 06 2015 - 11:01:26 CDT)
Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Odense, Denmark, Oct 12-16, 2015) Lela Vukovic (Wed May 06 2015 - 01:39:55 CDT)
Simulation Box Rescaling Phillips, Carolyn L. (Tue May 05 2015 - 18:02:28 CDT)
RE: namd-l digest V1 #1668 Bennion, Brian (Mon May 04 2015 - 10:42:12 CDT)
Re: atom ID in VMD and NAMD Axel Kohlmeyer (Mon May 04 2015 - 07:25:49 CDT)
Re: atom ID in VMD and NAMD Maxim Igaev (Mon May 04 2015 - 07:18:38 CDT)
Re: atom ID in VMD and NAMD Axel Kohlmeyer (Mon May 04 2015 - 07:04:22 CDT)
Re: atom ID in VMD and NAMD Maxim Igaev (Mon May 04 2015 - 06:47:09 CDT)
atom ID in VMD and NAMD Maxim Igaev (Mon May 04 2015 - 03:16:09 CDT)
RE: namd-l digest V1 #1668 Ern Seang Ong (Sun May 03 2015 - 23:14:28 CDT)
mail reg DCD error Vidhya Sankar (Sun May 03 2015 - 09:44:50 CDT)
Re: Simulated Annealing with many frequent restarts Maxim Belkin (Fri May 01 2015 - 11:49:41 CDT)
Re: Simulated Annealing with many frequent restarts Phillips, Carolyn L. (Fri May 01 2015 - 11:24:13 CDT)
Re: Simulated Annealing with many frequent restarts Maxim Belkin (Fri May 01 2015 - 11:18:21 CDT)
RE: Problems in running AutoIMD Bennion, Brian (Fri May 01 2015 - 11:00:35 CDT)
Re: Simulated Annealing with many frequent restarts Phillips, Carolyn L. (Fri May 01 2015 - 10:16:43 CDT)
Re: Simulated Annealing with many frequent restarts Maxim Belkin (Fri May 01 2015 - 09:46:21 CDT)
proper order for par files in namd Mayne, Christopher G (Fri May 01 2015 - 09:21:11 CDT)
Re: Simulated Annealing with many frequent restarts Francesco Pietra (Fri May 01 2015 - 01:21:28 CDT)
Problems in running AutoIMD Ern Seang Ong (Thu Apr 30 2015 - 23:33:47 CDT)
Simulated Annealing with many frequent restarts Phillips, Carolyn L. (Thu Apr 30 2015 - 18:51:19 CDT)
RE: performance question Norman Geist (Wed Apr 29 2015 - 03:24:46 CDT)
Re: performance question Thomas C. Bishop (Tue Apr 28 2015 - 15:53:42 CDT)
RE: performance question Bennion, Brian (Tue Apr 28 2015 - 15:06:13 CDT)
Re: performance question Thomas C. Bishop (Tue Apr 28 2015 - 14:32:16 CDT)
RE: performance question Norman Geist (Tue Apr 28 2015 - 02:51:06 CDT)
performance question Thomas C. Bishop (Mon Apr 27 2015 - 15:54:10 CDT)
RE: Which Binary to use? Norman Geist (Mon Apr 27 2015 - 01:59:17 CDT)
question about restart conf file oguz gurbulak (Sun Apr 26 2015 - 07:10:44 CDT)
RE: proper order for par files in namd (solved) Bennion, Brian (Fri Apr 24 2015 - 18:21:22 CDT)
proper order for par files in namd Bennion, Brian (Fri Apr 24 2015 - 17:05:16 CDT)
Re: Re: Problems to parametrize molecules Evandro Semighini (Fri Apr 24 2015 - 14:26:50 CDT)
Re: Re: Problems to parametrize molecules Mayne, Christopher G (Fri Apr 24 2015 - 14:22:55 CDT)
RE: Re: Problems to parametrize molecules Bennion, Brian (Fri Apr 24 2015 - 14:02:59 CDT)
Re: Re: Problems to parametrize molecules Evandro Semighini (Fri Apr 24 2015 - 13:58:25 CDT)
Re: Re: Problems to parametrize molecules Evandro Semighini (Fri Apr 24 2015 - 13:54:33 CDT)
Re: Re: Problems to parametrize molecules Mayne, Christopher G (Fri Apr 24 2015 - 13:53:01 CDT)
RE: Re: Problems to parametrize molecules Bennion, Brian (Fri Apr 24 2015 - 13:46:52 CDT)
Re: Re: Problems to parametrize molecules Evandro Semighini (Fri Apr 24 2015 - 12:49:31 CDT)
RE: Re: Problems to parametrize molecules Bennion, Brian (Fri Apr 24 2015 - 12:27:51 CDT)
Re: Re: Problems to parametrize molecules Evandro Semighini (Fri Apr 24 2015 - 10:04:37 CDT)
Re: Patches for namd 2.10 Ã…ke Sandgren (Fri Apr 24 2015 - 06:06:53 CDT)
Patches for namd 2.10 Ã…ke Sandgren (Fri Apr 24 2015 - 01:09:35 CDT)
Re: Which Binary to use? Sourav Ray (Fri Apr 24 2015 - 00:45:44 CDT)
Which Binary to use? Arijit Ghosh (Fri Apr 24 2015 - 00:10:49 CDT)
Re: How to output CCC per residue from MDFF Ryan McGreevy (Thu Apr 23 2015 - 22:15:49 CDT)
How to output CCC per residue from MDFF Michael Yuchi (Thu Apr 23 2015 - 21:48:11 CDT)
Re: How to save a structure after minimizing for 1000 steps? Chitrak Gupta (Thu Apr 23 2015 - 16:35:58 CDT)
Re: How to save a structure after minimizing for 1000 steps? Aron Broom (Thu Apr 23 2015 - 16:28:47 CDT)
How to save a structure after minimizing for 1000 steps? Arijit Ghosh (Thu Apr 23 2015 - 16:15:40 CDT)
Re: energy minimization in namd Branko (Thu Apr 23 2015 - 11:57:06 CDT)
Re: energy minimization in namd Brian Radak (Thu Apr 23 2015 - 11:51:26 CDT)
Re: energy minimization in namd Chitrak Gupta (Thu Apr 23 2015 - 11:44:51 CDT)
energy minimization in namd Hasan haska (Thu Apr 23 2015 - 11:29:43 CDT)
RE: Equilibration for a reverse FEP run Matthew Ralph Adendorff (Thu Apr 23 2015 - 10:16:08 CDT)
Re: Equilibration for a reverse FEP run Chris Chipot (Thu Apr 23 2015 - 10:04:32 CDT)
Equilibration for a reverse FEP run Matthew Ralph Adendorff (Thu Apr 23 2015 - 09:54:41 CDT)
restart simulation oguz gurbulak (Thu Apr 23 2015 - 09:22:38 CDT)
polarizable carbon nanotubes ibrahim khalil (Tue Apr 21 2015 - 11:00:36 CDT)
Re: Calculating RMSF per residue Abir Ganguly (Tue Apr 21 2015 - 02:58:40 CDT)
energy minimization Dhiraj Srivastava (Mon Apr 20 2015 - 21:57:55 CDT)
Re: Calculating RMSF per residue Aron Broom (Mon Apr 20 2015 - 15:59:23 CDT)
Calculating RMSF per residue Abir Ganguly (Mon Apr 20 2015 - 12:58:24 CDT)
Re: Mail reg Parameter file Fotis Baltoumas (Mon Apr 20 2015 - 08:48:36 CDT)
Mail reg Parameter file Vidhya Sankar (Mon Apr 20 2015 - 07:57:34 CDT)
Re: Re: Problems to parametrize molecules Mayne, Christopher G (Sun Apr 19 2015 - 18:59:20 CDT)
Re: Re: Problems to parametrize molecules Evandro Semighini (Sun Apr 19 2015 - 18:47:21 CDT)
TIP4P topology and parameter files oguz gurbulak (Sun Apr 19 2015 - 05:18:41 CDT)
Re: slow heating of system Maxim Belkin (Sun Apr 19 2015 - 04:08:03 CDT)
slow heating of system Dhiraj Srivastava (Sun Apr 19 2015 - 00:55:58 CDT)
Re: Calculation of PMF between protein domains NAMD Chola Regmi (Fri Apr 17 2015 - 18:50:25 CDT)
Re: Calculation of PMF between protein domains NAMD Jeff Comer (Fri Apr 17 2015 - 18:22:17 CDT)
Re: Calculation of PMF between protein domains NAMD Aron Broom (Fri Apr 17 2015 - 18:00:09 CDT)
Re: Calculation of PMF between protein domains NAMD Aron Broom (Fri Apr 17 2015 - 17:57:48 CDT)
