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NAMD-L: By Subject

By Subject

2588 messages sorted by: [ author ] [ date ] [ thread ] [ attachment ]
About this archive

Starting: Sat Jan 02 2016 - 22:55:30 CST
Ending: Sat Dec 30 2017 - 12:48:03 CST

• Haohao Fu (Fri Dec 29 2017 - 21:36:33 CST)
• Shahee Islam (Mon Dec 04 2017 - 03:57:36 CST)
• Vermaas, Joshua (Fri Dec 01 2017 - 08:35:31 CST)
• Victor Ovchinnikov (Thu Mar 23 2017 - 16:34:22 CDT)
• 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)
• "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL
  • João Ribeiro (Mon Jul 17 2017 - 14:45:43 CDT)
  • João Ribeiro (Tue Jun 27 2017 - 13:46:57 CDT)
• "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)
• "Periodic cell has become too small for original patch grid!" with membrane system on GPU
  • David Hardy (Fri Aug 25 2017 - 14:39:24 CDT)
  • James Starlight (Thu Jul 20 2017 - 06:03:29 CDT)
• (1) Failure running QM-MM with ORCA and (2) problems preparing input with transition metals
  • Francesco Pietra (Mon Jan 02 2017 - 01:38:54 CST)
• (no subject)
  • Suresh Ghimire (Fri Dec 29 2017 - 19:57:56 CST)
  • Suresh Ghimire (Fri Dec 22 2017 - 09:54:23 CST)
  • Shahee Islam (Fri Dec 01 2017 - 02:28:17 CST)
  • Marco Antonio Ramirez Martinez (Thu Mar 23 2017 - 13:23:33 CDT)
  • Debaditya Mukherjee (Tue Mar 21 2017 - 23:38:56 CDT)
  • Debaditya Mukherjee (Fri Mar 10 2017 - 23:40:50 CST)
  • Debaditya Mukherjee (Wed Mar 08 2017 - 22:52:17 CST)
  • Raul Araya (Tue Jan 03 2017 - 14:22:09 CST)
  • 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)
• ++idlepoll
  • Zeki Zeybek (Mon Feb 06 2017 - 02:59:51 CST)
  • Francesco Pietra (Mon Feb 06 2017 - 02:37:33 CST)
  • Zeki Zeybek (Mon Feb 06 2017 - 01:21:19 CST)
• ------------- Processor 0 Exiting: Called CmiAbort ------------
  • Pardis Tabaee (Thu Mar 17 2016 - 12:09:43 CDT)
• -nan values and fatal error
  • Vermaas, Joshua (Thu Sep 07 2017 - 12:15:51 CDT)
  • Natasha Gupta (Thu Sep 07 2017 - 11:24:29 CDT)
• 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)
• 2.12, cufft problems on a GTX 1070 ?
  • Nicholas M Glykos (Sun Jan 01 2017 - 03:56:32 CST)
• 2.12, cufft problems on a GTX 1070 ? [SOLVED]
  • Nicholas M. Glykos (Wed Jan 11 2017 - 12:51:54 CST)
• 2016 ISQBP Meeting: early registration / abstract submission deadline approaching
  • Vlad Cojocaru (Thu Mar 17 2016 - 03:49:47 CDT)
• [NAMD] File Missing in Nanopore Tutorial
  • The Cromicus Productions (Mon Sep 11 2017 - 22:38:23 CDT)
• [NAMD] How to build and simulate a periodic DNA in NAMD
  • The Cromicus Productions (Sun Jun 18 2017 - 17:47:39 CDT)
  • Vermaas, Joshua (Tue Jun 13 2017 - 12:09:32 CDT)
  • The Cromicus Productions (Tue Jun 13 2017 - 05:42:00 CDT)
  • Vermaas, Joshua (Fri Jun 09 2017 - 12:42:49 CDT)
  • The Cromicus Productions (Fri Jun 09 2017 - 12:31:08 CDT)
  • The Cromicus Productions (Sun May 07 2017 - 00:03:43 CDT)
  • The Cromicus Productions (Sat May 06 2017 - 23:30:26 CDT)
  • The Cromicus Productions (Sat May 06 2017 - 19:02:57 CDT)
  • Nielsen, Steven (Sat May 06 2017 - 13:49:13 CDT)
  • The Cromicus Productions (Sat May 06 2017 - 13:14:34 CDT)
• [NAMD] Obtain dynamical matrix away from equilibrium
  • The Cromicus Productions (Thu Feb 09 2017 - 12:02:35 CST)
• [NAMD] Outputting PMF at half the time using Metadynamics
  • Giacomo Fiorin (Sun May 14 2017 - 22:20:14 CDT)
  • The Cromicus Productions (Sun May 14 2017 - 14:04:32 CDT)
• [NAMD] Patch 5MC2
  • The Cromicus Productions (Thu Nov 30 2017 - 12:25:55 CST)
  • The Cromicus Productions (Wed Nov 29 2017 - 17:45:16 CST)
• [NAMD] Problem with colvar "tilt"
  • Jérôme Hénin (Mon May 15 2017 - 08:42:37 CDT)
  • Giacomo Fiorin (Fri May 12 2017 - 14:00:25 CDT)
  • Ajasja LjubetiÄ� (Fri May 12 2017 - 13:41:54 CDT)
  • The Cromicus Productions (Fri May 12 2017 - 13:29:17 CDT)
  • Giacomo Fiorin (Fri May 12 2017 - 08:43:41 CDT)
  • The Cromicus Productions (Fri May 12 2017 - 08:34:33 CDT)
• [NAMD] Question about patches
  • JC Gumbart (Tue Dec 26 2017 - 09:26:12 CST)
  • Lennart Nilsson (Tue Dec 26 2017 - 04:43:30 CST)
  • The Cromicus Productions (Mon Dec 25 2017 - 18:04:43 CST)
  • The Cromicus Productions (Mon Dec 25 2017 - 17:53:36 CST)
  • The Cromicus Productions (Mon Dec 25 2017 - 17:29:06 CST)
  • Lennart Nilsson (Mon Dec 25 2017 - 09:17:51 CST)
  • Natalia Ostrowska (Mon Dec 25 2017 - 01:58:35 CST)
  • JC Gumbart (Sun Dec 24 2017 - 15:16:10 CST)
  • The Cromicus Productions (Sun Dec 24 2017 - 03:49:07 CST)
• [NAMD] Running NAMD in Stampede2
  • Chitrak Gupta (Sun Oct 01 2017 - 19:21:52 CDT)
  • The Cromicus Productions (Fri Sep 29 2017 - 14:59:34 CDT)
• [NAMD] Simulations in guanidinium chloride
  • The Cromicus Productions (Tue Sep 12 2017 - 15:57:13 CDT)
• [NAMD] Too many collective variables?
