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NAMD-L: By Subject

By Subject

3750 messages sorted by: [ author ] [ date ] [ thread ] [ attachment ]
About this archive

Starting: Thu Jan 03 2013 - 06:24:44 CST
Ending: Tue Dec 30 2014 - 07:38:36 CST

• Gianluca Interlandi (Thu Aug 28 2014 - 00:16:37 CDT)
• Jim Phillips (Tue Aug 26 2014 - 10:38:36 CDT)
• Ajasja LjubetiÄ� (Tue Jul 22 2014 - 13:18:02 CDT)
• Aron Broom (Tue Jul 22 2014 - 12:36:33 CDT)
• Jérôme Hénin (Tue Jul 22 2014 - 12:21:26 CDT)
• Jason Swails (Tue Jul 22 2014 - 12:06:31 CDT)
• Kenno Vanommeslaeghe (Tue Jul 22 2014 - 11:58:25 CDT)
• Jérôme Hénin (Tue Jul 22 2014 - 11:57:54 CDT)
• Aaron Larsen (Tue Jul 22 2014 - 11:38:27 CDT)
• Kenno Vanommeslaeghe (Mon Jul 14 2014 - 15:58:25 CDT)
• Gianluca Interlandi (Mon Jul 14 2014 - 13:26:57 CDT)
• Branko (Mon Jul 14 2014 - 13:24:43 CDT)
• Aron Broom (Mon Jul 14 2014 - 13:18:14 CDT)
• manish kesherwani (Wed Apr 16 2014 - 13:21:34 CDT)
• Aron Broom (Tue Apr 15 2014 - 13:47:48 CDT)
• Kenno Vanommeslaeghe (Tue Apr 15 2014 - 12:14:07 CDT)
• Boyang Wang (Thu Feb 20 2014 - 00:53:46 CST)
• Axel Kohlmeyer (Sun Sep 01 2013 - 10:40:27 CDT)
• Aron Broom (Thu Jun 20 2013 - 10:19:40 CDT)
• Aron Broom (Thu Apr 25 2013 - 09:34:41 CDT)
• Aron Broom (Tue Mar 26 2013 - 13:02:52 CDT)
• Jérôme Hénin (Tue Mar 26 2013 - 12:35:01 CDT)
• linux freaker (Tue Mar 26 2013 - 12:57:20 CDT)
• Aron Broom (Mon Mar 25 2013 - 16:48:45 CDT)
• Jérôme Hénin (Mon Mar 25 2013 - 16:12:10 CDT)
• amin_at_imtech.res.in (Fri Feb 22 2013 - 00:31:16 CST)
• "BAK" format files
  • Ramin Ekhteiari (Mon Nov 24 2014 - 06:52:20 CST)
• "Beefier" benchmark
  • Phil Greer (Tue Aug 19 2014 - 11:30:38 CDT)
  • Aron Broom (Tue Aug 19 2014 - 11:15:29 CDT)
  • Maxime Boissonneault (Tue Aug 19 2014 - 11:14:31 CDT)
  • Phil Greer (Tue Aug 19 2014 - 11:10:28 CDT)
  • Maxime Boissonneault (Tue Aug 19 2014 - 10:48:30 CDT)
• "Hands-on" Workshop on Computational Biophysics at Lake Tahoe, August 4-8, 2014
  • David Brandon (Thu Apr 03 2014 - 11:17:33 CDT)
• 'Hands-on' Workshop on Computational Biophysics using VMD, NAMD, and ProDy, June 10-14, 2013 in Pittsburgh, PA
  • David Brandon (Fri Mar 08 2013 - 12:08:25 CST)
• (no subject)
  • tillmann.utesch_at_mailbox.tu-berlin.de (Wed Nov 26 2014 - 03:20:51 CST)
  • flavio seixas (Tue Nov 25 2014 - 19:13:24 CST)
  • BIPLAB NANDI (Wed Aug 27 2014 - 22:13:06 CDT)
  • ukulililixl (Tue Aug 26 2014 - 01:22:20 CDT)
  • Shalton Evans (Sat Aug 09 2014 - 23:00:48 CDT)
  • sudipta.mml (Sat Aug 02 2014 - 20:01:46 CDT)
  • Carlos Navarrro Retamal (Tue Jul 22 2014 - 11:43:10 CDT)
  • Mitul Saha (Tue Jul 22 2014 - 11:27:04 CDT)
  • Eifler, Jay Q. (UMKC-Student) (Mon Jul 14 2014 - 13:05:36 CDT)
  • sudipta.mml (Mon Jul 07 2014 - 01:08:12 CDT)
  • zmhoseyni (Thu Jul 03 2014 - 22:36:44 CDT)
  • zmhoseyni (Wed Jul 02 2014 - 00:25:31 CDT)
  • zmhoseyni (Wed May 21 2014 - 04:48:25 CDT)
  • zmhoseyni (Mon May 19 2014 - 04:18:48 CDT)
  • Boshra Moradi (Tue May 06 2014 - 16:35:44 CDT)
  • manish kesherwani (Tue Apr 15 2014 - 00:02:12 CDT)
  • Boyang Wang (Thu Feb 20 2014 - 00:05:03 CST)
  • sutapa dutta (Fri Nov 22 2013 - 05:04:36 CST)
  • buksanbio_at_gmail.com (Sat Oct 05 2013 - 16:12:07 CDT)
  • Arman Imen (Thu Sep 26 2013 - 05:49:15 CDT)
  • rasti_at_ut.ac.ir (Fri Sep 20 2013 - 05:19:37 CDT)
  • Nadia Salami (Sun Sep 01 2013 - 10:26:51 CDT)
  • kaushik chakraborty (Sun Aug 25 2013 - 11:41:34 CDT)
  • JAGODINSKY, JUSTIN (Fri Jul 12 2013 - 09:12:51 CDT)
  • Mihaela Drenscko (Thu Jun 20 2013 - 10:14:07 CDT)
  • Ganesh Shahane (Thu Apr 25 2013 - 08:51:59 CDT)
  • Ganesh Shahane (Thu Apr 25 2013 - 01:25:29 CDT)
  • Tina Stokelj (Thu Apr 11 2013 - 00:07:11 CDT)
  • Mohammad Jomah I Abu Saude (mbusaude) (Wed Apr 10 2013 - 17:30:08 CDT)
  • Mihaela Drenscko (Tue Mar 26 2013 - 12:41:35 CDT)
  • Riley Workman (Mon Mar 25 2013 - 15:07:09 CDT)
  • Francesco Pietra (Thu Feb 28 2013 - 10:59:57 CST)
  • Moema Monteiro (Wed Feb 27 2013 - 15:08:10 CST)
  • Titis Sekar Humani (Fri Feb 22 2013 - 00:05:07 CST)
  • forough askari (Sun Jan 27 2013 - 10:06:36 CST)
  • forough askari (Tue Jan 22 2013 - 16:32:34 CST)
  • forough askari (Mon Jan 21 2013 - 18:38:10 CST)
  • Maria Saeed (Tue Jan 15 2013 - 01:03:27 CST)
• *** glibc detected *** namd2: invalid fastbin entry (free)
  • Wesley Lay (Thu May 22 2014 - 15:19:11 CDT)
• +p option on Windows 7
  • Kukol, Andreas (Wed Jul 30 2014 - 09:56:28 CDT)
• .inpcrd to .pdb
  • Jason Swails (Sun Dec 21 2014 - 20:04:39 CST)
  • Shalton Evans (Sun Dec 21 2014 - 13:56:30 CST)
• .psf file in VMD
  • Lili Zhang (Thu Oct 03 2013 - 12:10:56 CDT)
• 1-5 Intramolecular repulsions
  • cuiyoutian_at_163.com (Wed Nov 05 2014 - 15:12:43 CST)
  • Axel Kohlmeyer (Wed Nov 05 2014 - 15:12:43 CST)
  • rocwhite168 (Wed Nov 05 2014 - 14:55:05 CST)
  • Rebecca Lindsey (Wed Nov 05 2014 - 13:07:49 CST)
  • rocwhite168 (Wed Nov 05 2014 - 13:02:55 CST)
  • Jeffrey Potoff (Wed Nov 05 2014 - 12:51:02 CST)
  • Kenno Vanommeslaeghe (Wed Nov 05 2014 - 12:33:12 CST)
  • Rebecca Lindsey (Wed Nov 05 2014 - 11:54:40 CST)
• 11/22/2014 6:32:52 PM
  • jeremy adler (Sat Nov 22 2014 - 00:32:52 CST)
• 2-residue patch for Asn-Lys side chain amide bond
  • Kenno Vanommeslaeghe (Fri Jul 25 2014 - 12:20:46 CDT)
• 2-residue patch for hydrocarbon staple
  • Kenno Vanommeslaeghe (Thu Jul 24 2014 - 15:48:52 CDT)
• 2014 Aspen Center for Physics Workshop
  • MARK PLUMMER (Fri May 24 2013 - 14:50:54 CDT)
• 2014 Biophysics Workshop In Aspen Colorado
  • MARK PLUMMER (Tue Jun 11 2013 - 20:39:57 CDT)
• 2d periodic box
  • Pavan G (Sun Mar 31 2013 - 12:50:49 CDT)
  • Pavan G (Fri Mar 29 2013 - 08:56:33 CDT)
  • Pavan G (Fri Mar 29 2013 - 08:39:59 CDT)
  • Pavan G (Wed Mar 27 2013 - 12:51:25 CDT)
• 50% system CPU usage when parallel running NAMD on Rocks cluster
  • Axel Kohlmeyer (Wed Dec 18 2013 - 07:04:24 CST)
  • ÖÜêÇêÀ (Wed Dec 18 2013 - 06:43:18 CST)
  • Axel Kohlmeyer (Wed Dec 18 2013 - 01:28:34 CST)
  • ÖÜêÇêÀ (Tue Dec 17 2013 - 08:12:33 CST)
  • ÖÜêÇêÀ (Sat Dec 14 2013 - 07:55:47 CST)
  • ÖÜêÇêÀ (Tue Dec 10 2013 - 06:51:31 CST)
  • ÖÜêÇêÀ (Sun Dec 08 2013 - 09:11:31 CST)
  • ÖÜêÇêÀ (Sat Nov 30 2013 - 21:06:18 CST)
  • ÖÜêÇêÀ (Tue Dec 03 2013 - 07:43:07 CST)
• 6 equilibration steps at charmm gui server
  • Sunhwan Jo (Thu Apr 03 2014 - 09:34:23 CDT)
  • Ramin Ekhteiari (Thu Apr 03 2014 - 04:32:58 CDT)
• [ANN] MDTraj 1.0: Trajectory Analysis in Python
  • Ivan Gregoretti (Tue Sep 09 2014 - 12:09:49 CDT)
  • Robert McGibbon (Mon Sep 08 2014 - 17:19:00 CDT)
• [charm] Charm 6.5.0 compilation issue
  • Ake Sandgren (Fri Jan 11 2013 - 12:21:43 CST)
• [Checkpoint] BLCR and NAMD
  • Joseph Farran (Fri Oct 25 2013 - 12:33:29 CDT)
  • Joseph Farran (Wed Oct 23 2013 - 13:46:00 CDT)
• [External] Boost value in aMD simulation
  • James Starlight (Fri Aug 22 2014 - 11:54:05 CDT)
  • James Starlight (Tue Aug 19 2014 - 13:45:58 CDT)
  • James Starlight (Tue Aug 19 2014 - 04:56:58 CDT)
  • Thomas Evangelidis (Mon Aug 18 2014 - 04:21:25 CDT)
  • James Starlight (Mon Aug 18 2014 - 03:25:53 CDT)
  • James Starlight (Thu Jul 24 2014 - 01:13:09 CDT)
  • Thomas Evangelidis (Wed Jul 23 2014 - 16:37:47 CDT)
  • James Starlight (Wed Jul 23 2014 - 15:32:53 CDT)
  • Thomas Evangelidis (Wed Jul 23 2014 - 15:02:25 CDT)
  • James Starlight (Wed Jul 23 2014 - 14:24:45 CDT)
• [OT] A new method for quantifying convergence of MD simulations
  • Nicholas M Glykos (Mon Oct 21 2013 - 12:37:45 CDT)
• [SOLVED] Charmrun> error x attaching to node
  • Norman Geist (Tue Apr 30 2013 - 05:09:05 CDT)
• [SUSPICIOUS MESSAGE] Reg System Prepartion namd
  • Kenno Vanommeslaeghe (Thu Oct 17 2013 - 16:15:10 CDT)
• A fancy problem in calculating the protonated glutamic acid modelled by adding the patch of GLUP
  • Yize Hu (Sat Jun 01 2013 - 03:17:27 CDT)
  • Jérôme Hénin (Fri May 31 2013 - 10:30:01 CDT)
  • Yize Hu (Fri May 31 2013 - 10:20:52 CDT)
• A larger protein data bank for performance benchmark
  • Rebecca Swett (Mon May 13 2013 - 20:52:17 CDT)
  • Gianluca Interlandi (Tue May 14 2013 - 00:02:34 CDT)
  • Aron Broom (Mon May 13 2013 - 22:56:35 CDT)
  • linux freaker (Mon May 13 2013 - 21:02:59 CDT)
  • linux freaker (Mon May 13 2013 - 19:51:51 CDT)
  • Ajasja LjubetiÄ� (Mon May 13 2013 - 12:13:46 CDT)
  • Cesar Millan (Mon May 13 2013 - 11:52:30 CDT)
  • linux freaker (Mon May 13 2013 - 11:49:10 CDT)
• a problem about pbc in a namd trajectory
  • ½ùÏþ½Ü (Mon Aug 26 2013 - 02:44:23 CDT)
• A problem in ABF simulations
  • Jeff Comer (Mon Nov 24 2014 - 11:44:45 CST)
  • Azadeh Alavi (Sat Nov 22 2014 - 05:50:03 CST)
• aa_ref-monomer-noh.dcd file in the tutorial of shape-based coarse grained (SBCG) simulation
  • sunyeping (Mon Mar 10 2014 - 20:01:13 CDT)
• aa_ref-monomer-noh.dcd in shape-based coarse grained simulation
  • sunyeping (Sat Mar 08 2014 - 20:09:26 CST)
• ABF
  • Chris Chipot (Thu May 09 2013 - 01:09:27 CDT)
  • karthik kumar (Wed May 08 2013 - 23:34:17 CDT)
  • karthik kumar (Mon Apr 15 2013 - 07:38:26 CDT)
  • karthik kumar (Sat Apr 13 2013 - 06:45:12 CDT)
  • Giacomo Fiorin (Thu Apr 04 2013 - 16:09:15 CDT)
  • Giacomo Fiorin (Thu Apr 04 2013 - 11:24:57 CDT)
  • karthik kumar (Thu Apr 04 2013 - 10:53:58 CDT)
• ABF - distance between two domains
  • Nadeem A. Vellore (Wed Feb 27 2013 - 15:45:49 CST)
  • Nadeem A. Vellore (Wed Feb 27 2013 - 15:12:35 CST)
• ABF calculations in NAMD
  • Johny Telecaster (Mon Nov 18 2013 - 07:36:58 CST)
• ABF force distribution
  • Kasra Fattah (Sat Mar 01 2014 - 18:20:11 CST)
  • Jérôme Hénin (Thu Feb 27 2014 - 06:59:48 CST)
  • MEHRAN MB (Tue Feb 18 2014 - 10:50:59 CST)
  • Kasra Fattah (Thu Feb 13 2014 - 14:56:42 CST)
• ABF hBond
  • Giacomo Fiorin (Mon Aug 25 2014 - 10:18:12 CDT)
  • Charles Whidborne (Mon Aug 25 2014 - 02:52:45 CDT)
• ABF historyFile and distFile
  • Sridhar Kumar Kannam (Thu Aug 29 2013 - 22:58:33 CDT)
• abf integrate on two dimensional pmf
  • Ajasja LjubetiÄ� (Tue Oct 08 2013 - 03:20:52 CDT)
  • Nadeem A. Vellore (Mon Oct 07 2013 - 21:25:11 CDT)
• ABF simulation fails with "FATAL ERROR: Low global exclusion count!"
  • Maria Pikoula (Fri Feb 28 2014 - 12:50:27 CST)
  • Jérôme Hénin (Fri Feb 28 2014 - 11:58:59 CST)
  • Maria Pikoula (Fri Feb 28 2014 - 11:42:47 CST)
  • Giacomo Fiorin (Tue Feb 25 2014 - 20:19:28 CST)
  • Maria Pikoula (Tue Feb 25 2014 - 11:02:24 CST)
• ABF simulation, free energy to remove a DNA strand
  • Thomas C. Bishop (Tue Aug 05 2014 - 10:17:07 CDT)
  • Jérôme Hénin (Tue Aug 05 2014 - 03:15:46 CDT)
  • Charles Whidborne (Tue Aug 05 2014 - 01:54:14 CDT)
• ABF simulations
  • MEHRAN MB (Tue Feb 18 2014 - 10:38:25 CST)
  • Aron Broom (Fri Feb 14 2014 - 07:34:46 CST)
  • Abir Ganguly (Thu Feb 13 2014 - 22:50:10 CST)
  • Aron Broom (Mon Feb 10 2014 - 11:20:54 CST)
  • Abir Ganguly (Sat Feb 08 2014 - 15:38:01 CST)
• ABF simulations with barriers (adsorption)
  • Jérôme Hénin (Thu Jun 13 2013 - 04:45:19 CDT)
  • Jérôme Hénin (Tue Jun 11 2013 - 07:09:06 CDT)
  • Zachary Ulissi (Mon Jun 10 2013 - 12:26:49 CDT)
• ABF subdividing the reaction coordinate
  • Aron Broom (Wed Jul 10 2013 - 17:44:57 CDT)
  • Pedro Swagger (Wed Jul 10 2013 - 17:15:44 CDT)
  • Aron Broom (Wed Jul 10 2013 - 17:01:01 CDT)
  • Pedro Swagger (Wed Jul 10 2013 - 16:45:15 CDT)
  • Aron Broom (Wed Jul 10 2013 - 16:22:28 CDT)
  • Pedro Swagger (Wed Jul 10 2013 - 16:00:37 CDT)
• ABF thermostats and energy introduced into the system
  • JC Gumbart (Wed Feb 27 2013 - 15:29:49 CST)
  • Ajasja LjubetiÄ� (Wed Feb 27 2013 - 11:29:28 CST)
  • Ajasja LjubetiÄ� (Wed Feb 27 2013 - 06:26:39 CST)
  • Ajasja LjubetiÄ� (Tue Feb 26 2013 - 03:10:27 CST)
  • Ajasja LjubetiÄ� (Tue Feb 26 2013 - 02:52:54 CST)
  • JC Gumbart (Mon Feb 25 2013 - 16:32:13 CST)
  • Jérôme Hénin (Mon Feb 25 2013 - 08:01:52 CST)
  • Ajasja LjubetiÄ� (Mon Feb 25 2013 - 07:07:39 CST)
• ABF with the RMSD colvar
  • George Patargias (Mon Sep 29 2014 - 05:25:01 CDT)
  • Jérôme Hénin (Mon Sep 22 2014 - 08:37:00 CDT)
  • George Patargias (Mon Sep 22 2014 - 06:21:45 CDT)
  • Jérôme Hénin (Fri Sep 19 2014 - 10:46:45 CDT)
  • George Patargias (Fri Sep 19 2014 - 10:12:40 CDT)
  • Jérôme Hénin (Wed Sep 17 2014 - 07:13:05 CDT)
  • George Patargias (Wed Sep 17 2014 - 06:43:44 CDT)
  • Giacomo Fiorin (Fri Apr 25 2014 - 09:41:54 CDT)
  • George Patargias (Fri Apr 25 2014 - 05:20:31 CDT)
  • Giacomo Fiorin (Wed Apr 16 2014 - 13:41:54 CDT)
  • George Patargias (Wed Apr 16 2014 - 05:14:05 CDT)
  • Giacomo Fiorin (Tue Apr 15 2014 - 10:06:44 CDT)
  • George Patargias (Tue Apr 15 2014 - 05:22:46 CDT)
  • Aron Broom (Fri Jun 07 2013 - 09:50:12 CDT)
  • George Patargias (Fri Jun 07 2013 - 09:43:45 CDT)
  • Jérôme Hénin (Fri Jun 07 2013 - 09:07:57 CDT)
  • George Patargias (Fri Jun 07 2013 - 08:51:22 CDT)
• ABF zCoord analog in colvars ?
  • Jérôme Hénin (Wed Jun 05 2013 - 08:44:16 CDT)
  • Arturas (Wed Jun 05 2013 - 08:41:15 CDT)
• ABF/colvar error in NAMD2.9
  • Harish Vashisth (Tue Jul 22 2014 - 14:39:15 CDT)
  • Niklaus Johner (Tue Jul 22 2014 - 13:32:12 CDT)
  • Aron Broom (Tue Jul 22 2014 - 13:08:48 CDT)
  • Harish Vashisth (Tue Jul 22 2014 - 13:00:04 CDT)
  • Aron Broom (Tue Jul 22 2014 - 12:32:06 CDT)
  • Jérôme Hénin (Tue Jul 22 2014 - 11:56:06 CDT)
  • Aron Broom (Tue Jul 22 2014 - 11:30:49 CDT)
  • Jérôme Hénin (Tue Jul 22 2014 - 11:29:47 CDT)
  • Harish Vashisth (Tue Jul 22 2014 - 11:23:13 CDT)
• ABF: Distances in colvars.traj not identical with VMD exported distances
  • Maximilian Ebert (Tue Oct 29 2013 - 10:02:05 CDT)
  • Giacomo Fiorin (Tue Oct 29 2013 - 09:33:36 CDT)
  • Maximilian Ebert (Tue Oct 29 2013 - 07:13:04 CDT)
  • Giacomo Fiorin (Mon Oct 28 2013 - 16:28:15 CDT)
  • Maximilian Ebert (Mon Oct 28 2013 - 16:21:45 CDT)
• abf_integrate
  • Giacomo Fiorin (Tue Jun 11 2013 - 15:03:29 CDT)
  • Kasra Fattah (Tue Jun 11 2013 - 14:54:34 CDT)
• About "add solvation"
  • Francesco Pietra (Mon Jan 21 2013 - 03:42:54 CST)
• About a REMD tutorial
  • Francesco Pietra (Sat Sep 07 2013 - 09:35:51 CDT)
• About asterisk in IC statements in topology files
  • Kevin C Chan (Tue Jul 08 2014 - 02:30:25 CDT)
• About Bond Deletion
  • Axel Kohlmeyer (Thu Apr 11 2013 - 00:32:45 CDT)
  • Vidhya Sankar (Wed Apr 10 2013 - 22:12:33 CDT)
• About Constraint Failure
  • Kenno Vanommeslaeghe (Tue Oct 15 2013 - 12:33:23 CDT)
  • Vidhya Sankar (Tue Oct 15 2013 - 04:57:04 CDT)
• About converting NAMD dcd file into CHARMM dcd file
  • Kenno Vanommeslaeghe (Fri Jun 13 2014 - 21:18:52 CDT)
  • Mo Chen (Fri Jun 13 2014 - 18:41:30 CDT)
• About electrostatic treatment
  • David Hardy (Sat May 31 2014 - 12:01:34 CDT)
  • Mo Chen (Fri May 30 2014 - 19:39:31 CDT)
  • Mo Chen (Fri May 30 2014 - 19:35:50 CDT)
• About Fiorin-Klein-Henin recent colvar examples
  • Giacomo Fiorin (Fri Jun 21 2013 - 09:59:06 CDT)
  • Francesco Pietra (Fri Jun 21 2013 - 03:50:35 CDT)
• About Free energy tutorial for Membrane-Protein system
  • Vidhya Sankar (Sun Dec 15 2013 - 03:26:34 CST)
• about interaction between protein and its image in namd simulation
  • Aron Broom (Tue Jul 09 2013 - 13:10:50 CDT)
  • Liqun Zhang (Tue Jul 09 2013 - 12:16:37 CDT)
• About keep_water_out.tcl
  • zeynab mohamad hoseyni (Thu Feb 20 2014 - 05:21:23 CST)
• About Membrane anlysis
  • Thomas Evangelidis (Wed Dec 18 2013 - 10:45:52 CST)
  • Jeffrey Potoff (Wed Dec 18 2013 - 09:50:03 CST)
  • Vidhya Sankar (Wed Dec 18 2013 - 09:09:22 CST)
• About Muticore Linux Ibnstalltion if NAmd
  • Kenno Vanommeslaeghe (Tue Sep 24 2013 - 11:32:07 CDT)
  • Aron Broom (Fri Sep 20 2013 - 23:29:04 CDT)
  • Vidhya Sankar (Fri Sep 20 2013 - 22:50:38 CDT)
• About NAMD
  • Douglas Houston (Tue Nov 18 2014 - 09:32:59 CST)
  • Dennis Lam (Tue Jun 25 2013 - 11:20:15 CDT)
• About Namd Compilation
  • Vidhya Sankar (Sat Dec 28 2013 - 11:12:02 CST)
• About Namd Installation
  • Axel Kohlmeyer (Sun Jun 16 2013 - 01:23:15 CDT)
  • Vidhya Sankar (Sun Jun 16 2013 - 00:14:04 CDT)
• About Number of atoms in fixed atoms PDB doesn't match coordinate PDB
  • Sridhar Kumar Kannam (Sat Jan 25 2014 - 23:49:47 CST)
  • Vidhya Sankar (Sat Jan 25 2014 - 21:01:01 CST)
• About PLUMED with NAMD VMD
  • davide branduardi (Wed Feb 27 2013 - 02:41:14 CST)
  • Giacomo Fiorin (Wed Feb 27 2013 - 02:39:27 CST)
  • Francesco Pietra (Wed Feb 27 2013 - 02:16:28 CST)
• About Psfgen error for Lipid molecules
  • Vidhya Sankar (Sun Jan 19 2014 - 07:29:51 CST)
• About Psfgen for cyclic peptide
  • Vidhya Sankar (Sun Nov 03 2013 - 00:08:11 CDT)
• About Psfgen for membrane
  • Vidhya Sankar (Wed Sep 18 2013 - 10:56:30 CDT)
• About restaring Simulation
  • Aron Broom (Sat Oct 05 2013 - 07:10:17 CDT)
  • Vidhya Sankar (Sat Oct 05 2013 - 02:56:01 CDT)
• About Tcl8.3 error in namd2.8
  • Phil Miller (Wed Jan 01 2014 - 09:33:57 CST)
  • Vidhya Sankar (Wed Jan 01 2014 - 08:20:20 CST)
• About the scope of show_replicas.vmd
  • Kenno Vanommeslaeghe (Tue Sep 24 2013 - 11:19:21 CDT)
  • Francesco Pietra (Fri Sep 20 2013 - 12:39:16 CDT)
  • Kenno Vanommeslaeghe (Fri Sep 20 2013 - 12:22:39 CDT)
  • Francesco Pietra (Fri Sep 20 2013 - 02:33:19 CDT)
  • Niklaus Johner (Thu Sep 19 2013 - 12:30:05 CDT)
  • Jason Swails (Thu Sep 19 2013 - 11:19:24 CDT)
  • Francesco Pietra (Thu Sep 19 2013 - 10:53:58 CDT)
  • Niklaus Johner (Thu Sep 19 2013 - 09:48:11 CDT)
  • Francesco Pietra (Thu Sep 19 2013 - 01:48:16 CDT)
• about the vdw Interpolation calculation in NAMD source code
  • ¬Óíï¿ (Thu Nov 20 2014 - 20:35:48 CST)
  • Jim Phillips (Thu Nov 20 2014 - 16:00:29 CST)
  • ¬Óíï¿ (Thu Nov 20 2014 - 09:32:10 CST)
  • Jim Phillips (Thu Nov 20 2014 - 08:29:27 CST)
  • Jeff Comer (Thu Nov 20 2014 - 08:20:54 CST)
  • ¬Óíï¿ (Thu Nov 20 2014 - 02:44:40 CST)
• About Usage of Topolgy and Parameter
  • Kenno Vanommeslaeghe (Mon Oct 14 2013 - 11:09:59 CDT)
  • Vidhya Sankar (Mon Oct 14 2013 - 08:24:20 CDT)
  • Kenno Vanommeslaeghe (Mon Oct 14 2013 - 00:26:01 CDT)
  • Vidhya Sankar (Sun Oct 13 2013 - 06:59:39 CDT)
• About Warning in compilation of Namd
  • Axel Kohlmeyer (Sat Jan 04 2014 - 06:21:55 CST)
  • Vidhya Sankar (Sat Jan 04 2014 - 03:41:57 CST)
• Accelerated MD (aMD)
  • Thomas Evangelidis (Sat Jul 26 2014 - 06:38:20 CDT)
  • Ramin Ekhteiari (Sat Jul 26 2014 - 06:06:25 CDT)
• accelerated MD and External Electric Field
  • Thomas Evangelidis (Tue Nov 05 2013 - 07:10:24 CST)
• accelerated MD as the engine for loop refirement
  • Gianluca Interlandi (Tue Jul 15 2014 - 02:05:30 CDT)
  • Ramin Ekhteiari (Tue Jul 15 2014 - 01:30:12 CDT)
  • Tristan Croll (Mon Jul 14 2014 - 18:18:05 CDT)
  • Chris Ing (Mon Jul 14 2014 - 16:53:07 CDT)
  • James Starlight (Mon Jul 14 2014 - 05:16:46 CDT)
  • Tristan Croll (Mon Jul 14 2014 - 00:40:11 CDT)
  • James Starlight (Sun Jul 13 2014 - 14:05:10 CDT)
  • James Starlight (Sat Jul 12 2014 - 09:28:21 CDT)
  • Gianluca Interlandi (Thu Jul 10 2014 - 17:59:24 CDT)
  • Kenno Vanommeslaeghe (Thu Jul 10 2014 - 17:32:38 CDT)
  • James Starlight (Thu Jul 10 2014 - 04:39:17 CDT)
  • Ajasja LjubetiÄ� (Wed Jul 09 2014 - 15:22:15 CDT)
  • Gianluca Interlandi (Wed Jul 09 2014 - 15:08:17 CDT)
  • James Starlight (Wed Jul 09 2014 - 14:39:08 CDT)
• Accelerated MD in NAMD
  • James Starlight (Sat Mar 08 2014 - 09:24:47 CST)
  • James Starlight (Fri Nov 08 2013 - 06:36:51 CST)
  • James Starlight (Fri Nov 08 2013 - 00:53:41 CST)
  • James Starlight (Thu Nov 07 2013 - 13:18:47 CST)
  • Jeff Wereszczynski (Thu Nov 07 2013 - 10:46:59 CST)
  • Thomas Evangelidis (Thu Nov 07 2013 - 09:59:39 CST)
  • Jeff Wereszczynski (Thu Nov 07 2013 - 08:19:53 CST)
  • James Starlight (Thu Nov 07 2013 - 06:48:45 CST)
  • Thomas Evangelidis (Thu Nov 07 2013 - 04:32:04 CST)
  • James Starlight (Thu Nov 07 2013 - 01:09:45 CST)
  • James Starlight (Wed Nov 06 2013 - 23:28:44 CST)
  • Jeff Wereszczynski (Wed Nov 06 2013 - 19:24:58 CST)
  • Thomas Evangelidis (Wed Nov 06 2013 - 15:21:52 CST)
  • Jeff Wereszczynski (Wed Nov 06 2013 - 15:03:00 CST)
  • James Starlight (Wed Nov 06 2013 - 12:50:36 CST)
  • Jeff Wereszczynski (Wed Nov 06 2013 - 12:00:29 CST)
  • James Starlight (Wed Nov 06 2013 - 01:29:53 CST)
  • James Starlight (Sun Nov 03 2013 - 08:17:51 CST)
• accelerated MD log
  • Felipe Merino (Mon Mar 31 2014 - 03:57:30 CDT)
• Accelerated MD parameters
  • Gianluca Interlandi (Tue Mar 26 2013 - 19:37:56 CDT)
• accelerated MD parameters for dual boost mode
  • Huihui Liu (Thu Oct 31 2013 - 10:04:23 CDT)
• Accelerated MD with transmembrane protein
  • Francesco Pietra (Sat Apr 12 2014 - 08:24:00 CDT)
  • Kevin Kastner (Fri Apr 11 2014 - 13:06:28 CDT)
  • Francesco Pietra (Fri Apr 11 2014 - 12:16:40 CDT)
  • Jeff Wereszczynski (Fri Apr 11 2014 - 11:50:20 CDT)
  • Francesco Pietra (Fri Apr 11 2014 - 11:39:10 CDT)
  • Jeff Wereszczynski (Fri Apr 11 2014 - 07:19:20 CDT)
  • Felipe Merino (Fri Apr 11 2014 - 03:27:09 CDT)
  • Kevin Kastner (Thu Apr 10 2014 - 13:40:26 CDT)
• Accelerated Molecular Dynamics logs
  • Johny Telecaster (Sat Mar 08 2014 - 09:37:05 CST)
• Accelerated molecular dynamics: Energy value in output file
  • Kapil jain (Tue Aug 19 2014 - 23:53:20 CDT)
• accelMD on GPUs
  • Francesco Pietra (Sat Mar 29 2014 - 02:38:58 CDT)
• Accumulating free energy change for applying colvar restraint
  • Jérôme Hénin (Mon Oct 07 2013 - 09:06:15 CDT)
  • Randy J. Zauhar (Mon Oct 07 2013 - 08:50:07 CDT)
• Adaptive tempering exception error
  • Matthew Ralph Adendorff (Sun Nov 17 2013 - 09:52:27 CST)
• Adaptive tempering floating point exception
  • Stober, Spencer T (Fri Oct 18 2013 - 13:21:03 CDT)
  • Stober, Spencer T (Fri Sep 27 2013 - 09:56:10 CDT)
• Add acetyle and amin Group to peptide
  • Axel Kohlmeyer (Mon Dec 30 2013 - 03:55:11 CST)
  • Alireza Mansouri (Mon Dec 30 2013 - 03:30:19 CST)
• Adding HEME parameters
  • Yarrow Madrona (Sat Mar 09 2013 - 17:54:03 CST)
• Adding hydrogen atoms to the crystall structure
  • Thomas Evangelidis (Tue Feb 18 2014 - 16:04:23 CST)
  • MEHRAN MB (Tue Feb 18 2014 - 15:54:55 CST)
  • Thomas Evangelidis (Tue Feb 18 2014 - 14:56:21 CST)
  • zeynab mohamad hoseyni (Tue Feb 18 2014 - 14:30:00 CST)
  • Thomas Evangelidis (Tue Feb 18 2014 - 10:44:56 CST)
  • MEHRAN MB (Tue Feb 18 2014 - 10:10:53 CST)
  • zeynab mohamad hoseyni (Sun Feb 16 2014 - 09:54:40 CST)
• alchElecLambdaStart (Thermodynamic Integration)
  • Javad Noroozi (Fri Jun 06 2014 - 13:55:28 CDT)
• alchemical free energy simulations with parmtop
  • Jim Phillips (Fri Dec 05 2014 - 14:49:55 CST)
  • hannes.loeffler_at_stfc.ac.uk (Thu Dec 04 2014 - 11:52:49 CST)
  • Jim Phillips (Thu Dec 04 2014 - 11:09:22 CST)
  • hannes.loeffler_at_stfc.ac.uk (Tue Dec 02 2014 - 12:39:41 CST)
  • Jim Phillips (Tue Dec 02 2014 - 12:06:40 CST)
  • Hannes Loeffler (Mon Dec 01 2014 - 03:20:17 CST)
  • Hannes Loeffler (Tue Jun 17 2014 - 04:35:59 CDT)
• Alignment
  • Axel Kohlmeyer (Thu Sep 04 2014 - 07:53:23 CDT)
  • Zeinab Emami (Thu Sep 04 2014 - 07:12:14 CDT)
• All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable.
  • JC Gumbart (Tue Aug 20 2013 - 13:14:27 CDT)
  • Kenno Vanommeslaeghe (Thu Aug 15 2013 - 22:25:07 CDT)
  • Lucas (Thu Aug 15 2013 - 17:26:07 CDT)
  • Paul Rigor (Thu Aug 15 2013 - 11:15:40 CDT)
  • Lucas (Thu Aug 15 2013 - 01:53:22 CDT)
  • Lucas (Wed Aug 14 2013 - 17:09:56 CDT)
  • Lucas (Tue Aug 13 2013 - 13:06:06 CDT)
• Altering extrabonds forces during MD
  • Bryan Roessler (Tue Apr 15 2014 - 09:53:02 CDT)
• Always 24-way SMP?
  • Andrew Pearson (Tue Feb 26 2013 - 08:14:52 CST)
  • Andrew Pearson (Mon Feb 25 2013 - 11:50:13 CST)
  • Andrew Pearson (Mon Feb 25 2013 - 06:28:05 CST)
  • Andrew Pearson (Fri Feb 22 2013 - 12:29:58 CST)
• Amorphous Structure code or builder
  • Rawan Al Nsour (Thu Feb 28 2013 - 14:47:14 CST)
• analysis of simulation output
  • James Starlight (Thu Jun 27 2013 - 13:25:38 CDT)
• Analysis problem (Data vector empty)
  • Stephan Grein (Tue Jul 29 2014 - 04:06:27 CDT)
• analyzing NAMD trajectory with NAMD Energy
  • Axel Kohlmeyer (Mon Jul 29 2013 - 10:42:44 CDT)
  • Markus Dahlgren (Mon Jul 29 2013 - 10:40:54 CDT)
  • Axel Kohlmeyer (Mon Jul 29 2013 - 10:31:22 CDT)
  • Markus Dahlgren (Mon Jul 29 2013 - 10:13:42 CDT)
• angles between residues
  • luca belmonte (Tue Dec 30 2014 - 07:38:14 CST)
• anisotropic pressure control
  • Maxim Igaev (Wed Nov 26 2014 - 05:10:09 CST)
  • Maxim Igaev (Wed Nov 26 2014 - 04:04:49 CST)
  • Maxim Igaev (Wed Nov 26 2014 - 03:47:41 CST)
  • Maxim Igaev (Wed Nov 26 2014 - 02:48:51 CST)
• Annealing of SiO
  • nadia salami (Fri Aug 02 2013 - 23:07:58 CDT)
• Annealing process of silica with excluded block
  • Marzieh Alishahi (Mon Sep 15 2014 - 09:40:21 CDT)
  • Jeff Comer (Mon Sep 15 2014 - 09:30:57 CDT)
  • Marzieh Alishahi (Fri Sep 12 2014 - 10:22:51 CDT)
• Announcement: Hands-On Workshop On Computational Biophysics
  • Danielle Chandler (Wed Dec 17 2014 - 10:24:50 CST)
  • Danielle Chandler (Tue Oct 07 2014 - 11:30:07 CDT)
  • Danielle Chandler (Wed Aug 27 2014 - 13:05:05 CDT)
  • Danielle Chandler (Tue Aug 12 2014 - 09:31:17 CDT)
• Any alternative to colvars for minimization?
  • Giacomo Fiorin (Thu Jun 06 2013 - 08:25:34 CDT)
  • Francesco Pietra (Thu Jun 06 2013 - 01:36:40 CDT)
• apoa1 slow Phase 1
  • Jan Fredin (Thu Aug 15 2013 - 16:25:11 CDT)
• APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
  • Jim Phillips (Thu Nov 13 2014 - 15:47:52 CST)
  • Bin He (Thu Nov 13 2014 - 01:53:42 CST)
• Apply magnetic field through TCLBC
  • Hongbo Du (Mon Mar 03 2014 - 16:23:55 CST)
  • Axel Kohlmeyer (Mon Mar 03 2014 - 11:46:25 CST)
  • Kenno Vanommeslaeghe (Mon Mar 03 2014 - 11:33:06 CST)
  • Hongbo Du (Fri Feb 28 2014 - 11:22:04 CST)
• Apply torque with NAMD
  • Jérôme Hénin (Tue Feb 12 2013 - 07:08:35 CST)
  • George Patargias (Tue Feb 12 2013 - 05:30:28 CST)
• Approaching Deadline December 1st 2013 - Advanced LAMMPS and Scientific Software Development Workshop at ICTP in March 2014
  • Axel Kohlmeyer (Tue Nov 19 2013 - 03:46:45 CST)
• Are coordinates in the tclForces module loaded as wrapped?
  • Salvatore Mario Cosseddu (Tue Apr 16 2013 - 05:12:08 CDT)
• Are random forces applied at every step (when using the langevin thermostat) ?
  • Ajasja LjubetiÄ� (Tue Apr 30 2013 - 10:48:46 CDT)
  • Jérôme Hénin (Mon Apr 29 2013 - 03:58:22 CDT)
  • Ajasja LjubetiÄ� (Fri Apr 26 2013 - 15:21:56 CDT)
• Aron Broom on NVIDIA CUDA Spotlight
  • Devang Sachdev (Wed May 22 2013 - 19:59:11 CDT)
• Asking for Free energy calculation advice
  • Aron Broom (Fri Dec 06 2013 - 11:48:03 CST)
  • Kasra Fattah (Thu Dec 05 2013 - 14:18:20 CST)
• Asking help on results of our GPU benchmark
  • 周文昌 (Tue Dec 23 2014 - 14:05:30 CST)
  • 周文昌 (Mon Dec 22 2014 - 12:11:18 CST)
  • 周文昌 (Fri Dec 19 2014 - 16:06:33 CST)
  • 周文昌 (Thu Dec 18 2014 - 13:24:59 CST)
  • 周文昌 (Wed Dec 17 2014 - 15:13:24 CST)
• Assessing convergence in FEP calculations
  • Gianluca Interlandi (Thu Aug 28 2014 - 14:00:08 CDT)
• Assigning atom serial number after the first 99999 atoms
  • Shyno Mathew (Fri Aug 30 2013 - 11:07:49 CDT)
• Assigning different temperatures to simulation
  • Jhonatam Cordeiro Rodrigues (Thu Apr 03 2014 - 15:24:09 CDT)
  • Jérôme Hénin (Wed Apr 02 2014 - 03:16:30 CDT)
  • Jérôme Hénin (Wed Apr 02 2014 - 02:35:40 CDT)
  • Jhonatam Cordeiro Rodrigues (Wed Apr 02 2014 - 00:42:17 CDT)
  • Jhonatam Cordeiro Rodrigues (Tue Apr 01 2014 - 15:29:36 CDT)
• Assigning Partial Charges to FE in Active Site Superoxide Dismutase.
  • Roy Fernando (Wed Jan 23 2013 - 13:39:04 CST)
• Atom indices in collective variable definition
  • Jérôme Hénin (Fri Sep 06 2013 - 09:56:06 CDT)
  • Aron Broom (Fri Sep 06 2013 - 09:47:30 CDT)
  • Randy J. Zauhar (Fri Sep 06 2013 - 09:40:09 CDT)
• Atom numbering
  • Giacomo Fiorin (Sat Jun 22 2013 - 10:41:35 CDT)
  • Felipe Merino (Sat Jun 22 2013 - 05:34:53 CDT)
• Atom selection in Tcl Force script with Amber partop file
  • Daniel Torrente (Fri Aug 15 2014 - 18:21:23 CDT)
  • Daniel Torrente (Fri Aug 15 2014 - 19:01:23 CDT)
  • Maxim Belkin (Fri Aug 15 2014 - 18:33:18 CDT)
  • Daniel Torrente (Fri Aug 15 2014 - 18:25:23 CDT)
  • Maxim Belkin (Fri Aug 15 2014 - 16:48:12 CDT)
  • Daniel Torrente (Fri Aug 15 2014 - 12:25:49 CDT)
• Atomselect for coor, vel, xsc
  • Kevin C Chan (Fri Nov 21 2014 - 04:20:16 CST)
  • Axel Kohlmeyer (Fri Nov 14 2014 - 09:02:47 CST)
  • Josh Vermaas (Fri Nov 14 2014 - 08:58:29 CST)
  • Kevin C Chan (Thu Nov 13 2014 - 22:49:02 CST)
• atomselect option for extracting protein-ligand complex
  • Axel Kohlmeyer (Mon Feb 17 2014 - 16:22:38 CST)
  • KK R (Mon Feb 17 2014 - 16:16:43 CST)
• automatic extraction of RMSD values of the heavy atoms of residues from NAMD output?