Re: Calculation of PMF between protein domains NAMD Josh Vermaas (Fri Apr 17 2015 - 17:54:37 CDT)
Re: Calculation of PMF between protein domains NAMD Giacomo Fiorin (Fri Apr 17 2015 - 17:48:33 CDT)
Re: Calculation of PMF between protein domains NAMD Josh Vermaas (Fri Apr 17 2015 - 17:43:49 CDT)
Calculation of PMF between protein domains NAMD Chola Regmi (Fri Apr 17 2015 - 17:26:03 CDT)
Re: Can NAMD simulation solve the problem of coordinate clash in a structural model? Tristan Croll (Fri Apr 17 2015 - 16:50:07 CDT)
Problems when running FEP for mutation ASP to GLY Yunhui Peng (Fri Apr 17 2015 - 13:53:03 CDT)
Re: Problems to parametrize molecules Mayne, Christopher G (Fri Apr 17 2015 - 11:16:16 CDT)
Re: Problems to parametrize molecules Evandro Semighini (Thu Apr 16 2015 - 15:28:23 CDT)
Re: Problems to parametrize molecules Evandro Semighini (Thu Apr 16 2015 - 14:53:54 CDT)
Re: Running two molecule coarse-grained simulation Prathit Chatterjee (Thu Apr 16 2015 - 11:37:21 CDT)
RE: Is there any point in running NAMD over an ethernet-linked cluster? Norman Geist (Thu Apr 16 2015 - 10:39:38 CDT)
Re: Running two molecule coarse-grained simulation Sourav Ray (Thu Apr 16 2015 - 06:27:30 CDT)
Re: Is there any point in running NAMD over an ethernet-linked cluster? Douglas Houston (Thu Apr 16 2015 - 05:10:12 CDT)
RE: Problems to parametrize molecules Bennion, Brian (Wed Apr 15 2015 - 15:44:53 CDT)
Re: Problems to parametrize molecules Evandro Semighini (Wed Apr 15 2015 - 15:37:12 CDT)
RE: Problems to parametrize molecules Bennion, Brian (Wed Apr 15 2015 - 13:04:21 CDT)
Re: Running two molecule coarse-grained simulation Prathit Chatterjee (Wed Apr 15 2015 - 09:24:32 CDT)
Re: Running two molecule coarse-grained simulation Sourav Ray (Wed Apr 15 2015 - 09:05:43 CDT)
Re: Running two molecule coarse-grained simulation Sourav Ray (Wed Apr 15 2015 - 05:51:29 CDT)
Running two molecule coarse-grained simulation Sourav Ray (Wed Apr 15 2015 - 05:39:18 CDT)
CHARMM parameter file Fransiska Kurniawan (Wed Apr 15 2015 - 04:11:00 CDT)
RE: Problems to parametrize molecules Bennion, Brian (Tue Apr 14 2015 - 15:57:28 CDT)
Re: Problems to parametrize molecules Evandro Semighini (Tue Apr 14 2015 - 15:51:17 CDT)
RE: Problems to parametrize molecules Bennion, Brian (Tue Apr 14 2015 - 15:45:41 CDT)
Problems to parametrize molecules Evandro Semighini (Tue Apr 14 2015 - 15:30:03 CDT)
Re: strange behavior of ABF Danilo Di Maio (Tue Apr 14 2015 - 12:48:13 CDT)
RE: REMD on GPU cluster Norman Geist (Tue Apr 14 2015 - 11:01:49 CDT)
Re: NetworkView plugin for the non-namd trajectories Vlad Cojocaru (Tue Apr 14 2015 - 10:13:47 CDT)
bilayer simulation keeps crashing Chitrak Gupta (Tue Apr 14 2015 - 10:00:27 CDT)
NetworkView plugin for the non-namd trajectories James Starlight (Tue Apr 14 2015 - 09:34:57 CDT)
Re: REMD on GPU cluster Michael Feig (Tue Apr 14 2015 - 08:00:16 CDT)
strange behavior of ABF Danilo Di Maio (Tue Apr 14 2015 - 05:41:24 CDT)
RE: REMD on GPU cluster Norman Geist (Tue Apr 14 2015 - 02:10:03 CDT)
REMD on GPU cluster Michael Feig (Mon Apr 13 2015 - 17:09:05 CDT)
Can't find documentation of known bug in NAMD 2.9 Klas Karis (Mon Apr 13 2015 - 12:02:25 CDT)
TIP4P water for MD Abhishek TYAGI (Mon Apr 13 2015 - 07:44:51 CDT)
Can NAMD simulation solve the problem of coordinate clash in a structural model? sunyeping (Sun Apr 12 2015 - 21:19:18 CDT)
Re: Can NAMD simulation solve the problem of coordinate clash in a structural model? sunyeping (Sun Apr 12 2015 - 21:18:30 CDT)
Re: Trouble using the extForces parameters David Hardy (Sat Apr 11 2015 - 12:05:49 CDT)
Trouble using the extForces parameters Duster, Adam (Sat Apr 11 2015 - 04:11:42 CDT)
Reg: topology file amidated and acetylated disulfide bridged Cystine Akshay Bhatnagar (Fri Apr 10 2015 - 05:05:42 CDT)
Immediate PhD Opening Computational Structural Biology Of Membrane Proteins Marawan Hussien (Thu Apr 09 2015 - 19:18:53 CDT)
Immediate Postdoctoral Position Opening Marawan Hussien (Thu Apr 09 2015 - 18:10:32 CDT)
Re: Daily cron stalls running NAMD outputs Vlastimil ZÃma (Wed Apr 08 2015 - 02:41:23 CDT)
Re: Algorithm used by NAMD David Hardy (Fri Apr 03 2015 - 11:18:46 CDT)
Re: timestep querry Abhishek TYAGI (Thu Apr 02 2015 - 23:07:39 CDT)
Re: problem restarting multiple walker metadynamics Amy Rice (Thu Apr 02 2015 - 14:54:56 CDT)
Algorithm used by NAMD Gurpreet Kaur Dhindsa (Thu Apr 02 2015 - 09:55:36 CDT)
Re: timestep querry Brian Radak (Thu Apr 02 2015 - 14:17:47 CDT)
Re: Minimisation not converged Kevin C Chan (Wed Apr 01 2015 - 22:26:19 CDT)
Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Wed Apr 01 2015 - 15:05:30 CDT)
Re: timestep querry Abhishek TYAGI (Wed Apr 01 2015 - 11:15:49 CDT)
Re: timestep querry Aron Broom (Wed Apr 01 2015 - 10:51:31 CDT)
timestep querry Abhishek TYAGI (Wed Apr 01 2015 - 10:28:12 CDT)
Re: Daily cron stalls running NAMD outputs Vlastimil ZÃma (Wed Apr 01 2015 - 07:08:28 CDT)
Daily cron stalls running NAMD outputs Vlastimil ZÃma (Wed Apr 01 2015 - 03:04:26 CDT)
Re: Enerygy Minimization of a homology modelled structure in NAMD JÃ©rÃ´me HÃ©nin (Wed Apr 01 2015 - 02:07:59 CDT)
problem about namdstats.tcl Hasan haska (Wed Apr 01 2015 - 01:34:32 CDT)
Minimisation not converged Kevin C Chan (Wed Apr 01 2015 - 01:20:37 CDT)
Enerygy Minimization of a homology modelled structure in NAMD Arijit Ghosh (Tue Mar 31 2015 - 22:46:49 CDT)
Re: ABF with external electric field Giacomo Fiorin (Tue Mar 31 2015 - 13:16:15 CDT)
Re: ABF with external electric field Jeff Comer (Tue Mar 31 2015 - 11:41:35 CDT)
ABF with external electric field Bala subramanian (Tue Mar 31 2015 - 10:42:24 CDT)
Re: Dipole Moment Watcher, Ibuprofen Branko (Tue Mar 31 2015 - 04:12:14 CDT)
Dipole Moment Watcher, Ibuprofen JAVAD NOROOZI (Tue Mar 31 2015 - 01:01:46 CDT)
Re: problem restarting multiple walker metadynamics Amy Rice (Mon Mar 30 2015 - 13:23:24 CDT)
Enerygy Minimization of a homology modelled structure in NAMD Arijit Ghosh (Mon Mar 30 2015 - 00:21:35 CDT)
Enerygy Minimization of a homology modelled structure in NAMD Arijit Ghosh (Sun Mar 29 2015 - 21:16:03 CDT)
Re: pressure value Jeff Comer (Sun Mar 29 2015 - 16:54:09 CDT)
Re: pressure value Brian Radak (Sun Mar 29 2015 - 15:30:42 CDT)