  • Giacomo Fiorin (Thu Oct 26 2017 - 15:34:51 CDT)
  • The Cromicus Productions (Thu Oct 26 2017 - 15:11:19 CDT)
• [NAMD] Using ABF to study separation of two molecules
  • Giacomo Fiorin (Mon Jan 23 2017 - 09:15:16 CST)
  • The Cromicus Productions (Mon Jan 23 2017 - 09:12:39 CST)
  • Giacomo Fiorin (Mon Jan 23 2017 - 08:43:26 CST)
  • The Cromicus Productions (Mon Jan 23 2017 - 01:00:48 CST)
• [NAMD] Using as collective variable the minimum of a set of distances
  • Giacomo Fiorin (Mon Jan 30 2017 - 17:07:07 CST)
  • The Cromicus Productions (Mon Jan 30 2017 - 16:53:34 CST)
  • Jérôme Hénin (Sun Jan 29 2017 - 10:25:38 CST)
  • The Cromicus Productions (Sat Jan 28 2017 - 17:07:52 CST)
• [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 (Mon Mar 13 2017 - 17:04:00 CDT)
  • 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 FEP with multichain receptor
  • Jérôme Hénin (Tue Jul 11 2017 - 11:52:23 CDT)
  • Francesco Pietra (Tue Jul 11 2017 - 11:28:48 CDT)
  • Jérôme Hénin (Tue Jul 11 2017 - 08:12:51 CDT)
  • Francesco Pietra (Sun Jul 09 2017 - 00:44:14 CDT)
  • Jérôme Hénin (Sat Jul 08 2017 - 15:07:36 CDT)
  • Francesco Pietra (Sat Jul 08 2017 - 11:08:41 CDT)
  • Jérôme Hénin (Sat Jul 08 2017 - 05:46:31 CDT)
  • Francesco Pietra (Fri Jul 07 2017 - 10:21:52 CDT)
• ABF for dihedrals
  • Giacomo Fiorin (Thu Aug 03 2017 - 12:53:19 CDT)
  • Albers, Thomas (Thu Aug 03 2017 - 12:48:24 CDT)
• ABF vs Umbrella Sampling entrance barrier heights discrepancy
  • Jérôme Hénin (Thu Aug 10 2017 - 14:11:42 CDT)
  • Olya Kravchenko (Thu Aug 10 2017 - 12:45:48 CDT)
  • Jérôme Hénin (Sun Aug 06 2017 - 10:17:44 CDT)
  • Olya Kravchenko (Wed Aug 02 2017 - 13:39:16 CDT)
• ABF with alpha colvar?
