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NAMD-L: By Subject

By Subject

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

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

• Vermaas, Joshua (Thu Dec 08 2016 - 10:17:25 CST)
• Kenneth Huang (Tue Jul 26 2016 - 08:09:12 CDT)
• Boyang Wang (Tue Jul 19 2016 - 23:33:49 CDT)
• Chitrak Gupta (Wed Jun 01 2016 - 13:03:34 CDT)
• Chitrak Gupta (Wed Jun 01 2016 - 08:57:57 CDT)
• Chitrak Gupta (Tue May 10 2016 - 13:57:03 CDT)
• Srijita Paul (Tue May 10 2016 - 08:41:10 CDT)
• Chitrak Gupta (Mon May 09 2016 - 11:07:14 CDT)
• Maxim Belkin (Mon May 09 2016 - 09:38:23 CDT)
• Jeff Comer (Sun May 08 2016 - 20:19:44 CDT)
• Abhishek TYAGI (Sat May 07 2016 - 07:45:54 CDT)
• Chitrak Gupta (Sat Apr 23 2016 - 23:19:09 CDT)
• Peter Freddolino (Fri Apr 22 2016 - 12:26:51 CDT)
• Srijita Paul (Fri Apr 22 2016 - 05:39:12 CDT)
• Akshay Bhatnagar (Fri Apr 22 2016 - 02:30:13 CDT)
• Peter Freddolino (Tue Apr 19 2016 - 10:03:52 CDT)
• Peter Freddolino (Sat Apr 16 2016 - 20:14:41 CDT)
• Jeff Comer (Wed Apr 13 2016 - 08:32:23 CDT)
• Jeff Comer (Tue Apr 12 2016 - 08:56:29 CDT)
• Chitrak Gupta (Fri Apr 08 2016 - 16:40:46 CDT)
• Chitrak Gupta (Fri Apr 08 2016 - 10:01:07 CDT)
• Ajasja LjubetiÄ� (Wed Jan 27 2016 - 03:39:04 CST)
• Zhe Wu (Wed Oct 21 2015 - 14:16:02 CDT)
• Norman Geist (Thu Feb 05 2015 - 07:55:53 CST)
• "implausibly old time stamp" for charm++ 6.7 in CVS
  • Jim Phillips (Mon Dec 21 2015 - 10:04:11 CST)
  • Brian Radak (Wed Dec 16 2015 - 11:42:29 CST)
• "Jump" in Energy and Volume graphs of my MD
  • David Hardy (Fri Apr 01 2016 - 12:09:44 CDT)
  • Daniela Rivas (Thu Mar 31 2016 - 11:21:03 CDT)
  • Peter Freddolino (Thu Mar 31 2016 - 09:13:46 CDT)
  • Peter Freddolino (Wed Mar 30 2016 - 19:33:49 CDT)
  • Peter Freddolino (Wed Mar 30 2016 - 15:56:22 CDT)
  • Daniela Rivas (Wed Mar 30 2016 - 15:49:01 CDT)
  • Peter Freddolino (Wed Mar 30 2016 - 15:23:46 CDT)
  • Daniela Rivas (Wed Mar 30 2016 - 15:04:07 CDT)
• "missing operator at _@_ in expression" for if statement
  • Norman Geist (Tue Jul 28 2015 - 01:33:01 CDT)
  • Simon Kit Sang Chu (Mon Jul 27 2015 - 19:39:51 CDT)
• "UNABLE TO FIND BOND PARAMETERS" but bond is defined in stream file
  • Josh Vermaas (Fri Sep 04 2015 - 10:29:38 CDT)
  • Bryan Roessler (Fri Sep 04 2015 - 00:07:49 CDT)
• "Unknown command-line option +replicas"
  • Norman Geist (Tue Mar 03 2015 - 08:35:47 CST)
  • Mitul Saha (Mon Mar 02 2015 - 23:33:11 CST)
• (no subject)
  • Tom King (Fri Dec 09 2016 - 16:43:07 CST)
  • Nehir NALINCI (Thu Dec 08 2016 - 01:06:44 CST)
  • Santanu Santra (Mon Oct 31 2016 - 23:22:58 CDT)
  • Sourav Pal (Mon Oct 03 2016 - 02:44:00 CDT)
  • krishna (Mon Aug 29 2016 - 03:03:21 CDT)
  • krishna (Tue Jul 26 2016 - 00:56:38 CDT)
  • d.ronika_at_iitg.ernet.in (Tue Jul 19 2016 - 22:52:43 CDT)
  • Srijita Paul (Tue May 31 2016 - 23:29:11 CDT)
  • Srijita Paul (Tue May 31 2016 - 05:03:47 CDT)
  • Srijita Paul (Sat May 07 2016 - 06:17:48 CDT)
  • Srijita Paul (Fri Apr 22 2016 - 01:19:21 CDT)
  • Srijita Paul (Sat Apr 16 2016 - 00:06:47 CDT)
  • Srijita Paul (Wed Apr 13 2016 - 07:08:28 CDT)
  • Srijita Paul (Tue Apr 12 2016 - 07:33:41 CDT)
  • Srijita Paul (Fri Apr 08 2016 - 08:00:25 CDT)
  • Srijita Paul (Tue Jan 26 2016 - 23:06:12 CST)
  • Srijita Paul (Tue Jan 26 2016 - 23:02:28 CST)
  • Srijita Paul (Wed Jan 06 2016 - 22:25:56 CST)
  • Srijita Paul (Tue Dec 22 2015 - 00:06:49 CST)
  • Mattia Felice Palermo (Wed Oct 21 2015 - 04:07:03 CDT)
  • Ma'Mon Hatmal (Thu Feb 05 2015 - 06:32:09 CST)
• +p option on Windows 7
  • Jim Phillips (Wed May 20 2015 - 11:58:13 CDT)
  • Norman Geist (Mon May 18 2015 - 02:39:30 CDT)
  • Kukol, Andreas (Fri May 15 2015 - 05:07:55 CDT)
• ------------- Processor 0 Exiting: Called CmiAbort ------------
  • Pardis Tabaee (Thu Mar 17 2016 - 12:09:43 CDT)
• -xHost
  • Gianluca Interlandi (Mon Jul 06 2015 - 13:08:37 CDT)
• 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD
  • Lachele Foley (Tue Mar 17 2015 - 21:46:19 CDT)
  • clarkzhy (Tue Mar 17 2015 - 21:18:48 CDT)
  • Lachele Foley (Tue Mar 17 2015 - 21:15:41 CDT)
  • clarkzhy (Tue Mar 17 2015 - 20:33:41 CDT)
• 16 total processes killed (some possibly by mpirun during cleanup)
  • Shalton Evans (Mon Nov 02 2015 - 14:34:13 CST)
• 2.11 how to remove charmrun remote-shell options
  • Jim Phillips (Tue Dec 20 2016 - 23:29:12 CST)
  • Scott Brozell (Tue Dec 20 2016 - 19:05:08 CST)
  • Scott Brozell (Wed Jan 13 2016 - 12:04:54 CST)
• 2016 ISQBP Meeting: early registration / abstract submission deadline approaching
  • Vlad Cojocaru (Thu Mar 17 2016 - 03:49:47 CDT)
• [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED)
  • Brunner, Robert Kraemer (Tue Jan 12 2016 - 14:31:36 CST)
  • Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 14:04:36 CST)
  • Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 09:44:54 CST)
  • Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 07:27:59 CST)
• A common tool to read the output of NAMD run
  • Ajasja LjubetiÄ� (Mon Nov 28 2016 - 08:34:47 CST)
  • Richard Overstreet (Mon Nov 28 2016 - 08:08:03 CST)
  • Harish Srinivasan (Mon Nov 28 2016 - 06:28:00 CST)
• A problem in ABF simulation
  • Jérôme Hénin (Wed Dec 14 2016 - 10:29:51 CST)
  • 宋瑞ç�© (Wed Dec 14 2016 - 05:45:28 CST)
  • Karteek Bejagam (Tue Nov 29 2016 - 12:14:44 CST)
  • Jérôme Hénin (Tue Nov 29 2016 - 08:16:02 CST)
  • 宋瑞ç�© (Tue Nov 29 2016 - 04:28:21 CST)
• ABF calculations - reaction coordinate
  • Giacomo Fiorin (Mon Nov 16 2015 - 20:30:56 CST)
  • Mohan maruthi sena (Mon Nov 16 2015 - 19:15:15 CST)
• ABF error on NAMD 2.10
  • Giacomo Fiorin (Mon Nov 02 2015 - 08:51:52 CST)
  • Haleh a (Mon Nov 02 2015 - 08:45:29 CST)
  • Giacomo Fiorin (Mon Nov 02 2015 - 07:49:46 CST)
  • Jérôme Hénin (Mon Nov 02 2015 - 07:47:25 CST)
  • Haleh a (Mon Nov 02 2015 - 05:55:59 CST)
• ABF with external electric field
  • Giacomo Fiorin (Tue Mar 31 2015 - 13:16:15 CDT)
  • Jeff Comer (Tue Mar 31 2015 - 11:41:35 CDT)
  • Bala subramanian (Tue Mar 31 2015 - 10:42:24 CDT)
• about "small molecules" in OPLS-AAM FF
  • Francesco Pietra (Wed Oct 07 2015 - 16:14:12 CDT)
• about angles in coordination complexes
  • luca belmonte (Wed Feb 04 2015 - 04:37:28 CST)
  • luca belmonte (Mon Jan 26 2015 - 11:51:11 CST)
  • luca belmonte (Mon Jan 26 2015 - 10:55:10 CST)
  • Jérôme Hénin (Mon Jan 26 2015 - 10:50:35 CST)
  • luca belmonte (Mon Jan 26 2015 - 10:28:17 CST)
  • Jérôme Hénin (Mon Jan 26 2015 - 10:20:37 CST)
  • luca belmonte (Mon Jan 26 2015 - 10:02:27 CST)
  • Jérôme Hénin (Mon Jan 26 2015 - 09:56:07 CST)
  • luca belmonte (Mon Jan 26 2015 - 09:28:16 CST)
  • luca belmonte (Mon Jan 26 2015 - 08:39:17 CST)
• about command replicaRecv and replicaSend
  • jc guo (Mon Oct 19 2015 - 02:09:43 CDT)
• about compiling NAMD using intel icc and impi
  • XSC (Fri Jan 23 2015 - 04:00:29 CST)
• about deca alanine tutorial setup
  • Branko (Mon Nov 02 2015 - 16:26:57 CST)
  • Ajasja LjubetiÄ� (Mon Nov 02 2015 - 16:14:28 CST)
  • Jessen Lucas (Mon Nov 02 2015 - 15:22:16 CST)
• about hydrogen bond analysis
  • Mo Chen (Tue Mar 24 2015 - 16:19:37 CDT)
  • Hasan haska (Tue Mar 24 2015 - 16:07:08 CDT)
• about langevin dynamics
  • Norman Geist (Mon Mar 09 2015 - 01:44:18 CDT)
  • Gisella Alfonsino (Sun Mar 08 2015 - 05:36:28 CDT)
• About parseFEP error
  • Atsutoshi Okabe (Wed Feb 03 2016 - 08:01:21 CST)
• About pbc
  • Jeff Comer (Tue Nov 15 2016 - 17:40:12 CST)
  • Francesco Pietra (Tue Nov 08 2016 - 15:10:56 CST)
• about re install
  • sunyeping (Tue Oct 20 2015 - 02:09:33 CDT)
  • jc guo (Tue Oct 20 2015 - 01:20:08 CDT)
• about replica exchange
  • Jeff Comer (Fri Oct 16 2015 - 16:17:13 CDT)
  • jc guo (Fri Oct 16 2015 - 10:43:23 CDT)
• about replica exchange example in lib of 2.10 NAMD
  • Jeff Comer (Tue Oct 20 2015 - 20:10:00 CDT)
  • jc guo (Fri Oct 16 2015 - 00:11:18 CDT)
• About the TMDInitialRMSD parameter in targeted molecular dynamics
  • sunyeping (Tue Oct 20 2015 - 12:06:22 CDT)
• about User-Defined Forces
  • ¸ß¾ü (Mon Jan 18 2016 - 03:28:31 CST)
• accelerated MD new variant
  • Brian Radak (Mon Nov 30 2015 - 09:48:36 CST)
  • Vlad Cojocaru (Mon Nov 30 2015 - 10:00:35 CST)
  • Vlad Cojocaru (Sun Nov 29 2015 - 03:53:20 CST)
• accelMD and GBIS?
  • Brian Radak (Fri Feb 27 2015 - 18:15:13 CST)
• accessing values of 'extendedLagrangian' fictious degree of freedom
  • Jérôme Hénin (Fri Apr 29 2016 - 04:37:36 CDT)
  • Prabhakar Bhimalapuram (Thu Apr 28 2016 - 12:23:36 CDT)
  • Jérôme Hénin (Wed Apr 27 2016 - 04:24:18 CDT)
  • Prabhakar Bhimalapuram (Tue Apr 26 2016 - 22:01:58 CDT)
• ACS COMP Division awards deadline this week
  • Carlos Simmerling (Wed Sep 28 2016 - 11:34:52 CDT)
• adaptive biasing force with RMSD colvar
  • Jérôme Hénin (Sun Mar 20 2016 - 05:49:54 CDT)
  • Haleh a (Thu Mar 17 2016 - 11:39:45 CDT)
• Adaptive Tempering - Velocity Rescaling
  • Sachin Natesh (Mon Aug 31 2015 - 09:45:16 CDT)
• Adaptive tempering implementation in NAMD differs
  • Nicholas M Glykos (Fri Sep 25 2015 - 04:36:52 CDT)
  • Sachin Natesh (Thu Sep 24 2015 - 20:28:36 CDT)
  • Sachin Natesh (Wed Sep 23 2015 - 10:28:05 CDT)
  • Nicholas M. Glykos (Wed Sep 23 2015 - 05:45:40 CDT)
• Adaptive tempering implementation in NAMD differs from original paper?
  • Sachin Natesh (Tue Sep 22 2015 - 19:45:22 CDT)
• Add ions/molecules different from Autoionize defaults
  • Tristan Croll (Tue Dec 29 2015 - 07:12:10 CST)
  • Peter Freddolino (Sun Dec 27 2015 - 22:04:00 CST)
  • Josh Vermaas (Sun Dec 27 2015 - 06:25:50 CST)
  • Peter Freddolino (Sat Dec 26 2015 - 21:12:23 CST)
  • Ardavan Mehdizadeh (Fri Dec 25 2015 - 12:28:43 CST)
  • amin_at_imtech.res.in (Fri Dec 25 2015 - 07:16:46 CST)
  • Peter Freddolino (Thu Dec 24 2015 - 08:45:43 CST)
  • Ardavan Mehdizadeh (Thu Dec 24 2015 - 07:37:39 CST)
  • Ardavan Mehdizadeh (Thu Dec 24 2015 - 07:37:01 CST)
  • Ardavan Mehdizadeh (Wed Dec 23 2015 - 12:05:36 CST)
• adjust water box size in RBCG
  • Yongcheng Zhou (Sun Feb 01 2015 - 16:03:54 CST)
• Adsorption energy of protein in vacuum
  • Abhishek TYAGI (Mon May 23 2016 - 19:52:56 CDT)
  • Jeff Comer (Mon May 23 2016 - 12:02:17 CDT)
  • Abhishek TYAGI (Sun May 22 2016 - 22:46:38 CDT)
  • Madhulika Gupta (Sat May 21 2016 - 10:20:34 CDT)
  • Ana Celia Vila Verde (Sat May 21 2016 - 04:17:54 CDT)
  • Madhulika Gupta (Fri May 20 2016 - 06:01:05 CDT)
• Aggregation related analysis scripts
  • Aditya Ranganathan (Wed Feb 25 2015 - 01:13:42 CST)
  • Jeff Comer (Tue Feb 24 2015 - 15:39:12 CST)
  • Jérôme Hénin (Tue Feb 24 2015 - 09:39:01 CST)
  • Aditya Ranganathan (Tue Feb 24 2015 - 02:28:10 CST)
• Alchemical FEP calculation involving glycine
  • Jérôme Hénin (Thu Mar 12 2015 - 04:26:18 CDT)
  • jostmey . (Wed Mar 11 2015 - 17:57:02 CDT)
  • Chris Chipot (Tue Mar 10 2015 - 05:59:57 CDT)
  • jostmey . (Mon Mar 09 2015 - 23:58:31 CDT)
• Alchemical FEP calculations in Implicit Solvent
  • jostmey . (Mon Feb 23 2015 - 14:45:13 CST)
  • jostmey . (Mon Feb 23 2015 - 13:21:57 CST)
  • MEHRAN MB (Mon Feb 23 2015 - 13:08:56 CST)
  • jostmey . (Mon Feb 23 2015 - 13:04:15 CST)
• Alchemify Possibilities
  • David Huggins (Tue Apr 26 2016 - 09:28:15 CDT)
  • Jérôme Hénin (Mon Apr 25 2016 - 11:31:32 CDT)
  • Brian Radak (Mon Apr 25 2016 - 11:15:19 CDT)
  • David Huggins (Mon Apr 25 2016 - 11:03:10 CDT)
• Alchemy Shift Coefficient at Low Density Regime (TI)
  • Brian Radak (Thu Feb 05 2015 - 13:44:14 CST)
  • JAVAD NOROOZI (Wed Feb 04 2015 - 02:58:15 CST)
• Algorithm used by NAMD
  • David Hardy (Fri Apr 03 2015 - 11:18:46 CDT)
  • Gurpreet Kaur Dhindsa (Thu Apr 02 2015 - 09:55:36 CDT)
• Amber forcefield in namd simulation in parallel version
  • Teerapong Pirojsirikul (Fri Dec 02 2016 - 03:30:11 CST)
  • Santanu Santra (Fri Dec 02 2016 - 00:05:35 CST)
  • Santanu Santra (Thu Dec 01 2016 - 23:00:45 CST)
  • Santanu Santra (Thu Dec 01 2016 - 06:36:24 CST)
• aMD and GPU acceleration
  • Thomas Albers (Thu Oct 22 2015 - 13:53:09 CDT)
• aMD doesn't work when some atoms are fixed
  • sunyeping (Mon Jul 18 2016 - 20:41:34 CDT)
• Amino acid as ligand
  • Dhiraj Srivastava (Mon Apr 25 2016 - 12:22:24 CDT)
• An script for ACF
  • faride badalkhani (Tue Jun 07 2016 - 16:37:13 CDT)
• Analysis plugins for Martini Coarse Grained protein simulations
  • Fotis Baltoumas (Sat Feb 07 2015 - 05:25:50 CST)
  • Aditya Ranganathan (Sat Feb 07 2015 - 03:55:33 CST)
• angle between 2 vectors as collective variable
  • Vlad Cojocaru (Thu Mar 26 2015 - 11:04:09 CDT)
  • Giacomo Fiorin (Thu Mar 26 2015 - 10:16:25 CDT)
  • Vlad Cojocaru (Thu Mar 26 2015 - 10:03:36 CDT)
  • Giacomo Fiorin (Thu Mar 26 2015 - 09:58:26 CDT)
  • Vlad Cojocaru (Thu Mar 26 2015 - 09:17:41 CDT)
• ANGLE PARAMETERS FOR NH3 HC NH3
  • Francesco Pietra (Tue Oct 27 2015 - 11:12:20 CDT)
• anionic cysteine
  • Tristan Croll (Wed Dec 09 2015 - 04:23:03 CST)
  • Francesco Pietra (Wed Dec 09 2015 - 04:13:54 CST)
  • Tristan Croll (Tue Dec 08 2015 - 22:00:12 CST)
  • Francesco Pietra (Tue Dec 08 2015 - 08:50:19 CST)
• Announcement: "Hands-On" Workshop on Computational Biophysics in Urbana, IL (April 6-10,2015)
  • Lela Vukovic (Mon Feb 16 2015 - 14:44:55 CST)
• Announcement: 'Hands On' Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015)
  • Emad Tajkhorshid (Wed May 20 2015 - 00:43:55 CDT)
  • Sourav Ray (Wed May 20 2015 - 00:33:00 CDT)
• Announcement: Hands-On Workshop On Computational Biophysics
  • Danielle Chandler (Wed Jan 07 2015 - 12:30:35 CST)
• Announcement: Workshop on Simulation Based Drug Discovery (San Diego, CA, Sept 21-25, 2015)
  • Lela Vukovic (Fri Jun 12 2015 - 21:06:22 CDT)
• Announcement: ‘Hands On’ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015)
  • Lela Vukovic (Wed May 20 2015 - 00:06:46 CDT)
• Announcement: ‘Hands On’ Workshop on Computational Biophysics (Lake Tahoe, CA, Aug 3-7, 2015)
  • Lela Vukovic (Tue Mar 24 2015 - 15:50:58 CDT)
• Announcement: ‘Hands On’ Workshop on Computational Biophysics (Odense, Denmark, Oct 12-16, 2015)
  • Lela Vukovic (Wed May 06 2015 - 01:39:55 CDT)
• Announcement: ‘Hands On’ Workshop on Computational Biophysics (Pittsburgh, PA, June 1-5, 2015)
  • Lela Vukovic (Wed Mar 04 2015 - 13:07:25 CST)
• Aoid protein to reach periodic boundary
  • Jeff Comer (Tue Jan 12 2016 - 09:30:36 CST)
  • Felipe Merino (Tue Jan 12 2016 - 06:13:43 CST)
  • Branko (Tue Jan 12 2016 - 05:41:21 CST)
  • Jérôme Hénin (Tue Jan 12 2016 - 05:34:22 CST)
  • Dharmeshkumar Patel (Mon Jan 11 2016 - 18:15:16 CST)
• ApoA1 simulation
  • Kostas Malavazos (Wed Oct 21 2015 - 05:21:28 CDT)
• Applying "selectionRule" in Multiple Walker ABF
  • Souvik Sinha (Thu Jun 23 2016 - 03:07:13 CDT)
  • Marlon Sidore (Wed Jun 22 2016 - 11:00:32 CDT)
  • Jeff Comer (Wed Jun 22 2016 - 09:49:31 CDT)
  • Souvik Sinha (Tue May 31 2016 - 01:27:08 CDT)
  • Souvik Sinha (Fri May 27 2016 - 09:43:28 CDT)
• applying a force to some atoms
  • Jérôme Hénin (Sun Jun 28 2015 - 15:54:42 CDT)
  • jing liang (Sat Jun 27 2015 - 06:22:02 CDT)
• applying constant force only within certain part of simulation cell?
  • Ajasja LjubetiÄ� (Thu Mar 03 2016 - 15:27:35 CST)
  • Olya Kravchenko (Thu Mar 03 2016 - 14:00:33 CST)
• Appropriate FF for a specific solvent
  • faride badalkhani (Thu Mar 17 2016 - 10:48:57 CDT)
• Are there features NOT or POORLY supported on GPU ?
  • sonia ziada (Tue Nov 15 2016 - 01:34:34 CST)
  • Brian Radak (Mon Nov 14 2016 - 14:46:40 CST)
  • Chris Goedde (Mon Nov 14 2016 - 14:30:16 CST)
  • Brian Radak (Mon Nov 14 2016 - 14:24:13 CST)
  • sonia ziada (Mon Nov 14 2016 - 04:11:43 CST)
• Asking help on results of our GPU benchmark
  • Axel Kohlmeyer (Mon Jan 05 2015 - 10:36:24 CST)
• atom ID in VMD and NAMD
  • Axel Kohlmeyer (Mon May 04 2015 - 07:25:49 CDT)
  • Maxim Igaev (Mon May 04 2015 - 07:18:38 CDT)
  • Axel Kohlmeyer (Mon May 04 2015 - 07:04:22 CDT)
  • Maxim Igaev (Mon May 04 2015 - 06:47:09 CDT)
  • Jérôme Hénin (Mon May 04 2015 - 04:52:06 CDT)
  • Maxim Igaev (Mon May 04 2015 - 03:16:09 CDT)
• atom types in PSF/PRM/RTF
  • hannes.loeffler_at_stfc.ac.uk (Sun May 31 2015 - 07:43:34 CDT)
  • Jason Swails (Thu May 28 2015 - 13:55:44 CDT)
  • Hannes Loeffler (Thu May 28 2015 - 13:19:14 CDT)
  • Josh Vermaas (Fri May 22 2015 - 09:55:44 CDT)
  • Aaron Larsen (Fri May 22 2015 - 07:34:37 CDT)
  • Hannes Loeffler (Fri May 22 2015 - 04:42:45 CDT)
• Atoms moving too fast; simulation has become unstable
  • Peter Freddolino (Mon Sep 21 2015 - 07:53:14 CDT)
  • Monika Madhavi (Mon Sep 21 2015 - 00:58:32 CDT)
  • Peter Freddolino (Thu Sep 17 2015 - 23:01:32 CDT)
  • Monika Madhavi (Thu Sep 17 2015 - 22:58:12 CDT)
  • Peter Freddolino (Thu Sep 17 2015 - 21:44:09 CDT)
  • Monika Madhavi (Thu Sep 17 2015 - 04:42:40 CDT)
  • Peter Freddolino (Mon Aug 31 2015 - 08:30:48 CDT)
  • Sourav Ray (Mon Aug 31 2015 - 06:29:30 CDT)
  • farzad kiani (Mon Aug 31 2015 - 06:17:38 CDT)
  • Monika Madhavi (Mon Aug 31 2015 - 05:42:48 CDT)
• atoms sequence in improper, OPLS, TOPOTOOLS, CHARMM
  • AnkiReddy katha (Thu May 07 2015 - 06:17:27 CDT)
• Atomselect within radial pair distribution function g(r)
  • Chitrak Gupta (Wed Sep 30 2015 - 08:09:16 CDT)
  • Aditya Ranganathan (Wed Sep 30 2015 - 03:55:37 CDT)
• ATP - CGENFF
  • JC Gumbart (Thu Jun 09 2016 - 09:36:37 CDT)
  • Benjamin Hill (Tue Jun 07 2016 - 19:34:15 CDT)
• Attempting modification to accumulate "Langevin heat"
  • Brian Radak (Tue Jun 30 2015 - 10:43:40 CDT)
• autocorrelation function
  • faride badalkhani (Thu Jun 02 2016 - 09:06:04 CDT)
• Autocorrelation function of Rg goes down without fluctuation around zero
  • Brian Radak (Wed Sep 07 2016 - 09:17:03 CDT)
  • faride badalkhani (Wed Sep 07 2016 - 01:14:08 CDT)
  • Brian Radak (Tue Sep 06 2016 - 16:43:30 CDT)
  • faride badalkhani (Mon Sep 05 2016 - 06:03:13 CDT)
  • Brian Radak (Tue Aug 23 2016 - 14:28:36 CDT)
  • faride badalkhani (Tue Aug 23 2016 - 14:16:28 CDT)
  • Brian Radak (Tue Aug 23 2016 - 13:59:31 CDT)
  • faride badalkhani (Mon Aug 22 2016 - 07:34:17 CDT)
  • faride badalkhani (Fri Aug 19 2016 - 04:00:59 CDT)
  • Lennart Nilsson (Fri Aug 19 2016 - 01:42:03 CDT)
  • faride badalkhani (Thu Aug 18 2016 - 13:50:23 CDT)
  • Lennart Nilsson (Thu Aug 18 2016 - 13:29:40 CDT)
  • Brian Radak (Thu Aug 18 2016 - 11:37:31 CDT)
  • faride badalkhani (Thu Aug 18 2016 - 11:31:05 CDT)
  • faride badalkhani (Thu Aug 18 2016 - 11:27:39 CDT)
  • Brian Radak (Thu Aug 18 2016 - 11:20:22 CDT)
  • faride badalkhani (Thu Aug 18 2016 - 11:16:57 CDT)
  • Brian Radak (Thu Aug 18 2016 - 11:00:16 CDT)
  • faride badalkhani (Thu Aug 18 2016 - 10:31:53 CDT)
  • Brian Radak (Thu Aug 18 2016 - 10:21:30 CDT)
  • faride badalkhani (Thu Aug 18 2016 - 10:16:34 CDT)
  • Brian Radak (Thu Aug 18 2016 - 09:47:02 CDT)
  • faride badalkhani (Thu Aug 18 2016 - 04:21:07 CDT)
• Autoionize and topology
  • Josh Vermaas (Wed Apr 27 2016 - 08:11:15 CDT)
  • Dhiraj Srivastava (Tue Apr 26 2016 - 22:07:04 CDT)
• Automate QwikMD set up for a large number of NAMD jobs?
  • Danny Xu (Tue Dec 20 2016 - 15:24:36 CST)
• Automatic PSF builder for cyclic peptide
  • Aditya Ranganathan (Sun Sep 20 2015 - 08:20:24 CDT)
  • Nikhil Maroli (Sun Sep 20 2015 - 07:04:36 CDT)
• AW: "Jump" in Energy and Volume graphs of my MD
  • Jeff Comer (Thu Mar 31 2016 - 08:44:50 CDT)
  • Brian Radak (Thu Mar 31 2016 - 07:56:32 CDT)
  • Norman Geist (Thu Mar 31 2016 - 01:00:46 CDT)
• AW: 16 total processes killed (some possibly by mpirun during cleanup)
  • Norman Geist (Tue Nov 03 2015 - 00:25:15 CST)
• AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED)
  • Norman Geist (Wed Jan 13 2016 - 02:17:01 CST)
  • Norman Geist (Tue Jan 12 2016 - 13:23:21 CST)
  • Norman Geist (Tue Jan 12 2016 - 08:31:52 CST)
• AW: about angles in coordination complexes
  • Norman Geist (Tue Jan 27 2015 - 02:23:29 CST)
  • Norman Geist (Mon Jan 26 2015 - 09:24:39 CST)
• AW: about command replicaRecv and replicaSend
  • Norman Geist (Mon Oct 19 2015 - 02:43:43 CDT)
• AW: about compiling NAMD using intel icc and impi
  • Norman Geist (Fri Jan 23 2015 - 04:59:43 CST)
• AW: Amber forcefield in namd simulation in parallel version
  • Norman Geist (Fri Dec 02 2016 - 01:59:20 CST)
  • Norman Geist (Thu Dec 01 2016 - 07:58:00 CST)
• AW: applying constant force only within certain part of simulation cell?
  • Norman Geist (Fri Mar 04 2016 - 02:27:49 CST)
• AW: Asking help on results of our GPU benchmark
  • Norman Geist (Mon Jan 05 2015 - 00:37:40 CST)
• AW: AW: AW: AW: warnings while using amber files
  • Norman Geist (Mon Jan 05 2015 - 08:56:36 CST)
• AW: AW: AW: warnings while using amber files
  • amin_at_imtech.res.in (Mon Jan 05 2015 - 07:34:30 CST)
  • Norman Geist (Mon Jan 05 2015 - 06:35:46 CST)
• AW: AW: AW: why does the transition seem to be irreversible in aMD
  • sunyeping (Wed May 25 2016 - 00:48:18 CDT)
  • Norman Geist (Tue May 24 2016 - 00:57:09 CDT)
  • Norman Geist (Mon May 23 2016 - 08:42:04 CDT)
  • sunyeping (Mon May 23 2016 - 03:53:37 CDT)
  • Brian Radak (Tue Apr 05 2016 - 09:42:27 CDT)
  • Norman Geist (Tue Apr 05 2016 - 04:31:27 CDT)
• AW: AW: Periodic Box Dimension (WrapAll is on)
  • Norman Geist (Tue Jan 20 2015 - 02:07:47 CST)
• AW: AW: problem with +devices using
  • Norman Geist (Tue Apr 05 2016 - 08:21:37 CDT)
• AW: AW: Regarding NAMD installation
  • Norman Geist (Mon Aug 17 2015 - 05:22:11 CDT)
• AW: AW: Replica Exchange: Equilibrating at each temperature
  • Norman Geist (Fri Jun 03 2016 - 01:39:54 CDT)
• AW: AW: Tcl script for simulated tempering?
  • Norman Geist (Wed Mar 16 2016 - 05:10:14 CDT)
  • Norman Geist (Tue Mar 15 2016 - 10:21:11 CDT)
• AW: AW: Testing NAMD scalability
  • Éric Germaneau (Mon Mar 21 2016 - 22:20:54 CDT)
  • Norman Geist (Mon Mar 21 2016 - 03:31:30 CDT)
• AW: AW: Trigger DCD frame from TCL?