pressure value Hasan haska (Sun Mar 29 2015 - 14:23:28 CDT)
Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Sat Mar 28 2015 - 17:50:19 CDT)
Re: problem restarting multiple walker metadynamics Amy Rice (Fri Mar 27 2015 - 11:48:02 CDT)
Re: error while running namd on CRAY XC40 machine Santosh Kumar Chaudhary (Fri Mar 27 2015 - 01:00:51 CDT)
Re: angle between 2 vectors as collective variable Vlad Cojocaru (Thu Mar 26 2015 - 11:04:09 CDT)
Re: angle between 2 vectors as collective variable Giacomo Fiorin (Thu Mar 26 2015 - 10:16:25 CDT)
Re: angle between 2 vectors as collective variable Vlad Cojocaru (Thu Mar 26 2015 - 10:03:36 CDT)
Re: angle between 2 vectors as collective variable Giacomo Fiorin (Thu Mar 26 2015 - 09:58:26 CDT)
angle between 2 vectors as collective variable Vlad Cojocaru (Thu Mar 26 2015 - 09:17:41 CDT)
bond angle and dihedral values oguz gurbulak (Thu Mar 26 2015 - 03:55:03 CDT)
Re: Restraining angle between bond vector and coordinate vector Seth Axen (Wed Mar 25 2015 - 19:01:40 CDT)
Fwd: FW: NAMD Brian Radak (Wed Mar 25 2015 - 11:35:27 CDT)
Re: Reg: solvating in a non-standard solvent Akshay Bhatnagar (Wed Mar 25 2015 - 02:38:00 CDT)
Parallelization of External Program Forces btreece_at_andrew.cmu.edu (Tue Mar 24 2015 - 18:49:26 CDT)
Re: about hydrogen bond analysis Mo Chen (Tue Mar 24 2015 - 16:19:37 CDT)
about hydrogen bond analysis Hasan haska (Tue Mar 24 2015 - 16:07:08 CDT)
Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Lake Tahoe, CA, Aug 3-7, 2015) Lela Vukovic (Tue Mar 24 2015 - 15:50:58 CDT)
GPU Programming workshop @ ICTP: deadline extended for participants not requiring visa and financial support Axel Kohlmeyer (Tue Mar 24 2015 - 14:17:40 CDT)
Re: NAMD nightly build compilation Vlad Cojocaru (Tue Mar 24 2015 - 12:51:47 CDT)
NAMD nightly build compilation Vlad Cojocaru (Tue Mar 24 2015 - 12:07:03 CDT)
Re: NAMD Subbarao Kanchi (Tue Mar 24 2015 - 01:48:39 CDT)
Re: Restraining angle between bond vector and coordinate vector Jeff Comer (Mon Mar 23 2015 - 18:17:18 CDT)
Restraining angle between bond vector and coordinate vector Seth Axen (Mon Mar 23 2015 - 15:26:37 CDT)
Re: error while running namd on CRAY XC40 machine Jim Phillips (Mon Mar 23 2015 - 13:59:47 CDT)
Immediate Postdoctoral Position Opening Marawan Hussien (Sun Mar 22 2015 - 16:08:16 CDT)
number of close contacts and contact area Abhishek TYAGI (Sun Mar 22 2015 - 04:37:57 CDT)
error while running namd on CRAY XC40 machine Santosh Kumar Chaudhary (Sun Mar 22 2015 - 02:40:31 CDT)
Re: Reg: solvating in a non-standard solvent Akshay Bhatnagar (Thu Mar 19 2015 - 23:38:24 CDT)
Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Thu Mar 19 2015 - 18:39:06 CDT)
Re: problem restarting multiple walker metadynamics Amy Rice (Thu Mar 19 2015 - 17:44:25 CDT)
Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Thu Mar 19 2015 - 17:26:27 CDT)
Re: problem restarting multiple walker metadynamics Amy Rice (Thu Mar 19 2015 - 17:24:29 CDT)
Re: Reg: solvating in a non-standard solvent Maxim Belkin (Thu Mar 19 2015 - 12:06:38 CDT)
Re: Reg: solvating in a non-standard solvent Maxim Belkin (Thu Mar 19 2015 - 11:59:28 CDT)
Re: Reg: solvating in a non-standard solvent Jeff Comer (Thu Mar 19 2015 - 09:02:10 CDT)
Re: DCD Error Abhishek TYAGI (Thu Mar 19 2015 - 03:59:56 CDT)
Re: Reg: solvating in a non-standard solvent Akshay Bhatnagar (Thu Mar 19 2015 - 01:40:55 CDT)
Re: DCD Error Atanu Maity (Wed Mar 18 2015 - 23:32:32 CDT)
Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2 Sadegh Faramarzi Ganjabad (Wed Mar 18 2015 - 17:50:58 CDT)
Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2 Josh Vermaas (Wed Mar 18 2015 - 17:42:03 CDT)
Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2 Jeff Comer (Wed Mar 18 2015 - 17:35:39 CDT)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2 Sadegh Faramarzi Ganjabad (Wed Mar 18 2015 - 16:47:50 CDT)
Re: DCD Error Abhishek Tyagi (Wed Mar 18 2015 - 10:13:07 CDT)
Re: DCD Error Josh Vermaas (Wed Mar 18 2015 - 10:06:43 CDT)
Re: DCD Error Maxim Belkin (Wed Mar 18 2015 - 10:06:34 CDT)
Re: DCD Error btreece_at_andrew.cmu.edu (Wed Mar 18 2015 - 10:05:58 CDT)
Re: DCD Error Abhishek Tyagi (Wed Mar 18 2015 - 09:51:17 CDT)
Re: Reg: solvating in a non-standard solvent Jeff Comer (Wed Mar 18 2015 - 09:44:12 CDT)
Re: DCD Error Josh Vermaas (Wed Mar 18 2015 - 09:36:52 CDT)
Re: DCD Error Abhishek Tyagi (Wed Mar 18 2015 - 09:29:42 CDT)
Re: DCD Error btreece_at_andrew.cmu.edu (Wed Mar 18 2015 - 09:27:28 CDT)
Re: Reg: solvating in a non-standard solvent Josh Vermaas (Wed Mar 18 2015 - 09:08:24 CDT)
Re: DCD Error manish kesherwani (Wed Mar 18 2015 - 08:10:18 CDT)
Re: Reg: solvating in a non-standard solvent Branko (Wed Mar 18 2015 - 07:19:45 CDT)
DCD Error Abhishek TYAGI (Wed Mar 18 2015 - 06:23:58 CDT)
Reg: solvating in a non-standard solvent Akshay Bhatnagar (Wed Mar 18 2015 - 01:29:20 CDT)
Re: Re: 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD Lachele Foley (Tue Mar 17 2015 - 21:46:19 CDT)
Re: Re: 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD clarkzhy (Tue Mar 17 2015 - 21:18:48 CDT)
Re: 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD Lachele Foley (Tue Mar 17 2015 - 21:15:41 CDT)
1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD clarkzhy (Tue Mar 17 2015 - 20:33:41 CDT)
Re: Restarting an abruptly interrupted simulation Prathit Chatterjee (Tue Mar 17 2015 - 02:03:52 CDT)
Restarting an abruptly interrupted simulation Sourav Ray (Tue Mar 17 2015 - 01:30:21 CDT)
Re: Updated Link: Postdoc positions available at IBM (bio-molecular modeling and MD) Sourav Ray (Mon Mar 16 2015 - 12:30:29 CDT)
Truncated octahedron : Problems in PBC when reading a dcd file with NAMD Panel Nicolas (M.) (Mon Mar 16 2015 - 11:18:00 CDT)
Updated Link: Postdoc positions available at IBM (bio-molecular modeling and MD) Payel Das (Mon Mar 16 2015 - 10:50:46 CDT)
Postdoc positions available at IBM (bio-molecular modeling and MD) Payel Das (Mon Mar 16 2015 - 09:15:05 CDT)
Re: equilibrate the bulk water system Axel Kohlmeyer (Sun Mar 15 2015 - 21:30:06 CDT)
Re: equilibrate the bulk water system Hasan haska (Sat Mar 14 2015 - 14:38:03 CDT)
Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Sun Mar 15 2015 - 10:47:17 CDT)
Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Sun Mar 15 2015 - 10:45:14 CDT)
Re: equilibrate the bulk water system Abhishek Tyagi (Fri Mar 13 2015 - 09:49:20 CDT)
Re: equilibrate the bulk water system Maxim Belkin (Fri Mar 13 2015 - 11:28:35 CDT)
Re: Dihedral calculation with colvars Giacomo Fiorin (Fri Mar 13 2015 - 10:05:20 CDT)
Re: equilibrate the bulk water system Hasan haska (Fri Mar 13 2015 - 06:57:15 CDT)
Re: problem restarting multiple walker metadynamics Amy Rice (Thu Mar 12 2015 - 17:26:10 CDT)
Re: Colvar with variable axis Mitchell Gleed (Thu Mar 12 2015 - 10:49:21 CDT)
Re: Restarting NAMD simulation Sourav Ray (Thu Mar 12 2015 - 09:16:26 CDT)
RE: Restarting NAMD simulation Norman Geist (Thu Mar 12 2015 - 09:13:14 CDT)
Restarting NAMD simulation Sourav Ray (Thu Mar 12 2015 - 08:30:27 CDT)
Re: Colvar with variable axis Giacomo Fiorin (Thu Mar 12 2015 - 08:25:54 CDT)
Re: Colvar with variable axis Mitchell Gleed (Thu Mar 12 2015 - 07:59:56 CDT)
Re: Colvar with variable axis Giacomo Fiorin (Thu Mar 12 2015 - 06:23:31 CDT)
PACE Force Field and NAMD 2.10 Fotis Baltoumas (Thu Mar 12 2015 - 06:18:07 CDT)
Re: Dihedral calculation with colvars Kevin C Chan (Thu Mar 12 2015 - 06:13:00 CDT)
Colvar with variable axis Mitchell Gleed (Thu Mar 12 2015 - 06:01:56 CDT)
Re: Dihedral calculation with colvars Kevin C Chan (Thu Mar 12 2015 - 01:20:46 CDT)
Re: Dihedral calculation with colvars Aron Broom (Wed Mar 11 2015 - 23:17:09 CDT)
Dihedral calculation with colvars Kevin C Chan (Wed Mar 11 2015 - 23:05:45 CDT)
Re: problem restarting multiple walker metadynamics Amy Rice (Wed Mar 11 2015 - 22:49:51 CDT)
Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Wed Mar 11 2015 - 18:29:36 CDT)
Re: Alchemical FEP calculation involving glycine jostmey . (Wed Mar 11 2015 - 17:57:02 CDT)
problem restarting multiple walker metadynamics Amy Rice (Wed Mar 11 2015 - 14:59:46 CDT)
vdw parameter error | atom type <-> name problem Art (Wed Mar 11 2015 - 14:03:38 CDT)
Fwd: No steric clashes, still not minimizing Francesco Pietra (Wed Mar 11 2015 - 12:28:44 CDT)
RE: equilibrate the bulk water system Norman Geist (Wed Mar 11 2015 - 02:03:46 CDT)
No steric clashes, still not minimizing Francesco Pietra (Wed Mar 11 2015 - 06:38:40 CDT)
Re: Dihedral definition in NAMD Kevin C Chan (Wed Mar 11 2015 - 05:03:54 CDT)
Re: Dihedral definition in NAMD Giacomo Fiorin (Wed Mar 11 2015 - 03:13:27 CDT)
Re: Dihedral definition in NAMD Josh Vermaas (Tue Mar 10 2015 - 13:32:12 CDT)
equilibrate the bulk water system Hasan haska (Tue Mar 10 2015 - 16:51:30 CDT)
Re: Dihedral definition in NAMD Kevin C Chan (Tue Mar 10 2015 - 22:22:34 CDT)
Re: Dihedral definition in NAMD Giacomo Fiorin (Tue Mar 10 2015 - 18:46:42 CDT)
Re: Dihedral definition in NAMD Kevin C Chan (Tue Mar 10 2015 - 13:13:00 CDT)
Re: Dihedral definition in NAMD Giacomo Fiorin (Tue Mar 10 2015 - 09:49:00 CDT)
Re: Dihedral definition in NAMD Giacomo Fiorin (Tue Mar 10 2015 - 09:33:15 CDT)
Re: Dihedral definition in NAMD Josh Vermaas (Tue Mar 10 2015 - 09:30:21 CDT)
Re: Dihedral definition in NAMD Kevin C Chan (Tue Mar 10 2015 - 09:24:23 CDT)
Re: Dihedral definition in NAMD Josh Vermaas (Tue Mar 10 2015 - 09:14:27 CDT)
Re: Dihedral definition in NAMD Kevin C Chan (Tue Mar 10 2015 - 06:52:53 CDT)
Re: Dihedral definition in NAMD Giacomo Fiorin (Tue Mar 10 2015 - 06:28:26 CDT)
Dihedral definition in NAMD Kevin C Chan (Tue Mar 10 2015 - 06:19:16 CDT)
Re: Alchemical FEP calculation involving glycine Chris Chipot (Tue Mar 10 2015 - 05:59:57 CDT)
Alchemical FEP calculation involving glycine jostmey . (Mon Mar 09 2015 - 23:58:31 CDT)
Topology and Parameter File Fransiska Kurniawan (Mon Mar 09 2015 - 01:52:36 CDT)
RE: about langevin dynamics Norman Geist (Mon Mar 09 2015 - 01:44:18 CDT)
about langevin dynamics Gisella Alfonsino (Sun Mar 08 2015 - 05:36:28 CDT)
energy groups in NAMD Andre Ribeiro (Fri Mar 06 2015 - 14:22:34 CST)
energy groups in NAMD Andre Ribeiro (Fri Mar 06 2015 - 14:23:14 CST)
Re: NAMD warning: Randomization of stack point is turned on in kernal, thread migration may not work! Axel Kohlmeyer (Thu Mar 05 2015 - 11:40:42 CST)
NAMD warning: Randomization of stack point is turned on in kernal, thread migration may not work! Yarrow Madrona (Thu Mar 05 2015 - 10:58:11 CST)
Re: namd simulation Abhishek TYAGI (Thu Mar 05 2015 - 04:46:29 CST)
Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Pittsburgh, PA, June 1-5, 2015) Lela Vukovic (Wed Mar 04 2015 - 13:07:25 CST)
RE: BUG: NAMD-2.10 CUDA REMD segfault with TCL exec randomly Norman Geist (Wed Mar 04 2015 - 04:40:07 CST)
BUG: NAMD-2.10 CUDA REMD segfault with TCL exec randomly Norman Geist (Wed Mar 04 2015 - 01:47:42 CST)
Re: Multicore-CUDA NAMD output hangs Mitchell Gleed (Tue Mar 03 2015 - 10:34:20 CST)
RE: "Unknown command-line option +replicas" Norman Geist (Tue Mar 03 2015 - 08:35:47 CST)
namd simulation Urszula Uciechowska (Tue Mar 03 2015 - 08:20:25 CST)
"Unknown command-line option +replicas" Mitul Saha (Mon Mar 02 2015 - 23:33:11 CST)
Re:Re: How to let NAMD terminate automatically at a given time Qing Lv (Mon Mar 02 2015 - 22:20:40 CST)
RE: How to let NAMD terminate automatically at a given time Norman Geist (Tue Mar 03 2015 - 02:35:36 CST)
RE: How to let NAMD terminate automatically at a given time hannes.loeffler_at_stfc.ac.uk (Mon Mar 02 2015 - 14:17:16 CST)
Re: How to let NAMD terminate automatically at a given time Jeff Comer (Mon Mar 02 2015 - 13:58:14 CST)
RE: How to let NAMD terminate automatically at a given time hannes.loeffler_at_stfc.ac.uk (Mon Mar 02 2015 - 13:19:08 CST)
Re: WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM? Jeff Comer (Mon Mar 02 2015 - 10:45:28 CST)
Re: How to let NAMD terminate automatically at a given time Dong Luo (Mon Mar 02 2015 - 09:27:22 CST)
Re: WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM? Richard Overstreet (Sun Mar 01 2015 - 16:56:39 CST)
WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM? Amin Dehkharghani (Sun Mar 01 2015 - 14:58:08 CST)
How to let NAMD terminate automatically at a given time ÂÀÇç (Fri Feb 27 2015 - 20:02:18 CST)
accelMD and GBIS? Brian Radak (Fri Feb 27 2015 - 18:15:13 CST)
Re: scaling non-bonded interactiion parameter for specific pairs MEHRAN MB (Fri Feb 27 2015 - 14:01:29 CST)