  • Giacomo Fiorin (Sat Jan 21 2017 - 15:21:21 CST)
  • Douglas Houston (Sat Jan 21 2017 - 11:30:49 CST)
• ABF: umbrella_int.awk
  • Francesco Pietra (Sat Jul 15 2017 - 08:45:00 CDT)
  • Giacomo Fiorin (Sat Jul 15 2017 - 07:04:13 CDT)
  • yjcoshc_at_gmail.com (Sat Jul 15 2017 - 07:02:33 CDT)
  • Francesco Pietra (Sat Jul 15 2017 - 03:36:33 CDT)
  • Giacomo Fiorin (Fri Jul 14 2017 - 08:21:10 CDT)
  • Giacomo Fiorin (Fri Jul 14 2017 - 08:20:15 CDT)
  • Francesco Pietra (Fri Jul 14 2017 - 03:39:48 CDT)
  • Jérôme Hénin (Thu Jul 13 2017 - 13:14:33 CDT)
  • Francesco Pietra (Thu Jul 13 2017 - 10:32:40 CDT)
• about colvar module in NAMD
  • Jessen Lucas (Wed Feb 01 2017 - 13:01:24 CST)
  • Jessen Lucas (Wed Feb 01 2017 - 13:00:04 CST)
  • Giacomo Fiorin (Wed Feb 01 2017 - 12:49:24 CST)
  • Giacomo Fiorin (Wed Feb 01 2017 - 12:34:57 CST)
  • Giacomo Fiorin (Wed Feb 01 2017 - 12:31:36 CST)
  • Jessen Lucas (Wed Feb 01 2017 - 11:47:41 CST)
• about GaMD reweighting
  • Radak, Brian K (Tue Jun 06 2017 - 11:29:09 CDT)
  • Francesco Pietra (Tue Jun 06 2017 - 10:58:40 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 the performance of RAMD
  • Francesco Pietra (Sat Nov 11 2017 - 00:46:49 CST)
  • vlad.cojocaru_at_mpi-muenster.mpg.de (Fri Nov 10 2017 - 13:38:17 CST)
  • Giacomo Fiorin (Fri Nov 10 2017 - 13:14:40 CST)
  • Francesco Pietra (Fri Nov 10 2017 - 10:55:42 CST)
• About the robustness of ABF and FEB protein-ligand
  • Francesco Pietra (Wed Jun 28 2017 - 09:40:15 CDT)
• about User-Defined Forces
  • ¸ß¾ü (Mon Jan 18 2016 - 03:28:31 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)
• 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)
• 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)
• Amber force filed input failure on GPU
  • Bata Zsófia (Wed Oct 25 2017 - 10:40:06 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 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)
• analyze NAMD trajectory in Curves+
  • Radak, Brian K (Mon Mar 06 2017 - 12:03:25 CST)
  • Oleksii Zdorevskyi (Mon Mar 06 2017 - 11:46:03 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)
• 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 constant force on water molecules in a particular direction
  • Jérôme Hénin (Mon Sep 11 2017 - 05:12:50 CDT)
  • Sanjib Paul (Mon Sep 11 2017 - 01:22:48 CDT)
  • Giacomo Fiorin (Wed Sep 06 2017 - 07:08:34 CDT)
  • Sanjib Paul (Wed Sep 06 2017 - 06:14:16 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 KNL a good choice for classical MD?
  • Francesco Pietra (Sun Aug 06 2017 - 03:04:31 CDT)
  • Francesco Pietra (Sat Aug 05 2017 - 02:02:09 CDT)
  • Vermaas, Joshua (Fri Aug 04 2017 - 16:34:28 CDT)
  • Francesco Pietra (Fri Aug 04 2017 - 15:51:48 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)
• atom selection error
  • Shahee Islam (Tue Dec 12 2017 - 01:31:22 CST)
  • Peter Freddolino (Mon Dec 11 2017 - 14:26:26 CST)
  • Vermaas, Joshua (Mon Dec 11 2017 - 11:28:09 CST)
  • Brian Radak (Mon Dec 11 2017 - 11:14:36 CST)
  • Atanu Maity (Mon Dec 11 2017 - 08:30:55 CST)
  • Shahee Islam (Mon Dec 11 2017 - 00:52:18 CST)
  • Peter Freddolino (Mon Dec 11 2017 - 00:38:19 CST)
  • Shahee Islam (Mon Dec 11 2017 - 00:33:38 CST)
  • Peter Freddolino (Mon Dec 11 2017 - 00:24:47 CST)
  • Shahee Islam (Mon Dec 11 2017 - 00:04:47 CST)
  • Peter Freddolino (Fri Dec 08 2017 - 11:54:00 CST)
  • Brian Radak (Fri Dec 08 2017 - 10:41:57 CST)
  • Shahee Islam (Fri Dec 08 2017 - 08:22:51 CST)
  • Peter Freddolino (Fri Dec 08 2017 - 07:59:51 CST)
  • Shahee Islam (Fri Dec 08 2017 - 02:33:19 CST)
• Atoms too fast/periodic cell too small with ABF protein-ligand
  • Francesco Pietra (Sun Jun 25 2017 - 05:56:01 CDT)
• ATP - CGENFF
  • JC Gumbart (Thu Jun 09 2016 - 09:36:37 CDT)
  • Benjamin Hill (Tue Jun 07 2016 - 19:34:15 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)
• 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: ++idlepoll
  • Norman Geist (Mon Feb 06 2017 - 02:15:12 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: 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: AW: AW: not a number in NAMD log file
  • Norman Geist (Mon Jan 30 2017 - 01:44:14 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: NAMD-2.12 CUDA2 and PMECUDA problems
  • Norman Geist (Wed Aug 30 2017 - 03:47:53 CDT)
• AW: AW: problem with +devices using
  • Norman Geist (Tue Apr 05 2016 - 08:21:37 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: 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: building system with or without water for metadynamics
  • Norman Geist (Wed Oct 18 2017 - 01:35:32 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: Change pressure during simulation
  • Norman Geist (Wed Nov 15 2017 - 01:28:06 CST)
• AW: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED)
  • Norman Geist (Tue Jan 12 2016 - 02:16:38 CST)
• 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: FATAL ERROR CUDA error during equilibration using NAMD
  • Norman Geist (Thu Sep 01 2016 - 01:15:55 CDT)
• AW: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
  • Norman Geist (Fri Feb 10 2017 - 05:34:40 CST)