  • Norman Geist (Thu Nov 10 2016 - 02:09:22 CST)
• AW: AW: warnings while using amber files
  • amin_at_imtech.res.in (Mon Jan 05 2015 - 04:39:58 CST)
  • Norman Geist (Mon Jan 05 2015 - 03:19:13 CST)
• AW: AW: why does the transition seem to be irreversible in aMD
  • sunyeping (Tue Apr 05 2016 - 04:10:59 CDT)
  • Norman Geist (Tue Apr 05 2016 - 03:06:43 CDT)
• AW: calculating replica exchange acceptance ratio
  • Norman Geist (Tue Jan 26 2016 - 08:03:40 CST)
  • Norman Geist (Mon Jan 25 2016 - 05:51:31 CST)
  • Norman Geist (Mon Jan 25 2016 - 04:37:56 CST)
  • Norman Geist (Mon Jan 25 2016 - 01:13:51 CST)
• AW: Changing Boundary conditions from PBC to non-periodic
  • Norman Geist (Fri Nov 20 2015 - 01:52:26 CST)
• AW: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED)
  • Norman Geist (Tue Jan 12 2016 - 02:16:38 CST)
• AW: Compilation of NAMD from Source (Cray XC40)
  • Jim Phillips (Tue Oct 13 2015 - 17:00:08 CDT)
  • Richter, Stefan (Tue Oct 13 2015 - 13:10:44 CDT)
• AW: Enabling GPU for Replica exchange umbrella sampling
  • Norman Geist (Mon Jan 25 2016 - 01:06:05 CST)
  • Norman Geist (Fri Jan 22 2016 - 03:09:24 CST)
• AW: Energy increase with fixed atoms in POPC membrane
  • Norman Geist (Mon Feb 22 2016 - 02:04:39 CST)
  • Norman Geist (Fri Feb 19 2016 - 01:47:51 CST)
  • Norman Geist (Thu Feb 18 2016 - 02:03:09 CST)
• AW: Energy minimization
  • Vermaas, Joshua (Wed Aug 17 2016 - 10:55:14 CDT)
  • d.ronika_at_iitg.ernet.in (Wed Aug 17 2016 - 05:09:01 CDT)
  • Norman Geist (Tue Aug 16 2016 - 23:53:20 CDT)
• AW: ERROR in CUDA run
  • Norman Geist (Thu Dec 17 2015 - 09:24:20 CST)
• AW: error parsing config file while executing
  • Norman Geist (Mon Jan 05 2015 - 00:26:37 CST)
• AW: Failure MD with par7/rst7 amber input
  • Norman Geist (Wed Jan 07 2015 - 03:28:15 CST)
• AW: FATAL ERROR CUDA error during equilibration using NAMD
  • Norman Geist (Thu Sep 01 2016 - 01:15:55 CDT)
• AW: feature request: external initiated clean exit
  • Daniel Möller (Fri Aug 21 2015 - 19:21:54 CDT)
• AW: global does not work in configuration and callback function
  • Norman Geist (Sat Oct 24 2015 - 08:30:48 CDT)
• AW: GPU accelerated MD
  • Norman Geist (Fri Oct 23 2015 - 05:00:05 CDT)
• AW: GPU configuration suggestions
  • Norman Geist (Tue Mar 22 2016 - 05:20:52 CDT)
  • Norman Geist (Tue Mar 22 2016 - 04:26:39 CDT)
  • Norman Geist (Tue Mar 22 2016 - 03:44:44 CDT)
  • Norman Geist (Tue Mar 22 2016 - 02:28:40 CDT)
• AW: How to calculate the temperature for a subset of my simulation
  • Norman Geist (Wed Oct 21 2015 - 02:24:09 CDT)
  • Norman Geist (Tue Oct 20 2015 - 01:23:57 CDT)
• AW: How to continue RMSD of previous production simulation
  • Norman Geist (Sat Dec 03 2016 - 05:45:35 CST)
  • Norman Geist (Sat Dec 03 2016 - 05:51:18 CST)
• AW: How to replace NAMD Eletrostatic Forces
  • Norman Geist (Fri Aug 05 2016 - 02:33:51 CDT)
• AW: Is GPU double-precision floating point performance important for NAMD?
  • Norman Geist (Fri Jun 03 2016 - 01:49:06 CDT)
• AW: is there a method equivalent to conformational flooding in NAMD 2.10
  • Norman Geist (Mon Jan 12 2015 - 00:53:25 CST)
• AW: NAMD 2.11 on CRAY XK with CPU+GPU
  • Jim Phillips (Tue Dec 06 2016 - 15:54:31 CST)
  • Norman Geist (Thu Dec 01 2016 - 01:04:38 CST)
• AW: NAMD Question: Generating ensemble of structures
  • Norman Geist (Wed Aug 31 2016 - 01:29:49 CDT)
• AW: NAMD running on a Cluster of Ubuntu Linux
  • Norman Geist (Mon Oct 10 2016 - 01:27:59 CDT)
• AW: NAMD slows at startup phase 1 smp problem
  • Norman Geist (Tue Jan 13 2015 - 05:52:43 CST)
  • Norman Geist (Tue Jan 13 2015 - 05:50:39 CST)
  • Norman Geist (Tue Jan 13 2015 - 01:22:03 CST)
• AW: NAMD2.11 DCD HEADER PROBLEM
  • Norman Geist (Thu Sep 15 2016 - 01:09:39 CDT)
• AW: NPT with graphene
  • Norman Geist (Tue Nov 15 2016 - 03:04:09 CST)
• AW: NVT and NPT simulationd
  • Norman Geist (Thu Dec 15 2016 - 02:20:28 CST)
  • Norman Geist (Wed Dec 14 2016 - 01:33:16 CST)
• AW: Occasional performance slow down using NAMD with Xeon Phi
  • Norman Geist (Mon Apr 04 2016 - 01:47:27 CDT)
• AW: On-the-fly modification of tclforces script?
  • Norman Geist (Tue Nov 10 2015 - 04:18:02 CST)
• AW: PBC BUG in coorfile + pair interaction
  • Norman Geist (Mon Jan 25 2016 - 02:33:18 CST)
  • Norman Geist (Thu Jan 21 2016 - 04:32:33 CST)
• AW: PBC in lipid bilayer: receptor vs. ligand
  • Norman Geist (Wed Jan 27 2016 - 09:35:05 CST)
• AW: periodic boundary condition in XY, hard wall in Z - errors
  • Norman Geist (Thu Mar 10 2016 - 01:05:33 CST)
• AW: Periodic Box Dimension (WrapAll is on)
  • JAVAD NOROOZI (Tue Jan 20 2015 - 01:37:18 CST)
  • Norman Geist (Tue Jan 20 2015 - 00:39:59 CST)
• AW: Probelm with Lone Pairs on TIP4 model
  • Norman Geist (Tue Jan 06 2015 - 05:34:59 CST)
• AW: problem in running targeted MD
  • Norman Geist (Mon Feb 29 2016 - 01:37:21 CST)
  • Norman Geist (Fri Feb 26 2016 - 01:57:15 CST)
  • Norman Geist (Thu Feb 25 2016 - 01:38:33 CST)
• AW: Problem running REMD simulation
  • Norman Geist (Thu Aug 27 2015 - 03:42:10 CDT)
  • Norman Geist (Tue Aug 25 2015 - 03:50:15 CDT)
• AW: problem with +devices using
  • nikolaev_at_spbau.ru (Tue Apr 05 2016 - 07:41:17 CDT)
  • Norman Geist (Tue Apr 05 2016 - 07:09:22 CDT)
• AW: problem with water molecules angle in MD simulation
  • Norman Geist (Thu Jan 29 2015 - 01:56:18 CST)
  • Norman Geist (Wed Jan 28 2015 - 10:50:47 CST)
  • Norman Geist (Wed Jan 28 2015 - 04:08:53 CST)
  • Norman Geist (Tue Jan 27 2015 - 02:28:18 CST)
  • Norman Geist (Mon Jan 26 2015 - 02:43:41 CST)
• AW: problems compiling NAMD with mpicxx from mvapich2
  • Norman Geist (Mon Jan 26 2015 - 02:36:17 CST)
• AW: problems running amber parm7
  • Norman Geist (Tue Jan 20 2015 - 02:10:44 CST)
  • Norman Geist (Tue Jan 20 2015 - 01:38:30 CST)
  • Norman Geist (Tue Jan 20 2015 - 00:19:40 CST)
• AW: Reason: FATAL ERROR: Unknown command-line option ++local
  • Norman Geist (Tue Oct 11 2016 - 00:33:25 CDT)
  • sunyeping (Mon Oct 10 2016 - 21:55:27 CDT)
  • Norman Geist (Mon Oct 10 2016 - 01:24:44 CDT)
• AW: Reducing the amount of work being done on CPU
  • Norman Geist (Tue Sep 01 2015 - 12:47:56 CDT)
• AW: Regarding NAMD installation
  • Pragya Priyadarshini (Mon Aug 17 2015 - 04:38:29 CDT)
  • Norman Geist (Mon Aug 17 2015 - 04:32:19 CDT)
• AW: regarding PME grid setting problem
  • Norman Geist (Mon Jan 05 2015 - 00:48:11 CST)
• AW: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark
  • Norman Geist (Tue Oct 20 2015 - 03:53:51 CDT)
  • Norman Geist (Tue Oct 20 2015 - 01:29:19 CDT)
• AW: REMD and sortreplicas program
  • Norman Geist (Tue Sep 13 2016 - 01:19:34 CDT)
  • Norman Geist (Mon Sep 12 2016 - 01:38:01 CDT)
  • Norman Geist (Mon Sep 12 2016 - 01:05:39 CDT)
  • Norman Geist (Thu Sep 08 2016 - 01:41:21 CDT)
• AW: replica exchange module
  • Norman Geist (Tue Oct 27 2015 - 03:08:42 CDT)
  • Norman Geist (Mon Oct 26 2015 - 03:21:01 CDT)
  • Norman Geist (Mon Oct 26 2015 - 02:11:47 CDT)
• AW: Replica Exchange: Equilibrating at each temperature
  • Horia Jalily Hasani (Tue Jun 07 2016 - 11:21:09 CDT)
  • Horia Jalily Hasani (Thu Jun 02 2016 - 10:59:56 CDT)
  • Norman Geist (Thu Jun 02 2016 - 01:33:55 CDT)
  • Norman Geist (Tue May 31 2016 - 08:41:23 CDT)
  • Norman Geist (Tue May 31 2016 - 04:24:52 CDT)
• AW: Running gromacs in namd
  • Norman Geist (Thu Dec 01 2016 - 01:06:23 CST)
  • Norman Geist (Wed Nov 30 2016 - 02:45:09 CST)
  • Norman Geist (Tue Nov 29 2016 - 01:36:48 CST)
• AW: Running multi-node jobs on Sun Grid Engine
  • Norman Geist (Mon Apr 04 2016 - 05:32:12 CDT)
  • Norman Geist (Mon Apr 04 2016 - 01:50:27 CDT)
• AW: selection error in forces script
  • Norman Geist (Tue Mar 08 2016 - 01:35:26 CST)
• AW: Simulation of metalo-binding proteins
  • Daniel Möller (Wed Nov 23 2016 - 15:52:53 CST)
• AW: Simulation runs only in background
  • Daniel Möller (Wed Jun 01 2016 - 04:44:55 CDT)
• AW: stepspercycle
  • Gianluca Interlandi (Mon Oct 19 2015 - 12:31:23 CDT)
  • Norman Geist (Mon Oct 19 2015 - 01:25:18 CDT)
• AW: Tcl script for simulated tempering?
  • Radak, Brian K (Wed Mar 16 2016 - 10:17:07 CDT)
  • Radak, Brian K (Tue Mar 15 2016 - 13:01:56 CDT)
  • Brian Radak (Tue Mar 15 2016 - 08:14:11 CDT)
  • Norman Geist (Tue Mar 15 2016 - 02:53:21 CDT)
• AW: Temperature assignment REMD
  • Norman Geist (Mon Jan 05 2015 - 01:29:55 CST)
• AW: Tempreture Profile along z axis
  • Norman Geist (Fri Jan 09 2015 - 02:23:04 CST)
• AW: Testing NAMD scalability
  • Eric Germaneau (Mon Mar 21 2016 - 03:15:06 CDT)
  • Norman Geist (Mon Mar 21 2016 - 02:45:31 CDT)
• AW: time per step during GPU-accelerated Implicit Solvent calculations
  • Thomas Albers (Wed Nov 18 2015 - 08:38:07 CST)
  • Jim Phillips (Mon Nov 16 2015 - 08:55:26 CST)
  • Norman Geist (Mon Nov 16 2015 - 01:52:00 CST)
• AW: Trigger DCD frame from TCL?
  • Jim Phillips (Wed Nov 09 2016 - 16:48:00 CST)
  • Brian Radak (Wed Nov 09 2016 - 07:34:48 CST)
  • Norman Geist (Wed Nov 09 2016 - 02:48:33 CST)
  • Norman Geist (Wed Nov 09 2016 - 02:05:50 CST)
• AW: Turning off and back on fixed atoms
  • Brian Radak (Sat Oct 29 2016 - 12:04:57 CDT)
  • Norman Geist (Fri Oct 28 2016 - 04:40:22 CDT)
• AW: Tutorial example of replica exchange
  • Norman Geist (Thu Mar 10 2016 - 16:53:22 CST)
  • Norman Geist (Thu Mar 10 2016 - 02:03:38 CST)
• AW: velocity computation
  • Norman Geist (Tue Feb 09 2016 - 02:22:54 CST)
  • Norman Geist (Mon Feb 08 2016 - 00:51:46 CST)
• AW: vmd-l: Error connecting to localhost on port 3000 and IMD connection ended unexpectedly; connection terminated.
  • Norman Geist (Thu Oct 27 2016 - 07:50:19 CDT)
• AW: vmd-l: moving atoms and updating distances
  • Norman Geist (Mon Feb 15 2016 - 00:11:47 CST)
• AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800
  • Jim Phillips (Fri Mar 11 2016 - 09:45:19 CST)
  • Josh Vermaas (Fri Mar 11 2016 - 09:29:09 CST)
  • Greipel.Joachim_at_mh-hannover.de (Fri Mar 11 2016 - 01:47:27 CST)
  • Norman Geist (Thu Mar 10 2016 - 16:43:55 CST)
• AW: warnings while using amber files
  • amin_at_imtech.res.in (Mon Jan 05 2015 - 02:50:52 CST)
  • Norman Geist (Mon Jan 05 2015 - 00:42:51 CST)
• AW: why does the transition seem to be irreversible in aMD
  • sunyeping (Tue Apr 05 2016 - 02:47:39 CDT)
  • Norman Geist (Tue Apr 05 2016 - 02:29:42 CDT)
• AW: Why the computational speed does not increase with the increase of GPUs?
  • Norman Geist (Fri Oct 23 2015 - 03:49:49 CDT)
  • sunyeping (Fri Oct 23 2015 - 02:57:48 CDT)
  • Norman Geist (Thu Oct 22 2015 - 02:27:54 CDT)
• AW: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓʼþ
  • ZOU Changling (Sun Feb 28 2016 - 19:36:06 CST)
  • Norman Geist (Fri Feb 26 2016 - 06:10:11 CST)
• backbone constraint
  • Josh Vermaas (Wed Jul 22 2015 - 08:59:48 CDT)
  • Urszula Uciechowska (Wed Jul 22 2015 - 02:59:37 CDT)
• Bad initial structure?
  • faride badalkhani (Thu Apr 14 2016 - 13:50:14 CDT)
• Basic validation of CGenFF
  • Peter Freddolino (Mon Mar 21 2016 - 08:19:53 CDT)
  • faride badalkhani (Mon Mar 21 2016 - 07:31:05 CDT)
• Best Practices for Nucleobase Parameterization
  • Mayne, Christopher G (Wed May 20 2015 - 08:12:55 CDT)
  • Aaron Larsen (Mon May 18 2015 - 11:30:22 CDT)
• Bias-exchange metadynamics
  • Fidan Sumbul (Sun Oct 18 2015 - 18:16:34 CDT)
• Biasing potential of a Metadynamics Simulation
  • Giacomo Fiorin (Tue Oct 27 2015 - 15:55:13 CDT)
  • Fidan Sumbul (Tue Oct 27 2015 - 14:38:16 CDT)
  • Giacomo Fiorin (Tue Oct 27 2015 - 13:14:06 CDT)
  • Fidan Sumbul (Tue Oct 27 2015 - 13:05:02 CDT)
• bilayer simulation keeps crashing
  • Chitrak Gupta (Tue Apr 14 2015 - 10:00:27 CDT)
• Binding energy of organic molecules/small peptides on the surface of Silicon Dioxide
  • Roshan Shrestha (Thu May 26 2016 - 10:29:01 CDT)
• bond angle and dihedral values
  • oguz gurbulak (Thu Mar 26 2015 - 03:55:03 CDT)
• bond energy high
  • Ipsita Basu (Wed Feb 03 2016 - 05:15:35 CST)
• bond lengths and angles constraints
  • oguz gurbulak (Tue Jun 23 2015 - 10:04:53 CDT)
• BONDS vs DOUBLE in topology file
  • Gianluca Interlandi (Fri Oct 09 2015 - 12:42:43 CDT)
  • Josh Vermaas (Fri Oct 09 2015 - 09:46:07 CDT)
  • Gianluca Interlandi (Fri Oct 09 2015 - 00:42:05 CDT)
• Bubble in water during membrane simulations
  • Kevin Chan (Mon Nov 16 2015 - 10:41:21 CST)
  • Giacomo Fiorin (Mon Nov 16 2015 - 09:48:42 CST)
  • Kevin C Chan (Mon Nov 16 2015 - 02:12:29 CST)
• buffer overflow with long file paths in psfgen in NAMD 2.11b2?
  • Jim Phillips (Tue Dec 08 2015 - 16:41:22 CST)
  • Brian Radak (Tue Dec 08 2015 - 15:54:28 CST)
• BUG: NAMD-2.10 CUDA REMD segfault with TCL exec randomly
  • Norman Geist (Wed Mar 04 2015 - 04:40:07 CST)
  • Norman Geist (Wed Mar 04 2015 - 01:47:42 CST)
• Building PSF for the system prepared by Packmol
  • Radak, Brian K (Thu Jun 09 2016 - 14:16:46 CDT)
  • faride badalkhani (Thu Jun 09 2016 - 09:27:31 CDT)
• calculating replica exchange acceptance ratio
  • Chitrak Gupta (Wed Jan 27 2016 - 04:18:38 CST)
  • Chitrak Gupta (Mon Jan 25 2016 - 09:58:31 CST)
  • Chitrak Gupta (Mon Jan 25 2016 - 09:51:48 CST)
  • Chitrak Gupta (Mon Jan 25 2016 - 02:54:15 CST)
  • Chitrak Gupta (Sun Jan 24 2016 - 23:16:09 CST)
• Calculating RMSF per residue
  • Abir Ganguly (Tue Apr 21 2015 - 02:58:40 CDT)
  • Aron Broom (Mon Apr 20 2015 - 15:59:23 CDT)
  • Abir Ganguly (Mon Apr 20 2015 - 12:58:24 CDT)
• Calculating the spin angle collective variable value
  • Marlon SIDORE (Mon May 11 2015 - 09:06:46 CDT)
  • Giacomo Fiorin (Mon May 11 2015 - 08:57:41 CDT)
  • Marlon SIDORE (Mon May 11 2015 - 08:48:51 CDT)
  • Giacomo Fiorin (Mon May 11 2015 - 08:40:34 CDT)
  • Marlon SIDORE (Mon May 11 2015 - 03:51:38 CDT)
• Calculation of PMF between protein domains NAMD
  • Chola Regmi (Wed May 13 2015 - 18:14:49 CDT)
  • Chola Regmi (Fri Apr 17 2015 - 18:50:25 CDT)
  • Jeff Comer (Fri Apr 17 2015 - 18:22:17 CDT)
  • Aron Broom (Fri Apr 17 2015 - 18:00:09 CDT)
  • Aron Broom (Fri Apr 17 2015 - 17:57:48 CDT)
  • Josh Vermaas (Fri Apr 17 2015 - 17:54:37 CDT)
  • Giacomo Fiorin (Fri Apr 17 2015 - 17:48:33 CDT)
  • Josh Vermaas (Fri Apr 17 2015 - 17:43:49 CDT)
  • Chola Regmi (Fri Apr 17 2015 - 17:26:03 CDT)
• Calculation of the water inside of protein during trajectory
  • James Starlight (Tue Feb 03 2015 - 09:51:07 CST)
• call "NAMD" from another program
  • bay__gulf618_at_sina.com (Sat Jul 11 2015 - 22:21:09 CDT)
  • Ajasja LjubetiÄ� (Fri Jul 10 2015 - 02:50:31 CDT)
  • Thomas C Bishop (Fri Jul 10 2015 - 02:38:00 CDT)
  • Aron Broom (Thu Jul 09 2015 - 17:59:08 CDT)
  • Ma'Mon Hatmal (Thu Jul 09 2015 - 17:53:24 CDT)
• Can 'nonbonded interaction parameters' be ignored in the parameter file?
  • ¶¡êÏ (Tue May 26 2015 - 20:43:52 CDT)
• Can NAMD handle two different LJ cutoffs in a single simulation?
  • Lewis Martin (Mon Sep 14 2015 - 23:17:36 CDT)
• Can NAMD simulation solve the problem of coordinate clash in a structural model?
  • Tristan Croll (Fri Apr 17 2015 - 16:50:07 CDT)
  • sunyeping (Sun Apr 12 2015 - 21:19:18 CDT)
  • sunyeping (Sun Apr 12 2015 - 21:18:30 CDT)
• Can't find documentation of known bug in NAMD 2.9
  • Klas Karis (Mon Apr 13 2015 - 12:02:25 CDT)
• Can't start SMP NAMD - Problem clearly is in front of the monitor
  • Jim Phillips (Tue Nov 17 2015 - 12:45:51 CST)
  • Vogel, Alexander (Tue Nov 17 2015 - 03:18:05 CST)
• cell basis vectors
  • faride badalkhani (Wed Apr 20 2016 - 13:59:11 CDT)
• cellBasisVectors
  • faride badalkhani (Wed Mar 09 2016 - 10:27:53 CST)
• cgenff
  • Benjamin Hill (Mon Jun 06 2016 - 14:48:30 CDT)
• CGENFF validation
  • faride badalkhani (Fri Mar 18 2016 - 15:12:56 CDT)
• Changing Boundary conditions from PBC to non-periodic
  • Gianluca Interlandi (Thu Nov 19 2015 - 14:30:16 CST)
  • Mahdi Tavakol (Thu Nov 19 2015 - 12:30:23 CST)
• charge group
  • faride badalkhani (Fri Mar 18 2016 - 13:36:14 CDT)
  • Josh Vermaas (Fri Mar 18 2016 - 11:36:21 CDT)
  • faride badalkhani (Fri Mar 18 2016 - 11:23:39 CDT)
  • Josh Vermaas (Fri Mar 18 2016 - 11:10:51 CDT)
  • faride badalkhani (Fri Mar 18 2016 - 10:56:42 CDT)
• Charm++ warning> fences and atomic operations not available in native assembly
  • Ern Seang Ong (Thu Aug 20 2015 - 02:56:40 CDT)
• charm36 for ATP and MG
  • Radhika Anoop (Wed Sep 09 2015 - 05:09:39 CDT)
  • Julian Gamboa (Tue Sep 08 2015 - 11:19:03 CDT)
  • Josh Vermaas (Tue Sep 08 2015 - 11:13:19 CDT)
  • Radhika Anoop (Tue Sep 08 2015 - 00:55:48 CDT)
• charmc rpath
  • Scott Brozell (Thu Jan 21 2016 - 22:04:41 CST)
• CHARMM parameter file
  • Fransiska Kurniawan (Wed Apr 15 2015 - 04:11:00 CDT)
• Charmm++ error
  • Sourav Ray (Sun Nov 20 2016 - 17:12:02 CST)
  • Sourav Ray (Sun Nov 20 2016 - 17:10:44 CST)
  • matthew reeves (Sun Nov 20 2016 - 11:29:25 CST)
• CHARMM22-STAR force field for NAMD
  • JC Gumbart (Tue Nov 01 2016 - 21:28:04 CDT)
  • Nicholas M. Glykos (Tue Nov 01 2016 - 13:15:48 CDT)
  • Nicholas M. Glykos (Tue Nov 01 2016 - 13:07:39 CDT)
• CHARMM36 alleged missing CC CT1 NH2 angle params
  • Francesco Pietra (Mon May 16 2016 - 02:45:55 CDT)
• CHARMM36 and TIP3
  • Josh Vermaas (Tue Apr 26 2016 - 19:49:04 CDT)
  • Dhiraj Srivastava (Tue Apr 26 2016 - 17:01:10 CDT)
  • Brian Radak (Tue Apr 26 2016 - 13:57:05 CDT)
  • Dhiraj Srivastava (Tue Apr 26 2016 - 13:37:49 CDT)
• clarification
  • sem ciccioni (Mon Apr 18 2016 - 16:21:08 CDT)
• Coarse Grain Angle Parameter Issue
  • Fotis Baltoumas (Sat Jun 18 2016 - 00:23:37 CDT)
  • Nisler, Collin R. (Fri Jun 17 2016 - 22:37:42 CDT)
• Coarse grained instability: atoms moving too fast
  • Marlon Sidore (Mon Oct 05 2015 - 06:47:41 CDT)
• Coarse-grained simulation with Polarizable Water crashing
  • Fotis Baltoumas (Sat May 21 2016 - 17:14:36 CDT)
  • Sourav Ray (Sat May 21 2016 - 11:39:42 CDT)
  • Sourav Ray (Mon May 16 2016 - 15:31:14 CDT)
  • Jeff Comer (Mon May 16 2016 - 12:04:43 CDT)
  • Sourav Ray (Sun May 15 2016 - 17:08:31 CDT)
  • Sourav Ray (Sun May 15 2016 - 16:34:18 CDT)
• Collecting average energies via Tcl callback?
  • Subbarao Kanchi (Thu Oct 13 2016 - 19:20:39 CDT)
  • Brian Radak (Thu Oct 13 2016 - 11:19:40 CDT)
• Colvar orientation and CoG
  • Jérôme Hénin (Fri Jun 17 2016 - 04:43:06 CDT)
  • Nicolas Martin (Thu Jun 16 2016 - 09:02:28 CDT)
• Colvar with variable axis
  • Mitchell Gleed (Thu Mar 12 2015 - 10:49:21 CDT)
  • Jérôme Hénin (Thu Mar 12 2015 - 08:53:45 CDT)
  • Giacomo Fiorin (Thu Mar 12 2015 - 08:25:54 CDT)
  • Mitchell Gleed (Thu Mar 12 2015 - 07:59:56 CDT)
  • Giacomo Fiorin (Thu Mar 12 2015 - 06:23:31 CDT)
  • Mitchell Gleed (Thu Mar 12 2015 - 06:01:56 CDT)
• colvars and drude don't play nice?
  • JC Gumbart (Sat Jan 17 2015 - 15:34:43 CST)
  • Jim Phillips (Fri Jan 16 2015 - 16:57:58 CST)
  • Giacomo Fiorin (Fri Jan 16 2015 - 11:04:44 CST)
  • Giacomo Fiorin (Wed Jan 14 2015 - 10:07:23 CST)
  • JC Gumbart (Wed Jan 14 2015 - 09:58:28 CST)
  • Giacomo Fiorin (Tue Jan 13 2015 - 18:31:38 CST)
  • JC Gumbart (Tue Jan 13 2015 - 18:08:42 CST)
• colvars angle centerReference
  • Giacomo Fiorin (Wed Jan 07 2015 - 14:00:02 CST)
• Colvars Boundary potentials do not look harmonic
  • Panel Nicolas (M.) (Thu Jun 04 2015 - 08:08:49 CDT)
  • Jeff Comer (Wed Jun 03 2015 - 11:54:28 CDT)
  • Jérôme Hénin (Wed Jun 03 2015 - 10:15:04 CDT)
  • Panel Nicolas (M.) (Wed Jun 03 2015 - 10:00:53 CDT)
• Colvars crossing "upperboundary" limit
  • Giacomo Fiorin (Tue May 10 2016 - 15:25:18 CDT)
  • Sourav Ray (Thu May 05 2016 - 05:33:26 CDT)
• Colvars order in the pmf file
  • Jérôme Hénin (Mon Jun 06 2016 - 11:18:51 CDT)
  • Marlon Sidore (Mon Jun 06 2016 - 10:49:01 CDT)
  • Giacomo Fiorin (Mon Jun 06 2016 - 09:57:38 CDT)
  • Marlon Sidore (Mon Jun 06 2016 - 09:14:53 CDT)
• colvars: keyword "name" is not supported, or not recognized in this context.
  • Francesco Pietra (Thu Jan 15 2015 - 09:52:16 CST)
• Colvars: Unable to restrict rotation and translation along y and z axes
  • Giacomo Fiorin (Fri May 20 2016 - 10:33:27 CDT)
  • Sourav Ray (Fri May 20 2016 - 01:31:38 CDT)
  • Giacomo Fiorin (Wed May 18 2016 - 08:23:14 CDT)
  • Sourav Ray (Wed May 18 2016 - 07:22:00 CDT)
• Combination of top_all36_cgenff with top_all36_prot
  • faride badalkhani (Mon Feb 29 2016 - 15:03:31 CST)
• Combining Drude structures
  • Jeff Comer (Mon May 16 2016 - 16:25:32 CDT)
• Combining parameter files from CHARMM
  • Josh Vermaas (Mon Jun 15 2015 - 11:10:43 CDT)
  • Branko (Mon Jun 15 2015 - 07:39:49 CDT)
  • Kevin C Chan (Mon Jun 15 2015 - 07:29:36 CDT)
  • Branko (Mon Jun 15 2015 - 05:12:57 CDT)
  • Kevin C Chan (Mon Jun 15 2015 - 03:08:06 CDT)
  • Branko (Fri Jun 05 2015 - 05:17:56 CDT)
  • Kevin C Chan (Fri Jun 05 2015 - 04:51:13 CDT)
• Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED)
  • Tim.Ho_at_csiro.au (Thu Jan 14 2016 - 22:02:44 CST)
  • Tim.Ho_at_csiro.au (Thu Jan 14 2016 - 16:00:28 CST)
  • Downs, Andrew S CTR USARMY ARL (US) (Thu Jan 14 2016 - 09:24:50 CST)
• Compilation error across Intel 14,15 and 16 (UNCLASSIFIED)
  • Tim.Ho_at_csiro.au (Wed Jan 13 2016 - 22:28:53 CST)
  • Downs, Andrew S CTR USARMY ARL (US) (Mon Jan 11 2016 - 13:10:19 CST)
• Compilation of NAMD for CUDA and replica exchange
  • #YEO JINGJIE# (Fri Apr 29 2016 - 13:53:44 CDT)
• Compilation of NAMD from Source (Cray XC40)
  • Stefan Richter (Wed Oct 14 2015 - 04:38:17 CDT)
  • Vlad Cojocaru (Tue Oct 13 2015 - 15:04:02 CDT)
  • Jim Phillips (Tue Oct 13 2015 - 10:03:39 CDT)
  • Richter, Stefan (Tue Oct 13 2015 - 09:26:06 CDT)
• Compilation with OpenMPI
  • Kevin C Chan (Mon Jul 20 2015 - 05:02:10 CDT)
  • Kevin C Chan (Tue Jul 14 2015 - 00:11:38 CDT)
  • Kevin C Chan (Sun Jul 12 2015 - 01:13:30 CDT)
• Compile NAMD - Projections
  • Stefan Richter (Thu Oct 15 2015 - 04:40:44 CDT)
  • Kostas Malavazos (Wed Oct 14 2015 - 11:45:04 CDT)
• compile psfgen as shared object or Tcl package?
  • Brian Radak (Wed Feb 18 2015 - 15:47:27 CST)
• Compressibility of Berendesen Barostat (Simulations Near Critical Point)
  • JAVAD NOROOZI (Fri Feb 13 2015 - 00:37:42 CST)
• compute capability
  • Josh Vermaas (Mon Jan 25 2016 - 09:52:37 CST)
  • Stefano Guglielmo (Sun Jan 24 2016 - 17:15:43 CST)
• concerning paratools
  • Mayne, Christopher G (Thu Dec 03 2015 - 14:11:52 CST)
  • luca belmonte (Thu Dec 03 2015 - 04:36:04 CST)
• configuration file question
  • Jeff Comer (Thu Feb 26 2015 - 17:34:09 CST)
  • Hasan haska (Thu Feb 26 2015 - 16:49:55 CST)
• constant velocity pulling
  • Jamal Zanjani (Thu Mar 31 2016 - 06:04:18 CDT)
• Constant velocity SMD
  • maral hassani (Tue Jun 09 2015 - 07:14:16 CDT)
• Constraint bonds that does not include hydrogrens
  • Jeff Comer (Thu Dec 22 2016 - 13:24:30 CST)
  • Karteek Bejagam (Thu Dec 22 2016 - 10:00:08 CST)
  • Jeff Comer (Thu Dec 22 2016 - 09:38:50 CST)
  • Karteek Bejagam (Wed Dec 21 2016 - 23:00:55 CST)
• Constraint failure in RATTLE algorithm
  • Stefano Guglielmo (Tue Mar 01 2016 - 19:18:05 CST)
• Constraint failure in RATTLE algorithm for atom 538
  • Chitrak Gupta (Tue Apr 05 2016 - 11:04:08 CDT)
  • Olya Kravchenko (Tue Apr 05 2016 - 10:29:38 CDT)
  • faride badalkhani (Tue Apr 05 2016 - 10:18:25 CDT)
  • Chitrak Gupta (Tue Apr 05 2016 - 10:10:44 CDT)
  • Brian Radak (Tue Apr 05 2016 - 10:04:40 CDT)
  • faride badalkhani (Tue Apr 05 2016 - 09:57:30 CDT)
• constraint failure in Rattle algorithm for atom 54134
  • Life Sciences Inc (Mon Oct 26 2015 - 13:37:42 CDT)
  • Chitrak Gupta (Mon Oct 26 2015 - 13:01:16 CDT)
  • Chitrak Gupta (Mon Oct 26 2015 - 09:10:59 CDT)
  • Tristan Croll (Mon Oct 26 2015 - 01:59:47 CDT)
  • Chitrak Gupta (Mon Oct 26 2015 - 08:31:44 CDT)
  • Life Sciences Inc (Sun Oct 25 2015 - 19:42:57 CDT)
• Constraint failure in RATTLE algorithm for atom 6!