Re: scaling non-bonded interactiion parameter for specific pairs Jeff Comer (Fri Feb 27 2015 - 13:58:31 CST)
scaling non-bonded interactiion parameter for specific pairs MEHRAN MB (Fri Feb 27 2015 - 13:15:11 CST)
Re: configuration file question Jeff Comer (Thu Feb 26 2015 - 17:34:09 CST)
configuration file question Hasan haska (Thu Feb 26 2015 - 16:49:55 CST)
Re: vmd-l: Re: velocity IO with psfgen? John Stone (Thu Feb 26 2015 - 12:47:52 CST)
Re: vmd-l: Re: velocity IO with psfgen? Maxim Belkin (Thu Feb 26 2015 - 12:14:24 CST)
Re: vmd-l: Re: velocity IO with psfgen? Brian Radak (Thu Feb 26 2015 - 11:42:22 CST)
Re: vmd-l: Re: velocity IO with psfgen? John Stone (Thu Feb 26 2015 - 11:03:15 CST)
Re: velocity IO with psfgen? Brian Radak (Thu Feb 26 2015 - 10:56:57 CST)
Re: velocity IO with psfgen? Ajasja LjubetiÄ (Thu Feb 26 2015 - 10:37:55 CST)
Re: vmd-l: velocity IO with psfgen? John Stone (Thu Feb 26 2015 - 10:24:36 CST)
velocity IO with psfgen? Brian Radak (Thu Feb 26 2015 - 09:41:04 CST)
Re: Aggregation related analysis scripts Aditya Ranganathan (Wed Feb 25 2015 - 01:13:42 CST)
Re: Aggregation related analysis scripts Jeff Comer (Tue Feb 24 2015 - 15:39:12 CST)
Rotating Constraints Sourav Purohit (Tue Feb 24 2015 - 14:23:26 CST)
Questions about lambda scheme in free energy perturbation Jian Dai (Tue Feb 24 2015 - 08:59:57 CST)
Aggregation related analysis scripts Aditya Ranganathan (Tue Feb 24 2015 - 02:28:10 CST)
Re: Alchemical FEP calculations in Implicit Solvent jostmey . (Mon Feb 23 2015 - 14:45:13 CST)
Re: Alchemical FEP calculations in Implicit Solvent jostmey . (Mon Feb 23 2015 - 13:21:57 CST)
Re: Alchemical FEP calculations in Implicit Solvent MEHRAN MB (Mon Feb 23 2015 - 13:08:56 CST)
Alchemical FEP calculations in Implicit Solvent jostmey . (Mon Feb 23 2015 - 13:04:15 CST)
Re: FATAL ERROR: Low global exclusion count! Jeff Comer (Wed Feb 18 2015 - 18:59:28 CST)
Re: FATAL ERROR: Low global exclusion count! Akshata Rudrapatna (Wed Feb 18 2015 - 18:32:03 CST)
My Plight Syed Kashif Zafar (Wed Feb 18 2015 - 18:28:19 CST)
FATAL ERROR: Low global exclusion count! Yongcheng Zhou (Wed Feb 18 2015 - 18:29:33 CST)
Re: Maximum limit for "run" parameter Jim Phillips (Wed Feb 18 2015 - 17:49:41 CST)
Re: GPU Multinodes problem Jim Phillips (Wed Feb 18 2015 - 17:36:26 CST)
Re: Maximum limit for "run" parameter Axel Kohlmeyer (Wed Feb 18 2015 - 17:15:30 CST)
Re: Maximum limit for "run" parameter Jim Phillips (Wed Feb 18 2015 - 17:10:36 CST)
GPU Multinodes problem horacio poblete (Wed Feb 18 2015 - 15:59:07 CST)
compile psfgen as shared object or Tcl package? Brian Radak (Wed Feb 18 2015 - 15:47:27 CST)
Multicore-CUDA NAMD output hangs Mitchell Gleed (Wed Feb 18 2015 - 15:12:21 CST)
NAMD Source, Molecule.c , Mass Critaria JAVAD NOROOZI (Wed Feb 18 2015 - 12:55:25 CST)
Maximum limit for "run" parameter Mitul Saha (Tue Feb 17 2015 - 18:50:38 CST)
multiple thermostats in adaptive tempering Igaev, Maxim (Wed Feb 18 2015 - 11:20:52 CST)
Re: Incorrect atom count in binary file Mihaela Drenscko (Wed Feb 18 2015 - 07:34:15 CST)
RE: Incorrect atom count in binary file Norman Geist (Wed Feb 18 2015 - 03:13:52 CST)
Incorrect atom count in binary file Mihaela Drenscko (Tue Feb 17 2015 - 18:59:43 CST)
Re: making dipeptides with psfgen - CMAP terms? Brian Radak (Tue Feb 17 2015 - 16:10:49 CST)
Re: making dipeptides with psfgen - CMAP terms? Jim Phillips (Tue Feb 17 2015 - 13:53:04 CST)
Re: making dipeptides with psfgen - CMAP terms? Brian Radak (Tue Feb 17 2015 - 12:06:54 CST)
making dipeptides with psfgen - CMAP terms? Brian Radak (Tue Feb 17 2015 - 09:42:59 CST)
Putting multiple copies of peptide in a box Aditya Ranganathan (Tue Feb 17 2015 - 03:39:14 CST)
Announcement: "Hands-On" Workshop on Computational Biophysics in Urbana, IL (April 6-10,2015) Lela Vukovic (Mon Feb 16 2015 - 14:44:55 CST)
Re: GBIS in NAMD 2.10 CUDA with IMD Tristan Croll (Sun Feb 15 2015 - 20:38:40 CST)
Re: GBIS in NAMD 2.10 CUDA with IMD Jim Phillips (Sat Feb 14 2015 - 12:18:25 CST)
problem with equilibration of membrane-protein system Azadeh Alavi (Sat Feb 14 2015 - 05:35:59 CST)
Compressibility of Berendesen Barostat (Simulations Near Critical Point) JAVAD NOROOZI (Fri Feb 13 2015 - 00:37:42 CST)
Re: PSF generated with PSFGEN [problem in CP2K] - Problem with CGenFF naming? Christian Jorgensen (Thu Feb 12 2015 - 13:01:13 CST)
Re: PSF generated with PSFGEN [problem in CP2K] - Problem with CGenFF naming? Jim Phillips (Thu Feb 12 2015 - 12:32:42 CST)
Re: GBIS in NAMD 2.10 CUDA with IMD Jim Phillips (Thu Feb 12 2015 - 12:29:25 CST)
PSF generated with PSFGEN [problem in CP2K] - Problem with CGenFF naming? Christian Jorgensen (Thu Feb 12 2015 - 10:16:00 CST)
single strand DNA in hairpin conformation Urszula Uciechowska (Thu Feb 12 2015 - 03:14:55 CST)
Re: GBIS in NAMD 2.10 CUDA with IMD Tristan Croll (Wed Feb 11 2015 - 15:09:11 CST)
Re: GBIS in NAMD 2.10 CUDA with IMD Jim Phillips (Wed Feb 11 2015 - 10:51:31 CST)
Re: vmd-l: GBIS in NAMD 2.10 CUDA with IMD John Stone (Wed Feb 11 2015 - 10:03:39 CST)
Re: Grid forces visualisation Jeff Comer (Wed Feb 11 2015 - 08:16:41 CST)
Grid forces visualisation Charan Thota (Wed Feb 11 2015 - 06:13:12 CST)
GBIS in NAMD 2.10 CUDA with IMD Tristan Croll (Wed Feb 11 2015 - 04:18:11 CST)
LangevinPistonPeriod (Simulation Near Critical Point) JAVAD NOROOZI (Tue Feb 10 2015 - 03:15:23 CST)
Re: namd-1: Simulation Terminating Early Akshata Rudrapatna (Mon Feb 09 2015 - 20:54:55 CST)
Re: namd-1: Simulation Terminating Early Jim Phillips (Mon Feb 09 2015 - 13:33:09 CST)
Re: on-the-fly parameter introspection Jim Phillips (Mon Feb 09 2015 - 13:18:02 CST)
New web server for setup of membrane simulation systems Chen, Po-chia (Sun Feb 08 2015 - 06:17:35 CST)
RE: namd-1: Simulation Terminating Early Norman Geist (Mon Feb 09 2015 - 03:09:57 CST)
Spikes in the Energy Plot Viswanath Pasumarthi (Mon Feb 09 2015 - 02:26:08 CST)
namd-1: Simulation Terminating Early Akshata Rudrapatna (Sat Feb 07 2015 - 15:06:33 CST)
Re: Analysis plugins for Martini Coarse Grained protein simulations Fotis Baltoumas (Sat Feb 07 2015 - 05:25:50 CST)
Analysis plugins for Martini Coarse Grained protein simulations Aditya Ranganathan (Sat Feb 07 2015 - 03:55:33 CST)