  • Norman Geist (Wed Feb 08 2017 - 02:22:17 CST)
• 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: High pressure calculations
  • faride badalkhani (Sat Feb 04 2017 - 06:11:52 CST)
  • Francesco Pietra (Sat Feb 04 2017 - 06:00:53 CST)
  • Andrey KALINICHEV (Sat Feb 04 2017 - 05:54:36 CST)
  • Norman Geist (Sat Feb 04 2017 - 05:33:49 CST)
• 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: Movie in VMD
  • Daniel Möller (Sun Aug 27 2017 - 08:13:39 CDT)
• 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 performance monitor
  • Norman Geist (Wed Jan 18 2017 - 01:10:26 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-2.12 CUDA2 and PMECUDA problems
  • Norman Geist (Fri Sep 01 2017 - 03:23:28 CDT)
  • Nicholas M Glykos (Wed Aug 30 2017 - 03:05:17 CDT)
  • Norman Geist (Wed Aug 30 2017 - 02:13:41 CDT)
• AW: NAMD-2.12 handful of issues with CUDA
  • Norman Geist (Fri Mar 10 2017 - 05:41:10 CST)
  • Norman Geist (Fri Mar 10 2017 - 04:55:47 CST)
• AW: NAMD2.11 DCD HEADER PROBLEM
  • Norman Geist (Thu Sep 15 2016 - 01:09:39 CDT)
• AW: not a number in NAMD log file
  • Mohaddeseh Habibzadeh (Wed Jan 18 2017 - 06:44:58 CST)
  • Norman Geist (Wed Jan 18 2017 - 01:14:12 CST)
• 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: Organic Solvent & Water Simulation
  • Norman Geist (Wed Jun 21 2017 - 02:31:42 CDT)
• 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: 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 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: question about GPU
  • Norman Geist (Wed Feb 08 2017 - 02:24:53 CST)
  • Norman Geist (Tue Feb 07 2017 - 03:15:30 CST)
  • Norman Geist (Mon Feb 06 2017 - 09:47:28 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: 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: REMD on HPC
  • HOUSTON Douglas (Tue Mar 07 2017 - 02:33:29 CST)
  • Vermaas, Joshua (Mon Mar 06 2017 - 09:47:23 CST)
  • Norman Geist (Mon Mar 06 2017 - 09:26:00 CST)
• 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: Scaling behaviour of NAMD on hosts with GPU accelerators
  • Norman Geist (Fri Mar 24 2017 - 08:25:52 CDT)
• AW: Scaling behaviour of NAMD on hosts with GPU accelrators
  • Maxime Boissonneault (Fri Mar 24 2017 - 06:42:04 CDT)
  • Norman Geist (Fri Mar 24 2017 - 05:47:39 CDT)
  • Norman Geist (Fri Mar 24 2017 - 05:35:00 CDT)
  • Norman Geist (Fri Mar 24 2017 - 05:27:46 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: Solvent box fluctuations
  • Götz, Alexander (Wed Mar 29 2017 - 03:37:59 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: Testing NAMD scalability
  • Eric Germaneau (Mon Mar 21 2016 - 03:15:06 CDT)
  • Norman Geist (Mon Mar 21 2016 - 02:45:31 CDT)
• 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: Building NAMD 2.12 from Source with IB and CUDA
  • Greipel.Joachim_at_mh-hannover.de (Thu Mar 02 2017 - 05:53:58 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: 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: 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)
• 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)
• basis set for QM-MM dft
  • Francesco Pietra (Thu Jan 26 2017 - 01:19:29 CST)
  • Marcelo C. R. Melo (Wed Jan 25 2017 - 13:18:36 CST)
  • Francesco Pietra (Wed Jan 25 2017 - 09:15:43 CST)
• Best NAMD distribution for COEUS cluster?
  • Bassam Haddad (Thu Apr 13 2017 - 15:27:10 CDT)
• Bias-exchange metadynamics
  • Giacomo Fiorin (Sun Nov 19 2017 - 17:30:49 CST)
  • Azadeh Alavizargar (Fri Nov 17 2017 - 05:07:56 CST)
• Binding energy of organic molecules/small peptides on the surface of Silicon Dioxide
  • Roshan Shrestha (Thu May 26 2016 - 10:29:01 CDT)
• bond energy high
  • Ipsita Basu (Wed Feb 03 2016 - 05:15:35 CST)
• Bond-jitter/Total-energy-spikes during energy minimization in vacuum
  • Eric Smoll (Mon May 01 2017 - 02:58:10 CDT)
• Build NAMD with CUDA for unix workstation (centos 7)
  • Haohao Fu (Wed Sep 20 2017 - 03:25:16 CDT)
  • Daipayan Sarkar (Wed Sep 20 2017 - 03:04:32 CDT)
  • Haohao Fu (Wed Sep 20 2017 - 02:22:17 CDT)
  • Daipayan Sarkar (Wed Sep 20 2017 - 01:54:25 CDT)
• Building namd 2.12 from source an ARM64 architecture
  • istamkos_at_auth.gr (Fri Sep 29 2017 - 17:38:21 CDT)
  • Fotis Baltoumas (Wed Sep 27 2017 - 18:15:36 CDT)
  • Vermaas, Joshua (Wed Sep 27 2017 - 18:09:31 CDT)
  • istamkos_at_auth.gr (Wed Sep 27 2017 - 17:06:00 CDT)
• 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)
• building system with or without water for metadynamics
  • Giacomo Fiorin (Tue Oct 17 2017 - 21:34:55 CDT)
  • Vermaas, Joshua (Tue Oct 17 2017 - 19:06:12 CDT)
  • Rabeta Yeasmin (Tue Oct 17 2017 - 16:52:38 CDT)
• calculate cumulative dG
  • Nehad Elsalamouny (Wed Aug 30 2017 - 19:20:09 CDT)
  • Brian Radak (Tue Aug 29 2017 - 10:08:25 CDT)
  • Nehad Elsalamouny (Tue Aug 29 2017 - 00:18:16 CDT)
• Calculating electrostatic force from NAMD trajectory
  • Ben Lowe (Fri Jul 07 2017 - 02:14:30 CDT)
  • sunyeping (Mon Jul 03 2017 - 21:42:56 CDT)
  • Ben Lowe (Mon Jul 03 2017 - 21:35:50 CDT)
• Calculating gradient of the potential (force field) on each atom.