  • faride badalkhani (Tue Apr 26 2016 - 16:47:59 CDT)
  • faride badalkhani (Tue Apr 26 2016 - 16:46:40 CDT)
  • Radak, Brian K (Tue Apr 26 2016 - 16:40:45 CDT)
  • Bennion, Brian (Tue Apr 26 2016 - 16:29:09 CDT)
  • Radak, Brian K (Tue Apr 26 2016 - 16:26:30 CDT)
  • faride badalkhani (Tue Apr 26 2016 - 16:22:02 CDT)
  • Jeff Comer (Tue Apr 26 2016 - 16:14:50 CDT)
  • faride badalkhani (Mon Apr 25 2016 - 10:42:52 CDT)
• Controlling water diffusion
  • Evandro Semighini (Sun Jul 19 2015 - 21:42:17 CDT)
  • Peter Freddolino (Sun Jul 19 2015 - 21:13:15 CDT)
  • Evandro Semighini (Fri Jul 17 2015 - 07:44:36 CDT)
  • Peter Freddolino (Thu Jul 16 2015 - 21:54:49 CDT)
  • Evandro Semighini (Thu Jul 16 2015 - 14:21:50 CDT)
• Conversion from c6 and c12 = 0 to sigma epsilon
  • Brian Radak (Sat May 14 2016 - 15:39:48 CDT)
  • Sourav Ray (Sat May 14 2016 - 06:29:49 CDT)
• Conversion from GROMACS .top .itp to CHARMM .psf .par combo
  • Roshan Shrestha (Sat May 28 2016 - 10:04:08 CDT)
  • Sourav Ray (Sat May 28 2016 - 10:00:54 CDT)
• convert .xyz file in .psf file for non-protein molecule
  • grenier_at_cinam.univ-mrs.fr (Fri Sep 09 2016 - 02:51:25 CDT)
  • Radak, Brian K (Thu Sep 08 2016 - 12:39:04 CDT)
  • Axel Kohlmeyer (Thu Sep 08 2016 - 10:41:07 CDT)
  • grenier_at_cinam.univ-mrs.fr (Thu Sep 08 2016 - 10:20:03 CDT)
• COORDINATE DCD FILE WAS NOT CREATED
  • Mihaela Drenscko (Thu Sep 15 2016 - 15:42:20 CDT)
• Coordinate DCD file was not created during restart of adaptive biasing force simulation using colvars.
  • Jérôme Hénin (Thu Sep 22 2016 - 14:34:27 CDT)
  • Jérôme Hénin (Thu Sep 22 2016 - 05:04:25 CDT)
  • Zach Bonham (Wed Sep 21 2016 - 15:15:45 CDT)
• Corrfunc output not generated
  • Giacomo Fiorin (Thu Apr 14 2016 - 17:41:44 CDT)
  • Giacomo Fiorin (Tue Apr 12 2016 - 22:00:04 CDT)
  • Giacomo Fiorin (Tue Apr 12 2016 - 16:16:00 CDT)
  • Sourav Ray (Mon Apr 11 2016 - 12:38:39 CDT)
• Could I run aMD in Drude force field?
  • Brian Radak (Thu Feb 05 2015 - 13:50:15 CST)
  • dream (Thu Feb 05 2015 - 02:14:04 CST)
• Crashes with dihedral PC
  • Giacomo Fiorin (Tue Nov 15 2016 - 22:40:17 CST)
  • Jiyong Park (Tue Nov 15 2016 - 20:28:32 CST)
• Crazy rigid water molecules
  • Brian Radak (Thu Nov 19 2015 - 15:40:55 CST)
• Create psf file
  • Asma el-magboub (Mon Jun 22 2015 - 18:43:13 CDT)
  • Mayne, Christopher G (Mon Jun 22 2015 - 10:01:23 CDT)
  • Raed Ahmed Abdelsalam Shalaby (Mon Jun 22 2015 - 05:54:32 CDT)
  • Fransiska Kurniawan (Sat Jun 20 2015 - 17:56:52 CDT)
• Cyclic peptide Nanotube
  • Nikhil Maroli (Fri Oct 02 2015 - 08:52:59 CDT)
• Daily cron stalls running NAMD outputs
  • Jérôme Hénin (Wed Apr 08 2015 - 03:16:22 CDT)
  • Vlastimil Zíma (Wed Apr 08 2015 - 02:41:23 CDT)
  • Vlastimil Zíma (Wed Apr 01 2015 - 07:08:28 CDT)
  • Vlastimil Zíma (Wed Apr 01 2015 - 03:04:26 CDT)
• DCD Error
  • Abhishek TYAGI (Thu Mar 19 2015 - 03:59:56 CDT)
  • Atanu Maity (Wed Mar 18 2015 - 23:32:32 CDT)
  • Abhishek Tyagi (Wed Mar 18 2015 - 10:13:07 CDT)
  • Josh Vermaas (Wed Mar 18 2015 - 10:06:43 CDT)
  • Maxim Belkin (Wed Mar 18 2015 - 10:06:34 CDT)
  • btreece_at_andrew.cmu.edu (Wed Mar 18 2015 - 10:05:58 CDT)
  • Abhishek Tyagi (Wed Mar 18 2015 - 09:51:17 CDT)
  • Josh Vermaas (Wed Mar 18 2015 - 09:36:52 CDT)
  • Abhishek Tyagi (Wed Mar 18 2015 - 09:29:42 CDT)
  • btreece_at_andrew.cmu.edu (Wed Mar 18 2015 - 09:27:28 CDT)
  • manish kesherwani (Wed Mar 18 2015 - 08:10:18 CDT)
  • Abhishek TYAGI (Wed Mar 18 2015 - 06:23:58 CDT)
• dcd file frame number
  • Dhiraj Srivastava (Thu Sep 29 2016 - 22:22:54 CDT)
• Dear NAMD users
  • msa5 (Thu Nov 03 2016 - 17:18:00 CDT)
• Debugging and Force Checking?
  • Jérôme Hénin (Mon Jul 20 2015 - 12:42:20 CDT)
  • Brian Radak (Mon Jul 20 2015 - 09:32:44 CDT)
• Determining the PMF with Adaptive Biasing Forces
  • sunyzero (Tue Dec 08 2015 - 22:00:19 CST)
  • Jérôme Hénin (Tue Dec 08 2015 - 09:09:58 CST)
  • Souvik Sinha (Tue Dec 08 2015 - 01:42:34 CST)
  • sunyzero (Mon Dec 07 2015 - 23:48:55 CST)
  • sunyzero (Mon Dec 07 2015 - 20:02:35 CST)
• Diagnosing CUDA (non)performance
  • Brian Radak (Mon Oct 31 2016 - 13:37:13 CDT)
  • Chris Goedde (Mon Oct 31 2016 - 07:48:31 CDT)
• did anyone built NAMD with PLUMED on XSEDE
  • Maksym Korablyov (Thu Sep 01 2016 - 09:36:07 CDT)
• DIDN'T FIND vdW PARAMETER FOR ATOM TYPE SG3O1
  • Srijita Paul (Fri Dec 25 2015 - 00:41:47 CST)
• Dielectric constant of water from MSM and PME simulations
  • Otello Maria Roscioni (Mon Oct 26 2015 - 12:29:02 CDT)
  • Zhe Wu (Fri Oct 23 2015 - 10:46:41 CDT)
  • Zhe Wu (Fri Oct 23 2015 - 10:31:04 CDT)
  • Axel Kohlmeyer (Fri Oct 23 2015 - 09:47:38 CDT)
  • Mattia Felice Palermo (Fri Oct 23 2015 - 08:57:37 CDT)
• Different trajectories with and without restarting
  • Grzegorz Nawrocki (Mon May 18 2015 - 15:04:17 CDT)
  • Axel Kohlmeyer (Sat May 16 2015 - 00:06:27 CDT)
  • Grzegorz Nawrocki (Fri May 15 2015 - 21:08:40 CDT)
  • Axel Kohlmeyer (Fri May 15 2015 - 18:26:53 CDT)
  • btreece_at_andrew.cmu.edu (Fri May 15 2015 - 18:26:09 CDT)
  • Grzegorz Nawrocki (Fri May 15 2015 - 18:09:57 CDT)
• Dihedral calculation with colvars
  • Giacomo Fiorin (Fri Mar 13 2015 - 10:05:20 CDT)
  • Jérôme Hénin (Fri Mar 13 2015 - 09:42:21 CDT)
  • Jérôme Hénin (Thu Mar 12 2015 - 06:29:22 CDT)
  • Kevin C Chan (Thu Mar 12 2015 - 06:13:00 CDT)
  • Jérôme Hénin (Thu Mar 12 2015 - 05:27:07 CDT)
  • Kevin C Chan (Thu Mar 12 2015 - 01:20:46 CDT)
  • Aron Broom (Wed Mar 11 2015 - 23:17:09 CDT)
  • Kevin C Chan (Wed Mar 11 2015 - 23:05:45 CDT)
• Dihedral definition in NAMD
  • Kevin C Chan (Wed Mar 11 2015 - 05:03:54 CDT)
  • Giacomo Fiorin (Wed Mar 11 2015 - 03:13:27 CDT)
  • Josh Vermaas (Tue Mar 10 2015 - 13:32:12 CDT)
  • Kevin C Chan (Tue Mar 10 2015 - 22:22:34 CDT)
  • Giacomo Fiorin (Tue Mar 10 2015 - 18:46:42 CDT)
  • Kevin C Chan (Tue Mar 10 2015 - 13:13:00 CDT)
  • Giacomo Fiorin (Tue Mar 10 2015 - 09:49:00 CDT)
  • Giacomo Fiorin (Tue Mar 10 2015 - 09:33:15 CDT)
  • Josh Vermaas (Tue Mar 10 2015 - 09:30:21 CDT)
  • Kevin C Chan (Tue Mar 10 2015 - 09:24:23 CDT)
  • Josh Vermaas (Tue Mar 10 2015 - 09:14:27 CDT)
  • Kevin C Chan (Tue Mar 10 2015 - 06:52:53 CDT)
  • Giacomo Fiorin (Tue Mar 10 2015 - 06:28:26 CDT)
  • Kevin C Chan (Tue Mar 10 2015 - 06:19:16 CDT)
• Dihedral missing
  • faride badalkhani (Thu Apr 28 2016 - 17:54:15 CDT)
• Dihedral parameter missing
  • Josh Vermaas (Mon Apr 04 2016 - 16:30:27 CDT)
  • faride badalkhani (Mon Apr 04 2016 - 16:26:03 CDT)
• Dipole Moment Watcher, Ibuprofen
  • Branko (Tue Mar 31 2015 - 04:12:14 CDT)
  • JAVAD NOROOZI (Tue Mar 31 2015 - 01:01:46 CDT)
• DNA not translocating under electric field
  • Athreya, Nagendra Bala Murali (Wed Nov 30 2016 - 21:20:55 CST)
• does fixedAtoms modify velocities?
  • Brian Radak (Tue Jul 07 2015 - 12:48:23 CDT)
  • Brian Radak (Tue Jul 07 2015 - 12:25:32 CDT)
• DOF during alchemical simulations
  • Brian Radak (Tue Dec 01 2015 - 10:08:08 CST)
  • Hannes Loeffler (Tue Dec 01 2015 - 08:19:00 CST)
  • Grace Brannigan (Mon Nov 30 2015 - 14:45:55 CST)
  • Brian Radak (Mon Nov 30 2015 - 12:30:33 CST)
  • Grace Brannigan (Mon Nov 30 2015 - 12:05:36 CST)
  • Brian Radak (Mon Nov 30 2015 - 09:36:55 CST)
  • Jérôme Hénin (Fri Nov 27 2015 - 03:31:25 CST)
  • Aron Broom (Thu Nov 26 2015 - 12:28:27 CST)
  • Jérôme Hénin (Thu Nov 26 2015 - 12:00:01 CST)
  • Brian Radak (Wed Nov 25 2015 - 10:31:11 CST)
• download stmv files for benchmarking
  • Bennion, Brian (Wed Jun 01 2016 - 14:29:22 CDT)
• Drude Prepper error in genic
  • Francesco Pietra (Mon Jun 13 2016 - 01:33:15 CDT)
• dual-boost aMD and the dV value in the output file
  • Ozge Sensoy (Sun Jan 18 2015 - 14:00:47 CST)
• dynamic_cast & runtime type information
  • Éric Germaneau (Wed Mar 23 2016 - 19:43:44 CDT)
  • Éric Germaneau (Fri Mar 18 2016 - 11:46:10 CDT)
• Dynamics of an interface Water/Hexane
  • Maxim Belkin (Fri Apr 15 2016 - 07:39:43 CDT)
  • Amy Rice (Wed Apr 13 2016 - 11:32:09 CDT)
  • Jean-François Fabre (Wed Apr 13 2016 - 07:54:17 CDT)
• Early bird extended! ISQBP2016 meeting - Bergen Norway
  • Vlad Cojocaru (Mon Apr 18 2016 - 14:35:38 CDT)
• eBiothon platform
  • eBiothon Admin Team (Mon Aug 03 2015 - 10:07:36 CDT)
• Editing Patch Grid Dimensions
  • Ryan Gordon (Thu Feb 05 2015 - 12:08:20 CST)
  • Jim Phillips (Thu Feb 05 2015 - 10:32:28 CST)
  • Ryan Gordon (Thu Feb 05 2015 - 10:00:28 CST)
• electrostatics cutoff parameters
  • Z (Mon Jun 08 2015 - 09:06:00 CDT)
• Enabling GPU for Replica exchange umbrella sampling
  • Abhishek TYAGI (Mon Jan 25 2016 - 01:49:23 CST)
  • Abhishek TYAGI (Sat Jan 23 2016 - 13:05:26 CST)
  • Norman Geist (Fri Jan 22 2016 - 03:07:59 CST)
  • Abhishek TYAGI (Thu Jan 21 2016 - 22:02:59 CST)
• Enabling GPU for REUS
  • Abhishek TYAGI (Wed Jan 20 2016 - 21:12:50 CST)
• Energy decomposition analyse in NAMD
  • sunyzero (Mon Dec 28 2015 - 20:23:28 CST)
• Energy gradient in colvars.state file
  • Giacomo Fiorin (Mon Feb 29 2016 - 14:25:35 CST)
  • Carlo Guardiani (Mon Feb 29 2016 - 13:09:31 CST)
• energy groups in NAMD
  • Andre Ribeiro (Fri Mar 06 2015 - 14:22:34 CST)
  • Andre Ribeiro (Fri Mar 06 2015 - 14:23:14 CST)
• Energy increase with fixed atoms in POPC membrane
  • Tristan Croll (Fri Feb 19 2016 - 10:51:52 CST)
  • Mihaela Drenscko (Wed Feb 17 2016 - 16:27:15 CST)
• Energy minimization
  • Aron Broom (Tue Aug 16 2016 - 09:57:04 CDT)
  • d.ronika_at_iitg.ernet.in (Mon Aug 15 2016 - 00:05:12 CDT)
  • Dhiraj Srivastava (Mon Apr 20 2015 - 21:57:55 CDT)
• Energy minimization in NAMD
  • Ajasja LjubetiÄ� (Tue Aug 09 2016 - 11:27:41 CDT)
  • Ajasja LjubetiÄ� (Tue Aug 09 2016 - 04:24:08 CDT)
  • Ajasja LjubetiÄ� (Mon Aug 08 2016 - 15:54:58 CDT)
  • Faramarz Joodaki (Mon Aug 08 2016 - 11:37:45 CDT)
  • Branko (Thu Apr 23 2015 - 11:57:06 CDT)
  • Brian Radak (Thu Apr 23 2015 - 11:51:26 CDT)
  • Chitrak Gupta (Thu Apr 23 2015 - 11:44:51 CDT)
  • Hasan haska (Thu Apr 23 2015 - 11:29:43 CDT)
• energy output
  • Jeffrey Potoff (Wed Dec 09 2015 - 11:56:45 CST)
  • Deng, Jinxia (Nancy) (Wed Dec 09 2015 - 13:12:11 CST)
  • Branko (Wed Dec 09 2015 - 11:51:45 CST)
  • Chitrak Gupta (Wed Dec 09 2015 - 11:47:57 CST)
  • Deng, Jinxia (Nancy) (Wed Dec 09 2015 - 11:39:14 CST)
• Energy output values
  • Brian Radak (Tue Dec 06 2016 - 13:35:47 CST)
  • matthew reeves (Tue Dec 06 2016 - 13:16:00 CST)
• Enerygy Minimization of a homology modelled structure in NAMD
  • Jérôme Hénin (Wed Apr 01 2015 - 02:07:59 CDT)
  • Arijit Ghosh (Tue Mar 31 2015 - 22:46:49 CDT)
  • Arijit Ghosh (Mon Mar 30 2015 - 00:21:35 CDT)
  • Arijit Ghosh (Sun Mar 29 2015 - 21:16:03 CDT)
• equilibrate the bulk water system
  • Axel Kohlmeyer (Sun Mar 15 2015 - 21:30:06 CDT)
  • Hasan haska (Sat Mar 14 2015 - 14:38:03 CDT)
  • Abhishek Tyagi (Fri Mar 13 2015 - 09:49:20 CDT)
  • Maxim Belkin (Fri Mar 13 2015 - 11:28:35 CDT)
  • Hasan haska (Fri Mar 13 2015 - 06:57:15 CDT)
  • Norman Geist (Wed Mar 11 2015 - 02:03:46 CDT)
  • Hasan haska (Tue Mar 10 2015 - 16:51:30 CDT)
• Equilibration and production run
  • Ajasja LjubetiÄ� (Mon May 16 2016 - 03:23:29 CDT)
  • dhirajks_at_gmail.com (Mon May 16 2016 - 01:25:32 CDT)
• equilibration error
  • faride badalkhani (Wed Mar 09 2016 - 15:22:25 CST)
• Equilibration fails for long time ,NPT
  • Nikhil Maroli (Sun Jan 03 2016 - 11:42:32 CST)
• Equilibration for a reverse FEP run
  • Matthew Ralph Adendorff (Thu Apr 23 2015 - 10:16:08 CDT)
  • Chris Chipot (Thu Apr 23 2015 - 10:04:32 CDT)
  • Matthew Ralph Adendorff (Thu Apr 23 2015 - 09:54:41 CDT)
• Equivalent of gromacs' "rdd" option
  • Marlon Sidore (Mon Jul 25 2016 - 10:44:48 CDT)
  • Fotis Baltoumas (Mon Jul 25 2016 - 10:26:05 CDT)
  • Axel Kohlmeyer (Mon Jul 25 2016 - 10:16:08 CDT)
  • Fotis Baltoumas (Mon Jul 25 2016 - 10:08:18 CDT)
  • Marlon Sidore (Mon Jul 25 2016 - 02:56:06 CDT)
  • Fotis Baltoumas (Fri Jul 22 2016 - 11:05:50 CDT)
  • Marlon Sidore (Fri Jul 22 2016 - 10:16:57 CDT)
  • Marlon Sidore (Fri Jul 22 2016 - 10:12:47 CDT)
• Error applying PME to simulation set up
  • Axel Kohlmeyer (Wed May 13 2015 - 08:00:00 CDT)
  • Sourav Ray (Wed May 13 2015 - 06:02:51 CDT)
  • Norman Geist (Wed May 13 2015 - 05:08:45 CDT)
  • Sourav Ray (Wed May 13 2015 - 04:24:41 CDT)
• Error associated with protected variable initialization: Nightly Build version
  • Sourav Ray (Tue May 17 2016 - 13:50:54 CDT)
• Error during Opt. Charges while using FF Took Kit
  • Aaron Larsen (Wed May 20 2015 - 16:38:19 CDT)
• ERROR in CUDA run
  • Jim Phillips (Thu Dec 17 2015 - 19:50:54 CST)
  • Lara rajam (Thu Dec 17 2015 - 08:50:49 CST)
• Error in Metadynamics Simulation
  • Fidan Sumbul (Fri Oct 23 2015 - 06:08:40 CDT)
  • Giacomo Fiorin (Thu Oct 22 2015 - 15:41:57 CDT)
  • Fidan Sumbul (Wed Oct 21 2015 - 16:31:30 CDT)
• Error in NAMD Controller Class Reference- Adaptive Tempering
  • Jeff Comer (Fri Sep 11 2015 - 08:12:15 CDT)
  • Jeff Comer (Fri Sep 11 2015 - 08:10:02 CDT)
  • Sachin Natesh (Thu Sep 10 2015 - 19:13:41 CDT)
• Error in TI derivatives for staggered lambda scaling?
  • Brian Radak (Tue Jul 21 2015 - 13:41:28 CDT)
• error in writing colvars state file
  • Jérôme Hénin (Fri Jun 05 2015 - 05:33:07 CDT)
  • Bennion, Brian (Thu Jun 04 2015 - 16:30:07 CDT)
  • Bennion, Brian (Thu Jun 04 2015 - 16:24:44 CDT)
• error reading colvars.conf in REUS
  • Chitrak Gupta (Mon Nov 16 2015 - 08:42:08 CST)
  • Giacomo Fiorin (Wed Nov 11 2015 - 11:00:21 CST)
  • Chitrak Gupta (Tue Nov 10 2015 - 20:18:11 CST)
  • Giacomo Fiorin (Fri Nov 06 2015 - 14:41:42 CST)
  • Chitrak Gupta (Thu Nov 05 2015 - 16:45:48 CST)
• error running min
  • Jeff Comer (Tue Feb 03 2015 - 08:32:57 CST)
  • Urszula Uciechowska (Tue Feb 03 2015 - 08:23:28 CST)
• error when use Charmm_Gui prepared *.inp for NAMD
  • Jeffrey Potoff (Thu Dec 03 2015 - 08:44:53 CST)
  • Deng, Jinxia (Nancy) (Thu Dec 03 2015 - 09:52:20 CST)
  • Josh Vermaas (Thu Dec 03 2015 - 08:50:36 CST)
  • Chitrak Gupta (Thu Dec 03 2015 - 08:49:59 CST)
  • Deng, Jinxia (Nancy) (Thu Dec 03 2015 - 08:37:14 CST)
• error while running namd on CRAY XC40 machine
  • Santosh Kumar Chaudhary (Fri Mar 27 2015 - 01:00:51 CDT)
  • Jim Phillips (Mon Mar 23 2015 - 13:59:47 CDT)
  • Santosh Kumar Chaudhary (Sun Mar 22 2015 - 02:40:31 CDT)
• Error: Constraint failure in RATTLE algorithm for atom 5380! in NAMD
  • Mahya Hemmat (Mon Jul 06 2015 - 11:06:39 CDT)
• ERROR: ofstream_namd::close() called when file is not open
  • Giacomo Fiorin (Mon Apr 18 2016 - 07:36:01 CDT)
  • Souvik Sinha (Mon Apr 18 2016 - 06:54:37 CDT)
  • Giacomo Fiorin (Mon Apr 18 2016 - 06:40:09 CDT)
  • Souvik Sinha (Mon Apr 18 2016 - 02:36:33 CDT)
• Excessively high dE_avg values in FEP output (NAMD CVS)
  • Radak, Brian K (Fri May 20 2016 - 11:58:43 CDT)
  • Jérôme Hénin (Fri May 20 2016 - 10:25:03 CDT)
  • Brian Radak (Fri May 20 2016 - 07:47:33 CDT)
  • Reza Salari (Thu May 19 2016 - 16:21:08 CDT)
  • Brian Radak (Wed May 18 2016 - 13:25:44 CDT)
  • Jérôme Hénin (Tue May 17 2016 - 14:44:52 CDT)
  • Reza Salari (Tue May 17 2016 - 14:20:32 CDT)
  • Giacomo Fiorin (Mon May 16 2016 - 18:51:55 CDT)
  • Reza Salari (Mon May 16 2016 - 16:29:32 CDT)
  • Reza Salari (Mon May 16 2016 - 12:42:27 CDT)
• excluding non-bonded interactions between two proteins
  • Peter Freddolino (Wed May 04 2016 - 19:14:34 CDT)
  • JC Gumbart (Wed May 04 2016 - 19:04:43 CDT)
  • Peter Freddolino (Wed May 04 2016 - 18:41:18 CDT)
  • JC Gumbart (Wed May 04 2016 - 18:16:26 CDT)
• Exit Command Failure
  • Jeff Comer (Thu Jun 23 2016 - 08:45:54 CDT)
  • Sarah Sweger (Thu Jun 23 2016 - 08:01:09 CDT)
• extendedLagrangian for non-scalar colvar
  • Jerome Karp (Thu Dec 10 2015 - 12:05:51 CST)
  • Jérôme Hénin (Thu Dec 10 2015 - 11:18:39 CST)
  • Jerome Karp (Thu Dec 10 2015 - 10:45:27 CST)
• external computational power for NAMD
  • Roshan Shrestha (Thu May 26 2016 - 21:35:39 CDT)
  • Deng, Jinxia (Nancy) (Thu May 26 2016 - 12:59:40 CDT)
  • Deng, Jinxia (Nancy) (Thu May 26 2016 - 12:02:54 CDT)
• external HPC resource
  • Mahya Hemmat (Thu Feb 18 2016 - 17:10:12 CST)
  • Deng, Jinxia (Nancy) (Thu Feb 18 2016 - 10:23:36 CST)
• extra bonds
  • Josh Vermaas (Fri Jul 03 2015 - 09:08:25 CDT)
  • Lara rajam (Thu Jul 02 2015 - 12:35:14 CDT)
  • Josh Vermaas (Thu Jul 02 2015 - 09:48:22 CDT)
  • Lara rajam (Thu Jul 02 2015 - 09:20:59 CDT)
• Extracting data
  • Stephan Grein (Thu Feb 05 2015 - 03:44:29 CST)
  • Jeff Comer (Wed Feb 04 2015 - 08:39:33 CST)
  • Axel Kohlmeyer (Wed Feb 04 2015 - 08:24:25 CST)
  • Jeff Comer (Wed Feb 04 2015 - 07:56:42 CST)
  • Stephan Grein (Wed Feb 04 2015 - 05:56:47 CST)
  • Stephan Grein (Wed Feb 04 2015 - 05:55:37 CST)
• Failure MD with par7/rst7 amber input
  • Francesco Pietra (Fri Jan 09 2015 - 02:31:55 CST)
  • Francesco Pietra (Wed Jan 07 2015 - 02:55:16 CST)
• FATAL ERROR CUDA error during equilibration using NAMD
  • Abraham A. Gutierrez Hernandez (Tue Aug 30 2016 - 18:27:38 CDT)
• FATAL ERROR: cuda_check_progress polled 1000000 times over 101.178648 s on step 6418536
  • sunyeping (Thu Dec 01 2016 - 17:27:36 CST)
• FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2
  • Sadegh Faramarzi Ganjabad (Wed Mar 18 2015 - 17:50:58 CDT)
  • Josh Vermaas (Wed Mar 18 2015 - 17:42:03 CDT)
  • Jeff Comer (Wed Mar 18 2015 - 17:35:39 CDT)
  • Sadegh Faramarzi Ganjabad (Wed Mar 18 2015 - 16:47:50 CDT)
• FATAL ERROR: Duplicate bond when going from nvt to npt
  • Radak, Brian K (Mon Dec 12 2016 - 09:33:46 CST)
  • Marlon Sidore (Mon Dec 12 2016 - 04:02:17 CST)
• FATAL ERROR: Incorrect atom count in binary file min.coor
  • Urszula Uciechowska (Fri Jul 24 2015 - 03:27:31 CDT)
• FATAL ERROR: Low global exclusion count!
  • Jeff Comer (Wed Feb 18 2015 - 18:59:28 CST)
  • Akshata Rudrapatna (Wed Feb 18 2015 - 18:32:03 CST)
  • Yongcheng Zhou (Wed Feb 18 2015 - 18:29:33 CST)
• FATAL ERROR: Unable to access config file ubq_ws_eq.log
  • Jim Phillips (Thu Nov 12 2015 - 22:45:32 CST)
  • Hugo Siles (Thu Nov 12 2015 - 16:40:41 CST)
• FATAL ERROR: UNABLE TO FIND BOND PARAMETERS
  • Jeff Comer (Wed Jan 07 2015 - 20:15:30 CST)
  • Mihaela Drenscko (Wed Jan 07 2015 - 19:58:27 CST)
• FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CTL2 OC301 (ATOMS 25 45)
  • Sourav Ray (Fri Jun 12 2015 - 13:49:00 CDT)
  • Danielle Grodi (Fri Jun 12 2015 - 13:39:30 CDT)
• Fatal Error: vdw atom type CC3161
  • Allen, Caley R (Wed Aug 03 2016 - 13:46:17 CDT)
  • Chitrak Gupta (Wed Aug 03 2016 - 10:11:51 CDT)
  • Allen, Caley R (Wed Aug 03 2016 - 09:53:37 CDT)
• feature request: external initiated clean exit
  • Peter Freddolino (Fri Aug 21 2015 - 20:04:42 CDT)
  • Peter Freddolino (Fri Aug 21 2015 - 17:09:40 CDT)
  • Axel Kohlmeyer (Fri Aug 21 2015 - 17:03:32 CDT)
  • Peter Freddolino (Fri Aug 21 2015 - 16:47:55 CDT)
  • Peter Freddolino (Fri Aug 21 2015 - 16:44:27 CDT)
  • Parag Khuraswar (Fri Aug 21 2015 - 07:58:53 CDT)
  • Daniel Möller (Fri Aug 21 2015 - 07:37:02 CDT)
• FEP double annihilation
  • Carlo Guardiani (Fri Sep 23 2016 - 13:28:30 CDT)
• FEP method- Free energy of solvation of ligand
  • hannes.loeffler_at_stfc.ac.uk (Wed Jul 22 2015 - 03:10:42 CDT)
  • Felipe Merino (Wed Jul 22 2015 - 03:07:32 CDT)
  • Mohan maruthi sena (Wed Jul 22 2015 - 02:25:40 CDT)
• FEP Restart file
  • Jérôme Hénin (Wed Jan 21 2015 - 08:57:20 CST)
  • g_at_ut#@m! (Wed Jan 21 2015 - 08:26:15 CST)
• FEP using separated topologies
  • Jérôme Hénin (Thu Nov 12 2015 - 08:48:12 CST)
  • David Huggins (Thu Nov 12 2015 - 07:46:54 CST)
• FEP utility for binding estimation
  • HERBERT MAX VENTHUR PEÂ¥A (Mon Sep 14 2015 - 10:35:17 CDT)
• FEP, big variations in dG within a window
  • Felipe Merino (Mon Jan 05 2015 - 10:27:30 CST)
  • Jonasson Gabriella (Mon Jan 05 2015 - 09:44:31 CST)
• FEP/REMD with NAMD2.11 - missing alchLambda?
  • Nathan Lim (Wed Apr 06 2016 - 20:42:58 CDT)
• FES analysis
  • Giacomo Fiorin (Tue May 24 2016 - 16:00:51 CDT)
  • Stefano Guglielmo (Tue May 24 2016 - 15:46:21 CDT)
• Few doubt on the numbers implying in REMD simulatio
  • Nicholus Bhattacharjee (Thu Apr 07 2016 - 03:34:44 CDT)
• Few doubt on the numbers implying in REMD simulation
  • Chitrak Gupta (Tue Apr 12 2016 - 10:00:21 CDT)
  • Nicholus Bhattacharjee (Tue Apr 12 2016 - 07:06:42 CDT)
  • Nicholus Bhattacharjee (Tue Apr 05 2016 - 10:00:50 CDT)
• FFTK - error
  • Mayne, Christopher G (Mon Jun 08 2015 - 11:56:34 CDT)
  • Mohan maruthi sena (Sat Jun 06 2015 - 18:35:44 CDT)
• ffTK fitting dihedrals
  • Seth Axen (Tue May 17 2016 - 01:36:02 CDT)
• firstTimestep error message
  • Laura Joana (Mon May 23 2016 - 05:55:51 CDT)
• fix disulfide bond in coarse grain(CG) model for NAMD
  • Deng, Jinxia (Nancy) (Mon Oct 24 2016 - 11:46:11 CDT)
• fix disulfide bridge in coarse grain MD
  • Fotis Baltoumas (Wed Oct 19 2016 - 12:36:11 CDT)
  • Deng, Jinxia (Nancy) (Wed Oct 19 2016 - 11:54:59 CDT)
• force units conversion
  • Maxim Belkin (Fri Mar 25 2016 - 14:12:22 CDT)
  • Maxim Belkin (Fri Mar 25 2016 - 10:42:40 CDT)
  • Olya Kravchenko (Thu Mar 24 2016 - 14:15:05 CDT)
• Force-field for DOPI lipid
  • Josh Vermaas (Sun May 24 2015 - 08:27:46 CDT)
  • Kevin C Chan (Sat May 23 2015 - 13:58:30 CDT)
• Format of colvars.state
  • Jérôme Hénin (Thu Aug 27 2015 - 04:27:00 CDT)
  • Hossein Mohammadiarani (Wed Aug 26 2015 - 18:05:19 CDT)
  • Jérôme Hénin (Mon Aug 24 2015 - 13:04:50 CDT)
  • Hossein Mohammadiarani (Mon Aug 24 2015 - 12:53:14 CDT)
• free energy calculation along image index in us
  • ÂÀСӨ (Wed Jun 24 2015 - 02:27:35 CDT)
• Free energy calculation using MM-GBSA with NAMD
  • Jeff Comer (Wed Jun 15 2016 - 09:10:21 CDT)
  • Sneha Menon (Wed Jun 15 2016 - 05:50:41 CDT)
• free energy changes via FEP method
  • Haleh a (Thu Dec 17 2015 - 05:42:15 CST)
  • Gianluca Interlandi (Wed Dec 16 2015 - 12:49:26 CST)
  • Brian Radak (Wed Dec 16 2015 - 12:15:10 CST)
  • Haleh a (Tue Dec 15 2015 - 09:59:10 CST)
• Free energy profiles in ABF tutorial
  • Giacomo Fiorin (Mon Nov 16 2015 - 07:52:31 CST)
  • Haleh a (Mon Nov 16 2015 - 06:35:30 CST)
• Free Energy Workshop, Münster, March 9-11, 2015
  • Vlad Cojocaru (Fri Jan 09 2015 - 03:19:04 CST)
• fructose 1,6 bisphosphate forcefield parameters.
  • Dhiraj Srivastava (Wed Dec 02 2015 - 00:06:45 CST)
• Fw (5): zmhoseyni
  • zmhoseyni (Mon Dec 19 2016 - 13:47:30 CST)
• Fwd: all atom equilibrium of yeast PGK simulation with NAMD
  • Qing Li (Tue Feb 03 2015 - 21:14:36 CST)
• Fwd: ANGLE PARAMETERS FOR NH3 HC NH3
  • Tristan Croll (Wed Oct 28 2015 - 20:36:08 CDT)
  • Francesco Pietra (Tue Oct 27 2015 - 13:33:59 CDT)
  • Josh Vermaas (Tue Oct 27 2015 - 11:24:47 CDT)
  • Francesco Pietra (Tue Oct 27 2015 - 11:19:48 CDT)
• Fwd: Appropriate FF for a specific solvent
  • faride badalkhani (Fri Mar 18 2016 - 10:53:15 CDT)
• Fwd: colvars: keyword "name" is not supported, or not recognized in this context.