  • Maxim Belkin (Mon Aug 04 2014 - 11:25:15 CDT)
  • Andras Borosy (Mon Aug 04 2014 - 05:32:53 CDT)
• autopsf (patch)
  • Cenk Denktas (Tue Jul 15 2014 - 12:41:48 CDT)
• AW:
  • flavio seixas (Wed Nov 26 2014 - 09:53:23 CST)
  • Norman Geist (Wed Nov 26 2014 - 02:26:35 CST)
  • Norman Geist (Thu Feb 20 2014 - 00:41:55 CST)
  • Norman Geist (Fri Jun 21 2013 - 03:11:07 CDT)
  • Titis Sekar Humani (Fri Feb 22 2013 - 00:57:11 CST)
  • Norman Geist (Fri Feb 22 2013 - 00:49:17 CST)
• AW: "Beefier" benchmark
  • Maxime Boissonneault (Wed Aug 20 2014 - 09:20:15 CDT)
  • Norman Geist (Wed Aug 20 2014 - 01:38:51 CDT)
• AW: 50% system CPU usage when parallel running NAMD on Rocks cluster
  • Norman Geist (Wed Dec 18 2013 - 02:06:09 CST)
  • Norman Geist (Mon Dec 16 2013 - 01:08:54 CST)
  • Norman Geist (Mon Dec 16 2013 - 01:07:28 CST)
  • Norman Geist (Tue Dec 10 2013 - 08:19:45 CST)
  • Norman Geist (Mon Dec 09 2013 - 01:19:28 CST)
  • Norman Geist (Tue Dec 03 2013 - 08:47:54 CST)
• AW: [SOLVED] Charmrun> error x attaching to node
  • Norman Geist (Tue Apr 30 2013 - 07:09:22 CDT)
• AW: A larger protein data bank for performance benchmark
  • Norman Geist (Tue May 14 2013 - 10:30:08 CDT)
  • linux freaker (Tue May 14 2013 - 01:30:42 CDT)
  • linux freaker (Tue May 14 2013 - 01:28:23 CDT)
  • linux freaker (Tue May 14 2013 - 00:58:52 CDT)
  • Norman Geist (Tue May 14 2013 - 00:46:34 CDT)
• AW: a problem about pbc in a namd trajectory
  • Norman Geist (Mon Aug 26 2013 - 03:44:14 CDT)
• AW: About Bond Deletion
  • Norman Geist (Thu Apr 11 2013 - 00:57:43 CDT)
• AW: About Constraint Failure
  • Norman Geist (Wed Oct 16 2013 - 00:31:03 CDT)
• AW: About NAMD
  • Douglas Houston (Wed Nov 26 2014 - 05:28:39 CST)
  • Norman Geist (Wed Nov 19 2014 - 01:10:11 CST)
• AW: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable.
  • Norman Geist (Fri Aug 16 2013 - 00:22:44 CDT)
  • Norman Geist (Thu Aug 15 2013 - 02:12:58 CDT)
  • Norman Geist (Thu Aug 15 2013 - 00:50:54 CDT)
  • Norman Geist (Wed Aug 14 2013 - 00:41:31 CDT)
• AW: Always 24-way SMP?
  • Norman Geist (Wed Feb 27 2013 - 01:53:27 CST)
  • Norman Geist (Tue Feb 26 2013 - 00:27:27 CST)
  • Norman Geist (Mon Feb 25 2013 - 09:06:05 CST)
  • Norman Geist (Mon Feb 25 2013 - 00:55:26 CST)
• AW: anisotropic pressure control
  • Norman Geist (Wed Nov 26 2014 - 05:04:20 CST)
  • Norman Geist (Wed Nov 26 2014 - 03:22:31 CST)
• AW: Any alternative to colvars for minimization?
  • Jérôme Hénin (Thu Jun 06 2013 - 05:07:25 CDT)
  • Norman Geist (Thu Jun 06 2013 - 02:27:26 CDT)
• AW: apoa1 slow Phase 1
  • Norman Geist (Fri Aug 16 2013 - 00:32:09 CDT)
• AW: Are random forces applied at every step (when using the langevin thermostat) ?
  • Norman Geist (Mon Apr 29 2013 - 01:55:37 CDT)
• AW: Asking help on results of our GPU benchmark
  • Norman Geist (Tue Dec 23 2014 - 02:34:58 CST)
  • Norman Geist (Mon Dec 22 2014 - 01:16:12 CST)
  • Norman Geist (Fri Dec 19 2014 - 00:30:22 CST)
  • Norman Geist (Thu Dec 18 2014 - 02:39:51 CST)
• AW: Assigning different temperatures to simulation
  • Norman Geist (Wed Apr 02 2014 - 02:45:57 CDT)
  • Norman Geist (Wed Apr 02 2014 - 00:06:08 CDT)
  • Norman Geist (Wed Apr 02 2014 - 00:02:58 CDT)
• AW: Assigning Partial Charges to FE in Active Site Superoxide Dismutase.
  • Norman Geist (Thu Jan 24 2013 - 01:23:18 CST)
• AW: AW: "Beefier" benchmark
  • Maxime Boissonneault (Thu Aug 21 2014 - 07:32:10 CDT)
  • Norman Geist (Thu Aug 21 2014 - 03:04:01 CDT)
• AW: AW: AW: "Beefier" benchmark
  • Maxime Boissonneault (Thu Aug 21 2014 - 09:04:42 CDT)
  • Norman Geist (Thu Aug 21 2014 - 08:43:05 CDT)
• AW: AW: AW: AW: AW: Using nodelist file causes namd to hang
  • Norman Geist (Thu Jun 19 2014 - 05:09:43 CDT)
• AW: AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process.
  • Maxime Boissonneault (Mon Aug 25 2014 - 07:34:34 CDT)
  • Norman Geist (Mon Aug 25 2014 - 01:07:21 CDT)
• AW: AW: AW: AW: Using nodelist file causes namd to hang
  • Douglas Houston (Thu Jun 19 2014 - 04:56:28 CDT)
  • Norman Geist (Thu Jun 19 2014 - 02:19:03 CDT)
• AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process.
  • Maxime Boissonneault (Fri Aug 22 2014 - 08:59:26 CDT)
  • Norman Geist (Fri Aug 22 2014 - 08:56:32 CDT)
• AW: AW: AW: Hybrid MPI + Multicore + Cuda build
  • Norman Geist (Fri Aug 15 2014 - 00:39:36 CDT)
• AW: AW: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast"
  • eprates_at_iqm.unicamp.br (Wed Nov 06 2013 - 11:17:19 CST)
  • Norman Geist (Tue Nov 05 2013 - 03:04:53 CST)
• AW: AW: AW: pbc error
  • Norman Geist (Tue Sep 03 2013 - 04:55:03 CDT)
• AW: AW: AW: Using nodelist file causes namd to hang
  • Douglas Houston (Thu Aug 28 2014 - 07:54:30 CDT)
  • Norman Geist (Thu Aug 28 2014 - 06:08:47 CDT)
  • Norman Geist (Tue Jun 24 2014 - 08:50:06 CDT)
  • Norman Geist (Wed Jun 18 2014 - 07:52:29 CDT)
  • Douglas Houston (Wed Jun 18 2014 - 07:57:59 CDT)
  • Norman Geist (Wed Apr 09 2014 - 07:09:53 CDT)
  • Norman Geist (Tue Apr 08 2014 - 07:30:15 CDT)
• AW: AW: benchmark info
  • Norman Geist (Fri Mar 07 2014 - 01:40:25 CST)
• AW: AW: charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program"
  • Norman Geist (Mon Dec 02 2013 - 05:27:37 CST)
• AW: AW: Coarse-Grained fatal error!
  • Norman Geist (Mon May 06 2013 - 01:09:08 CDT)
• AW: AW: CUDA problem?
  • Norman Geist (Thu Jan 17 2013 - 00:01:27 CST)
  • Ajasja LjubetiÄ� (Wed Jan 16 2013 - 10:04:02 CST)
  • Norman Geist (Wed Jan 16 2013 - 00:21:57 CST)
  • Eric Hill (Tue Jan 15 2013 - 01:12:53 CST)
• AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process.
  • Maxime Boissonneault (Fri Aug 22 2014 - 08:22:43 CDT)
  • Norman Geist (Fri Aug 22 2014 - 08:21:25 CDT)
• AW: AW: hi every body,
  • Kenno Vanommeslaeghe (Thu Aug 22 2013 - 22:30:11 CDT)
  • Norman Geist (Thu Aug 22 2013 - 04:39:38 CDT)
• AW: AW: How to refer to side-chain via tcl-force scripting?
  • zeynab mohamad hoseyni (Mon Jun 16 2014 - 11:20:46 CDT)
  • zeynab mohamad hoseyni (Sat Jun 14 2014 - 09:03:09 CDT)
  • Tristan Croll (Sat Jun 14 2014 - 01:09:39 CDT)
  • zeynab mohamad hoseyni (Fri Jun 13 2014 - 23:01:42 CDT)
  • Norman Geist (Fri Jun 13 2014 - 03:26:33 CDT)
• AW: AW: Hybrid MPI + Multicore + Cuda build
  • Maxime Boissonneault (Thu Aug 14 2014 - 11:53:16 CDT)
  • Norman Geist (Thu Aug 14 2014 - 08:14:30 CDT)
• AW: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast"
  • eprates_at_iqm.unicamp.br (Mon Nov 04 2013 - 09:59:14 CST)
  • Norman Geist (Mon Nov 04 2013 - 09:02:04 CST)
• AW: AW: Minimisation of protein in a water box
  • Norman Geist (Mon Apr 22 2013 - 01:22:48 CDT)
• AW: AW: NAMD and NUMA
  • Kenno Vanommeslaeghe (Fri May 09 2014 - 11:45:09 CDT)
  • Norman Geist (Fri May 09 2014 - 02:11:19 CDT)
• AW: AW: Question to NAMD source
  • Jim Phillips (Mon Sep 08 2014 - 08:43:00 CDT)
  • Norman Geist (Mon Sep 08 2014 - 04:40:10 CDT)
  • Norman Geist (Mon Sep 08 2014 - 01:19:49 CDT)
• AW: AW: smd simulation
  • Norman Geist (Thu Feb 28 2013 - 03:10:01 CST)
• AW: AW: Using nodelist file causes namd to hang
  • Douglas Houston (Thu Aug 28 2014 - 05:43:48 CDT)
  • Norman Geist (Thu Aug 28 2014 - 02:47:58 CDT)
  • Douglas Houston (Tue Jun 24 2014 - 08:42:20 CDT)
  • Norman Geist (Fri Jun 20 2014 - 05:15:02 CDT)
  • Douglas Houston (Wed Jun 18 2014 - 07:24:00 CDT)
  • Norman Geist (Mon Jun 16 2014 - 02:19:28 CDT)
  • Douglas Houston (Mon Jun 02 2014 - 04:50:40 CDT)
  • Douglas Houston (Wed Apr 09 2014 - 06:16:35 CDT)
  • Norman Geist (Wed Apr 09 2014 - 05:53:50 CDT)
  • Douglas Houston (Tue Apr 08 2014 - 07:13:42 CDT)
  • Norman Geist (Tue Apr 08 2014 - 06:22:41 CDT)
• AW: AW: vmd-l: Occupancy maps
  • Norman Geist (Tue Aug 13 2013 - 03:28:25 CDT)
  • Norman Geist (Mon Aug 12 2013 - 01:47:30 CDT)
• AW: AW: Xeon vs i7 and ECC vs SDRAM
  • Norman Geist (Thu Jun 26 2014 - 00:59:13 CDT)
  • Norman Geist (Wed Jun 25 2014 - 01:47:38 CDT)
• AW: benchmark info
  • Norman Geist (Fri Feb 28 2014 - 01:18:46 CST)
• AW: BUG: TCL coorfile command
  • Norman Geist (Mon Dec 02 2013 - 01:43:41 CST)
• AW: Build polymer from monomer
  • Sindu (Fri Apr 26 2013 - 01:22:46 CDT)
  • Norman Geist (Fri Apr 26 2013 - 01:07:13 CDT)
• AW: Building crystal polymer
  • Norman Geist (Fri May 17 2013 - 07:39:30 CDT)
• AW: Bulk properties of polymers
  • Sindu (Wed May 08 2013 - 03:46:35 CDT)
  • Axel Kohlmeyer (Wed May 08 2013 - 03:39:25 CDT)
  • Sindu (Wed May 08 2013 - 02:33:18 CDT)
  • Norman Geist (Wed May 08 2013 - 02:13:56 CDT)
• AW: C++ API
  • Norman Geist (Thu Jun 20 2013 - 01:01:53 CDT)
• AW: Can I define a simulation box but turn off the PBC at the same time?
  • Jérôme Hénin (Mon May 13 2013 - 03:17:29 CDT)
  • Norman Geist (Mon May 13 2013 - 00:22:55 CDT)
• AW: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact?
  • Norman Geist (Wed Mar 20 2013 - 02:47:06 CDT)
• AW: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact?
  • Norman Geist (Tue Mar 19 2013 - 10:18:35 CDT)
• AW: catdcd error
  • Norman Geist (Mon Aug 19 2013 - 08:53:59 CDT)
• AW: catdcd output and .psf file atom count mismatch
  • Norman Geist (Tue May 07 2013 - 00:47:33 CDT)
• AW: cell origin problem
  • Norman Geist (Thu Sep 26 2013 - 00:59:57 CDT)
  • Norman Geist (Wed Sep 25 2013 - 00:44:46 CDT)
• AW: charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program"
  • Frank Thommen (Mon Dec 02 2013 - 04:07:42 CST)
  • Norman Geist (Mon Dec 02 2013 - 02:05:24 CST)
• AW: charm-gui membrane builder
  • Norman Geist (Mon Sep 16 2013 - 09:16:41 CDT)
• AW: Coarse-Grained fatal error!
  • Norman Geist (Fri May 03 2013 - 00:25:54 CDT)
• AW: Coarse-grained reverse transformation
  • Norman Geist (Mon May 13 2013 - 00:43:00 CDT)
• AW: Colvar cannot be ran on supercomputer newton
  • Branko (Wed Aug 07 2013 - 11:25:38 CDT)
  • Branko (Wed Aug 07 2013 - 03:04:23 CDT)
  • Norman Geist (Wed Aug 07 2013 - 02:18:25 CDT)
  • Norman Geist (Tue Aug 06 2013 - 09:57:32 CDT)
• AW: Constraint failure in RATTLE
  • Norman Geist (Tue Apr 01 2014 - 00:11:28 CDT)
  • Norman Geist (Mon Mar 31 2014 - 00:43:09 CDT)
• AW: Constraint failure in RATTLE algorithm
  • Norman Geist (Thu Jun 19 2014 - 02:29:16 CDT)
• AW: converting dcd files to netcdf or ascii
  • Norman Geist (Thu Feb 28 2013 - 09:05:59 CST)
• AW: Coordinate vs. time plots
  • Norman Geist (Thu Mar 21 2013 - 01:49:37 CDT)
• AW: coordinates in namd
  • Norman Geist (Tue Jun 03 2014 - 01:40:14 CDT)
• AW: Coordinates of Carbon atoms on Graphite
  • Norman Geist (Thu Sep 26 2013 - 00:45:38 CDT)
  • Norman Geist (Wed Sep 25 2013 - 09:16:24 CDT)
  • Norman Geist (Wed Sep 25 2013 - 08:35:15 CDT)
  • Norman Geist (Wed Sep 25 2013 - 00:49:32 CDT)
• AW: CUDA error in cuda_check_local_progress
  • Norman Geist (Tue Apr 22 2014 - 00:39:49 CDT)
  • Norman Geist (Thu Apr 17 2014 - 04:50:10 CDT)
  • Norman Geist (Thu Apr 17 2014 - 03:21:44 CDT)
• AW: DCD writing error on cluster
  • Norman Geist (Mon Jun 10 2013 - 00:48:28 CDT)
• AW: Dihedrals multiplicity!
  • Kenno Vanommeslaeghe (Thu Feb 20 2014 - 10:35:55 CST)
  • Kenno Vanommeslaeghe (Tue Feb 18 2014 - 20:12:14 CST)
  • Anna Borlsky (Tue Feb 18 2014 - 03:11:42 CST)
  • Kenno Vanommeslaeghe (Mon Feb 17 2014 - 12:44:19 CST)
  • hannes.loeffler_at_stfc.ac.uk (Mon Feb 17 2014 - 11:43:47 CST)
  • Kenno Vanommeslaeghe (Mon Feb 17 2014 - 10:56:29 CST)
  • Kenno Vanommeslaeghe (Sun Feb 16 2014 - 12:45:16 CST)
  • hannes.loeffler_at_stfc.ac.uk (Sun Feb 16 2014 - 02:34:16 CST)
  • Kenno Vanommeslaeghe (Sat Feb 15 2014 - 22:15:33 CST)
  • Anna Borlsky (Sat Feb 15 2014 - 11:51:16 CST)
  • Kenno Vanommeslaeghe (Sat Feb 15 2014 - 11:30:42 CST)
  • Anna Borlsky (Sat Feb 15 2014 - 04:34:49 CST)
  • Kenno Vanommeslaeghe (Thu Feb 13 2014 - 19:48:12 CST)
  • Kenno Vanommeslaeghe (Thu Feb 13 2014 - 17:53:49 CST)
  • Norman Geist (Thu Feb 13 2014 - 14:23:52 CST)
• AW: DNA surrounded by a shell of water in a big box with vacuum
  • Norman Geist (Tue Jan 15 2013 - 00:39:59 CST)
• AW: Does MOLLY really retain bond motion for water?
  • Norman Geist (Mon Jun 03 2013 - 00:43:15 CDT)
• AW: Drifting water molecules
  • Axel Kohlmeyer (Thu Nov 28 2013 - 04:17:47 CST)
  • Norman Geist (Thu Nov 28 2013 - 02:59:56 CST)
• AW: Error
  • Norman Geist (Thu Oct 17 2013 - 00:38:22 CDT)
• AW: Error in distributing the cores for a single processor
  • Norman Geist (Thu Apr 11 2013 - 01:20:57 CDT)
• AW: Error on write to binary file
  • Norman Geist (Tue Dec 23 2014 - 02:42:04 CST)
• AW: ERROR: Constraint failure in RATTLE algorithm for atom 593!
  • Norman Geist (Mon Feb 04 2013 - 09:33:08 CST)
• AW: explicit NVT simulation
  • Norman Geist (Mon Sep 09 2013 - 01:26:14 CDT)
• AW: Exploding vdW energies in automatically generated POPC membranes
  • Norman Geist (Tue May 07 2013 - 00:17:36 CDT)
  • Norman Geist (Tue May 07 2013 - 00:16:20 CDT)
• AW: Extract KE, PE and total energy from log file
  • Norman Geist (Mon Nov 04 2013 - 01:13:05 CST)
• AW: Fatal error..
  • Norman Geist (Mon Jun 23 2014 - 03:33:27 CDT)
• AW: FATAL ERROR: error parsing config file while executing <feff>
  • Jim Phillips (Mon Nov 10 2014 - 16:00:19 CST)
  • Jim Phillips (Mon Nov 10 2014 - 15:44:39 CST)
  • Norman Geist (Mon Nov 10 2014 - 08:20:48 CST)
  • Norman Geist (Mon Nov 10 2014 - 00:56:24 CST)
• AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory
  • Douglas Houston (Fri Dec 19 2014 - 08:40:04 CST)
  • Maxime Boissonneault (Fri Dec 19 2014 - 08:18:38 CST)
  • Douglas Houston (Fri Dec 19 2014 - 02:12:48 CST)
  • Norman Geist (Fri Dec 19 2014 - 00:35:26 CST)
• AW: FEP on an amino acid ligand
  • Norman Geist (Wed Jan 23 2013 - 01:21:09 CST)
  • Norman Geist (Tue Jan 22 2013 - 00:28:38 CST)
• AW: First meeting with NAMD
  • Norman Geist (Mon Jun 10 2013 - 00:35:06 CDT)
  • Norman Geist (Thu Jun 06 2013 - 02:23:05 CDT)
  • Norman Geist (Tue Jun 04 2013 - 02:16:18 CDT)
• AW: Fixed and SMD atoms
  • Norman Geist (Tue Oct 22 2013 - 03:37:09 CDT)
  • Norman Geist (Mon Oct 21 2013 - 01:37:28 CDT)
• AW: fixed atom/Constraint failure in RATTLE algorithm/
  • Norman Geist (Tue Jun 04 2013 - 02:01:10 CDT)
  • Norman Geist (Mon Jun 03 2013 - 00:23:43 CDT)
• AW: Fixing atoms while equilibration
  • Norman Geist (Mon Sep 01 2014 - 02:26:11 CDT)
• AW: floating point reproduceability
  • Norman Geist (Fri Apr 19 2013 - 02:09:33 CDT)
  • Norman Geist (Thu Apr 18 2013 - 02:15:11 CDT)
• AW: GPU/CPU workstation optimal simulation parameters for NAMD2.9 performance
  • Norman Geist (Wed Feb 19 2014 - 01:38:53 CST)
• AW: GPUs silently stop working during simulation when oversubscribed
  • Norman Geist (Thu Feb 28 2013 - 05:41:04 CST)
  • Norman Geist (Thu Feb 28 2013 - 03:21:00 CST)
• AW: H-bonds cutoff angle criterian
  • Norman Geist (Sun Jan 20 2013 - 23:46:48 CST)
• AW: H-bonds cutoff angle criterian. .
  • Anurag Sharma (Mon Jan 21 2013 - 01:11:46 CST)
  • Martin, Erik W (Mon Jan 21 2013 - 01:07:11 CST)
• AW: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!"
  • Norman Geist (Tue May 21 2013 - 01:02:42 CDT)
• AW: hi every body,
  • Norman Geist (Thu Aug 22 2013 - 02:16:39 CDT)
• AW: how to apply force SMD method on an anisotropic geometry
  • Anurag Sharma (Fri Jun 21 2013 - 20:38:47 CDT)
  • Anurag Sharma (Thu Jun 13 2013 - 09:41:24 CDT)
  • Jérôme Hénin (Thu Jun 13 2013 - 02:54:42 CDT)
  • Norman Geist (Thu Jun 13 2013 - 01:56:48 CDT)
• AW: how to do a vacuum minimization without electrostatics and periodic boundary conditions?
  • Norman Geist (Thu Jun 06 2013 - 02:12:01 CDT)
• AW: How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory
  • Norman Geist (Tue Apr 29 2014 - 02:21:20 CDT)
  • Norman Geist (Tue Apr 29 2014 - 02:20:33 CDT)
• AW: how to get cell vectors in tcl forces script
  • Norman Geist (Thu Mar 13 2014 - 08:34:58 CDT)
  • Norman Geist (Wed Mar 12 2014 - 09:59:12 CDT)
  • Norman Geist (Wed Mar 12 2014 - 07:54:50 CDT)
  • Norman Geist (Wed Mar 12 2014 - 02:29:43 CDT)
• AW: How to refer to side-chain via tcl-force scripting?
  • zeynab mohamad hoseyni (Fri Jun 13 2014 - 03:21:08 CDT)
  • Norman Geist (Fri Jun 13 2014 - 02:56:03 CDT)
  • Norman Geist (Fri Jun 13 2014 - 02:53:41 CDT)
• AW: Hybrid MPI + Multicore + Cuda build
  • Maxime Boissonneault (Thu Aug 14 2014 - 07:19:37 CDT)
  • Norman Geist (Thu Aug 14 2014 - 02:13:32 CDT)
• AW: ibverb&&smp build NAMD
  • Norman Geist (Mon Sep 01 2014 - 02:17:13 CDT)
  • Norman Geist (Thu Aug 28 2014 - 05:25:13 CDT)
• AW: inconsistency between "Benchmark" and "Timing" output
  • Norman Geist (Tue Nov 26 2013 - 01:08:31 CST)
• AW: information about simulation speed
  • Norman Geist (Wed Dec 03 2014 - 02:31:26 CST)
• AW: Job script for multi node job
  • Norman Geist (Fri Feb 14 2014 - 06:03:47 CST)
  • Norman Geist (Fri Feb 14 2014 - 05:12:56 CST)
• AW: keeping Crystal angles constant
  • Norman Geist (Thu Jan 16 2014 - 02:36:51 CST)
  • Norman Geist (Thu Jan 16 2014 - 02:13:08 CST)
• AW: LES very slow
  • Norman Geist (Tue Mar 12 2013 - 01:51:40 CDT)
  • Norman Geist (Thu Mar 07 2013 - 00:47:59 CST)
  • Norman Geist (Wed Mar 06 2013 - 01:03:39 CST)
  • Norman Geist (Tue Mar 05 2013 - 00:08:42 CST)
  • Norman Geist (Mon Mar 04 2013 - 01:27:27 CST)
  • Norman Geist (Thu Feb 28 2013 - 00:37:07 CST)
  • Norman Geist (Wed Feb 27 2013 - 01:19:51 CST)
  • Norman Geist (Tue Feb 26 2013 - 00:42:30 CST)
• AW: Link between simulations
  • Norman Geist (Wed Apr 24 2013 - 02:09:13 CDT)
  • Norman Geist (Mon Apr 22 2013 - 01:34:43 CDT)
• AW: Loading Velocity DCD file
  • Norman Geist (Thu Dec 18 2014 - 02:31:16 CST)
• AW: Log file is not being updated
  • Norman Geist (Mon Feb 10 2014 - 07:32:10 CST)
  • Norman Geist (Mon Feb 10 2014 - 06:42:06 CST)
• AW: making patch
  • Norman Geist (Wed Aug 28 2013 - 02:46:00 CDT)
• AW: Martini RBCG simulation frequently crashing with "atoms moving too fast"
  • eprates_at_iqm.unicamp.br (Mon Nov 04 2013 - 08:42:53 CST)
  • Norman Geist (Mon Nov 04 2013 - 01:17:46 CST)
• AW: MD crashes at 300K after warm up MD
  • Norman Geist (Wed Mar 20 2013 - 02:36:02 CDT)
• AW: Minimisation of protein in a water box
  • Rajan Vatassery (Fri Apr 19 2013 - 18:18:28 CDT)
  • Norman Geist (Fri Apr 19 2013 - 02:03:15 CDT)
  • Norman Geist (Tue Apr 16 2013 - 01:31:31 CDT)
• AW: Movie of a channel trajectory
  • Norman Geist (Mon Apr 07 2014 - 02:05:25 CDT)
• AW: moving out of the box
  • Ariel Talavera Perez (Thu Feb 20 2014 - 07:48:07 CST)
  • MEHRAN MB (Mon Feb 17 2014 - 11:48:44 CST)
  • Ariel Talavera Perez (Mon Feb 17 2014 - 06:51:36 CST)
  • Ariel Talavera Perez (Mon Feb 17 2014 - 04:39:29 CST)
  • Felipe Merino (Sat Feb 15 2014 - 04:50:15 CST)
  • Aron Broom (Fri Feb 14 2014 - 13:25:54 CST)
  • Kenno Vanommeslaeghe (Fri Feb 14 2014 - 13:15:37 CST)
  • Aaron Larsen (Fri Feb 14 2014 - 09:10:36 CST)
  • Ariel Talavera Perez (Fri Feb 14 2014 - 08:38:01 CST)
  • Norman Geist (Thu Feb 13 2014 - 14:24:53 CST)
  • Norman Geist (Thu Feb 13 2014 - 14:21:26 CST)
• AW: Mysterious slow down in parallel
  • Norman Geist (Mon Oct 28 2013 - 01:50:58 CDT)
• AW: NAMD 2.10 Manual
  • Norman Geist (Fri Aug 22 2014 - 08:46:07 CDT)
• AW: NAMD 2.10b1 CUDA PME offload
  • Norman Geist (Tue Aug 26 2014 - 10:24:50 CDT)
• AW: NAMD 2.9 CUDA compilation
  • Norman Geist (Tue Mar 12 2013 - 02:53:06 CDT)
  • Norman Geist (Tue Mar 12 2013 - 01:57:00 CDT)
• AW: NAMD 2.9 install on CLuster mpirun/charmrun with ibverb version ?
  • Norman Geist (Thu Nov 14 2013 - 06:43:49 CST)
• AW: namd 2.9 tip4p-2005
  • Norman Geist (Wed Jan 16 2013 - 00:01:40 CST)
• AW: NAMD and NUMA
  • Kenno Vanommeslaeghe (Mon May 12 2014 - 12:06:53 CDT)
  • Norman Geist (Mon May 12 2014 - 01:12:54 CDT)
  • Joseph Farran (Thu May 08 2014 - 11:33:25 CDT)
  • Joseph Farran (Thu May 08 2014 - 11:28:46 CDT)
  • Norman Geist (Thu May 08 2014 - 01:53:12 CDT)
• AW: NAMD CUDA performance
  • Norman Geist (Wed Sep 11 2013 - 01:53:54 CDT)
• AW: NAMD error LInux 3.11.10-21-desktop kernel AMD opternon 6272
  • Norman Geist (Thu Nov 06 2014 - 01:43:36 CST)
• AW: NAMD Multicore CUDA usage
  • Norman Geist (Tue Jun 10 2014 - 02:33:13 CDT)
• AW: NAMD PERFORMANCE ON NVIDIA K20 GPU
  • Kenno Vanommeslaeghe (Tue Sep 17 2013 - 18:42:55 CDT)
  • Norman Geist (Mon Sep 16 2013 - 02:05:34 CDT)
• AW: NAMD related
  • Norman Geist (Mon Jun 10 2013 - 10:24:11 CDT)
• AW: namd scale-up
  • Norman Geist (Fri Sep 06 2013 - 02:09:19 CDT)
  • Norman Geist (Thu Sep 05 2013 - 08:55:10 CDT)
  • Norman Geist (Thu Sep 05 2013 - 07:58:23 CDT)
  • Norman Geist (Thu Sep 05 2013 - 01:32:45 CDT)
• AW: NAMD with Intel Xeon Phi coprocessors ?
  • Norman Geist (Mon Mar 11 2013 - 02:05:28 CDT)
• AW: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation??
  • Norman Geist (Tue Jun 10 2014 - 02:43:11 CDT)
• AW: NAMD-SMP-Ibverbs-CUDA assistance
  • Norman Geist (Wed May 14 2014 - 00:42:51 CDT)
• AW: NAMD/VMD installation on Linux Clusters with InfiniBand
  • Norman Geist (Thu May 30 2013 - 05:14:55 CDT)
  • Norman Geist (Thu May 23 2013 - 01:24:51 CDT)
• AW: NAMD2.9 single-node benchmarks, 0-2 Kepler GPU's.
  • Norman Geist (Thu May 02 2013 - 01:13:08 CDT)
• AW: NAMD_2.9_Linux-x86_64-ibverbs RUNS on QueenBee RUN TIME VARIATION
  • Norman Geist (Tue Nov 19 2013 - 09:07:42 CST)
• AW: NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults
  • Norman Geist (Wed Jun 11 2014 - 03:07:21 CDT)
• AW: NamdMemoryReduction - genCompressedPsf
  • Norman Geist (Fri Mar 22 2013 - 02:28:53 CDT)
  • Norman Geist (Tue Mar 19 2013 - 02:50:33 CDT)
  • Norman Geist (Tue Mar 12 2013 - 01:58:11 CDT)
  • Norman Geist (Mon Mar 11 2013 - 01:56:40 CDT)
  • Norman Geist (Fri Mar 08 2013 - 01:04:34 CST)
• AW: NBFIX 1-4 scaling term ignored for CHARMM format parameters
  • Kenno Vanommeslaeghe (Thu Aug 08 2013 - 11:16:59 CDT)
  • Norman Geist (Thu Aug 08 2013 - 00:27:43 CDT)
• AW: Nvidia GPUs
  • Norman Geist (Wed Aug 21 2013 - 03:22:12 CDT)
• AW: parallel code in tclforce script
  • Norman Geist (Thu Sep 05 2013 - 01:45:08 CDT)
• AW: paricle type in residue based coarse graining of NAMD
  • Norman Geist (Tue Jun 24 2014 - 03:13:21 CDT)
• AW: Pass a runtime parameter into the configuration file
  • Norman Geist (Wed Oct 16 2013 - 00:45:18 CDT)
• AW: pbc error
  • Norman Geist (Mon Sep 02 2013 - 01:44:18 CDT)
• AW: Percentage of Residues in Ramachandran Plot regions versus time of trajectory
  • Norman Geist (Tue Jan 29 2013 - 08:27:01 CST)
  • Norman Geist (Mon Jan 28 2013 - 00:08:17 CST)
• AW: problem in solvating a graphene layer created using VMD-nanotube builder
  • Norman Geist (Tue Mar 05 2013 - 00:18:44 CST)
• AW: problem with ptch ...
  • Norman Geist (Tue Aug 27 2013 - 03:40:58 CDT)
• AW: Problem with replica exchange
  • Norman Geist (Tue Dec 17 2013 - 05:43:32 CST)
• AW: problem with runiing namd through infiniband
  • Norman Geist (Fri May 31 2013 - 01:04:09 CDT)
  • Norman Geist (Thu May 30 2013 - 05:05:59 CDT)
  • Norman Geist (Wed May 29 2013 - 00:22:58 CDT)
• AW: Protein unfolding and Coarse grained
  • Norman Geist (Fri May 17 2013 - 07:41:17 CDT)
• AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs
  • Aron Broom (Sun Dec 15 2013 - 00:51:33 CST)
  • Norman Geist (Fri Dec 13 2013 - 01:43:43 CST)
  • Norman Geist (Fri Dec 13 2013 - 00:47:03 CST)
  • dbaogen (Thu Dec 12 2013 - 23:58:49 CST)
  • Aron Broom (Thu Dec 12 2013 - 19:25:58 CST)
  • dbaogen (Thu Dec 12 2013 - 19:02:30 CST)
  • Norman Geist (Tue Dec 10 2013 - 08:18:03 CST)
• AW: question about '+devices'
  • Norman Geist (Wed Oct 08 2014 - 02:13:08 CDT)
• AW: Question about accelerated MD
  • Ryan McGreevy (Wed Mar 26 2014 - 11:19:17 CDT)
  • Mare Libero (Wed Mar 26 2014 - 11:35:38 CDT)
  • Thomas Evangelidis (Wed Mar 26 2014 - 10:36:51 CDT)
  • Mare Libero (Wed Mar 26 2014 - 10:12:13 CDT)
  • Norman Geist (Wed Mar 26 2014 - 02:34:20 CDT)
• AW: question about CUDA-enabled
  • Norman Geist (Mon Dec 01 2014 - 02:56:08 CST)
  • Norman Geist (Mon Dec 01 2014 - 02:05:20 CST)
• AW: Question about how much used from CPU?
  • Norman Geist (Tue Nov 19 2013 - 03:06:14 CST)
• AW: Question about loading velocity files on VMD
  • Norman Geist (Sun Aug 11 2013 - 23:48:35 CDT)
• AW: Question regarding reverse CG to all-atom
  • Norman Geist (Tue Jan 21 2014 - 06:18:10 CST)
• AW: Question to NAMD source
  • Jim Phillips (Fri Sep 05 2014 - 14:34:55 CDT)
  • Norman Geist (Fri Sep 05 2014 - 01:32:29 CDT)
• AW: questions regarding the source code in NAMD
  • Norman Geist (Fri Aug 23 2013 - 06:59:34 CDT)
• AW: RATTLE algorithm
  • Norman Geist (Wed Feb 27 2013 - 01:24:05 CST)
  • Norman Geist (Tue Feb 26 2013 - 00:38:53 CST)
• AW: rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs
  • Norman Geist (Mon Oct 14 2013 - 01:15:13 CDT)
• AW: recent comparison of NAMD to other MD engines
  • Norman Geist (Fri Jan 24 2014 - 13:22:51 CST)
  • Norman Geist (Fri Jan 24 2014 - 01:01:04 CST)
  • Norman Geist (Thu Jan 23 2014 - 01:32:54 CST)
• AW: Reg: deformation of water box during equilibration
  • Norman Geist (Tue Jun 10 2014 - 02:23:04 CDT)
• AW: Reg: minimization
  • Norman Geist (Thu Sep 25 2014 - 05:23:26 CDT)
• AW: Reg: movement of protein outside box
  • Norman Geist (Fri Jun 13 2014 - 03:09:20 CDT)
  • Norman Geist (Tue Jun 10 2014 - 07:26:58 CDT)
  • Norman Geist (Tue Jun 10 2014 - 02:47:32 CDT)
• AW: Reg: QM/MM calculations in NAMD
  • Norman Geist (Mon Nov 10 2014 - 08:12:44 CST)
• AW: Regarding installing Namd 2.9 on windows xp 32 bit system
  • Norman Geist (Wed Feb 27 2013 - 01:30:58 CST)
• AW: Regarding NAMD and MD simulations
  • Joel Moniz (Tue Jul 08 2014 - 22:17:19 CDT)
  • Norman Geist (Mon Jul 07 2014 - 02:48:08 CDT)
• AW: Regarding Temperature calculation from velocity trajectory of NAMD-2.9
  • Norman Geist (Fri Jul 11 2014 - 02:51:44 CDT)
  • Norman Geist (Thu Jul 10 2014 - 05:08:50 CDT)
• AW: REMD
  • Norman Geist (Tue Feb 18 2014 - 02:59:07 CST)
• AW: remd across gpus
  • Norman Geist (Mon Mar 31 2014 - 04:13:21 CDT)
  • Norman Geist (Mon Mar 31 2014 - 00:39:03 CDT)
• AW: REMD on IBM iDataPlex DX360M3
  • Norman Geist (Wed Jul 09 2014 - 02:24:27 CDT)
  • Norman Geist (Tue Jul 08 2014 - 01:12:46 CDT)
  • Norman Geist (Thu Jul 03 2014 - 05:42:02 CDT)
  • Norman Geist (Thu Jul 03 2014 - 05:38:48 CDT)
  • Norman Geist (Thu Jul 03 2014 - 04:28:46 CDT)
• AW: remd run command question
  • Norman Geist (Tue Mar 05 2013 - 00:14:22 CST)
• AW: Replica exchange, colvars & harmonic restraints
  • Norman Geist (Tue Jul 30 2013 - 00:38:02 CDT)
• AW: Require Suggestion
  • Norman Geist (Wed Feb 19 2014 - 01:42:09 CST)
• AW: residue_rmsd.tcl segmentation fault
  • John Xi (Fri Apr 04 2014 - 07:04:45 CDT)
  • Norman Geist (Fri Apr 04 2014 - 03:18:08 CDT)
  • Norman Geist (Fri Apr 04 2014 - 02:53:45 CDT)
• AW: Restart simulation of an equilibrated bilayer with sugar molecules inserted
  • Norman Geist (Mon Mar 18 2013 - 01:39:50 CDT)
• AW: Runaway cuda-enabled namd2 processes
  • Norman Geist (Wed Dec 04 2013 - 05:41:20 CST)
• AW: Running Charmrun/NAMD with more than 10 processes fails
  • Norman Geist (Tue Dec 16 2014 - 04:06:49 CST)
• AW: Running CUDA-enabled NAMD on multiple nodes without InfiniBand?
  • Norman Geist (Thu Dec 04 2014 - 01:08:09 CST)
  • Norman Geist (Mon Dec 01 2014 - 09:19:24 CST)
• AW: running namd in parallel
  • Norman Geist (Fri Aug 02 2013 - 03:43:52 CDT)
• AW: running NAMD on Amazon EC2?
  • Norman Geist (Thu Feb 14 2013 - 01:30:58 CST)
• AW: Running namd on linux in cpu+gpu mode
  • Norman Geist (Sun Jan 20 2013 - 23:52:48 CST)
• AW: Running NAMD on SGE cluster - multiple modes and cores
  • Norman Geist (Thu Dec 05 2013 - 04:33:12 CST)
  • Norman Geist (Thu Dec 05 2013 - 04:57:18 CST)
  • Norman Geist (Thu Dec 05 2013 - 04:06:31 CST)
  • Norman Geist (Thu Dec 05 2013 - 02:58:07 CST)
  • Norman Geist (Wed Dec 04 2013 - 07:36:48 CST)
  • Norman Geist (Tue Dec 03 2013 - 06:12:08 CST)
• AW: Running NAMD via GROMACS topology
  • Norman Geist (Mon Aug 11 2014 - 00:33:15 CDT)
• AW: Scaling on 64 core nodes?
  • Norman Geist (Fri Feb 15 2013 - 01:43:58 CST)
• AW: Scaling problem: 4 nodes OK, 5 fails to start
  • Norman Geist (Mon Jan 21 2013 - 00:02:25 CST)
  • Norman Geist (Thu Jan 17 2013 - 00:14:37 CST)
• AW: secondary structure analysis
  • Norman Geist (Thu Jan 10 2013 - 00:16:07 CST)
• AW: Self-Assemble Monolayer--Periodic Boundary Conditions
  • Norman Geist (Tue Sep 30 2014 - 01:38:57 CDT)
• AW: Separate water coordinates from graphite
  • Norman Geist (Thu Nov 14 2013 - 06:34:46 CST)
  • Norman Geist (Thu Nov 14 2013 - 01:26:31 CST)
  • Norman Geist (Wed Nov 13 2013 - 04:58:35 CST)
• AW: Should PME be used for electrostatic interaction energy calculations?
  • Norman Geist (Thu Jun 19 2014 - 02:46:48 CDT)
  • Norman Geist (Thu Jun 19 2014 - 02:25:49 CDT)
• AW: Simulation crash during NPT equilibration
  • Norman Geist (Fri Apr 11 2014 - 06:31:49 CDT)
• AW: slice of water box
  • Norman Geist (Thu Apr 10 2014 - 01:46:05 CDT)
• AW: smd simulation
  • Jacqueline Schmidt (Thu Feb 28 2013 - 01:12:36 CST)
  • Norman Geist (Thu Feb 28 2013 - 00:48:19 CST)
• AW: solvated system for minimization
  • Norman Geist (Mon Apr 22 2013 - 09:14:20 CDT)
• AW: spectrum simulation
  • Norman Geist (Mon Feb 25 2013 - 01:01:05 CST)
• AW: Suggestions while building a GPU-machine (CUDA) for NAMD use!