  • Brian Radak (Fri Jan 13 2017 - 11:34:11 CST)
  • Wasut Pornpatcharapong (Thu Jan 12 2017 - 17:37:55 CST)
• 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)
• Can large number of atoms define in colvariables reduce the computational speed in adaptive biased force (ABF) simulation via lowering the GPU utility?
  • sunyeping (Thu Apr 27 2017 - 00:34:49 CDT)
  • Giacomo Fiorin (Wed Apr 26 2017 - 13:34:12 CDT)
  • sunyeping (Wed Apr 26 2017 - 12:51:17 CDT)
• Carma/grcarma v.1.7 released.
  • Nicholas M Glykos (Mon Mar 06 2017 - 10:31:26 CST)
• Cascade MDFF
  • Ryan McGreevy (Thu Mar 09 2017 - 10:53:42 CST)
  • Ryan McGreevy (Thu Mar 09 2017 - 08:25:56 CST)
  • Luba Simhaev (Thu Mar 09 2017 - 02:34:08 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)
• Center of mass drift
  • M. Wong (Sat Jun 03 2017 - 04:44:18 CDT)
  • David Hardy (Fri Jun 02 2017 - 12:35:12 CDT)
  • Radak, Brian K (Fri Jun 02 2017 - 10:10:01 CDT)
  • M. Wong (Fri Jun 02 2017 - 04:10:50 CDT)
• cgenff
  • Benjamin Hill (Mon Jun 06 2016 - 14:48:30 CDT)
• CGENFF validation
  • faride badalkhani (Fri Mar 18 2016 - 15:12:56 CDT)
• Change pressure during simulation
  • Monika Madhavi (Wed Nov 15 2017 - 01:07:39 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++ Fatal Error Question
  • Oscar Bastidas (Mon Feb 20 2017 - 11:36:53 CST)
• Charm++ fatal error with QM-MM MOPAC
  • Marcelo C. R. Melo (Tue Jan 17 2017 - 15:52:04 CST)
  • Marcelo C. R. Melo (Mon Jan 16 2017 - 15:52:41 CST)
  • Francesco Pietra (Sun Jan 15 2017 - 02:53:17 CST)
  • Francesco Pietra (Sun Jan 15 2017 - 01:55:20 CST)
  • Francesco Pietra (Tue Jan 10 2017 - 10:50:58 CST)
  • Francesco Pietra (Tue Jan 10 2017 - 10:40:39 CST)
  • Marcelo C. R. Melo (Tue Jan 10 2017 - 08:11:02 CST)
  • Francesco Pietra (Tue Jan 10 2017 - 01:56:35 CST)
• Charm++ supports RoCE ?