  • Francesco Pietra (Thu Jan 15 2015 - 10:54:47 CST)
  • Jérôme Hénin (Thu Jan 15 2015 - 10:34:22 CST)
  • Francesco Pietra (Thu Jan 15 2015 - 10:10:14 CST)
• Fwd: H-bonds in charmm36 with namd2.11
  • Francesco Pietra (Sun May 22 2016 - 01:46:52 CDT)
• Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech
  • JC Gumbart (Wed Sep 09 2015 - 18:15:34 CDT)
  • JC Gumbart (Wed Sep 09 2015 - 10:13:31 CDT)
• Fwd: ISQBP 2016 meeting - registration opened!
  • Vlad Cojocaru (Mon Mar 14 2016 - 03:13:10 CDT)
• Fwd: Local minima on minimiztion with colvars
  • Francesco Pietra (Thu Jan 22 2015 - 02:55:09 CST)
  • Francesco Pietra (Wed Jan 21 2015 - 13:01:33 CST)
• Fwd: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file
  • zeynab hoseyni (Mon Dec 26 2016 - 06:45:28 CST)
  • zeynab hoseyni (Sun Dec 25 2016 - 14:31:53 CST)
• Fwd: namd on Windows 10
  • Branko (Fri Feb 05 2016 - 08:13:51 CST)
• Fwd: No steric clashes, still not minimizing
  • Francesco Pietra (Wed Mar 11 2015 - 12:28:44 CDT)
• Fwd: problem with angle parameters
  • faride badalkhani (Wed Mar 30 2016 - 10:01:22 CDT)
• Fwd: Regarding problem in generating psf file of heparin and heparan sulfate
  • siddharth kamal (Thu Jul 16 2015 - 07:44:46 CDT)
• Fwd: Regarding system forces in NAMD
  • sruthi c k (Fri Jan 08 2016 - 03:38:26 CST)
• Fwd: TIP4P and CHARMM27
  • Francesco Pietra (Thu Dec 03 2015 - 12:19:58 CST)
  • Peter Freddolino (Wed Dec 02 2015 - 12:51:43 CST)
  • Francesco Pietra (Wed Dec 02 2015 - 11:47:58 CST)
  • Francesco Pietra (Tue Dec 01 2015 - 03:22:31 CST)
  • Jim Phillips (Mon Nov 30 2015 - 16:21:44 CST)
  • Francesco Pietra (Fri Nov 27 2015 - 15:54:56 CST)
  • Peter Freddolino (Fri Nov 27 2015 - 11:37:48 CST)
  • Francesco Pietra (Fri Nov 27 2015 - 11:35:25 CST)
  • Peter Freddolino (Fri Nov 27 2015 - 10:26:05 CST)
  • Francesco Pietra (Fri Nov 27 2015 - 10:18:28 CST)
  • Peter Freddolino (Fri Nov 27 2015 - 09:41:00 CST)
  • Francesco Pietra (Fri Nov 27 2015 - 09:17:35 CST)
• Fwd: Urey-Bradley parameters
  • Brian Radak (Mon Mar 14 2016 - 10:25:22 CDT)
  • faride badalkhani (Mon Mar 14 2016 - 07:20:08 CDT)
• GBIS error
  • sunyeping (Sat Jan 02 2016 - 22:55:10 CST)
• GBIS in NAMD 2.10 CUDA with IMD
  • Tristan Croll (Sun Feb 15 2015 - 20:38:40 CST)
  • Jim Phillips (Sat Feb 14 2015 - 12:18:25 CST)
  • Jim Phillips (Thu Feb 12 2015 - 12:29:25 CST)
  • Tristan Croll (Wed Feb 11 2015 - 15:09:11 CST)
  • Jim Phillips (Wed Feb 11 2015 - 10:51:31 CST)
  • Tristan Croll (Wed Feb 11 2015 - 04:18:11 CST)
• GBIS intrinsic radii set from aber parm7
  • Norman Geist (Fri Dec 16 2016 - 02:04:15 CST)
• Generalized Born solvation models supported by NAMD
  • Chitrak Gupta (Tue Aug 02 2016 - 17:54:08 CDT)
  • Aron Broom (Tue Aug 02 2016 - 09:41:09 CDT)
  • Chitrak Gupta (Fri Jul 29 2016 - 16:05:02 CDT)
  • Aron Broom (Fri Jul 29 2016 - 14:24:21 CDT)
  • Thomas Evangelidis (Fri Jul 29 2016 - 13:18:08 CDT)
  • Aron Broom (Fri Jul 29 2016 - 12:25:49 CDT)
  • Thomas Evangelidis (Fri Jul 29 2016 - 11:20:46 CDT)
  • Aron Broom (Fri Jul 29 2016 - 10:55:51 CDT)
  • Thomas Evangelidis (Fri Jul 29 2016 - 10:26:13 CDT)
• Generate psf file in x-plor format
  • Nehad Elsalamouny (Thu Nov 17 2016 - 19:04:06 CST)
  • Vermaas, Joshua (Thu Nov 17 2016 - 18:56:55 CST)
  • Nehad Elsalamouny (Thu Nov 17 2016 - 16:59:53 CST)
  • Nehad Elsalamouny (Thu Nov 17 2016 - 14:44:40 CST)
  • Vermaas, Joshua (Thu Nov 17 2016 - 14:56:01 CST)
  • Vermaas, Joshua (Thu Nov 17 2016 - 09:47:42 CST)
  • Nehad Elsalamouny (Thu Nov 17 2016 - 06:07:39 CST)
• Generating solvent models.
  • VINAYAK BHAT (Sun Jul 05 2015 - 04:06:27 CDT)
• get seed
  • Jérôme Hénin (Fri Jul 01 2016 - 12:39:28 CDT)
  • Laura Joana (Fri Jul 01 2016 - 11:52:46 CDT)
• Getting cluster with defined criteria
  • Brian Radak (Sun Dec 04 2016 - 17:54:21 CST)
  • Peter Mawanga (Sun Dec 04 2016 - 07:05:35 CST)
• Getting Infinity in Calculation of Free Energy using SMD
  • Ebru Çetin (Tue Jun 23 2015 - 00:23:19 CDT)
• Getting residue mapping correpond to bead using SBCG (Shape based CG) Model in Coarse Grain Builder VMD
  • Christian Bope Domilongo (Fri Jan 09 2015 - 09:18:32 CST)
  • Jeff Comer (Fri Jan 09 2015 - 08:23:03 CST)
  • Christian Bope Domilongo (Fri Jan 09 2015 - 04:31:44 CST)
• global does not work in configuration and callback function
  • jc guo (Sat Oct 24 2015 - 08:51:33 CDT)
  • jc guo (Sat Oct 24 2015 - 01:46:21 CDT)
• GPU accelerated MD
  • Nikhil Maroli (Fri Oct 23 2015 - 04:12:24 CDT)
• GPU acceleration using K40 and k80
  • Atanu Maity (Wed Sep 14 2016 - 00:32:00 CDT)
• GPU configuration suggestions
  • daniel aguayo (Tue Mar 22 2016 - 06:59:16 CDT)
  • Nikhil Maroli (Tue Mar 22 2016 - 04:31:33 CDT)
  • Nikhil Maroli (Tue Mar 22 2016 - 00:52:25 CDT)
• GPU Multinodes problem
  • Jim Phillips (Wed Feb 18 2015 - 17:36:26 CST)
  • horacio poblete (Wed Feb 18 2015 - 15:59:07 CST)
• GPU Programming workshop @ ICTP: deadline extended for participants not requiring visa and financial support
  • Axel Kohlmeyer (Tue Mar 24 2015 - 14:17:40 CDT)
• Gradual Heating Periodic Error
  • Jackson Cavett (Tue Sep 13 2016 - 15:39:42 CDT)
  • Hardy, David Joseph (Tue Sep 13 2016 - 14:13:52 CDT)
  • david gae (Tue Sep 13 2016 - 12:03:07 CDT)
  • Jackson Cavett (Tue Sep 13 2016 - 10:32:22 CDT)
  • david gae (Tue Sep 13 2016 - 09:27:25 CDT)
  • Ajasja LjubetiÄ� (Tue Sep 13 2016 - 09:15:38 CDT)
  • Jackson Cavett (Tue Sep 13 2016 - 09:01:43 CDT)
  • Jackson Cavett (Tue Sep 13 2016 - 08:34:30 CDT)
• gradual heating problem
  • Radak, Brian K (Mon May 09 2016 - 10:12:01 CDT)
  • dhirajks_at_gmail.com (Sun May 08 2016 - 11:21:13 CDT)
  • Brian Radak (Sun May 08 2016 - 11:04:31 CDT)
  • Dhiraj Srivastava (Sun May 08 2016 - 10:27:39 CDT)
• Graphene Oxide Parameter File
  • Jeff Comer (Sat Aug 20 2016 - 16:25:07 CDT)
  • Marisol Oswald (Sat Aug 20 2016 - 14:25:38 CDT)
• graphene with proteins
  • Zeina Salman (Mon Sep 26 2016 - 16:02:36 CDT)
  • Jeff Comer (Mon Sep 26 2016 - 15:18:07 CDT)
  • Zeina Salman (Sun Sep 25 2016 - 19:42:51 CDT)
• Grid forces visualisation
  • Jeff Comer (Wed Feb 11 2015 - 08:16:41 CST)
  • Charan Thota (Wed Feb 11 2015 - 06:13:12 CST)
• gromacs to charmm conversion
  • Francesco Pietra (Fri Oct 23 2015 - 02:34:15 CDT)
• group selection in TCL script for use in NAMD
  • Allen, Caley R (Wed Jul 27 2016 - 13:35:05 CDT)
• H-bonds in charmm36 with namd2.11
  • Francesco Pietra (Tue May 24 2016 - 04:30:13 CDT)
  • JC Gumbart (Mon May 23 2016 - 08:59:24 CDT)
  • Francesco Pietra (Sun May 22 2016 - 01:43:55 CDT)
  • JC Gumbart (Sat May 21 2016 - 18:44:09 CDT)
  • Francesco Pietra (Fri May 20 2016 - 16:18:22 CDT)
• Half of the structure goes out of the simulation box!
  • Ana Celia Vila Verde (Fri Sep 30 2016 - 07:31:03 CDT)
  • Richard Overstreet (Fri Sep 30 2016 - 06:25:19 CDT)
  • faride badalkhani (Fri Sep 30 2016 - 05:18:51 CDT)
• Hamiltonian Replica Exchange MD Simulation in NAMD
  • Fidan Sumbul (Tue Jan 27 2015 - 14:07:31 CST)
  • JC Gumbart (Tue Jan 27 2015 - 08:52:42 CST)
  • Fidan Sumbul (Fri Jan 23 2015 - 13:04:19 CST)
• Hands-On Workshop on Computational Biophysics: June 6-10 in Pittsburgh, PA
  • Jodi Ann Hadden (Wed Mar 09 2016 - 14:34:10 CST)
• Hands-On Workshop on Computational Biophysics: November 14-18 in Atlanta, GA
  • Jodi Ann Hadden (Thu Sep 29 2016 - 00:27:31 CDT)
  • Jodi Ann Hadden (Tue Aug 16 2016 - 15:41:22 CDT)
• Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL
  • Jodi Ann Hadden (Fri Sep 16 2016 - 15:35:45 CDT)
  • Jodi Ann Hadden (Wed Sep 07 2016 - 18:06:53 CDT)
  • Jodi Ann Hadden (Tue Aug 16 2016 - 15:21:32 CDT)
• Hands-On Workshop on Integrative Modeling and Simulations
  • Jodi Ann Hadden (Wed Nov 16 2016 - 11:28:03 CST)
• Have GPU-accelerated NAMD Questions? Join us for a Live Webinar
  • MARK (Fri May 20 2016 - 13:07:08 CDT)
• HBB2-pol
  • R. Charbel MAROUN (Fri Mar 25 2016 - 09:01:46 CDT)
• heating in NPT ensemble
  • Radak, Brian K (Fri May 06 2016 - 10:04:07 CDT)
  • Dhiraj Srivastava (Thu May 05 2016 - 17:39:35 CDT)
• Help about Drude Prepper
  • Francesco Pietra (Tue Jun 07 2016 - 10:06:48 CDT)
• heparin
  • Lara rajam (Sat Aug 29 2015 - 18:48:08 CDT)
• Hi All
  • msa5 (Tue Nov 01 2016 - 22:06:01 CDT)
• Histidine C-H---O hydrogen bonding
  • Branko (Thu Jan 29 2015 - 12:53:52 CST)
  • Tanner, John J. (Thu Jan 29 2015 - 12:51:42 CST)
  • eprates_at_iqm.unicamp.br (Thu Jan 29 2015 - 11:39:57 CST)
  • eprates_at_iqm.unicamp.br (Thu Jan 29 2015 - 11:36:33 CST)
  • Josh Vermaas (Thu Jan 29 2015 - 09:21:27 CST)
  • eprates_at_iqm.unicamp.br (Thu Jan 29 2015 - 09:03:17 CST)
• How can I find the proper number of solvent molecules in the simulation?
  • Brian Radak (Mon Jun 06 2016 - 09:49:42 CDT)
  • faride badalkhani (Mon Jun 06 2016 - 09:25:50 CDT)
• how does NAMD calculate intramolecular electrostatic interactions between Drude pairs?
  • Ana Celia Vila Verde (Thu Nov 26 2015 - 01:13:38 CST)
  • Ana Celia Vila Verde (Mon Nov 23 2015 - 09:27:00 CST)
• How occupancy relates to force in SMD
  • daneshkaftroody_v_at_mech.sharif.ir (Mon Nov 02 2015 - 10:41:11 CST)
• How to calculate the temperature for a subset of my simulation
  • Josh Vermaas (Tue Oct 20 2015 - 14:03:32 CDT)
  • Jhonatam Cordeiro Rodrigues (Tue Oct 20 2015 - 13:47:53 CDT)
  • Jhonatam Cordeiro Rodrigues (Tue Oct 20 2015 - 12:20:46 CDT)
  • Jhonatam Cordeiro Rodrigues (Mon Oct 19 2015 - 15:08:27 CDT)
• How to continue RMSD of previous production simulation
  • Chitrak Gupta (Fri Dec 02 2016 - 12:43:05 CST)
  • Farhad Jahanfar (Fri Dec 02 2016 - 12:21:36 CST)
• How to create 3'-3' phosphodiester linkage for a DNA.
  • Susmita Ghosh (Mon Nov 28 2016 - 23:50:26 CST)
• how to create two namd jobs in a single script with 2 x dual cuda gpus?
  • nam kim (Sat Aug 01 2015 - 16:36:15 CDT)
  • nam kim (Sat Aug 01 2015 - 16:33:04 CDT)
• how to get the restart files from the dcd file?
  • Azadeh Alavi (Mon Dec 21 2015 - 07:10:47 CST)
  • Azadeh Alavi (Sun Dec 20 2015 - 14:30:07 CST)
  • Jeff Comer (Sun Dec 20 2015 - 12:46:16 CST)
  • Jeff Comer (Sun Dec 20 2015 - 12:06:17 CST)
  • Azadeh Alavi (Sun Dec 20 2015 - 03:02:36 CST)
• How to let NAMD terminate automatically at a given time
  • Qing Lv (Mon Mar 02 2015 - 22:20:40 CST)
  • Norman Geist (Tue Mar 03 2015 - 02:35:36 CST)
  • hannes.loeffler_at_stfc.ac.uk (Mon Mar 02 2015 - 14:17:16 CST)
  • Jeff Comer (Mon Mar 02 2015 - 13:58:14 CST)
  • hannes.loeffler_at_stfc.ac.uk (Mon Mar 02 2015 - 13:19:08 CST)
  • Jérôme Hénin (Mon Mar 02 2015 - 11:12:40 CST)
  • Dong Luo (Mon Mar 02 2015 - 09:27:22 CST)
  • ÂÀÇç (Fri Feb 27 2015 - 20:02:18 CST)
• how to not overwrite a modified file? (while producing coordinates for ABF/US windows)
  • Olya Kravchenko (Sat Aug 06 2016 - 07:18:56 CDT)
• How to output CCC per residue from MDFF
  • Ryan McGreevy (Thu Apr 23 2015 - 22:15:49 CDT)
  • Michael Yuchi (Thu Apr 23 2015 - 21:48:11 CDT)
• how to reassign dcdfreq??
  • Faramarz Joodaki (Wed Jul 13 2016 - 08:02:23 CDT)
  • Faramarz Joodaki (Wed Jul 13 2016 - 08:01:09 CDT)
  • Marlon Sidore (Wed Jul 13 2016 - 03:35:52 CDT)
  • Radak, Brian K (Tue Jul 12 2016 - 13:22:08 CDT)
  • Faramarz Joodaki (Mon Jul 11 2016 - 22:17:54 CDT)
• How to replace NAMD Eletrostatic Forces
  • Emerson Macedo (Fri Aug 05 2016 - 10:45:12 CDT)
  • Giacomo Fiorin (Fri Aug 05 2016 - 09:45:05 CDT)
  • Ajasja LjubetiÄ� (Fri Aug 05 2016 - 02:46:00 CDT)
  • Jérôme Hénin (Thu Aug 04 2016 - 17:21:40 CDT)
  • Brian Radak (Thu Aug 04 2016 - 15:17:17 CDT)
  • Emerson Macedo (Thu Aug 04 2016 - 13:15:38 CDT)
• how to rerun a namd trajectory in order to complement the missing snapshots?
  • Brian Radak (Fri Aug 19 2016 - 07:54:54 CDT)
  • sunyeping (Thu Aug 18 2016 - 22:35:51 CDT)
• How to save a structure after minimizing for 1000 steps?
  • Chitrak Gupta (Thu Apr 23 2015 - 16:35:58 CDT)
  • Aron Broom (Thu Apr 23 2015 - 16:28:47 CDT)
  • Arijit Ghosh (Thu Apr 23 2015 - 16:15:40 CDT)
• How to use a proper force constant to decrease computational cost while keeping calculation precision?
  • Radak, Brian K (Wed Apr 20 2016 - 16:22:09 CDT)
  • Ana Celia Vila Verde (Wed Apr 20 2016 - 03:03:08 CDT)
  • wliu (Wed Apr 20 2016 - 02:18:01 CDT)
• Hybrid coarse-grained/all-atom simulation
  • Mahya Hemmat (Mon Sep 28 2015 - 14:25:24 CDT)
• hyper-branched polymers
  • faride badalkhani (Tue May 24 2016 - 09:24:41 CDT)
• I can not run fixed protein in membrane with NAMD
  • Chitrak Gupta (Mon Jun 29 2015 - 14:41:11 CDT)
  • R.L. Ma (Sat Jun 27 2015 - 21:27:18 CDT)
• I cannot make MD simulation constant in pressure
  • Peter Freddolino (Mon May 23 2016 - 22:56:48 CDT)
  • Faramarz Joodaki (Mon May 23 2016 - 22:44:21 CDT)
  • Peter Freddolino (Mon May 23 2016 - 21:01:23 CDT)
  • Faramarz Joodaki (Mon May 23 2016 - 18:29:14 CDT)
  • Jeff Comer (Mon May 23 2016 - 16:06:17 CDT)
  • Faramarz Joodaki (Mon May 23 2016 - 14:41:54 CDT)
• Immediate PhD Opening Computational Structural Biology Of Membrane Proteins
  • Marawan Hussien (Thu Apr 09 2015 - 19:18:53 CDT)
• Immediate Postdoctoral Position Opening
  • Marawan Hussien (Thu Apr 09 2015 - 18:10:32 CDT)
  • Marawan Hussien (Sun Mar 22 2015 - 16:08:16 CDT)
• Including two parameters for protein-ligand simulation
  • Payal Chatterjee (Wed Oct 28 2015 - 03:08:16 CDT)
  • Abhishek TYAGI (Wed Oct 28 2015 - 01:59:21 CDT)
  • Nikhil Maroli (Wed Oct 28 2015 - 01:52:30 CDT)
• inconsistency in ABF results for helix unfolding
  • JC Gumbart (Wed Jan 28 2015 - 15:40:30 CST)
  • Giacomo Fiorin (Wed Jan 28 2015 - 14:52:54 CST)
  • MEHRAN MB (Wed Jan 28 2015 - 14:50:14 CST)
  • Ajasja LjubetiÄ� (Wed Jan 28 2015 - 04:05:37 CST)
  • gmail (Wed Jan 28 2015 - 03:49:54 CST)
  • MEHRAN MB (Tue Jan 27 2015 - 17:09:19 CST)
• Inconsistent atom count
  • Laura Joana (Tue Jul 05 2016 - 12:04:44 CDT)
• Incorrect atom count in binary file
  • Mihaela Drenscko (Wed Feb 18 2015 - 07:34:15 CST)
  • Norman Geist (Wed Feb 18 2015 - 03:13:52 CST)
  • Mihaela Drenscko (Tue Feb 17 2015 - 18:59:43 CST)
• initial structure
  • faride badalkhani (Mon Apr 18 2016 - 10:17:30 CDT)
  • faride badalkhani (Fri Apr 15 2016 - 14:18:03 CDT)
• Instability in harmonic restraints when equilibrating large systems
  • Tristan Croll (Fri Jul 24 2015 - 16:52:05 CDT)
• installing NAMD 2.11
  • Chitrak Gupta (Thu Mar 10 2016 - 11:30:44 CST)
  • faride badalkhani (Wed Mar 09 2016 - 07:54:23 CST)
  • Ajasja LjubetiÄ� (Wed Mar 09 2016 - 07:38:39 CST)
  • faride badalkhani (Wed Mar 09 2016 - 07:32:46 CST)
• instantaneous pressure and temp change for multiple run calls?
  • Radak, Brian K (Tue Mar 22 2016 - 13:21:53 CDT)
• INTERNAL COORDINATES
  • Josh Vermaas (Tue Mar 01 2016 - 08:28:33 CST)
  • faride badalkhani (Tue Mar 01 2016 - 07:52:09 CST)
• interpretation of eigenvec colvar?
  • JC Gumbart (Tue Aug 23 2016 - 22:12:48 CDT)
  • Giacomo Fiorin (Tue Aug 23 2016 - 20:29:37 CDT)
  • JC Gumbart (Tue Aug 23 2016 - 20:02:37 CDT)
• Interrupted Molecular Dynamics Simulation
  • Daniela Rivas (Wed Jul 29 2015 - 10:25:29 CDT)
  • Axel Kohlmeyer (Tue Jul 28 2015 - 10:53:28 CDT)
  • Felipe Merino (Tue Jul 28 2015 - 10:34:17 CDT)
  • Purushottam Dixit (Tue Jul 28 2015 - 09:51:22 CDT)
  • Daniela Rivas (Tue Jul 28 2015 - 09:45:07 CDT)
  • Chitrak Gupta (Tue Jul 28 2015 - 09:34:21 CDT)
  • Felipe Merino (Tue Jul 28 2015 - 02:03:00 CDT)
  • Daniela Rivas (Mon Jul 27 2015 - 19:21:00 CDT)
  • Chitrak Gupta (Mon Jul 27 2015 - 12:29:25 CDT)
  • Daniela Rivas (Mon Jul 27 2015 - 10:32:29 CDT)
• Intramolecular interaction energy of protein in vacuum from NAMD simualtions
  • dayanidhi mohanta (Sat Jul 09 2016 - 08:26:13 CDT)
• Introducing PDBManip
  • Ali Khanlarkhani (Tue Aug 16 2016 - 10:10:05 CDT)
• ION CHANNEL gating mechanism
  • Shambo Hore (Sat Sep 03 2016 - 05:42:46 CDT)
• ion escapes the channel during US simulation
  • Vermaas, Joshua (Thu Sep 01 2016 - 10:27:16 CDT)
  • Olya Kravchenko (Thu Sep 01 2016 - 10:17:08 CDT)
  • Vermaas, Joshua (Thu Sep 01 2016 - 09:44:22 CDT)
  • Olya Kravchenko (Thu Sep 01 2016 - 09:03:14 CDT)
  • Amy Rice (Wed Aug 31 2016 - 10:40:16 CDT)
  • Olya Kravchenko (Tue Aug 30 2016 - 16:17:26 CDT)
• Is GPU double-precision floating point performance important for NAMD?
  • Mert Gür (Fri Jun 03 2016 - 09:20:42 CDT)
  • Mert Gür (Thu Jun 02 2016 - 16:48:07 CDT)
• Is it possible to perform NVT FEP on a fluid system?
  • Radak, Brian K (Tue Aug 09 2016 - 10:22:59 CDT)
  • Jeffrey Potoff (Tue Aug 09 2016 - 12:10:10 CDT)
  • Radak, Brian K (Tue Aug 09 2016 - 11:51:05 CDT)
  • B.W.J. Irwin (Tue Aug 09 2016 - 11:23:58 CDT)
  • B.W.J. Irwin (Tue Aug 09 2016 - 05:22:08 CDT)
• Is it possible to rename atoms with psfgen?
  • Brian Radak (Fri Jan 30 2015 - 10:35:43 CST)
  • Jim Phillips (Thu Jan 29 2015 - 13:11:46 CST)
  • Brian Radak (Wed Jan 28 2015 - 09:54:16 CST)
• is it possible to restrict the access of ions to certain volume?
  • Olya Kravchenko (Mon Oct 31 2016 - 15:55:28 CDT)
  • Giacomo Fiorin (Mon Oct 31 2016 - 15:43:34 CDT)
  • Olya Kravchenko (Mon Oct 31 2016 - 15:28:40 CDT)
• is there a method equivalent to conformational flooding in NAMD 2.10
  • Jérôme Hénin (Mon Jan 12 2015 - 04:44:58 CST)
  • Thomas Evangelidis (Mon Jan 12 2015 - 04:32:17 CST)
  • Thomas Evangelidis (Sun Jan 11 2015 - 07:43:36 CST)
• is there a way to prevent ions from entering the channel?
  • Olya Kravchenko (Thu Jul 21 2016 - 12:56:57 CDT)
• Is there any point in running NAMD over an ethernet-linked cluster?
  • Norman Geist (Thu Apr 16 2015 - 10:39:38 CDT)
  • Douglas Houston (Thu Apr 16 2015 - 05:10:12 CDT)
• Ispopetide bond
  • Milica UtjeÅ¡anović (Fri Oct 02 2015 - 14:30:04 CDT)
• K40 benchmark problem in NAMD
  • sonia ziada (Thu Nov 17 2016 - 01:54:59 CST)
  • Atanu Maity (Thu Nov 17 2016 - 01:27:04 CST)
• keyword "outputaccumulatedwork" is not supported, or not recognized in this context.
  • Sridhar Kumar Kannam (Thu Oct 15 2015 - 02:24:52 CDT)
  • Jérôme Hénin (Thu Oct 15 2015 - 01:43:25 CDT)
  • Sridhar Kumar Kannam (Thu Oct 15 2015 - 00:54:00 CDT)
  • Giacomo Fiorin (Wed Oct 14 2015 - 06:33:28 CDT)
  • Sridhar Kumar Kannam (Wed Oct 14 2015 - 05:41:58 CDT)
  • Jérôme Hénin (Wed Oct 14 2015 - 05:14:41 CDT)
  • Marlon Sidore (Wed Oct 14 2015 - 05:12:16 CDT)
  • Jérôme Hénin (Wed Oct 14 2015 - 05:05:54 CDT)
  • Sridhar Kumar Kannam (Tue Oct 13 2015 - 23:39:14 CDT)
• Lambda-exchange multiple-copy alchemical free energy calculations
  • 岡部篤俊 (Tue Aug 18 2015 - 09:54:40 CDT)
• LangevinDamping Coefficient for MARTINI
  • Mahdi Tavakol (Wed Dec 23 2015 - 05:33:48 CST)
• LangevinPistonPeriod (Simulation Near Critical Point)
  • JAVAD NOROOZI (Tue Feb 10 2015 - 03:15:23 CST)
• LAST CALL: Free Energy Workshop, Münster, March 9-11, 2015
  • Vlad Cojocaru (Tue Feb 03 2015 - 14:34:42 CST)
• LCPO parameters P1-P4
  • yandong Huang (Sat Jan 31 2015 - 13:24:55 CST)
  • yandong Huang (Mon Jan 26 2015 - 12:30:21 CST)
• Lennard-Jones and Electrostatic Forces and Energies
  • Brian Radak (Tue Oct 27 2015 - 08:50:27 CDT)
  • Kostas Malavazos (Mon Oct 26 2015 - 13:54:28 CDT)
• Lennard-Jones potential in coarse grained MD
  • Yongcheng Zhou (Sun Jan 31 2016 - 00:16:37 CST)
  • bay__gulf618_at_sina.com (Sat Jan 30 2016 - 01:19:17 CST)
  • Yongcheng Zhou (Sat Jan 30 2016 - 00:36:20 CST)
• Ligand jump out of the protein through NPT ensemle runs
  • mahdi K (Fri Nov 25 2016 - 06:40:31 CST)
• Lipid Bilayer Shearing
  • Vermaas, Joshua (Tue Aug 16 2016 - 13:06:52 CDT)
  • Sachin Natesh (Tue Aug 16 2016 - 13:01:45 CDT)
  • Vermaas, Joshua (Tue Aug 16 2016 - 12:25:06 CDT)
  • Sachin Natesh (Tue Aug 16 2016 - 12:01:15 CDT)
• LJ Parameters for Au and S and harmonic constraints
  • Jeff Comer (Fri Apr 08 2016 - 12:52:50 CDT)
  • Madhulika Gupta (Fri Apr 08 2016 - 03:24:34 CDT)
  • Ana Celia Vila Verde (Fri Apr 08 2016 - 02:55:45 CDT)
  • Madhulika Gupta (Fri Apr 08 2016 - 02:18:29 CDT)
• LJ parameters for Pd surface
  • Axel Kohlmeyer (Fri May 06 2016 - 08:36:59 CDT)
  • Madhulika Gupta (Fri May 06 2016 - 08:33:03 CDT)
• LJ Parameters on hydrogen for TIP4P water models
  • Shayon Bhattacharya (Wed Sep 30 2015 - 16:39:45 CDT)
  • Peter Freddolino (Wed Sep 30 2015 - 08:14:45 CDT)
  • Brian Radak (Tue Sep 29 2015 - 14:52:44 CDT)
  • Shayon Bhattacharya (Tue Sep 29 2015 - 14:04:44 CDT)
  • Peter Freddolino (Tue Sep 29 2015 - 13:25:07 CDT)
  • Shayon Bhattacharya (Tue Sep 29 2015 - 10:20:36 CDT)
• LJcorrection + switching?
  • Peter Freddolino (Tue Sep 15 2015 - 20:11:32 CDT)
  • Brian Radak (Tue Sep 01 2015 - 09:31:34 CDT)
• LJcorrection and alchemy?
  • Brian Radak (Fri Jan 30 2015 - 14:15:01 CST)
  • Brian Radak (Fri Jan 30 2015 - 12:10:53 CST)
• LJcorrection option in NAMD
  • Grace Brannigan (Mon Jun 27 2016 - 06:41:33 CDT)
  • JC Gumbart (Mon Jun 27 2016 - 00:23:12 CDT)
  • Brian Radak (Wed Jun 22 2016 - 17:22:07 CDT)
  • Brian Radak (Wed Jun 22 2016 - 17:04:02 CDT)
  • Grace Brannigan (Tue Jun 21 2016 - 13:03:24 CDT)
  • Jérôme Hénin (Tue Jun 21 2016 - 09:48:12 CDT)
  • Brian Radak (Tue Jun 21 2016 - 07:36:06 CDT)
  • Yue Qian (Mon Jun 20 2016 - 17:09:04 CDT)
• Local minima on minimiztion with colvars
  • Francesco Pietra (Wed Jan 21 2015 - 12:45:14 CST)
• Looking for benchmarks on k80's
  • rswett_at_chem.wayne.edu (Thu Aug 13 2015 - 10:40:45 CDT)
• Low global exclusion count error
  • Brian Radak (Fri Dec 02 2016 - 09:25:30 CST)
  • B.W.J. Irwin (Fri Dec 02 2016 - 04:43:49 CST)
  • faride badalkhani (Thu Dec 01 2016 - 15:21:03 CST)
• Low global exclusion count errors!
  • Jim Phillips (Tue Dec 06 2016 - 15:59:34 CST)
  • faride badalkhani (Thu Nov 24 2016 - 10:28:53 CST)
• Lowe-Andersen, Langevin and velocity rescaling thermostats (lipid bilayers)
  • Jeff Comer (Wed Apr 06 2016 - 08:49:16 CDT)
  • Brian Radak (Mon Apr 04 2016 - 09:44:37 CDT)
  • Loison Claire (Mon Apr 04 2016 - 07:16:22 CDT)
• LSU SuperMIC
  • Kenneth Huang (Tue Jan 19 2016 - 17:15:39 CST)
  • Jeff Comer (Tue Jan 19 2016 - 16:21:39 CST)
• mail reg compilation of mdenergy
  • Vidhya Sankar (Tue Oct 25 2016 - 20:20:07 CDT)
  • Axel Kohlmeyer (Wed Oct 19 2016 - 14:27:04 CDT)
  • David Hardy (Wed Oct 19 2016 - 14:11:32 CDT)
  • Vidhya Sankar (Wed Oct 19 2016 - 12:08:12 CDT)
• mail reg DCD error
  • Vidhya Sankar (Sun May 03 2015 - 09:44:50 CDT)
• Mail reg Parameter file
  • Fotis Baltoumas (Mon Apr 20 2015 - 08:48:36 CDT)
  • Vidhya Sankar (Mon Apr 20 2015 - 07:57:34 CDT)
• mail reg parameters
  • sena (Fri Dec 25 2015 - 22:29:17 CST)
  • Vidhya Sankar (Fri Dec 25 2015 - 20:51:57 CST)
• making dipeptides with psfgen - CMAP terms?