  • Norman Geist (Wed May 29 2013 - 00:27:44 CDT)
• AW: TclForces and efficient PBC corrections
  • Norman Geist (Tue Nov 12 2013 - 01:55:16 CST)
  • Norman Geist (Tue Nov 12 2013 - 01:19:01 CST)
• AW: TclForces wrapmode FATAL ERROR: Setting parameter wrapmode from script failed
  • Norman Geist (Thu May 08 2014 - 01:54:10 CDT)
• AW: Trouble loading frames from large DCD files
  • Norman Geist (Fri Dec 20 2013 - 01:52:23 CST)
• AW: Two GPU-based workstation
  • Norman Geist (Mon Nov 11 2013 - 03:26:06 CST)
  • Norman Geist (Mon Nov 11 2013 - 03:23:53 CST)
  • Norman Geist (Mon Nov 11 2013 - 01:09:38 CST)
  • Norman Geist (Thu Nov 07 2013 - 01:51:43 CST)
  • Norman Geist (Mon Nov 04 2013 - 05:15:06 CST)
  • Norman Geist (Mon Nov 04 2013 - 02:27:40 CST)
  • Norman Geist (Mon Nov 04 2013 - 01:04:00 CST)
  • Norman Geist (Wed Oct 30 2013 - 11:09:44 CDT)
  • Norman Geist (Tue Oct 29 2013 - 09:46:10 CDT)
  • Norman Geist (Tue Oct 29 2013 - 05:00:15 CDT)
  • Norman Geist (Tue Oct 29 2013 - 04:13:17 CDT)
• AW: Using nodelist file causes namd to hang
  • Norman Geist (Thu Sep 18 2014 - 12:32:23 CDT)
  • Douglas Houston (Thu Sep 18 2014 - 05:35:30 CDT)
  • Douglas Houston (Wed Aug 27 2014 - 12:47:24 CDT)
  • Ajasja LjubetiÄ� (Wed Aug 27 2014 - 12:32:53 CDT)
  • Douglas Houston (Wed Aug 27 2014 - 09:30:42 CDT)
  • Douglas Houston (Fri Jun 20 2014 - 05:00:05 CDT)
  • Norman Geist (Fri Jun 20 2014 - 02:25:11 CDT)
  • Douglas Houston (Fri Jun 13 2014 - 12:17:15 CDT)
  • Norman Geist (Wed Apr 09 2014 - 05:28:51 CDT)
  • Douglas Houston (Wed Apr 09 2014 - 04:28:37 CDT)
  • Norman Geist (Wed Apr 09 2014 - 00:21:40 CDT)
  • Douglas Houston (Tue Apr 08 2014 - 07:21:19 CDT)
  • Douglas Houston (Tue Apr 08 2014 - 05:52:52 CDT)
  • Norman Geist (Tue Apr 08 2014 - 05:06:03 CDT)
• AW: Various questions
  • Douglas Houston (Wed Jan 22 2014 - 04:30:17 CST)
  • Norman Geist (Wed Jan 22 2014 - 02:42:07 CST)
• AW: VDW energy is negative but total energy is positive
  • Norman Geist (Mon Sep 09 2013 - 01:14:20 CDT)
• AW: velocity manipulation
  • Norman Geist (Thu Oct 16 2014 - 08:26:37 CDT)
  • Norman Geist (Thu Oct 16 2014 - 08:11:59 CDT)
  • Norman Geist (Thu Oct 16 2014 - 07:27:28 CDT)
• AW: vmd-l: AMD vs. nvidia support
  • Axel Kohlmeyer (Thu Dec 12 2013 - 09:23:37 CST)
  • Aron Broom (Thu Dec 12 2013 - 09:10:52 CST)
  • Norman Geist (Thu Dec 12 2013 - 01:05:22 CST)
• AW: vmd-l: Creating custom molecule in VMD scripting
  • Norman Geist (Tue Oct 29 2013 - 07:16:46 CDT)
• AW: vmd-l: Error: Maximum number of bonds exceeded
  • Norman Geist (Mon Sep 09 2013 - 01:06:38 CDT)
• AW: vmd-l: fftk-charges
  • Norman Geist (Mon Oct 21 2013 - 01:23:48 CDT)
• AW: vmd-l: Finding particles that are close
  • Norman Geist (Tue Oct 08 2013 - 06:48:07 CDT)
• AW: vmd-l: how to enable multiple core rendering?
  • Norman Geist (Thu Sep 05 2013 - 01:01:40 CDT)
• AW: vmd-l: matching part of two models
  • Norman Geist (Mon Aug 26 2013 - 04:58:04 CDT)
• AW: vmd-l: non-orthorhombic PBCs
  • Norman Geist (Thu Sep 26 2013 - 00:49:18 CDT)
• AW: vmd-l: Occupancy maps
  • Axel Kohlmeyer (Mon Aug 12 2013 - 01:14:52 CDT)
  • Norman Geist (Mon Aug 12 2013 - 00:14:36 CDT)
• AW: vmd-l: SangbaeLee: question about pbc wrap
  • Norman Geist (Fri Aug 30 2013 - 02:15:30 CDT)
• AW: vmd-l: Stray PME grid
  • Norman Geist (Wed Oct 01 2014 - 02:27:31 CDT)
• AW: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD
  • Norman Geist (Tue Nov 11 2014 - 07:03:53 CST)
  • Norman Geist (Tue Nov 11 2014 - 02:48:52 CST)
  • Norman Geist (Mon Nov 10 2014 - 00:53:15 CST)
• AW: Why does my volume suddenly expand as I increase temperature.
  • Norman Geist (Tue Nov 12 2013 - 01:23:47 CST)
• AW: wrapping in two dimensions
  • Norman Geist (Mon Oct 20 2014 - 01:14:02 CDT)
  • Norman Geist (Fri Oct 17 2014 - 02:21:07 CDT)
• AW: writedcd problem
  • Norman Geist (Tue Sep 03 2013 - 03:47:16 CDT)
• AW: Xeon vs i7 and ECC vs SDRAM
  • Kenno Vanommeslaeghe (Wed Jun 25 2014 - 10:26:26 CDT)
  • Gianluca Interlandi (Wed Jun 25 2014 - 01:14:48 CDT)
  • Norman Geist (Wed Jun 25 2014 - 00:31:47 CDT)
• AW: 回å¤�： Shift (or offset) of the lipid bilayer along Z axis during equilibration
  • Norman Geist (Mon Jun 10 2013 - 00:42:35 CDT)
• Bad global bond count
  • Fugui (Mon May 06 2013 - 15:26:52 CDT)
• Bad global crossterm count!
  • Mitul Saha (Tue Jul 08 2014 - 16:48:51 CDT)
  • Mitul Saha (Tue Jul 08 2014 - 16:46:17 CDT)
• BAR-estimator error of ParseFEP plugin version 1.5 in VMD 1.9.1
  • Chris Chipot (Tue May 07 2013 - 00:44:08 CDT)
  • dbaogen (Tue May 07 2013 - 00:10:40 CDT)
• Basic question about impropers
  • Victor (Wed Jun 19 2013 - 11:29:11 CDT)
  • Wenhao Liu (Tue Jun 18 2013 - 18:30:12 CDT)
• benchmark info
  • Hassan Kianinejad (Thu Feb 27 2014 - 16:34:08 CST)
• bilayer creation
  • Richard Wood (Mon Sep 09 2013 - 15:50:18 CDT)
  • Axel Kohlmeyer (Mon Sep 09 2013 - 15:15:24 CDT)
  • Richard Wood (Mon Sep 09 2013 - 14:58:39 CDT)
  • Axel Kohlmeyer (Mon Sep 09 2013 - 14:15:56 CDT)
  • Richard Wood (Mon Sep 09 2013 - 14:00:43 CDT)
• binding free energy calculation
  • Aron Broom (Mon Apr 22 2013 - 10:12:45 CDT)
  • yp sun (Sun Apr 21 2013 - 07:42:52 CDT)
• Biotin force field
  • Kenno Vanommeslaeghe (Thu Oct 03 2013 - 13:28:51 CDT)
  • Zack Scholl (Thu Oct 03 2013 - 10:44:25 CDT)
• BKS potential
  • Marzieh Alishahi (Sat Aug 03 2013 - 13:39:33 CDT)
  • nadia salami (Sat Aug 03 2013 - 12:54:40 CDT)
  • sheida bagherzadeh (Sat Jul 06 2013 - 05:00:08 CDT)
  • sheida bagherzadeh (Mon Jul 01 2013 - 02:15:13 CDT)
• BLCR and NAMD
  • Paul Hargrove (Fri Nov 08 2013 - 01:54:48 CST)
  • Phil Miller (Thu Nov 07 2013 - 22:47:14 CST)
  • Joseph Farran (Thu Nov 07 2013 - 22:56:44 CST)
• Bonds in XPLOR format
  • Kenno Vanommeslaeghe (Wed Oct 23 2013 - 13:49:24 CDT)
  • Sunhwan Jo (Wed Oct 23 2013 - 13:28:27 CDT)
  • Mihaela Drenscko (Wed Oct 23 2013 - 13:23:10 CDT)
  • David Hardy (Wed Oct 23 2013 - 13:14:23 CDT)
  • Mihaela Drenscko (Wed Oct 23 2013 - 13:00:05 CDT)
• Boost value in aMD simulation
  • James Starlight (Wed Jul 23 2014 - 06:30:12 CDT)
• boron nitride nanotube
  • Axel Kohlmeyer (Thu Jun 12 2014 - 05:46:33 CDT)
  • Z (Thu Jun 12 2014 - 05:28:33 CDT)
  • Axel Kohlmeyer (Mon Jun 09 2014 - 04:19:24 CDT)
  • Z (Mon Jun 09 2014 - 02:58:02 CDT)
• Bug in T-REMD with colvars
  • Francesco Pietra (Tue Dec 03 2013 - 01:55:14 CST)
• BUG Report: NAMD 2.10 Nightly Build from 11.Sep
  • Norman Geist (Fri Oct 11 2013 - 06:23:14 CDT)
• bugs in NAMD_TI script?
  • shunzhou Wan (Wed Jul 31 2013 - 11:57:28 CDT)
• Build polymer from monomer
  • Sindu (Thu Apr 25 2013 - 23:48:17 CDT)
• Building crystal polymer
  • Shaikh Abdul Rajjak (Fri May 17 2013 - 00:59:09 CDT)
• building namd on a Cray XE6 with Interlagos procs
  • Giovanni Settanni (Tue May 20 2014 - 09:03:22 CDT)
• Bulk properties of polymers
  • Sindu (Wed May 08 2013 - 03:33:15 CDT)
  • Axel Kohlmeyer (Wed May 08 2013 - 02:28:50 CDT)
  • Sindu (Tue May 07 2013 - 23:34:20 CDT)
• C++ API
  • Aron Broom (Thu Jun 20 2013 - 01:12:19 CDT)
  • Stephan Grein (Wed Jun 19 2013 - 08:20:11 CDT)
• Calculate binding free energy
  • Aron Broom (Sun Feb 24 2013 - 22:46:17 CST)
  • yp sun (Sun Feb 24 2013 - 19:22:08 CST)
• Calculating density for a molecule
  • Jeffrey Potoff (Fri Feb 07 2014 - 13:17:17 CST)
  • Research Jubilant (Fri Feb 07 2014 - 11:36:41 CST)
• calculating free energy
  • Aron Broom (Sat Jun 28 2014 - 15:53:02 CDT)
  • Alireza Mansouri (Sat Jun 28 2014 - 12:22:40 CDT)
• Calculating pressure on each direction
  • Bala subramanian (Thu Oct 24 2013 - 10:25:20 CDT)
  • Bala subramanian (Thu Oct 24 2013 - 07:53:07 CDT)
• Calculating the force needed to constrain a protein
  • Maxim Belkin (Fri Jul 18 2014 - 11:43:27 CDT)
  • Shane.OMahony (Fri Jul 18 2014 - 11:18:05 CDT)
• Call for participation: ISQBP Meeting, Telluride 15-19.06.2014
  • Vlad Cojocaru (Mon Mar 10 2014 - 11:38:09 CDT)
• Can a small langevinDamping coefficient lead to 'ERROR: atoms moving too fast'?
  • Jose Borreguero (Tue Aug 27 2013 - 16:25:38 CDT)
  • Gianluca Interlandi (Mon Aug 26 2013 - 11:56:47 CDT)
  • Ajasja LjubetiÄ� (Mon Aug 26 2013 - 08:49:08 CDT)
  • Jose Borreguero (Mon Aug 26 2013 - 08:24:32 CDT)
• Can I define a simulation box but turn off the PBC at the same time?
  • ÕÔÀöÄÈ (Thu May 09 2013 - 03:49:48 CDT)
• can i use swap partition to increase ram in namd?
  • Axel Kohlmeyer (Mon Nov 25 2013 - 09:26:13 CST)
  • k.manzoorolajdad (Mon Nov 25 2013 - 09:18:15 CST)
• Can NAMD does Langevin Dynamics Simulation
  • Jeff Comer (Thu Nov 13 2014 - 15:11:10 CST)
  • Jeff Comer (Thu Nov 13 2014 - 14:37:13 CST)
  • Fidan Sumbul (Thu Nov 13 2014 - 10:41:39 CST)
  • Jeff Comer (Wed Nov 12 2014 - 16:37:31 CST)
  • Fidan Sumbul (Wed Nov 12 2014 - 14:48:25 CST)
• Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact?
  • somedatta pal (Thu Mar 21 2013 - 23:49:13 CDT)
  • Grace Brannigan (Wed Mar 20 2013 - 08:45:51 CDT)
  • somedatta pal (Wed Mar 20 2013 - 00:37:21 CDT)
• Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact?
  • Axel Kohlmeyer (Tue Mar 19 2013 - 01:15:42 CDT)
  • somedatta pal (Tue Mar 19 2013 - 00:35:22 CDT)
  • Axel Kohlmeyer (Tue Mar 19 2013 - 00:04:12 CDT)
  • somedatta pal (Mon Mar 18 2013 - 23:58:43 CDT)
• CAN'T FIND DIHEDRAL PARAMETERS FOR CPH1 NR2 FE NPH
  • Roy Fernando (Tue Jan 07 2014 - 08:05:22 CST)
  • Katherine Parra Pulido (Mon Jan 06 2014 - 23:33:49 CST)
• can't run multiple jobs with multiple gpus
  • Gordon Wells (Thu Apr 04 2013 - 19:10:02 CDT)
  • Gordon Wells (Wed Apr 03 2013 - 15:42:44 CDT)
• Cannot find colvar dih1 (dih colvars)
  • Francesco Pietra (Tue Dec 23 2014 - 11:15:31 CST)
• carboxyl NBFIX on proteins
  • Jeff Comer (Thu Nov 20 2014 - 10:46:35 CST)
  • Giacomo Fiorin (Thu Nov 20 2014 - 10:05:10 CST)
  • Jeff Comer (Thu Nov 20 2014 - 09:18:45 CST)
• Carma v.1.3 available for download
  • Nicholas M Glykos (Sun Nov 24 2013 - 04:33:05 CST)
• Carma v.1.4 released.
  • Nicholas M Glykos (Mon Oct 27 2014 - 06:09:24 CDT)
• catdcd error
  • Suresh (Mon Aug 19 2013 - 08:43:35 CDT)
  • Niklaus Johner (Mon Aug 19 2013 - 08:26:24 CDT)
  • Revthi Sanker (Mon Aug 19 2013 - 07:15:04 CDT)
• catdcd output and .psf file atom count mismatch
  • Izhar Karbat (Mon May 06 2013 - 17:18:53 CDT)
• CatDCD windows binaries
  • Axel Kohlmeyer (Fri Jul 19 2013 - 04:56:00 CDT)
• cell origin problem
  • Haleh Abdizadeh (Wed Sep 25 2013 - 15:06:19 CDT)
  • Aron Broom (Wed Sep 25 2013 - 14:53:19 CDT)
  • Haleh Abdizadeh (Wed Sep 25 2013 - 14:00:49 CDT)
  • Haleh Abdizadeh (Tue Sep 24 2013 - 09:53:17 CDT)
• Cellulose MD simulations
  • Munir S. Skaf (Fri Feb 01 2013 - 07:46:07 CST)
  • Patriche Simona (Thu Jan 31 2013 - 04:39:33 CST)
• center of mass calculation in the tcl interface
  • Aron Broom (Sun Feb 24 2013 - 14:48:38 CST)
  • Jacqueline Schmidt (Sun Feb 24 2013 - 13:02:21 CST)
• Center of mass motion included in Temperature?
  • Jérôme Hénin (Fri Aug 02 2013 - 15:24:56 CDT)
  • Kenno Vanommeslaeghe (Fri Aug 02 2013 - 11:15:09 CDT)
  • Norman Geist (Thu Aug 01 2013 - 04:53:34 CDT)
• CGenFF atom type N-
  • Francesco Pietra (Mon Nov 24 2014 - 02:55:04 CST)
• CHAMBER generated .prmtop file is not compatable with namd2
  • Jason Swails (Mon Sep 16 2013 - 04:55:09 CDT)
  • sudipta (Sun Sep 15 2013 - 23:51:48 CDT)
• change in pdb..
  • Joaquim Rui de Castro Rodrigues (Wed Jun 11 2014 - 13:03:18 CDT)
  • Axel Kohlmeyer (Wed Jun 11 2014 - 20:55:34 CDT)
  • Gurpreet Kaur Dhindsa (Wed Jun 11 2014 - 20:34:29 CDT)
  • Ivan Gregoretti (Wed Jun 11 2014 - 10:29:05 CDT)
  • Gurpreet Kaur Dhindsa (Wed Jun 11 2014 - 09:39:31 CDT)
  • Gurpreet Kaur Dhindsa (Sat Jun 07 2014 - 18:37:41 CDT)
• changing damping coefficient during simulation
  • Gozde Eskici (Tue Mar 18 2014 - 10:20:25 CDT)
• Changing NAMD XY restraint
  • Beaven, Andrew (Fri Aug 02 2013 - 16:29:05 CDT)
• Charge distribution
  • Kenno Vanommeslaeghe (Fri Nov 01 2013 - 13:52:54 CDT)
  • Peterson J (Fri Nov 01 2013 - 00:28:34 CDT)
• Charm 6.5.0 compilation issue
  • Dmitry Osolodkin (Fri Jan 11 2013 - 07:17:21 CST)
  • Dmitry Osolodkin (Sun Jan 06 2013 - 13:28:27 CST)
• charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program"
  • Frank Thommen (Sat Nov 30 2013 - 14:51:55 CST)
• charm-gui membrane builder
  • James Starlight (Fri Nov 01 2013 - 04:23:07 CDT)
  • James Starlight (Thu Sep 19 2013 - 01:04:39 CDT)
  • James Starlight (Tue Sep 17 2013 - 15:30:31 CDT)
  • James Starlight (Tue Sep 17 2013 - 14:32:17 CDT)
  • Kenno Vanommeslaeghe (Tue Sep 17 2013 - 14:26:09 CDT)
  • Niklaus Johner (Tue Sep 17 2013 - 13:22:45 CDT)
  • James Starlight (Tue Sep 17 2013 - 12:12:21 CDT)
  • Aron Broom (Tue Sep 17 2013 - 00:55:57 CDT)
  • James Starlight (Tue Sep 17 2013 - 00:33:30 CDT)
  • Niklaus Johner (Fri Sep 13 2013 - 09:01:51 CDT)
  • James Starlight (Fri Sep 13 2013 - 02:06:07 CDT)
  • Niklaus Johner (Thu Sep 12 2013 - 13:08:53 CDT)
  • James Starlight (Thu Sep 12 2013 - 06:24:51 CDT)
  • Sunhwan Jo (Wed Sep 11 2013 - 17:41:02 CDT)
  • James Starlight (Wed Sep 11 2013 - 15:15:23 CDT)
  • Sunhwan Jo (Wed Sep 11 2013 - 13:32:58 CDT)
  • James Starlight (Wed Sep 11 2013 - 12:20:59 CDT)
  • James Starlight (Tue Sep 10 2013 - 11:29:17 CDT)
  • James Starlight (Sun Sep 08 2013 - 23:52:00 CDT)
  • Grace Brannigan (Sun Sep 08 2013 - 01:02:31 CDT)
  • Cesar Millan (Sun Sep 08 2013 - 11:51:56 CDT)
  • James Starlight (Sun Sep 08 2013 - 11:44:04 CDT)
  • Sunhwan Jo (Sun Sep 08 2013 - 08:35:10 CDT)
  • James Starlight (Sat Sep 07 2013 - 23:56:42 CDT)
  • Emilia Wu (Sat Sep 07 2013 - 09:16:19 CDT)
  • James Starlight (Sat Sep 07 2013 - 04:04:10 CDT)
  • Sunhwan Jo (Fri Sep 06 2013 - 15:13:45 CDT)
  • James Starlight (Fri Sep 06 2013 - 15:03:41 CDT)
  • James Starlight (Fri Sep 06 2013 - 11:24:56 CDT)
  • Sunhwan Jo (Fri Sep 06 2013 - 07:39:34 CDT)
  • James Starlight (Fri Sep 06 2013 - 06:21:15 CDT)
• CHARMGUI and ligands parametrisation
  • James Starlight (Tue Sep 24 2013 - 15:35:09 CDT)
  • Kenno Vanommeslaeghe (Tue Sep 24 2013 - 10:54:37 CDT)
  • Sunhwan Jo (Tue Sep 24 2013 - 10:34:40 CDT)
  • James Starlight (Tue Sep 24 2013 - 09:38:30 CDT)
• Charmm
  • Kenno Vanommeslaeghe (Thu Feb 20 2014 - 12:53:55 CST)
  • Gianluca Interlandi (Thu Feb 20 2014 - 12:10:22 CST)
  • Kenno Vanommeslaeghe (Thu Feb 20 2014 - 10:40:41 CST)
  • Peter Reinke (Thu Feb 20 2014 - 02:31:35 CST)
• CHARMM-c36, glycans and RATTLE
  • Tristan Croll (Fri Aug 16 2013 - 06:26:33 CDT)
  • Tristan Croll (Fri Aug 16 2013 - 05:51:17 CDT)
  • Sunhwan Jo (Thu Aug 15 2013 - 09:31:26 CDT)
  • Tristan Croll (Thu Aug 15 2013 - 04:13:59 CDT)
  • Tristan Croll (Thu Aug 15 2013 - 01:23:50 CDT)
  • Sunhwan Jo (Thu Aug 15 2013 - 01:09:40 CDT)
  • Tristan Croll (Thu Aug 15 2013 - 01:05:32 CDT)
  • Tristan Croll (Wed Aug 14 2013 - 23:50:36 CDT)
• CHARMM36 and NAMD
  • Kenno Vanommeslaeghe (Tue Feb 18 2014 - 20:23:37 CST)
  • Douglas Houston (Tue Feb 18 2014 - 04:02:38 CST)
• chloromethyl ketone patch?
  • Jesper Madsen (Tue Feb 11 2014 - 16:49:21 CST)
• choose the best equilibrium arrangement of water molecules
  • Boshra Moradi (Tue May 06 2014 - 16:55:17 CDT)
• Choosing of windows and width for Umbrella Sampling
  • Kevin C Chan (Mon Dec 08 2014 - 09:39:46 CST)
  • Giacomo Fiorin (Mon Dec 08 2014 - 08:29:49 CST)
  • Kevin C Chan (Mon Dec 08 2014 - 06:48:19 CST)
• Citating colvars module
  • Giacomo Fiorin (Tue Jan 21 2014 - 11:12:55 CST)
  • Salvatore Mario Cosseddu (Tue Jan 21 2014 - 11:20:50 CST)
• citing SODIUM program
  • Shyno Mathew (Sat Jan 04 2014 - 10:45:36 CST)
• CNT coarse grain
  • Ramin Ekhteiari (Sat Jan 12 2013 - 03:29:59 CST)
  • hamid mosaddeghi (Fri Jan 11 2013 - 06:01:51 CST)
• Coarse grain parameter files
  • JAGODINSKY, JUSTIN (Fri Jul 12 2013 - 09:47:50 CDT)
• Coarse-Grained fatal error!
  • Fugui (Thu May 02 2013 - 07:49:20 CDT)
• Coarse-grained reverse transformation
  • Fugui (Sat May 11 2013 - 10:21:04 CDT)
• coarse-grained simulation: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C5M P5 (ATOMS 1 2)
  • Khaled Barakat (Sun Mar 23 2014 - 22:44:02 CDT)
• code implementation based on NAMD source code
  • Teerapong Pirojsirikul (Thu May 29 2014 - 17:39:21 CDT)
• colavrs ABF restart not matching
  • Kasra Fattah (Tue Dec 10 2013 - 12:02:53 CST)
  • Giacomo Fiorin (Tue Dec 10 2013 - 11:40:38 CST)
  • Kasra Fattah (Tue Dec 10 2013 - 11:30:50 CST)
• Collective variable data analysis using WHAM
  • Narasimhan LOGANATHAN (Wed Feb 20 2013 - 11:55:31 CST)
• Collective variable module
  • naresh kumar (Mon Apr 14 2014 - 10:11:37 CDT)
  • Giacomo Fiorin (Fri Apr 11 2014 - 12:49:20 CDT)
  • naresh kumar (Fri Apr 11 2014 - 12:01:32 CDT)
  • Giacomo Fiorin (Thu Apr 10 2014 - 14:06:18 CDT)
  • naresh kumar (Thu Apr 10 2014 - 12:54:02 CDT)
  • Giacomo Fiorin (Thu Apr 10 2014 - 12:03:27 CDT)
  • naresh kumar (Thu Apr 10 2014 - 11:36:07 CDT)
• collective variables new paper
  • Giacomo Fiorin (Mon Jun 17 2013 - 17:48:11 CDT)
• Collective Variables to Restrain Ions Away From Protein
  • Aron Broom (Sun Apr 20 2014 - 00:27:37 CDT)
  • Aron Broom (Thu Apr 17 2014 - 23:15:35 CDT)
  • Chris Ing (Thu Apr 17 2014 - 18:36:06 CDT)
• Colvar cannot be ran on supercomputer newton
  • Ajasja LjubetiÄ� (Tue Aug 06 2013 - 09:08:25 CDT)
  • Tian Li (Tue Aug 06 2013 - 08:35:44 CDT)
• colvar DistanceZ
  • Kevin C Chan (Wed Nov 26 2014 - 20:32:24 CST)
  • Jérôme Hénin (Wed Nov 26 2014 - 07:35:37 CST)
  • Kevin C Chan (Wed Nov 26 2014 - 07:25:03 CST)
  • Jérôme Hénin (Wed Nov 26 2014 - 05:07:19 CST)
  • Kevin C Chan (Tue Nov 25 2014 - 21:03:55 CST)
• colvar keyword ForceNoPBC
  • Giacomo Fiorin (Wed Feb 27 2013 - 23:50:16 CST)
  • Nadeem A. Vellore (Wed Feb 27 2013 - 23:46:09 CST)
• COLVAR metadynamics: center of mass of atoms crossing simulation box
  • Lorenz Ripka (Fri May 23 2014 - 07:35:23 CDT)
  • Giacomo Fiorin (Tue May 20 2014 - 11:41:56 CDT)
  • Lorenz Ripka (Mon May 19 2014 - 03:44:36 CDT)
  • Lorenz Ripka (Mon May 19 2014 - 07:17:47 CDT)
• COLVAR related quesion
  • Giacomo Fiorin (Tue Mar 11 2014 - 16:19:24 CDT)
  • Abir Ganguly (Tue Mar 11 2014 - 16:06:20 CDT)
• Colvar: minimal distance between 2 groups of atoms
  • Vlad Cojocaru (Tue Nov 18 2014 - 03:40:53 CST)
  • Jérôme Hénin (Mon Nov 17 2014 - 13:13:07 CST)
  • Vlad Cojocaru (Mon Nov 17 2014 - 12:12:42 CST)
  • Ajasja LjubetiÄ� (Mon Nov 17 2014 - 11:30:45 CST)
  • Vlad Cojocaru (Mon Nov 17 2014 - 10:49:57 CST)
  • Ajasja LjubetiÄ� (Mon Nov 17 2014 - 10:28:20 CST)
  • Vlad Cojocaru (Mon Nov 17 2014 - 10:14:58 CST)
  • Jérôme Hénin (Mon Nov 17 2014 - 10:07:38 CST)
  • Vlad Cojocaru (Mon Nov 17 2014 - 09:57:37 CST)
  • Giacomo Fiorin (Mon Nov 17 2014 - 08:49:18 CST)
  • Vlad Cojocaru (Mon Nov 17 2014 - 07:41:31 CST)
• colvars and parallel-tempering with namd2.10
  • Francesco Pietra (Fri Aug 23 2013 - 02:57:53 CDT)
  • Francesco Pietra (Mon Aug 19 2013 - 01:46:36 CDT)
  • Francesco Pietra (Mon Aug 19 2013 - 01:41:12 CDT)
  • Giacomo Fiorin (Sun Aug 18 2013 - 10:40:59 CDT)
  • Francesco Pietra (Sat Aug 17 2013 - 11:51:08 CDT)
  • Axel Kohlmeyer (Tue Aug 13 2013 - 12:07:52 CDT)
  • Giacomo Fiorin (Tue Aug 13 2013 - 12:00:45 CDT)
  • Sunhwan Jo (Tue Aug 13 2013 - 11:17:44 CDT)
  • Giacomo Fiorin (Tue Aug 13 2013 - 10:51:39 CDT)
  • Sunhwan Jo (Tue Aug 13 2013 - 10:29:08 CDT)
  • Jérôme Hénin (Tue Aug 13 2013 - 09:51:30 CDT)
  • Sunhwan Jo (Mon Aug 12 2013 - 10:29:23 CDT)
  • Francesco Pietra (Mon Aug 12 2013 - 09:54:25 CDT)
• colvars angle centerReference
  • Jeff Comer (Wed Dec 10 2014 - 09:22:10 CST)
  • Giacomo Fiorin (Wed Dec 10 2014 - 08:44:22 CST)
  • Jeff Comer (Wed Dec 10 2014 - 08:41:06 CST)
  • Jim Phillips (Wed Dec 10 2014 - 07:31:11 CST)
  • Giacomo Fiorin (Tue Dec 09 2014 - 21:54:55 CST)
  • Jeff Comer (Tue Dec 09 2014 - 21:41:26 CST)
  • Giacomo Fiorin (Tue Dec 09 2014 - 18:35:22 CST)
  • Jeff Comer (Fri Dec 05 2014 - 15:00:44 CST)
• colvars configuration file example
  • Giacomo Fiorin (Wed Apr 03 2013 - 15:09:12 CDT)
  • Martin, Erik W (Wed Apr 03 2013 - 15:04:41 CDT)
• Colvars error
  • Kevin C Chan (Tue Nov 25 2014 - 21:11:41 CST)
  • Kevin C Chan (Tue Nov 25 2014 - 05:11:55 CST)
  • Giacomo Fiorin (Tue Nov 25 2014 - 08:53:58 CST)
  • Subbarao Kanchi (Tue Nov 25 2014 - 06:30:36 CST)
  • Subbarao Kanchi (Tue Nov 25 2014 - 02:08:45 CST)
  • Kevin C Chan (Tue Nov 25 2014 - 00:57:45 CST)
  • Kevin C Chan (Tue Nov 25 2014 - 00:10:05 CST)
• colvars fatal error
  • Jérôme Hénin (Wed Nov 05 2014 - 02:54:43 CST)
  • Leili Zhang (Tue Nov 04 2014 - 22:44:05 CST)
• Colvars keyword problem
  • Jérôme Hénin (Mon May 05 2014 - 10:01:03 CDT)
  • Sofya Lushchekina (Mon May 05 2014 - 09:32:11 CDT)
• Colvars periodic boundary treatment question
  • Giacomo Fiorin (Tue Dec 03 2013 - 16:07:12 CST)
  • Kasra Fattah (Tue Dec 03 2013 - 15:57:04 CST)
  • Jérôme Hénin (Tue Dec 03 2013 - 12:39:25 CST)
  • Kasra Fattah (Sat Nov 30 2013 - 22:25:46 CST)
  • Jérôme Hénin (Sat Nov 30 2013 - 19:04:48 CST)
  • Kasra Fattah (Sat Nov 30 2013 - 13:12:42 CST)
• colvars replica exchange oddity
  • JC Gumbart (Tue Oct 14 2014 - 22:27:07 CDT)
• Colvars RMSD syntax with a moving reference frame
  • Mayne, Christopher G (Fri Aug 02 2013 - 16:38:21 CDT)
  • Giacomo Fiorin (Fri Aug 02 2013 - 13:17:49 CDT)
  • Jérôme Hénin (Fri Aug 02 2013 - 10:29:12 CDT)
  • Mayne, Christopher G (Fri Aug 02 2013 - 10:14:47 CDT)
• Colvars simulation running slow?
  • Ajasja LjubetiÄ� (Wed Sep 10 2014 - 19:58:48 CDT)
  • Tristan Croll (Wed Sep 10 2014 - 19:51:15 CDT)
  • Tristan Croll (Wed Sep 10 2014 - 17:15:35 CDT)
  • Jérôme Hénin (Wed Sep 10 2014 - 02:13:00 CDT)
  • Tristan Croll (Tue Sep 09 2014 - 20:31:06 CDT)
• colvars with replica exchange molecular dynamics
  • Francesco Pietra (Fri Jan 31 2014 - 01:38:21 CST)
  • Giacomo Fiorin (Thu Jan 30 2014 - 17:32:47 CST)
  • Francesco Pietra (Tue Jan 14 2014 - 02:25:19 CST)
  • Giacomo Fiorin (Mon Jan 13 2014 - 15:17:25 CST)
  • Francesco Pietra (Mon Jan 13 2014 - 14:29:41 CST)
• Combining interleaved and top posting is considered harmful.
  • Jim Phillips (Thu Aug 28 2014 - 11:29:10 CDT)
  • Nicholas M Glykos (Thu Aug 28 2014 - 11:11:40 CDT)
• Combining several proteins of the same type together
  • Lili Zhang (Mon Oct 14 2013 - 13:54:56 CDT)
• Compile NAMD with FFTW3 and MPI
  • Axel Kohlmeyer (Tue Nov 19 2013 - 02:50:48 CST)
  • Chan Tabris C (Tue Nov 19 2013 - 02:45:00 CST)
• Compile NAMD2.9 on Xeon Phi
  • Devang Jane (Thu Aug 08 2013 - 13:15:38 CDT)
• compiling namd-lite
  • Hassan Kianinejad (Thu Mar 06 2014 - 19:08:28 CST)
  • Hassan Kianinejad (Thu Mar 06 2014 - 18:55:54 CST)
• Compiling with Open64 4.5.2.1 for AMD Opteron 6378
  • David Chin (Mon Mar 24 2014 - 10:44:54 CDT)
• Computational Biophysics Workshop using NAMD and VMD, November 18-22, 2013, Urbana, Illinois, USA
  • David Brandon (Fri Aug 23 2013 - 14:07:30 CDT)
• Computational Electrostatics for Biological Application (CEBA'13) - July 1-3 2013 - Genoa - Italy
  • Walter Rocchia (Fri Apr 19 2013 - 04:59:23 CDT)
• computing forces on atoms by postprocessing a dcd file generated with FEP enabled
  • Harris, Robert C. (Wed Sep 03 2014 - 14:05:40 CDT)
• Conceptual questions about GPU acceleration
  • Axel Kohlmeyer (Sat Apr 27 2013 - 12:20:06 CDT)
  • Andrew DeYoung (Sat Apr 27 2013 - 11:46:49 CDT)
• confines volume effects
  • Nicholas M Glykos (Fri Feb 15 2013 - 04:04:29 CST)
  • Martin, Erik W (Thu Feb 14 2013 - 12:30:39 CST)
• Constant pressure energy minimization
  • FX (Wed Feb 20 2013 - 02:18:43 CST)
• Constant Pressure, Variable Volume, Minimization
  • Josh Vermaas (Thu Dec 18 2014 - 13:17:35 CST)
  • Miss. State (Thu Dec 18 2014 - 13:01:05 CST)
• Constant volume energy minimization
  • Jérôme Hénin (Wed Feb 20 2013 - 04:29:50 CST)
  • Michael Mazack (Tue Feb 19 2013 - 16:18:00 CST)
  • FX (Tue Feb 19 2013 - 16:06:53 CST)
• Constraining two sets of atoms
  • Natnael Doilicho (Tue Sep 16 2014 - 12:06:38 CDT)
• Constraint failure in RATTLE
  • Massimiliano Porrini (Mon Mar 31 2014 - 11:48:38 CDT)
  • Francesco Pietra (Mon Mar 31 2014 - 02:29:48 CDT)
  • Massimiliano Porrini (Sun Mar 30 2014 - 06:49:34 CDT)
  • Francesco Pietra (Sun Mar 30 2014 - 02:31:54 CDT)
• Constraint failure in RATTLE algorithm
  • Douglas Houston (Tue Jul 01 2014 - 04:29:38 CDT)
  • Kenno Vanommeslaeghe (Fri Jun 27 2014 - 10:37:19 CDT)
  • Douglas Houston (Fri Jun 27 2014 - 09:29:42 CDT)
  • Aron Broom (Sun Jun 22 2014 - 23:02:28 CDT)
  • Tristan Croll (Sat Jun 21 2014 - 18:43:43 CDT)
  • Douglas Houston (Fri Jun 20 2014 - 08:31:56 CDT)
  • Aron Broom (Thu Jun 19 2014 - 09:15:49 CDT)
  • Aron Broom (Thu Jun 19 2014 - 10:37:59 CDT)
  • Douglas Houston (Thu Jun 19 2014 - 09:51:33 CDT)
  • Douglas Houston (Thu Jun 19 2014 - 05:26:53 CDT)
  • Tristan Croll (Wed Jun 18 2014 - 20:29:08 CDT)
  • Aron Broom (Wed Jun 18 2014 - 14:07:04 CDT)
  • Axel Kohlmeyer (Wed Jun 18 2014 - 13:23:05 CDT)
  • Douglas Houston (Wed Jun 18 2014 - 12:29:48 CDT)
• Constraint failure in RATTLE algorithm occurs during NAMD simulation with amber force field
  • Gianluca Interlandi (Thu Aug 29 2013 - 22:58:38 CDT)
  • sunyeping (Thu Aug 29 2013 - 21:32:22 CDT)
• constraint file from amber prmtop/inpcrd
  • amin_at_imtech.res.in (Sat May 24 2014 - 14:32:55 CDT)
• Convergence of Sampling and Deciding on Simulation Length
  • Nikolaos Glykos (Tue Jul 16 2013 - 12:16:12 CDT)
  • Aron Broom (Tue Jul 16 2013 - 09:59:15 CDT)
  • Aditya Ranganathan (Tue Jul 16 2013 - 06:08:15 CDT)
• converting dcd files to netcdf or ascii
  • Daniel Abergel (Thu Feb 28 2013 - 07:04:41 CST)
• Coordinate vs. time plots
  • Ajasja LjubetiÄ� (Thu Mar 28 2013 - 07:53:47 CDT)
  • Mihaela Drenscko (Thu Mar 28 2013 - 06:11:44 CDT)
  • Mihaela Drenscko (Wed Mar 20 2013 - 17:17:46 CDT)
• coordinates in namd
  • Tristan Croll (Tue Jun 03 2014 - 02:25:49 CDT)
  • Research Jubilant (Mon Jun 02 2014 - 23:34:52 CDT)
• Coordinates of Carbon atoms on Graphite
  • Mihaela Drenscko (Tue Sep 24 2013 - 11:47:28 CDT)
• Cost of a colvar calculation
  • Branko (Wed Jul 23 2014 - 07:45:31 CDT)
  • George Patargias (Wed Jul 23 2014 - 01:33:23 CDT)
  • Jo, Sunhwan (Tue Jul 22 2014 - 19:02:20 CDT)
  • Giacomo Fiorin (Tue Jul 22 2014 - 17:31:23 CDT)
  • Jo, Sunhwan (Tue Jul 22 2014 - 13:06:12 CDT)
  • Jérôme Hénin (Tue Jul 22 2014 - 11:20:56 CDT)
  • Axel Kohlmeyer (Tue Jul 22 2014 - 11:02:47 CDT)
  • Aron Broom (Tue Jul 22 2014 - 10:56:45 CDT)
  • Ivan Gregoretti (Tue Jul 22 2014 - 08:41:41 CDT)
  • Jérôme Hénin (Tue Jul 22 2014 - 07:43:30 CDT)
  • Branko (Tue Jul 22 2014 - 07:44:04 CDT)
  • Ivan Gregoretti (Tue Jul 22 2014 - 07:33:14 CDT)
  • Jérôme Hénin (Tue Jul 22 2014 - 06:56:42 CDT)
  • George Patargias (Tue Jul 22 2014 - 06:27:52 CDT)
• create psf file without hydrogens
  • Revthi Sanker (Fri Nov 21 2014 - 03:23:19 CST)
  • Tristan Croll (Thu Nov 20 2014 - 14:22:06 CST)
  • Revthi Sanker (Thu Nov 20 2014 - 12:26:48 CST)
• creating coarse grain model with martini force field
  • ¼­¿ëÀÏ (Mon Sep 02 2013 - 01:58:10 CDT)
• Cross-correlation analysis in multidomain proteins
  • James Starlight (Thu Mar 13 2014 - 05:32:22 CDT)
• cuda error
  • subbarao kanchi (Mon Apr 08 2013 - 03:37:11 CDT)
  • subbarao kanchi (Sat Mar 30 2013 - 10:53:13 CDT)
  • Aron Broom (Fri Mar 29 2013 - 18:40:46 CDT)
  • subbarao kanchi (Fri Mar 29 2013 - 12:36:50 CDT)
• CUDA error in cuda_check_local_progress
  • Abhishek TYAGI (Thu Apr 17 2014 - 04:23:44 CDT)
  • Abhishek TYAGI (Thu Apr 17 2014 - 04:07:36 CDT)
  • Abhishek TYAGI (Thu Apr 17 2014 - 02:41:11 CDT)
• CUDA error in cuda_check_remote_progress on Pe 2
  • Francesco Pietra (Fri Apr 05 2013 - 09:55:44 CDT)
• CUDA error memcpy to exclusions: invalid argument
  • Axel Kohlmeyer (Tue Aug 27 2013 - 05:15:45 CDT)
  • Haleh Abdizadeh (Tue Aug 27 2013 - 05:13:11 CDT)
  • Axel Kohlmeyer (Tue Aug 27 2013 - 04:15:23 CDT)
  • Haleh Abdizadeh (Tue Aug 27 2013 - 04:06:29 CDT)
• CUDA Fatal Error While Trying to Run Under Windows 8.1
  • Jim Phillips (Thu Nov 06 2014 - 13:00:35 CST)
  • Branko (Thu Nov 06 2014 - 12:15:59 CST)
  • Justin Sanders (Thu Nov 06 2014 - 12:01:58 CST)
• CUDA vd non-CUDA for minimization
  • Kenno Vanommeslaeghe (Mon Oct 21 2013 - 11:34:26 CDT)
  • Francesco Pietra (Sat Oct 19 2013 - 02:28:50 CDT)
  • Kenno Vanommeslaeghe (Fri Oct 18 2013 - 13:55:00 CDT)
  • Francesco Pietra (Fri Oct 18 2013 - 12:13:04 CDT)
• Current bias values
  • Ajasja LjubetiÄ� (Wed May 08 2013 - 02:54:11 CDT)
  • Siri Søndergaard (Wed May 01 2013 - 20:39:50 CDT)
• Current CVS broken? (SortedArray.h)
  • Michael Mazack (Wed Feb 06 2013 - 09:00:43 CST)
  • Michael Mazack (Tue Feb 05 2013 - 14:24:42 CST)
  • Chris Harrison (Tue Feb 05 2013 - 13:20:58 CST)
  • Michael Mazack (Tue Feb 05 2013 - 12:52:26 CST)
• DCD file doubles a monomer
  • JC Gumbart (Tue Feb 26 2013 - 20:58:04 CST)
  • JC Gumbart (Tue Feb 26 2013 - 19:50:08 CST)
  • Eduard Schreiner (Tue Feb 26 2013 - 16:17:34 CST)
  • Patricia Campbell (Tue Feb 26 2013 - 15:01:18 CST)
  • Aron Broom (Tue Feb 26 2013 - 12:34:54 CST)
  • Patricia Campbell (Tue Feb 26 2013 - 12:13:53 CST)
  • Patricia Campbell (Tue Feb 26 2013 - 12:09:16 CST)
• dcd to pdb for trajectory analysis
  • bishop_at_latech.edu (Thu Jul 11 2013 - 13:01:33 CDT)
  • Aron Broom (Thu Jul 11 2013 - 09:49:30 CDT)
  • Gabriel Jara (Thu Jul 11 2013 - 09:43:16 CDT)
  • oguz gurbulak (Thu Jul 11 2013 - 07:40:11 CDT)
• DCD writing error on cluster
  • Rehan Zafar (Sun Jun 09 2013 - 14:01:44 CDT)
• Defining colvars groups of atoms for ABF
  • Maria Pikoula (Wed Aug 21 2013 - 04:13:57 CDT)
• delta-G calculation
  • Axel Kohlmeyer (Thu Sep 19 2013 - 03:09:43 CDT)
  • Yi Wang, PhD (Thu Sep 19 2013 - 03:08:28 CDT)
  • rasti_at_ut.ac.ir (Thu Sep 19 2013 - 03:02:33 CDT)
• Density of water box
  • Akshay Bhatnagar (Tue Jun 03 2014 - 07:26:41 CDT)
  • Ana Celia Vila Verde (Tue Jun 03 2014 - 06:29:02 CDT)
  • Akshay Bhatnagar (Tue Jun 03 2014 - 05:22:00 CDT)
• Detection of Internal water along MD trajectory
  • James Starlight (Mon Mar 17 2014 - 04:14:38 CDT)
• Determining HIS protonation state using PropKa vmd plug-in
  • zeynab mohamad hoseyni (Tue Feb 11 2014 - 06:30:09 CST)
• DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface
  • Norman Geist (Mon Oct 28 2013 - 09:17:36 CDT)
  • Norman Geist (Thu Oct 24 2013 - 11:53:37 CDT)
  • Norman Geist (Thu Oct 24 2013 - 11:51:38 CDT)
  • Jim Phillips (Thu Oct 24 2013 - 10:01:30 CDT)
  • Norman Geist (Thu Oct 24 2013 - 01:21:19 CDT)
• Difficulties with using the "rescalevels" command every MD timestep
  • Spencer, Jacob (Thu Jan 09 2014 - 09:48:37 CST)
• diffusion of protein into water box
  • Axel Kohlmeyer (Mon Nov 25 2013 - 07:13:57 CST)
  • Ramin Ekhteiari (Mon Nov 25 2013 - 02:30:39 CST)
  • Axel Kohlmeyer (Sun Nov 24 2013 - 08:24:47 CST)
  • Ramin Ekhteiari (Sun Nov 24 2013 - 08:21:04 CST)
  • Axel Kohlmeyer (Sun Nov 24 2013 - 08:14:52 CST)
  • Ramin Ekhteiari (Sun Nov 24 2013 - 08:06:27 CST)
• dihedral parameter conversion
  • JC Gumbart (Fri May 03 2013 - 00:21:10 CDT)
  • Markus Dahlgren (Thu May 02 2013 - 10:08:51 CDT)
  • JC Gumbart (Thu May 02 2013 - 09:41:30 CDT)
  • Markus Dahlgren (Thu May 02 2013 - 09:16:36 CDT)
  • JC Gumbart (Thu May 02 2013 - 08:17:00 CDT)
• Dihedrals multiplicity!