  • Hyun (Mon Mar 20 2017 - 22:22:40 CDT)
  • Hyun (Thu Mar 16 2017 - 18:06:01 CDT)
• charmc rpath
  • Scott Brozell (Thu Jan 21 2016 - 22:04:41 CST)
• charmm parameters for buffer molecules
  • Martin, Erik W (Fri Apr 07 2017 - 15:10:46 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)
• CHARMRUN ERROR
  • Scott Brozell (Fri May 19 2017 - 11:17:18 CDT)
  • Zeki Zeybek (Thu May 18 2017 - 13:38:26 CDT)
  • Scott Brozell (Thu May 18 2017 - 13:28:52 CDT)
  • Zeki Zeybek (Thu May 18 2017 - 02:27:27 CDT)
  • Zeki Zeybek (Fri May 12 2017 - 02:05:13 CDT)
  • Boonstra, S. (Thu May 11 2017 - 15:03:38 CDT)
  • Zeki Zeybek (Thu May 11 2017 - 02:39:43 CDT)
• Choice of bromide ion LJ parameters
  • Harish Srinivasan (Tue Mar 07 2017 - 07:03:16 CST)
• 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 Grain of a Calcium Binding Protein
  • Ajasja LjubetiÄ� (Wed Aug 09 2017 - 10:51:34 CDT)
  • Nisler, Collin R. (Wed Aug 09 2017 - 10:31:24 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)
• coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion"
  • Yaxin An (Fri Jun 09 2017 - 10:38:33 CDT)
  • Peter Freddolino (Fri Jun 09 2017 - 10:10:21 CDT)
  • Richard Overstreet (Fri Jun 09 2017 - 09:45:06 CDT)
  • Yaxin An (Fri Jun 09 2017 - 09:39:28 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)
• Collective variable remains at zero during Umbrella Sampling
  • Giacomo Fiorin (Mon Jul 10 2017 - 21:46:53 CDT)
  • Hemanth Vemuri (Sun Jul 09 2017 - 23:59:18 CDT)
• Colvar distance xy to restrain ions
  • Azadeh Alavizargar (Fri Jan 13 2017 - 15:00:16 CST)
  • Olya Kravchenko (Thu Jan 12 2017 - 10:39:00 CST)
  • Jérôme Hénin (Thu Jan 12 2017 - 04:40:41 CST)
  • Azadeh Alavizargar (Thu Jan 12 2017 - 04:30:42 CST)
  • Jérôme Hénin (Thu Jan 12 2017 - 04:09:12 CST)
  • Azadeh Alavizargar (Thu Jan 12 2017 - 02:42:25 CST)
• colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12
  • Giacomo Fiorin (Tue May 16 2017 - 12:18:18 CDT)
  • Vlad Cojocaru (Tue May 16 2017 - 10:50:10 CDT)
  • Giacomo Fiorin (Tue May 16 2017 - 09:39:59 CDT)
  • Vlad Cojocaru (Tue May 16 2017 - 09:36:38 CDT)
  • Jérôme Hénin (Tue May 16 2017 - 09:08:46 CDT)
  • Vlad Cojocaru (Tue May 16 2017 - 08:20:31 CDT)
  • Vlad Cojocaru (Mon May 15 2017 - 04:18:28 CDT)
• Colvar Error
  • Souvik Sinha (Mon Dec 04 2017 - 12:34:36 CST)
  • Jérôme Hénin (Mon Dec 04 2017 - 12:19:31 CST)
  • Souvik Sinha (Mon Dec 04 2017 - 08:37:09 CST)
  • Giacomo Fiorin (Mon Dec 04 2017 - 08:03:05 CST)
  • Souvik Sinha (Mon Dec 04 2017 - 07:33:12 CST)
• Colvar orientation and CoG
  • Jérôme Hénin (Fri Jun 17 2016 - 04:43:06 CDT)
  • Nicolas Martin (Thu Jun 16 2016 - 09:02:28 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 not scaling well in NAMD 2.10
  • Chitrak Gupta (Fri Feb 24 2017 - 11:46:32 CST)
  • Giacomo Fiorin (Thu Feb 23 2017 - 21:58:43 CST)
  • Jérôme Hénin (Thu Feb 23 2017 - 17:36:52 CST)
  • Chitrak Gupta (Thu Feb 23 2017 - 17:25:14 CST)
• 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 to restrain peptide close to lipid
  • Giacomo Fiorin (Sun May 21 2017 - 11:31:42 CDT)
  • Chitrak Gupta (Sat May 20 2017 - 16:10:35 CDT)
  • Giacomo Fiorin (Thu Apr 27 2017 - 15:13:14 CDT)
  • Chitrak Gupta (Thu Apr 27 2017 - 15:11:17 CDT)
  • Giacomo Fiorin (Wed Apr 26 2017 - 18:46:50 CDT)
  • Jeff Comer (Wed Apr 26 2017 - 15:31:33 CDT)
  • Chitrak Gupta (Wed Apr 26 2017 - 15:15:10 CDT)
  • Chitrak Gupta (Wed Apr 26 2017 - 15:01:23 CDT)
• Colvars wall boundaries for CoordNum
  • Giacomo Fiorin (Thu Jun 08 2017 - 19:42:46 CDT)
  • Wasut Pornpatcharapong (Thu Jun 08 2017 - 19:27:50 CDT)
• colvars/rmsd: Error: definition for atom group "atoms" not found.
  • Victor Kwan (Sun Dec 03 2017 - 15:15:38 CST)
  • Bogdan Marekha (Sun Dec 03 2017 - 06:35:28 CST)
  • Victor Kwan (Sun Dec 03 2017 - 05:12:06 CST)
• colvars: Did the orthogonality requirements of colvars change in ABF?
  • Jérôme Hénin (Tue Oct 17 2017 - 08:23:44 CDT)
  • yjcoshc (Mon Oct 16 2017 - 22:23:06 CDT)
  • Giacomo Fiorin (Mon Oct 16 2017 - 21:43:40 CDT)
  • yjcoshc (Mon Oct 16 2017 - 20:20:29 CDT)
• colvars: Error: Feature unavailable:compute total collective force only from one group center
  • Giacomo Fiorin (Wed Mar 01 2017 - 02:04:00 CST)
  • Bennion, Brian (Mon Feb 27 2017 - 17:36:53 CST)
  • Bennion, Brian (Fri Feb 24 2017 - 10:33:28 CST)
  • Giacomo Fiorin (Thu Feb 23 2017 - 21:50:08 CST)
  • Bennion, Brian (Thu Feb 23 2017 - 14:58:54 CST)
  • Bennion, Brian (Thu Feb 23 2017 - 14:35:22 CST)
  • Giacomo Fiorin (Thu Feb 23 2017 - 14:44:00 CST)
  • Bennion, Brian (Thu Feb 23 2017 - 10:38:39 CST)
  • Giacomo Fiorin (Thu Feb 23 2017 - 03:10:20 CST)
  • Ajasja LjubetiÄ� (Thu Feb 23 2017 - 01:36:03 CST)
  • Bennion, Brian (Wed Feb 22 2017 - 18:17:44 CST)
• colvars: Error: keyword "translatereference" is not supported, or not recognized in this context.