  • Brian Radak (Tue Feb 17 2015 - 16:10:49 CST)
  • Jim Phillips (Tue Feb 17 2015 - 13:53:04 CST)
  • Brian Radak (Tue Feb 17 2015 - 12:06:54 CST)
  • Brian Radak (Tue Feb 17 2015 - 09:42:59 CST)
• Making NAMD aware of Tcl packages?
  • Brian Radak (Thu Mar 31 2016 - 16:12:20 CDT)
  • Giacomo Fiorin (Thu Mar 31 2016 - 11:36:20 CDT)
  • Brian Radak (Thu Mar 31 2016 - 10:20:42 CDT)
  • Giacomo Fiorin (Thu Mar 31 2016 - 10:17:30 CDT)
  • Brian Radak (Thu Mar 31 2016 - 10:11:07 CDT)
• Manganese force field
  • Taejin Kim (Fri Mar 18 2016 - 14:07:35 CDT)
• Martini CG models parameters errors
  • Mahad Gatti (Wed Sep 28 2016 - 05:40:51 CDT)
  • Fotis Baltoumas (Mon Sep 26 2016 - 14:58:52 CDT)
  • Vermaas, Joshua (Mon Sep 26 2016 - 10:48:56 CDT)
  • Mahad Gatti (Mon Sep 26 2016 - 04:01:32 CDT)
  • Vermaas, Joshua (Thu Sep 22 2016 - 10:36:40 CDT)
  • Mahad Gatti (Thu Sep 22 2016 - 10:07:34 CDT)
• Martini polarizable water topology and/or psf file
  • Sourav Ray (Thu May 12 2016 - 17:30:57 CDT)
• maximum coordinate is negative for z
  • faride badalkhani (Fri Apr 01 2016 - 12:23:38 CDT)
  • Maxim Belkin (Fri Apr 01 2016 - 12:21:05 CDT)
  • Aron Broom (Fri Apr 01 2016 - 12:16:52 CDT)
  • faride badalkhani (Fri Apr 01 2016 - 12:14:17 CDT)
• Maximum dihedral angle
  • Mahdi Tavakol (Sun Jul 31 2016 - 03:19:16 CDT)
• Maximum limit for "run" parameter
  • Jim Phillips (Wed Feb 18 2015 - 17:49:41 CST)
  • Axel Kohlmeyer (Wed Feb 18 2015 - 17:15:30 CST)
  • Jim Phillips (Wed Feb 18 2015 - 17:10:36 CST)
  • Mitul Saha (Tue Feb 17 2015 - 18:50:38 CST)
• MD Simulation of accelerated MD using GPU
  • jeevan gc (Fri Oct 16 2015 - 08:25:29 CDT)
  • jeevan gc (Wed Oct 14 2015 - 16:21:36 CDT)
  • Kenneth Huang (Mon Oct 12 2015 - 20:09:26 CDT)
  • Brian Radak (Mon Oct 12 2015 - 20:01:24 CDT)
  • jeevan gc (Mon Oct 12 2015 - 17:19:15 CDT)
  • jeevan gc (Mon Oct 12 2015 - 17:07:39 CDT)
• MD simulation of Linear Molecules (like 2-butyne£©
  • ԬС¾§ (Mon Dec 21 2015 - 20:30:09 CST)
  • Jim Phillips (Sat Dec 19 2015 - 21:53:01 CST)
  • ԬС¾§ (Fri Dec 18 2015 - 20:26:26 CST)
• MD trajectory analysis
  • Deng, Jinxia (Nancy) (Thu Jan 28 2016 - 13:02:14 CST)
• MDFF based on known EM maps
  • Ryan McGreevy (Tue Jun 28 2016 - 12:20:46 CDT)
  • giulia palermo (Tue Jun 28 2016 - 12:08:12 CDT)
• MDFF with two symmetry groups
  • Benjamin.Haberl_at_physik.uni-muenchen.de (Tue May 17 2016 - 14:48:19 CDT)
• Message about timing in *log file.
  • Jim Phillips (Mon Feb 02 2015 - 00:15:09 CST)
  • Dawid das (Sun Feb 01 2015 - 05:05:39 CST)
• metadynamics and pmf file
  • Giacomo Fiorin (Tue Jul 05 2016 - 16:29:10 CDT)
  • Stefano Guglielmo (Mon Jul 04 2016 - 19:43:23 CDT)
• Metadynamics simulation with Radius of Gyration and RMSD variation - 1
  • Giacomo Fiorin (Mon Apr 11 2016 - 10:02:45 CDT)
  • Sourav Ray (Sat Apr 09 2016 - 12:03:36 CDT)
• Metadynamics simulation with Radius of Gyration and RMSD variation - 2
  • Sourav Ray (Mon Apr 11 2016 - 11:10:57 CDT)
  • Giacomo Fiorin (Mon Apr 11 2016 - 10:08:14 CDT)
  • Sourav Ray (Sat Apr 09 2016 - 14:53:15 CDT)
  • Sourav Ray (Sat Apr 09 2016 - 12:11:53 CDT)
• Metadynamics: writeHillsTrajectory
  • Chola Regmi (Thu Jul 30 2015 - 16:48:15 CDT)
  • Chola Regmi (Thu Jul 30 2015 - 16:37:53 CDT)
• Minimisation goes to several values
  • Kevin C Chan (Thu Jun 25 2015 - 11:32:10 CDT)
• Minimisation not converged
  • Jérôme Hénin (Thu Apr 02 2015 - 06:52:36 CDT)
  • Kevin C Chan (Wed Apr 01 2015 - 22:26:19 CDT)
  • Jérôme Hénin (Wed Apr 01 2015 - 02:14:12 CDT)
  • Kevin C Chan (Wed Apr 01 2015 - 01:20:37 CDT)
• Minimization error
  • Vermaas, Joshua (Wed Dec 07 2016 - 11:36:44 CST)
  • Santanu Santra (Tue Dec 06 2016 - 23:00:04 CST)
• Minimization failing on one machine only
  • David Hardy (Fri Oct 21 2016 - 15:16:47 CDT)
  • Chris Goedde (Fri Oct 21 2016 - 14:11:42 CDT)
  • Ajasja LjubetiÄ� (Sat Oct 15 2016 - 01:50:29 CDT)
  • Chris Goedde (Fri Oct 14 2016 - 15:34:10 CDT)
• Minimization without MD
  • Ajasja LjubetiÄ� (Thu Jul 16 2015 - 17:18:20 CDT)
  • Simon Kit Sang Chu (Thu Jul 16 2015 - 15:37:39 CDT)
  • Simon Kit Sang Chu (Thu Jul 16 2015 - 16:21:40 CDT)
• minimization, heating, equilibration and production run in one script
  • Dhiraj Srivastava (Thu Apr 28 2016 - 10:05:55 CDT)
• Missing atom type for hydroperoxide
  • Radak, Brian K (Tue Jun 14 2016 - 12:58:25 CDT)
  • Jean-François Fabre (Tue Jun 14 2016 - 10:48:55 CDT)
• Mixing all_36_cgenff with all_36_prot
  • Tristan Croll (Mon Mar 28 2016 - 14:36:33 CDT)
  • Francesco Pietra (Sat Mar 26 2016 - 13:02:27 CDT)
• model.conf
  • Mai Aamer (Thu Jul 09 2015 - 17:09:01 CDT)
• modify input file for production phase MD
  • Branko (Fri Dec 04 2015 - 11:50:53 CST)
  • Deng, Jinxia (Nancy) (Fri Dec 04 2015 - 11:31:26 CST)
• Modifying equilibrium distance for a specific region of carbon nanotube in the parameter file
  • jashnvareh 1395 (Mon Dec 26 2016 - 08:30:59 CST)
• Modifying equilibrium distance for part of carbon nanotubes in parameter file
  • jashnvareh 1395 (Tue Dec 27 2016 - 02:55:42 CST)
• Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file
  • zeynab mohamad hoseyni (Sun Dec 25 2016 - 12:46:28 CST)
  • Abhishek TYAGI (Mon Dec 26 2016 - 08:59:58 CST)
  • zeynab hoseyni (Sun Dec 25 2016 - 12:51:46 CST)
• More FEP using separated topologies
  • Jérôme Hénin (Fri May 27 2016 - 23:00:20 CDT)
  • David Huggins (Fri May 27 2016 - 15:21:01 CDT)
• Msd
  • Radak, Brian K (Mon Jul 25 2016 - 12:48:13 CDT)
  • Mahdiye Azadpour (Sat Jul 23 2016 - 23:21:09 CDT)
• much larger diameter of ssDNA,
  • Aliasghar Alizadeh-Mojarad (Sat Jun 04 2016 - 04:22:41 CDT)
• multicore vs ibverbs
  • Gianluca Interlandi (Sat Jul 04 2015 - 12:52:40 CDT)
• Multicore-CUDA NAMD output hangs
  • Mitchell Gleed (Tue Mar 03 2015 - 10:34:20 CST)
  • Mitchell Gleed (Wed Feb 18 2015 - 15:12:21 CST)
• multipld .dcd analysis by VMD
  • Zhao Qin (Thu Jan 21 2016 - 12:40:25 CST)
  • Deng, Jinxia (Nancy) (Wed Jan 20 2016 - 13:53:21 CST)
• Multiple Dihedral in CHARMM parameters
  • Jérôme Hénin (Mon Jan 19 2015 - 04:57:07 CST)
  • JAVAD NOROOZI (Mon Jan 19 2015 - 01:19:37 CST)
• Multiple NAMD calculations on windows
  • Mai Aamer (Mon Nov 02 2015 - 16:40:06 CST)
• multiple output .dcd files??
  • Deng, Jinxia (Nancy) (Tue Dec 08 2015 - 08:43:02 CST)
  • Jim Phillips (Mon Dec 07 2015 - 16:43:12 CST)
  • Deng, Jinxia (Nancy) (Mon Dec 07 2015 - 14:56:53 CST)
• multiple run commands freeze when using MTS?
  • Brian Radak (Thu Nov 03 2016 - 15:45:40 CDT)
• Multiple Tcouple
  • JAVAD NOROOZI (Mon Jan 12 2015 - 03:35:01 CST)
• Multiple tcouple (Nonequilbirium molecular dynamics)
  • JAVAD NOROOZI (Tue Jan 06 2015 - 03:51:07 CST)
• multiple thermostats in adaptive tempering
  • Igaev, Maxim (Wed Feb 18 2015 - 11:20:52 CST)
• Multiple-replicas metadynamics / Well-tempered metadynamics
  • Giacomo Fiorin (Fri Jun 12 2015 - 14:21:15 CDT)
  • Yerko Escalona (Fri Jun 12 2015 - 14:15:39 CDT)
• My Plight
  • Syed Kashif Zafar (Wed Feb 18 2015 - 18:28:19 CST)
• NAMD
  • Brian Radak (Wed Mar 25 2015 - 11:35:27 CDT)
  • Subbarao Kanchi (Tue Mar 24 2015 - 01:48:39 CDT)
• NAMD "unable to find improper parameters"
  • Asma El-Magboub (Thu Jan 22 2015 - 21:32:09 CST)
• namd "WARNING: ignoring command" problem
  • Shambo Hore (Tue May 31 2016 - 12:11:35 CDT)
• NAMD - wrap atoms, not center of mass
  • Josh Vermaas (Fri Oct 16 2015 - 10:48:35 CDT)
  • Sourav Ray (Fri Oct 16 2015 - 10:27:09 CDT)
  • Stanislav Q=A0imko?= (Fri Oct 16 2015 - 10:20:28 CDT)
• NAMD 2.10 Building from Source
  • Giacomo Fiorin (Thu Jul 09 2015 - 16:05:02 CDT)
  • Kumar, Amit (Thu Jul 09 2015 - 16:02:07 CDT)
  • Giacomo Fiorin (Thu Jul 09 2015 - 15:45:32 CDT)
  • Kumar, Amit (Thu Jul 09 2015 - 15:28:07 CDT)
• namd 2.10 crashes when using more than 1 CPU for FEP simulation
  • Tien Huynh (Tue Oct 27 2015 - 21:58:14 CDT)
• NAMD 2.10 on IBM POWER(8) machines
  • Baker D.J. (Thu Jun 25 2015 - 07:00:49 CDT)
• NAMD 2.10 with multiple-replica support
  • Jim Phillips (Mon Feb 02 2015 - 00:11:26 CST)
  • Branko (Sat Jan 31 2015 - 14:06:06 CST)
• NAMD 2.10 with MVAPICH2-GDR?
  • Jim Phillips (Fri Jan 16 2015 - 16:54:35 CST)
  • David Chin (Thu Jan 15 2015 - 08:41:04 CST)
• NAMD 2.11 CUDA forces IBverbs
  • Jim Phillips (Fri Nov 13 2015 - 08:31:50 CST)
  • Norman Geist (Fri Nov 13 2015 - 06:00:18 CST)
• NAMD 2.11 CUDA freezes on windows 8
  • Ajasja LjubetiÄ� (Wed Mar 16 2016 - 13:08:59 CDT)
• NAMD 2.11 on CRAY XK with CPU+GPU
  • P.-L. Chau (Wed Nov 30 2016 - 17:47:07 CST)
• NAMD 2.11 released
  • Jeff Comer (Wed Jan 06 2016 - 08:35:12 CST)
  • JC Gumbart (Tue Jan 05 2016 - 16:16:03 CST)
  • Ajasja LjubetiÄ� (Thu Dec 24 2015 - 02:35:34 CST)
  • Francesco Pietra (Thu Dec 24 2015 - 01:22:37 CST)
  • Jeff Comer (Wed Dec 23 2015 - 19:38:21 CST)
  • Jim Phillips (Tue Dec 22 2015 - 21:37:31 CST)
  • Branko (Tue Dec 22 2015 - 16:19:37 CST)
  • Jim Phillips (Tue Dec 22 2015 - 10:38:50 CST)
• NAMD 2.11b1 multicore CUDA: Incorrect number of exclusions
  • Jim Phillips (Fri Dec 04 2015 - 16:52:30 CST)
  • Jeff Comer (Thu Dec 03 2015 - 14:20:42 CST)
• NAMD 2.11b1 released
  • Jim Phillips (Fri Nov 27 2015 - 20:10:42 CST)
  • Norman Geist (Fri Nov 27 2015 - 01:22:44 CST)
  • sunyeping (Thu Nov 26 2015 - 23:26:33 CST)
  • Jim Phillips (Thu Nov 12 2015 - 22:41:32 CST)
  • sunyeping (Thu Nov 12 2015 - 20:29:18 CST)
  • Tien Huynh (Thu Nov 12 2015 - 11:24:00 CST)
  • Jim Phillips (Thu Nov 12 2015 - 11:15:27 CST)
  • Jim Phillips (Thu Nov 12 2015 - 06:55:42 CST)
  • sunyeping (Thu Nov 12 2015 - 02:39:43 CST)
  • Tristan Croll (Wed Nov 11 2015 - 20:11:00 CST)
  • Jeff Comer (Tue Nov 10 2015 - 13:18:06 CST)
  • Tien Huynh (Tue Nov 10 2015 - 11:10:25 CST)
  • Jim Phillips (Tue Nov 10 2015 - 09:39:44 CST)
• NAMD 2.11b2 released
  • Jim Phillips (Sun Dec 06 2015 - 22:01:09 CST)
• NAMD 2.12 released
  • Francesco Pietra (Tue Dec 27 2016 - 01:40:40 CST)
  • Angelo Rossi (Mon Dec 26 2016 - 15:53:42 CST)
  • Francesco Pietra (Mon Dec 26 2016 - 04:17:27 CST)
  • Jim Phillips (Fri Dec 23 2016 - 12:57:34 CST)
• NAMD 2.12b1 released
  • Jim Phillips (Thu Nov 03 2016 - 17:06:48 CDT)
• NAMD Anisotropic pressure control
  • Mahdi Tavakol (Fri Sep 18 2015 - 11:51:29 CDT)
  • Fotis Baltoumas (Fri Sep 18 2015 - 09:50:14 CDT)
  • Jérôme Hénin (Fri Sep 18 2015 - 09:44:50 CDT)
  • Mahdi Tavakol (Fri Sep 18 2015 - 08:50:04 CDT)
• NAMD breaks with wrong timestep
  • Götz, Alexander (Sat Oct 22 2016 - 10:19:42 CDT)
  • Brian Radak (Fri Oct 21 2016 - 15:20:19 CDT)
  • Axel Kohlmeyer (Fri Oct 21 2016 - 10:54:00 CDT)
  • Vermaas, Joshua (Fri Oct 21 2016 - 10:49:22 CDT)
  • Brian Radak (Fri Oct 21 2016 - 10:41:46 CDT)
  • Götz, Alexander (Fri Oct 21 2016 - 08:23:33 CDT)
• NAMD Developer Workshop: May 26-27 in Chicago, IL
  • Jodi Ann Hadden (Fri Apr 15 2016 - 13:14:22 CDT)
  • Jodi Ann Hadden (Wed Mar 09 2016 - 14:31:56 CST)
• NAMD Energies
  • Peter Freddolino (Wed Dec 14 2016 - 13:54:52 CST)
  • Giacomo Fiorin (Wed Dec 14 2016 - 13:53:02 CST)
  • Radak, Brian K (Wed Dec 14 2016 - 13:42:36 CST)
  • Giacomo Fiorin (Wed Dec 14 2016 - 13:47:16 CST)
  • Chris Goedde (Wed Dec 14 2016 - 13:13:01 CST)
• NAMD Equil Config
  • Jackson Cavett (Thu Sep 22 2016 - 07:24:53 CDT)
• NAMD equilibrium step
  • Brian Radak (Tue Aug 23 2016 - 13:55:47 CDT)
  • d.ronika_at_iitg.ernet.in (Mon Aug 22 2016 - 00:34:01 CDT)
• NAMD Execution Error
  • Vermaas, Joshua (Mon Oct 31 2016 - 14:09:02 CDT)
  • Oscar Bastidas (Sun Oct 30 2016 - 18:46:19 CDT)
• NAMD GPU+ibverbs on multiple nodes: timeout problems
  • Robert Sawko (Thu Nov 17 2016 - 05:51:21 CST)
• NAMD How to calculate ns/day
  • Abhishek TYAGI (Thu Dec 08 2016 - 01:38:04 CST)
  • Shikha Sharma (Wed Dec 07 2016 - 23:01:44 CST)
  • Ajasja LjubetiÄ� (Wed Dec 07 2016 - 16:59:45 CST)
  • Jan Fredin (Wed Dec 07 2016 - 16:02:16 CST)
• NAMD hybrid configuration: Atoms moving too fast error
  • Puneet Singh (Mon Jul 27 2015 - 06:41:38 CDT)
• namd ibverbs
  • Kevin C Chan (Thu Jul 23 2015 - 05:38:49 CDT)
  • Gianluca Interlandi (Thu Jul 16 2015 - 17:09:40 CDT)
  • Maxime Boissonneault (Thu Jul 16 2015 - 16:43:06 CDT)
  • Gianluca Interlandi (Thu Jul 16 2015 - 16:20:34 CDT)
  • Gianluca Interlandi (Thu Jul 16 2015 - 16:06:37 CDT)
  • Maxime Boissonneault (Thu Jul 16 2015 - 15:59:19 CDT)
  • Gianluca Interlandi (Thu Jul 16 2015 - 15:56:14 CDT)
  • Maxime Boissonneault (Thu Jul 16 2015 - 15:50:36 CDT)
  • Gianluca Interlandi (Thu Jul 16 2015 - 15:31:34 CDT)
  • Maxime Boissonneault (Thu Jul 16 2015 - 12:59:50 CDT)
• NAMD Implicit GB Parameters
  • Samuel Bowerman (Mon Feb 01 2016 - 12:41:03 CST)
• NAMD installation
  • Puneet (Sat Nov 26 2016 - 01:41:14 CST)
• namd leaves zombie processes on nodes?
  • JC Gumbart (Mon May 23 2016 - 10:01:45 CDT)
• NAMD nightly build compilation
  • Vlad Cojocaru (Fri May 08 2015 - 04:11:52 CDT)
  • Vlad Cojocaru (Fri May 08 2015 - 03:12:16 CDT)
  • Jérôme Hénin (Thu May 07 2015 - 09:11:53 CDT)
  • Vlad Cojocaru (Thu May 07 2015 - 08:40:00 CDT)
  • Vlad Cojocaru (Tue Mar 24 2015 - 12:51:47 CDT)
  • Vlad Cojocaru (Tue Mar 24 2015 - 12:07:03 CDT)
• NAMD Non-features
  • Axel Kohlmeyer (Wed Jan 21 2015 - 15:54:49 CST)
  • JAVAD NOROOZI (Wed Jan 21 2015 - 15:24:43 CST)
  • Jeff Comer (Wed Jan 21 2015 - 09:35:27 CST)
  • Axel Kohlmeyer (Wed Jan 21 2015 - 05:31:57 CST)
  • Axel Kohlmeyer (Wed Jan 21 2015 - 05:24:41 CST)
  • Jérôme Hénin (Wed Jan 21 2015 - 04:38:17 CST)
  • JAVAD NOROOZI (Wed Jan 21 2015 - 01:54:50 CST)
• NAMD on TACC (Darter)
  • Chitrak Gupta (Thu Dec 10 2015 - 17:35:15 CST)
  • Jim Phillips (Thu Dec 10 2015 - 10:03:56 CST)
  • Chitrak Gupta (Wed Dec 09 2015 - 07:49:53 CST)
  • Jim Phillips (Tue Dec 08 2015 - 22:41:19 CST)
  • Chitrak Gupta (Tue Dec 08 2015 - 22:19:12 CST)
  • Jim Phillips (Tue Dec 08 2015 - 22:15:15 CST)
  • Chitrak Gupta (Tue Dec 08 2015 - 18:16:29 CST)
• namd on Windows 10
  • Kostas Malavazos (Thu Feb 04 2016 - 14:14:09 CST)
  • Branko (Thu Feb 04 2016 - 12:24:14 CST)
• NAMD parallelisation / patch grid
  • P.-L. Chau (Tue Dec 27 2016 - 04:37:15 CST)
• NAMD Question: Generating ensemble of structures
  • Brian Radak (Thu Sep 01 2016 - 08:44:10 CDT)
  • Oscar Bastidas (Wed Aug 31 2016 - 00:52:20 CDT)
• NAMD Question: How to run on 2-chain system
  • Oscar Bastidas (Wed Oct 26 2016 - 20:08:18 CDT)
• NAMD Question: NAMD Message "364"-What does it mean?
  • Oscar Bastidas (Thu Oct 27 2016 - 03:34:17 CDT)
• NAMD Recipe for Success with GPUs!
  • MARK (Thu May 05 2016 - 11:35:42 CDT)
• NAMD related theoretical questions
  • Kostas Malavazos (Wed Jul 20 2016 - 12:33:11 CDT)
• NAMD Repeated failures launching tasks
  • Kumar, Amit (Mon May 11 2015 - 13:47:40 CDT)
• NAMD running on a Cluster of Ubuntu Linux
  • Marisol Oswald (Sun Oct 09 2016 - 18:37:55 CDT)
• namd simulation
  • Abhishek TYAGI (Thu Mar 05 2015 - 04:46:29 CST)
  • Urszula Uciechowska (Tue Mar 03 2015 - 08:20:25 CST)
• namd simulation with TIP5P
  • Monika Madhavi (Fri Oct 02 2015 - 01:16:41 CDT)
  • Shanshan Wu (Tue Feb 03 2015 - 18:36:34 CST)
• NAMD slows at startup phase 1 smp problem
  • Jim Phillips (Thu Jan 15 2015 - 14:20:58 CST)
  • Alexander Tzanov (Thu Jan 15 2015 - 10:05:16 CST)
  • Jim Phillips (Wed Jan 14 2015 - 17:16:19 CST)
  • Ryan Gordon (Mon Jan 12 2015 - 12:24:31 CST)
• NAMD Source, Molecule.c , Mass Critaria
  • JAVAD NOROOZI (Wed Feb 18 2015 - 12:55:25 CST)
• NAMD survey starting
  • Jim Phillips (Tue Mar 15 2016 - 13:34:00 CDT)
• NAMD warning: Randomization of stack point is turned on in kernal, thread migration may not work!
  • Axel Kohlmeyer (Thu Mar 05 2015 - 11:40:42 CST)
  • Yarrow Madrona (Thu Mar 05 2015 - 10:58:11 CST)
• namd-1: Fatal Error: Unable to Open CHARMM Parameter File
  • Akshata Rudrapatna (Thu Feb 05 2015 - 06:32:40 CST)
  • Jim Phillips (Tue Feb 03 2015 - 18:48:35 CST)
  • Branko (Tue Feb 03 2015 - 16:14:32 CST)
  • David Hardy (Tue Feb 03 2015 - 15:54:49 CST)
  • David Hardy (Tue Feb 03 2015 - 15:32:57 CST)
  • Akshata Rudrapatna (Tue Feb 03 2015 - 14:43:55 CST)
• namd-1: Simulation Terminating Early
  • Akshata Rudrapatna (Mon Feb 09 2015 - 20:54:55 CST)
  • Jim Phillips (Mon Feb 09 2015 - 13:33:09 CST)
  • Norman Geist (Mon Feb 09 2015 - 03:09:57 CST)
  • Akshata Rudrapatna (Sat Feb 07 2015 - 15:06:33 CST)
• namd-I: How to assume the thickness of membrane when applying external Electric field ?
  • Adelman, Joshua Lev (Tue Jan 13 2015 - 08:36:01 CST)
  • Axel Kohlmeyer (Tue Jan 13 2015 - 07:21:49 CST)
  • Vy Phan (Tue Jan 13 2015 - 00:20:31 CST)
• namd-l digest V1 #1668
  • Bennion, Brian (Mon May 04 2015 - 10:42:12 CDT)
  • Ern Seang Ong (Sun May 03 2015 - 23:14:28 CDT)
• namd-l digest V1 #1726
  • nader zabarjad (Sun Aug 02 2015 - 10:41:55 CDT)
• NAMD-Replica exchange
  • ZOU Changling (Wed May 27 2015 - 04:31:28 CDT)
• NAMD/VMD: generating psf for Abeta, ACE patch
  • Tristan Croll (Tue Sep 15 2015 - 17:53:20 CDT)
  • Mona Habibi (Tue Sep 15 2015 - 15:31:37 CDT)
• namd2 or charmrun ++local ?
  • Giacomo Fiorin (Fri Jun 17 2016 - 13:18:48 CDT)
  • Laura Joana (Fri Jun 17 2016 - 11:35:05 CDT)
• namd2 seg fault NAMD_2.11_Source Linux-x86_64-g++
  • Doug Stetner (Tue Jul 12 2016 - 22:51:40 CDT)
• NAMD2.11 DCD HEADER PROBLEM
  • Marco Sant (Wed Sep 14 2016 - 06:37:02 CDT)
  • Sourav Ray (Wed Sep 14 2016 - 06:10:20 CDT)
  • Marco Sant (Wed Sep 14 2016 - 05:35:31 CDT)
• NAMD2.11 source code not compiling
  • Madhulika Gupta (Fri Nov 20 2015 - 01:20:05 CST)
  • Madhulika Gupta (Wed Nov 18 2015 - 10:31:55 CST)
  • Jim Phillips (Wed Nov 18 2015 - 09:21:13 CST)
  • Madhulika Gupta (Wed Nov 18 2015 - 02:47:38 CST)
• NAMD2.12b1 and CUDA
  • Jeff Comer (Thu Nov 10 2016 - 17:23:04 CST)
  • Jim Phillips (Thu Nov 10 2016 - 16:20:31 CST)
  • Giacomo Fiorin (Thu Nov 10 2016 - 11:09:04 CST)
  • Jeff Comer (Thu Nov 10 2016 - 09:09:50 CST)
• namd2.22b CUDA Phi
  • Jim Phillips (Sat Dec 05 2015 - 08:50:57 CST)
  • Francesco Pietra (Sat Dec 05 2015 - 01:06:49 CST)
• NAMD_2.12b1 build on Cray XC40 is failing
  • Ianni, James C CTR USARMY RDECOM ARL (US) (Mon Dec 12 2016 - 14:35:32 CST)
• NAMD_CUDA
  • Jim Phillips (Tue Dec 20 2016 - 23:30:12 CST)
  • Sana Saeed (Thu Dec 15 2016 - 20:23:18 CST)
• namdenergy and bigdcd
  • Grant Schauer (Thu Jun 02 2016 - 23:58:23 CDT)
• NBFIX parameters for Calcium ion
  • Azadeh Alavi (Thu Jun 09 2016 - 04:49:04 CDT)
• Need help with TCL script
  • Vermaas, Joshua (Mon Nov 14 2016 - 14:17:08 CST)
  • Nicholus Bhattacharjee (Mon Nov 14 2016 - 13:10:13 CST)
• NetworkView plugin for the non-namd trajectories
  • Vlad Cojocaru (Tue Apr 14 2015 - 10:13:47 CDT)
  • James Starlight (Tue Apr 14 2015 - 09:34:57 CDT)
• New web server for setup of membrane simulation systems
  • Chen, Po-chia (Sun Feb 08 2015 - 06:17:35 CST)
• NH4+ params
  • Mikhail Suyetin (Sat Oct 24 2015 - 11:56:15 CDT)
  • Thomas Albers (Sat Oct 24 2015 - 09:26:17 CDT)
  • Mikhail Suyetin (Fri Oct 23 2015 - 16:38:55 CDT)
• No parameter for ribose ring, Charmm 27
  • JC Gumbart (Mon May 30 2016 - 07:19:44 CDT)
  • Benjamin Hill (Sun May 29 2016 - 11:12:07 CDT)
  • Lennart Nilsson (Fri May 27 2016 - 15:28:43 CDT)
  • JC Gumbart (Fri May 27 2016 - 14:14:17 CDT)
  • Benjamin Hill (Fri May 27 2016 - 05:51:40 CDT)
  • Lennart Nilsson (Fri May 27 2016 - 05:42:02 CDT)
  • JC Gumbart (Thu May 26 2016 - 18:42:52 CDT)
  • Benjamin Hill (Thu May 26 2016 - 17:18:43 CDT)
• no response from mail list
  • Giacomo Fiorin (Tue Nov 01 2016 - 09:36:49 CDT)
  • Peter Freddolino (Mon Oct 31 2016 - 20:36:12 CDT)
  • sunyeping (Mon Oct 31 2016 - 20:32:18 CDT)
  • Oscar Bastidas (Mon Oct 31 2016 - 20:16:50 CDT)
  • sunyeping (Mon Oct 31 2016 - 19:23:09 CDT)
• No steric clashes, still not minimizing
  • Francesco Pietra (Wed Mar 11 2015 - 06:38:40 CDT)
• node file for NAMD
  • Sourav Ray (Sat Sep 12 2015 - 01:13:32 CDT)
  • Sourav Ray (Sat Sep 12 2015 - 01:11:30 CDT)
  • Abhishek Tyagi (Fri Sep 11 2015 - 22:55:16 CDT)
  • Parag Khuraswar (Fri Sep 11 2015 - 08:02:54 CDT)
  • Parag Khuraswar (Tue Sep 01 2015 - 23:28:06 CDT)
• Non respect of sequence of commands in command file
  • Josh Vermaas (Fri Feb 12 2016 - 11:04:28 CST)
  • R. Charbel MAROUN (Fri Feb 12 2016 - 05:11:39 CST)
• non-bonded energy of individual atoms
  • Bärwinkel, Tom (Fri Jun 12 2015 - 09:17:46 CDT)
• non-standard solvants
  • faride badalkhani (Wed Jun 01 2016 - 11:55:28 CDT)
• not able to view trajectory in VMD
  • Axel Kohlmeyer (Fri Jun 26 2015 - 13:04:20 CDT)
  • Lara rajam (Fri Jun 26 2015 - 12:55:01 CDT)
• NPT with graphene
  • Jeff Comer (Tue Nov 15 2016 - 08:10:57 CST)
  • Richard Overstreet (Mon Nov 14 2016 - 15:03:43 CST)
  • Richard Overstreet (Mon Nov 14 2016 - 11:29:27 CST)
• number of close contacts and contact area
  • Abhishek TYAGI (Sun Mar 22 2015 - 04:37:57 CDT)
• Number of pdb and psf atoms are not the same!
  • Francesco Pietra (Wed Dec 16 2015 - 09:23:41 CST)
• NVE simulations in NAMD - the right choice of timesteps and parameters
  • Brian Radak (Tue Nov 29 2016 - 12:52:15 CST)
  • Vlad Cojocaru (Tue Nov 29 2016 - 11:09:40 CST)
  • Axel Kohlmeyer (Tue Nov 29 2016 - 10:16:11 CST)
  • Brian Radak (Tue Nov 29 2016 - 10:04:53 CST)
  • Felipe Merino (Tue Nov 29 2016 - 07:03:45 CST)
  • Harish Srinivasan (Tue Nov 29 2016 - 04:54:32 CST)
• NVT and NPT simulationd
  • faride badalkhani (Thu Dec 15 2016 - 14:38:24 CST)
  • faride badalkhani (Wed Dec 14 2016 - 12:14:08 CST)
  • faride badalkhani (Wed Dec 14 2016 - 11:09:40 CST)
  • faride badalkhani (Tue Dec 13 2016 - 23:50:53 CST)
• nvt input file
  • Branko (Fri Jul 17 2015 - 08:44:24 CDT)
  • Urszula Uciechowska (Fri Jul 17 2015 - 08:25:21 CDT)
• nvt run error
  • Felipe Merino (Tue Jul 21 2015 - 03:28:40 CDT)
  • Urszula Uciechowska (Tue Jul 21 2015 - 02:54:10 CDT)
• Occasional performance slow down using NAMD with Xeon Phi
  • Mattia Felice Palermo (Fri Apr 01 2016 - 09:53:37 CDT)
• On-the-fly modification of tclforces script?