  • Jeffrey Potoff (Thu Feb 13 2014 - 11:34:16 CST)
  • Jeffrey Potoff (Thu Feb 13 2014 - 10:51:12 CST)
  • Anna Borlsky (Thu Feb 13 2014 - 09:24:46 CST)
• Dioxygen atom type with CHARMM36
  • Francesco Pietra (Wed Nov 12 2014 - 01:17:44 CST)
  • Kenno Vanommeslaeghe (Tue Nov 11 2014 - 14:19:40 CST)
  • Francesco Pietra (Tue Nov 11 2014 - 13:34:13 CST)
  • Kenno Vanommeslaeghe (Tue Nov 11 2014 - 12:46:48 CST)
  • Francesco Pietra (Tue Nov 11 2014 - 11:19:17 CST)
  • Kenno Vanommeslaeghe (Tue Nov 11 2014 - 11:07:25 CST)
  • Francesco Pietra (Tue Nov 11 2014 - 10:11:00 CST)
• Dioxygen params charmm36
  • Francesco Pietra (Wed Oct 29 2014 - 16:27:17 CDT)
• direction of pull in namd
  • Leandro Martínez (Tue Jan 29 2013 - 10:46:15 CST)
  • Leandro Martínez (Tue Jan 29 2013 - 08:09:01 CST)
  • raghav singh (Tue Jan 29 2013 - 07:18:49 CST)
• Distance Constraints in ABF Simulation
  • Vince Cho (Wed Dec 25 2013 - 05:31:26 CST)
• distanceZ - harmonic restraints
  • Narasimhan LOGANATHAN (Mon Mar 18 2013 - 13:38:55 CDT)
  • Narasimhan LOGANATHAN (Mon Mar 18 2013 - 13:37:45 CDT)
  • Aron Broom (Mon Mar 18 2013 - 12:35:47 CDT)
  • Jérôme Hénin (Mon Mar 18 2013 - 12:04:03 CDT)
  • Narasimhan LOGANATHAN (Mon Mar 18 2013 - 12:14:46 CDT)
• DNA surrounded by a shell of water in a big box with vacuum
  • Bikan Tan (Mon Jan 14 2013 - 11:01:06 CST)
• DNA terminals and charges
  • Jack Bulat (Tue Jan 15 2013 - 22:13:24 CST)
  • Siri Søndergaard (Tue Jan 15 2013 - 20:45:40 CST)
• Does MOLLY really retain bond motion for water?
  • Francesco Pietra (Sun Jun 02 2013 - 08:45:04 CDT)
• Does NAMD have some way to test the result?
  • Jérôme Hénin (Sat Oct 04 2014 - 04:20:57 CDT)
  • Axel Kohlmeyer (Fri Oct 03 2014 - 22:17:05 CDT)
  • ukulililixl (Fri Oct 03 2014 - 21:50:52 CDT)
• Does NAMD read the PDB element field?
  • Albrecht Goez (Fri Feb 01 2013 - 02:52:15 CST)
• Does stray PME charges with T-REMD mean insufficient resources and can explicit water abandoned for implicit GB?
  • Francesco Pietra (Wed Sep 11 2013 - 09:24:59 CDT)
• Drifting water molecules
  • Axel Kohlmeyer (Wed Nov 27 2013 - 16:56:17 CST)
  • Mihaela Drenscko (Wed Nov 27 2013 - 16:45:10 CST)
• Drude polarizable force field
  • Hadi (Sat Jul 06 2013 - 02:06:15 CDT)
• Dual boost accelerated md energy parameters?
  • Thomas Evangelidis (Mon May 12 2014 - 14:11:45 CDT)
  • Per Larsson (Mon May 12 2014 - 13:54:48 CDT)
• dynamic_cast cannot be done without runtime type information
  • Jérôme Hénin (Mon Mar 11 2013 - 10:31:27 CDT)
  • Jérôme Hénin (Mon Mar 11 2013 - 10:16:24 CDT)
• editing the code of the non bonded pair potentials
  • Asaf Farhi (Fri Aug 30 2013 - 19:54:45 CDT)
  • Gianluca Interlandi (Fri Aug 30 2013 - 18:33:06 CDT)
  • Victor (Fri Aug 30 2013 - 18:19:04 CDT)
  • Gianluca Interlandi (Fri Aug 30 2013 - 18:00:08 CDT)
  • Victor (Fri Aug 30 2013 - 14:29:58 CDT)
  • Axel Kohlmeyer (Fri Aug 30 2013 - 14:08:53 CDT)
  • Joshua Adelman (Fri Aug 30 2013 - 14:06:12 CDT)
  • Axel Kohlmeyer (Fri Aug 30 2013 - 13:59:26 CDT)
  • Asaf Farhi (Fri Aug 30 2013 - 13:55:21 CDT)
  • Kenno Vanommeslaeghe (Fri Aug 30 2013 - 13:47:15 CDT)
  • Asaf Farhi (Fri Aug 30 2013 - 13:14:33 CDT)
  • Axel Kohlmeyer (Fri Aug 30 2013 - 09:10:35 CDT)
  • Asaf Farhi (Fri Aug 30 2013 - 05:26:41 CDT)
  • Axel Kohlmeyer (Fri Aug 30 2013 - 04:34:46 CDT)
  • Asaf Farhi (Fri Aug 30 2013 - 04:31:44 CDT)
  • Asaf Farhi (Fri Aug 30 2013 - 04:27:19 CDT)
• Effect of phi, psi cross term map (CMAP) correction on result of MD simulation
  • Axel Kohlmeyer (Wed Mar 13 2013 - 04:20:08 CDT)
  • dbaogen (Wed Mar 13 2013 - 04:13:42 CDT)
• efficient way to apply time-dependent electric field
  • Jim Phillips (Thu Sep 04 2014 - 11:18:00 CDT)
  • Azadeh Alavi (Thu Sep 04 2014 - 05:38:12 CDT)
• eigenvector colvar
  • Steven Mike (Thu Aug 29 2013 - 13:24:41 CDT)
  • Giacomo Fiorin (Thu Aug 29 2013 - 09:00:56 CDT)
  • Steven Mike (Wed Aug 28 2013 - 23:14:49 CDT)
• Electronic density profile of lipid bilayer.
  • Subbarao Kanchi (Sun Apr 06 2014 - 20:32:54 CDT)
• Empirical force fields: release new version of RED Server Dev/PyRED
  • FyD (Mon May 05 2014 - 06:07:18 CDT)
• Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014
  • FyD (Tue Dec 09 2014 - 02:43:22 CST)
• Energy Correction Term For PME Electrostatics in a Charged Periodic System
  • David Huggins (Wed Sep 18 2013 - 05:02:52 CDT)
• Energy term in output file of Accelerated dynamics
  • Kapil jain (Sun Aug 10 2014 - 21:39:32 CDT)
  • Kapil jain (Fri Aug 08 2014 - 02:14:56 CDT)
• Epoxy CHARMM
  • Rawan Al Nsour (Thu Feb 21 2013 - 18:11:41 CST)
• Equilibration of the membrane bilayers with CUDA-support
  • Axel Kohlmeyer (Wed Sep 11 2013 - 02:14:13 CDT)
  • James Starlight (Wed Sep 11 2013 - 01:31:05 CDT)
  • Axel Kohlmeyer (Tue Sep 10 2013 - 09:14:55 CDT)
  • James Starlight (Tue Sep 10 2013 - 09:06:11 CDT)
  • James Starlight (Mon Sep 09 2013 - 10:16:40 CDT)
• Equilibration of the membrane-protein system done in CHARMM-GUI
  • James Starlight (Thu Nov 14 2013 - 07:32:44 CST)
  • James Starlight (Fri Nov 08 2013 - 06:38:26 CST)
  • Kenno Vanommeslaeghe (Wed Nov 06 2013 - 14:03:05 CST)
  • Sunhwan Jo (Wed Nov 06 2013 - 09:29:54 CST)
  • James Starlight (Wed Nov 06 2013 - 09:02:45 CST)
  • Sunhwan Jo (Wed Nov 06 2013 - 08:07:25 CST)
  • James Starlight (Wed Nov 06 2013 - 00:51:22 CST)
• Error
  • Kenno Vanommeslaeghe (Mon Oct 21 2013 - 12:17:41 CDT)
  • Kenno Vanommeslaeghe (Wed Oct 16 2013 - 21:21:20 CDT)
  • Mihaela Drenscko (Wed Oct 16 2013 - 20:15:29 CDT)
• error : segmentation fault
  • Faezeh Mottaghitalab (Wed Jan 01 2014 - 05:18:30 CST)
• Error compiling NAMD2.9 after patching with PLUMED2.1
  • Rubén Granero (Tue Dec 16 2014 - 12:07:45 CST)
  • Jim Phillips (Tue Dec 16 2014 - 09:22:04 CST)
  • Rubén Granero (Tue Dec 16 2014 - 07:39:02 CST)
  • Jim Phillips (Mon Dec 15 2014 - 08:37:26 CST)
  • Rubén Granero (Mon Dec 15 2014 - 06:47:27 CST)
• Error in distributing the cores for a single processor
  • Axel Kohlmeyer (Thu Apr 11 2013 - 00:44:20 CDT)
  • Axel Kohlmeyer (Thu Apr 11 2013 - 00:33:33 CDT)
  • Priyanka Purkayastha (Wed Apr 10 2013 - 23:36:00 CDT)
• Error in implicit solvent MD
  • Aron Broom (Wed Mar 27 2013 - 15:39:39 CDT)
  • Fugui (Wed Mar 27 2013 - 15:08:19 CDT)
• Error in PSF gen
  • Ivana (Wed Jun 19 2013 - 10:14:36 CDT)
  • Vibhor Agrawal (Tue Jun 18 2013 - 22:36:32 CDT)
  • Ivana (Mon Jun 17 2013 - 14:39:00 CDT)
  • Vibhor Agrawal (Sat Jun 15 2013 - 21:18:13 CDT)
• ERROR IN TIP4P WATER SIMULATION IN NAMD2.9
  • Roman Shirokov (Tue Sep 03 2013 - 16:44:57 CDT)
  • Uday Midya (Sun Aug 11 2013 - 07:09:05 CDT)
  • Uday Midya (Sun Aug 11 2013 - 02:19:47 CDT)
• error message
  • Richard Wood (Tue Jun 03 2014 - 19:13:26 CDT)
• Error on write to binary file
  • Mihaela Drenscko (Mon Dec 22 2014 - 18:02:54 CST)
• error when doing minimization with the charmm Drude FF
  • Frank Haverkort (Fri Aug 30 2013 - 08:48:43 CDT)
  • Frank Haverkort (Wed Aug 28 2013 - 05:23:49 CDT)
• Error when running MIC version of namd on Stampede
  • Chen Wei (Fri Feb 21 2014 - 09:49:38 CST)
• error while making psf file for bacteriorhodopsin system
  • Faezeh Mottaghitalab (Fri May 09 2014 - 13:10:55 CDT)
  • Kenno Vanommeslaeghe (Fri May 09 2014 - 11:38:08 CDT)
  • Kenno Vanommeslaeghe (Thu May 08 2014 - 15:57:52 CDT)
  • Faezeh Mottaghitalab (Thu May 08 2014 - 15:11:26 CDT)
• Error while running the infiniband version.
  • Shubhra Ghosh Dastidar (Wed Jun 12 2013 - 07:52:36 CDT)
• Error with dummy atoms
  • George Patargias (Wed Nov 27 2013 - 11:07:40 CST)
• Error with NAMD Energy
  • Anurag Sharma (Mon Mar 25 2013 - 13:05:00 CDT)
• Error with show_replicas.vmd
  • Francesco Pietra (Tue Sep 03 2013 - 04:44:55 CDT)
• ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG!
  • Axel Kohlmeyer (Mon Feb 17 2014 - 21:39:00 CST)
  • Axel Kohlmeyer (Mon Feb 17 2014 - 17:26:41 CST)
  • Miss. State (Mon Feb 17 2014 - 17:05:09 CST)
• ERROR: CALCULATED VDWA/B FORCES DOES NOT MATCH ENERGY
  • Shalton Evans (Mon Feb 03 2014 - 21:13:41 CST)
• ERROR: Constraint failure in RATTLE algorithm for atom 474!
  • suresh satpati (Tue Apr 09 2013 - 00:54:41 CDT)
• ERROR: Constraint failure in RATTLE algorithm for atom 593!
  • Nutan Preety (Mon Feb 04 2013 - 06:26:44 CST)
• ERROR: Could not translate the value....into a Vector for the option 'cellOrigin'
  • Jose Borreguero (Mon Jul 15 2013 - 16:35:08 CDT)
  • Axel Kohlmeyer (Mon Jul 15 2013 - 16:25:22 CDT)
  • Jose Borreguero (Mon Jul 15 2013 - 16:19:31 CDT)
• ERROR: Molecule destroyed by fatal error
  • Axel Kohlmeyer (Mon Jan 27 2014 - 13:37:58 CST)
  • Marlet Martinez (Mon Jan 27 2014 - 13:31:18 CST)
• Evaluate energy of "protein + two closest ions"
  • Xiaodong Pang (Tue Aug 06 2013 - 17:25:45 CDT)
• exchange force constants
  • Lu Hong (Mon Jul 21 2014 - 11:25:25 CDT)
  • Sunhwan Jo (Mon Jul 21 2014 - 09:30:08 CDT)
  • Lu Hong (Mon Jul 21 2014 - 08:50:24 CDT)
• excluded interactions (NNB) in psf file for FEP simulations
  • Aman (Tue Aug 27 2013 - 10:16:38 CDT)
• Excluding non bonded interactions between segments
  • Fotis Baltoumas (Tue Apr 08 2014 - 07:08:40 CDT)
  • Jérôme Hénin (Tue Apr 08 2014 - 06:56:22 CDT)
  • Fotis Baltoumas (Tue Apr 08 2014 - 06:57:35 CDT)
  • Jérôme Hénin (Wed Apr 02 2014 - 08:09:21 CDT)
  • Fotis Baltoumas (Wed Apr 02 2014 - 07:40:29 CDT)
• expected speed up after fixing atoms?
  • Jose Borreguero (Wed Sep 24 2014 - 14:26:06 CDT)
  • JC Gumbart (Wed Sep 24 2014 - 14:15:54 CDT)
  • Kenno Vanommeslaeghe (Wed Sep 24 2014 - 14:06:46 CDT)
  • Aron Broom (Wed Sep 24 2014 - 14:07:32 CDT)
  • Jose Borreguero (Wed Sep 24 2014 - 13:41:02 CDT)
  • Aron Broom (Wed Sep 24 2014 - 13:10:45 CDT)
  • Jose Borreguero (Wed Sep 24 2014 - 12:44:48 CDT)
• explicit membrane in implicit solvent
  • Kenno Vanommeslaeghe (Mon Nov 03 2014 - 10:46:24 CST)
  • Gisella Alfonsino (Mon Nov 03 2014 - 05:00:36 CST)
• explicit NVT simulation
  • Hailey Bureau (Tue Sep 10 2013 - 10:35:24 CDT)
  • Kenno Vanommeslaeghe (Mon Sep 09 2013 - 13:46:20 CDT)
  • Axel Kohlmeyer (Mon Sep 09 2013 - 13:02:37 CDT)
  • Kenno Vanommeslaeghe (Mon Sep 09 2013 - 12:24:29 CDT)
  • Axel Kohlmeyer (Mon Sep 09 2013 - 09:06:19 CDT)
  • Jérôme Hénin (Mon Sep 09 2013 - 08:31:03 CDT)
  • Axel Kohlmeyer (Mon Sep 09 2013 - 08:17:45 CDT)
  • Hailey Bureau (Mon Sep 09 2013 - 08:07:19 CDT)
  • Hailey Bureau (Sun Sep 08 2013 - 17:54:26 CDT)
• Exploding vdW energies in automatically generated POPC membranes
  • Lucas (Mon May 06 2013 - 15:33:47 CDT)
• Extent of Sampling possible using classical all-atom MD Simulations
  • Aditya Ranganathan (Tue Oct 01 2013 - 08:22:42 CDT)
• Extract KE, PE and total energy from log file
  • Mihaela Drenscko (Sat Nov 02 2013 - 17:49:06 CDT)
  • Ajasja LjubetiÄ� (Thu Oct 31 2013 - 18:05:37 CDT)
  • Aron Broom (Thu Oct 31 2013 - 15:39:05 CDT)
  • Mihaela Drenscko (Thu Oct 31 2013 - 15:15:04 CDT)
• Extracting Kinetic Energy of Certain Atoms
  • JAVAD NOROOZI (Wed Dec 17 2014 - 03:19:09 CST)
• FAD topology and parameters
  • Kenno Vanommeslaeghe (Tue Feb 18 2014 - 20:01:28 CST)
  • Tanner, John J. (Mon Feb 17 2014 - 10:15:52 CST)
  • flavio seixas (Mon Feb 17 2014 - 06:01:14 CST)
  • Tanner, John J. (Sun Feb 16 2014 - 15:30:38 CST)
• fail to guess missing coordinates
  • Liqi Feng (Tue May 07 2013 - 13:30:21 CDT)
• Failure of namd2.10 in keeping trace of cell in t-remd
  • Francesco Pietra (Tue Feb 18 2014 - 05:44:34 CST)
• Failure with compilation namd2.9-cuda_plumed1.3_recon
  • Francesco Pietra (Sat Jun 22 2013 - 12:15:26 CDT)
• Fatal Error by charmc.../usr/bin/ld: cannot find -lsrfftw. Please help!
  • Jose Borreguero (Tue Feb 12 2013 - 17:26:12 CST)
• FATAL ERROR Unknown parameter in charmm parameter file
  • Kenno Vanommeslaeghe (Mon Jul 01 2013 - 15:07:30 CDT)
  • Cat Chenal (Mon Jul 01 2013 - 13:19:27 CDT)
• Fatal error..
  • Gurpreet Kaur Dhindsa (Sun Jun 22 2014 - 17:32:16 CDT)
• FATAL ERROR: Bad global bond count!
  • Peterson J (Wed Jun 12 2013 - 11:01:23 CDT)
• FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE
  • zeynab mohamad hoseyni (Thu Feb 20 2014 - 13:31:50 CST)
• FATAL ERROR: error parsing config file while executing <feff>
  • Mihaela Drenscko (Sun Nov 09 2014 - 11:39:11 CST)
• FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small.
  • Sandhyaa Subramanian (Wed Sep 03 2014 - 02:37:32 CDT)
  • Sandhyaa Subramanian (Wed Sep 03 2014 - 02:34:06 CDT)
  • Tristan Croll (Wed Sep 03 2014 - 02:26:27 CDT)
  • Tristan Croll (Tue Sep 02 2014 - 17:27:20 CDT)
  • Sandhyaa Subramanian (Sat Aug 30 2014 - 09:06:14 CDT)
• FATAL ERROR: PME offload requires exactly one CUDA device per process.
  • Maxime Boissonneault (Fri Aug 22 2014 - 06:40:06 CDT)
• FATAL ERROR: seek failed while writing DCD file: No such file or directory
  • Douglas Houston (Fri Dec 19 2014 - 08:33:31 CST)
  • Douglas Houston (Thu Dec 18 2014 - 14:39:51 CST)
• FATAL ERROR: Setting parameter colvars from script failed!
  • Jérôme Hénin (Tue Sep 30 2014 - 13:28:48 CDT)
  • Jérôme Hénin (Tue Sep 30 2014 - 13:04:27 CDT)
  • Jérôme Hénin (Tue Sep 30 2014 - 10:17:02 CDT)
  • Mihaela Drenscko (Tue Sep 30 2014 - 09:27:18 CDT)
• FATAL ERROR: Setting parameter tclForces from script failed!
  • zeynab mohamad hoseyni (Tue Apr 22 2014 - 02:43:23 CDT)
• FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C NH3 (ATOMS 105 107)
  • Kenno Vanommeslaeghe (Fri Jul 25 2014 - 16:44:15 CDT)
  • Cenk Denktas (Fri Jul 25 2014 - 15:30:40 CDT)
• Fe-N bond parameters
  • Francesco Pietra (Sun Apr 28 2013 - 09:55:16 CDT)
• FEP calculations: optimizing the dlambda, number of steps
  • Shyno Mathew (Thu Dec 12 2013 - 09:37:22 CST)
  • Jérôme Hénin (Thu Dec 12 2013 - 03:05:30 CST)
  • Shyno Mathew (Wed Dec 11 2013 - 15:37:08 CST)
  • Shyno Mathew (Wed Dec 11 2013 - 15:00:01 CST)
  • Shyno Mathew (Tue Dec 10 2013 - 10:28:10 CST)
  • Shyno Mathew (Tue Dec 03 2013 - 17:12:43 CST)
  • Shyno Mathew (Fri Nov 22 2013 - 12:09:37 CST)
  • Shyno Mathew (Fri Nov 22 2013 - 11:01:18 CST)
  • Jérôme Hénin (Fri Nov 22 2013 - 10:49:17 CST)
  • Shyno Mathew (Fri Nov 22 2013 - 10:32:44 CST)
  • Jérôme Hénin (Fri Nov 22 2013 - 04:21:54 CST)
  • Shyno Mathew (Thu Nov 21 2013 - 13:33:34 CST)
  • Jérôme Hénin (Tue Nov 19 2013 - 04:25:39 CST)
  • Shyno Mathew (Mon Nov 18 2013 - 23:21:35 CST)
  • Jérôme Hénin (Mon Nov 18 2013 - 17:32:09 CST)
  • Shyno Mathew (Mon Nov 18 2013 - 12:56:19 CST)
  • Shyno Mathew (Mon Nov 18 2013 - 11:44:59 CST)
  • Shyno Mathew (Fri Nov 15 2013 - 14:41:13 CST)
  • Shyno Mathew (Fri Nov 15 2013 - 15:02:06 CST)
• FEP Error - TCL
  • Jérôme Hénin (Tue Nov 12 2013 - 16:17:13 CST)
  • Jérôme Hénin (Wed Oct 30 2013 - 11:07:33 CDT)
  • Eudes Fileti (Tue Oct 29 2013 - 14:28:17 CDT)
• FEP error using CUDA
  • Gianluca Interlandi (Sun Apr 13 2014 - 23:14:03 CDT)
  • Sadegh Faramarzi Ganjabad (Sun Apr 13 2014 - 22:42:12 CDT)
• FEP failure - FFTW problem?
  • JC Gumbart (Fri Sep 20 2013 - 14:16:37 CDT)
• FEP is in kj/mol
  • Javad Noroozi (Sun Apr 27 2014 - 08:32:33 CDT)
• FEP of water molecule in binding pocket
  • Monika Sharma (Wed May 28 2014 - 15:35:33 CDT)
• FEP on an amino acid ligand
  • JC Gumbart (Wed Jan 23 2013 - 18:10:00 CST)
  • Gordon Wells (Wed Jan 23 2013 - 17:18:46 CST)
  • JC Gumbart (Wed Jan 23 2013 - 16:45:19 CST)
  • Gordon Wells (Wed Jan 23 2013 - 14:44:41 CST)
  • JC Gumbart (Wed Jan 23 2013 - 11:29:57 CST)
  • JC Gumbart (Wed Jan 23 2013 - 11:16:32 CST)
  • Thomas Albers (Wed Jan 23 2013 - 09:30:36 CST)
  • JC Gumbart (Wed Jan 23 2013 - 08:24:25 CST)
  • Jérôme Hénin (Wed Jan 23 2013 - 08:13:30 CST)
  • Thomas Albers (Wed Jan 23 2013 - 07:36:36 CST)
  • Thomas Albers (Tue Jan 22 2013 - 16:36:59 CST)
  • Thomas Albers (Mon Jan 21 2013 - 19:44:20 CST)
• FEP OpenMPI Error
  • Andrew Miglino (Fri Mar 22 2013 - 10:43:43 CDT)
• FEP result analysis
  • Javad Noroozi (Sat Mar 01 2014 - 03:37:29 CST)
• FEP simulation on membrane protein
  • Kapil jain (Sun Jul 21 2013 - 22:37:44 CDT)
• FEP simulation: protein moving out of water box.
  • Niklaus Johner (Tue Nov 05 2013 - 21:21:48 CST)
  • venkata agasthya (Tue Nov 05 2013 - 19:39:51 CST)
• FEP, Ewald size-dependence charge correction
  • JC Gumbart (Sat Sep 13 2014 - 18:38:44 CDT)
  • Sebastian Stolzenberg (Fri Sep 12 2014 - 13:21:10 CDT)
  • Sebastian Stolzenberg (Sun Sep 07 2014 - 10:23:17 CDT)
  • Sebastian Stolzenberg (Tue Sep 02 2014 - 15:12:17 CDT)
• ffTK and phase angles
  • Kenno Vanommeslaeghe (Thu Jun 19 2014 - 20:01:05 CDT)
  • Benjamin Hill (Thu Jun 19 2014 - 17:43:28 CDT)
• FFTK Atom types
  • Francesco Pietra (Wed Mar 27 2013 - 02:21:13 CDT)
• ffTK problem: initial parameter fiel is viod of atoms!
  • Mayne, Christopher G (Mon Oct 20 2014 - 11:45:39 CDT)
  • Zeinab Emami (Mon Oct 20 2014 - 11:33:25 CDT)
  • Mayne, Christopher G (Mon Oct 20 2014 - 09:55:55 CDT)
  • Zeinab Emami (Wed Oct 15 2014 - 07:42:57 CDT)
• ffTK problem: initial parameter file is void of of atoms!
  • Zeinab Emami (Thu Oct 16 2014 - 04:15:55 CDT)
• ffTK problem: OPT.Charges
  • Zeinab Emami (Fri Nov 07 2014 - 09:14:15 CST)
• file for fixed atoms is not found! - but the file exist actually
  • Rebecca Swett (Fri Apr 05 2013 - 09:23:54 CDT)
  • Sridhar Kumar Kannam (Fri Apr 05 2013 - 01:24:44 CDT)
  • Ramya Gamini (Fri Apr 05 2013 - 00:25:56 CDT)
  • Sridhar Kumar Kannam (Thu Apr 04 2013 - 21:33:52 CDT)
• Final link of namd2 executable fails under AIX with xlC compiler
  • Mark Cheeseman (Mon Mar 25 2013 - 17:07:05 CDT)
• First meeting with NAMD
  • Kenno Vanommeslaeghe (Fri Sep 13 2013 - 12:19:52 CDT)
  • James Starlight (Fri Sep 13 2013 - 08:41:12 CDT)
  • James Starlight (Fri Jun 07 2013 - 00:13:55 CDT)
  • James Starlight (Thu Jun 06 2013 - 06:31:42 CDT)
  • James Starlight (Wed Jun 05 2013 - 05:22:28 CDT)
  • Giacomo Fiorin (Tue Jun 04 2013 - 10:05:52 CDT)
  • James Starlight (Tue Jun 04 2013 - 09:46:54 CDT)
  • Giacomo Fiorin (Tue Jun 04 2013 - 09:38:15 CDT)
  • James Starlight (Tue Jun 04 2013 - 09:33:19 CDT)
  • Ajasja LjubetiÄ� (Tue Jun 04 2013 - 08:45:44 CDT)
  • Branko (Tue Jun 04 2013 - 08:46:07 CDT)
  • James Starlight (Tue Jun 04 2013 - 08:25:06 CDT)
  • James Starlight (Tue Jun 04 2013 - 03:13:10 CDT)
  • James Starlight (Mon Jun 03 2013 - 13:08:01 CDT)
  • Giacomo Fiorin (Mon Jun 03 2013 - 09:16:05 CDT)
  • James Starlight (Mon Jun 03 2013 - 09:08:58 CDT)
• Fixed and SMD atoms
  • Mihaela Drenscko (Sat Oct 19 2013 - 14:16:47 CDT)
• fixed atom/Constraint failure in RATTLE algorithm/
  • MEHRAN MB (Tue Jun 04 2013 - 10:26:47 CDT)
  • MEHRAN MB (Fri May 31 2013 - 11:33:03 CDT)
• Fixed atoms.
  • Maxim Belkin (Thu Jun 05 2014 - 17:14:48 CDT)
  • Aron Broom (Thu Jun 05 2014 - 17:03:12 CDT)
  • Gurpreet Kaur Dhindsa (Thu Jun 05 2014 - 16:15:05 CDT)
• FixedAtoms and Reference group in spinangle colvar
  • nicolas martin (Thu May 22 2014 - 07:06:08 CDT)
  • Jérôme Hénin (Thu May 22 2014 - 07:00:25 CDT)
  • nicolas martin (Thu May 22 2014 - 06:21:02 CDT)
  • Giacomo Fiorin (Sun May 11 2014 - 17:27:29 CDT)
  • nicolas martin (Sun May 11 2014 - 16:52:42 CDT)
  • Jérôme Hénin (Fri May 09 2014 - 13:53:56 CDT)
  • nicolas martin (Fri May 09 2014 - 09:01:28 CDT)
• Fixing atoms while equilibration
  • Kenno Vanommeslaeghe (Mon Sep 01 2014 - 10:52:07 CDT)
  • Axel Kohlmeyer (Mon Sep 01 2014 - 08:14:37 CDT)
  • Siva Dasetty (Mon Sep 01 2014 - 08:07:59 CDT)
  • Axel Kohlmeyer (Mon Sep 01 2014 - 07:48:34 CDT)
  • Siva Dasetty (Mon Sep 01 2014 - 07:33:57 CDT)
  • Siva Dasetty (Fri Aug 29 2014 - 20:12:21 CDT)
• Fixing Langevin piston to allow off-diagonal stress (and why does the source say "FIX THIS"?)
  • FX (Wed Mar 06 2013 - 16:36:04 CST)
  • FX (Wed Mar 06 2013 - 04:43:49 CST)
• Flags for TIP3 water with NAMD/AMBER FF
  • Francesco Pietra (Tue May 28 2013 - 10:46:01 CDT)
• floating point reproduceability
  • Axel Kohlmeyer (Fri Apr 19 2013 - 03:02:11 CDT)
  • Thomas Brian (Thu Apr 18 2013 - 23:28:31 CDT)
  • Thomas Brian (Wed Apr 17 2013 - 17:08:34 CDT)
• Folic acid parameters
  • Haleh a (Wed Oct 01 2014 - 01:42:20 CDT)
  • Kenno Vanommeslaeghe (Tue Sep 30 2014 - 11:37:03 CDT)
  • Kenno Vanommeslaeghe (Tue Sep 30 2014 - 10:43:21 CDT)
  • Fotis Baltoumas (Tue Sep 30 2014 - 10:06:43 CDT)
  • Haleh a (Tue Sep 30 2014 - 08:44:38 CDT)
• Force field design
  • Axel Kohlmeyer (Thu Jul 24 2014 - 14:35:11 CDT)
  • Thomas Evangelidis (Thu Jul 24 2014 - 14:31:31 CDT)
  • Gianluca Interlandi (Thu Jul 24 2014 - 14:22:41 CDT)
  • Kenno Vanommeslaeghe (Thu Jul 24 2014 - 11:12:18 CDT)
  • R.J. Swett (Wed Jul 23 2014 - 23:03:48 CDT)
  • Abhishek TYAGI (Wed Jul 23 2014 - 19:57:40 CDT)
  • Gianluca Interlandi (Wed Jul 23 2014 - 23:30:58 CDT)
  • Axel Kohlmeyer (Wed Jul 23 2014 - 22:06:21 CDT)
  • Kenno Vanommeslaeghe (Wed Jul 23 2014 - 18:20:53 CDT)
  • Abhishek TYAGI (Wed Jul 23 2014 - 00:23:36 CDT)
  • Abhishek TYAGI (Tue Jul 22 2014 - 23:04:23 CDT)
  • Axel Kohlmeyer (Wed Jul 23 2014 - 05:13:16 CDT)
  • Axel Kohlmeyer (Tue Jul 22 2014 - 23:36:30 CDT)
  • Abhishek TYAGI (Tue Jul 22 2014 - 05:40:00 CDT)
  • Axel Kohlmeyer (Tue Jul 22 2014 - 11:14:16 CDT)
  • Kenno Vanommeslaeghe (Tue Jul 22 2014 - 10:40:37 CDT)
  • Mayne, Christopher G (Tue Jul 22 2014 - 09:01:58 CDT)
  • Kenno Vanommeslaeghe (Mon Jul 21 2014 - 10:47:12 CDT)
  • Abhishek TYAGI (Sat Jul 19 2014 - 07:44:53 CDT)
  • Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:24:29 CDT)
  • Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:06:23 CDT)
  • Mayne, Christopher G (Wed Jul 16 2014 - 10:46:48 CDT)
  • Sunhwan Jo (Wed Jul 16 2014 - 07:37:19 CDT)
  • Gianluca Interlandi (Wed Jul 16 2014 - 00:32:49 CDT)
  • Gianluca Interlandi (Tue Jul 15 2014 - 22:32:35 CDT)
  • Aron Broom (Tue Jul 15 2014 - 21:58:07 CDT)
  • Abhishek TYAGI (Tue Jul 15 2014 - 11:55:35 CDT)
• Force field for sulfated tyrosines
  • Kenno Vanommeslaeghe (Mon May 05 2014 - 13:11:47 CDT)
  • Shaon Chakrabarti (Sun May 04 2014 - 21:35:38 CDT)
• force field parameter for graphene oxide
  • Kenno Vanommeslaeghe (Fri Mar 07 2014 - 11:28:50 CST)
  • Asis Jana (Fri Mar 07 2014 - 07:58:34 CST)
• Force Field Parameters for PEG
  • Axel Kohlmeyer (Mon Feb 24 2014 - 10:49:58 CST)
  • Roy Fernando (Mon Feb 24 2014 - 10:48:08 CST)
  • Aron Broom (Mon Feb 24 2014 - 10:29:42 CST)
  • Roy Fernando (Mon Feb 24 2014 - 10:22:47 CST)
  • Roy Fernando (Wed Nov 06 2013 - 13:58:57 CST)
  • Kenno Vanommeslaeghe (Wed Nov 06 2013 - 13:27:41 CST)
  • Roy Fernando (Wed Nov 06 2013 - 12:21:46 CST)
• forward
  • Gianluca Interlandi (Thu Sep 05 2013 - 21:43:40 CDT)
  • minh nhut (Thu Sep 05 2013 - 21:01:00 CDT)
• Free energy calculation of proton transfer with FEP
  • Huihui Liu (Sat Apr 27 2013 - 03:49:10 CDT)
• Free Energy Calculation Question
  • Jérôme Hénin (Thu Jun 20 2013 - 16:18:57 CDT)
  • Aron Broom (Thu Jun 20 2013 - 16:22:34 CDT)
  • Kasra Fattah (Thu Jun 20 2013 - 15:28:28 CDT)
• Free Energy Calculation Using Thermodynamic Integration
  • Javad Noroozi (Mon Mar 17 2014 - 02:06:08 CDT)
• Free energy calculations
  • Jérôme Hénin (Tue May 28 2013 - 05:36:55 CDT)
  • karthik kumar (Mon May 27 2013 - 07:47:33 CDT)
• free energy methods cheat-sheet/comparison chart
  • Dale l. Schruben (Mon Mar 25 2013 - 21:06:22 CDT)
  • Giacomo Fiorin (Mon Mar 25 2013 - 17:11:29 CDT)
  • Niklaus Johner (Mon Mar 25 2013 - 17:06:36 CDT)
  • Aron Broom (Mon Mar 25 2013 - 16:43:54 CDT)
  • Niklaus Johner (Mon Mar 25 2013 - 16:17:06 CDT)
  • Jeffrey Potoff (Mon Mar 25 2013 - 15:09:53 CDT)
  • Thomas C. Bishop (Mon Mar 25 2013 - 14:56:11 CDT)
  • JC Gumbart (Mon Mar 25 2013 - 14:50:04 CDT)
  • Aron Broom (Mon Mar 25 2013 - 14:28:00 CDT)
  • Thomas C. Bishop (Mon Mar 25 2013 - 13:49:16 CDT)
• Free Energy Perturbation
  • Jérôme Hénin (Thu Feb 27 2014 - 07:05:00 CST)
  • Javad Noroozi (Tue Feb 25 2014 - 00:36:30 CST)
• Free Energy using atomic coordinates as CVs
  • Jérôme Hénin (Fri Jul 12 2013 - 05:12:23 CDT)
  • Teerapong Pirojsirikul (Thu Jul 11 2013 - 17:59:31 CDT)
• Free Energy Workshop, Münster, March 9-11Q_2015?=
  • Vlad Cojocaru (Fri Dec 19 2014 - 12:02:00 CST)
• full electrostatics and pairlistdist
  • Jonathan Phillips (Fri Apr 18 2014 - 05:51:02 CDT)
  • Jason Swails (Wed Apr 16 2014 - 08:27:34 CDT)
  • Jonathan Phillips (Mon Apr 14 2014 - 16:25:04 CDT)
• FullDirect Electrostatics
  • Adrian (Tue Jul 23 2013 - 09:51:53 CDT)
• Fwd:
  • manish kesherwani (Sun Nov 24 2013 - 06:29:35 CST)
• Fwd: [External] Boost value in aMD simulation
  • Thomas Evangelidis (Thu Aug 21 2014 - 06:05:05 CDT)
  • Thomas Evangelidis (Tue Aug 19 2014 - 05:24:17 CDT)
• Fwd: About "add solvation"
  • Francesco Pietra (Mon Jan 21 2013 - 03:49:06 CST)
• Fwd: Bug in T-REMD with colvars
  • Francesco Pietra (Tue Dec 03 2013 - 13:31:24 CST)
  • Francesco Pietra (Tue Dec 03 2013 - 02:55:43 CST)
• Fwd: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact?
  • somedatta pal (Tue Mar 19 2013 - 02:54:35 CDT)
• Fwd: Cannot find colvar dih1 (dih colvars)
  • Francesco Pietra (Wed Dec 24 2014 - 05:53:54 CST)
  • Maxim Belkin (Tue Dec 23 2014 - 15:59:09 CST)
  • Jeff Comer (Tue Dec 23 2014 - 15:35:37 CST)
  • Francesco Pietra (Tue Dec 23 2014 - 15:01:39 CST)
  • Francesco Pietra (Tue Dec 23 2014 - 14:23:04 CST)
• Fwd: charm-gui membrane builder
  • James Starlight (Mon Sep 16 2013 - 07:07:43 CDT)
• Fwd: colvars with replica exchange molecular dynamics
  • Francesco Pietra (Thu Jan 30 2014 - 04:38:47 CST)
  • Francesco Pietra (Wed Jan 29 2014 - 10:40:22 CST)
• Fwd: Constraint failure in RATTLE
  • Francesco Pietra (Sun Mar 30 2014 - 03:07:50 CDT)
• Fwd: CUDA error in cuda_check_remote_progress on Pe 2
  • Francesco Pietra (Sat Apr 06 2013 - 04:49:21 CDT)
  • Francesco Pietra (Fri Apr 05 2013 - 10:04:48 CDT)
  • Francesco Pietra (Fri Apr 05 2013 - 09:58:58 CDT)
• Fwd: deca-alanin folding by remd parallel tempering
  • Francesco Pietra (Wed Sep 04 2013 - 04:35:45 CDT)
• Fwd: Error in PSF gen
  • Vibhor Agrawal (Mon Jun 17 2013 - 11:48:27 CDT)
• Fwd: Failure of namd2.10 in keeping trace of cell in t-remd
  • Francesco Pietra (Tue Feb 18 2014 - 12:45:35 CST)
• Fwd: Failure with compilation namd2.9-cuda_plumed1.3_recon
  • Francesco Pietra (Mon Jun 24 2013 - 04:48:24 CDT)
• Fwd: Getting extra atoms by Patching!
  • Sadegh Faramarzi Ganjabad (Thu May 08 2014 - 15:49:14 CDT)
• Fwd: Inconsistency in fast table energy vs force
  • Francesco Pietra (Sat Apr 13 2013 - 05:27:01 CDT)
• Fwd: Low global exclusion count on parallel tempering, not on MD
  • Francesco Pietra (Thu Aug 22 2013 - 03:32:18 CDT)
  • Francesco Pietra (Wed Aug 21 2013 - 11:27:44 CDT)
• Fwd: Majordomo results
  • Kuldeep Roy (Wed Jan 01 2014 - 16:33:22 CST)
  • farzad kiani (Wed Jan 01 2014 - 14:57:29 CST)
  • Faezeh Mottaghitalab (Wed Jan 01 2014 - 05:19:11 CST)
• Fwd: membrane lipid involvement of cholesterol
  • Thomas Evangelidis (Sat Jul 26 2014 - 06:39:30 CDT)
• Fwd: NAMD + PLUMED COMPILATION
  • Francesco Pietra (Fri Mar 01 2013 - 00:52:14 CST)
• Fwd: NAMD 2.9 CUDA compilation
  • Francesco Pietra (Mon Mar 11 2013 - 10:56:51 CDT)
• Fwd: NAMD tcouple atoms moving too fast
  • Tao Qu (Thu Jun 06 2013 - 15:04:56 CDT)
• Fwd: PCIexpress 3.0 for MD with NAMD on GPUs
  • Francesco Pietra (Tue Nov 19 2013 - 02:50:42 CST)
  • Francesco Pietra (Mon Nov 18 2013 - 03:13:05 CST)
  • Francesco Pietra (Sun Nov 17 2013 - 09:06:51 CST)
• Fwd: PCL dcd files
  • Mihaela Drenscko (Mon Sep 29 2014 - 11:38:30 CDT)
• Fwd: Pressure in NPT ensamble
  • Cobalto Tetracloruro (Fri May 31 2013 - 11:15:49 CDT)
• Fwd: question about CUDA-enabled
  • maryam atabay (Mon Nov 24 2014 - 05:08:04 CST)
• Fwd: Reg: solvation in DMSO
  • Kenno Vanommeslaeghe (Wed Sep 03 2014 - 14:43:59 CDT)
  • Akshay Bhatnagar (Wed Sep 03 2014 - 02:36:04 CDT)
• Fwd: Regarding Temperature calculation from velocity trajectory of NAMD-2.9
  • Shailesh Pandey (Thu Jul 10 2014 - 09:31:03 CDT)
• Fwd: REMD on IBM iDataPlex DX360M3
  • Francesco Pietra (Tue Jul 08 2014 - 00:41:54 CDT)
• Fwd: replica exchange and colvars
  • Francesco Pietra (Wed Jul 31 2013 - 02:49:11 CDT)
• Fwd: Restarting T-REMD with colvars
  • Francesco Pietra (Tue Nov 05 2013 - 01:53:50 CST)
  • Francesco Pietra (Tue Nov 05 2013 - 01:48:45 CST)
• Fwd: Stray PME grid charges on increasing number of replicas and T-range with T-REMD
  • Francesco Pietra (Tue Sep 10 2013 - 05:33:03 CDT)
• Fwd: TCL command "run" erratic
  • Francesco Pietra (Mon Mar 17 2014 - 02:22:26 CDT)
  • Aron Broom (Sun Mar 16 2014 - 15:58:34 CDT)
  • Francesco Pietra (Sun Mar 16 2014 - 14:57:53 CDT)
  • Francesco Pietra (Sun Mar 16 2014 - 14:48:12 CDT)
• Fwd: Troubles to converge while running bidirectional FEP
  • GALLY Jose Manuel (Thu Jun 27 2013 - 02:12:24 CDT)
• Fwd: vmd-l: HEME acting unplanar
  • Francesco Pietra (Wed Apr 24 2013 - 15:07:54 CDT)
• GBIS CUDA not yet compatible with fixed atoms
  • Siva Dasetty (Fri Sep 05 2014 - 18:01:13 CDT)
  • Aron Broom (Fri Sep 05 2014 - 16:50:39 CDT)
  • Siva Dasetty (Fri Sep 05 2014 - 15:24:45 CDT)
  • Jim Phillips (Fri Sep 05 2014 - 15:16:04 CDT)
  • Siva Dasetty (Fri Sep 05 2014 - 10:03:12 CDT)
• GBIS using CUDA enabled NAMD
  • Siva Dasetty (Wed Sep 17 2014 - 09:36:03 CDT)
  • Jim Phillips (Wed Sep 10 2014 - 16:32:32 CDT)
  • David Hardy (Wed Sep 10 2014 - 14:46:22 CDT)
  • Siva Dasetty (Tue Sep 09 2014 - 18:59:01 CDT)
• Generalized Born Implicit solvation with implicit membrane
  • Thomas Evangelidis (Fri Mar 14 2014 - 14:22:36 CDT)
  • Fotis Baltoumas (Fri Mar 14 2014 - 08:28:45 CDT)
• Generating .psf for amorphous disaccharide
  • JC Gumbart (Sat Mar 01 2014 - 21:41:45 CST)
  • Maxwell Wesley Terban (Fri Feb 28 2014 - 13:10:56 CST)
• Generating topology files for crystalline materials
  • Axel Kohlmeyer (Sun Feb 10 2013 - 16:05:16 CST)
  • FX (Sun Feb 10 2013 - 15:58:31 CST)
  • Axel Kohlmeyer (Sun Feb 10 2013 - 15:11:55 CST)
  • Axel Kohlmeyer (Sun Feb 10 2013 - 14:54:45 CST)
  • FX (Sun Feb 10 2013 - 14:02:16 CST)
  • Axel Kohlmeyer (Sun Feb 10 2013 - 12:22:09 CST)
  • FX (Sun Feb 10 2013 - 12:05:26 CST)
• Geometric center of a residue over time
  • Sindu (Wed Jul 24 2013 - 05:33:32 CDT)
• get topology and parameter file for the ligand.