  • Haohao Fu (Sun Dec 17 2017 - 23:54:10 CST)
  • Victor Kwan (Sun Dec 17 2017 - 22:35:33 CST)
• colvars: keepFreeEnergyFiles doesn't work in latest colvars version
  • yjcoshc_at_gmail.com (Sat Sep 30 2017 - 22:41:30 CDT)
  • Giacomo Fiorin (Sat Sep 30 2017 - 12:32:26 CDT)
  • yjcoshc (Fri Sep 29 2017 - 21:38:13 CDT)
• 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)
• 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 2.12 fails
  • David Hardy (Fri Apr 28 2017 - 10:41:18 CDT)
  • Vlad Cojocaru (Fri Apr 28 2017 - 10:36:12 CDT)
  • Vlad Cojocaru (Fri Apr 28 2017 - 10:24:18 CDT)
  • Vlad Cojocaru (Fri Apr 28 2017 - 10:23:24 CDT)
  • David Hardy (Fri Apr 28 2017 - 10:15:04 CDT)
  • Vlad Cojocaru (Fri Apr 28 2017 - 09:14:58 CDT)
  • David Hardy (Thu Apr 27 2017 - 12:36:35 CDT)
  • Vermaas, Joshua (Thu Apr 27 2017 - 11:37:08 CDT)
  • Vlad Cojocaru (Thu Apr 27 2017 - 10:02:19 CDT)
• Compilation of NAMD for CUDA and replica exchange
  • #YEO JINGJIE# (Fri Apr 29 2016 - 13:53:44 CDT)
• Compiling charm/NAMD with an alternative gcc, e.g. gcc 6.x
  • Radak, Brian K (Mon Feb 06 2017 - 11:27:58 CST)
  • Greipel.Joachim_at_mh-hannover.de (Mon Feb 06 2017 - 08:54:08 CST)
• Compiling NAMD on stampede 2.
  • Giacomo Fiorin (Fri Jul 21 2017 - 12:47:07 CDT)
  • Chitrak Gupta (Fri Jul 21 2017 - 12:20:38 CDT)
  • Giacomo Fiorin (Thu Jul 20 2017 - 11:45:18 CDT)
  • Chitrak Gupta (Thu Jul 20 2017 - 11:29:37 CDT)
  • Giacomo Fiorin (Thu Jul 20 2017 - 11:20:29 CDT)
  • Chitrak Gupta (Thu Jul 20 2017 - 11:09:29 CDT)
  • Giacomo Fiorin (Wed Jul 19 2017 - 20:14:30 CDT)
  • Chitrak Gupta (Wed Jul 19 2017 - 17:47:07 CDT)
• compute capability
  • Josh Vermaas (Mon Jan 25 2016 - 09:52:37 CST)
  • Stefano Guglielmo (Sun Jan 24 2016 - 17:15:43 CST)
• Concatenating log files
  • Roshan Shrestha (Wed Sep 06 2017 - 12:00:34 CDT)
  • Bennion, Brian (Wed Sep 06 2017 - 11:50:53 CDT)
  • Roshan Shrestha (Wed Sep 06 2017 - 11:39:06 CDT)
  • Brian Radak (Wed Sep 06 2017 - 11:32:02 CDT)
  • Vermaas, Joshua (Wed Sep 06 2017 - 11:14:52 CDT)
  • Roshan Shrestha (Wed Sep 06 2017 - 11:07:51 CDT)
• Configuration of new HPC Cluster for NAMD and GROMACS
  • Vogel, Alexander (Tue Aug 01 2017 - 05:45:57 CDT)
  • Vermaas, Joshua (Mon Jul 31 2017 - 13:57:50 CDT)
  • Vogel, Alexander (Mon Jul 31 2017 - 05:36:30 CDT)
• constant velocity pulling
  • Jamal Zanjani (Thu Mar 31 2016 - 06:04:18 CDT)
• Constrain on DNA when using ABF for protein-DNA system
  • Vlad Cojocaru (Fri Oct 06 2017 - 08:28:43 CDT)
  • Giacomo Fiorin (Fri Oct 06 2017 - 08:15:40 CDT)
  • Vlad Cojocaru (Fri Oct 06 2017 - 08:08:33 CDT)
  • Jérôme Hénin (Fri Oct 06 2017 - 07:52:43 CDT)
  • Mehdi Bagherpour (Thu Oct 05 2017 - 13:25:33 CDT)
• Constraining and imparting motion to a geometry
  • Jérôme Hénin (Fri Sep 08 2017 - 03:56:55 CDT)
  • Abhaysinh Gaikwad (Thu Sep 07 2017 - 14:35:01 CDT)
  • Jérôme Hénin (Mon Sep 04 2017 - 07:42:47 CDT)
  • Abhaysinh Gaikwad (Fri Sep 01 2017 - 14:47:21 CDT)
• Constraining bonds that aren't hydrogens - splitPatch usefulness ?