  • John Stone (Fri Nov 13 2015 - 20:17:53 CST)
  • Tristan Croll (Fri Nov 13 2015 - 19:28:39 CST)
  • John Stone (Fri Nov 13 2015 - 19:05:34 CST)
  • Tristan Croll (Fri Nov 13 2015 - 18:14:28 CST)
  • Tristan Croll (Fri Nov 13 2015 - 16:48:21 CST)
  • Tristan Croll (Tue Nov 10 2015 - 16:03:38 CST)
  • Jim Phillips (Tue Nov 10 2015 - 09:53:42 CST)
  • Tristan Croll (Tue Nov 10 2015 - 04:27:19 CST)
  • Tristan Croll (Tue Nov 10 2015 - 03:01:19 CST)
• on-the-fly parameter introspection
  • Jim Phillips (Mon Feb 09 2015 - 13:18:02 CST)
  • Brian Radak (Thu Feb 05 2015 - 13:54:51 CST)
• OpenGL Display Window, "Key 2", SMD with NAMD
  • Zeinab Emami (Sun Dec 20 2015 - 11:57:52 CST)
• Opinions on Haptic Feedback Devices with NAMD/VMD
  • Axel Kohlmeyer (Fri Mar 25 2016 - 08:52:33 CDT)
  • Ben Fritch (Fri Mar 25 2016 - 08:37:31 CDT)
  • Ben Fritch (Thu Mar 24 2016 - 14:29:02 CDT)
• OPLS force field in NAMD
  • Peter Freddolino (Sat Jun 20 2015 - 22:20:00 CDT)
  • AnkiReddy katha (Sat Jun 20 2015 - 16:17:31 CDT)
  • farzad kiani (Sat Jun 20 2015 - 15:28:39 CDT)
  • oguz gurbulak (Sat Jun 20 2015 - 11:43:02 CDT)
• OPLS force-field in NAMD
  • AnkiReddy katha (Thu May 07 2015 - 02:12:03 CDT)
• OPLS in NAMD
  • AnkiReddy katha (Thu May 07 2015 - 04:40:47 CDT)
  • AnkiReddy katha (Thu May 07 2015 - 04:17:23 CDT)
• OPLS/AA force field
  • oguz gurbulak (Wed Aug 05 2015 - 09:00:01 CDT)
• OPLSAA to CHARMM
  • Francesco Pietra (Fri Nov 06 2015 - 00:59:02 CST)
  • Francesco Pietra (Thu Nov 05 2015 - 10:21:42 CST)
• optimising namd ibverb runs
  • Jim Phillips (Wed May 20 2015 - 12:28:37 CDT)
  • Aaron Larsen (Mon May 18 2015 - 08:48:18 CDT)
  • Norman Geist (Mon May 18 2015 - 08:16:11 CDT)
  • Thanassis Silis (Mon May 18 2015 - 06:48:03 CDT)
• output files are not stored when running namd-2.10 ibverbs
  • Thanassis Silis (Fri May 08 2015 - 05:07:50 CDT)
  • Thanassis Silis (Thu May 07 2015 - 10:29:26 CDT)
• Output temperature not agreeing with tcouple temperature
  • Karson Bader (Fri May 13 2016 - 12:07:52 CDT)
• Output to a file
  • Mahdi Tavakol (Mon Oct 05 2015 - 01:31:55 CDT)
• OutputAccumulatedWork...where's the output?
  • Giacomo Fiorin (Mon Dec 14 2015 - 13:32:17 CST)
  • Bryan Roessler (Mon Dec 14 2015 - 12:41:08 CST)
  • Giacomo Fiorin (Mon Dec 14 2015 - 10:55:36 CST)
  • Bryan Roessler (Sun Dec 13 2015 - 19:36:26 CST)
• Outward tilting which colvar to use
  • Jérôme Hénin (Thu Oct 01 2015 - 07:11:45 CDT)
  • Nicolas Martin (Thu Oct 01 2015 - 05:13:01 CDT)
• Overflow in LJcorrection?
  • Jim Phillips (Mon Dec 07 2015 - 16:35:27 CST)
  • Peter Freddolino (Sat Dec 05 2015 - 21:15:12 CST)
  • Peter Freddolino (Sat Dec 05 2015 - 17:57:22 CST)
  • Jason Swails (Sat Dec 05 2015 - 07:54:57 CST)
  • Brian Radak (Thu Dec 03 2015 - 16:26:19 CST)
  • Jason Swails (Thu Dec 03 2015 - 16:18:40 CST)
  • Brian Radak (Thu Dec 03 2015 - 16:15:59 CST)
  • Jason Swails (Thu Dec 03 2015 - 16:15:15 CST)
  • Brian Radak (Thu Dec 03 2015 - 16:10:59 CST)
  • Jason Swails (Thu Dec 03 2015 - 16:04:28 CST)
  • Brian Radak (Thu Dec 03 2015 - 15:59:27 CST)
  • Peter Freddolino (Thu Dec 03 2015 - 15:55:49 CST)
  • Jason Swails (Thu Dec 03 2015 - 15:55:30 CST)
  • Brian Radak (Thu Dec 03 2015 - 15:45:38 CST)
• Oxidized cysteine parameters for CHARMM36
  • Brian Radak (Fri Sep 30 2016 - 09:35:08 CDT)
  • Gergely Gyimesi (Fri Sep 30 2016 - 08:40:04 CDT)
• PACE Force Field and NAMD 2.10
  • Fotis Baltoumas (Thu Mar 12 2015 - 06:18:07 CDT)
• Packing of different system
  • Srijita Paul (Thu Apr 07 2016 - 10:51:32 CDT)
• Parallelization of External Program Forces
  • btreece_at_andrew.cmu.edu (Tue Mar 24 2015 - 18:49:26 CDT)
• parameterization of cations
  • faride badalkhani (Wed May 04 2016 - 11:28:59 CDT)
• parameterizing a new solvent
  • faride badalkhani (Tue May 03 2016 - 08:54:06 CDT)
• Parameterizing a novel peptide
  • Bryan Roessler (Tue Sep 15 2015 - 12:06:12 CDT)
  • Bennion, Brian (Tue Sep 15 2015 - 11:15:56 CDT)
  • Peter Freddolino (Mon Sep 14 2015 - 22:00:56 CDT)
  • Mayne, Christopher G (Mon Sep 14 2015 - 21:38:04 CDT)
  • Peter Freddolino (Mon Sep 14 2015 - 21:08:55 CDT)
  • Mayne, Christopher G (Mon Sep 14 2015 - 08:48:57 CDT)
  • Tomek StÄ™pniewski (Fri Sep 11 2015 - 18:16:27 CDT)
  • Bryan Roessler (Fri Sep 11 2015 - 17:14:05 CDT)
• Parameterizing residues of a polymer
  • faride badalkhani (Tue Mar 22 2016 - 12:47:57 CDT)
  • faride badalkhani (Tue Mar 22 2016 - 09:17:46 CDT)
• Parameters for determining run time
  • Oscar Bastidas (Tue Nov 08 2016 - 15:33:00 CST)
  • Peter Freddolino (Tue Nov 08 2016 - 15:10:04 CST)
  • Brian Radak (Tue Nov 08 2016 - 09:18:15 CST)
  • Vermaas, Joshua (Mon Nov 07 2016 - 18:43:03 CST)
  • Peter Freddolino (Mon Nov 07 2016 - 21:21:51 CST)
  • Richard Overstreet (Mon Nov 07 2016 - 19:12:59 CST)
  • Oscar Bastidas (Mon Nov 07 2016 - 16:10:34 CST)
• Parameters for HS(CH2)11NH2
  • Deng, Jinxia (Nancy) (Sun May 22 2016 - 14:03:37 CDT)
  • Natnael Doilicho (Fri May 20 2016 - 19:06:55 CDT)
• parameters problem in sulfated molecules
  • siddharth kamal (Wed Sep 02 2015 - 08:33:11 CDT)
  • Bennion, Brian (Tue Sep 01 2015 - 12:27:17 CDT)
  • Peter Freddolino (Tue Sep 01 2015 - 12:25:02 CDT)
  • Lara rajam (Tue Sep 01 2015 - 12:12:42 CDT)
• Particle Mesh Ewald with Martini
  • Sourav Ray (Mon May 16 2016 - 10:55:14 CDT)
• Patch-size Error (not like the other ones)
  • Norman Geist (Mon Jul 27 2015 - 02:32:33 CDT)
  • Jeffrey Potoff (Fri Jul 24 2015 - 13:38:52 CDT)
  • Merrill, Dante (Fri Jul 24 2015 - 13:14:28 CDT)
• Patches for namd 2.10
  • Ã…ke Sandgren (Fri Apr 24 2015 - 06:06:53 CDT)
  • Jérôme Hénin (Fri Apr 24 2015 - 04:38:39 CDT)
  • Ã…ke Sandgren (Fri Apr 24 2015 - 01:09:35 CDT)
• patching SO3 group to GAG
  • Lara rajam (Thu Sep 03 2015 - 22:45:34 CDT)
  • Peter Freddolino (Thu Sep 03 2015 - 20:36:45 CDT)
  • Lara rajam (Thu Sep 03 2015 - 19:13:21 CDT)
• PBC BUG in coorfile + pair interaction
  • Norman Geist (Thu Jan 21 2016 - 03:50:59 CST)
• PBC in lipid bilayer: receptor vs. ligand
  • R. Charbel MAROUN (Mon Feb 01 2016 - 10:39:06 CST)
  • Jeff Comer (Thu Jan 28 2016 - 12:38:45 CST)
  • R. Charbel MAROUN (Thu Jan 28 2016 - 11:59:14 CST)
  • Josh Vermaas (Thu Jan 28 2016 - 11:09:08 CST)
  • R. Charbel MAROUN (Thu Jan 28 2016 - 11:03:17 CST)
  • Josh Vermaas (Thu Jan 28 2016 - 09:43:21 CST)
  • R. Charbel MAROUN (Thu Jan 28 2016 - 05:26:33 CST)
  • Josh Vermaas (Wed Jan 27 2016 - 09:22:40 CST)
  • Ajasja LjubetiÄ� (Wed Jan 27 2016 - 09:21:11 CST)
  • R. Charbel MAROUN (Wed Jan 27 2016 - 07:54:34 CST)
• PDB File of Primary structure and Simulation
  • Emerson Macedo (Fri Sep 02 2016 - 11:19:18 CDT)
• pdb files to dcd
  • Josh Vermaas (Tue Nov 03 2015 - 14:40:53 CST)
  • Amitkumar Majhi (Tue Nov 03 2015 - 14:33:21 CST)
• performance drop during run
  • Chitrak Gupta (Fri Jul 29 2016 - 10:41:32 CDT)
• performance of GPU calculations
  • Hao Dong (Sun Nov 06 2016 - 21:11:40 CST)
• performance question
  • Norman Geist (Wed Apr 29 2015 - 03:24:46 CDT)
  • Thomas C. Bishop (Tue Apr 28 2015 - 15:53:42 CDT)
  • Bennion, Brian (Tue Apr 28 2015 - 15:06:13 CDT)
  • Thomas C. Bishop (Tue Apr 28 2015 - 14:32:16 CDT)
  • Norman Geist (Tue Apr 28 2015 - 02:51:06 CDT)
  • Thomas C. Bishop (Mon Apr 27 2015 - 15:54:10 CDT)
• Performing MD simulations with protein and halide ions (iodide, bromide, chloride)
  • Stojanoski, Vlatko (Sat Oct 17 2015 - 15:49:19 CDT)
  • Branko (Sat Oct 17 2015 - 15:42:11 CDT)
  • Stojanoski, Vlatko (Sat Oct 17 2015 - 15:31:43 CDT)
  • Branko (Sat Oct 17 2015 - 14:35:37 CDT)
  • Stojanoski, Vlatko (Sat Oct 17 2015 - 14:05:29 CDT)
• periodic boundary condition in XY, hard wall in Z - errors
  • Maxim Belkin (Tue Mar 15 2016 - 15:50:18 CDT)
  • Olya Kravchenko (Tue Mar 15 2016 - 14:48:58 CDT)
  • Maxim Belkin (Mon Mar 14 2016 - 11:24:35 CDT)
  • Olya Kravchenko (Fri Mar 11 2016 - 21:42:23 CST)
  • Maxim Belkin (Fri Mar 11 2016 - 15:31:50 CST)
  • Olya Kravchenko (Fri Mar 11 2016 - 14:57:55 CST)
  • Maxim Belkin (Fri Mar 11 2016 - 14:39:06 CST)
  • Maxim Belkin (Fri Mar 11 2016 - 14:34:35 CST)
  • Olya Kravchenko (Thu Mar 10 2016 - 20:01:12 CST)
  • Maxim Belkin (Thu Mar 10 2016 - 15:58:45 CST)
  • Olya Kravchenko (Thu Mar 10 2016 - 11:21:00 CST)
  • Olya Kravchenko (Wed Mar 09 2016 - 21:23:05 CST)
• Periodic Box Dimension (WrapAll is on)
  • JAVAD NOROOZI (Mon Jan 19 2015 - 23:55:19 CST)
• Permeation of liquid through Silicon Dioxide Crystal
  • Roshan Shrestha (Fri Jun 10 2016 - 07:30:00 CDT)
• Ph.D. positions available
  • Ivaylo Nikolaev Ivanov (Tue May 17 2016 - 10:10:41 CDT)
• PhD and postdoctoral positions in biomolecular simulation
  • Allison, Jane (Thu Jan 07 2016 - 19:01:29 CST)
• Phi vs GPU
  • Francesco Pietra (Wed Feb 04 2015 - 01:52:43 CST)
• plumed
  • Stefano Guglielmo (Sun Feb 28 2016 - 10:21:32 CST)
• PME Seg Fault
  • Vibhor Agrawal (Mon Aug 10 2015 - 11:31:56 CDT)
  • Richard Overstreet (Mon Aug 10 2015 - 09:11:27 CDT)
• PME vs. cutoff with switching function
  • JC Gumbart (Mon Jun 27 2016 - 00:33:36 CDT)
  • Benjamin Brown (Fri Jun 17 2016 - 10:25:44 CDT)
• PMEGridSize and parameters controlling electrostatic interactions.
  • Maxim Belkin (Sun Jan 25 2015 - 21:20:58 CST)
  • Jeff Comer (Sun Jan 25 2015 - 18:11:17 CST)
  • Maxim Belkin (Sat Jan 24 2015 - 14:11:59 CST)
  • Dawid das (Sat Jan 24 2015 - 13:48:44 CST)
• PMEProcessors setting on one node
  • dhirajks_at_gmail.com (Sun May 08 2016 - 21:22:54 CDT)
• PMF Calculation
  • Brian Radak (Sun Aug 14 2016 - 16:36:06 CDT)
  • Crystal Liu (Fri Aug 12 2016 - 19:15:46 CDT)
• PMF calculation input files
  • Jérôme Hénin (Wed Aug 24 2016 - 15:22:47 CDT)
  • Olya Kravchenko (Wed Aug 24 2016 - 16:23:30 CDT)
  • Vermaas, Joshua (Tue Aug 23 2016 - 11:02:01 CDT)
  • Olya Kravchenko (Tue Aug 23 2016 - 10:01:05 CDT)
  • Vermaas, Joshua (Mon Aug 22 2016 - 16:27:34 CDT)
  • Olya Kravchenko (Mon Aug 22 2016 - 15:10:57 CDT)
  • Vermaas, Joshua (Mon Aug 22 2016 - 11:23:58 CDT)
  • Olya Kravchenko (Mon Aug 22 2016 - 10:30:28 CDT)
• PMF calculation using ABF
  • Souvik Sinha (Tue May 10 2016 - 08:57:52 CDT)
• PMF decompostion
  • Azadeh Alavi (Mon Sep 12 2016 - 13:34:22 CDT)
  • Radak, Brian K (Mon Sep 12 2016 - 12:31:48 CDT)
  • Azadeh Alavi (Mon Sep 12 2016 - 06:49:50 CDT)
• PMF with ABF for ion channels in a spherical molecule
  • Aron Broom (Fri Jul 01 2016 - 18:42:21 CDT)
  • Olya Kravchenko (Fri Jul 01 2016 - 15:50:15 CDT)
  • Aron Broom (Tue Jun 28 2016 - 16:37:49 CDT)
  • Olya Kravchenko (Tue Jun 28 2016 - 16:20:13 CDT)
  • Aron Broom (Tue Jun 28 2016 - 15:57:14 CDT)
  • Olya Kravchenko (Tue Jun 28 2016 - 15:35:53 CDT)
  • Aron Broom (Sun Jun 26 2016 - 15:13:36 CDT)
  • Olya Kravchenko (Fri Jun 24 2016 - 17:01:13 CDT)
• polarizable carbon nanotubes
  • ibrahim khalil (Tue Apr 21 2015 - 11:00:36 CDT)
• Polymer moves to the edge of water box during the simulation
  • faride badalkhani (Thu Apr 14 2016 - 09:56:07 CDT)
  • faride badalkhani (Wed Apr 13 2016 - 12:55:28 CDT)
  • faride badalkhani (Wed Apr 13 2016 - 08:32:29 CDT)
  • Josh Vermaas (Wed Apr 13 2016 - 08:02:36 CDT)
  • faride badalkhani (Tue Apr 12 2016 - 17:02:19 CDT)
  • Josh Vermaas (Tue Apr 12 2016 - 16:54:35 CDT)
  • faride badalkhani (Tue Apr 12 2016 - 16:49:21 CDT)
• polymerization simulations
  • Giacomo Fiorin (Thu Jul 09 2015 - 15:51:38 CDT)
  • L. Signorile (Thu Jul 09 2015 - 13:06:51 CDT)
• Possible bug in DCD writer, number of frames not in NSET but in 5-ZEROS
  • Norman Geist (Wed Jul 06 2016 - 07:26:01 CDT)
• Post Doctoral Fellow Opening at IBM for Biomolecular Modeling
  • Tien Huynh (Tue Apr 05 2016 - 18:30:43 CDT)
• Postdoc in Theoretical and Computational Biophysics
  • Aksimentiev, Oleksii (Mon Jun 08 2015 - 11:51:11 CDT)
• Postdoc position available
  • Ivaylo Nikolaev Ivanov (Tue May 17 2016 - 10:05:18 CDT)
• Postdoc positions available at IBM (bio-molecular modeling and MD)
  • Payel Das (Mon Mar 16 2015 - 09:15:05 CDT)
• Postdoctoral opening in biomolecular modeling at IBM
  • Payel Das (Mon Mar 21 2016 - 16:38:19 CDT)
• Potential per TS looks wierd
  • faride badalkhani (Mon Jun 27 2016 - 13:18:33 CDT)
• preparing dsDNA
  • Urszula Uciechowska (Fri Feb 06 2015 - 05:58:43 CST)
• PRES and water-ions issues with charmm36
  • Francesco Pietra (Thu Dec 10 2015 - 15:30:14 CST)
• Pressure coupling options
  • Chitrak Gupta (Sun Jun 28 2015 - 15:54:05 CDT)
  • Josh Vermaas (Sat Jun 27 2015 - 19:36:17 CDT)
  • Kevin C Chan (Fri Jun 26 2015 - 23:32:05 CDT)
• Pressure Profile.
  • msa5 (Thu Nov 17 2016 - 11:06:48 CST)
• pressure value
  • Jeff Comer (Sun Mar 29 2015 - 16:54:09 CDT)
  • Brian Radak (Sun Mar 29 2015 - 15:30:42 CDT)
  • Hasan haska (Sun Mar 29 2015 - 14:23:28 CDT)
• Probelm with Lone Pairs on TIP4 model
  • JAVAD NOROOZI (Tue Jan 06 2015 - 04:07:23 CST)
• problem about namdstats.tcl
  • Hasan haska (Wed Apr 01 2015 - 01:34:32 CDT)
• problem in minimization
  • Ma'Mon Hatmal (Tue Nov 08 2016 - 00:01:28 CST)
• problem in running targeted MD
  • giulia palermo (Wed Feb 24 2016 - 19:56:11 CST)
• Problem on merging multi-psf files into one
  • wliu (Sun Oct 18 2015 - 07:52:11 CDT)
• problem restarting multiple walker metadynamics
  • Amy Rice (Thu Apr 02 2015 - 14:54:56 CDT)
  • Giacomo Fiorin (Wed Apr 01 2015 - 15:05:30 CDT)
  • Amy Rice (Mon Mar 30 2015 - 13:23:24 CDT)
  • Giacomo Fiorin (Sat Mar 28 2015 - 17:50:19 CDT)
  • Amy Rice (Fri Mar 27 2015 - 11:48:02 CDT)
  • Giacomo Fiorin (Thu Mar 19 2015 - 18:39:06 CDT)
  • Amy Rice (Thu Mar 19 2015 - 17:44:25 CDT)
  • Giacomo Fiorin (Thu Mar 19 2015 - 17:26:27 CDT)
  • Amy Rice (Thu Mar 19 2015 - 17:24:29 CDT)
  • Giacomo Fiorin (Sun Mar 15 2015 - 10:47:17 CDT)
  • Giacomo Fiorin (Sun Mar 15 2015 - 10:45:14 CDT)
  • Amy Rice (Thu Mar 12 2015 - 17:26:10 CDT)
  • Amy Rice (Wed Mar 11 2015 - 22:49:51 CDT)
  • Giacomo Fiorin (Wed Mar 11 2015 - 18:29:36 CDT)
  • Amy Rice (Wed Mar 11 2015 - 14:59:46 CDT)
• Problem running REMD simulation
  • Nicholus Bhattacharjee (Thu Aug 27 2015 - 03:00:31 CDT)
  • Peter Freddolino (Wed Aug 26 2015 - 08:28:57 CDT)
  • Peter Freddolino (Tue Aug 25 2015 - 23:25:00 CDT)
  • Nicholus Bhattacharjee (Tue Aug 25 2015 - 04:59:07 CDT)
  • Douglas Houston (Tue Aug 25 2015 - 04:16:55 CDT)
  • Nicholus Bhattacharjee (Tue Aug 25 2015 - 03:01:36 CDT)
  • Nicholus Bhattacharjee (Thu Aug 20 2015 - 03:47:33 CDT)
• problem with +devices using
  • nikolaev_at_spbau.ru (Tue Apr 05 2016 - 06:35:23 CDT)
• Problem with alpha colvar in NAMD 2.12b1
  • JC Gumbart (Fri Dec 09 2016 - 16:58:23 CST)
  • Giacomo Fiorin (Fri Dec 09 2016 - 17:14:34 CST)
  • Giacomo Fiorin (Thu Dec 08 2016 - 16:04:41 CST)
  • Amy Rice (Thu Dec 08 2016 - 15:23:16 CST)
• problem with angle parameters
  • Radak, Brian K (Wed Mar 30 2016 - 11:09:12 CDT)
  • faride badalkhani (Wed Mar 30 2016 - 09:01:20 CDT)
• problem with bringing down the pressure
  • Josh Vermaas (Thu Mar 10 2016 - 19:26:12 CST)
  • faride badalkhani (Thu Mar 10 2016 - 11:31:36 CST)
• problem with equilibration of membrane-protein system
  • Azadeh Alavi (Sat Feb 14 2015 - 05:35:59 CST)
• Problem with iron ion (FE2+)
  • Tristan Croll (Tue Aug 25 2015 - 03:56:51 CDT)
  • Josh Vermaas (Mon Aug 24 2015 - 14:17:20 CDT)
  • Branko (Mon Aug 24 2015 - 13:40:17 CDT)
  • Daniela Rivas (Mon Aug 24 2015 - 13:16:15 CDT)
  • Branko (Mon Aug 24 2015 - 13:09:01 CDT)
  • Daniela Rivas (Mon Aug 24 2015 - 12:51:59 CDT)
• Problem with Kinetic Energy of Atomselection
  • JAVAD NOROOZI (Wed Jan 07 2015 - 00:53:38 CST)
• Problem with minimization
  • Abhishek TYAGI (Thu Oct 27 2016 - 06:13:10 CDT)
  • Ma'Mon Hatmal (Thu Oct 27 2016 - 05:22:52 CDT)
• Problem with tcl intepreter
  • Belkin, Maxim (Tue Nov 03 2015 - 10:53:53 CST)
  • Bryan Roessler (Thu Oct 29 2015 - 20:06:58 CDT)
  • Bryan Roessler (Thu Oct 29 2015 - 20:00:31 CDT)
  • Axel Kohlmeyer (Thu Oct 29 2015 - 19:54:34 CDT)
  • Josh Vermaas (Thu Oct 29 2015 - 19:45:12 CDT)
  • Bryan Roessler (Thu Oct 29 2015 - 19:24:53 CDT)
• Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1
  • Pardis Tabaee (Fri May 06 2016 - 08:05:10 CDT)
• Problem with using autoPSF on TMCL lipid
  • Giacomo Fiorin (Fri Dec 16 2016 - 11:18:21 CST)
  • Jeff Comer (Fri Dec 16 2016 - 10:40:17 CST)
  • salehesam101 . (Fri Dec 16 2016 - 10:11:47 CST)
• problem with water molecules angle in MD simulation
  • Axel Kohlmeyer (Fri Jan 30 2015 - 05:32:06 CST)
  • Tristan Croll (Fri Jan 30 2015 - 02:43:42 CST)
  • Shoresh Shafei (Fri Jan 30 2015 - 02:28:17 CST)
  • Tristan Croll (Fri Jan 30 2015 - 02:25:32 CST)
  • Shoresh (Tue Jan 27 2015 - 10:30:54 CST)
  • Shoresh Shafei (Sun Jan 25 2015 - 19:06:23 CST)
• problems compiling NAMD with mpicxx from mvapich2
  • Jose Borreguero (Mon Jan 26 2015 - 08:27:41 CST)
  • Jose Borreguero (Sat Jan 24 2015 - 11:49:02 CST)
• Problems in NAMD's code about real implementation of function named ComputeNonbondedUtil:calc_pair_energy
  • Peter Freddolino (Sat Jan 30 2016 - 21:00:17 CST)
  • yeguoqiao (Fri Jan 29 2016 - 09:05:31 CST)
• Problems in running AutoIMD
  • Bennion, Brian (Fri May 01 2015 - 11:00:35 CDT)
  • Ern Seang Ong (Thu Apr 30 2015 - 23:33:47 CDT)
• problems running amber parm7
  • Francesco Pietra (Tue Jan 20 2015 - 01:56:02 CST)
  • Francesco Pietra (Tue Jan 20 2015 - 01:25:17 CST)
  • Francesco Pietra (Mon Jan 19 2015 - 13:03:44 CST)
• Problems to parametrize molecules
  • Evandro Semighini (Fri Apr 24 2015 - 14:26:50 CDT)
  • Mayne, Christopher G (Fri Apr 24 2015 - 14:22:55 CDT)
  • Bennion, Brian (Fri Apr 24 2015 - 14:02:59 CDT)
  • Evandro Semighini (Fri Apr 24 2015 - 13:58:25 CDT)
  • Evandro Semighini (Fri Apr 24 2015 - 13:54:33 CDT)
  • Mayne, Christopher G (Fri Apr 24 2015 - 13:53:01 CDT)
  • Bennion, Brian (Fri Apr 24 2015 - 13:46:52 CDT)
  • Evandro Semighini (Fri Apr 24 2015 - 12:49:31 CDT)
  • Bennion, Brian (Fri Apr 24 2015 - 12:27:51 CDT)
  • Evandro Semighini (Fri Apr 24 2015 - 10:04:37 CDT)
  • Mayne, Christopher G (Sun Apr 19 2015 - 18:59:20 CDT)
  • Evandro Semighini (Sun Apr 19 2015 - 18:47:21 CDT)
  • Mayne, Christopher G (Fri Apr 17 2015 - 11:16:16 CDT)
  • Evandro Semighini (Thu Apr 16 2015 - 15:28:23 CDT)
  • Evandro Semighini (Thu Apr 16 2015 - 14:53:54 CDT)
  • Bennion, Brian (Wed Apr 15 2015 - 15:44:53 CDT)
  • Evandro Semighini (Wed Apr 15 2015 - 15:37:12 CDT)
  • Bennion, Brian (Wed Apr 15 2015 - 13:04:21 CDT)
  • Bennion, Brian (Tue Apr 14 2015 - 15:57:28 CDT)
  • Evandro Semighini (Tue Apr 14 2015 - 15:51:17 CDT)
  • Bennion, Brian (Tue Apr 14 2015 - 15:45:41 CDT)
  • Evandro Semighini (Tue Apr 14 2015 - 15:30:03 CDT)
• Problems when running FEP for mutation ASP to GLY
  • Yunhui Peng (Fri Apr 17 2015 - 13:53:03 CDT)
• Problems with GLUP and ASPP with CHARMM36
  • Francesco Pietra (Fri Dec 11 2015 - 09:35:48 CST)
  • Josh Vermaas (Fri Dec 11 2015 - 09:25:11 CST)
  • Francesco Pietra (Fri Dec 11 2015 - 09:21:34 CST)
  • Josh Vermaas (Fri Dec 11 2015 - 08:45:00 CST)
  • Francesco Pietra (Fri Dec 11 2015 - 05:07:03 CST)
• Problems with wrapAll
  • Sonu Kumar (Fri Jul 22 2016 - 13:08:33 CDT)
  • Vermaas, Joshua (Fri Jul 22 2016 - 11:55:30 CDT)
  • MEHRAN MB (Fri Jul 22 2016 - 11:35:12 CDT)
  • Sonu Kumar (Fri Jul 22 2016 - 06:58:13 CDT)
  • Vermaas, Joshua (Thu Jul 21 2016 - 11:14:48 CDT)
  • Sonu Kumar (Thu Jul 21 2016 - 00:52:55 CDT)
• Processing 64-window FEP
  • Matthew Ralph Adendorff (Sun May 10 2015 - 08:44:08 CDT)
• proper order for par files in namd
  • Mayne, Christopher G (Fri May 01 2015 - 09:21:11 CDT)
  • Bennion, Brian (Fri Apr 24 2015 - 17:05:16 CDT)
• proper order for par files in namd (solved)
  • Bennion, Brian (Fri Apr 24 2015 - 18:21:22 CDT)
• protein-DNA complex
  • Vlad Cojocaru (Thu Jul 16 2015 - 10:59:19 CDT)
  • Urszula Uciechowska (Thu Jul 16 2015 - 09:40:25 CDT)
• protonating ASP and GLU
  • Brian Radak (Tue Dec 13 2016 - 13:20:27 CST)
  • Giacomo Fiorin (Tue Dec 13 2016 - 13:06:05 CST)
  • Nehad Elsalamouny (Tue Dec 13 2016 - 12:48:35 CST)
  • Brian Radak (Tue Dec 13 2016 - 08:27:28 CST)
  • Nehad Elsalamouny (Tue Dec 13 2016 - 05:58:51 CST)
• PSF for CYCLIC PEPTIDE :
  • bay__gulf618_at_sina.com (Sat Sep 26 2015 - 21:26:01 CDT)
  • Nikhil Maroli (Sat Sep 26 2015 - 05:45:17 CDT)
• PSF for cyclic peptide nanotube
  • Nikhil Maroli (Fri Oct 02 2015 - 08:36:47 CDT)
• psf for cyclic peptide nanotube:psf ready for one ring but required for 8 ring
  • Nikhil Maroli (Sat Sep 26 2015 - 06:50:31 CDT)
• PSF generated with PSFGEN [problem in CP2K] - Problem with CGenFF naming?
  • Christian Jorgensen (Thu Feb 12 2015 - 13:01:13 CST)
  • Jim Phillips (Thu Feb 12 2015 - 12:32:42 CST)
  • Christian Jorgensen (Thu Feb 12 2015 - 10:16:00 CST)
• psfgen - pdbalias when using readpsf
  • Peter Freddolino (Thu Dec 15 2016 - 15:37:40 CST)
  • Vermaas, Joshua (Thu Dec 15 2016 - 15:26:11 CST)
  • Peter Freddolino (Thu Dec 15 2016 - 15:03:23 CST)
  • Brian Radak (Thu Dec 15 2016 - 14:48:01 CST)
  • Peter Freddolino (Thu Dec 15 2016 - 14:40:40 CST)
  • Brian Radak (Thu Dec 15 2016 - 14:28:56 CST)
• PSFgen with RNA-like nucleotide monophosphates
  • Aaron Larsen (Wed May 06 2015 - 11:01:26 CDT)
• psfgen: creating segments without extra hydrogens?
  • Brian Radak (Sun Aug 14 2016 - 16:39:59 CDT)
  • Emerson Macedo (Sat Aug 13 2016 - 13:58:49 CDT)
• Putting multiple copies of peptide in a box
  • Aditya Ranganathan (Tue Feb 17 2015 - 03:39:14 CST)
• Q=B4=D7=D4"=C2=C0=D0=A1=D3=A8"_<lv-xy11@mail?= s.tsinghua.edu.cn>µÄÓʼþ
  • ÂÀСӨ (Fri Sep 25 2015 - 09:19:53 CDT)
• Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?=
  • ZOU Changling (Mon Feb 29 2016 - 02:43:31 CST)
  • ZOU Changling (Fri Feb 26 2016 - 05:20:03 CST)
  • ZOU Changling (Wed Nov 25 2015 - 06:39:26 CST)
  • ZOU Changling (Wed Nov 18 2015 - 00:25:35 CST)
• Queries regarding metadynamics and .pmf visualization
  • Giacomo Fiorin (Tue Nov 15 2016 - 10:40:15 CST)
• query for system size in pmf calculation
  • Giacomo Fiorin (Fri Nov 20 2015 - 08:52:35 CST)
  • Atanu Maity (Fri Nov 20 2015 - 05:24:47 CST)
• query in the equilibration step
  • d.ronika_at_iitg.ernet.in (Thu Sep 08 2016 - 07:32:32 CDT)
• Query on colvar distanceZ
  • Giacomo Fiorin (Mon Nov 21 2016 - 11:10:57 CST)
  • Karteek Bejagam (Sat Nov 19 2016 - 10:12:36 CST)
  • Bala subramanian (Sat Nov 19 2016 - 08:18:57 CST)
• query on OuputTotalforce Vs OnesiteTotal force ?