  • Kenno Vanommeslaeghe (Wed Oct 16 2013 - 17:21:38 CDT)
  • Ramin Ekhteiari (Wed Oct 16 2013 - 12:14:15 CDT)
• getting different dihedral energy with two identical backbones
  • Joyce Yang (Mon Sep 29 2014 - 21:15:54 CDT)
  • Jim Phillips (Fri Sep 26 2014 - 17:18:24 CDT)
  • Joyce Yang (Wed Sep 24 2014 - 16:45:52 CDT)
• Getting extra atoms by Patching!
  • Kenno Vanommeslaeghe (Thu May 08 2014 - 12:38:10 CDT)
  • Kenno Vanommeslaeghe (Mon May 05 2014 - 11:45:48 CDT)
  • Michelle Kuttel (Sat May 03 2014 - 01:11:50 CDT)
  • Sadegh Faramarzi Ganjabad (Fri May 02 2014 - 18:51:31 CDT)
• Gold nanoparticle
  • Kenno Vanommeslaeghe (Fri Sep 27 2013 - 13:30:35 CDT)
  • Luca Bellucci (Fri Sep 27 2013 - 03:10:09 CDT)
  • Dr. Eddie (Thu Sep 26 2013 - 09:42:36 CDT)
  • lcbllcc_at_gmail.com (Thu Sep 26 2013 - 04:07:26 CDT)
  • Ana Celia Vila Verde (Thu Sep 26 2013 - 03:22:47 CDT)
  • Axel Kohlmeyer (Wed Sep 25 2013 - 12:37:13 CDT)
  • Dr. Eddie (Wed Sep 25 2013 - 11:52:48 CDT)
  • Axel Kohlmeyer (Wed Sep 25 2013 - 11:34:39 CDT)
  • Dr. Eddie (Wed Sep 25 2013 - 11:25:45 CDT)
• GPU/CPU workstation optimal simulation parameters for NAMD2.9 performance
  • Pino, James Christopher (Tue Feb 18 2014 - 12:00:34 CST)
• GPUs silently stop working during simulation when oversubscribed
  • Benjamin Merget (Thu Feb 28 2013 - 04:04:30 CST)
  • Benjamin Merget (Thu Feb 28 2013 - 02:51:39 CST)
• Graphene simualtion
  • Abhishek TYAGI (Mon Oct 20 2014 - 03:28:51 CDT)
• grcarma : a graphical user interface to carma
  • Lenin Domínguez (Sun Jan 05 2014 - 18:20:50 CST)
  • Nicholas M Glykos (Wed Apr 17 2013 - 09:33:24 CDT)
• gromacs to NAMD
  • Axel Kohlmeyer (Tue Jul 09 2013 - 15:48:45 CDT)
  • Peterson J (Tue Jul 09 2013 - 14:55:46 CDT)
• Guideline for selecting water box size.
  • Aron Broom (Sun Feb 16 2014 - 19:12:30 CST)
  • Hyuntae Na (Sun Feb 16 2014 - 18:49:00 CST)
• H-Bond measurements
  • Stephan Grein (Thu Aug 14 2014 - 01:57:40 CDT)
• H-bonds cutoff angle criterian
  • Anurag Sharma (Sun Jan 20 2013 - 10:54:07 CST)
  • Anurag Sharma (Thu Jan 17 2013 - 20:52:40 CST)
• harmonic restraints between multiple atom pairs
  • Tristan Croll (Mon Nov 03 2014 - 23:20:09 CST)
  • Neelanjana Sengupta (Mon Nov 03 2014 - 22:42:33 CST)
• Help regarding PMF with SMD
  • Katherine Parra Pulido (Thu Aug 01 2013 - 10:06:03 CDT)
• Help to solve the error
  • Flora Chettiar (Thu Mar 27 2014 - 01:47:09 CDT)
  • Ivan Gregoretti (Thu Mar 27 2014 - 07:20:50 CDT)
  • Ivan Gregoretti (Wed Mar 26 2014 - 17:11:58 CDT)
  • Flora Chettiar (Wed Mar 26 2014 - 04:00:46 CDT)
• Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!"
  • Aron Broom (Mon May 20 2013 - 21:38:01 CDT)
  • Corey Fugate (Mon May 20 2013 - 17:28:21 CDT)
  • Aron Broom (Mon May 20 2013 - 14:07:56 CDT)
  • Corey Fugate (Mon May 20 2013 - 11:57:14 CDT)
  • Aron Broom (Mon May 20 2013 - 11:16:35 CDT)
  • Corey Fugate (Mon May 20 2013 - 11:08:07 CDT)
• HEME acting unplanar
  • Yarrow Madrona (Sun Apr 21 2013 - 17:48:43 CDT)
• HEME B PARAMETERS
  • Kenno Vanommeslaeghe (Thu Oct 31 2013 - 13:06:26 CDT)
  • Sadegh Faramarzi Ganjabad (Wed Oct 30 2013 - 02:30:09 CDT)
• Hexagonal cell instability during lipid bilayer sim in NAMD 2.9
  • Michael Bokoch (Mon Jul 07 2014 - 21:42:54 CDT)
• hey! you! why did my simulation crash?
  • Edward Lyman (Wed Mar 26 2014 - 10:42:46 CDT)
• Hi
  • Axel Kohlmeyer (Thu Dec 12 2013 - 09:24:31 CST)
  • Gurpreet Kaur Dhindsa (Thu Dec 12 2013 - 09:19:31 CST)
• hi every body,
  • rasti (Wed Aug 21 2013 - 17:19:05 CDT)
• HMMM model
  • Tristan Croll (Wed Oct 30 2013 - 22:51:50 CDT)
• how does NAMD calculate intramolecular electrostatic interactions between Drude pairs?
  • Ana Celia Vila Verde (Thu Aug 29 2013 - 04:07:02 CDT)
• How I can to change the force field function in NAMD for protein phi-value analysis
  • Felipe Merino (Mon Oct 07 2013 - 09:15:48 CDT)
  • Giacomo Fiorin (Mon Oct 07 2013 - 08:30:34 CDT)
  • Juan José Galano Frutos (Mon Oct 07 2013 - 04:55:44 CDT)
• How Pressureprofile output are averaged ?
  • namd_chcwaaa_at_yahoo.com.cn (Fri Jan 04 2013 - 23:21:39 CST)
• How to Amend a PBD file for NAMD
  • Zeinab Emami (Wed Oct 01 2014 - 09:27:15 CDT)
• How to apply a magnetic field with NAMD
  • Faezeh Mottaghitalab (Wed Jun 25 2014 - 15:40:43 CDT)
  • Kenno Vanommeslaeghe (Wed Jun 25 2014 - 10:08:11 CDT)
  • Axel Kohlmeyer (Tue Jun 24 2014 - 19:43:42 CDT)
  • Ajasja LjubetiÄ� (Tue Jun 24 2014 - 16:52:06 CDT)
  • Faezeh Mottaghitalab (Tue Jun 24 2014 - 16:00:48 CDT)
• how to apply force SMD method on an anisotropic geometry
  • Anurag Sharma (Fri Jun 21 2013 - 20:47:47 CDT)
  • Anurag Sharma (Wed Jun 12 2013 - 15:39:34 CDT)
• How to apply Symmetry boundary on NAMD
  • zhangxing (Tue Nov 19 2013 - 17:52:50 CST)
• How to compile NAMD2.9 in IBM AIX UNIX$B!)(B
  • Mengyuan Zhu (Thu Dec 12 2013 - 12:24:42 CST)
• How to converse Coarse-Grained structure into all-atom structure
  • Axel Kohlmeyer (Mon May 06 2013 - 05:09:01 CDT)
  • Fugui (Mon May 06 2013 - 05:02:10 CDT)
• how to convert CHARMM TIP3P to traditional TIP3P
  • Jeffrey Potoff (Wed Mar 06 2013 - 09:07:55 CST)
  • subbarao kanchi (Wed Mar 06 2013 - 05:56:27 CST)
• how to do a vacuum minimization without electrostatics and periodic boundary conditions?
  • Aron Broom (Wed Jun 05 2013 - 10:47:48 CDT)
  • Jose Borreguero (Wed Jun 05 2013 - 10:20:27 CDT)
• How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory
  • zeynab mohamad hoseyni (Mon Apr 28 2014 - 23:12:57 CDT)
• how to fix the problem
  • Jeff Comer (Sat Nov 15 2014 - 08:33:54 CST)
  • Jeff Comer (Fri Nov 14 2014 - 20:02:44 CST)
  • Jeff Comer (Fri Nov 14 2014 - 20:02:09 CST)
  • Liqun Zhang (Fri Nov 14 2014 - 17:19:37 CST)
• How to get cell information from within calcforces in TclForces
  • Salvatore Mario Cosseddu (Fri Feb 08 2013 - 17:35:52 CST)
• how to get cell vectors in tcl forces script
  • Cosseddu, Salvatore (Thu Mar 13 2014 - 13:11:01 CDT)
  • Thomas Evangelidis (Thu Mar 13 2014 - 11:47:28 CDT)
  • Hongbo Du (Thu Mar 13 2014 - 11:32:32 CDT)
  • Thomas Evangelidis (Thu Mar 13 2014 - 06:11:48 CDT)
  • Thomas Evangelidis (Wed Mar 12 2014 - 09:26:46 CDT)
  • Cosseddu, Salvatore (Wed Mar 12 2014 - 09:01:35 CDT)
  • Cosseddu, Salvatore (Wed Mar 12 2014 - 07:05:43 CDT)
  • Thomas Evangelidis (Tue Mar 11 2014 - 15:14:17 CDT)
• How to maintain Density constant?
  • Tristan Croll (Thu Mar 06 2014 - 16:30:43 CST)
  • Kenno Vanommeslaeghe (Thu Mar 06 2014 - 12:39:08 CST)
  • Morgan, Brittany (Thu Mar 06 2014 - 12:26:02 CST)
  • Roy Fernando (Thu Mar 06 2014 - 12:03:37 CST)
  • Morgan, Brittany (Thu Mar 06 2014 - 11:41:12 CST)
  • Roy Fernando (Thu Mar 06 2014 - 11:28:23 CST)
  • Kenno Vanommeslaeghe (Thu Mar 06 2014 - 10:55:28 CST)
  • Ivan Gregoretti (Thu Mar 06 2014 - 10:34:43 CST)
  • Kenno Vanommeslaeghe (Thu Mar 06 2014 - 09:57:24 CST)
  • Ivan Gregoretti (Thu Mar 06 2014 - 07:23:29 CST)
  • Kenno Vanommeslaeghe (Wed Mar 05 2014 - 16:51:30 CST)
  • Roy Fernando (Wed Mar 05 2014 - 15:43:59 CST)
• How to optimize parameters in command for NAMD CUDA GPU MD calculations?
  • Aron Broom (Thu Sep 12 2013 - 15:41:50 CDT)
  • Michael Shokhen (Thu Sep 12 2013 - 14:59:21 CDT)
• How to parametrize new atom types in Namd
  • Dian Jiao (Fri Jan 17 2014 - 15:44:50 CST)
• How to prepare FEP input files for double mutant
  • Aman (Wed Aug 28 2013 - 15:05:19 CDT)
• how to quantify and visualize the flow of water into a protein
  • Mo Chen (Tue Jul 08 2014 - 19:43:35 CDT)
  • Joshua Adelman (Tue Jul 08 2014 - 19:36:02 CDT)
  • Maxim Belkin (Tue Jul 08 2014 - 19:20:12 CDT)
  • Thomas Evangelidis (Tue Jul 08 2014 - 19:12:40 CDT)
  • Thomas Evangelidis (Tue Jul 08 2014 - 19:04:01 CDT)
  • Maxim Belkin (Tue Jul 08 2014 - 18:40:15 CDT)
  • Thomas Evangelidis (Tue Jul 08 2014 - 18:20:48 CDT)
• How to recenter a waterbox with ions around my protein?
  • Thomas Evangelidis (Fri Mar 29 2013 - 08:47:33 CDT)
  • Maria Bykhovskaia (Thu Mar 28 2013 - 17:44:06 CDT)
• How to refer to side-chain via tcl-force scripting?
  • Tristan Croll (Fri Jun 13 2014 - 02:08:51 CDT)
  • zeynab mohamad hoseyni (Fri Jun 13 2014 - 00:53:12 CDT)
• How to remove center of mass translation of macromolecule
  • Jérôme Hénin (Mon Jun 17 2013 - 08:51:20 CDT)
  • Teerapong Pirojsirikul (Thu Jun 13 2013 - 20:56:29 CDT)
  • Giacomo Fiorin (Thu Jun 13 2013 - 20:09:49 CDT)
  • Teerapong Pirojsirikul (Thu Jun 13 2013 - 19:40:23 CDT)
  • Giacomo Fiorin (Thu Jun 13 2013 - 18:17:00 CDT)
  • Teerapong Pirojsirikul (Thu Jun 13 2013 - 17:38:07 CDT)
  • Jérôme Hénin (Wed Jun 12 2013 - 04:00:48 CDT)
  • Teerapong Pirojsirikul (Wed Jun 12 2013 - 03:05:36 CDT)
• How to replace NAMD electrostatics
  • Axel Kohlmeyer (Thu Nov 21 2013 - 12:02:42 CST)
  • Juba, Derek (Thu Nov 21 2013 - 11:41:06 CST)
  • Axel Kohlmeyer (Tue Nov 19 2013 - 17:03:48 CST)
  • Aron Broom (Tue Nov 19 2013 - 17:00:16 CST)
  • Axel Kohlmeyer (Tue Nov 19 2013 - 16:54:29 CST)
  • Axel Kohlmeyer (Tue Nov 19 2013 - 16:53:01 CST)
  • Juba, Derek (Tue Nov 19 2013 - 16:36:20 CST)
• How to setting tilt component in colvars module
  • ¼­¿ëÀÏ (Mon Sep 23 2013 - 22:54:26 CDT)
  • Giacomo Fiorin (Mon Sep 23 2013 - 09:43:35 CDT)
  • ¼­¿ëÀÏ (Mon Sep 23 2013 - 01:21:35 CDT)
• How to setup a system with two pulling directions
  • John Xi (Thu Apr 17 2014 - 19:48:39 CDT)
  • Felipe Merino (Thu Apr 17 2014 - 10:38:06 CDT)
  • John Xi (Wed Apr 16 2014 - 19:32:27 CDT)
• How to solvate a protein using C36 and not C27
  • zeynab mohamad hoseyni (Sat Jan 25 2014 - 11:08:14 CST)
  • zeynab mohamad hoseyni (Sat Jan 25 2014 - 10:48:31 CST)
• How to split large NAMD DCD file
  • Branko (Thu Jan 24 2013 - 11:15:17 CST)
  • flavio seixas (Thu Jan 24 2013 - 11:09:31 CST)
  • Michael Purdy (Thu Jan 24 2013 - 11:06:33 CST)
  • Aron Broom (Thu Jan 24 2013 - 11:06:45 CST)
  • snoze pa (Thu Jan 24 2013 - 10:49:58 CST)
• How to stop omega trans-cis switching
  • Kenno Vanommeslaeghe (Mon Mar 03 2014 - 13:01:10 CST)
  • Alex Utev (CMP) (Mon Mar 03 2014 - 12:11:25 CST)
  • Alex Utev (CMP) (Mon Mar 03 2014 - 12:10:08 CST)
• how to switch off protein-water electrostatic interaction keeping the protein-water vdw interactions intact
  • somedatta pal (Tue Mar 19 2013 - 02:57:09 CDT)
• How to use ParseFEP plugin to carry out FEP analysis for several forward and backward *.fepout files when lambda is from 0 to 1
  • Chris Chipot (Sun May 05 2013 - 02:44:48 CDT)
  • dbaogen (Sat May 04 2013 - 02:23:19 CDT)
• How to write dcd file within Tclforce script
  • Teerapong Pirojsirikul (Wed Feb 20 2013 - 17:56:31 CST)
• How we can merge protein and ligand complex?
  • Eric Hill (Tue Jan 15 2013 - 01:15:22 CST)
  • Maria Saeed (Tue Jan 15 2013 - 01:06:20 CST)
• Hwo to switch from NPT to NVT
  • Zeinab Emami (Fri Aug 15 2014 - 07:14:05 CDT)
  • Zeinab Emami (Fri Aug 15 2014 - 07:12:39 CDT)
• Hybrid MPI + Multicore + Cuda build
  • Maxime Boissonneault (Wed Aug 13 2014 - 11:46:59 CDT)
• Hydration of protein-lipid interface
  • zeynab mohamad hoseyni (Mon Feb 03 2014 - 10:27:20 CST)
• I have a question about pair interaction energy calculations.
  • Kenno Vanommeslaeghe (Thu Oct 31 2013 - 13:21:31 CDT)
  • ¼Û ¿¬È£ (Wed Oct 30 2013 - 02:14:32 CDT)
• I would like to unsubscribe
  • Ajasja LjubetiÄ� (Wed Sep 10 2014 - 10:03:21 CDT)
  • Giacomo Fiorin (Wed Sep 10 2014 - 09:21:11 CDT)
  • MEHRAN MB (Wed Sep 10 2014 - 09:19:54 CDT)
  • Maria Kopp (Wed Sep 10 2014 - 09:04:54 CDT)
• ibverb&&smp build NAMD
  • ukulililixl (Fri Aug 29 2014 - 06:41:21 CDT)
  • ukulililixl (Thu Aug 28 2014 - 04:30:47 CDT)
• iDataPlex
  • Francesco Pietra (Tue Mar 18 2014 - 04:03:29 CDT)
  • Andrew Emerson (Tue Mar 18 2014 - 03:15:30 CDT)
  • Francesco Pietra (Mon Mar 17 2014 - 13:12:32 CDT)
• if{} statements
  • Axel Kohlmeyer (Tue Mar 05 2013 - 08:15:21 CST)
  • Thomas C. Bishop (Tue Mar 05 2013 - 08:07:02 CST)
  • Hannes Loeffler (Tue Mar 05 2013 - 07:59:32 CST)
  • Axel Kohlmeyer (Tue Mar 05 2013 - 07:54:53 CST)
  • Thomas C. Bishop (Tue Mar 05 2013 - 07:46:29 CST)
• Implementation of ELASTIC NETWORK model in NAMD
  • Victor (Fri Aug 23 2013 - 12:29:01 CDT)
  • Vibhor Agrawal (Fri Aug 23 2013 - 10:57:17 CDT)
• Implementing the Virtual Bond Algorithm Using Colvars
  • Giacomo Fiorin (Thu Dec 18 2014 - 19:37:06 CST)
  • David Huggins (Wed Dec 17 2014 - 06:25:33 CST)
• implicit solvent
  • Aron Broom (Wed Mar 27 2013 - 12:30:09 CDT)
  • Giacomo Fiorin (Wed Mar 27 2013 - 12:26:15 CDT)
  • Aron Broom (Wed Mar 27 2013 - 12:20:30 CDT)
  • Axel Kohlmeyer (Wed Mar 27 2013 - 11:31:03 CDT)
  • Fugui (Wed Mar 27 2013 - 11:27:55 CDT)
• Implicit solvent lipid bilayer simulation in NAMD.
  • Kenno Vanommeslaeghe (Thu Sep 18 2014 - 15:39:49 CDT)
  • Subbarao Kanchi (Wed Sep 17 2014 - 14:27:10 CDT)
  • Aron Broom (Wed Sep 17 2014 - 13:54:57 CDT)
  • Jason Swails (Wed Sep 17 2014 - 13:47:53 CDT)
  • Subbarao Kanchi (Wed Sep 17 2014 - 13:41:34 CDT)
  • Siva Dasetty (Wed Sep 17 2014 - 13:23:53 CDT)
  • Subbarao Kanchi (Wed Sep 17 2014 - 12:04:44 CDT)
• Implicit water with explicit ions
  • Jason Swails (Thu Jul 18 2013 - 21:09:27 CDT)
  • adrian palacios (Thu Jul 18 2013 - 20:02:36 CDT)
  • Jason Swails (Thu Jul 18 2013 - 18:30:49 CDT)
  • Adrian (Thu Jul 18 2013 - 13:10:49 CDT)
• IMPROPER PARAMETERS FOR CA CA CA CA
  • Axel Kohlmeyer (Mon May 26 2014 - 16:47:44 CDT)
  • Kenno Vanommeslaeghe (Mon May 26 2014 - 16:42:29 CDT)
  • Z (Sat May 24 2014 - 10:50:49 CDT)
• Improve scaling for large amount of fixed atoms
  • Tristan Croll (Wed Mar 19 2014 - 21:15:40 CDT)
  • Norman Geist (Wed Mar 19 2014 - 03:19:38 CDT)
• Improving MDFF results
  • Kevin Chun Chan (Tue Oct 21 2014 - 10:56:00 CDT)
  • Tristan Croll (Tue Oct 21 2014 - 14:22:31 CDT)
  • Tristan Croll (Tue Oct 21 2014 - 00:36:21 CDT)
  • Kevin C Chan (Mon Oct 20 2014 - 22:15:59 CDT)
• improving tclforce efficiency, getting "Signal: segmentation violation" error
  • zeynab mohamad hoseyni (Sun Jun 15 2014 - 20:18:11 CDT)
• inconsistency between "Benchmark" and "Timing" output
  • Vlad Cojocaru (Mon Nov 25 2013 - 09:08:58 CST)
• Inconsistency in fast table energy vs force
  • Francesco Pietra (Sat Apr 13 2013 - 02:36:32 CDT)
• INCONSISTENCY messages and minimization in toturial 1-2-sphere
  • Yan Zhou (Wed Sep 03 2014 - 03:14:30 CDT)
• Incorporating some ions with specific location
  • Niklaus Johner (Tue Aug 13 2013 - 08:43:04 CDT)
  • Stephan Grein (Tue Aug 13 2013 - 03:04:10 CDT)
• incorrect bond
  • Nadia Salami (Wed Sep 18 2013 - 01:28:59 CDT)
  • Nadia Salami (Wed Sep 18 2013 - 01:11:08 CDT)
• Info: Pairlistdist is too small for 3 computes during timestep 115001
  • Subbarao Kanchi (Fri Dec 12 2014 - 16:26:26 CST)
  • Jim Phillips (Fri Dec 12 2014 - 15:49:06 CST)
  • Santosh Kumar Chaudhary (Fri Dec 12 2014 - 10:34:41 CST)
• information about simulation speed
  • Jeff Comer (Tue Dec 02 2014 - 18:09:54 CST)
  • Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:45:32 CST)
  • Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:35:14 CST)
  • Josh Vermaas (Tue Dec 02 2014 - 17:08:55 CST)
  • Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:22:28 CST)
  • Axel Kohlmeyer (Tue Dec 02 2014 - 17:07:15 CST)
  • Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:04:31 CST)
  • Axel Kohlmeyer (Tue Dec 02 2014 - 16:53:44 CST)
  • Kshatresh Dutta Dubey (Tue Dec 02 2014 - 16:50:11 CST)
• Inquiry about forceConstant
  • Jérôme Hénin (Tue Jul 22 2014 - 04:37:30 CDT)
  • Mo Chen (Mon Jul 21 2014 - 16:57:15 CDT)
  • Mo Chen (Mon Jul 21 2014 - 15:23:06 CDT)
  • Aron Broom (Mon Jul 21 2014 - 15:12:06 CDT)
  • Mo Chen (Mon Jul 21 2014 - 15:03:30 CDT)
• Inquiry about lipid membrane simulation
  • JC Gumbart (Wed Jun 18 2014 - 19:48:17 CDT)
  • Wonpil Im (Wed Jun 18 2014 - 14:53:31 CDT)
  • Sunhwan Jo (Wed Jun 18 2014 - 14:46:56 CDT)
  • Mo Chen (Wed Jun 18 2014 - 14:25:16 CDT)
  • Kenno Vanommeslaeghe (Wed Jun 18 2014 - 14:02:52 CDT)
  • Kenno Vanommeslaeghe (Wed Jun 18 2014 - 10:20:24 CDT)
  • Mo Chen (Tue Jun 17 2014 - 20:57:59 CDT)
• Insertion of GPCR in the POPC Bilayer
  • Vibhor Agrawal (Fri Jun 21 2013 - 11:34:22 CDT)
  • Ramin Ekhteiari (Fri Jun 21 2013 - 03:17:13 CDT)
  • Yi Wang, PhD (Thu Jun 20 2013 - 21:09:03 CDT)
  • Jeffrey Potoff (Thu Jun 20 2013 - 20:12:27 CDT)
  • Aron Broom (Thu Jun 20 2013 - 16:27:25 CDT)
  • Vibhor Agrawal (Thu Jun 20 2013 - 15:29:20 CDT)
• Inspiration for most efficient implementation of coarse grained forcefield.
  • Jim Phillips (Tue Dec 16 2014 - 09:30:40 CST)
  • Jérôme Hénin (Mon Dec 15 2014 - 15:41:22 CST)
  • Ajasja LjubetiÄ� (Mon Dec 15 2014 - 12:08:03 CST)
• Instability in thermodynamic integration
  • Maryam Sayadi (Sun Feb 16 2014 - 14:04:12 CST)
• Installation Protocol of NAMD on Linux Cluster
  • Viswanath Pasumarthi (Thu Aug 21 2014 - 14:46:27 CDT)
• Interaction energy definition
  • Aron Broom (Sat Nov 23 2013 - 07:09:54 CST)
  • nan li (Fri Nov 22 2013 - 15:21:31 CST)
  • Aron Broom (Fri Nov 22 2013 - 14:57:35 CST)
  • nan li (Fri Nov 22 2013 - 14:45:13 CST)
• Interactive molecular dynamics question
  • Axel Kohlmeyer (Sun Feb 09 2014 - 17:13:15 CST)
  • Chris Harrison (Sun Feb 09 2014 - 17:00:27 CST)
  • Mare Libero (Sun Feb 09 2014 - 15:05:51 CST)
• Intermolecular potential energy function in NAMD
  • Kenno Vanommeslaeghe (Fri Aug 01 2014 - 11:41:46 CDT)
  • Viswanath Pasumarthi (Fri Aug 01 2014 - 06:31:21 CDT)
• Invalid command error
  • Axel Kohlmeyer (Mon Jun 30 2014 - 07:44:41 CDT)
  • Adam Kells (Mon Jun 30 2014 - 06:49:07 CDT)
• Invitation to connect on LinkedIn
  • Gabriel Jara (Mon Jun 03 2013 - 08:46:22 CDT)
• Invitation to Submit Review Article Current Protein & Peptide Science (IF: 2.326)
  • Prija Ponnan (Fri Jun 27 2014 - 06:40:43 CDT)
• Ion Au+3 simulation
  • Kenno Vanommeslaeghe (Thu Jun 05 2014 - 17:27:37 CDT)
  • Aron Broom (Wed Jun 04 2014 - 16:00:23 CDT)
  • Kenno Vanommeslaeghe (Wed Jun 04 2014 - 10:32:46 CDT)
  • Daniel Torrente (Tue Jun 03 2014 - 16:17:38 CDT)
  • Aron Broom (Tue Jun 03 2014 - 16:21:52 CDT)
  • Axel Kohlmeyer (Tue Jun 03 2014 - 15:49:35 CDT)
  • Daniel Torrente (Tue Jun 03 2014 - 15:17:15 CDT)
  • Axel Kohlmeyer (Tue Jun 03 2014 - 14:38:35 CDT)
  • Daniel Torrente (Tue Jun 03 2014 - 13:31:40 CDT)
• Is it so different when setting reinitvels or not?
  • Zhao Lina (Wed Dec 17 2014 - 19:31:49 CST)
  • Jeff Comer (Wed Dec 17 2014 - 05:45:09 CST)
  • Zhao Lina (Wed Dec 17 2014 - 00:03:25 CST)
• is the aMD implementation compatible with AMBER force fields
  • Thomas Evangelidis (Wed Jun 18 2014 - 18:20:00 CDT)
  • Jeff Wereszczynski (Wed Jun 18 2014 - 13:14:11 CDT)
  • Thomas Evangelidis (Wed Jun 18 2014 - 06:20:06 CDT)
• Is there any point in running NAMD over an ethernet-linked cluster?
  • Nicholas M Glykos (Mon Sep 22 2014 - 03:40:59 CDT)
  • Axel Kohlmeyer (Mon Sep 22 2014 - 01:22:11 CDT)
  • Douglas Houston (Mon Sep 22 2014 - 00:23:41 CDT)
  • Nicholas M Glykos (Sun Sep 21 2014 - 13:21:53 CDT)
  • Douglas Houston (Sat Sep 20 2014 - 06:18:25 CDT)
• Issues with the "Keep Water Out" tcl script
  • peter.schmidtke_at_fr.netgrs.com (Thu Jan 03 2013 - 09:09:29 CST)
  • B Hartzoulakis (Thu Jan 03 2013 - 06:15:50 CST)
• jeremy adler
  • jeremy adler (Thu Oct 23 2014 - 06:21:43 CDT)
• Job script for multi node job
  • Phil Greer (Fri Feb 14 2014 - 09:04:37 CST)
  • Subbarao Kanchi (Fri Feb 14 2014 - 08:24:13 CST)
  • Subbarao Kanchi (Fri Feb 14 2014 - 05:22:55 CST)
  • Subbarao Kanchi (Fri Feb 14 2014 - 04:20:16 CST)
• Kb, Ktheta values for TIP3P water model
  • Viswanath Pasumarthi (Wed Aug 13 2014 - 02:27:24 CDT)
  • Maxim Belkin (Tue Aug 12 2014 - 23:11:43 CDT)
  • Axel Kohlmeyer (Tue Aug 12 2014 - 14:26:05 CDT)
  • Viswanath Pasumarthi (Tue Aug 12 2014 - 14:11:40 CDT)
  • Kenno Vanommeslaeghe (Tue Aug 12 2014 - 13:31:04 CDT)
  • Axel Kohlmeyer (Tue Aug 12 2014 - 12:27:25 CDT)
  • Viswanath Pasumarthi (Tue Aug 12 2014 - 12:19:00 CDT)
  • Maxim Belkin (Mon Aug 11 2014 - 18:05:41 CDT)
  • Kenno Vanommeslaeghe (Mon Aug 11 2014 - 14:08:41 CDT)
  • Viswanath Pasumarthi (Mon Aug 11 2014 - 12:56:00 CDT)
  • Axel Kohlmeyer (Mon Aug 11 2014 - 06:40:43 CDT)
  • Kenno Vanommeslaeghe (Sun Aug 10 2014 - 23:16:19 CDT)
  • Hadi (Sun Aug 10 2014 - 22:29:55 CDT)
  • Kenno Vanommeslaeghe (Sun Aug 10 2014 - 22:10:43 CDT)
  • Hadi (Sun Aug 10 2014 - 20:59:58 CDT)
  • Kenno Vanommeslaeghe (Sun Aug 10 2014 - 17:49:01 CDT)
  • Hadi (Thu Aug 07 2014 - 17:15:09 CDT)
  • Kenno Vanommeslaeghe (Thu Aug 07 2014 - 15:08:39 CDT)
  • Hadi (Thu Aug 07 2014 - 12:36:33 CDT)
  • Kenno Vanommeslaeghe (Thu Aug 07 2014 - 10:50:24 CDT)
  • Hadi (Wed Aug 06 2014 - 17:39:50 CDT)
  • Kenno Vanommeslaeghe (Wed Aug 06 2014 - 17:28:12 CDT)
  • Hadi (Wed Aug 06 2014 - 16:07:27 CDT)
  • Axel Kohlmeyer (Wed Aug 06 2014 - 15:48:57 CDT)
  • Hadi (Wed Aug 06 2014 - 15:40:22 CDT)
  • Axel Kohlmeyer (Wed Aug 06 2014 - 15:28:23 CDT)
  • Hadi (Wed Aug 06 2014 - 14:41:58 CDT)
  • Axel Kohlmeyer (Wed Aug 06 2014 - 14:11:01 CDT)
  • Hadi (Wed Aug 06 2014 - 13:57:26 CDT)
  • Kenno Vanommeslaeghe (Tue Aug 05 2014 - 15:00:49 CDT)
  • Axel Kohlmeyer (Tue Aug 05 2014 - 14:59:14 CDT)
  • Hadi (Tue Aug 05 2014 - 14:49:48 CDT)
  • Kenno Vanommeslaeghe (Tue Aug 05 2014 - 14:29:22 CDT)
  • Axel Kohlmeyer (Tue Aug 05 2014 - 14:28:04 CDT)
  • Hadi (Tue Aug 05 2014 - 14:10:14 CDT)
  • Kenno Vanommeslaeghe (Tue Aug 05 2014 - 13:41:12 CDT)
  • Hadi Dinpajooh (Tue Aug 05 2014 - 11:52:44 CDT)
  • Kenno Vanommeslaeghe (Tue Aug 05 2014 - 09:54:35 CDT)
  • Hadi (Tue Aug 05 2014 - 02:14:00 CDT)
  • Kenno Vanommeslaeghe (Thu Jul 31 2014 - 17:28:09 CDT)
  • JC Gumbart (Thu Jul 31 2014 - 16:24:06 CDT)
  • Axel Kohlmeyer (Thu Jul 31 2014 - 14:14:43 CDT)
  • Kenno Vanommeslaeghe (Thu Jul 31 2014 - 14:03:00 CDT)
  • JC Gumbart (Wed Jul 30 2014 - 10:27:16 CDT)
  • Kenno Vanommeslaeghe (Tue Jul 29 2014 - 23:21:58 CDT)
  • Hadi (Tue Jul 29 2014 - 17:59:19 CDT)
  • Viswanath Pasumarthi (Tue Jul 29 2014 - 16:38:28 CDT)
• keeping Crystal angles constant
  • Mohan maruthi sena (Wed Jan 15 2014 - 12:03:58 CST)
• Launching namd GPU-MPI vs GPU-binary
  • Francesco Pietra (Sat Jul 06 2013 - 02:54:00 CDT)
• Lennard Jones (LJ) parameters
  • Axel Kohlmeyer (Sun Oct 06 2013 - 15:36:22 CDT)
  • Bachir Aoun (Sun Oct 06 2013 - 15:23:36 CDT)
• LES very slow
  • Siri Søndergaard (Mon Feb 25 2013 - 18:00:02 CST)
• Ligand in association with water
  • Roy Fernando (Mon Mar 25 2013 - 09:40:44 CDT)
• Linear force ramp increments in ABF
  • Matthew Ralph Adendorff (Thu Aug 29 2013 - 14:56:30 CDT)
  • Jérôme Hénin (Thu Aug 29 2013 - 14:15:43 CDT)
  • Matthew Ralph Adendorff (Thu Aug 29 2013 - 13:40:42 CDT)
  • Jérôme Hénin (Thu Aug 29 2013 - 12:06:49 CDT)
  • Matthew Ralph Adendorff (Tue Aug 27 2013 - 12:44:41 CDT)
• Link between simulations
  • Thomas Evangelidis (Wed Apr 24 2013 - 04:30:12 CDT)
  • Suresh (Mon Apr 22 2013 - 01:37:00 CDT)
  • Mihaela Drenscko (Sat Apr 20 2013 - 15:18:36 CDT)
• Linuxtag
  • Gianluca Interlandi (Thu May 16 2013 - 14:38:40 CDT)
• Lipid bilayer tears apart during simulation
  • Jeffrey Potoff (Fri Jun 14 2013 - 15:46:10 CDT)
  • Peterson J (Fri Jun 14 2013 - 15:44:46 CDT)
  • Aron Broom (Fri Jun 14 2013 - 15:34:31 CDT)
  • Peterson J (Fri Jun 14 2013 - 15:14:02 CDT)
• Liquid Simulation Failure
  • Roy Fernando (Fri Jan 24 2014 - 18:54:44 CST)
• LJcorrection
  • Gianluca Interlandi (Wed Aug 28 2013 - 01:33:39 CDT)
• Loading and analysis of DCD file (~300 MB)
  • tillmann.utesch_at_mailbox.tu-berlin.de (Thu Jul 24 2014 - 07:00:09 CDT)
  • Ajasja LjubetiÄ� (Thu Jul 24 2014 - 09:30:12 CDT)
  • Stephan Grein (Thu Jul 24 2014 - 07:02:53 CDT)
  • Stephan Grein (Thu Jul 24 2014 - 06:45:54 CDT)
  • Stephan Grein (Thu Jul 24 2014 - 06:18:45 CDT)
• Loading Velocity DCD file
  • JAVAD NOROOZI (Wed Dec 17 2014 - 13:23:20 CST)
• local pressure profile for water liquid-vapor
  • Mashayak, Sikandar Yusufoddin (Wed Jul 10 2013 - 10:43:21 CDT)
• Locally Enhanced Sampling
  • Melina (Wed Mar 27 2013 - 13:23:06 CDT)
  • Melina (Mon Mar 18 2013 - 12:20:09 CDT)
• Log file is not being updated
  • BATUHAN KAV (Thu Feb 13 2014 - 11:05:13 CST)
  • BATUHAN KAV (Mon Feb 10 2014 - 06:44:08 CST)
  • BATUHAN KAV (Mon Feb 10 2014 - 06:01:41 CST)
  • Ajasja LjubetiÄ� (Mon Feb 10 2014 - 05:53:39 CST)
  • BATUHAN KAV (Mon Feb 10 2014 - 05:41:07 CST)
• Lone Pair on H2S
  • JAVAD NOROOZI (Tue Dec 30 2014 - 06:05:39 CST)
  • JAVAD NOROOZI (Tue Dec 30 2014 - 06:05:40 CST)
  • JAVAD NOROOZI (Sat Dec 27 2014 - 09:42:25 CST)
• lone pair velocities
  • Gergely Gyimesi (Wed Sep 25 2013 - 11:27:48 CDT)
• long running sim dies
  • ransun (Mon Oct 13 2014 - 09:12:33 CDT)
  • Tristan Croll (Mon Oct 13 2014 - 14:36:37 CDT)
  • Thomas C. Bishop (Mon Oct 13 2014 - 08:29:43 CDT)
• Loss of Translational entropy calculation in FEP
  • Daniel Torrente (Wed Jul 30 2014 - 16:57:08 CDT)
• Low global exclusion count on parallel tempering, not on MD
  • Francesco Pietra (Wed Aug 21 2013 - 10:45:05 CDT)
• Mac OS Binary for NAMD 2.10
  • Eudes Fileti (Thu Oct 24 2013 - 06:16:31 CDT)
• making patch
  • Kenno Vanommeslaeghe (Tue Aug 27 2013 - 19:07:40 CDT)
  • rasti_at_ut.ac.ir (Tue Aug 27 2013 - 18:41:06 CDT)
• Margin setup
  • Tian Li (Fri Aug 30 2013 - 08:37:03 CDT)
• Martini 2.2 and ElNeDyn in NAMD
  • XAvier Periole (Thu Jul 18 2013 - 03:30:00 CDT)
  • XAvier Periole (Wed Jul 03 2013 - 12:29:16 CDT)
• MARTINI Bad global angle count
  • thomas lemmin (Mon Mar 25 2013 - 04:40:07 CDT)
• Martini forcefield RBCG and ENM
  • Raul Araya (Fri Aug 15 2014 - 10:05:01 CDT)
• Martini RBCG
  • DENILSON FERREIRA DE OLIVEIRA (Mon Jan 14 2013 - 09:55:51 CST)
• Martini RBCG simulation frequently crashing with "atoms moving too fast"
  • eprates_at_iqm.unicamp.br (Sun Nov 03 2013 - 11:57:18 CST)
• MD crashes at 300K after warm up MD
  • Patricia Campbell (Tue Mar 19 2013 - 13:30:23 CDT)
• MD simulation Patch grid errors
  • Thomas Evangelidis (Tue Jan 14 2014 - 02:19:55 CST)
  • Jeffrey Potoff (Mon Jan 13 2014 - 22:34:42 CST)
  • Jiann George Pazhamalil (Mon Jan 13 2014 - 21:37:41 CST)
  • Jeffrey Potoff (Tue Jan 07 2014 - 18:03:29 CST)
  • Thomas Evangelidis (Tue Jan 07 2014 - 17:56:32 CST)
  • Jiann George Pazhamalil (Tue Jan 07 2014 - 17:33:06 CST)
• MD- GPU
  • Aron Broom (Thu Oct 03 2013 - 07:06:24 CDT)
  • Sagar Gore (Thu Oct 03 2013 - 06:51:02 CDT)
• MDFF - should hydrogens be included?
  • Geoffrey Kwai Wai Kong (Mon Mar 04 2013 - 00:19:26 CST)
• MDFF force threshold
  • Ivana (Thu May 02 2013 - 10:07:17 CDT)
• MDFF volumetric map
  • Ivana (Wed Feb 27 2013 - 11:43:03 CST)
• Mechanical Properties of protein
  • Maxim Belkin (Thu Oct 30 2014 - 20:27:58 CDT)
  • chin chun (Thu Oct 30 2014 - 19:18:11 CDT)
• medwater config
  • Hassan Kianinejad (Fri Apr 04 2014 - 19:15:32 CDT)
• Membrane and NPAT
  • hannes.loeffler_at_stfc.ac.uk (Mon Feb 17 2014 - 10:53:49 CST)
  • Kenno Vanommeslaeghe (Mon Feb 17 2014 - 10:43:03 CST)
  • José Villalaín (Mon Feb 17 2014 - 04:49:08 CST)
• membrane bilayer crosses the z axis boundaries of the box and separates into two layers
  • Thomas Evangelidis (Wed Dec 11 2013 - 14:29:33 CST)
• membrane lipid involvement of cholesterol
  • Ramin Ekhteiari (Sat Jul 26 2014 - 03:14:38 CDT)
• membrane protein simulation lipid bilayer question
  • Tian Li (Wed Oct 02 2013 - 19:48:35 CDT)
• Membrane/peptide system. Water moving from one layer to the other ...