Targeted MD and the MARTINI Coarse-Grained Force Field Fotis Baltoumas (Fri Feb 06 2015 - 10:06:55 CST)
preparing dsDNA Urszula Uciechowska (Fri Feb 06 2015 - 05:58:43 CST)
Re: Residue number changed to hexadecimal string Jim Phillips (Fri Feb 06 2015 - 00:38:00 CST)
Residue number changed to hexadecimal string K Miura (Thu Feb 05 2015 - 23:34:24 CST)
on-the-fly parameter introspection Brian Radak (Thu Feb 05 2015 - 13:54:51 CST)
Re: Could I run aMD in Drude force field? Brian Radak (Thu Feb 05 2015 - 13:50:15 CST)
Re: Alchemy Shift Coefficient at Low Density Regime (TI) Brian Radak (Thu Feb 05 2015 - 13:44:14 CST)
Re: Editing Patch Grid Dimensions Ryan Gordon (Thu Feb 05 2015 - 12:08:20 CST)
Re: Editing Patch Grid Dimensions Jim Phillips (Thu Feb 05 2015 - 10:32:28 CST)
Editing Patch Grid Dimensions Ryan Gordon (Thu Feb 05 2015 - 10:00:28 CST)
RE: Norman Geist (Thu Feb 05 2015 - 07:55:53 CST)
Re: namd-1: Fatal Error: Unable to Open CHARMM Parameter File Akshata Rudrapatna (Thu Feb 05 2015 - 06:32:40 CST)
(no subject) Ma'Mon Hatmal (Thu Feb 05 2015 - 06:32:09 CST)
Re: Extracting data Stephan Grein (Thu Feb 05 2015 - 03:44:29 CST)
Could I run aMD in Drude force field? dream (Thu Feb 05 2015 - 02:14:04 CST)
Re: Extracting data Jeff Comer (Wed Feb 04 2015 - 08:39:33 CST)
Re: Extracting data Axel Kohlmeyer (Wed Feb 04 2015 - 08:24:25 CST)
Re: Extracting data Jeff Comer (Wed Feb 04 2015 - 07:56:42 CST)
Re: Extracting data Stephan Grein (Wed Feb 04 2015 - 05:56:47 CST)
Extracting data Stephan Grein (Wed Feb 04 2015 - 05:55:37 CST)
Re: about angles in coordination complexes luca belmonte (Wed Feb 04 2015 - 04:37:28 CST)
Alchemy Shift Coefficient at Low Density Regime (TI) JAVAD NOROOZI (Wed Feb 04 2015 - 02:58:15 CST)
Phi vs GPU Francesco Pietra (Wed Feb 04 2015 - 01:52:43 CST)
Fwd: all atom equilibrium of yeast PGK simulation with NAMD Qing Li (Tue Feb 03 2015 - 21:14:36 CST)
Re: namd-1: Fatal Error: Unable to Open CHARMM Parameter File Jim Phillips (Tue Feb 03 2015 - 18:48:35 CST)
namd simulation with TIP5P Shanshan Wu (Tue Feb 03 2015 - 18:36:34 CST)
namd-1: Fatal Error: Unable to Open CHARMM Parameter File Branko (Tue Feb 03 2015 - 16:14:32 CST)
Re: namd-1: Fatal Error: Unable to Open CHARMM Parameter File David Hardy (Tue Feb 03 2015 - 15:54:49 CST)
Re: namd-1: Fatal Error: Unable to Open CHARMM Parameter File David Hardy (Tue Feb 03 2015 - 15:32:57 CST)
namd-1: Fatal Error: Unable to Open CHARMM Parameter File Akshata Rudrapatna (Tue Feb 03 2015 - 14:43:55 CST)
LAST CALL: Free Energy Workshop, MÃ¼nster, March 9-11, 2015 Vlad Cojocaru (Tue Feb 03 2015 - 14:34:42 CST)
Calculation of the water inside of protein during trajectory James Starlight (Tue Feb 03 2015 - 09:51:07 CST)
Re: error running min Jeff Comer (Tue Feb 03 2015 - 08:32:57 CST)
error running min Urszula Uciechowska (Tue Feb 03 2015 - 08:23:28 CST)
Re: vmd-l: vmd-I: Fatal Error: Unable to Open CHARMM Parameter File Ajasja LjubetiÄ (Tue Feb 03 2015 - 07:06:43 CST)
Re: Message about timing in *log file. Jim Phillips (Mon Feb 02 2015 - 00:15:09 CST)
Re: NAMD 2.10 with multiple-replica support Jim Phillips (Mon Feb 02 2015 - 00:11:26 CST)
adjust water box size in RBCG Yongcheng Zhou (Sun Feb 01 2015 - 16:03:54 CST)
Message about timing in *log file. Dawid das (Sun Feb 01 2015 - 05:05:39 CST)
NAMD 2.10 with multiple-replica support Branko (Sat Jan 31 2015 - 14:06:06 CST)
LCPO parameters P1-P4 yandong Huang (Sat Jan 31 2015 - 13:24:55 CST)
Re: LJcorrection and alchemy? Brian Radak (Fri Jan 30 2015 - 14:15:01 CST)
LJcorrection and alchemy? Brian Radak (Fri Jan 30 2015 - 12:10:53 CST)
Re: Is it possible to rename atoms with psfgen? Brian Radak (Fri Jan 30 2015 - 10:35:43 CST)
Re: problem with water molecules angle in MD simulation Axel Kohlmeyer (Fri Jan 30 2015 - 05:32:06 CST)
Re: problem with water molecules angle in MD simulation Tristan Croll (Fri Jan 30 2015 - 02:43:42 CST)
Re: problem with water molecules angle in MD simulation Shoresh Shafei (Fri Jan 30 2015 - 02:28:17 CST)
Re: problem with water molecules angle in MD simulation Tristan Croll (Fri Jan 30 2015 - 02:25:32 CST)
Re: Is it possible to rename atoms with psfgen? Jim Phillips (Thu Jan 29 2015 - 13:11:46 CST)
Re: Histidine C-H---O hydrogen bonding Branko (Thu Jan 29 2015 - 12:53:52 CST)
Re: Histidine C-H---O hydrogen bonding Tanner, John J. (Thu Jan 29 2015 - 12:51:42 CST)
Re: Histidine C-H---O hydrogen bonding eprates_at_iqm.unicamp.br (Thu Jan 29 2015 - 11:39:57 CST)
Re: Histidine C-H---O hydrogen bonding eprates_at_iqm.unicamp.br (Thu Jan 29 2015 - 11:36:33 CST)
Re: Histidine C-H---O hydrogen bonding Josh Vermaas (Thu Jan 29 2015 - 09:21:27 CST)
Histidine C-H---O hydrogen bonding eprates_at_iqm.unicamp.br (Thu Jan 29 2015 - 09:03:17 CST)
AW: problem with water molecules angle in MD simulation Norman Geist (Thu Jan 29 2015 - 01:56:18 CST)
Re: inconsistency in ABF results for helix unfolding JC Gumbart (Wed Jan 28 2015 - 15:40:30 CST)
Re: inconsistency in ABF results for helix unfolding Giacomo Fiorin (Wed Jan 28 2015 - 14:52:54 CST)
Re: inconsistency in ABF results for helix unfolding MEHRAN MB (Wed Jan 28 2015 - 14:50:14 CST)
AW: problem with water molecules angle in MD simulation Norman Geist (Wed Jan 28 2015 - 10:50:47 CST)
Is it possible to rename atoms with psfgen? Brian Radak (Wed Jan 28 2015 - 09:54:16 CST)
AW: problem with water molecules angle in MD simulation Norman Geist (Wed Jan 28 2015 - 04:08:53 CST)
Re: inconsistency in ABF results for helix unfolding Ajasja LjubetiÄ (Wed Jan 28 2015 - 04:05:37 CST)
Re: inconsistency in ABF results for helix unfolding gmail (Wed Jan 28 2015 - 03:49:54 CST)
inconsistency in ABF results for helix unfolding MEHRAN MB (Tue Jan 27 2015 - 17:09:19 CST)
Re: Hamiltonian Replica Exchange MD Simulation in NAMD Fidan Sumbul (Tue Jan 27 2015 - 14:07:31 CST)
Re: System unstable after turning electric field on. Jeff Comer (Tue Jan 27 2015 - 14:04:26 CST)
Re: System unstable after turning electric field on. Jeff Comer (Tue Jan 27 2015 - 13:22:38 CST)
System unstable after turning electric field on. Dawid das (Tue Jan 27 2015 - 11:26:50 CST)
Re: problem with water molecules angle in MD simulation Shoresh (Tue Jan 27 2015 - 10:30:54 CST)