  • Bala subramanian (Wed Nov 30 2016 - 07:39:14 CST)
  • Giacomo Fiorin (Tue Nov 29 2016 - 10:20:36 CST)
  • Giacomo Fiorin (Tue Nov 29 2016 - 10:14:34 CST)
  • Jérôme Hénin (Tue Nov 29 2016 - 10:12:44 CST)
  • Bala subramanian (Tue Nov 29 2016 - 09:39:39 CST)
• Query regarding colvar distanceZ
  • Peter Mawanga (Tue Dec 27 2016 - 20:47:16 CST)
  • Vermaas, Joshua (Tue Dec 27 2016 - 19:14:06 CST)
  • Peter Mawanga (Tue Dec 27 2016 - 19:07:07 CST)
  • Giacomo Fiorin (Tue Dec 27 2016 - 13:20:42 CST)
  • Peter Mawanga (Mon Dec 26 2016 - 11:39:48 CST)
  • Vermaas, Joshua (Mon Dec 26 2016 - 10:49:38 CST)
  • Peter Mawanga (Mon Dec 26 2016 - 09:17:34 CST)
  • Peter Mawanga (Mon Dec 26 2016 - 09:07:18 CST)
  • Vermaas, Joshua (Mon Dec 26 2016 - 08:12:23 CST)
  • Peter Mawanga (Mon Dec 26 2016 - 06:57:57 CST)
• Query regarding parameter file generation of a non standard residue
  • Vermaas, Joshua (Wed Sep 07 2016 - 16:49:15 CDT)
  • Mahrukh Imtiaz (Wed Sep 07 2016 - 15:12:14 CDT)
• Query regarding parameter file generation of non standard residue
  • Mahrukh Imtiaz (Thu Sep 08 2016 - 11:22:31 CDT)
  • Vermaas, Joshua (Thu Sep 08 2016 - 11:19:05 CDT)
  • Bennion, Brian (Thu Sep 08 2016 - 11:07:13 CDT)
  • Mahrukh Imtiaz (Thu Sep 08 2016 - 11:01:22 CDT)
  • Abhishek TYAGI (Thu Sep 08 2016 - 06:37:37 CDT)
  • Mahrukh Imtiaz (Thu Sep 08 2016 - 04:54:35 CDT)
  • Mahrukh Imtiaz (Thu Sep 08 2016 - 02:36:31 CDT)
  • Mahrukh Imtiaz (Thu Sep 08 2016 - 00:12:37 CDT)
• question about restart conf file
  • oguz gurbulak (Sun Apr 26 2015 - 07:10:44 CDT)
• question regarding rmsd
  • dhirajks_at_gmail.com (Thu Oct 06 2016 - 17:37:23 CDT)
  • Leandro Martínez (Wed Oct 05 2016 - 15:58:39 CDT)
  • Radak, Brian K (Wed Oct 05 2016 - 15:39:01 CDT)
  • Dhiraj Srivastava (Wed Oct 05 2016 - 14:02:32 CDT)
  • Pardis Tabaee (Wed Oct 05 2016 - 13:34:41 CDT)
  • Radak, Brian K (Wed Oct 05 2016 - 11:18:12 CDT)
  • Roshan Shrestha (Wed Oct 05 2016 - 11:07:09 CDT)
  • dhirajks_at_gmail.com (Wed Oct 05 2016 - 11:03:41 CDT)
  • Pardis Tabaee (Wed Oct 05 2016 - 10:55:01 CDT)
  • Dhiraj Srivastava (Tue Oct 04 2016 - 16:07:43 CDT)
• Questions about lambda scheme in free energy perturbation
  • Jérôme Hénin (Tue Feb 24 2015 - 16:18:21 CST)
  • Jian Dai (Tue Feb 24 2015 - 08:59:57 CST)
• RATTLE Error During Minimization of Charmm Gui Generated Bilayer
  • Chitrak Gupta (Fri Dec 18 2015 - 09:08:27 CST)
  • Jim Phillips (Thu Dec 17 2015 - 19:49:32 CST)
  • Chitrak Gupta (Wed Dec 16 2015 - 11:23:39 CST)
  • begüm alaybeyoÄŸlu (Wed Dec 16 2015 - 10:21:17 CST)
  • Chitrak Gupta (Wed Dec 16 2015 - 09:21:07 CST)
  • begüm alaybeyoÄŸlu (Wed Dec 16 2015 - 03:46:10 CST)
  • Chitrak Gupta (Tue Dec 15 2015 - 12:46:36 CST)
  • begüm alaybeyoÄŸlu (Tue Dec 15 2015 - 10:27:48 CST)
• Reason: FATAL ERROR: Unknown command-line option ++local
  • 孙业平 (Sun Oct 09 2016 - 14:09:47 CDT)
• Recipe for Success - GPU accelerated NAMD
  • Mark Berger (Wed May 04 2016 - 19:25:24 CDT)
• recommendations for a fast multicore workstation
  • Jeff Comer (Tue Nov 24 2015 - 11:56:54 CST)
• Recomposing the system splitted by periodicity
  • Tristan Croll (Thu Jun 11 2015 - 23:22:50 CDT)
  • Francesco Pietra (Thu Jun 11 2015 - 04:34:57 CDT)
• Recover the PMF along an unbiased CV
  • Jérôme Hénin (Thu Jan 14 2016 - 17:38:51 CST)
  • Felipe Merino (Thu Jan 14 2016 - 16:11:37 CST)
• Reducing the amount of work being done on CPU
  • Maxime Boissonneault (Tue Sep 01 2015 - 09:48:24 CDT)
• Reg. restarting a Thermodynamic Integration Run
  • Aditya Chattopadhyay (Mon Jan 12 2015 - 09:32:26 CST)
• Reg: simulating an amino acid in dichloromethane
  • Akshay Bhatnagar (Mon Jan 05 2015 - 06:46:07 CST)
  • Branko (Mon Jan 05 2015 - 05:39:13 CST)
  • Jeff Comer (Sat Jan 03 2015 - 00:34:17 CST)
  • Akshay Bhatnagar (Fri Jan 02 2015 - 23:18:45 CST)
• Reg: solvating in a non-standard solvent
  • Akshay Bhatnagar (Wed Mar 25 2015 - 02:38:00 CDT)
  • Akshay Bhatnagar (Thu Mar 19 2015 - 23:38:24 CDT)
  • Maxim Belkin (Thu Mar 19 2015 - 12:06:38 CDT)
  • Maxim Belkin (Thu Mar 19 2015 - 11:59:28 CDT)
  • Jeff Comer (Thu Mar 19 2015 - 09:02:10 CDT)
  • Akshay Bhatnagar (Thu Mar 19 2015 - 01:40:55 CDT)
  • Jeff Comer (Wed Mar 18 2015 - 09:44:12 CDT)
  • Josh Vermaas (Wed Mar 18 2015 - 09:08:24 CDT)
  • Branko (Wed Mar 18 2015 - 07:19:45 CDT)
  • Akshay Bhatnagar (Wed Mar 18 2015 - 01:29:20 CDT)
• Reg: topology file amidated and acetylated disulfide bridged Cystine
  • Akshay Bhatnagar (Fri Apr 10 2015 - 05:05:42 CDT)
• Regarding biasTemperature used in Well-tempered metadynamics
  • Giacomo Fiorin (Tue Oct 06 2015 - 09:01:52 CDT)
  • Vijay L. Roy (Tue Oct 06 2015 - 01:49:12 CDT)
• Regarding Bionanotechnology tutorial
  • arpita agarwal (Wed Apr 13 2016 - 20:07:26 CDT)
• Regarding FFTW routines usage in NAMD
  • Axel Kohlmeyer (Tue Oct 20 2015 - 08:10:09 CDT)
  • Puneet Singh (Tue Oct 20 2015 - 07:39:50 CDT)
• Regarding merging of .grad files obtained from ABF simulations
  • sruthi c k (Thu Jan 07 2016 - 04:31:11 CST)
  • Jérôme Hénin (Thu Jan 07 2016 - 04:07:17 CST)
  • sruthi c k (Thu Jan 07 2016 - 01:49:18 CST)
• Regarding NAMD installation
  • Sourav Ray (Mon Aug 17 2015 - 02:53:00 CDT)
  • Pragya Priyadarshini (Mon Aug 17 2015 - 02:45:13 CDT)
• regarding PME grid setting problem
  • amit banerjee (Sun Jan 04 2015 - 18:31:44 CST)
• Regarding problem in psfgen of heparin
  • Tristan Croll (Tue Oct 06 2015 - 18:44:21 CDT)
  • Tristan Croll (Mon Oct 05 2015 - 23:00:32 CDT)
  • siddharth kamal (Fri Oct 02 2015 - 14:20:15 CDT)
• Regarding radial distribution function graph
  • siddharth kamal (Thu Jun 16 2016 - 08:31:23 CDT)
• Regarding significance of days per ns (days/ns) parameter in NAMD benchmark
  • Brian Radak (Tue Oct 20 2015 - 09:46:32 CDT)
  • Puneet Singh (Tue Oct 20 2015 - 01:01:24 CDT)
• Regarding system forces in NAMD
  • sruthi c k (Fri Jan 08 2016 - 06:14:08 CST)
  • Giacomo Fiorin (Fri Jan 08 2016 - 08:36:45 CST)
  • sruthi c k (Thu Jan 07 2016 - 11:43:49 CST)
  • Giacomo Fiorin (Thu Jan 07 2016 - 09:18:35 CST)
  • Giacomo Fiorin (Thu Jan 07 2016 - 09:14:45 CST)
  • sruthi c k (Thu Jan 07 2016 - 09:13:57 CST)
  • Giacomo Fiorin (Thu Jan 07 2016 - 09:10:39 CST)
  • Jérôme Hénin (Thu Jan 07 2016 - 08:37:07 CST)
  • sruthi c k (Thu Jan 07 2016 - 06:49:51 CST)
• Regarding Trajectory files
  • Harish Srinivasan (Mon Dec 26 2016 - 23:44:52 CST)
  • Harish Srinivasan (Mon Dec 26 2016 - 23:44:03 CST)
  • Amit Kumar (Sun Dec 25 2016 - 23:18:26 CST)
• REMD
  • Vermaas, Joshua (Thu Nov 24 2016 - 11:07:06 CST)
  • kaushik chakraborty (Wed Nov 23 2016 - 13:58:51 CST)
• REMD and sortreplicas program
  • Horia Jalily Hasani (Tue Sep 13 2016 - 10:34:22 CDT)
  • Horia Jalily Hasani (Mon Sep 12 2016 - 11:21:55 CDT)
  • Horia Jalily Hasani (Thu Sep 08 2016 - 12:22:39 CDT)
  • Horia Jalily Hasani (Wed Sep 07 2016 - 19:10:49 CDT)
• REMD on GPU cluster
  • Norman Geist (Tue Apr 14 2015 - 11:01:49 CDT)
  • Michael Feig (Tue Apr 14 2015 - 08:00:16 CDT)
  • Norman Geist (Tue Apr 14 2015 - 02:10:03 CDT)
  • Michael Feig (Mon Apr 13 2015 - 17:09:05 CDT)
• Remembering Klaus Schulten
  • Thomas C. Bishop (Tue Nov 01 2016 - 09:33:31 CDT)
• Remembering resid
  • Kevin C Chan (Thu Jun 18 2015 - 11:48:50 CDT)
  • Chitrak Gupta (Thu Jun 18 2015 - 08:52:08 CDT)
  • Branko (Thu Jun 18 2015 - 08:54:40 CDT)
  • Kevin C Chan (Thu Jun 18 2015 - 08:42:34 CDT)
• Replica exchange
  • arpita agarwal (Fri Apr 22 2016 - 02:54:50 CDT)
  • arpita agarwal (Thu Apr 21 2016 - 00:43:44 CDT)
  • Jason Swails (Tue Jan 19 2016 - 15:06:24 CST)
  • Chitrak Gupta (Tue Jan 19 2016 - 14:40:20 CST)
  • Dr. Eddie (Tue Jan 19 2016 - 10:35:00 CST)
• replica exchange and GPU acceleration
  • Mitchell Gleed (Mon Jul 13 2015 - 01:32:14 CDT)
  • Norman Geist (Mon Jul 13 2015 - 00:51:11 CDT)
  • Mitchell Gleed (Sun Jul 12 2015 - 22:36:54 CDT)
  • Norman Geist (Mon Jul 06 2015 - 01:38:11 CDT)
  • Mitchell Gleed (Sat Jul 04 2015 - 10:49:22 CDT)
  • Norman Geist (Fri Jul 03 2015 - 03:16:17 CDT)
  • Mitchell Gleed (Wed Jul 01 2015 - 11:01:50 CDT)
  • Norman Geist (Wed Jul 01 2015 - 02:13:56 CDT)
  • Mitchell Gleed (Tue Jun 30 2015 - 18:09:27 CDT)
• replica exchange module
  • Jessen Lucas (Tue Oct 27 2015 - 03:42:23 CDT)
  • Jessen Lucas (Mon Oct 26 2015 - 22:49:20 CDT)
  • Jessen Lucas (Mon Oct 26 2015 - 03:25:46 CDT)
  • Jessen Lucas (Mon Oct 26 2015 - 02:25:49 CDT)
  • Jessen Lucas (Mon Oct 26 2015 - 01:29:43 CDT)
• Replica Exchange US, Colvar suggestion
  • Laurent Chaloin (Sat Feb 13 2016 - 02:02:24 CST)
  • Laurent Chaloin (Sat Feb 13 2016 - 01:53:46 CST)
  • Abhishek TYAGI (Sat Feb 13 2016 - 22:39:29 CST)
  • Giacomo Fiorin (Sat Feb 13 2016 - 13:21:00 CST)
  • Abhishek TYAGI (Sat Feb 13 2016 - 01:07:38 CST)
• Replica Exchange: Equilibrating at each temperature
  • Horia Jalily Hasani (Tue May 31 2016 - 11:18:08 CDT)
  • Horia Jalily Hasani (Mon May 30 2016 - 11:28:24 CDT)
• Repulsion of lipid bilayer during equilibration
  • Mahrukh Imtiaz (Fri Jul 22 2016 - 05:00:41 CDT)
• Residue number changed to hexadecimal string
  • Jim Phillips (Fri Feb 06 2015 - 00:38:00 CST)
  • K Miura (Thu Feb 05 2015 - 23:34:24 CST)
• restart a job
  • Ana Celia Vila Verde (Thu Apr 07 2016 - 02:43:32 CDT)
  • Life Sciences Inc (Wed Apr 06 2016 - 12:40:28 CDT)
  • Farideh Badalkhani Khamseh (Wed Apr 06 2016 - 11:57:49 CDT)
• restart error
  • Lara rajam (Mon Jul 20 2015 - 10:15:23 CDT)
• restart file - langevin options removed?
  • Olya Kravchenko (Thu Apr 28 2016 - 15:59:09 CDT)
  • Maxim Belkin (Thu Apr 28 2016 - 15:36:52 CDT)
  • Olya Kravchenko (Thu Apr 28 2016 - 15:28:57 CDT)
  • Maxim Belkin (Thu Apr 28 2016 - 15:17:35 CDT)
  • Josh Vermaas (Thu Apr 28 2016 - 15:16:41 CDT)
  • Olya Kravchenko (Thu Apr 28 2016 - 15:13:00 CDT)
  • Maxim Belkin (Thu Apr 28 2016 - 15:00:57 CDT)
  • Olya Kravchenko (Thu Apr 28 2016 - 14:49:45 CDT)
• Restart heating
  • Fotis Baltoumas (Fri Jan 16 2015 - 12:26:09 CST)
  • Francesco Pietra (Fri Jan 16 2015 - 12:04:33 CST)
• Restart multiple walker ABF
  • Atanu Maity (Mon May 23 2016 - 01:13:10 CDT)
  • Atanu Maity (Sun May 22 2016 - 23:55:32 CDT)
  • Jeff Comer (Thu May 19 2016 - 15:58:22 CDT)
  • Atanu Maity (Thu May 19 2016 - 03:36:30 CDT)
  • Atanu Maity (Thu May 19 2016 - 03:32:24 CDT)
• restart namd calculations
  • Bylund, Tatsiana (NIH/NIAID) [F] (Tue Jan 12 2016 - 16:55:09 CST)
• restart simulation
  • oguz gurbulak (Thu Apr 23 2015 - 09:22:38 CDT)
• Restarting ABF
  • Jérôme Hénin (Wed Mar 23 2016 - 04:28:51 CDT)
  • Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Tue Mar 22 2016 - 13:45:51 CDT)
• Restarting an abruptly interrupted simulation
  • Prathit Chatterjee (Tue Mar 17 2015 - 02:03:52 CDT)
  • Sourav Ray (Tue Mar 17 2015 - 01:30:21 CDT)
• Restarting NAMD simulation
  • Sourav Ray (Thu Mar 12 2015 - 09:16:26 CDT)
  • Norman Geist (Thu Mar 12 2015 - 09:13:14 CDT)
  • Sourav Ray (Thu Mar 12 2015 - 08:30:27 CDT)
• restarting simulation
  • Francesco Pietra (Mon Mar 14 2016 - 09:45:44 CDT)
• Restarting trajectories
  • Grzegorz Nawrocki (Thu May 21 2015 - 09:10:28 CDT)
  • Bennion, Brian (Wed May 20 2015 - 14:38:43 CDT)
  • Grzegorz Nawrocki (Wed May 20 2015 - 14:24:08 CDT)
  • Emad Tajkhorshid (Wed May 20 2015 - 12:32:12 CDT)
  • Michael Feig (Wed May 20 2015 - 11:18:12 CDT)
  • Maxim Belkin (Wed May 20 2015 - 11:11:33 CDT)
  • Josh Vermaas (Wed May 20 2015 - 11:07:42 CDT)
  • Axel Kohlmeyer (Wed May 20 2015 - 11:07:56 CDT)
  • Michael Feig (Wed May 20 2015 - 10:59:07 CDT)
  • Axel Kohlmeyer (Wed May 20 2015 - 10:49:11 CDT)
  • Bennion, Brian (Wed May 20 2015 - 10:42:46 CDT)
  • Michael Feig (Wed May 20 2015 - 02:47:08 CDT)
  • Michael Feig (Wed May 20 2015 - 03:01:37 CDT)
• Restraining angle between bond vector and coordinate vector
  • Seth Axen (Wed Mar 25 2015 - 19:01:40 CDT)
  • Jeff Comer (Mon Mar 23 2015 - 18:17:18 CDT)
  • Jérôme Hénin (Mon Mar 23 2015 - 15:45:02 CDT)
  • Seth Axen (Mon Mar 23 2015 - 15:26:37 CDT)
• restraint backbone to keep secondary structure in coarse grain MD
  • Deng, Jinxia (Nancy) (Wed Nov 09 2016 - 10:42:46 CST)
• Restraints on the outer solutes
  • Vibhor Agrawal (Mon Dec 28 2015 - 03:50:57 CST)
  • Diksha Dubey (Mon Dec 28 2015 - 03:39:00 CST)
• Returning energy values from .log file.
  • Ajasja LjubetiÄ� (Thu Dec 08 2016 - 02:30:28 CST)
  • Radak, Brian K (Wed Dec 07 2016 - 15:19:49 CST)
  • Ajasja LjubetiÄ� (Wed Dec 07 2016 - 14:41:54 CST)
  • Chitrak Gupta (Wed Dec 07 2016 - 14:36:57 CST)
  • matthew reeves (Wed Dec 07 2016 - 14:16:44 CST)
• Reverse Coarse Graining using VMD CG Builder
  • Peter Freddolino (Wed Oct 21 2015 - 11:25:44 CDT)
  • Peter Freddolino (Wed Oct 21 2015 - 10:49:38 CDT)
  • Ardavan Mehdizadeh (Wed Oct 21 2015 - 10:41:55 CDT)
  • Peter Freddolino (Wed Oct 21 2015 - 07:29:13 CDT)
  • Ardavan Mehdizadeh (Wed Oct 21 2015 - 03:15:35 CDT)
• Reverse osmosis simulation
  • Z (Thu Jan 22 2015 - 05:09:24 CST)
• Rigid bonds and non-bonded energy
  • Grzegorz Nawrocki (Wed Oct 21 2015 - 08:29:22 CDT)
  • Grzegorz Nawrocki (Tue Oct 20 2015 - 11:09:20 CDT)
  • Brian Radak (Tue Oct 20 2015 - 12:52:34 CDT)
  • Grzegorz Nawrocki (Tue Oct 20 2015 - 10:11:42 CDT)
  • Brian Radak (Tue Oct 20 2015 - 10:33:51 CDT)
  • Brian Radak (Mon Oct 19 2015 - 14:40:51 CDT)
  • Brian Radak (Fri Oct 16 2015 - 17:42:34 CDT)
  • Grzegorz Nawrocki (Fri Oct 16 2015 - 16:39:48 CDT)
• RMSD
  • faride badalkhani (Thu Jun 16 2016 - 14:13:40 CDT)
  • Brian Radak (Thu Jun 16 2016 - 14:11:29 CDT)
  • faride badalkhani (Thu Jun 16 2016 - 14:02:43 CDT)
  • Brian Radak (Thu Jun 16 2016 - 13:51:46 CDT)
  • faride badalkhani (Thu Jun 16 2016 - 12:42:32 CDT)
• RMSD based PMF calculation with umbrella sampling
  • Jérôme Hénin (Thu Dec 22 2016 - 05:06:35 CST)
  • Wang, X. Y. (Thu Dec 22 2016 - 04:26:21 CST)
• Rotating Constraints
  • Sourav Purohit (Tue Feb 24 2015 - 14:23:26 CST)
• rotation angle
  • Giacomo Fiorin (Wed Apr 20 2016 - 13:51:43 CDT)
  • giulia palermo (Wed Apr 20 2016 - 12:25:16 CDT)
• Ru surface potential
  • Madhulika Gupta (Mon Apr 11 2016 - 03:52:26 CDT)
• run NAMD 2.10 on Xeon Phi machine
  • Xiaoge Wang (Tue Jul 28 2015 - 12:50:23 CDT)
• run on sungle node
  • Alexander Tzanov (Wed Jun 24 2015 - 13:37:01 CDT)
  • Axel Kohlmeyer (Wed Jun 24 2015 - 11:16:34 CDT)
  • Josh Vermaas (Wed Jun 24 2015 - 11:14:16 CDT)
  • Alexander Tzanov (Wed Jun 24 2015 - 11:03:24 CDT)
  • Alexander Tzanov (Wed Jun 24 2015 - 09:56:18 CDT)
• Running a test simulation using GPU only (without any CPU core)
  • Axel Kohlmeyer (Thu Apr 28 2016 - 10:40:38 CDT)
  • Josh Vermaas (Thu Apr 28 2016 - 10:09:28 CDT)
  • Sourav Ray (Thu Apr 28 2016 - 10:04:29 CDT)
  • Brian Radak (Thu Apr 28 2016 - 10:00:42 CDT)
  • Sourav Ray (Thu Apr 28 2016 - 09:40:00 CDT)
• Running Charmm36
  • Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Fri Apr 08 2016 - 19:04:49 CDT)
• Running constant pH molecular dynamics (CpHMD)
  • Jason Swails (Thu Jul 09 2015 - 20:05:36 CDT)
  • Leonardo Herrera (Thu Jul 09 2015 - 19:00:02 CDT)
• Running CUDA on a laptop
  • Tristan Croll (Tue Jan 13 2015 - 19:14:31 CST)
  • Tristan Croll (Tue Jan 13 2015 - 18:29:59 CST)
• Running gromacs in namd
  • Subbarao Kanchi (Thu Dec 01 2016 - 01:42:24 CST)
  • Subbarao Kanchi (Thu Dec 01 2016 - 00:27:37 CST)
  • Subbarao Kanchi (Tue Nov 29 2016 - 04:25:06 CST)
  • Subbarao Kanchi (Tue Nov 29 2016 - 00:30:37 CST)
• Running multi-node jobs on Sun Grid Engine
  • Sourav Ray (Tue Apr 05 2016 - 00:19:23 CDT)
  • Sourav Ray (Mon Apr 04 2016 - 04:39:57 CDT)
  • Éric Germaneau (Sun Apr 03 2016 - 20:34:20 CDT)
  • Sourav Ray (Sun Apr 03 2016 - 10:49:30 CDT)
• running multicore version on a 2-CPU node
  • Gianluca Interlandi (Sat Jul 04 2015 - 15:33:25 CDT)
• running namd gpu version
  • Sanjana Anil Kumar Nair (Sat Aug 29 2015 - 05:21:41 CDT)
• Running REMD
  • Nicolas Martin (Wed Sep 21 2016 - 03:26:18 CDT)
  • Giacomo Fiorin (Mon Sep 19 2016 - 11:22:52 CDT)
  • Nicolas Martin (Wed Sep 14 2016 - 03:10:55 CDT)
• running simulations in successive steps
  • faride badalkhani (Mon May 16 2016 - 17:31:31 CDT)
• Running two molecule coarse-grained simulation
  • Prathit Chatterjee (Thu Apr 16 2015 - 11:37:21 CDT)
  • Sourav Ray (Thu Apr 16 2015 - 06:27:30 CDT)
  • Prathit Chatterjee (Wed Apr 15 2015 - 09:24:32 CDT)
  • Sourav Ray (Wed Apr 15 2015 - 09:05:43 CDT)
  • Sourav Ray (Wed Apr 15 2015 - 05:51:29 CDT)
  • Sourav Ray (Wed Apr 15 2015 - 05:39:18 CDT)
• running with replica exchange on stampede
  • Peter Freddolino (Sun May 24 2015 - 21:40:09 CDT)
• Sampling frequency
  • Jeff Comer (Tue Sep 01 2015 - 08:40:14 CDT)
  • Dr. Eddie (Mon Aug 31 2015 - 14:02:46 CDT)
• sausage plot for a namd trajectory in vmd
  • Thomas C. Bishop (Tue Aug 11 2015 - 10:30:23 CDT)
  • Aaron Larsen (Fri Jul 31 2015 - 05:44:17 CDT)
  • luca belmonte (Fri Jul 31 2015 - 05:01:02 CDT)
• scaling non-bonded interactiion parameter for specific pairs
  • MEHRAN MB (Fri Feb 27 2015 - 14:01:29 CST)
  • Jeff Comer (Fri Feb 27 2015 - 13:58:31 CST)
  • MEHRAN MB (Fri Feb 27 2015 - 13:15:11 CST)
• School on Molecular Dynamics and Enhanced Sampling Methods @ Temple University July 6-10, 2015
  • Axel Kohlmeyer (Fri May 08 2015 - 11:28:54 CDT)
• script error
  • Nikhil Maroli (Fri Oct 02 2015 - 08:44:13 CDT)
• Second Announcement: ‘Hands On’ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015)
  • Lela Vukovic (Tue Jun 16 2015 - 12:04:27 CDT)
• segmentation error
  • Giacomo Fiorin (Fri Mar 04 2016 - 10:54:29 CST)
  • Stefano Guglielmo (Fri Mar 04 2016 - 04:15:01 CST)
• segmentation fault (core dumped)
  • faride badalkhani (Wed Mar 30 2016 - 16:24:26 CDT)
• Segmentation Fault - Debug
  • Kumar, Amit (Mon Oct 05 2015 - 09:13:14 CDT)
• segmentation fault in ABF simulations
  • Jérôme Hénin (Mon Jan 25 2016 - 12:47:00 CST)
  • Azadeh Alavi (Mon Jan 25 2016 - 12:31:10 CST)
  • Jérôme Hénin (Mon Jan 25 2016 - 12:23:01 CST)
  • Azadeh Alavi (Mon Jan 25 2016 - 12:11:58 CST)
  • Jérôme Hénin (Mon Jan 25 2016 - 11:08:22 CST)
  • Azadeh Alavi (Mon Jan 25 2016 - 11:00:26 CST)
  • Jérôme Hénin (Mon Jan 25 2016 - 08:14:47 CST)
  • Azadeh Alavi (Mon Jan 25 2016 - 07:58:49 CST)
• segmentation fault when running with mpirun
  • Puneet Singh (Fri Jul 24 2015 - 08:05:23 CDT)
• selection error in forces script
  • Olya Kravchenko (Tue Mar 08 2016 - 00:08:00 CST)
  • Olya Kravchenko (Mon Mar 07 2016 - 23:02:34 CST)
• selectively assign HIE or HID for HIS residues
  • Jim Phillips (Tue Dec 06 2016 - 16:08:47 CST)
  • Nehad Elsalamouny (Tue Dec 06 2016 - 15:03:47 CST)
  • Vermaas, Joshua (Tue Dec 06 2016 - 11:03:38 CST)
  • Brian Radak (Mon Dec 05 2016 - 22:13:09 CST)
  • Nehad Elsalamouny (Mon Dec 05 2016 - 20:19:44 CST)
• Separate switchdist for electrostatic interactions
  • Fotis Baltoumas (Mon Nov 21 2016 - 09:54:33 CST)
  • Peter Mawanga (Mon Nov 21 2016 - 06:17:18 CST)
• setting up simulation in vmd using charmm 36 forcefield
  • JC Gumbart (Mon May 30 2016 - 07:29:44 CDT)
  • Rabeta Yeasmin (Fri May 27 2016 - 16:28:38 CDT)
• Setting up symmetry restraints in a homo-dimer with non-equal number of residues
  • Mark Hilge (Mon Dec 12 2016 - 16:55:07 CST)
  • Ryan McGreevy (Fri Dec 09 2016 - 12:46:04 CST)
  • Giacomo Fiorin (Fri Dec 09 2016 - 12:34:43 CST)
  • Mark Hilge (Fri Dec 09 2016 - 00:17:19 CST)
• Several questions about targeted molecular dynamics
  • sunyeping (Mon Oct 19 2015 - 04:54:09 CDT)
• Shear Stress modelling in NAMD
  • James Starlight (Sun Sep 11 2016 - 05:12:26 CDT)
• Should you cap C and N termini?
  • Gianluca Interlandi (Thu Feb 18 2016 - 12:57:24 CST)
  • Vlad Cojocaru (Thu Feb 18 2016 - 09:31:56 CST)
  • ashika torikora (Thu Feb 18 2016 - 07:09:10 CST)
• Shrinking a molecule (Colvars and Constant Pressure not working)
  • Sonu Kumar (Mon Aug 22 2016 - 15:21:48 CDT)
• Shrinking a polymer to match its density using pbc
  • Sonu Kumar (Wed Sep 28 2016 - 10:21:11 CDT)
• simulated annealing
  • Brian Radak (Thu Apr 07 2016 - 10:00:03 CDT)
  • faride badalkhani (Thu Apr 07 2016 - 08:14:10 CDT)
  • faride badalkhani (Wed Apr 06 2016 - 11:24:30 CDT)
• Simulated annealing error
  • Brian Radak (Thu Apr 07 2016 - 15:34:51 CDT)
  • faride badalkhani (Thu Apr 07 2016 - 13:13:38 CDT)
• Simulated Annealing with many frequent restarts
  • Maxim Belkin (Fri May 01 2015 - 11:49:41 CDT)
  • Phillips, Carolyn L. (Fri May 01 2015 - 11:24:13 CDT)
  • Maxim Belkin (Fri May 01 2015 - 11:18:21 CDT)
  • Phillips, Carolyn L. (Fri May 01 2015 - 10:16:43 CDT)
  • Maxim Belkin (Fri May 01 2015 - 09:46:21 CDT)
  • Francesco Pietra (Fri May 01 2015 - 01:21:28 CDT)
  • Phillips, Carolyn L. (Thu Apr 30 2015 - 18:51:19 CDT)
• Simulated annealing, in solvent or in vacuum?
  • Roshan Shrestha (Fri Sep 09 2016 - 03:17:37 CDT)
  • faride badalkhani (Thu Sep 08 2016 - 14:21:26 CDT)
• simulating graphene sheets (with bonds across boundaries) with water
  • upayan baul (Wed Sep 16 2015 - 05:40:38 CDT)
  • Axel Kohlmeyer (Tue Sep 15 2015 - 19:22:27 CDT)
  • Abhishek TYAGI (Tue Sep 15 2015 - 18:58:52 CDT)
  • upayan baul (Tue Sep 15 2015 - 06:57:20 CDT)
  • Abhishek TYAGI (Mon Sep 14 2015 - 19:28:04 CDT)
  • upayan baul (Mon Sep 14 2015 - 06:59:00 CDT)
• simulating TIP5P water
  • Monika Madhavi (Mon Oct 12 2015 - 05:10:35 CDT)
  • Monika Madhavi (Mon Oct 12 2015 - 03:44:50 CDT)
  • Peter Freddolino (Sat Oct 10 2015 - 21:33:50 CDT)
  • Monika Madhavi (Fri Oct 09 2015 - 05:29:35 CDT)
  • Monika Madhavi (Thu Oct 01 2015 - 23:36:51 CDT)
• Simulation Box Rescaling
  • Phillips, Carolyn L. (Tue May 05 2015 - 18:02:28 CDT)
• simulation of hyperbranched polymers
  • faride badalkhani (Tue Apr 19 2016 - 07:54:49 CDT)
• Simulation of metalo-binding proteins
  • luca belmonte (Fri Nov 25 2016 - 06:47:10 CST)
  • James Starlight (Thu Nov 24 2016 - 14:44:03 CST)
  • Francesco Pietra (Thu Nov 24 2016 - 14:41:58 CST)
  • James Starlight (Thu Nov 24 2016 - 14:01:08 CST)
  • Jérôme Hénin (Wed Nov 23 2016 - 14:11:44 CST)
  • James Starlight (Wed Nov 23 2016 - 13:52:38 CST)
• Simulation runs only in background
  • Marlon Sidore (Wed Jun 01 2016 - 04:09:16 CDT)
  • Roshan Shrestha (Wed Jun 01 2016 - 03:44:15 CDT)
• single strand DNA in hairpin conformation
  • Urszula Uciechowska (Thu Feb 12 2015 - 03:14:55 CST)
• size of water box and cellbasisvectors
  • Ajasja LjubetiÄ� (Wed Mar 30 2016 - 08:08:14 CDT)
  • faride badalkhani (Wed Mar 30 2016 - 07:51:14 CDT)
• slow heating of system
  • Maxim Belkin (Sun Apr 19 2015 - 04:08:03 CDT)
  • Dhiraj Srivastava (Sun Apr 19 2015 - 00:55:58 CDT)
• SMD Constant velocity pulling
  • jeevan gc (Wed Jul 27 2016 - 16:45:19 CDT)
  • Allen, Caley R (Wed Jul 27 2016 - 13:38:19 CDT)
  • Roshan Shrestha (Wed Jul 27 2016 - 12:59:49 CDT)
• SMD in NAMD
  • Madhulika Gupta (Sat Apr 23 2016 - 05:15:34 CDT)
• SMD or moving contraints
  • Kevin C Chan (Thu Oct 15 2015 - 21:50:20 CDT)
• SMD restraints
  • Allen, Caley R (Tue Nov 15 2016 - 13:30:17 CST)
  • Giacomo Fiorin (Tue Nov 15 2016 - 13:17:17 CST)
  • Vermaas, Joshua (Mon Nov 14 2016 - 16:26:01 CST)
  • Giacomo Fiorin (Mon Nov 14 2016 - 15:59:07 CST)
  • Giacomo Fiorin (Mon Nov 14 2016 - 15:17:59 CST)
  • Allen, Caley R (Mon Nov 14 2016 - 15:14:09 CST)
• SMD simulation problem
  • Madhulika Gupta (Sun May 22 2016 - 10:59:18 CDT)
  • Shambo Hore (Sun May 22 2016 - 10:37:52 CDT)
• SMD simulation problem.