  • Ajasja LjubetiÄ� (Wed Oct 23 2013 - 07:30:36 CDT)
  • Villalain Boullon, Jose (Wed Oct 23 2013 - 05:46:00 CDT)
• memory demands of REMD
  • Martin, Erik W (Fri Mar 08 2013 - 15:44:50 CST)
  • Martin, Erik W (Thu Mar 07 2013 - 18:27:55 CST)
  • Chris Harrison (Thu Mar 07 2013 - 18:19:39 CST)
  • Martin, Erik W (Thu Mar 07 2013 - 16:16:00 CST)
• memory problem
  • Adam Moser (Fri Jun 20 2014 - 15:01:30 CDT)
• Merging the two files......
  • Aron Broom (Tue Jun 17 2014 - 10:58:22 CDT)
  • Aron Broom (Tue Jun 17 2014 - 10:44:36 CDT)
  • Gurpreet Kaur Dhindsa (Tue Jun 17 2014 - 10:00:09 CDT)
• metadynamics
  • Francesco Pietra (Fri Apr 26 2013 - 11:02:19 CDT)
  • Francesco Pietra (Fri Apr 26 2013 - 10:58:40 CDT)
  • Aron Broom (Fri Apr 26 2013 - 10:19:40 CDT)
  • Niklaus Johner (Fri Apr 26 2013 - 10:17:00 CDT)
  • Axel Kohlmeyer (Fri Apr 26 2013 - 09:53:41 CDT)
  • Francesco Pietra (Fri Apr 26 2013 - 09:46:12 CDT)
• Metadynamics pmf restart
  • Giacomo Fiorin (Mon Jan 28 2013 - 14:43:56 CST)
  • Riley Workman (Mon Jan 28 2013 - 12:18:48 CST)
• Metadynamics test along eigenvector
  • Giacomo Fiorin (Tue Aug 26 2014 - 10:07:34 CDT)
  • Floquet Nicolas (Tue Aug 26 2014 - 02:58:00 CDT)
• Metadynamics with eigenvector
  • Giacomo Fiorin (Mon Aug 25 2014 - 10:17:22 CDT)
  • Nicolas Floquet (Mon Aug 25 2014 - 09:40:06 CDT)
• Method for solvation of protein
  • Dong Luo (Tue Oct 22 2013 - 10:57:17 CDT)
  • Xingcheng Lin (Mon Oct 21 2013 - 15:45:16 CDT)
• Minimisation issue
  • Aron Broom (Wed Jul 24 2013 - 15:25:06 CDT)
  • venkata agasthya (Wed Jul 24 2013 - 15:12:06 CDT)
• Minimisation of protein in a water box
  • Price, Gareth (Thu Apr 18 2013 - 19:15:31 CDT)
  • Rajan Vatassery (Mon Apr 15 2013 - 12:30:46 CDT)
  • Gareth Price (Sat Apr 13 2013 - 13:52:01 CDT)
• Minimisation problem
  • Aron Broom (Thu Jul 18 2013 - 13:26:52 CDT)
  • Rajan Vatassery (Thu Jul 18 2013 - 13:14:40 CDT)
  • venkata agasthya (Thu Jul 18 2013 - 12:42:08 CDT)
• minimization does not converge
  • Revthi Sanker (Mon Jul 08 2013 - 11:43:27 CDT)
• minimization with symmetry restrain
  • JC Gumbart (Fri Dec 13 2013 - 16:48:32 CST)
  • flavio seixas (Fri Dec 13 2013 - 12:31:39 CST)
• Minimization/Equilibrium problem, atoms moving too fast
  • Tristan Croll (Thu Jul 18 2013 - 21:08:02 CDT)
  • adrian palacios (Thu Jul 18 2013 - 20:32:57 CDT)
  • Tristan Croll (Thu Jul 18 2013 - 20:23:35 CDT)
  • Aron Broom (Thu Jul 18 2013 - 20:15:47 CDT)
  • adrian palacios (Thu Jul 18 2013 - 20:12:05 CDT)
  • Aron Broom (Thu Jul 18 2013 - 20:05:53 CDT)
  • adrian palacios (Thu Jul 18 2013 - 19:58:47 CDT)
  • Aron Broom (Thu Jul 18 2013 - 16:12:32 CDT)
  • Adrian (Thu Jul 18 2013 - 15:28:10 CDT)
• minimizer slowly moving atoms with bad contacts downhill
  • Axel Kohlmeyer (Fri Apr 12 2013 - 03:56:19 CDT)
  • Himani Raina (Fri Apr 12 2013 - 02:02:17 CDT)
• Misleading failure of VMD with charge/CGenFF from waterbox
  • Francesco Pietra (Sun Nov 23 2014 - 03:21:38 CST)
• MM-PBSA calculation
  • Hannes Loeffler (Wed Nov 06 2013 - 03:25:23 CST)
  • Ramin Ekhteiari (Wed Nov 06 2013 - 02:56:43 CST)
• MMPBSA calculation using NAMD
  • Aron Broom (Sun Sep 15 2013 - 17:49:19 CDT)
  • sudipta (Wed Sep 11 2013 - 07:37:57 CDT)
• MMPBSA Energy Calculations using VMD (Post-Processing)
  • James Starlight (Mon Apr 21 2014 - 14:27:38 CDT)
  • Jason Swails (Mon Apr 14 2014 - 13:02:08 CDT)
  • Kenno Vanommeslaeghe (Mon Apr 14 2014 - 12:24:33 CDT)
  • Jason Swails (Mon Apr 14 2014 - 07:31:05 CDT)
  • Jason Swails (Mon Apr 14 2014 - 07:26:59 CDT)
  • James Starlight (Mon Apr 14 2014 - 04:23:01 CDT)
  • James Starlight (Mon Apr 14 2014 - 00:56:50 CDT)
  • Jason Swails (Sat Apr 12 2014 - 06:53:32 CDT)
  • Vlad Cojocaru (Sat Apr 12 2014 - 03:46:19 CDT)
  • James Starlight (Sat Apr 12 2014 - 01:53:35 CDT)
  • Fotis Baltoumas (Thu Apr 10 2014 - 10:09:00 CDT)
  • Aditya Ranganathan (Thu Apr 10 2014 - 08:25:41 CDT)
• MMPBSA-like analysis
  • Hannes Loeffler (Wed Oct 30 2013 - 08:24:43 CDT)
  • Hannes Loeffler (Wed Oct 30 2013 - 06:02:54 CDT)
  • Hannes Loeffler (Tue Oct 29 2013 - 04:32:01 CDT)
  • Kenno Vanommeslaeghe (Fri Oct 25 2013 - 15:05:05 CDT)
  • Hannes Loeffler (Wed Oct 23 2013 - 02:39:29 CDT)
  • Revthi Sanker (Wed Oct 23 2013 - 01:19:40 CDT)
  • Kenno Vanommeslaeghe (Tue Oct 22 2013 - 11:56:59 CDT)
  • Revthi Sanker (Tue Oct 22 2013 - 11:12:52 CDT)
  • Jason Swails (Tue Oct 22 2013 - 05:01:32 CDT)
  • Peter Jones (Tue Oct 22 2013 - 04:21:24 CDT)
  • Revthi Sanker (Tue Oct 22 2013 - 02:04:49 CDT)
• modeling missing loops in starting structures
  • Thomas Evangelidis (Tue May 21 2013 - 17:12:44 CDT)
  • Martin, Erik W (Tue May 21 2013 - 17:08:06 CDT)
• Modify Molecule.C to avoid fatal error?
  • George Patargias (Thu Nov 28 2013 - 02:26:37 CST)
• Molecular Dynamics of Rigid Linear Molecules in NAMD.
  • Kenno Vanommeslaeghe (Sun Sep 28 2014 - 14:00:43 CDT)
  • Axel Kohlmeyer (Sun Sep 28 2014 - 13:31:59 CDT)
  • Kenno Vanommeslaeghe (Sun Sep 28 2014 - 13:06:06 CDT)
  • Aron Broom (Sun Sep 28 2014 - 10:25:13 CDT)
  • Mike Makowski (Sun Sep 28 2014 - 06:50:36 CDT)
  • Mike Makowski (Sun Sep 28 2014 - 03:03:10 CDT)
  • Javad Noroozi (Sun Sep 28 2014 - 00:44:28 CDT)
• Molecular Shape Searching on GPUs
  • MARK (Mon May 20 2013 - 13:13:55 CDT)
• Monitoring progress of an ongoing molecular dynamics simulation
  • Bennion, Brian (Fri Mar 07 2014 - 11:44:01 CST)
  • Ivan Gregoretti (Fri Mar 07 2014 - 10:57:31 CST)
  • Cosseddu, Salvatore (Fri Mar 07 2014 - 10:57:59 CST)
  • Axel Kohlmeyer (Fri Mar 07 2014 - 10:49:34 CST)
  • Cosseddu, Salvatore (Fri Mar 07 2014 - 10:43:29 CST)
  • Ivan Gregoretti (Fri Mar 07 2014 - 09:08:44 CST)
  • Douglas Houston (Fri Mar 07 2014 - 08:55:47 CST)
  • Ivan Gregoretti (Fri Mar 07 2014 - 08:52:43 CST)
  • Cosseddu, Salvatore (Fri Mar 07 2014 - 08:21:35 CST)
  • Ivan Gregoretti (Fri Mar 07 2014 - 08:08:11 CST)
• Morse potentail with charmm 27
  • Francesco Pietra (Sun Mar 24 2013 - 11:04:56 CDT)
• Movie of a channel trajectory
  • Javier Cáceres Delpiano (Sat Apr 05 2014 - 22:26:21 CDT)
• moving out of the box
  • Aaron Larsen (Thu Feb 13 2014 - 14:39:04 CST)
  • Ajasja LjubetiÄ� (Thu Feb 13 2014 - 10:08:36 CST)
  • Ariel Talavera Perez (Thu Feb 13 2014 - 09:57:16 CST)
• MPICH 3 with Namd2/Charm
  • Daniel Strahs (Mon Oct 13 2014 - 18:04:45 CDT)
• Multiple dihedral with multiplicity of 7 greater than max of 6
  • Kenno Vanommeslaeghe (Wed Apr 02 2014 - 14:05:49 CDT)
  • Axel Kohlmeyer (Wed Apr 02 2014 - 13:52:18 CDT)
  • Rawan Al Nsour (Wed Apr 02 2014 - 13:44:33 CDT)
  • Rawan Al Nsour (Wed Apr 02 2014 - 13:38:53 CDT)
• multiple harmonic constrains
  • Jeff Comer (Sat Nov 08 2014 - 14:54:50 CST)
  • Azadeh Alavi (Sat Nov 08 2014 - 01:36:16 CST)
• Multiple input and output files
  • Jim Phillips (Thu Nov 06 2014 - 12:50:36 CST)
  • Josh Vermaas (Wed Nov 05 2014 - 20:54:02 CST)
  • Axel Kohlmeyer (Wed Nov 05 2014 - 21:51:44 CST)
  • Debashis Kundu (Wed Nov 05 2014 - 20:20:37 CST)
• multiple vectors in SMD
  • Jérôme Hénin (Thu Jun 13 2013 - 02:56:44 CDT)
  • yp sun (Mon Jun 10 2013 - 22:35:50 CDT)
• My calcforces does not work properly after a unknown point of the simulation.
  • Salvatore Mario Cosseddu (Wed Mar 13 2013 - 15:35:11 CDT)
• Mysterious slow down in parallel
  • Gianluca Interlandi (Sun Oct 27 2013 - 01:12:21 CDT)
  • Joseph Farran (Sun Oct 27 2013 - 00:20:02 CDT)
  • Roy Fernando (Sat Oct 26 2013 - 22:06:49 CDT)
  • Axel Kohlmeyer (Sat Oct 26 2013 - 17:04:11 CDT)
  • Roy Fernando (Sat Oct 26 2013 - 10:05:13 CDT)
• NADH topology file
  • Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:39:02 CDT)
  • Kevin C Chan (Wed Jul 16 2014 - 01:51:22 CDT)
  • Kenno Vanommeslaeghe (Tue Jul 15 2014 - 09:44:10 CDT)
  • Kevin C Chan (Tue Jul 15 2014 - 05:41:51 CDT)
• NAMD "tCouple" option
  • Tao Qu (Wed Apr 17 2013 - 15:56:54 CDT)
• NAMD + PLUMED COMPILATION
  • Giacomo Fiorin (Thu Feb 28 2013 - 11:26:00 CST)
  • Francesco Pietra (Thu Feb 28 2013 - 11:02:28 CST)
• NAMD 2.10 Manual
  • Ajasja LjubetiÄ� (Fri Aug 22 2014 - 03:30:05 CDT)
  • Norman Geist (Fri Aug 22 2014 - 03:14:47 CDT)
• NAMD 2.10 released
  • Jim Phillips (Fri Dec 12 2014 - 16:35:38 CST)
• NAMD 2.10b1 CUDA PME offload
  • Jim Phillips (Tue Aug 26 2014 - 10:22:48 CDT)
  • Norman Geist (Tue Aug 26 2014 - 09:25:48 CDT)
• NAMD 2.10b1 released
  • Jim Phillips (Mon Aug 25 2014 - 07:49:51 CDT)
• NAMD 2.10b1: occasional corrupted frame in binary dcd output
  • Tristan Croll (Tue Dec 23 2014 - 16:39:46 CST)
• NAMD 2.10b2 released
  • Jim Phillips (Mon Nov 17 2014 - 14:22:52 CST)
• NAMD 2.9 Changing/Replacing atoms in multiple molecules
  • Tristan Croll (Fri Feb 21 2014 - 16:04:43 CST)
  • Kenno Vanommeslaeghe (Fri Feb 21 2014 - 12:38:25 CST)
  • Axel Kohlmeyer (Fri Feb 21 2014 - 08:11:33 CST)
  • Michal Skoczek (Fri Feb 21 2014 - 08:02:41 CST)
• NAMD 2.9 CUDA compilation
  • Francesco Pietra (Mon Mar 11 2013 - 10:40:11 CDT)
• NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart
  • Tristan Croll (Wed Jul 17 2013 - 19:02:25 CDT)
  • Kenno Vanommeslaeghe (Tue Jul 16 2013 - 11:29:09 CDT)
  • Tristan Croll (Tue Jul 16 2013 - 02:40:08 CDT)
  • Vibhor Agrawal (Tue Jul 16 2013 - 01:18:44 CDT)
  • Tristan Croll (Tue Jul 16 2013 - 00:59:49 CDT)
  • Tristan Croll (Tue Jul 16 2013 - 01:05:19 CDT)
  • Vibhor Agrawal (Tue Jul 16 2013 - 00:56:33 CDT)
  • Tristan Croll (Tue Jul 16 2013 - 00:14:36 CDT)
• NAMD 2.9 install on CLuster mpirun/charmrun with ibverb version ?
  • Axel Kohlmeyer (Thu Nov 14 2013 - 06:52:52 CST)
  • Nicolas Floquet (Thu Nov 14 2013 - 05:17:48 CST)
• NAMD 2.9 jobs hanging.
  • Bhupender Thakur (Mon Feb 18 2013 - 20:40:14 CST)
• NAMD 2.9 quits early without error message.
  • Ivan Gregoretti (Mon Mar 10 2014 - 18:45:17 CDT)
  • Roy Fernando (Sat Mar 08 2014 - 10:03:21 CST)
  • Aron Broom (Fri Mar 07 2014 - 17:31:37 CST)
  • Morgan, Brittany (Fri Mar 07 2014 - 11:45:15 CST)
  • Ivan Gregoretti (Fri Mar 07 2014 - 11:46:54 CST)
  • Ivan Gregoretti (Fri Mar 07 2014 - 11:36:17 CST)
• NAMD 2.9 Replica-exchange. FATAL ERROR: Unknown command-line option +replicas
  • ncskocze_at_cyf-kr.edu.pl (Fri Jan 04 2013 - 07:53:16 CST)
• namd 2.9 tip4p-2005
  • Guanglei Cui (Thu Apr 11 2013 - 10:31:33 CDT)
  • Daniele Gentili (Tue Jan 15 2013 - 06:23:14 CST)
• Namd and CUDA on Debian Wheezy
  • Vlastimil Zíma (Tue Feb 12 2013 - 07:11:38 CST)
• NAMD and NUMA
  • Brunner, Robert Kraemer (Fri May 09 2014 - 12:03:53 CDT)
  • Joseph Farran (Wed May 07 2014 - 13:54:51 CDT)
• NAMD and usable FFs
  • Kenno Vanommeslaeghe (Fri Oct 17 2014 - 11:15:18 CDT)
  • Francesco Pietra (Fri Oct 17 2014 - 03:12:48 CDT)
  • Kenno Vanommeslaeghe (Thu Oct 16 2014 - 17:53:13 CDT)
  • Francesco Pietra (Thu Oct 16 2014 - 16:41:59 CDT)
  • Kenno Vanommeslaeghe (Thu Oct 16 2014 - 13:45:05 CDT)
  • Kenno Vanommeslaeghe (Thu Oct 16 2014 - 13:37:11 CDT)
  • Josh Vermaas (Thu Oct 16 2014 - 13:05:27 CDT)
  • Francesco Pietra (Thu Oct 16 2014 - 12:59:10 CDT)
  • Josh Vermaas (Wed Oct 15 2014 - 09:20:08 CDT)
  • Francesco Pietra (Wed Oct 15 2014 - 04:34:31 CDT)
• NAMD and water models
  • Axel Kohlmeyer (Wed Oct 23 2013 - 23:22:16 CDT)
  • Mihaela Drenscko (Wed Oct 23 2013 - 20:13:17 CDT)
• NAMD build problems on PowerPC under Red Hat Enterprise
  • Lane, William (Wed Oct 16 2013 - 11:37:12 CDT)
• namd conf file
  • oguz gurbulak (Sat Sep 21 2013 - 05:52:23 CDT)
• NAMD configuration file
  • Hasan haska (Wed Jul 03 2013 - 17:12:22 CDT)
• namd coulomb conversion factor
  • Mohan maruthi sena (Sat Sep 27 2014 - 01:09:43 CDT)
• NAMD CUDA performance
  • Vlastimil Zíma (Wed Sep 11 2013 - 04:04:08 CDT)
  • Aron Broom (Tue Sep 10 2013 - 14:30:26 CDT)
  • Vlastimil Zíma (Tue Sep 10 2013 - 07:59:41 CDT)
• NAMD CVS_CUDA ERROR: "all CUDA-capable devices are busy or unavailable"
  • Samuel Bowerman (Mon Aug 11 2014 - 11:50:45 CDT)
• NAMD electrostatic interaction Failure
  • MEHRAN MB (Wed Sep 25 2013 - 10:53:25 CDT)
• NAMD electrostatic interaction Failure.
  • MEHRAN MB (Thu Sep 26 2013 - 17:27:31 CDT)
  • Kenno Vanommeslaeghe (Thu Sep 26 2013 - 16:59:20 CDT)
  • Mehran MB (Thu Sep 26 2013 - 10:12:16 CDT)
  • Kenno Vanommeslaeghe (Wed Sep 25 2013 - 19:32:11 CDT)
  • Mehran Bagheri (Wed Sep 25 2013 - 08:58:03 CDT)
• NAMD energy calculation
  • Ramin Ekhteiari (Wed Jun 25 2014 - 11:45:33 CDT)
• NAMD energy minimization
  • Axel Kohlmeyer (Sun Aug 31 2014 - 14:51:10 CDT)
  • Siva Dasetty (Sun Aug 31 2014 - 14:30:56 CDT)
• NAMD energy plugin
  • MEHRAN MB (Wed Jun 04 2014 - 15:16:09 CDT)
  • Kenno Vanommeslaeghe (Wed Jun 04 2014 - 14:16:48 CDT)
  • Kenno Vanommeslaeghe (Wed Jun 04 2014 - 14:10:39 CDT)
  • Ramin Ekhteiari (Wed Jun 04 2014 - 13:55:23 CDT)
  • Aron Broom (Wed Jun 04 2014 - 13:34:51 CDT)
  • Ramin Ekhteiari (Wed Jun 04 2014 - 12:45:36 CDT)
  • James Starlight (Thu Nov 07 2013 - 01:53:52 CST)
• NAMD energy plugin - dielectric constant
  • Ramin Ekhteiari (Mon Jul 07 2014 - 14:59:42 CDT)
• NAMD error LInux 3.11.10-21-desktop kernel AMD opternon 6272
  • Thomas C. Bishop (Tue Nov 11 2014 - 12:41:11 CST)
  • Thomas C. Bishop (Wed Nov 05 2014 - 09:48:15 CST)
• NAMD exiting on startup phase
  • Bryan Roessler (Mon Jun 24 2013 - 09:52:36 CDT)
• Namd grid forces -distance between molecule and surface
  • Mohan maruthi sena (Fri Jun 27 2014 - 05:20:29 CDT)
• namd ibverbs compile target
  • Bennion, Brian (Tue Oct 28 2014 - 18:04:52 CDT)
• NAMD Internal energy unit
  • Norman Geist (Wed Oct 23 2013 - 05:16:57 CDT)
• NAMD job submission on Kraken?
  • Giacomo Fiorin (Fri Aug 30 2013 - 15:37:56 CDT)
  • Martin, Erik W (Fri Aug 30 2013 - 15:36:03 CDT)
• NAMD mailing list unsubscribe instructions
  • Ajasja LjubetiÄ� (Sun Feb 03 2013 - 11:28:32 CST)
• NAMD Multicore CUDA usage
  • Ravi Abrol (Fri Jun 06 2014 - 14:20:10 CDT)
• NAMD on CRAY XE6m-200: dynamic linking in tcl not working
  • Harish Vashisth (Fri Jun 20 2014 - 18:49:59 CDT)
  • Harish Vashisth (Fri Jun 20 2014 - 15:17:34 CDT)
  • Axel Kohlmeyer (Fri Jun 20 2014 - 14:36:37 CDT)
  • Harish Vashisth (Fri Jun 20 2014 - 14:07:31 CDT)
• NAMD on Rescale
  • Istvan Jonyer (Mon Mar 10 2014 - 20:22:10 CDT)
• NAMD on SLURM
  • Abhishek TYAGI (Wed Nov 12 2014 - 21:07:16 CST)
  • Mitchell Gleed (Wed Nov 12 2014 - 12:57:16 CST)
  • Abhishek TYAGI (Wed Nov 05 2014 - 23:30:20 CST)
• NAMD on Stampede
  • Niklaus Johner (Wed Feb 27 2013 - 14:27:34 CST)
  • Zumot, Elia Nabil (Wed Feb 27 2013 - 14:15:51 CST)
  • hanif mahboobi (Wed Feb 27 2013 - 13:46:29 CST)
• NAMD on Stempede (and other MIC Coprocessor systems)
  • Chris Harrison (Fri Jan 11 2013 - 15:18:42 CST)
  • Jeff Wereszczynski (Fri Jan 11 2013 - 13:39:37 CST)
• Namd options from TCL
  • Ajasja LjubetiÄ� (Tue Oct 29 2013 - 04:44:50 CDT)
  • Norman Geist (Tue Oct 22 2013 - 10:26:37 CDT)
• NAMD Output files
  • Axel Kohlmeyer (Thu Apr 11 2013 - 00:35:05 CDT)
  • Rawan Al Nsour (Tue Apr 09 2013 - 08:02:26 CDT)
• NAMD PBS Parallel Job Error
  • Aditya Ranganathan (Mon Mar 04 2013 - 03:44:15 CST)
• NAMD PERFORMANCE ON NVIDIA K20 GPU
  • Neeraj Agrawal (Tue Sep 17 2013 - 18:13:34 CDT)
  • Aron Broom (Sat Sep 14 2013 - 20:19:23 CDT)
  • Neeraj Agrawal (Sat Sep 14 2013 - 18:59:08 CDT)
• NAMD post processing analysis....
  • linux freaker (Tue Mar 26 2013 - 21:09:31 CDT)
• NAMD Pressure profile calculations
  • Tao Qu (Wed Apr 02 2014 - 15:43:59 CDT)
• NAMD pressureProfile command
  • MEHRAN MB (Fri Jul 12 2013 - 12:33:48 CDT)
  • P.-L. Chau (Fri Jul 12 2013 - 11:48:30 CDT)
  • P.-L. Chau (Thu Jul 11 2013 - 04:05:45 CDT)
  • P.-L. Chau (Thu Jul 04 2013 - 16:52:00 CDT)
• NAMD related
  • Axel Kohlmeyer (Tue Jun 11 2013 - 03:01:12 CDT)
  • Anilkumar Naik (Tue Jun 11 2013 - 02:51:27 CDT)
  • Axel Kohlmeyer (Tue Jun 11 2013 - 02:27:51 CDT)
  • Anilkumar Naik (Tue Jun 11 2013 - 02:20:42 CDT)
  • Anilkumar Naik (Tue Jun 11 2013 - 02:14:17 CDT)
  • Anilkumar Naik (Tue Jun 11 2013 - 01:43:30 CDT)
  • Anilkumar Naik (Tue Jun 11 2013 - 00:16:33 CDT)
  • Anilkumar Naik (Mon Jun 10 2013 - 06:35:27 CDT)
• namd scale-up
  • Revthi Sanker (Wed Sep 18 2013 - 01:16:09 CDT)
  • Kenno Vanommeslaeghe (Tue Sep 17 2013 - 18:50:07 CDT)
  • Revthi Sanker (Sat Sep 14 2013 - 00:26:51 CDT)
  • Revthi Sanker (Fri Sep 06 2013 - 01:25:53 CDT)
  • Revthi Sanker (Thu Sep 05 2013 - 08:30:40 CDT)
  • Revthi Sanker (Thu Sep 05 2013 - 03:47:19 CDT)
  • Axel Kohlmeyer (Wed Sep 04 2013 - 03:00:30 CDT)
  • Revthi Sanker (Wed Sep 04 2013 - 02:43:24 CDT)
• namd simulation for solids withoy solvation
  • Subbusinger N (Fri Nov 14 2014 - 00:20:24 CST)
  • Kenno Vanommeslaeghe (Thu Nov 13 2014 - 11:50:51 CST)
  • Subbusinger N (Thu Nov 13 2014 - 00:02:42 CST)
• NAMD simulation with flag similar to -maxh in Gromacs
  • Dong Luo (Tue Oct 15 2013 - 11:50:45 CDT)
  • Xingcheng Lin (Tue Oct 15 2013 - 11:30:49 CDT)
• NAMD Tutorial - Water Sphere - Altering size of water sphere
  • Peter Murphy (Mon May 13 2013 - 11:16:20 CDT)
• namd with ff99sb
  • Francesco Pietra (Wed May 29 2013 - 01:27:32 CDT)
• NAMD with Intel Xeon Phi coprocessors ?
  • Christopher Neale (Fri Mar 08 2013 - 22:32:06 CST)
• NAMD with NVIDIA Quadro K5000?
  • Martin, Erik W (Tue Jan 15 2013 - 12:15:41 CST)
• NAMD with pbs script
  • k.manzoorolajdad (Tue Sep 03 2013 - 02:22:54 CDT)
  • Branko (Sun Aug 25 2013 - 10:20:28 CDT)
  • k.manzoorolajdad (Sun Aug 25 2013 - 09:36:58 CDT)
• NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation??
  • Ivan Gregoretti (Thu Jun 26 2014 - 08:34:16 CDT)
  • Shailesh Pandey (Thu Jun 26 2014 - 04:41:49 CDT)
  • Shailesh Pandey (Mon Jun 09 2014 - 12:54:03 CDT)
• NAMD-GPU
  • Aron Broom (Wed May 14 2014 - 09:54:20 CDT)
  • Axel Kohlmeyer (Wed May 14 2014 - 07:51:37 CDT)
  • Ramin Ekhteiari (Wed May 14 2014 - 07:19:10 CDT)
• namd-I: sub-routine code in NAMD
  • Axel Kohlmeyer (Thu Jan 03 2013 - 21:05:51 CST)
  • goldwheel87 (Thu Jan 03 2013 - 16:18:27 CST)
• namd-l digest V1 #1282
  • Istvan Jonyer (Fri Jan 17 2014 - 14:04:39 CST)
• namd-l digest V1 #979
  • Nutan Preety (Mon Feb 04 2013 - 06:18:55 CST)
• NAMD-Lite
  • Axel Kohlmeyer (Tue Apr 15 2014 - 18:22:54 CDT)
  • Gianluca Interlandi (Tue Apr 15 2014 - 18:16:50 CDT)
  • Axel Kohlmeyer (Tue Apr 15 2014 - 17:42:32 CDT)
  • Hassan Kianinejad (Tue Apr 15 2014 - 17:22:56 CDT)
• namd-slurm file
  • Ramin Ekhteiari (Wed Jul 02 2014 - 10:08:31 CDT)
• NAMD-SMP-Ibverbs-CUDA assistance
  • Matthew Ralph Adendorff (Tue May 13 2014 - 09:25:44 CDT)
• namd/bluegeneQ
  • Francesco Pietra (Mon Aug 05 2013 - 12:48:07 CDT)
• NAMD/MIC & CUDA on Stampede
  • Maxim Belkin (Thu Jul 17 2014 - 13:32:27 CDT)
  • Maxim Belkin (Wed Jul 16 2014 - 15:44:34 CDT)
  • Jeffery Klauda (Wed Jul 16 2014 - 13:28:27 CDT)
• NAMD/VMD installation on Linux Clusters with InfiniBand
  • Andrew Emerson (Mon May 27 2013 - 07:25:19 CDT)
  • Anilkumar Naik (Sun May 26 2013 - 00:46:47 CDT)
  • Axel Kohlmeyer (Sun May 26 2013 - 02:08:46 CDT)
  • Axel Kohlmeyer (Fri May 24 2013 - 22:42:08 CDT)
  • Axel Kohlmeyer (Fri May 24 2013 - 08:55:42 CDT)
  • Anilkumar Naik (Fri May 24 2013 - 08:25:10 CDT)
  • Anilkumar Naik (Fri May 24 2013 - 04:55:02 CDT)
  • Anilkumar Naik (Fri May 24 2013 - 08:31:09 CDT)
  • Anilkumar Naik (Wed May 22 2013 - 11:18:22 CDT)
• namd2 CUDA errors for non-superusers in Debian
  • Michael Mazack (Fri Feb 15 2013 - 22:55:07 CST)
  • Blake Mertz (Fri Feb 15 2013 - 13:46:39 CST)
  • Michael Mazack (Fri Feb 15 2013 - 08:47:47 CST)
  • Blake Mertz (Fri Feb 15 2013 - 08:42:57 CST)
  • Aron Broom (Thu Feb 14 2013 - 17:31:26 CST)
  • Blake Mertz (Thu Feb 14 2013 - 16:28:23 CST)
• NAMD2.9 single-node benchmarks, 0-2 Kepler GPU's.
  • Aron Broom (Tue Apr 30 2013 - 23:59:32 CDT)
  • Aaron Cann (Tue Apr 30 2013 - 21:17:02 CDT)
• NAMD_2.9_Linux-x86_64-ibverbs RUNS on QueenBee RUN TIME VARIATION
  • Thomas C. Bishop (Tue Nov 19 2013 - 08:06:31 CST)
• NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults
  • Axel Kohlmeyer (Wed Jun 11 2014 - 03:13:56 CDT)
  • Axel Kohlmeyer (Wed Jun 11 2014 - 02:42:48 CDT)
  • Vlastimil Zíma (Wed Jun 11 2014 - 02:36:44 CDT)
• NAMD_energy_plot
  • Jason Swails (Tue Jul 22 2014 - 17:22:29 CDT)
  • sananda chatterjee (Tue Jul 22 2014 - 17:08:56 CDT)
• NAMD_multiprocessor
  • Ramin Ekhteiari (Sat Sep 28 2013 - 04:40:19 CDT)
  • Shomesankar Bhunia (Sat Sep 28 2013 - 03:15:11 CDT)
  • Shomesankar Bhunia (Sat Sep 28 2013 - 03:08:23 CDT)
• namdenergy and namd
  • Dr. Eddie (Mon Jun 17 2013 - 08:43:44 CDT)
• NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance
  • Axel Kohlmeyer (Sun Feb 23 2014 - 20:57:18 CST)
  • sunyeping (Sun Feb 23 2014 - 20:29:02 CST)
• NamdMemoryReduction - genCompressedPsf
  • Sridhar Kumar Kannam (Thu Apr 04 2013 - 00:24:09 CDT)
  • JC Gumbart (Wed Apr 03 2013 - 22:50:22 CDT)
  • Sridhar Kumar Kannam (Wed Apr 03 2013 - 01:00:06 CDT)
  • Sridhar Kumar Kannam (Wed Apr 03 2013 - 00:05:39 CDT)
  • Sridhar Kumar Kannam (Thu Mar 21 2013 - 23:31:06 CDT)
  • Sridhar Kumar Kannam (Mon Mar 11 2013 - 17:18:12 CDT)
  • Sridhar Kumar Kannam (Sun Mar 10 2013 - 16:10:42 CDT)
  • Sridhar Kumar Kannam (Thu Mar 07 2013 - 21:39:20 CST)
• Nanotube Simulation
  • Samoylova, Olga M. (Tue Apr 15 2014 - 12:50:06 CDT)
  • Kenno Vanommeslaeghe (Tue Apr 15 2014 - 12:13:14 CDT)
  • Samoylova, Olga M. (Tue Apr 15 2014 - 09:49:31 CDT)
  • Axel Kohlmeyer (Mon Apr 14 2014 - 13:53:53 CDT)
  • Kenno Vanommeslaeghe (Mon Apr 14 2014 - 12:33:58 CDT)
  • Thomas C. Bishop (Mon Apr 14 2014 - 08:24:22 CDT)
  • Axel Kohlmeyer (Fri Apr 11 2014 - 17:41:04 CDT)
  • Kenno Vanommeslaeghe (Fri Apr 11 2014 - 17:18:18 CDT)
  • Axel Kohlmeyer (Fri Apr 11 2014 - 14:55:16 CDT)
  • Thomas C. Bishop (Fri Apr 11 2014 - 14:44:08 CDT)
  • MEHRAN MB (Fri Apr 11 2014 - 13:33:31 CDT)
  • Axel Kohlmeyer (Fri Apr 11 2014 - 13:30:47 CDT)
  • Miro Hodak (Fri Apr 11 2014 - 13:13:32 CDT)
  • Axel Kohlmeyer (Fri Apr 11 2014 - 12:05:50 CDT)
  • Miro Hodak (Fri Apr 11 2014 - 11:56:59 CDT)
  • Axel Kohlmeyer (Fri Apr 11 2014 - 03:36:44 CDT)
  • Miro Hodak (Thu Apr 10 2014 - 18:02:56 CDT)
• Nanotube tutorial
  • Adam Kells (Fri Jul 04 2014 - 13:19:33 CDT)
• NBFIX 1-4 scaling term ignored for CHARMM format parameters
  • Sunhwan Jo (Wed Aug 07 2013 - 15:21:33 CDT)
• negative VdW energy and Elect energy
  • ç¿�æž—å²½ (Tue Apr 30 2013 - 20:50:17 CDT)
• New empirical force field tools: Release of R.E.D. Server Dev./R.E.D. Python
  • FyD (Fri Nov 22 2013 - 04:18:53 CST)
• New partial charges after patching
  • Sadegh Faramarzi Ganjabad (Tue Jul 22 2014 - 06:28:57 CDT)
  • Sadegh Faramarzi Ganjabad (Tue Jul 22 2014 - 05:04:09 CDT)
  • Tristan Croll (Wed Jul 16 2014 - 18:44:39 CDT)
  • Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:53:47 CDT)
  • Sadegh Faramarzi Ganjabad (Wed Jul 16 2014 - 01:27:52 CDT)
  • Kenno Vanommeslaeghe (Fri Jul 11 2014 - 12:19:21 CDT)
  • Kenno Vanommeslaeghe (Thu Jun 19 2014 - 10:11:28 CDT)
  • Sadegh Faramarzi Ganjabad (Thu Jun 19 2014 - 03:21:33 CDT)
  • Kenno Vanommeslaeghe (Mon Jun 16 2014 - 10:23:02 CDT)
  • Sadegh Faramarzi Ganjabad (Sat Jun 14 2014 - 04:15:47 CDT)
• New: Colvars project page
  • Jérôme Hénin (Fri Jun 07 2013 - 11:43:42 CDT)
• Newbie GPU user, please help with my submission line
  • Jose Borreguero (Thu Oct 02 2014 - 14:03:24 CDT)
• Non standar solvent
  • bdrakuli (Tue Feb 18 2014 - 11:43:58 CST)
  • Roy Fernando (Tue Feb 18 2014 - 10:49:10 CST)
  • MEHRAN MB (Tue Feb 18 2014 - 10:12:26 CST)
  • Javad Noroozi (Sat Feb 15 2014 - 06:52:17 CST)
• Non-equilibrium effects in ABF runs
  • Q=AF=9B=E8=BF=90=E9=93=96?= (Fri Aug 16 2013 - 13:28:05 CDT)
  • Aron Broom (Tue Aug 13 2013 - 15:59:16 CDT)
  • Matthew Ralph Adendorff (Tue Aug 13 2013 - 11:38:57 CDT)
• non-neutralized system
  • Research Jubilant (Wed Jun 04 2014 - 10:29:47 CDT)
• non-planarity problem! NOE restraints!
  • Anna Borlsky (Thu Feb 13 2014 - 09:22:43 CST)
• Nonstandard ligand-DNA system
  • Saaz Sakrikar (Tue Jun 11 2013 - 16:47:13 CDT)
• Normal Mode Analysis in NAMD
  • Vibhor Agrawal (Thu Aug 15 2013 - 09:06:09 CDT)
• not fatal error but no more information
  • Wang (Thu Apr 04 2013 - 13:50:17 CDT)
• not reading improper angle from amber1.5 ff12SB
  • Jorgen Simonsen (Sun Jan 27 2013 - 16:06:20 CST)
• Nucleic acid stains parameters
  • Kenno Vanommeslaeghe (Mon Aug 25 2014 - 10:56:26 CDT)
  • Sebastián Gutiérrez (Mon Aug 25 2014 - 10:37:04 CDT)
• Nucleic acid-small molecule system
  • Saaz Sakrikar (Fri Jun 07 2013 - 01:45:49 CDT)
• Nvidia GPUs
  • Thomas C. Bishop (Tue Aug 20 2013 - 14:22:10 CDT)
  • Thomas Albers (Tue Aug 20 2013 - 13:27:28 CDT)
• NVT, NPT, order & combination
  • Kenno Vanommeslaeghe (Tue Aug 19 2014 - 12:17:27 CDT)
  • Zeinab Emami (Tue Aug 19 2014 - 03:23:26 CDT)
• obtaining cellBasisVectors from SCALE entries in the PDB file
  • Jose Borreguero (Fri Aug 23 2013 - 10:31:28 CDT)
• obtaining the system force
  • Giacomo Fiorin (Tue Dec 24 2013 - 10:51:10 CST)
  • Neelanjana Sengupta (Tue Dec 24 2013 - 00:26:59 CST)
• One Chain Simulation
  • Aron Broom (Tue Dec 10 2013 - 11:13:50 CST)
  • Rawan Al Nsour (Tue Dec 10 2013 - 11:06:10 CST)
• OpenMPI FEP Yields SegFaults and/or infinite dG
  • Andrew Miglino (Wed Apr 10 2013 - 12:51:05 CDT)
• Organic molecule and membrane. NAMD gives fatal error:
  • Kenno Vanommeslaeghe (Wed Sep 25 2013 - 12:33:54 CDT)
  • Aron Broom (Wed Sep 25 2013 - 08:35:14 CDT)
  • Villalain Boullon, Jose (Wed Sep 25 2013 - 08:27:59 CDT)
• Orientation colvar + metadynamics questions
  • Giacomo Fiorin (Thu Feb 21 2013 - 10:10:24 CST)
  • Jérôme Hénin (Thu Feb 21 2013 - 09:21:43 CST)
  • Benjamin Bouvier (Thu Feb 21 2013 - 07:37:06 CST)
  • Benjamin Bouvier (Thu Feb 21 2013 - 04:58:48 CST)
• Overestimated PMF
  • Aron Broom (Mon Jun 17 2013 - 14:13:09 CDT)
  • Felipe Merino (Mon Jun 17 2013 - 13:33:13 CDT)
  • Aron Broom (Mon Jun 17 2013 - 11:51:57 CDT)
  • JC Gumbart (Mon Jun 17 2013 - 11:37:10 CDT)
  • Felipe Merino (Mon Jun 17 2013 - 10:15:07 CDT)
  • Giacomo Fiorin (Mon Jun 17 2013 - 10:10:10 CDT)
  • Felipe Merino (Mon Jun 17 2013 - 09:43:07 CDT)
• pair interaction energy calculation
  • Behnam Rasti (Wed Sep 25 2013 - 06:20:35 CDT)
• pairInteraction and PME
  • Jason Swails (Wed Apr 03 2013 - 15:58:21 CDT)
• pairInteractionSelf interaction terms
  • Christopher Von Bargen (Thu Nov 07 2013 - 15:22:58 CST)
• parallel code in tclforce script
  • Axel Kohlmeyer (Fri Sep 06 2013 - 00:48:44 CDT)
  • Teerapong Pirojsirikul (Thu Sep 05 2013 - 18:48:42 CDT)
  • Axel Kohlmeyer (Thu Sep 05 2013 - 02:02:36 CDT)
  • Teerapong Pirojsirikul (Wed Sep 04 2013 - 22:03:15 CDT)
• parameter and topology files for martini polarizable water
  • Klas Karis (Thu Jul 10 2014 - 12:11:35 CDT)
  • Fotis Baltoumas (Thu Jul 10 2014 - 04:17:31 CDT)
  • Klas Karis (Wed Jul 09 2014 - 18:30:23 CDT)
• Parameter colvars
  • Giacomo Fiorin (Tue Oct 07 2014 - 13:04:53 CDT)
  • Z (Mon Oct 06 2014 - 22:05:28 CDT)
  • Grace Brannigan (Mon Oct 06 2014 - 15:56:18 CDT)
  • Giacomo Fiorin (Mon Oct 06 2014 - 15:25:06 CDT)
  • Z (Mon Oct 06 2014 - 11:20:41 CDT)
  • Jérôme Hénin (Mon Oct 06 2014 - 10:01:52 CDT)
  • Z (Mon Oct 06 2014 - 09:47:28 CDT)
  • Giacomo Fiorin (Mon Oct 06 2014 - 07:03:38 CDT)
  • Z (Mon Oct 06 2014 - 07:02:28 CDT)
  • Z (Mon Oct 06 2014 - 06:55:44 CDT)
  • Giacomo Fiorin (Mon Oct 06 2014 - 06:27:23 CDT)
  • Z (Mon Oct 06 2014 - 05:56:07 CDT)
  • Giacomo Fiorin (Mon Oct 06 2014 - 05:45:41 CDT)
  • Z (Mon Oct 06 2014 - 05:26:21 CDT)
• Parameter file for DGEBA
  • Sindu (Mon Mar 25 2013 - 03:56:40 CDT)
• Parameters for prosthetic groups
  • James Starlight (Mon Jun 24 2013 - 06:56:03 CDT)
• paricle type in residue based coarse graining of NAMD
  • Yongcheng Zhou (Mon Jun 23 2014 - 09:14:12 CDT)
  • Yongcheng Zhou (Mon Jun 23 2014 - 14:37:16 CDT)
• Pass a runtime parameter into the configuration file
  • Xingcheng Lin (Tue Oct 15 2013 - 17:55:48 CDT)
• Patch information for 1TUB.pdb in order to use "psfgen"
  • Roy Fernando (Tue Dec 10 2013 - 10:07:22 CST)
  • Lili Zhang (Tue Dec 10 2013 - 09:21:39 CST)
• Patch to connect monomers code
  • Kenno Vanommeslaeghe (Tue May 06 2014 - 13:33:49 CDT)
  • Kenno Vanommeslaeghe (Mon May 05 2014 - 13:11:36 CDT)
  • Rawan Al Nsour (Sun May 04 2014 - 12:15:12 CDT)
• Patching N- and C-Terms and their parameters
  • Peterson J (Thu May 02 2013 - 18:28:25 CDT)
• Patching protein with phosphoserine, phosphothreonine and phosphotyrosine patches
  • Rehan Zafar (Thu Sep 12 2013 - 03:41:08 CDT)
• pbc error
  • jinxj (Sun Sep 01 2013 - 21:38:48 CDT)
• PBC only along the z axis.