Re: Hamiltonian Replica Exchange MD Simulation in NAMD JC Gumbart (Tue Jan 27 2015 - 08:52:42 CST)
AW: problem with water molecules angle in MD simulation Norman Geist (Tue Jan 27 2015 - 02:28:18 CST)
AW: about angles in coordination complexes Norman Geist (Tue Jan 27 2015 - 02:23:29 CST)
LCPO parameters P1-P4 yandong Huang (Mon Jan 26 2015 - 12:30:21 CST)
Re: about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 11:51:11 CST)
Re: about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 10:55:10 CST)
Re: about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 10:28:17 CST)
Re: about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 10:02:27 CST)
Re: about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 09:28:16 CST)
AW: about angles in coordination complexes Norman Geist (Mon Jan 26 2015 - 09:24:39 CST)
about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 08:39:17 CST)
Re: problems compiling NAMD with mpicxx from mvapich2 Jose Borreguero (Mon Jan 26 2015 - 08:27:41 CST)
AW: problem with water molecules angle in MD simulation Norman Geist (Mon Jan 26 2015 - 02:43:41 CST)
AW: problems compiling NAMD with mpicxx from mvapich2 Norman Geist (Mon Jan 26 2015 - 02:36:17 CST)
Re: PMEGridSize and parameters controlling electrostatic interactions. Maxim Belkin (Sun Jan 25 2015 - 21:20:58 CST)
problem with water molecules angle in MD simulation Shoresh Shafei (Sun Jan 25 2015 - 19:06:23 CST)
Re: PMEGridSize and parameters controlling electrostatic interactions. Jeff Comer (Sun Jan 25 2015 - 18:11:17 CST)
Re: PMEGridSize and parameters controlling electrostatic interactions. Maxim Belkin (Sat Jan 24 2015 - 14:11:59 CST)
PMEGridSize and parameters controlling electrostatic interactions. Dawid das (Sat Jan 24 2015 - 13:48:44 CST)
problems compiling NAMD with mpicxx from mvapich2 Jose Borreguero (Sat Jan 24 2015 - 11:49:02 CST)
Hamiltonian Replica Exchange MD Simulation in NAMD Fidan Sumbul (Fri Jan 23 2015 - 13:04:19 CST)
NAMD "unable to find improper parameters" Asma El-Magboub (Thu Jan 22 2015 - 21:32:09 CST)
AW: about compiling NAMD using intel icc and impi Norman Geist (Fri Jan 23 2015 - 04:59:43 CST)
about compiling NAMD using intel icc and impi XSC (Fri Jan 23 2015 - 04:00:29 CST)
Re: tclBCArgs, passing floating point lists Jim Phillips (Thu Jan 22 2015 - 14:27:15 CST)
tclBCArgs, passing floating point lists btreece_at_andrew.cmu.edu (Thu Jan 22 2015 - 14:03:21 CST)
Reverse osmosis simulation Z (Thu Jan 22 2015 - 05:09:24 CST)
Re: Fwd: Local minima on minimiztion with colvars Francesco Pietra (Thu Jan 22 2015 - 02:55:09 CST)
Re: NAMD Non-features Axel Kohlmeyer (Wed Jan 21 2015 - 15:54:49 CST)
Re: NAMD Non-features JAVAD NOROOZI (Wed Jan 21 2015 - 15:24:43 CST)
Fwd: Local minima on minimiztion with colvars Francesco Pietra (Wed Jan 21 2015 - 13:01:33 CST)
Local minima on minimiztion with colvars Francesco Pietra (Wed Jan 21 2015 - 12:45:14 CST)
Re: NAMD Non-features Jeff Comer (Wed Jan 21 2015 - 09:35:27 CST)
FEP Restart file g_at_ut#@m! (Wed Jan 21 2015 - 08:26:15 CST)
Re: NAMD Non-features Axel Kohlmeyer (Wed Jan 21 2015 - 05:31:57 CST)
Re: NAMD Non-features Axel Kohlmeyer (Wed Jan 21 2015 - 05:24:41 CST)
NAMD Non-features JAVAD NOROOZI (Wed Jan 21 2015 - 01:54:50 CST)
Re: using NAMD with CHARMM36 ff Tristan Croll (Wed Jan 21 2015 - 01:37:05 CST)
AW: problems running amber parm7 Norman Geist (Tue Jan 20 2015 - 02:10:44 CST)
AW: AW: Periodic Box Dimension (WrapAll is on) Norman Geist (Tue Jan 20 2015 - 02:07:47 CST)
Re: problems running amber parm7 Francesco Pietra (Tue Jan 20 2015 - 01:56:02 CST)
AW: problems running amber parm7 Norman Geist (Tue Jan 20 2015 - 01:38:30 CST)
Re: AW: Periodic Box Dimension (WrapAll is on) JAVAD NOROOZI (Tue Jan 20 2015 - 01:37:18 CST)
Re: problems running amber parm7 Francesco Pietra (Tue Jan 20 2015 - 01:25:17 CST)
AW: Periodic Box Dimension (WrapAll is on) Norman Geist (Tue Jan 20 2015 - 00:39:59 CST)
AW: problems running amber parm7 Norman Geist (Tue Jan 20 2015 - 00:19:40 CST)
Periodic Box Dimension (WrapAll is on) JAVAD NOROOZI (Mon Jan 19 2015 - 23:55:19 CST)
problems running amber parm7 Francesco Pietra (Mon Jan 19 2015 - 13:03:44 CST)
Multiple Dihedral in CHARMM parameters JAVAD NOROOZI (Mon Jan 19 2015 - 01:19:37 CST)
dual-boost aMD and the dV value in the output file Ozge Sensoy (Sun Jan 18 2015 - 14:00:47 CST)
Re: using NAMD with CHARMM36 ff JC Gumbart (Sun Jan 18 2015 - 12:32:35 CST)
Re: using NAMD with CHARMM36 ff Branko (Sun Jan 18 2015 - 11:46:38 CST)
Steered NAMD using AMBER Forcefield [Config File] Zeinab Emami (Sun Jan 18 2015 - 10:07:51 CST)
Re: using NAMD with CHARMM36 ff JC Gumbart (Sat Jan 17 2015 - 19:36:55 CST)
using NAMD with CHARMM36 ff Maria Bykhovskaia (Sat Jan 17 2015 - 19:26:29 CST)
Re: colvars and drude don't play nice? JC Gumbart (Sat Jan 17 2015 - 15:34:43 CST)
Re: colvars and drude don't play nice? Jim Phillips (Fri Jan 16 2015 - 16:57:58 CST)
Re: NAMD 2.10 with MVAPICH2-GDR? Jim Phillips (Fri Jan 16 2015 - 16:54:35 CST)
Re: Restart heating Fotis Baltoumas (Fri Jan 16 2015 - 12:26:09 CST)
Restart heating Francesco Pietra (Fri Jan 16 2015 - 12:04:33 CST)
Re: colvars and drude don't play nice? Giacomo Fiorin (Fri Jan 16 2015 - 11:04:44 CST)
Re: NAMD slows at startup phase 1 smp problem Jim Phillips (Thu Jan 15 2015 - 14:20:58 CST)
NAMD 2.10 with MVAPICH2-GDR? David Chin (Thu Jan 15 2015 - 08:41:04 CST)
Re: Fwd: colvars: keyword "name" is not supported, or not recognized in this context. Francesco Pietra (Thu Jan 15 2015 - 10:54:47 CST)
Re: Fwd: colvars: keyword "name" is not supported, or not recognized in this context. JÃ©rÃ´me HÃ©nin (Thu Jan 15 2015 - 10:34:22 CST)
Fwd: colvars: keyword "name" is not supported, or not recognized in this context. Francesco Pietra (Thu Jan 15 2015 - 10:10:14 CST)
Re: NAMD slows at startup phase 1 smp problem Alexander Tzanov (Thu Jan 15 2015 - 10:05:16 CST)
colvars: keyword "name" is not supported, or not recognized in this context. Francesco Pietra (Thu Jan 15 2015 - 09:52:16 CST)
Re: NAMD slows at startup phase 1 smp problem Jim Phillips (Wed Jan 14 2015 - 17:16:19 CST)
Re: colvars and drude don't play nice? Giacomo Fiorin (Wed Jan 14 2015 - 10:07:23 CST)
Re: colvars and drude don't play nice? JC Gumbart (Wed Jan 14 2015 - 09:58:28 CST)