  • Shambo Hore (Sun May 29 2016 - 20:15:57 CDT)
• SMD with PBC
  • Mahdi Tavakol (Thu Dec 24 2015 - 00:22:36 CST)
• SMP NAMD reports threads greater than physical cores, even when distributed to other nodes
  • Jim Phillips (Sat Dec 19 2015 - 21:39:50 CST)
  • Tom Coles (Fri Dec 18 2015 - 15:16:01 CST)
  • Jim Phillips (Fri Dec 18 2015 - 09:38:15 CST)
  • Tom Coles (Thu Dec 17 2015 - 10:26:20 CST)
• Solvation free energy calculation with MM/GBSA
  • Neelanjana Sengupta (Fri Sep 25 2015 - 07:36:50 CDT)
  • Jeff Comer (Thu Sep 24 2015 - 08:27:26 CDT)
  • Abhishek TYAGI (Thu Sep 24 2015 - 07:40:43 CDT)
  • Neelanjana Sengupta (Thu Sep 24 2015 - 07:37:04 CDT)
  • Abhishek TYAGI (Thu Sep 24 2015 - 07:13:20 CDT)
  • Neelanjana Sengupta (Wed Sep 23 2015 - 06:51:28 CDT)
• solvent other than water
  • Jeff Comer (Wed Jan 06 2016 - 13:39:14 CST)
  • Deng, Jinxia (Nancy) (Wed Jan 06 2016 - 12:17:11 CST)
• Some questions on the Deca-Alanine ABF tutorial
  • Pardis Tabaee (Fri May 20 2016 - 09:52:09 CDT)
  • Pardis Tabaee (Fri May 20 2016 - 10:01:13 CDT)
  • Jérôme Hénin (Fri May 20 2016 - 08:07:03 CDT)
  • Jérôme Hénin (Fri May 20 2016 - 07:35:22 CDT)
  • sunyeping (Thu May 19 2016 - 22:41:05 CDT)
  • Jérôme Hénin (Thu May 19 2016 - 02:31:14 CDT)
  • sunyeping (Wed May 18 2016 - 20:29:46 CDT)
  • Jérôme Hénin (Wed May 18 2016 - 05:49:56 CDT)
  • sunyeping (Wed May 18 2016 - 03:06:08 CDT)
  • Jérôme Hénin (Tue May 17 2016 - 10:33:03 CDT)
  • sunyeping (Mon May 16 2016 - 04:19:33 CDT)
• Spawning too many gpu processes on the first node
  • Robert Sawko (Thu Dec 01 2016 - 13:10:12 CST)
• Spikes in the Energy Plot
  • Viswanath Pasumarthi (Mon Feb 09 2015 - 02:26:08 CST)
• startup phase 1 for benchmark
  • Branko (Tue May 12 2015 - 09:29:28 CDT)
• statistical error of mean force in (NAMD) ABF calculations
  • Jeff Comer (Thu Jul 02 2015 - 09:09:38 CDT)
  • Branko (Wed Jul 01 2015 - 05:09:48 CDT)
• steepest descent
  • Ma'Mon Hatmal (Tue Nov 08 2016 - 08:58:30 CST)
• Steered MD diminishing distances
  • Giacomo Fiorin (Sat Apr 02 2016 - 20:56:34 CDT)
  • giulia palermo (Sat Apr 02 2016 - 20:29:14 CDT)
• Steered NAMD using AMBER Forcefield [Config File]
  • Zeinab Emami (Sun Jan 18 2015 - 10:07:51 CST)
• stepspercycle
  • Gianluca Interlandi (Sun Oct 18 2015 - 20:20:26 CDT)
• strange behavior of ABF
  • Danilo Di Maio (Tue Apr 14 2015 - 12:48:13 CDT)
  • Jérôme Hénin (Tue Apr 14 2015 - 07:06:47 CDT)
  • Danilo Di Maio (Tue Apr 14 2015 - 05:41:24 CDT)
• Stray PME grid charges detected
  • Sourav Ray (Mon Apr 04 2016 - 13:12:41 CDT)
  • faride badalkhani (Mon Apr 04 2016 - 13:02:51 CDT)
  • Sourav Ray (Mon Apr 04 2016 - 05:26:56 CDT)
  • faride badalkhani (Sun Apr 03 2016 - 12:49:18 CDT)
• string method in NAMD 2.10
  • Jerome Karp (Tue Sep 22 2015 - 11:44:37 CDT)
  • Chris Chipot (Tue Sep 22 2015 - 10:46:28 CDT)
  • Jerome Karp (Tue Sep 22 2015 - 10:39:30 CDT)
  • Chris Chipot (Tue Sep 22 2015 - 10:26:53 CDT)
  • Jerome Karp (Tue Sep 22 2015 - 10:05:05 CDT)
  • Thomas Evangelidis (Tue Sep 22 2015 - 05:31:34 CDT)
  • Thomas Evangelidis (Tue Sep 22 2015 - 05:29:16 CDT)
  • Jerry Karp (Mon Sep 21 2015 - 10:46:45 CDT)
  • Jerome Karp (Mon Sep 21 2015 - 10:49:42 CDT)
• stripping off water from DCD file except structural water
  • Dhiraj Srivastava (Sun Oct 02 2016 - 22:57:24 CDT)
• Studying Folding of 870 Small Peptides. Computationally Feasible?
  • Brian Radak (Mon Dec 19 2016 - 09:32:10 CST)
  • Nicholas M. Glykos (Mon Dec 19 2016 - 03:36:15 CST)
  • Peter Freddolino (Sat Dec 17 2016 - 22:04:38 CST)
  • JC Gumbart (Sat Dec 17 2016 - 19:18:46 CST)
  • Eric A Brenner (Sat Dec 17 2016 - 19:02:39 CST)
  • JC Gumbart (Sat Dec 17 2016 - 18:48:50 CST)
  • Eric A Brenner (Sat Dec 17 2016 - 12:35:59 CST)
• Subscribe
  • Vijay L. Roy (Tue Oct 06 2015 - 01:22:14 CDT)
• substrate and membrane protein
  • Lucía Díaz (Mon Nov 02 2015 - 08:03:28 CST)
• Sugar phosphate topology and parameter
  • Dhiraj Srivastava (Thu Apr 14 2016 - 00:32:55 CDT)
• Switch function equation
  • Brian Radak (Mon Oct 03 2016 - 21:16:58 CDT)
  • Faramarz Joodaki (Sun Oct 02 2016 - 23:57:40 CDT)
• Switch off rescale temperature after some number of timesteps
  • Radak, Brian K (Wed Oct 26 2016 - 11:12:36 CDT)
  • Harish Srinivasan (Wed Oct 26 2016 - 01:05:50 CDT)
• System temperature check of specific atoms , sys temp of only coupled atoms?
  • Karson Bader (Thu Jul 21 2016 - 15:36:13 CDT)
• System unstable after turning electric field on.
  • Jeff Comer (Tue Jan 27 2015 - 14:04:26 CST)
  • Jeff Comer (Tue Jan 27 2015 - 13:22:38 CST)
  • Dawid das (Tue Jan 27 2015 - 11:26:50 CST)
• targetCenters in Umbrella Sampling
  • Vermaas, Joshua (Wed Aug 24 2016 - 18:04:31 CDT)
  • Olya Kravchenko (Wed Aug 24 2016 - 17:50:36 CDT)
• Targeted MD and the MARTINI Coarse-Grained Force Field
  • Fotis Baltoumas (Fri Feb 06 2015 - 10:06:55 CST)
• Tcl clock
  • Giacomo Fiorin (Wed Oct 05 2016 - 10:58:47 CDT)
  • Laura Joana (Wed Oct 05 2016 - 10:42:00 CDT)
  • Mayne, Christopher G (Wed Oct 05 2016 - 09:51:15 CDT)
  • Laura Joana (Tue Oct 04 2016 - 14:10:12 CDT)
• Tcl script for simulated tempering?
  • Radak, Brian K (Fri Mar 11 2016 - 16:12:21 CST)
• TCL Scripting for Force Calculations
  • Allen, Caley R (Mon May 02 2016 - 14:08:17 CDT)
  • Jérôme Hénin (Mon May 02 2016 - 11:37:19 CDT)
  • Allen, Caley R (Mon May 02 2016 - 10:48:56 CDT)
• tclBC during SMD and ABF simulations
  • Olya Kravchenko (Mon Nov 28 2016 - 19:44:01 CST)
  • Jérôme Hénin (Mon Nov 28 2016 - 12:45:48 CST)
  • Olya Kravchenko (Mon Nov 28 2016 - 12:36:47 CST)
• tclBC relective boundaries
  • Norman Geist (Mon Feb 01 2016 - 00:10:45 CST)
  • Art (Fri Jan 29 2016 - 17:27:02 CST)
  • Art (Fri Jan 29 2016 - 13:51:17 CST)
• tclBCArgs, passing floating point lists
  • Jim Phillips (Thu Jan 22 2015 - 14:27:15 CST)
  • btreece_at_andrew.cmu.edu (Thu Jan 22 2015 - 14:03:21 CST)
• Temperature assignment REMD
  • Yan Zhou (Mon Jan 05 2015 - 02:27:56 CST)
  • divya nayar (Sat Jan 03 2015 - 08:36:05 CST)
• Tempreture Profile along z axis
  • Jim Phillips (Thu Jan 08 2015 - 10:48:58 CST)
  • JAVAD NOROOZI (Thu Jan 08 2015 - 03:23:12 CST)
• Tesla K80 vs 3 x GTX 980Ti
  • JC Gumbart (Mon Jun 27 2016 - 00:26:31 CDT)
  • Aron Broom (Sun Jun 26 2016 - 15:07:13 CDT)
  • Nikhil Maroli (Sat Jun 25 2016 - 11:24:25 CDT)
  • Nikhil Maroli (Sat Jun 25 2016 - 08:02:25 CDT)
• test area method to calculate surface tension
  • Yan Shen (Thu Feb 25 2016 - 15:05:45 CST)
• Testing NAMD scalability
  • Éric Germaneau (Fri Mar 18 2016 - 20:31:31 CDT)
• The 2 NAMD tests "Alanin" and "tclforces" fail to run with "Atoms moving too fast" error
  • Sriram Adhyapak (Mon Jul 27 2015 - 20:36:14 CDT)
• The adaptTemp and Temp in Adaptive tempering
  • Chenyi L (Thu Jul 07 2016 - 19:51:03 CDT)
  • §³henyi (Thu Jun 09 2016 - 15:17:25 CDT)
• the method to move freely in one direction like a rigid body
  • Xiaokang Liu (Mon May 25 2015 - 05:46:40 CDT)
• The needed time for a MD simulation
  • faride badalkhani (Mon Sep 05 2016 - 10:11:08 CDT)
• The question about Network calculation
  • ÀîÎľê (Thu Jun 23 2016 - 03:28:47 CDT)
• The script of Umbrella sampling
  • JC Gumbart (Fri Dec 25 2015 - 12:49:51 CST)
  • sunyzero (Tue Dec 22 2015 - 03:33:13 CST)
• Thermodynamic integration question
  • Jérôme Hénin (Mon Sep 07 2015 - 01:44:15 CDT)
  • Randall Hall (Sat Sep 05 2015 - 23:28:57 CDT)
• Tilt angle clockwise rotation
  • Jérôme Hénin (Wed Jul 22 2015 - 11:04:55 CDT)
  • Nicolas Martin (Wed Jul 22 2015 - 08:34:47 CDT)
• time per step during GPU-accelerated Implicit Solvent calculations
  • Thomas Albers (Sun Nov 15 2015 - 19:11:26 CST)
• timestep querry
  • Abhishek TYAGI (Thu Apr 02 2015 - 23:07:39 CDT)
  • Brian Radak (Thu Apr 02 2015 - 14:17:47 CDT)
  • Abhishek TYAGI (Wed Apr 01 2015 - 11:15:49 CDT)
  • Aron Broom (Wed Apr 01 2015 - 10:51:31 CDT)
  • Abhishek TYAGI (Wed Apr 01 2015 - 10:28:12 CDT)
• TIP4P topology and parameter files
  • oguz gurbulak (Sun Apr 19 2015 - 05:18:41 CDT)
• TIP4P water for MD
  • Abhishek TYAGI (Mon Apr 13 2015 - 07:44:51 CDT)
• TIP4P water with flexible bonds
  • Jeff Comer (Wed May 18 2016 - 17:03:53 CDT)
  • Hartling, Kathryn (Wed May 18 2016 - 14:32:24 CDT)
• TIP4P/2005 par file by Jordi Faraudo
  • Monika Madhavi (Sat Jan 09 2016 - 14:38:50 CST)
  • Fotis Baltoumas (Sat Jan 09 2016 - 12:13:01 CST)
  • Monika Madhavi (Sat Jan 09 2016 - 07:16:17 CST)
• topology & force field parameters for Sorbitan monooleate (span 80)
  • Madhusoodanan M.R (Tue Jan 06 2015 - 20:32:39 CST)
• Topology and Parameter File
  • Fransiska Kurniawan (Mon Mar 09 2015 - 01:52:36 CDT)
• Topology and parameter files for liquid methane
  • Monika Madhavi (Wed Aug 31 2016 - 00:24:24 CDT)
• Topology and parameters for Sodium dodecanoate
  • Mayne, Christopher G (Wed Nov 04 2015 - 08:05:46 CST)
  • André Farias de Moura (Tue Nov 03 2015 - 12:57:34 CST)
  • Sadegh Faramarzi Ganjabad (Tue Nov 03 2015 - 11:21:45 CST)
• Topology Command in VMD
  • Josh Vermaas (Mon Jun 13 2016 - 08:22:33 CDT)
  • Eric Weine (Thu Jun 09 2016 - 19:27:39 CDT)
• Topology for drugs to do MD after docking
  • Evandro Semighini (Wed Oct 21 2015 - 11:48:21 CDT)
  • Nikhil Maroli (Wed Oct 21 2015 - 11:40:04 CDT)
• transition metal parameters
  • luca belmonte (Fri Jun 24 2016 - 03:04:02 CDT)
  • Francesca Lønstad Bleken (Fri Jun 24 2016 - 02:19:01 CDT)
• Trigger DCD frame from TCL?
  • Brian Radak (Tue Nov 08 2016 - 09:22:24 CST)
  • Norman Geist (Tue Nov 08 2016 - 09:12:04 CST)
• Triple-hybrid topology?
  • Tristan Croll (Tue Oct 06 2015 - 19:26:07 CDT)
• Trouble using the extForces parameters
  • David Hardy (Sat Apr 11 2015 - 12:05:49 CDT)
  • Duster, Adam (Sat Apr 11 2015 - 04:11:42 CDT)
• Truncated octahedron : Problems in PBC when reading a dcd file with NAMD
  • Panel Nicolas (M.) (Mon Mar 16 2015 - 11:18:00 CDT)
• Turning off and back on fixed atoms
  • Radak, Brian K (Thu Oct 27 2016 - 12:05:27 CDT)
  • Norman Geist (Thu Oct 27 2016 - 05:14:28 CDT)
• Tutorial example of replica exchange
  • Dr. Eddie (Fri Mar 11 2016 - 09:35:03 CST)
  • Dr. Eddie (Thu Mar 10 2016 - 12:26:19 CST)
  • Josh Vermaas (Thu Mar 10 2016 - 10:04:07 CST)
  • Dr. Eddie (Thu Mar 10 2016 - 09:46:50 CST)
  • Dr. Eddie (Tue Mar 08 2016 - 16:55:34 CST)
• Umbrella sampling colvars DistanceZ deviates a lot
  • Giacomo Fiorin (Wed Sep 14 2016 - 08:32:43 CDT)
  • Kevin C Chan (Tue Sep 13 2016 - 23:10:21 CDT)
  • Sourav Ray (Tue Sep 13 2016 - 15:22:47 CDT)
  • Giacomo Fiorin (Tue Sep 13 2016 - 15:16:14 CDT)
  • Tabris Chun Chan (Tue Sep 13 2016 - 12:27:25 CDT)
  • Giacomo Fiorin (Tue Sep 13 2016 - 11:23:56 CDT)
  • Kevin C Chan (Tue Sep 13 2016 - 11:19:08 CDT)
• Umbrella sampling of 2 CNT's taking distance as collective variable
  • Jérôme Hénin (Wed Jun 01 2016 - 10:26:27 CDT)
  • Giacomo Fiorin (Wed Jun 01 2016 - 05:07:50 CDT)
  • Kashish Punjani (Wed Jun 01 2016 - 01:16:45 CDT)
• Unable to compile Tachyon on Sun Grid Engine
  • Sourav Ray (Sat Jun 04 2016 - 08:03:44 CDT)
  • Sourav Ray (Sat Jun 04 2016 - 05:59:00 CDT)
  • Sourav Ray (Sat Jun 04 2016 - 04:20:29 CDT)
• UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
  • Anjela Manandhar (Mon Jul 13 2015 - 15:58:55 CDT)
• unbinding free energy using ABF
  • JC Gumbart (Tue Jul 05 2016 - 18:28:59 CDT)
  • Gabriel Jara (Fri Jul 01 2016 - 16:13:32 CDT)
  • JC Gumbart (Thu Jun 30 2016 - 15:51:09 CDT)
  • Gabriel Jara (Thu Jun 30 2016 - 13:25:27 CDT)
• Unexpected(?) callback behavior when minimizing before MD
  • Radak, Brian K (Tue Apr 12 2016 - 16:02:34 CDT)
• unix path length limits for namd
  • Shyam Saladi (Sun May 01 2016 - 19:21:27 CDT)
  • Chris Goedde (Sun May 01 2016 - 17:10:34 CDT)
• Updated Link: Postdoc positions available at IBM (bio-molecular modeling and MD)
  • Sourav Ray (Mon Mar 16 2015 - 12:30:29 CDT)
  • Payel Das (Mon Mar 16 2015 - 10:50:46 CDT)
• Urey-Bradley parameters
  • faride badalkhani (Fri Mar 11 2016 - 09:10:39 CST)
• Usage of velDCDfile and forceDCDfile keywords in viscosity calculations
  • Debashis Kundu (Mon Dec 14 2015 - 00:34:56 CST)
• Using a different potential with NAMD
  • Axel Kohlmeyer (Fri Jun 12 2015 - 09:39:47 CDT)
  • Peter Freddolino (Fri Jun 12 2015 - 09:25:32 CDT)
  • Wade, Alex (Fri Jun 12 2015 - 09:08:48 CDT)
• Using colvars for biasing potential in Umbrella Sampling
  • Giacomo Fiorin (Wed Jan 07 2015 - 10:08:11 CST)
  • begüm alaybeyoÄŸlu (Wed Jan 07 2015 - 10:01:17 CST)
• using colvars to constrain two atoms in a direction
  • Giacomo Fiorin (Wed Dec 14 2016 - 11:11:00 CST)
  • Hamed Fadaei (Wed Dec 14 2016 - 11:02:37 CST)
  • Giacomo Fiorin (Wed Dec 14 2016 - 10:49:31 CST)
  • Giacomo Fiorin (Wed Dec 14 2016 - 10:40:57 CST)
  • Hamed Fadaei (Wed Dec 14 2016 - 10:34:08 CST)
  • Giacomo Fiorin (Wed Dec 14 2016 - 10:22:39 CST)
  • Hamed Fadaei (Wed Dec 14 2016 - 10:15:20 CST)
• Using Mergestructs
  • Eric Weine (Tue May 31 2016 - 14:09:46 CDT)
• using NAMD with CHARMM36 ff
  • Tristan Croll (Wed Jan 21 2015 - 01:37:05 CST)
  • JC Gumbart (Sun Jan 18 2015 - 12:32:35 CST)
  • Branko (Sun Jan 18 2015 - 11:46:38 CST)
  • JC Gumbart (Sat Jan 17 2015 - 19:36:55 CST)
  • Maria Bykhovskaia (Sat Jan 17 2015 - 19:26:29 CST)
• Using NAMD with NMR structure
  • Pardis Tabaee (Mon Oct 24 2016 - 16:02:48 CDT)
  • Steve Chou (Mon Oct 24 2016 - 13:18:34 CDT)
  • Pardis Tabaee (Mon Oct 24 2016 - 11:26:09 CDT)
  • Pardis Tabaee (Mon Oct 24 2016 - 11:20:26 CDT)
  • Brian Radak (Mon Oct 24 2016 - 09:02:02 CDT)
  • Pardis Tabaee (Mon Oct 24 2016 - 06:13:04 CDT)
  • Peter Freddolino (Sun Oct 23 2016 - 05:55:08 CDT)
  • Oscar Bastidas (Sun Oct 23 2016 - 02:00:14 CDT)
• Using the multi-copy version of NAMD on a linux workstation
  • Avisek Das (Mon Jun 01 2015 - 12:22:46 CDT)
  • Norman Geist (Mon Jun 01 2015 - 02:43:36 CDT)
  • Avisek Das (Fri May 29 2015 - 14:43:18 CDT)
• Van der Waals and Electrostatic Forces - CUDA
  • Kostas Malavazos (Tue Nov 10 2015 - 11:11:37 CST)
• varying two colvar distances simultaneously
  • Giacomo Fiorin (Fri Mar 25 2016 - 17:22:37 CDT)
  • Chitrak Gupta (Fri Mar 25 2016 - 17:20:57 CDT)
  • Chitrak Gupta (Fri Mar 25 2016 - 10:58:08 CDT)
  • Giacomo Fiorin (Thu Mar 24 2016 - 16:53:46 CDT)
  • Chitrak Gupta (Thu Mar 24 2016 - 16:49:06 CDT)
• VDW energy diverged & VMD functions applied on cluster
  • Simon Kit Sang Chu (Sat Jul 18 2015 - 16:37:54 CDT)
• vdw parameter error | atom type <-> name problem
  • Art (Wed Mar 11 2015 - 14:03:38 CDT)
• velocity computation
  • Tristan Croll (Tue Feb 09 2016 - 03:04:40 CST)
  • Tristan Croll (Mon Feb 08 2016 - 12:33:16 CST)
  • 'Patrick Welche' (Mon Feb 08 2016 - 08:34:19 CST)
  • Patrick Welche (Fri Feb 05 2016 - 13:05:25 CST)
• velocity IO with psfgen?
  • John Stone (Thu Feb 26 2015 - 12:47:52 CST)
  • Maxim Belkin (Thu Feb 26 2015 - 12:14:24 CST)
  • Brian Radak (Thu Feb 26 2015 - 11:42:22 CST)
  • John Stone (Thu Feb 26 2015 - 11:03:15 CST)
  • Brian Radak (Thu Feb 26 2015 - 10:56:57 CST)
  • Ajasja LjubetiÄ� (Thu Feb 26 2015 - 10:37:55 CST)
  • Brian Radak (Thu Feb 26 2015 - 09:41:04 CST)
• Verification of NAMD Results
  • Kanzliersch, Lukas (Wed Aug 05 2015 - 15:32:38 CDT)
• Viscosity Calculation using EMD
  • Gaurab Sarkar (Mon Dec 14 2015 - 13:22:02 CST)
• visualizing and analyzing long simulation
  • Deng, Jinxia (Nancy) (Mon Oct 10 2016 - 10:51:42 CDT)
  • Richard Overstreet (Mon Oct 10 2016 - 11:48:28 CDT)
  • Dhiraj Srivastava (Mon Oct 10 2016 - 10:41:53 CDT)
• vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params
  • Pardis Tabaee (Fri May 20 2016 - 11:12:24 CDT)
  • Francesco Pietra (Tue May 17 2016 - 11:43:05 CDT)
  • JC Gumbart (Tue May 17 2016 - 09:29:52 CDT)
  • Francesco Pietra (Mon May 16 2016 - 08:54:45 CDT)
  • Francesco Pietra (Mon May 16 2016 - 08:54:31 CDT)
  • Peter Freddolino (Mon May 16 2016 - 07:46:47 CDT)
  • Francesco Pietra (Mon May 16 2016 - 04:30:29 CDT)
• vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech
  • Sourav Ray (Fri Sep 11 2015 - 11:15:47 CDT)
  • JC Gumbart (Fri Sep 11 2015 - 10:08:07 CDT)
  • Sourav Ray (Wed Sep 09 2015 - 22:51:54 CDT)
• vmd-l: GBIS in NAMD 2.10 CUDA with IMD
  • John Stone (Wed Feb 11 2015 - 10:03:39 CST)
• vmd-l: gromacs to charmm conversion
  • Ajasja LjubetiÄ� (Fri Oct 23 2015 - 03:28:28 CDT)
• vmd-l: Including two parameters for protein-ligand simulation
  • Sourav Ray (Wed Oct 28 2015 - 02:20:04 CDT)
• vmd-l: Inconsistent atom count
  • John Stone (Tue Jul 05 2016 - 12:54:26 CDT)
• vmd-l: Number of pdb and psf atoms are not the same!
  • Ashar Malik (Wed Dec 16 2015 - 09:57:47 CST)
  • Francesco Pietra (Wed Dec 16 2015 - 10:14:12 CST)
• vmd-l: PRES and water-ions issues with charmm36
  • Brian Radak (Thu Dec 10 2015 - 15:58:49 CST)
• vmd-l: script error
  • Nikhil Maroli (Sat Oct 03 2015 - 02:44:17 CDT)
  • John Stone (Fri Oct 02 2015 - 10:10:56 CDT)
• vmd-l: Topology for drugs to do MD after docking
  • Mayne, Christopher G (Wed Oct 21 2015 - 14:44:18 CDT)
• vmd-l: velocity IO with psfgen?
  • John Stone (Thu Feb 26 2015 - 10:24:36 CST)
• vmd-l: vmd-I: Fatal Error: Unable to Open CHARMM Parameter File
  • Ajasja LjubetiÄ� (Tue Feb 03 2015 - 07:06:43 CST)
• vmd-l: what is difference between "TOTAL", “TOTAL2" and "POTENTIAL" in the VMD plugin NAMD Plot?
  • 孙业平 (Mon Nov 09 2015 - 06:49:42 CST)
• vmd-l: Which VMD AND NAMD should install
  • John Stone (Tue Sep 22 2015 - 14:07:17 CDT)
• VMD-NAMD and PDB element column
  • Victor Ovchinnikov (Mon Dec 14 2015 - 16:27:41 CST)
  • Francesco Pietra (Mon Dec 14 2015 - 14:52:18 CST)
  • Francesco Pietra (Mon Dec 14 2015 - 14:42:21 CST)
  • Victor Ovchinnikov (Mon Dec 14 2015 - 09:47:54 CST)
  • Jim Phillips (Mon Dec 14 2015 - 09:04:21 CST)
  • Francesco Pietra (Sun Dec 13 2015 - 15:59:37 CST)
  • Jim Phillips (Sun Dec 13 2015 - 14:32:38 CST)
  • Francesco Pietra (Sun Dec 13 2015 - 13:39:11 CST)
  • Jim Phillips (Sun Dec 13 2015 - 12:17:57 CST)
  • Francesco Pietra (Sat Dec 12 2015 - 09:09:55 CST)
• water box and padding
  • Jeff Comer (Mon May 02 2016 - 11:10:45 CDT)
  • Brian Radak (Mon May 02 2016 - 09:54:43 CDT)
  • Dhiraj Srivastava (Sat Apr 30 2016 - 11:40:53 CDT)
• water box has a weird shape
  • Ana Celia Vila Verde (Thu Apr 07 2016 - 02:40:47 CDT)
  • Aron Broom (Wed Apr 06 2016 - 13:41:04 CDT)
  • faride badalkhani (Wed Apr 06 2016 - 13:21:28 CDT)
• water permeability calculation using NAMD trajectories
  • Pragya Priyadarshini (Tue Dec 13 2016 - 22:39:41 CST)
• water permeation through nanotube in lipid bilayer
  • Nikhil Maroli (Fri Jul 29 2016 - 07:18:45 CDT)
• Weird Bond In Non-Polar Tail
  • Axel Kohlmeyer (Thu Jun 18 2015 - 10:45:06 CDT)
  • Danielle Grodi (Thu Jun 18 2015 - 10:15:53 CDT)
• Weird psfgen bug?
  • Tristan Croll (Fri Oct 30 2015 - 03:22:06 CDT)
• WG: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800
  • Greipel.Joachim_at_mh-hannover.de (Mon Mar 14 2016 - 04:47:28 CDT)
• what exactly is the form of the cosine angle potential?
  • Fotis Baltoumas (Fri Jul 17 2015 - 08:47:55 CDT)
  • Charlesworth, Henry (Fri Jul 17 2015 - 08:08:50 CDT)
• where can I find the parameter file for chlorophenols?
  • Jeff Comer (Mon May 25 2015 - 14:35:46 CDT)
  • ¶¡êÏ (Sun May 24 2015 - 08:30:15 CDT)
• Which Binary to use?
  • Norman Geist (Mon Apr 27 2015 - 01:59:17 CDT)
  • Sourav Ray (Fri Apr 24 2015 - 00:45:44 CDT)
  • Arijit Ghosh (Fri Apr 24 2015 - 00:10:49 CDT)
• Which namd to use
  • Jim Phillips (Fri Nov 20 2015 - 11:11:30 CST)
  • Maxime Boissonneault (Fri Nov 20 2015 - 08:13:58 CST)
  • Jim Phillips (Fri Nov 20 2015 - 08:02:36 CST)
  • Maxime Boissonneault (Fri Nov 20 2015 - 07:29:45 CST)
• WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM?
  • Jeff Comer (Mon Mar 02 2015 - 10:45:28 CST)
  • Richard Overstreet (Sun Mar 01 2015 - 16:56:39 CST)
  • Amin Dehkharghani (Sun Mar 01 2015 - 14:58:08 CST)
• Which VMD AND NAMD should install
  • Nikhil Maroli (Sat Sep 19 2015 - 01:57:30 CDT)
• why does the transition seem to be irreversible in aMD
  • sunyeping (Mon Apr 04 2016 - 22:21:00 CDT)
• Why does the water box collapse in an aMD
  • sunyeping (Mon Jun 13 2016 - 21:11:00 CDT)
• Why the computational speed does not increase with the increase of GPUs?
  • sunyeping (Wed Oct 21 2015 - 22:18:17 CDT)
• Why the Lennard−Jones parameters E for anions are usually larger than cations?
  • Axel Kohlmeyer (Mon Jun 15 2015 - 05:36:16 CDT)
  • bay__gulf618_at_sina.com (Mon Jun 15 2015 - 04:02:44 CDT)
• Why wrapped and unwrapped trajectories show different energies over the time?
  • Brian Radak (Sun Apr 24 2016 - 09:03:07 CDT)
  • Jason Swails (Sun Apr 24 2016 - 00:23:50 CDT)
  • zeynab hoseyni (Sat Apr 23 2016 - 21:22:04 CDT)
• Why wrapped and unwrapped trajectories show different energies over time?
  • zeynab mohamad hoseyni (Sat Apr 23 2016 - 09:30:08 CDT)
• WHY!!! num_runs should be divisible by runs_per_frame * frames_per_restart -->REMD
  • Nicholus Bhattacharjee (Wed May 04 2016 - 10:07:53 CDT)
  • Peter Freddolino (Tue May 03 2016 - 11:08:17 CDT)
  • Nicholus Bhattacharjee (Fri Apr 22 2016 - 08:21:46 CDT)
• Would it be possible to continue a simulation from any snapshot of a trajectory?
  • sunyeping (Thu Nov 12 2015 - 20:57:20 CST)
  • Felipe Merino (Thu Nov 12 2015 - 03:33:05 CST)
  • sunyeping (Thu Nov 12 2015 - 02:45:51 CST)
• Wrapall on or off?
  • Radak, Brian K (Tue Sep 27 2016 - 10:50:33 CDT)
  • sunyeping (Tue Sep 27 2016 - 00:14:49 CDT)
• wrapping in NVT
  • Abhishek TYAGI (Wed Jul 22 2015 - 00:27:02 CDT)
  • Richard Overstreet (Wed Jul 22 2015 - 01:05:30 CDT)
  • Abhishek TYAGI (Tue Jul 21 2015 - 22:59:52 CDT)
• Wrapping molecules in a NAMD simulation
  • Sourav Ray (Mon Apr 04 2016 - 08:23:02 CDT)
• Writing number of atoms in a specific group to a file
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