  • Sridhar Kumar Kannam (Sat Jan 04 2014 - 18:25:28 CST)
  • David Hardy (Fri Jan 03 2014 - 17:18:47 CST)
  • Subbarao Kanchi (Fri Jan 03 2014 - 00:18:53 CST)
  • Sridhar Kumar Kannam (Thu Jan 02 2014 - 21:46:58 CST)
• pbc problem
  • jinxj (Tue Sep 03 2013 - 04:45:06 CDT)
  • jinxj (Mon Sep 02 2013 - 04:08:28 CDT)
• pbc wrap
  • Tugba Nogay (Fri Aug 02 2013 - 14:52:23 CDT)
• PCIexpress 3.0 for MD with NAMD on GPUs
  • Francesco Pietra (Thu Nov 21 2013 - 05:00:54 CST)
  • Johny Telecaster (Wed Nov 20 2013 - 10:32:41 CST)
  • Francesco Pietra (Mon Nov 18 2013 - 01:31:10 CST)
  • Johny Telecaster (Sun Nov 17 2013 - 14:23:22 CST)
  • Francesco Pietra (Sun Nov 17 2013 - 04:56:04 CST)
  • Thomas Albers (Sat Nov 16 2013 - 09:58:22 CST)
  • Lane, William (Fri Nov 15 2013 - 02:22:53 CST)
  • Francesco Pietra (Tue Nov 12 2013 - 01:46:45 CST)
  • Francesco Pietra (Mon Nov 11 2013 - 03:51:02 CST)
• PCL dcd files
  • Niklaus Johner (Tue Sep 30 2014 - 01:15:25 CDT)
  • Giacomo Fiorin (Mon Sep 29 2014 - 12:10:07 CDT)
  • Mihaela Drenscko (Mon Sep 29 2014 - 11:09:40 CDT)
• Peptide insertion into a membrane
  • Lucas (Thu Oct 17 2013 - 17:33:38 CDT)
  • Kenno Vanommeslaeghe (Thu Oct 17 2013 - 15:08:10 CDT)
  • Villalain Boullon, Jose (Thu Oct 17 2013 - 07:44:47 CDT)
• peptide tends to migrate out the water box
  • Kenno Vanommeslaeghe (Fri Apr 18 2014 - 10:27:09 CDT)
  • Francesco Pietra (Fri Apr 18 2014 - 03:14:49 CDT)
  • Ana Celia Vila Verde (Fri Apr 18 2014 - 02:12:40 CDT)
  • Francesco Pietra (Thu Apr 17 2014 - 17:02:01 CDT)
• Percentage of Residues in Ramachandran Plot regions versus time of trajectory
  • Aditya Ranganathan (Tue Jan 29 2013 - 09:51:31 CST)
  • Aditya Ranganathan (Tue Jan 29 2013 - 04:14:57 CST)
  • Aditya Ranganathan (Sun Jan 27 2013 - 22:45:13 CST)
• Performance difference of prcompiled binary VS source code
  • Nizar Masbukhin (Mon Oct 13 2014 - 19:23:43 CDT)
• periodic boundary conditions
  • Anna Borlsky (Fri Jan 10 2014 - 15:27:34 CST)
• Persistent margin errors
  • Norman Geist (Wed Apr 16 2014 - 07:49:47 CDT)
  • Vlastimil Zíma (Wed Apr 16 2014 - 05:28:56 CDT)
  • Vlastimil Zíma (Wed Feb 26 2014 - 06:38:23 CST)
• pH calculation
  • Jérôme Hénin (Mon Dec 02 2013 - 03:05:46 CST)
  • Nadia Salami (Sun Dec 01 2013 - 23:31:02 CST)
• Phosphorylating a residue with Amber ff
  • vapour (Tue Dec 03 2013 - 17:29:31 CST)
  • Charles McAnany (Sat Nov 30 2013 - 12:24:19 CST)
• PLUMED 2.0 announcement
  • Massimiliano Bonomi (Mon Oct 28 2013 - 06:51:47 CDT)
• PME: The Excluded Coulombic Interactions
  • Hadi (Fri Mar 21 2014 - 22:56:50 CDT)
• PMEGridSizeX (number of grid points) is very small.
  • Aron Broom (Wed Feb 05 2014 - 15:10:53 CST)
  • Maxim Belkin (Wed Feb 05 2014 - 12:44:35 CST)
  • Bennion, Brian (Wed Feb 05 2014 - 12:28:37 CST)
  • Rawan Al Nsour (Wed Feb 05 2014 - 12:00:57 CST)
• PMETolerance
  • Natalie Esther Smith (Tue Apr 08 2014 - 23:07:52 CDT)
• PMF and work distribution
  • Ajasja LjubetiÄ� (Thu Jun 26 2014 - 08:05:48 CDT)
  • Giacomo Fiorin (Wed Jun 25 2014 - 12:12:52 CDT)
  • Mustafa Tekpinar (Wed Jun 25 2014 - 05:50:30 CDT)
• PMF calculation crashes with constraint failure
  • Giacomo Fiorin (Sun Jan 26 2014 - 15:37:10 CST)
  • Magnus Andersson (Sat Jan 25 2014 - 11:02:11 CST)
• PMF calculations between membrane and nano particle simulations
  • Subbarao Kanchi (Tue Jul 08 2014 - 01:01:15 CDT)
  • Giacomo Fiorin (Mon Jul 07 2014 - 18:05:06 CDT)
  • Subbarao Kanchi (Thu Jul 03 2014 - 17:46:24 CDT)
  • Giacomo Fiorin (Thu Jul 03 2014 - 16:34:33 CDT)
  • Subbarao Kanchi (Thu Jul 03 2014 - 15:58:23 CDT)
• pmf command
  • Giacomo Fiorin (Thu Jul 25 2013 - 13:00:50 CDT)
  • Victor Ovchinnikov (Thu Jul 25 2013 - 12:56:52 CDT)
  • Pedro Swagger (Thu Jul 25 2013 - 12:35:00 CDT)
  • Pedro Swagger (Wed Jul 24 2013 - 15:30:40 CDT)
• PMF from ABF simulation not plateauing
  • Jérôme Hénin (Thu May 08 2014 - 17:37:20 CDT)
  • Aron Broom (Thu May 08 2014 - 13:56:37 CDT)
  • Riley Workman (Thu May 08 2014 - 12:08:13 CDT)
• Point group symmetry
  • bmaiti_at_andrew.cmu.edu (Mon Apr 07 2014 - 18:20:08 CDT)
• Polarizability Question!
  • Sai Kumar Ramadugu (Wed Feb 20 2013 - 11:46:06 CST)
• Polarization effect of gold cluster
  • Zhao Lina (Fri Feb 21 2014 - 06:30:34 CST)
  • Axel Kohlmeyer (Tue Feb 18 2014 - 06:32:07 CST)
  • Zhao Lina (Tue Feb 18 2014 - 06:20:20 CST)
• Polymer Layer/ Cutoff
  • Kenno Vanommeslaeghe (Thu May 15 2014 - 18:00:42 CDT)
  • Rawan Al Nsour (Thu May 15 2014 - 16:13:58 CDT)
  • Kenno Vanommeslaeghe (Thu May 15 2014 - 14:34:00 CDT)
  • Kenno Vanommeslaeghe (Thu May 15 2014 - 11:58:43 CDT)
  • Rawan Al Nsour (Thu May 15 2014 - 11:19:21 CDT)
• Poor scaling in NAMD simulations
  • Tristan Croll (Fri Nov 08 2013 - 22:11:41 CST)
• posting from Yahoo addresses disabled
  • Jim Phillips (Tue Apr 08 2014 - 17:45:15 CDT)
• Potential energy as collective variable
  • Giacomo Fiorin (Mon Mar 25 2013 - 11:55:41 CDT)
  • Austin B. Yongye (Mon Mar 25 2013 - 10:35:30 CDT)
• Potential energy in the boundaries
  • Nadia Salami (Tue Nov 05 2013 - 03:06:50 CST)
• Potential of mean force calculation using colvars in NADM 2.9 package
  • Jérôme Hénin (Fri May 17 2013 - 09:56:36 CDT)
  • Ajasja LjubetiÄ� (Fri May 17 2013 - 09:41:40 CDT)
  • Jérôme Hénin (Fri May 17 2013 - 09:21:24 CDT)
  • Jérôme Hénin (Thu May 16 2013 - 08:19:57 CDT)
  • Aron Broom (Thu May 16 2013 - 07:55:46 CDT)
  • ¼­¿ëÀÏ (Thu May 16 2013 - 02:06:53 CDT)
• pre residues and ligands interaction
  • Axel Kohlmeyer (Thu Nov 21 2013 - 06:55:04 CST)
  • Ramin Ekhteiari (Thu Nov 21 2013 - 06:48:15 CST)
• PREMD in NAMD
  • Matthew Ralph Adendorff (Mon Feb 10 2014 - 09:27:15 CST)
• pressure profile calculation problem
  • P.-L. Chau (Fri Jul 12 2013 - 10:47:05 CDT)
• pressure profile calculations
  • P.-L. Chau (Thu Jul 04 2013 - 16:43:32 CDT)
• pressure profile freezing
  • Thomas Brian (Wed May 22 2013 - 12:41:52 CDT)
  • Thomas Brian (Wed May 22 2013 - 11:57:59 CDT)
• Preventing rotation of a protein
  • Kenno Vanommeslaeghe (Thu Jul 18 2013 - 11:54:15 CDT)
  • Giacomo Fiorin (Thu Jul 18 2013 - 11:41:55 CDT)
  • Axel Kohlmeyer (Thu Jul 18 2013 - 11:32:28 CDT)
  • Kenno Vanommeslaeghe (Thu Jul 18 2013 - 11:25:43 CDT)
  • Thomas Albers (Thu Jul 18 2013 - 11:21:30 CDT)
  • Jérôme Hénin (Thu Jul 18 2013 - 06:00:19 CDT)
  • Boyang Wang (Wed Jul 17 2013 - 22:05:03 CDT)
  • Peter Jones (Wed Jul 17 2013 - 22:06:10 CDT)
  • Giacomo Fiorin (Wed Jul 17 2013 - 21:31:15 CDT)
  • Thomas Albers (Wed Jul 17 2013 - 21:18:16 CDT)
• problem compiling NAMD
  • Ivan Gregoretti (Tue Feb 25 2014 - 13:23:23 CST)
  • David Hardy (Tue Feb 25 2014 - 12:39:11 CST)
  • David Hardy (Mon Feb 24 2014 - 13:18:32 CST)
  • Hassan Kianinejad (Mon Feb 24 2014 - 10:48:51 CST)
• Problem during TMD
  • Peterson J (Wed Jun 26 2013 - 14:59:50 CDT)
• problem in calculating binding energy using MMGBSA with namd-2.9
  • Shailesh Pandey (Mon Sep 01 2014 - 07:31:34 CDT)
• Problem in creating dummy atom
  • Atanu Maity (Fri Nov 01 2013 - 01:43:09 CDT)
• problem in determining atom types and charges for ligand atoms to type in the topology file
  • Mamon Hatmal (Sun Sep 01 2013 - 16:16:38 CDT)
  • Kenno Vanommeslaeghe (Thu Aug 29 2013 - 16:05:27 CDT)
  • Branko (Thu Aug 29 2013 - 12:08:30 CDT)
  • Mamon Hatmal (Thu Aug 29 2013 - 11:28:27 CDT)
  • Kenno Vanommeslaeghe (Thu Aug 29 2013 - 09:00:58 CDT)
  • Mamon Hatmal (Thu Aug 29 2013 - 06:03:17 CDT)
• problem in finding atom types for ligand
  • Kenno Vanommeslaeghe (Tue Aug 27 2013 - 11:02:10 CDT)
  • Mamon Hatmal (Tue Aug 27 2013 - 06:54:38 CDT)
• problem in installation of charm-6.4.0 in bluegeneL]
  • Santosh Kumar Chaudhary (Fri Dec 19 2014 - 05:49:45 CST)
• Problem in running "Constant Velocity Pulling" example
  • Lili Zhang (Wed Oct 02 2013 - 12:25:56 CDT)
• Problem in SMD "Constant Velocity Pulling" on Ubiquitin example
  • Lili Zhang (Thu Oct 03 2013 - 08:53:48 CDT)
• problem in solvating a graphene layer created using VMD-nanotube builder
  • Yi Wang, PhD (Mon Mar 04 2013 - 22:10:47 CST)
  • Sridhar Kumar Kannam (Mon Mar 04 2013 - 21:37:15 CST)
• Problem of ATP mutated to dATP in solution using FEP method
  • dbaogen (Mon Aug 05 2013 - 02:14:24 CDT)
• problem of using SMD and TclForces keywords simultaneously
  • dbaogen (Fri Nov 15 2013 - 02:42:07 CST)
• Problem regarding the big DCD file
  • Nicholas M Glykos (Sat Jul 20 2013 - 07:29:04 CDT)
  • Axel Kohlmeyer (Fri Jul 19 2013 - 05:03:22 CDT)
  • Atanu Maity (Fri Jul 19 2013 - 01:05:08 CDT)
  • Axel Kohlmeyer (Thu Jul 18 2013 - 18:10:51 CDT)
  • Axel Kohlmeyer (Thu Jul 18 2013 - 12:37:28 CDT)
  • Kenno Vanommeslaeghe (Thu Jul 18 2013 - 12:36:34 CDT)
  • Ajasja LjubetiÄ� (Thu Jul 18 2013 - 12:08:27 CDT)
  • Vibhor Agrawal (Thu Jul 18 2013 - 11:42:23 CDT)
  • Axel Kohlmeyer (Tue Jul 16 2013 - 14:12:37 CDT)
  • Vibhor Agrawal (Tue Jul 16 2013 - 14:07:40 CDT)
• Problem regarding the Pre-Minimizer Bad Contacts Removal
  • Norman Geist (Wed Nov 27 2013 - 02:24:28 CST)
• Problem regarding the psfgen
  • Jack Bulat (Mon Jun 10 2013 - 12:21:32 CDT)
  • Vibhor Agrawal (Sat Jun 08 2013 - 14:17:52 CDT)
  • Jack Bulat (Fri Jun 07 2013 - 15:51:10 CDT)
  • Vibhor Agrawal (Fri Jun 07 2013 - 15:33:38 CDT)
  • Jack Bulat (Fri Jun 07 2013 - 15:02:58 CDT)
  • Vibhor Agrawal (Fri Jun 07 2013 - 14:55:28 CDT)
• problem with Dihedral
  • Kenno Vanommeslaeghe (Sun Oct 06 2013 - 21:42:57 CDT)
  • farzad kiani (Sun Oct 06 2013 - 07:27:01 CDT)
• problem with inorganic builder genCompressedPsf
  • Sridhar Kumar Kannam (Wed Apr 03 2013 - 01:05:07 CDT)
• Problem with psfgen for Carbohydrates
  • Aaron Oakley (Mon Jan 28 2013 - 16:53:24 CST)
  • Sai Kumar Ramadugu (Mon Jan 28 2013 - 13:28:06 CST)
• problem with ptch ...
  • rasti (Mon Aug 26 2013 - 15:21:36 CDT)
• Problem with replica exchange
  • Michal Skoczek (Tue Dec 17 2013 - 04:57:38 CST)
• problem with restraining a dihedral angle
  • Victor (Tue Aug 13 2013 - 19:19:59 CDT)
  • Sijia (Scarlett) Dong (Mon Aug 12 2013 - 18:55:33 CDT)
• problem with runiing namd through infiniband
  • Shubhra Ghosh Dastidar (Thu May 30 2013 - 05:15:40 CDT)
  • Shubhra Ghosh Dastidar (Wed May 29 2013 - 07:41:47 CDT)
  • Shubhra Ghosh Dastidar (Wed May 29 2013 - 05:13:10 CDT)
  • Shubhra Ghosh Dastidar (Tue May 28 2013 - 02:15:15 CDT)
• Problem with running FEP calculations
  • Eric Lang (Mon Apr 15 2013 - 20:21:53 CDT)
  • chipot (Mon Apr 15 2013 - 00:03:24 CDT)
  • Eric Lang (Sun Apr 14 2013 - 18:51:45 CDT)
• Problem with running namdenergy plugin from text interface
  • zeynab mohamad hoseyni (Mon Sep 22 2014 - 22:29:26 CDT)
  • Josh Vermaas (Mon Sep 22 2014 - 15:09:10 CDT)
  • zeynab mohamad hoseyni (Mon Sep 22 2014 - 14:53:04 CDT)
• Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1
  • Kenno Vanommeslaeghe (Fri Jul 05 2013 - 16:44:06 CDT)
  • Kenno Vanommeslaeghe (Fri Jul 05 2013 - 15:47:58 CDT)
  • Vibhor Agrawal (Fri Jul 05 2013 - 14:44:31 CDT)
  • Rajan Vatassery (Fri Jul 05 2013 - 14:16:59 CDT)
  • Sebastián Gutiérrez (Fri Jul 05 2013 - 14:03:08 CDT)
  • Kenno Vanommeslaeghe (Fri Jul 05 2013 - 12:21:20 CDT)
  • Vibhor Agrawal (Thu Jul 04 2013 - 21:28:54 CDT)
  • Kenno Vanommeslaeghe (Thu Jul 04 2013 - 19:49:35 CDT)
  • Vibhor Agrawal (Thu Jul 04 2013 - 02:31:27 CDT)
• problem with using patch LINK ...
  • Victor (Sun Aug 25 2013 - 11:28:45 CDT)
  • rasti (Sun Aug 25 2013 - 07:54:50 CDT)
  • rasti (Sat Aug 24 2013 - 07:50:16 CDT)
• problems about new molecule parameterization
  • Tian Li (Thu Jan 30 2014 - 22:28:36 CST)
• problems running ABF simulation
  • Giacomo Fiorin (Tue Sep 02 2014 - 02:45:26 CDT)
  • Charles Whidborne (Tue Sep 02 2014 - 00:37:40 CDT)
• Problems with energy minimization
  • James Starlight (Thu Apr 10 2014 - 05:32:48 CDT)
  • Hongbo Du (Wed Apr 09 2014 - 10:17:08 CDT)
  • Morgan, Brittany (Wed Apr 09 2014 - 10:20:05 CDT)
  • James Starlight (Wed Apr 09 2014 - 09:38:21 CDT)
  • Subbarao Kanchi (Wed Apr 09 2014 - 09:14:55 CDT)
  • James Starlight (Wed Apr 09 2014 - 09:07:28 CDT)
• problems with in text mode towards pdf and pdb files
  • Francesco Pietra (Sat Nov 22 2014 - 02:45:10 CST)
  • Jim Phillips (Fri Nov 21 2014 - 12:50:22 CST)
  • Josh Vermaas (Fri Nov 21 2014 - 10:54:56 CST)
  • Jim Phillips (Fri Nov 21 2014 - 10:54:20 CST)
  • Francesco Pietra (Fri Nov 21 2014 - 10:42:05 CST)
  • Francesco Pietra (Fri Nov 21 2014 - 10:06:28 CST)
  • Jim Phillips (Fri Nov 21 2014 - 09:56:11 CST)
  • Francesco Pietra (Fri Nov 21 2014 - 09:39:56 CST)
  • Jim Phillips (Fri Nov 21 2014 - 09:29:35 CST)
  • Francesco Pietra (Fri Nov 21 2014 - 09:09:52 CST)
• Protein Dielectric Constant in GBIS
  • hanif mahboobi (Mon Mar 04 2013 - 12:31:46 CST)
  • hanif mahboobi (Fri Mar 01 2013 - 02:58:01 CST)
• protein schematic representaton
  • francesco oteri (Mon Jun 10 2013 - 13:23:17 CDT)
• Protein solvation
  • Kipp Johnson (Sat May 10 2014 - 15:38:26 CDT)
  • farzad kiani (Sat May 10 2014 - 12:28:26 CDT)
• Protein unfolding and Coarse grained
  • Aron Broom (Fri May 17 2013 - 07:44:38 CDT)
  • Fugui (Fri May 17 2013 - 06:55:02 CDT)
• Protein-ligand affinity
  • James Starlight (Wed Oct 16 2013 - 14:42:42 CDT)
  • Kenno Vanommeslaeghe (Tue Oct 15 2013 - 15:51:03 CDT)
  • Kenno Vanommeslaeghe (Tue Oct 15 2013 - 15:50:25 CDT)
  • James Starlight (Tue Oct 15 2013 - 15:05:11 CDT)
  • Thomas Evangelidis (Tue Oct 15 2013 - 14:43:39 CDT)
  • Kenno Vanommeslaeghe (Tue Oct 15 2013 - 14:40:50 CDT)
  • James Starlight (Tue Oct 15 2013 - 13:43:30 CDT)
  • Aron Broom (Tue Oct 15 2013 - 12:44:33 CDT)
  • James Starlight (Tue Oct 15 2013 - 12:42:09 CDT)
  • Aron Broom (Mon Oct 14 2013 - 22:16:00 CDT)
  • James Starlight (Mon Oct 14 2013 - 13:20:17 CDT)
• Protein-ligand simulation
  • Aron Broom (Sat Jul 06 2013 - 13:28:15 CDT)
  • Branko (Sat Jul 06 2013 - 11:49:45 CDT)
  • Chris Chipot (Sat Jul 06 2013 - 03:02:05 CDT)
  • Kenno Vanommeslaeghe (Sat Jun 29 2013 - 12:36:32 CDT)
  • JC Gumbart (Sat Jun 29 2013 - 07:53:31 CDT)
  • James Starlight (Sat Jun 29 2013 - 00:02:32 CDT)
  • JC Gumbart (Fri Jun 28 2013 - 17:43:24 CDT)
  • Kenno Vanommeslaeghe (Fri Jun 28 2013 - 16:12:50 CDT)
  • James Starlight (Fri Jun 28 2013 - 14:55:55 CDT)
  • Kenno Vanommeslaeghe (Fri Jun 28 2013 - 12:22:12 CDT)
  • James Starlight (Fri Jun 28 2013 - 04:21:45 CDT)
  • James Starlight (Thu Jun 27 2013 - 23:35:21 CDT)
  • JC Gumbart (Thu Jun 27 2013 - 18:40:15 CDT)
  • James Starlight (Thu Jun 27 2013 - 13:18:59 CDT)
  • Kenno Vanommeslaeghe (Thu Jun 27 2013 - 10:50:25 CDT)
  • James Starlight (Thu Jun 27 2013 - 00:16:25 CDT)
  • JC Gumbart (Wed Jun 26 2013 - 15:21:09 CDT)
  • Kenno Vanommeslaeghe (Wed Jun 26 2013 - 14:07:09 CDT)
  • James Starlight (Wed Jun 26 2013 - 00:56:38 CDT)
  • Kenno Vanommeslaeghe (Tue Jun 25 2013 - 14:17:17 CDT)
  • James Starlight (Tue Jun 25 2013 - 13:39:02 CDT)
  • Kenno Vanommeslaeghe (Tue Jun 25 2013 - 13:09:27 CDT)
  • James Starlight (Tue Jun 25 2013 - 00:58:51 CDT)
  • Kenno Vanommeslaeghe (Mon Jun 24 2013 - 21:51:34 CDT)
  • JC Gumbart (Mon Jun 24 2013 - 18:43:42 CDT)
  • James Starlight (Mon Jun 24 2013 - 13:15:51 CDT)
  • Chris Chipot (Mon Jun 24 2013 - 07:02:24 CDT)
  • James Starlight (Mon Jun 24 2013 - 06:51:46 CDT)
• protein-membrane interface hydration
  • zeynab mohamad hoseyni (Tue Feb 18 2014 - 13:37:30 CST)
• protein-water interactions
  • somedatta pal (Mon Mar 18 2013 - 12:40:31 CDT)
• psf file does not contain cross-terms
  • Axel Kohlmeyer (Sun Feb 16 2014 - 12:10:01 CST)
  • zeynab mohamad hoseyni (Sun Feb 16 2014 - 12:00:30 CST)
• PSF file for a metalloprotein
  • Roy Fernando (Mon Dec 09 2013 - 09:57:32 CST)
  • Haleh Abdizadeh (Mon Dec 09 2013 - 07:29:55 CST)
• PSF files and long atom name
  • Reza (Mon Jun 10 2013 - 19:45:48 CDT)
  • Reza (Sun Jun 09 2013 - 14:40:17 CDT)
• psf generation error
  • Vasumathi Velachi (Fri Mar 08 2013 - 13:26:14 CST)
• Psfgen - bonding terms involving disulfide bridges
  • Reza (Fri Oct 04 2013 - 09:32:46 CDT)
  • Jérôme Hénin (Fri Oct 04 2013 - 06:55:47 CDT)
  • Reza (Sun Sep 22 2013 - 22:26:33 CDT)
• pThr topology
  • ÂÀСӨ (Tue Feb 18 2014 - 21:05:27 CST)
• pump / force application
  • Arturas (Thu Apr 11 2013 - 09:14:31 CDT)
  • Jérôme Hénin (Thu Apr 11 2013 - 08:38:20 CDT)
  • Arturas (Thu Apr 11 2013 - 08:54:34 CDT)
  • Jérôme Hénin (Thu Apr 11 2013 - 08:15:14 CDT)
  • Ivana (Thu Apr 11 2013 - 08:23:44 CDT)
  • Axel Kohlmeyer (Thu Apr 11 2013 - 08:23:10 CDT)
  • Arturas (Thu Apr 11 2013 - 08:19:46 CDT)
• puzzle of SMD in NAMD-2.9 and pull code in Gromacs
  • Axel Kohlmeyer (Wed Dec 11 2013 - 00:02:26 CST)
  • dbaogen (Tue Dec 10 2013 - 20:27:15 CST)
  • Axel Kohlmeyer (Tue Dec 10 2013 - 08:22:18 CST)
  • dbaogen (Tue Dec 10 2013 - 06:02:25 CST)
• Qh
  • Lurong Pan (Thu Sep 11 2014 - 08:22:22 CDT)
• QM-MM
  • Francesco Pietra (Fri May 31 2013 - 01:47:47 CDT)
• query about the cross term in psf
  • Josh Vermaas (Sat Dec 06 2014 - 14:22:32 CST)
  • Kshatresh Dutta Dubey (Sat Dec 06 2014 - 14:12:31 CST)
  • Josh Vermaas (Sat Dec 06 2014 - 13:49:06 CST)
  • Kshatresh Dutta Dubey (Sat Dec 06 2014 - 13:31:42 CST)
• query on constraintScaling in NAMD
  • Peterson J (Fri Jun 14 2013 - 15:47:25 CDT)
• Query regarding NAMD
  • linux freaker (Sun Mar 24 2013 - 05:13:43 CDT)
• question
  • Jérôme Hénin (Mon Mar 31 2014 - 12:26:01 CDT)
  • Eifler, Jay Q. (UMKC-Student) (Mon Mar 31 2014 - 11:47:16 CDT)
• question about '+devices'
  • ukulililixl (Wed Oct 08 2014 - 01:06:50 CDT)
• Question about accelerated MD
  • Mare Libero (Tue Mar 25 2014 - 17:14:27 CDT)
• Question about converting velocities DCD to ascii plain text
  • Axel Kohlmeyer (Sat Aug 03 2013 - 14:38:36 CDT)
  • Joe Janicki (Sat Aug 03 2013 - 13:24:11 CDT)
• question about CUDA-enabled
  • Abhishek TYAGI (Sun Nov 30 2014 - 02:57:53 CST)
  • Axel Kohlmeyer (Sat Nov 29 2014 - 19:22:55 CST)
  • Abhishek Tyagi (Sat Nov 29 2014 - 11:04:55 CST)
  • maryam atabay (Sat Nov 29 2014 - 10:19:49 CST)
  • maryam atabay (Tue Nov 25 2014 - 01:05:32 CST)
• question about FEP for amphiphile in lipid bilayer
  • Leonardo Darre (Wed Dec 10 2014 - 09:20:51 CST)
  • Giacomo Fiorin (Wed Dec 10 2014 - 08:41:25 CST)
  • Leonardo Darre (Wed Dec 10 2014 - 08:08:27 CST)
• question about force constant
  • Lurong Pan (Fri Jan 03 2014 - 09:02:13 CST)
• Question about how much used from CPU?
  • jafar azamat (Mon Nov 18 2013 - 02:50:14 CST)
• Question about loading velocity files on VMD
  • Ganesh Kamath (Fri Aug 09 2013 - 10:01:17 CDT)
• Question about NAMD
  • Norman Geist (Tue Jan 29 2013 - 00:24:26 CST)
  • johan strumpfer (Mon Jan 28 2013 - 02:02:13 CST)
• question about NAMD on Kraken.
  • Martin, Erik W (Mon Oct 14 2013 - 13:44:10 CDT)
• question about NVE ensamble
  • Felipe Merino (Thu Jul 18 2013 - 10:33:23 CDT)
  • Axel Kohlmeyer (Thu Jul 18 2013 - 03:13:56 CDT)
  • Hasan haska (Thu Jul 18 2013 - 01:56:18 CDT)
• question about setting up FEP calculations
  • Shyno Mathew (Thu Nov 14 2013 - 15:25:45 CST)
  • Jérôme Hénin (Sat Nov 02 2013 - 04:24:49 CDT)
  • Shyno Mathew (Fri Nov 01 2013 - 10:14:36 CDT)
  • Shyno Mathew (Fri Oct 18 2013 - 11:44:41 CDT)
  • Jérôme Hénin (Fri Oct 18 2013 - 04:33:54 CDT)
  • Shyno Mathew (Wed Oct 16 2013 - 16:21:09 CDT)
  • Jérôme Hénin (Tue Oct 15 2013 - 12:00:58 CDT)
  • Shyno Mathew (Tue Oct 15 2013 - 11:53:12 CDT)
  • Jérôme Hénin (Tue Oct 15 2013 - 11:29:51 CDT)
  • Shyno Mathew (Tue Oct 15 2013 - 11:21:51 CDT)
  • Jérôme Hénin (Tue Oct 15 2013 - 10:44:51 CDT)
  • Shyno Mathew (Mon Oct 14 2013 - 20:01:48 CDT)
  • Jérôme Hénin (Mon Oct 14 2013 - 14:32:34 CDT)
  • Shyno Mathew (Mon Oct 14 2013 - 10:48:46 CDT)
• question in NAMD with icc & cuda
  • ukulililixl (Mon Aug 25 2014 - 06:40:48 CDT)
• question on explicit solvent reproducibility
  • Hailey Bureau (Thu Sep 05 2013 - 16:31:52 CDT)
• question regarding interaction parameters
  • subbarao kanchi (Thu Jan 24 2013 - 12:36:57 CST)
  • Victor Ovchinnikov (Thu Jan 24 2013 - 10:37:22 CST)
  • subbarao kanchi (Thu Jan 24 2013 - 09:52:42 CST)
• Question regarding loss of translational entropy calculation in FEP tutorial
  • Sunhwan Jo (Tue Feb 04 2014 - 14:47:17 CST)
  • Aron Broom (Tue Feb 04 2014 - 14:22:31 CST)
  • Monika Sharma (Tue Feb 04 2014 - 14:05:49 CST)
  • Monika Sharma (Sun Jan 19 2014 - 11:32:02 CST)
• Question regarding reverse CG to all-atom
  • parikshit moitra (Tue Jan 21 2014 - 04:42:04 CST)
• Question to NAMD source
  • Jim Phillips (Thu Sep 04 2014 - 11:25:48 CDT)
  • Norman Geist (Thu Sep 04 2014 - 08:02:31 CDT)
• Questions on calling external program to calculate force with NAMD
  • Wasut Pornpatcharapong (Mon Feb 10 2014 - 15:41:48 CST)
• Questions regarding pressure difference
  • houyang chen (Wed Oct 02 2013 - 08:29:43 CDT)
  • houyang chen (Sun Sep 29 2013 - 22:55:10 CDT)
• questions regarding the source code in NAMD
  • Asaf Farhi (Fri Aug 23 2013 - 06:12:59 CDT)
• Random segfault for MPI based REMD at startup
  • Norman Geist (Wed Apr 02 2014 - 00:34:20 CDT)
• Rapid and accurate parameterization of new molecules in CHARMM
  • Kenno Vanommeslaeghe (Wed May 28 2014 - 10:35:07 CDT)
  • Aaron Larsen (Tue May 27 2014 - 19:22:22 CDT)
  • Kenno Vanommeslaeghe (Tue May 27 2014 - 17:58:42 CDT)
  • Tristan Croll (Tue May 27 2014 - 17:23:07 CDT)
  • JC Gumbart (Tue May 27 2014 - 09:19:40 CDT)
  • Aaron Larsen (Tue May 27 2014 - 08:21:06 CDT)
• RATTLE algorithm
  • Mihaela Drenscko (Mon Feb 25 2013 - 17:56:25 CST)
• RBCG and NAMD 2.9
  • Ramya Gamini (Wed Apr 16 2014 - 14:49:54 CDT)
  • Raul Araya (Wed Apr 16 2014 - 13:21:43 CDT)
• rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs
  • Thomas C. Bishop (Sun Oct 13 2013 - 22:29:51 CDT)
• RDF calculation of crystal system
  • Axel Kohlmeyer (Sat Aug 30 2014 - 01:49:16 CDT)
  • Fatemeh Omidbeygi (Sat Aug 30 2014 - 00:41:02 CDT)
• RDF calculation with NAMD
  • Ana Celia Vila Verde (Tue Jan 21 2014 - 11:23:57 CST)
  • Dian Jiao (Tue Jan 14 2014 - 15:05:32 CST)
• RE : AW: vmd-l: Occupancy maps
  • Andrei Tudor (Mon Aug 12 2013 - 10:40:27 CDT)
• Reaction field treatment
  • Chris Chipot (Mon Jul 01 2013 - 14:29:56 CDT)
  • Axel Kohlmeyer (Mon Jul 01 2013 - 00:25:32 CDT)
  • Axel Kohlmeyer (Sat Jun 29 2013 - 08:21:54 CDT)
  • Neelanjana Sengupta (Fri Jun 28 2013 - 01:24:08 CDT)
• Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT
  • Anna Chailyan (Thu Sep 19 2013 - 08:40:58 CDT)
  • Kenno Vanommeslaeghe (Wed Sep 18 2013 - 16:52:41 CDT)
  • Teerapong Pirojsirikul (Wed Sep 18 2013 - 15:45:54 CDT)
  • Grace Brannigan (Wed Sep 18 2013 - 11:59:02 CDT)
  • Teerapong Pirojsirikul (Wed Sep 18 2013 - 12:20:24 CDT)
  • Kenno Vanommeslaeghe (Wed Sep 18 2013 - 13:50:04 CDT)
  • Niklaus Johner (Wed Sep 18 2013 - 10:29:40 CDT)
  • Anna Chailyan (Wed Sep 18 2013 - 10:01:10 CDT)
  • Kenno Vanommeslaeghe (Tue Sep 17 2013 - 18:20:38 CDT)
  • Niklaus Johner (Tue Sep 17 2013 - 11:35:45 CDT)
  • Anna Chailyan (Tue Sep 17 2013 - 11:10:29 CDT)
• reassigning temperatures
  • Martin, Erik W (Thu Jan 03 2013 - 08:19:24 CST)
• reassignTemp question
  • Martin, Erik W (Tue Oct 29 2013 - 18:55:08 CDT)
  • Aron Broom (Tue Oct 29 2013 - 16:44:52 CDT)
  • Ajasja LjubetiÄ� (Tue Oct 29 2013 - 16:26:41 CDT)
  • Aron Broom (Tue Oct 29 2013 - 15:40:46 CDT)
  • Martin, Erik W (Tue Oct 29 2013 - 15:26:46 CDT)
• Reassure fluctuations in course of simulation
  • James Starlight (Mon Jan 20 2014 - 03:19:51 CST)
• recent comparison of NAMD to other MD engines
  • Bennion, Brian (Fri Jan 24 2014 - 12:59:21 CST)
  • Tristan Croll (Fri Jan 24 2014 - 02:44:05 CST)
  • JC Gumbart (Thu Jan 23 2014 - 11:14:22 CST)
  • Hannes Loeffler (Thu Jan 23 2014 - 04:05:18 CST)
  • Giacomo Fiorin (Wed Jan 22 2014 - 20:38:29 CST)
  • Bennion, Brian (Wed Jan 22 2014 - 18:22:03 CST)
• Reduce percent use of cpu
  • jafar azamat (Tue Dec 03 2013 - 02:31:53 CST)
• Reg : MD simulation with DMSO instead of water
  • Kenno Vanommeslaeghe (Tue Jun 17 2014 - 13:13:02 CDT)
  • Axel Kohlmeyer (Tue Jun 17 2014 - 06:12:55 CDT)
  • Akshay Bhatnagar (Tue Jun 17 2014 - 06:04:58 CDT)
• Reg Lack of Lack of VDW parameters
  • Vidhya Sankar (Wed Oct 09 2013 - 10:57:58 CDT)
• Reg loadtotalforces.
  • aravind chandrasekaran (Mon Jul 29 2013 - 06:24:31 CDT)
• Reg Membrane Builder
  • Sunhwan Jo (Wed Sep 18 2013 - 12:26:06 CDT)
  • Vidhya Sankar (Wed Sep 18 2013 - 12:08:59 CDT)
• reg Parameters
  • Kenno Vanommeslaeghe (Sun Sep 29 2013 - 14:11:14 CDT)
  • Vidhya Sankar (Sun Sep 29 2013 - 08:35:10 CDT)
• Reg Reading of files durin simulation
  • Vidhya Sankar (Sat Sep 28 2013 - 03:52:32 CDT)
• Reg VDw Parameters
  • Kenno Vanommeslaeghe (Fri Sep 27 2013 - 13:36:47 CDT)
  • Vidhya Sankar (Fri Sep 27 2013 - 11:18:30 CDT)
• Reg: deciding cell basis vector
  • Aron Broom (Mon Jul 21 2014 - 12:39:39 CDT)
  • Akshay Bhatnagar (Mon Jul 21 2014 - 08:57:57 CDT)
• Reg: deformation of water box during equilibration
  • Branko (Sat Jun 07 2014 - 05:05:35 CDT)
  • Aron Broom (Fri Jun 06 2014 - 22:28:02 CDT)
  • Akshay Bhatnagar (Fri Jun 06 2014 - 21:15:30 CDT)
  • Aron Broom (Fri Jun 06 2014 - 12:37:30 CDT)
  • Akshay Bhatnagar (Fri Jun 06 2014 - 11:35:34 CDT)
• Reg: dielectric constant calculations in NAMD
  • Akshay Bhatnagar (Fri Oct 31 2014 - 00:51:24 CDT)
• Reg: error in log file
  • Jim Phillips (Thu Oct 30 2014 - 10:46:01 CDT)
  • Akshay Bhatnagar (Tue Oct 21 2014 - 20:36:48 CDT)
• Reg: LangevinPistonDecay and LangevinPistonPeriod
  • Akshay Bhatnagar (Thu Jul 24 2014 - 02:04:25 CDT)
• Reg: minimization
  • Akshay Bhatnagar (Thu Sep 25 2014 - 04:52:40 CDT)
  • Akshay Bhatnagar (Thu Sep 25 2014 - 04:51:52 CDT)
  • Axel Kohlmeyer (Wed Sep 24 2014 - 23:44:35 CDT)
  • Akshay Bhatnagar (Wed Sep 24 2014 - 23:35:16 CDT)
• Reg: movement of protein outside box
  • Aron Broom (Mon Jun 09 2014 - 22:09:28 CDT)
  • Akshay Bhatnagar (Mon Jun 09 2014 - 20:46:56 CDT)
• Reg: QM/MM calculations in NAMD
  • Akshay Bhatnagar (Mon Nov 10 2014 - 07:05:40 CST)
• Reg: solvation in DMSO
  • Akshay Bhatnagar (Mon Sep 01 2014 - 00:01:44 CDT)
• Regarding colvar distancez
  • Cosseddu, Salvatore (Sat Mar 08 2014 - 07:44:39 CST)
  • Subbarao Kanchi (Sat Mar 08 2014 - 05:00:28 CST)
• regarding editing protonated glutamate in the pdb file via psfgen
  • Prathit Chatterjee (Tue Nov 05 2013 - 00:53:17 CST)
• regarding editing protonated glutamate in the pdb file via psfgen . .
  • Martin, Erik W (Tue Nov 05 2013 - 01:38:20 CST)
• Regarding free energy cost incurred by using pseudo bonds
  • Sharmon (Thu Jul 10 2014 - 13:29:29 CDT)
• Regarding installing Namd 2.9 on windows xp 32 bit system
  • Himani Raina (Tue Feb 26 2013 - 04:08:25 CST)
• Regarding Membrane Builder
  • Vidhya Sankar (Fri Sep 20 2013 - 08:40:51 CDT)
• Regarding NAMD and MD simulations
  • Joel Moniz (Mon Jul 07 2014 - 01:42:04 CDT)
• Regarding Production Run in NAMD
  • amit banerjee (Wed Jul 10 2013 - 00:14:34 CDT)
• Regarding Temperature calculation from velocity trajectory of NAMD-2.9
  • Shailesh Pandey (Fri Jul 11 2014 - 06:14:59 CDT)
  • Shailesh Pandey (Thu Jul 10 2014 - 04:30:20 CDT)
• Regarding the Protein-Ligand Free Energy Tutorial
  • Aron Broom (Wed Sep 11 2013 - 00:39:18 CDT)
• Release of ConcatXY
  • Ali Khanlarkhani (Tue Nov 12 2013 - 16:18:36 CST)
• REMD
  • Boshra Moradi (Tue Feb 18 2014 - 02:08:53 CST)
• remd across gpus
  • Francesco Pietra (Mon Mar 31 2014 - 02:41:24 CDT)
  • Francesco Pietra (Sat Mar 29 2014 - 02:29:12 CDT)
• REMD history file and question
  • Ivana (Mon Jul 08 2013 - 11:22:36 CDT)
  • Martin, Erik W (Mon Jul 08 2013 - 10:23:00 CDT)
• REMD on IBM iDataPlex DX360M3
  • Francesco Pietra (Tue Jul 08 2014 - 12:14:10 CDT)
  • Francesco Pietra (Thu Jul 03 2014 - 09:42:41 CDT)
  • Francesco Pietra (Thu Jul 03 2014 - 04:53:32 CDT)
  • Francesco Pietra (Thu Jul 03 2014 - 01:15:21 CDT)
• remd restart
  • Francesco Pietra (Thu Aug 22 2013 - 06:00:40 CDT)
• remd run command question
  • Martin, Erik W (Mon Mar 04 2013 - 12:59:56 CST)
• REMD-GPU
  • Francesco Pietra (Thu Jul 04 2013 - 02:36:59 CDT)
• Remove tjwang@iastate.edu from the list pls
  • Norman Geist (Mon Jan 21 2013 - 00:04:57 CST)
• Repelling extracellular regions of the protein from membrane in NAMD MD simulation
  • Sahu, Indra (Sat Feb 09 2013 - 14:58:24 CST)
  • Sahu, Indra (Sun Feb 10 2013 - 11:43:43 CST)
• replica exchange and colvars
  • Francesco Pietra (Wed Jul 31 2013 - 02:34:05 CDT)
• Replica exchange and colvars - Missing Stage from restart
  • Jérôme Hénin (Sun Sep 15 2013 - 15:41:54 CDT)
  • Andrei Tudor (Sat Sep 14 2013 - 10:04:43 CDT)
• Replica exchange on single physical node
  • Francesco Pietra (Sat Jul 06 2013 - 10:37:43 CDT)
  • Francesco Pietra (Sat Jul 06 2013 - 09:19:42 CDT)
• replica exchange parallel tempering BlueGene/Q
  • Francesco Pietra (Mon Aug 12 2013 - 02:25:42 CDT)
  • Francesco Pietra (Sun Aug 11 2013 - 01:15:04 CDT)
• Replica Exchange Simulation in NAMD Precompiled binary in single node.