Re: Running CUDA on a laptop Tristan Croll (Tue Jan 13 2015 - 19:14:31 CST)
Re: colvars and drude don't play nice? Giacomo Fiorin (Tue Jan 13 2015 - 18:31:38 CST)
Running CUDA on a laptop Tristan Croll (Tue Jan 13 2015 - 18:29:59 CST)
colvars and drude don't play nice? JC Gumbart (Tue Jan 13 2015 - 18:08:42 CST)
Re: namd-I: How to assume the thickness of membrane when applying external Electric field ? Adelman, Joshua Lev (Tue Jan 13 2015 - 08:36:01 CST)
Re: namd-I: How to assume the thickness of membrane when applying external Electric field ? Axel Kohlmeyer (Tue Jan 13 2015 - 07:21:49 CST)
AW: NAMD slows at startup phase 1 smp problem Norman Geist (Tue Jan 13 2015 - 05:52:43 CST)
AW: NAMD slows at startup phase 1 smp problem Norman Geist (Tue Jan 13 2015 - 05:50:39 CST)
AW: NAMD slows at startup phase 1 smp problem Norman Geist (Tue Jan 13 2015 - 01:22:03 CST)
namd-I: How to assume the thickness of membrane when applying external Electric field ? Vy Phan (Tue Jan 13 2015 - 00:20:31 CST)
NAMD slows at startup phase 1 smp problem Ryan Gordon (Mon Jan 12 2015 - 12:24:31 CST)
Reg. restarting a Thermodynamic Integration Run Aditya Chattopadhyay (Mon Jan 12 2015 - 09:32:26 CST)
Re: is there a method equivalent to conformational flooding in NAMD 2.10 JÃ©rÃ´me HÃ©nin (Mon Jan 12 2015 - 04:44:58 CST)
Re: is there a method equivalent to conformational flooding in NAMD 2.10 Thomas Evangelidis (Mon Jan 12 2015 - 04:32:17 CST)
Multiple Tcouple JAVAD NOROOZI (Mon Jan 12 2015 - 03:35:01 CST)
AW: is there a method equivalent to conformational flooding in NAMD 2.10 Norman Geist (Mon Jan 12 2015 - 00:53:25 CST)
is there a method equivalent to conformational flooding in NAMD 2.10 Thomas Evangelidis (Sun Jan 11 2015 - 07:43:36 CST)
Re: Getting residue mapping correpond to bead using SBCG (Shape based CG) Model in Coarse Grain Builder VMD Christian Bope Domilongo (Fri Jan 09 2015 - 09:18:32 CST)
Re: Getting residue mapping correpond to bead using SBCG (Shape based CG) Model in Coarse Grain Builder VMD Jeff Comer (Fri Jan 09 2015 - 08:23:03 CST)
Getting residue mapping correpond to bead using SBCG (Shape based CG) Model in Coarse Grain Builder VMD Christian Bope Domilongo (Fri Jan 09 2015 - 04:31:44 CST)
Free Energy Workshop, MÃ¼nster, March 9-11, 2015 Vlad Cojocaru (Fri Jan 09 2015 - 03:19:04 CST)
Re: Failure MD with par7/rst7 amber input Francesco Pietra (Fri Jan 09 2015 - 02:31:55 CST)
AW: Tempreture Profile along z axis Norman Geist (Fri Jan 09 2015 - 02:23:04 CST)
Re: Tempreture Profile along z axis Jim Phillips (Thu Jan 08 2015 - 10:48:58 CST)
Tempreture Profile along z axis JAVAD NOROOZI (Thu Jan 08 2015 - 03:23:12 CST)
Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS Jeff Comer (Wed Jan 07 2015 - 20:15:30 CST)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS Mihaela Drenscko (Wed Jan 07 2015 - 19:58:27 CST)
Re: colvars angle centerReference Giacomo Fiorin (Wed Jan 07 2015 - 14:00:02 CST)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Wed Jan 07 2015 - 12:30:35 CST)
Re: Using colvars for biasing potential in Umbrella Sampling Giacomo Fiorin (Wed Jan 07 2015 - 10:08:11 CST)
Using colvars for biasing potential in Umbrella Sampling begÃ¼m alaybeyoÄŸlu (Wed Jan 07 2015 - 10:01:17 CST)
AW: Failure MD with par7/rst7 amber input Norman Geist (Wed Jan 07 2015 - 03:28:15 CST)
Failure MD with par7/rst7 amber input Francesco Pietra (Wed Jan 07 2015 - 02:55:16 CST)
Problem with Kinetic Energy of Atomselection JAVAD NOROOZI (Wed Jan 07 2015 - 00:53:38 CST)
topology & force field parameters for Sorbitan monooleate (span 80) Madhusoodanan M.R (Tue Jan 06 2015 - 20:32:39 CST)
AW: Probelm with Lone Pairs on TIP4 model Norman Geist (Tue Jan 06 2015 - 05:34:59 CST)
Probelm with Lone Pairs on TIP4 model JAVAD NOROOZI (Tue Jan 06 2015 - 04:07:23 CST)
Multiple tcouple (Nonequilbirium molecular dynamics) JAVAD NOROOZI (Tue Jan 06 2015 - 03:51:07 CST)
Re: Asking help on results of our GPU benchmark Axel Kohlmeyer (Mon Jan 05 2015 - 10:36:24 CST)
Re: FEP, big variations in dG within a window Felipe Merino (Mon Jan 05 2015 - 10:27:30 CST)
AW: Asking help on results of our GPU benchmark Norman Geist (Mon Jan 05 2015 - 00:37:40 CST)
FEP, big variations in dG within a window Jonasson Gabriella (Mon Jan 05 2015 - 09:44:31 CST)
AW: AW: AW: AW: warnings while using amber files Norman Geist (Mon Jan 05 2015 - 08:56:36 CST)
Re: AW: AW: AW: warnings while using amber files amin_at_imtech.res.in (Mon Jan 05 2015 - 07:34:30 CST)
Re: Reg: simulating an amino acid in dichloromethane Akshay Bhatnagar (Mon Jan 05 2015 - 06:46:07 CST)
AW: AW: AW: warnings while using amber files Norman Geist (Mon Jan 05 2015 - 06:35:46 CST)
Re: Reg: simulating an amino acid in dichloromethane Branko (Mon Jan 05 2015 - 05:39:13 CST)
Re: AW: AW: warnings while using amber files amin_at_imtech.res.in (Mon Jan 05 2015 - 04:39:58 CST)
AW: AW: warnings while using amber files Norman Geist (Mon Jan 05 2015 - 03:19:13 CST)
Re: AW: warnings while using amber files amin_at_imtech.res.in (Mon Jan 05 2015 - 02:50:52 CST)
Re: Temperature assignment REMD Yan Zhou (Mon Jan 05 2015 - 02:27:56 CST)
AW: Temperature assignment REMD Norman Geist (Mon Jan 05 2015 - 01:29:55 CST)
AW: regarding PME grid setting problem Norman Geist (Mon Jan 05 2015 - 00:48:11 CST)
AW: warnings while using amber files Norman Geist (Mon Jan 05 2015 - 00:42:51 CST)
AW: error parsing config file while executing Norman Geist (Mon Jan 05 2015 - 00:26:37 CST)
regarding PME grid setting problem amit banerjee (Sun Jan 04 2015 - 18:31:44 CST)
Temperature assignment REMD divya nayar (Sat Jan 03 2015 - 08:36:05 CST)
Re: Reg: simulating an amino acid in dichloromethane Jeff Comer (Sat Jan 03 2015 - 00:34:17 CST)
Reg: simulating an amino acid in dichloromethane Akshay Bhatnagar (Fri Jan 02 2015 - 23:18:45 CST)

Last message date: Tue Dec 27 2016 - 20:48:03 CST
Archived on: Tue Dec 27 2016 - 23:22:47 CST

2670 messages sorted by: [ author ] [ thread ] [ subject ] [ attachment ]
About this archive

Home

Overview

Publications

Research

Software

NAMD

VMD

GPU Computing

Lattice Microbes

Atomic Resolution Brownian Dynamics

MDFF

QwikMD

VND (Neuronal)

Other

Outreach

NAMD-L: By Date

By Date