  • Nizar Masbukhin (Thu Oct 16 2014 - 17:09:05 CDT)
• Replica exchange, colvars & harmonic restraints
  • Giacomo Fiorin (Mon Jul 29 2013 - 16:22:56 CDT)
  • Andrei Tudor (Mon Jul 29 2013 - 13:36:22 CDT)
• Replica-exchange metadynamics scripts
  • Robert Elder (Thu Feb 14 2013 - 18:29:53 CST)
• Require Suggestion
  • amit banerjee (Tue Feb 18 2014 - 23:39:40 CST)
• Resample trajectory files
  • Ajasja LjubetiÄ� (Mon Jul 15 2013 - 16:02:04 CDT)
  • Vibhor Agrawal (Mon Jul 15 2013 - 15:52:58 CDT)
• residue_rmsd.tcl segmentation fault
  • Axel Kohlmeyer (Fri Apr 04 2014 - 04:12:38 CDT)
  • Axel Kohlmeyer (Fri Apr 04 2014 - 03:03:55 CDT)
  • John Xi (Thu Apr 03 2014 - 21:49:05 CDT)
• Restart files are empy
  • Aron Broom (Mon Jul 22 2013 - 08:33:42 CDT)
  • Alessandro Mascioni (Sun Jul 21 2013 - 12:24:23 CDT)
• restart files not written.
  • Yarrow Madrona (Fri May 10 2013 - 14:11:00 CDT)
  • Aron Broom (Thu May 09 2013 - 20:52:19 CDT)
  • Yarrow Madrona (Thu May 09 2013 - 19:25:57 CDT)
• Restart simulation of an equilibrated bilayer with sugar molecules inserted
  • Keller Wenger (Sun Mar 17 2013 - 09:51:27 CDT)
• Restarting an FEP simulation
  • Shyno Mathew (Sat Mar 22 2014 - 14:00:06 CDT)
  • Shyno Mathew (Mon Mar 10 2014 - 11:58:02 CDT)
  • Shyno Mathew (Wed Mar 05 2014 - 12:43:48 CST)
• Restarting simulation
  • MEHRAN MB (Fri Jul 05 2013 - 15:52:04 CDT)
  • James Starlight (Tue Jul 02 2013 - 00:45:37 CDT)
• Restarting T-REMD with colvars
  • Francesco Pietra (Tue Nov 05 2013 - 13:58:55 CST)
  • Francesco Pietra (Mon Nov 04 2013 - 10:19:30 CST)
• Restoring simulation from the previous run
  • James Starlight (Wed Mar 19 2014 - 09:38:18 CDT)
  • James Starlight (Wed Mar 19 2014 - 03:32:31 CDT)
• restrain ligand in z-interval
  • Magnus Andersson (Mon Apr 15 2013 - 06:37:26 CDT)
• restrain ligand to z-interval
  • Ajasja LjubetiÄ� (Mon Apr 15 2013 - 08:22:07 CDT)
  • Magnus Andersson (Mon Apr 15 2013 - 06:29:07 CDT)
• restrain noe's in random.inp
  • Vanessa Gameiro (Tue Dec 03 2013 - 04:12:38 CST)
• restraining bonds
  • Kenno Vanommeslaeghe (Tue Sep 02 2014 - 11:04:37 CDT)
  • Kenno Vanommeslaeghe (Mon Sep 01 2014 - 10:37:17 CDT)
  • Tristan Croll (Mon Sep 01 2014 - 01:09:05 CDT)
  • Tristan Croll (Mon Sep 01 2014 - 00:57:28 CDT)
  • Tristan Croll (Mon Sep 01 2014 - 00:45:22 CDT)
  • Neelanjana Sengupta (Sun Aug 31 2014 - 23:50:24 CDT)
• Restraints between ion and small molecule
  • Daniel Torrente (Mon Jul 14 2014 - 20:51:55 CDT)
  • Aron Broom (Mon Jul 14 2014 - 21:13:44 CDT)
  • Kenno Vanommeslaeghe (Thu Jun 26 2014 - 14:43:47 CDT)
  • Aron Broom (Thu Jun 26 2014 - 13:55:13 CDT)
  • Kenno Vanommeslaeghe (Thu Jun 26 2014 - 13:21:42 CDT)
  • Kenno Vanommeslaeghe (Thu Jun 26 2014 - 13:16:31 CDT)
  • Daniel Torrente (Thu Jun 26 2014 - 11:53:49 CDT)
• Retaining conformation
  • Tristan Croll (Sat Jul 20 2013 - 05:15:17 CDT)
  • Jérôme Hénin (Thu Jul 18 2013 - 06:01:09 CDT)
  • Riley Workman (Wed Jul 17 2013 - 14:52:44 CDT)
• Reverse coarse-graining Error: CG Builder
  • Sanket Avinash Deshmukh (Fri Dec 13 2013 - 00:42:25 CST)
• RE£º NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance
  • Axel Kohlmeyer (Sun Feb 23 2014 - 21:26:40 CST)
• RE： NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance
  • sunyeping (Wed Mar 12 2014 - 09:42:34 CDT)
  • sunyeping (Mon Feb 24 2014 - 03:32:06 CST)
  • sunyeping (Sun Feb 23 2014 - 21:13:52 CST)
• RE： The water box shrinks at the start of the MD simulation
  • sunyeping (Sun Jul 27 2014 - 19:19:15 CDT)
• Re：tutorial-l: Protein structure distorted after Energy minimization with NAMD
  • sunyeping (Wed Oct 08 2014 - 21:58:02 CDT)
• RMSD calculation
  • Mert Gür (Fri Aug 02 2013 - 22:22:35 CDT)
  • Vibhor Agrawal (Fri Aug 02 2013 - 21:44:47 CDT)
• Root mean square deviation..........
  • Gurpreet Kaur Dhindsa (Tue Aug 12 2014 - 12:58:38 CDT)
• RSMDTT keyword for nucleic acids
  • Aaron Larsen (Wed Feb 05 2014 - 14:43:13 CST)
• Rule of thumb for equilibration
  • Aron Broom (Mon Jul 28 2014 - 09:59:04 CDT)
  • Stephan Grein (Mon Jul 28 2014 - 09:45:43 CDT)
• run NAMD command in GPU
  • Axel Kohlmeyer (Tue Jul 16 2013 - 14:11:35 CDT)
  • Adrian (Tue Jul 16 2013 - 14:05:17 CDT)
• Runaway cuda-enabled namd2 processes
  • Tim.Ho_at_csiro.au (Tue Dec 03 2013 - 21:31:42 CST)
• runaway minimizations
  • Bennion, Brian (Thu Feb 20 2014 - 12:06:54 CST)
• Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations)
  • Tristan Croll (Fri Feb 21 2014 - 01:44:39 CST)
  • Norman Geist (Fri Feb 21 2014 - 01:34:55 CST)
  • Tristan Croll (Thu Feb 20 2014 - 17:52:22 CST)
  • Bennion, Brian (Thu Feb 20 2014 - 11:53:31 CST)
  • Tristan Croll (Wed Feb 19 2014 - 17:53:43 CST)
  • Tristan Croll (Wed Feb 12 2014 - 17:51:13 CST)
  • Bennion, Brian (Wed Feb 12 2014 - 10:57:12 CST)
  • Tristan Croll (Tue Feb 11 2014 - 20:07:59 CST)
• running a calculation during simulation
  • Jérôme Hénin (Tue Oct 21 2014 - 04:03:13 CDT)
  • Ajasja LjubetiÄ� (Tue Oct 21 2014 - 02:52:21 CDT)
  • Maxim Belkin (Mon Oct 20 2014 - 18:00:03 CDT)
  • Josh Vermaas (Mon Oct 20 2014 - 16:38:57 CDT)
  • btreece_at_andrew.cmu.edu (Mon Oct 20 2014 - 16:08:12 CDT)
• running benchmarks on NAMD-Lite
  • Hassan Kianinejad (Fri Mar 14 2014 - 17:35:21 CDT)
• Running Charmrun/NAMD with more than 10 processes fails
  • K Miura (Tue Dec 16 2014 - 02:53:36 CST)
• Running CUDA-enabled NAMD on multiple nodes without InfiniBand?
  • Michel van der List (Wed Dec 03 2014 - 12:06:03 CST)
  • Michel van der List (Mon Dec 01 2014 - 08:40:46 CST)
• running Linux-x86_64-multicore precompiled version at 2 hexa-core CPUs?
  • Axel Kohlmeyer (Thu Jul 17 2014 - 09:35:59 CDT)
  • Andras Borosy (Thu Jul 17 2014 - 09:27:46 CDT)
• running Multiple-replicas metadynamics
  • Osvalds Verners (Fri May 16 2014 - 14:21:28 CDT)
  • Giacomo Fiorin (Fri May 16 2014 - 14:00:41 CDT)
  • Osvalds Verners (Fri May 16 2014 - 13:01:08 CDT)
• Running NAMD in multiprocessor single machine
  • Aron Broom (Thu Oct 17 2013 - 19:31:20 CDT)
  • Roy Fernando (Thu Oct 17 2013 - 16:28:02 CDT)
  • Roy Fernando (Thu Oct 17 2013 - 16:02:58 CDT)
• running NAMD in parallel
  • Jim Phillips (Sat Nov 29 2014 - 16:51:06 CST)
  • Kshatresh Dutta Dubey (Fri Nov 28 2014 - 19:29:43 CST)
  • Revthi Sanker (Thu Aug 01 2013 - 23:39:02 CDT)
• running NAMD on Amazon EC2?
  • Axel Kohlmeyer (Thu Feb 14 2013 - 14:53:56 CST)
  • Cloud Computing (Thu Feb 14 2013 - 14:48:04 CST)
  • Cloud Computing (Thu Feb 14 2013 - 14:38:38 CST)
  • Dong Luo (Thu Feb 14 2013 - 10:54:21 CST)
  • Ajasja LjubetiÄ� (Thu Feb 14 2013 - 02:39:06 CST)
  • Cloud Computing (Wed Feb 13 2013 - 16:05:03 CST)
• Running namd on linux in cpu+gpu mode
  • James Starlight (Sat Jan 19 2013 - 01:19:53 CST)
• Running NAMD on SGE cluster - multiple modes and cores
  • Anna Gorska (Fri Dec 06 2013 - 07:23:29 CST)
  • Anna Gorska (Thu Dec 05 2013 - 04:14:05 CST)
  • Anna Gorska (Thu Dec 05 2013 - 05:09:27 CST)
  • Anna Gorska (Tue Dec 03 2013 - 09:23:30 CST)
  • Anna Gorska (Tue Dec 03 2013 - 05:25:37 CST)
• Running NAMD via GROMACS topology
  • Mike Makowski (Sun Aug 10 2014 - 18:05:21 CDT)
  • Mike Makowski (Sun Aug 10 2014 - 17:44:35 CDT)
• Same NAMD files give error in Linux but not in Windows ....
  • Axel Kohlmeyer (Tue Oct 01 2013 - 03:54:56 CDT)
  • Villalain Boullon, Jose (Tue Oct 01 2013 - 03:49:55 CDT)
• SASA calculation
  • Siva Dasetty (Thu Sep 04 2014 - 09:03:56 CDT)
• Scaling on 64 core nodes?
  • Rebecca Swett (Thu Feb 14 2013 - 08:37:44 CST)
• Scaling problem: 4 nodes OK, 5 fails to start
  • Stober, Spencer T (Thu Jan 17 2013 - 08:31:53 CST)
  • Stober, Spencer T (Wed Jan 16 2013 - 13:39:08 CST)
• Scaling problem: 4 nodes OK, 5 nodes fail
  • Stober, Spencer T (Wed Jan 16 2013 - 13:46:07 CST)
• Scaling solvent-solute intermolecular interactions
  • Jason Swails (Wed May 14 2014 - 10:20:57 CDT)
  • Michael Bellucci (Wed May 14 2014 - 08:50:36 CDT)
  • Jason Swails (Tue May 13 2014 - 16:57:14 CDT)
  • Axel Kohlmeyer (Tue May 13 2014 - 15:17:53 CDT)
  • Michael Bellucci (Tue May 13 2014 - 15:09:06 CDT)
  • Axel Kohlmeyer (Tue May 13 2014 - 13:56:02 CDT)
  • Michael Bellucci (Tue May 13 2014 - 13:34:13 CDT)
• School on Molecular Dynamics with NAMD and LAMMPS in Philadelphia, August 18-22 2014
  • Axel Kohlmeyer (Thu Jul 17 2014 - 14:48:33 CDT)
• secondary structure analysis
  • Ajasja LjubetiÄ� (Fri Jan 11 2013 - 03:34:55 CST)
  • Nicholas M Glykos (Fri Jan 11 2013 - 02:57:26 CST)
  • Martin, Erik W (Wed Jan 09 2013 - 14:20:36 CST)
• Segmentation fault - colvar
  • Peterson J (Mon Sep 16 2013 - 23:02:55 CDT)
• segmentation fault in accelMD
  • Anna Modzelewska (Mon Jul 28 2014 - 05:56:05 CDT)
• Selecting GPU for namd2
  • Francesco Pietra (Mon May 06 2013 - 02:27:57 CDT)
• Self-Assemble Monolayer--Periodic Boundary Conditions
  • Natnael Doilicho (Wed Oct 01 2014 - 16:14:52 CDT)
  • Natnael Doilicho (Mon Sep 29 2014 - 18:03:18 CDT)
• Separate water coordinates from graphite
  • Mihaela Drenscko (Tue Nov 12 2013 - 13:57:01 CST)
• Set exact molarity in cell
  • Stephan Grein (Thu Aug 28 2014 - 09:08:42 CDT)
• Setting constraints for SMD simulation
  • Charles Whidborne (Mon Sep 15 2014 - 20:20:39 CDT)
• setting the polarizabilities for the Drude force field
  • Hadi (Fri Aug 02 2013 - 13:28:46 CDT)
  • Kenno Vanommeslaeghe (Fri Aug 02 2013 - 11:01:26 CDT)
  • Hadi Dinpajooh (Thu Aug 01 2013 - 13:39:42 CDT)
  • Frank Haverkort (Thu Aug 01 2013 - 06:48:59 CDT)
• Setting up membrane protein simulation from existing conformation?
  • Per Larsson (Wed May 07 2014 - 15:12:53 CDT)
  • Kenno Vanommeslaeghe (Wed May 07 2014 - 14:44:00 CDT)
  • Per Larsson (Wed May 07 2014 - 14:17:41 CDT)
• setting up namd simulation in IBM Blue Gene/L
  • Santosh Kumar Chaudhary (Sat Dec 20 2014 - 01:53:14 CST)
  • Jim Phillips (Fri Dec 19 2014 - 12:55:33 CST)
  • hannes.loeffler_at_stfc.ac.uk (Thu Dec 18 2014 - 01:43:11 CST)
  • hannes.loeffler_at_stfc.ac.uk (Thu Dec 18 2014 - 01:36:36 CST)
  • Santosh Kumar Chaudhary (Thu Dec 18 2014 - 00:09:48 CST)
  • hannes.loeffler_at_stfc.ac.uk (Wed Dec 17 2014 - 07:07:23 CST)
  • Santosh Kumar Chaudhary (Wed Dec 17 2014 - 06:21:17 CST)
• Sevoflurane parameters (psf file)
  • Mikhail Suyetin (Mon May 06 2013 - 13:25:38 CDT)
  • Jérôme Hénin (Mon May 06 2013 - 03:42:42 CDT)
  • Mikhail Suyetin (Fri May 03 2013 - 15:07:00 CDT)
  • Branko (Fri May 03 2013 - 13:14:27 CDT)
  • Mikhail Suyetin (Fri May 03 2013 - 09:41:19 CDT)
• SHAKE or RATTLE algorithm
  • David Hardy (Fri Apr 04 2014 - 16:28:54 CDT)
  • Axel Kohlmeyer (Fri Apr 04 2014 - 15:44:45 CDT)
  • Ramin Ekhteiari (Fri Apr 04 2014 - 15:08:04 CDT)
• Sherical BC energy conservation
  • Norman Geist (Mon Nov 25 2013 - 03:18:37 CST)
• Shift (or offset) of the lipid bilayer along Z axis during equilibration
  • Aron Broom (Fri Jun 07 2013 - 20:56:46 CDT)
  • ç¿�æž—å²½ (Fri Jun 07 2013 - 20:36:44 CDT)
• Should I use a precompiled binary?
  • Bennion, Brian (Fri May 24 2013 - 15:45:02 CDT)
  • Andrew DeYoung (Fri May 24 2013 - 15:36:41 CDT)
• Should PME be used for electrostatic interaction energy calculations?
  • Thomas Evangelidis (Thu Jun 19 2014 - 02:38:50 CDT)
  • Fotis Baltoumas (Wed Jun 18 2014 - 12:59:16 CDT)
• Siginificant speedup by updating nvidia driver
  • Norman Geist (Mon Aug 25 2014 - 11:06:38 CDT)
• Silent crash NAMD-multicore-CUDA
  • Aron Broom (Tue Aug 19 2014 - 11:17:04 CDT)
  • MEHRAN MB (Tue Aug 19 2014 - 11:06:34 CDT)
  • MEHRAN MB (Thu Jul 31 2014 - 18:27:55 CDT)
  • Aron Broom (Wed Jul 30 2014 - 17:50:54 CDT)
  • MEHRAN MB (Wed Jul 30 2014 - 17:23:10 CDT)
• Simulated Annealing for a polymer
  • Rawan Al Nsour (Mon Feb 04 2013 - 13:13:54 CST)
• Simulated Annealing/ Cooling
  • Rawan Al Nsour (Tue Feb 26 2013 - 09:43:32 CST)
• Simulation at different time-steps
  • Aron Broom (Tue Jul 16 2013 - 23:47:17 CDT)
  • Mare Libero (Tue Jul 16 2013 - 22:02:58 CDT)
• Simulation at high pressure
  • Rawan Al Nsour (Sat Mar 23 2013 - 13:45:25 CDT)
  • Gianluca Interlandi (Fri Mar 22 2013 - 15:10:42 CDT)
  • Rawan Al Nsour (Fri Mar 22 2013 - 14:20:49 CDT)
• Simulation continuously crashes after minimization
  • Cruz-Chu Eduardo Roberto (Tue Feb 12 2013 - 17:00:57 CST)
  • Patricia Campbell (Tue Feb 12 2013 - 15:01:37 CST)
  • Patricia Campbell (Tue Feb 12 2013 - 14:52:03 CST)
• Simulation crash during NPT equilibration
  • James Starlight (Fri Apr 11 2014 - 05:58:17 CDT)
• simulation crashes frequently with "atoms moving too fast"
  • eprates_at_iqm.unicamp.br (Fri Nov 01 2013 - 16:26:57 CDT)
• Simulation Do not Run in the Cluster
  • Roy Fernando (Sun Sep 21 2014 - 12:16:44 CDT)
• Simulation in Collective sub-space
  • Giacomo Fiorin (Tue Jun 25 2013 - 16:54:04 CDT)
  • James Starlight (Tue Jun 25 2013 - 13:21:18 CDT)
  • Giacomo Fiorin (Tue Jun 25 2013 - 08:03:48 CDT)
  • James Starlight (Tue Jun 25 2013 - 07:52:41 CDT)
• Simulation in NPT ensemble
  • James Starlight (Fri Jun 28 2013 - 15:28:40 CDT)
• Simulation of a membrane protein with large extracellular domains
  • Jim Phillips (Thu Nov 13 2014 - 16:05:08 CST)
  • Josh Vermaas (Thu Nov 13 2014 - 08:35:43 CST)
  • Fotis Baltoumas (Thu Nov 13 2014 - 07:30:54 CST)
• Simulation of a protein and calcium ions
  • Axel Kohlmeyer (Wed Oct 09 2013 - 02:45:01 CDT)
  • Stephan Matthias Grein (Wed Oct 09 2013 - 02:39:27 CDT)
  • Kenno Vanommeslaeghe (Tue Oct 08 2013 - 11:37:19 CDT)
  • Ajasja LjubetiÄ� (Tue Oct 08 2013 - 08:21:38 CDT)
  • Stephan Matthias Grein (Tue Oct 08 2013 - 04:49:53 CDT)
  • Ajasja LjubetiÄ� (Tue Oct 08 2013 - 04:08:56 CDT)
  • Axel Kohlmeyer (Tue Oct 08 2013 - 03:29:40 CDT)
  • Ajasja LjubetiÄ� (Tue Oct 08 2013 - 03:29:28 CDT)
  • Stephan Matthias Grein (Tue Oct 08 2013 - 03:15:44 CDT)
• Simulation of a protein and ions
  • Stephan Matthias Grein (Tue Oct 08 2013 - 03:29:05 CDT)
• Simulation of Protein with Ions
  • Aron Broom (Wed Jul 03 2013 - 06:02:21 CDT)
  • Stephan Grein (Wed Jul 03 2013 - 02:47:03 CDT)
• Simulation of the membrane protein
  • Niklaus Johner (Thu Sep 05 2013 - 12:23:00 CDT)
  • James Starlight (Thu Sep 05 2013 - 10:52:29 CDT)
  • James Starlight (Thu Sep 05 2013 - 02:48:10 CDT)
  • James Starlight (Thu Sep 05 2013 - 00:35:26 CDT)
  • Aron Broom (Wed Sep 04 2013 - 12:26:00 CDT)
  • James Starlight (Wed Sep 04 2013 - 11:16:35 CDT)
• simulation options available with GPU
  • Ana Celia Vila Verde (Tue Sep 16 2014 - 02:52:51 CDT)
  • Ana Celia Vila Verde (Tue Sep 16 2014 - 02:58:28 CDT)
• Simulation results from NVT has a cavity
  • Kenno Vanommeslaeghe (Mon Oct 21 2013 - 12:25:58 CDT)
  • Xingcheng Lin (Sat Oct 19 2013 - 13:49:12 CDT)
• simultaneous simulation for protein in water and SMD
  • Aron Broom (Thu Oct 03 2013 - 13:02:55 CDT)
  • Axel Kohlmeyer (Thu Oct 03 2013 - 12:40:05 CDT)
  • amit banerjee (Thu Oct 03 2013 - 12:36:23 CDT)
  • Axel Kohlmeyer (Thu Oct 03 2013 - 07:39:03 CDT)
  • amit banerjee (Thu Oct 03 2013 - 07:33:04 CDT)
• Single point energy calc with gaussian/namd... log file interpretation
  • Axel Kohlmeyer (Sat Feb 23 2013 - 02:30:10 CST)
  • Stober, Spencer T (Fri Feb 22 2013 - 16:31:01 CST)
• slice of water box
  • Hongbo Du (Wed Apr 09 2014 - 20:22:04 CDT)
  • Boshra Moradi (Wed Apr 09 2014 - 17:13:12 CDT)
• Slow vacuum/GBIS simulations (time to completion keeps increasing)
  • Aron Broom (Wed Jul 03 2013 - 07:40:54 CDT)
  • Ole Juul Andersen (Wed Jul 03 2013 - 07:28:20 CDT)
  • Axel Kohlmeyer (Wed Jul 03 2013 - 06:19:36 CDT)
  • Aron Broom (Wed Jul 03 2013 - 06:12:30 CDT)
  • Ole Juul Andersen (Wed Jul 03 2013 - 05:06:46 CDT)
  • Aron Broom (Tue Jul 02 2013 - 13:10:49 CDT)
  • Ole Juul Andersen (Tue Jul 02 2013 - 12:57:14 CDT)
  • Aron Broom (Tue Jul 02 2013 - 12:45:17 CDT)
  • Ole Juul Andersen (Tue Jul 02 2013 - 12:33:45 CDT)
• SMD and torque application
  • George Patargias (Sun Feb 03 2013 - 14:42:09 CST)
• SMD constant velocity not constant
  • Axel Kohlmeyer (Wed Oct 29 2014 - 20:04:28 CDT)
  • Charles Whidborne (Wed Oct 29 2014 - 19:25:08 CDT)
• smd force is too high
  • Yi Wang, PhD (Mon Mar 18 2013 - 20:07:26 CDT)
  • Jérôme Hénin (Mon Mar 18 2013 - 12:07:40 CDT)
  • Yi Wang, PhD (Sat Mar 16 2013 - 09:35:44 CDT)
  • Jacqueline Schmidt (Fri Mar 15 2013 - 12:35:52 CDT)
  • Aron Broom (Fri Mar 15 2013 - 12:10:55 CDT)
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• unsubscriber e-mail office pool anybody?
  • Axel Kohlmeyer (Thu Mar 07 2013 - 03:04:16 CST)
  • Ajasja LjubetiÄ� (Tue Mar 05 2013 - 08:39:01 CST)
  • Axel Kohlmeyer (Tue Mar 05 2013 - 08:36:45 CST)
  • Aaron Oakley (Tue Mar 05 2013 - 07:31:42 CST)
  • Jérôme Hénin (Tue Mar 05 2013 - 07:02:47 CST)
  • Axel Kohlmeyer (Tue Mar 05 2013 - 07:11:44 CST)
• unsuscribe
  • Cat Chenal (Thu Apr 10 2014 - 09:49:18 CDT)
  • Rehan Zafar (Tue Oct 29 2013 - 11:30:35 CDT)
  • Cat Chenal (Tue Oct 29 2013 - 09:45:33 CDT)
  • Cat Chenal (Mon Aug 12 2013 - 10:01:42 CDT)
  • Cat Chenal (Thu Aug 08 2013 - 12:20:16 CDT)
• use of colvars to restrain the absolute positions of all atoms in a large system
  • Abir Ganguly (Wed Jul 10 2013 - 12:11:10 CDT)
  • Jérôme Hénin (Wed Jul 10 2013 - 05:07:16 CDT)
  • Abir Ganguly (Tue Jul 09 2013 - 17:35:31 CDT)
  • Aron Broom (Tue Jul 09 2013 - 17:18:35 CDT)
  • Giacomo Fiorin (Tue Jul 09 2013 - 17:16:19 CDT)
  • Abir Ganguly (Tue Jul 09 2013 - 17:01:15 CDT)
• useGroupPressure
  • Anna Borlsky (Fri Jan 10 2014 - 17:09:32 CST)
• using CHARMM-format Amber parameters in NAMD
  • Basheer (Wed Aug 20 2014 - 22:15:22 CDT)
  • Kenno Vanommeslaeghe (Wed Aug 20 2014 - 10:27:20 CDT)
  • Mike Makowski (Tue Aug 19 2014 - 23:34:13 CDT)
  • Basheer Subei (Tue Aug 19 2014 - 19:16:43 CDT)
• Using CNS parameter file to create NAMD topology and parameter files
  • Roy Fernando (Wed Jan 23 2013 - 13:21:35 CST)
• Using CosntantArea in membrane simulation
  • Peterson J (Wed Jun 19 2013 - 16:53:06 CDT)
• Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction .......
  • Niklaus Johner (Wed Jul 24 2013 - 08:45:19 CDT)
  • Aron Broom (Wed Jul 24 2013 - 12:03:47 CDT)
  • Kenno Vanommeslaeghe (Wed Jul 24 2013 - 11:07:42 CDT)
  • Villalain Boullon, Jose (Wed Jul 24 2013 - 03:37:20 CDT)
• Using negatively charged phospholipids and no neutralization, membrane expands in the xy direction .......
  • Kenno Vanommeslaeghe (Thu Jul 25 2013 - 11:12:23 CDT)
  • Villalain Boullon, Jose (Thu Jul 25 2013 - 05:52:05 CDT)
• Using nodelist file causes namd to hang
  • Douglas Houston (Sat Sep 20 2014 - 06:14:29 CDT)
  • Douglas Houston (Thu Jun 19 2014 - 12:25:25 CDT)
  • Douglas Houston (Wed Apr 09 2014 - 04:49:17 CDT)
  • Douglas Houston (Tue Apr 08 2014 - 08:50:15 CDT)
  • Douglas Houston (Tue Apr 08 2014 - 04:29:34 CDT)
• Using position-dependent diffusion to simulate long colvars trajectories
  • Ajasja LjubetiÄ� (Thu Apr 03 2014 - 07:36:28 CDT)
• Using the CHARMM36 forcefield with NAMD
  • Kenno Vanommeslaeghe (Fri May 09 2014 - 11:50:45 CDT)
  • Kenno Vanommeslaeghe (Wed Apr 23 2014 - 12:28:33 CDT)
  • Alex Utev (CMP) (Wed Apr 23 2014 - 11:15:08 CDT)
• Using volmap to calculate the water density around certain residues
  • Axel Kohlmeyer (Mon Nov 04 2013 - 02:32:22 CST)
  • bharat gupta (Mon Nov 04 2013 - 02:25:22 CST)
• utilizing mic coprocs on Stampede
  • Edward Lyman (Tue Jun 18 2013 - 14:46:47 CDT)
• vacuum minimisation-reg
  • Niklaus Johner (Wed Jul 24 2013 - 08:38:49 CDT)
  • Revthi Sanker (Thu Jul 25 2013 - 02:40:42 CDT)
  • Revthi Sanker (Wed Jul 24 2013 - 02:37:12 CDT)
• variable force constant
  • Aron Broom (Thu Jul 10 2014 - 13:00:32 CDT)
  • Lu Hong (Thu Jul 10 2014 - 12:34:58 CDT)
• Various questions
  • Douglas Houston (Tue Feb 04 2014 - 07:26:05 CST)
  • Norman Geist (Mon Feb 03 2014 - 04:34:48 CST)
  • Douglas Houston (Mon Feb 03 2014 - 03:52:42 CST)
  • Douglas Houston (Wed Jan 22 2014 - 08:31:03 CST)
  • Douglas Houston (Tue Jan 21 2014 - 09:42:14 CST)
• VDW component: NAMD vs. CHARMM
  • Jérôme Hénin (Thu Apr 04 2013 - 09:56:46 CDT)
  • Shubhra Ghosh Dastidar (Thu Apr 04 2013 - 09:20:23 CDT)
• VDW energy is negative but total energy is positive
  • Bennion, Brian (Tue Sep 10 2013 - 10:57:23 CDT)
  • Bennion, Brian (Mon Sep 09 2013 - 10:25:53 CDT)
  • dayanidhi mohanta (Fri Sep 06 2013 - 23:18:51 CDT)
• VDW energy: positive or negative?
  • Kenno Vanommeslaeghe (Wed Mar 05 2014 - 17:21:12 CST)
  • Jason Swails (Tue Mar 04 2014 - 20:04:38 CST)
  • Kenno Vanommeslaeghe (Tue Mar 04 2014 - 19:14:15 CST)
  • PANAGIOTA KYRIAKOU (Tue Mar 04 2014 - 18:24:54 CST)
  • Kenno Vanommeslaeghe (Tue Mar 04 2014 - 17:50:50 CST)
  • Axel Kohlmeyer (Tue Mar 04 2014 - 17:28:08 CST)
  • PANAGIOTA KYRIAKOU (Tue Mar 04 2014 - 17:20:53 CST)
• vdW-only fep between two ions
  • Christopher Rowley (Tue Nov 04 2014 - 14:43:08 CST)
• vdwForceSwitching and PME
  • Adrian (Wed Jul 24 2013 - 22:48:20 CDT)
• velocity manipulation
  • Ajasja LjubetiÄ� (Thu Oct 16 2014 - 08:24:34 CDT)
  • Axel Kohlmeyer (Thu Oct 16 2014 - 08:21:17 CDT)
  • mostafa raeesi (Thu Oct 16 2014 - 06:37:02 CDT)
• Very long simulation
  • flavio seixas (Mon Mar 04 2013 - 17:39:26 CST)
  • Axel Kohlmeyer (Mon Mar 04 2013 - 06:10:43 CST)
  • Mihaela Drenscko (Mon Mar 04 2013 - 05:55:07 CST)
• vibrational modes calculation
  • Mortaza Aghtar (Mon Sep 23 2013 - 08:55:27 CDT)
• vmd-l: About PLUMED with NAMD VMD
  • andrea spitaleri (Thu Feb 28 2013 - 02:46:34 CST)
  • John Stone (Wed Feb 27 2013 - 10:10:48 CST)
• vmd-l: Accelerated MD (aMD)
  • Juan R. Perilla (Sun Jul 27 2014 - 20:23:00 CDT)
• vmd-l: citing SODIUM program
  • John Stone (Tue Jan 14 2014 - 09:19:27 CST)
• vmd-l: Error with show_replicas.vmd
  • John Stone (Tue Sep 03 2013 - 10:57:26 CDT)
• vmd-l: FFTK Atom types
  • Francesco Pietra (Wed Mar 27 2013 - 10:54:21 CDT)
  • Mayne, Christopher G (Wed Mar 27 2013 - 08:06:05 CDT)
• vmd-l: ffTK problem: OPT.Charges
  • Zeinab Emami (Fri Nov 07 2014 - 11:13:04 CST)
  • Mayne, Christopher G (Fri Nov 07 2014 - 10:51:57 CST)
• vmd-l: fftk-charges
  • Kenno Vanommeslaeghe (Mon Oct 21 2013 - 12:53:59 CDT)
  • rodolfo gonzalez (Mon Oct 21 2013 - 01:57:55 CDT)
• vmd-l: making psf files
  • Kenno Vanommeslaeghe (Mon Oct 13 2014 - 12:18:31 CDT)
  • Zeinab Emami (Mon Oct 13 2014 - 04:55:06 CDT)
• vmd-l: membrane lipid involvement of cholesterol
  • Richard Wood (Sat Jul 26 2014 - 09:07:57 CDT)
  • Richard Wood (Sat Jul 26 2014 - 06:26:59 CDT)
• vmd-l: NAMD energy calculation
  • Morgan, Brittany (Wed Jul 02 2014 - 11:58:22 CDT)
  • Ramin Ekhteiari (Tue Jul 01 2014 - 12:07:47 CDT)
  • Morgan, Brittany (Tue Jul 01 2014 - 09:26:44 CDT)
  • John Stone (Mon Jun 30 2014 - 22:59:28 CDT)
• vmd-l: Suggestions on parameterizing a ligand to simulate in NAMD
  • Peterson J (Mon May 20 2013 - 23:48:48 CDT)
  • Mayne, Christopher G (Mon May 20 2013 - 14:32:42 CDT)
  • Jiawei Xu (Mon May 20 2013 - 14:11:50 CDT)
• Volume Entry
  • Axel Kohlmeyer (Sun Feb 16 2014 - 17:33:03 CST)
  • Rawan Al Nsour (Sun Feb 16 2014 - 16:36:04 CST)
  • Aron Broom (Sun Feb 16 2014 - 15:28:27 CST)
  • Rawan Al Nsour (Sun Feb 16 2014 - 15:16:44 CST)
  • Aron Broom (Sun Feb 16 2014 - 13:57:33 CST)
  • Axel Kohlmeyer (Sun Feb 16 2014 - 13:51:37 CST)
  • Rawan Al Nsour (Sun Feb 16 2014 - 13:08:05 CST)
  • Axel Kohlmeyer (Sun Feb 16 2014 - 10:38:13 CST)
  • Rawan Al Nsour (Sun Feb 16 2014 - 10:29:18 CST)
  • Axel Kohlmeyer (Mon Feb 10 2014 - 11:09:18 CST)
  • Rawan Al Nsour (Mon Feb 10 2014 - 11:04:06 CST)
  • Axel Kohlmeyer (Mon Feb 10 2014 - 10:45:37 CST)
  • Axel Kohlmeyer (Mon Feb 10 2014 - 10:12:49 CST)
  • Rawan Al Nsour (Mon Feb 10 2014 - 10:08:19 CST)
• VRPN cannot connect to Falcon
  • George Patargias (Wed Oct 15 2014 - 04:58:11 CDT)
• VRPN compilation error
  • Axel Kohlmeyer (Tue Oct 14 2014 - 08:54:12 CDT)
  • George Patargias (Tue Oct 14 2014 - 08:43:59 CDT)
• warnings while using amber files
  • amin_at_imtech.res.in (Thu Dec 25 2014 - 21:54:38 CST)
  • amin_at_imtech.res.in (Thu Dec 25 2014 - 05:14:20 CST)
• Water density in the solvate plugin
  • Kenno Vanommeslaeghe (Mon Jul 29 2013 - 10:34:11 CDT)
  • Axel Kohlmeyer (Fri Jul 26 2013 - 10:58:57 CDT)
  • David Cohen-Tanugi (Fri Jul 26 2013 - 10:50:20 CDT)
• water layer in membrane protein modeling
  • Ajasja LjubetiÄ� (Thu Jul 18 2013 - 10:00:19 CDT)
  • Kong, Ren (Thu Jul 18 2013 - 09:24:06 CDT)
• water-protein interation
  • Hongbo Du (Fri Nov 14 2014 - 09:03:37 CST)
  • sunyeping (Fri Nov 14 2014 - 02:32:11 CST)
• WG: questions regarding the source code in NAMD
  • Norman Geist (Wed Aug 28 2013 - 10:49:31 CDT)
• WHAM analysis for Umbrella sampling
  • Ada Zhan (Wed May 01 2013 - 15:10:03 CDT)
  • Aron Broom (Wed May 01 2013 - 14:12:23 CDT)
  • Ada Zhan (Wed May 01 2013 - 13:59:46 CDT)
  • Aron Broom (Wed May 01 2013 - 13:09:53 CDT)
  • Chris Chipot (Wed May 01 2013 - 12:58:18 CDT)
  • Ada Zhan (Wed May 01 2013 - 12:20:15 CDT)
  • Chris Chipot (Wed May 01 2013 - 02:01:44 CDT)
  • Aron Broom (Tue Apr 30 2013 - 17:27:57 CDT)
  • Ada Zhan (Tue Apr 30 2013 - 17:18:37 CDT)
  • Jérôme Hénin (Tue Apr 30 2013 - 04:07:52 CDT)
  • Aron Broom (Mon Apr 29 2013 - 15:17:00 CDT)
  • Ada Zhan (Mon Apr 29 2013 - 14:41:37 CDT)
• What does "outputSystemForce" output?
  • Giacomo Fiorin (Wed Jun 05 2013 - 17:17:04 CDT)
  • Ivan Mikhaylov (Wed Jun 05 2013 - 17:14:50 CDT)
  • Giacomo Fiorin (Wed Jun 05 2013 - 16:49:20 CDT)
  • Ivan Mikhaylov (Wed Jun 05 2013 - 16:28:48 CDT)
• what to do with this error
  • Pavan (Fri Dec 06 2013 - 08:03:31 CST)
  • Liqun Zhang (Tue Dec 03 2013 - 14:21:34 CST)
• which namd versions compatible with CUDA 5.5 and other CUDA woes
  • Robert Wohlhueter (Sun Sep 28 2014 - 12:00:17 CDT)
  • Jim Phillips (Fri Sep 26 2014 - 17:25:29 CDT)
  • Robert Wohlhueter (Mon Sep 22 2014 - 13:39:19 CDT)
• whidth value of orientation in colvars
  • Giacomo Fiorin (Fri Jan 10 2014 - 16:20:45 CST)
  • ¼­¿ëÀÏ (Thu Jan 09 2014 - 18:28:22 CST)
  • Giacomo Fiorin (Thu Jan 09 2014 - 07:31:15 CST)
  • ¼­¿ëÀÏ (Thu Jan 09 2014 - 02:27:59 CST)
• Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD
  • Bin He (Tue Nov 11 2014 - 06:19:06 CST)
  • Bin He (Mon Nov 10 2014 - 13:51:15 CST)
  • Bin He (Sat Nov 08 2014 - 01:24:32 CST)
• Why does my volume suddenly expand as I increase temper ature.. .
  • Martin, Erik W (Tue Nov 12 2013 - 09:14:29 CST)
• Why does my volume suddenly expand as I increase temperature.
  • Aron Broom (Mon Nov 11 2013 - 19:12:33 CST)
  • Martin, Erik W (Mon Nov 11 2013 - 17:55:05 CST)
• Why RDF increases as r increase instead of constant
  • Arash Azari (Mon Nov 03 2014 - 01:32:27 CST)
  • Kenno Vanommeslaeghe (Sun Nov 02 2014 - 18:25:41 CST)
  • Kenno Vanommeslaeghe (Sun Nov 02 2014 - 12:38:04 CST)
  • Nifeng Guo hui (Sat Nov 01 2014 - 17:07:32 CDT)
• Widom test particle insertion in NAMD
  • Javad Noroozi (Mon Feb 17 2014 - 00:40:08 CST)
• Will there be a NAMD2.9 for IBM AIX UNIX?
  • Mengyuan Zhu (Fri Dec 13 2013 - 11:06:48 CST)
• Window for FEP calculations
  • Gianluca Interlandi (Tue Aug 26 2014 - 19:35:33 CDT)
• Workshop on GPU Programming for Molecular Modeling, August 2-4, 2013, in Urbana, Illinois
  • David Brandon (Tue Jun 11 2013 - 17:41:43 CDT)
• Workshop on GPU Programming for Molecular Modeling, in Urbana, Illinois, July 22-24, 2014
  • David Brandon (Fri Apr 18 2014 - 16:49:02 CDT)
• Workshop on Very Large System Simulation Workshop, Urbana, IL, August 11-15, 2014
  • David Brandon (Sat May 17 2014 - 18:22:07 CDT)
• wrapping a protein
  • Maxim Belkin (Wed Aug 20 2014 - 17:53:46 CDT)
  • Maria Bykhovskaia (Wed Aug 20 2014 - 17:40:30 CDT)
• wrapping in two dimensions
  • Maria Bykhovskaia (Thu Oct 16 2014 - 15:33:34 CDT)
• wrapping option in namd
  • Christian Jorgensen (Mon Jun 23 2014 - 04:59:50 CDT)
  • MEHRAN MB (Tue Apr 01 2014 - 21:44:36 CDT)
  • Research Jubilant (Wed Mar 19 2014 - 22:38:16 CDT)
  • Ivan Gregoretti (Wed Mar 19 2014 - 21:58:30 CDT)
  • Research Jubilant (Wed Mar 19 2014 - 21:34:57 CDT)
• write pdb
  • bay__gulf618_at_sina.com (Thu Feb 20 2014 - 00:31:36 CST)
• writedcd problem
  • jinxj (Mon Sep 02 2013 - 09:32:00 CDT)
• Xeon vs i7 and ECC vs SDRAM
  • Gianluca Interlandi (Tue Jun 24 2014 - 23:07:02 CDT)
  • Gianluca Interlandi (Tue Jun 24 2014 - 20:02:49 CDT)
• xplor psf used for namd
  • Jana, Suvamay (Mon Nov 25 2013 - 20:07:31 CST)
• XY constraints with center of mass movements
  • Aron Broom (Mon Dec 09 2013 - 12:00:33 CST)
  • Peterson J (Mon Dec 09 2013 - 11:29:12 CST)
• zeroMomentum for water droplet
  • David Hardy (Wed Dec 04 2013 - 09:32:41 CST)
  • Axel Kohlmeyer (Tue Dec 03 2013 - 22:38:16 CST)
  • Mihaela Drenscko (Tue Dec 03 2013 - 17:38:43 CST)
• zinc finger with ASP
  • FIDAN SUMBUL (Thu Jun 27 2013 - 09:47:22 CDT)
• ´ð¸´£ºRE£º NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance
  • Axel Kohlmeyer (Mon Feb 24 2014 - 04:34:22 CST)
• 回å¤�： Shift (or offset) of the lipid bilayer along Z axis during equilibration
  • ç¿�æž—å²½ (Fri Jun 07 2013 - 21:30:12 CDT)
• 崔幼æ�¬ 自动回å¤�: Multiple input and output files
  • cuiyoutian_at_163.com (Wed Nov 05 2014 - 20:20:37 CST)
• ÅÙÇÏÉ ÊèÌêç:
  • Mamon Hatmal (Tue Dec 03 2013 - 05:14:42 CST)
• ç­”å¤�：RE： NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance
  • sunyeping (Mon Feb 24 2014 - 03:37:02 CST)