  • Jeff Comer (Wed Mar 22 2017 - 08:56:57 CDT)
  • Marlon Sidore (Wed Mar 22 2017 - 07:08:50 CDT)
• Constraining bonds that don't include hydrogens
  • Marlon Sidore (Thu Jan 05 2017 - 08:11:06 CST)
• Constraint bonds that does not include hydrogrens
  • Karteek Bejagam (Fri Dec 30 2016 - 18:14:17 CST)
  • 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 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)
• Continuing SMD from restart files
  • Kevin Chun Chan (Mon Apr 24 2017 - 08:32:18 CDT)
  • Kevin C Chan (Wed Apr 19 2017 - 08:20:03 CDT)
• convergence criterion of free energy perturbation (FEP) simulations for pKa calculation
  • Brian Radak (Fri Oct 06 2017 - 14:28:56 CDT)
  • Sadegh Faramarzi Ganjabad (Fri Oct 06 2017 - 14:19:56 CDT)
  • Brian Radak (Fri Oct 06 2017 - 14:11:27 CDT)
  • Sadegh Faramarzi Ganjabad (Fri Oct 06 2017 - 14:04:39 CDT)
  • Brian Radak (Thu Oct 05 2017 - 15:30:28 CDT)
  • Sadegh Faramarzi Ganjabad (Thu Oct 05 2017 - 13:36:07 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)
• Converting x,y,z coordinates to dcd file
  • Vermaas, Joshua (Mon Jun 12 2017 - 10:17:24 CDT)
  • Kashish Punjani (Sun Jun 11 2017 - 12:44:18 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)
• CPU/GPU energy difference
  • Boonstra, S. (Mon Feb 27 2017 - 05:08:28 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)
• Creating psf file DNA
  • Vermaas, Joshua (Wed Aug 30 2017 - 10:11:27 CDT)
  • Vermaas, Joshua (Thu Jul 06 2017 - 18:02:37 CDT)
  • Roshan Shrestha (Thu Jul 06 2017 - 17:53:51 CDT)
  • Vermaas, Joshua (Thu Jul 06 2017 - 12:33:05 CDT)
  • Roshan Shrestha (Thu Jul 06 2017 - 11:47:54 CDT)
• Creating psf file for ligand
  • João Ribeiro (Thu Aug 24 2017 - 13:19:32 CDT)
  • Roshan Shrestha (Thu Aug 24 2017 - 12:58:07 CDT)
  • Nikhil Maroli (Wed Aug 23 2017 - 10:07:59 CDT)
  • Nikhil Maroli (Mon Aug 21 2017 - 12:33:07 CDT)
  • Roshan Shrestha (Sat Aug 12 2017 - 09:38:59 CDT)
  • Roshan Shrestha (Sat Aug 12 2017 - 09:34:29 CDT)
• Cross-term (CMAP)
  • Faramarz Joodaki (Sat Jul 08 2017 - 07:25:27 CDT)
  • Faramarz Joodaki (Fri Jul 07 2017 - 18:04:48 CDT)
• cuda errors when running NAMD
  • sunyeping (Fri Mar 03 2017 - 18:51:34 CST)
• Custum made residue addition
  • Chitrak Gupta (Fri Apr 28 2017 - 08:11:31 CDT)
  • Chitrak Gupta (Thu Apr 27 2017 - 14:46:27 CDT)
  • Zeki Zeybek (Thu Apr 27 2017 - 08:08:17 CDT)
• dcd file frame number
  • Dhiraj Srivastava (Thu Sep 29 2016 - 22:22:54 CDT)
• dcd to pdb conversion
  • Srijita Paul (Wed Jan 04 2017 - 13:05:28 CST)
  • Radak, Brian K (Wed Jan 04 2017 - 10:43:35 CST)
  • sonu2kd_at_gmail.com (Wed Jan 04 2017 - 06:26:49 CST)
  • Srijita Paul (Wed Jan 04 2017 - 06:18:21 CST)
• Dear NAMD users
  • msa5 (Thu Nov 03 2016 - 17:18:00 CDT)
• Define a colvar from other colvars
  • Giacomo Fiorin (Thu Dec 14 2017 - 14:57:56 CST)
  • Bogdan Marekha (Thu Dec 14 2017 - 14:53:11 CST)
  • Vermaas, Joshua (Thu Dec 14 2017 - 14:40:22 CST)
  • Ben Adams (Thu Dec 14 2017 - 13:50:29 CST)
• Define spheres using NAMD
  • Dushyant Sahoo (Sun Feb 19 2017 - 12:17:37 CST)
• Defining colvars based on a region
  • Giacomo Fiorin (Mon Mar 20 2017 - 20:00:09 CDT)
  • Bob Faith (Mon Mar 20 2017 - 19:48:00 CDT)
• Defining custom Colvars to measure pmf with Umbrella Sampling
  • Giacomo Fiorin (Thu Jun 22 2017 - 09:15:21 CDT)
  • Hemanth Vemuri (Thu Jun 22 2017 - 01:34:15 CDT)
  • Hemanth Vemuri (Thu Jun 22 2017 - 00:26:31 CDT)
  • Radak, Brian K (Wed Jun 21 2017 - 11:16:49 CDT)
  • Vermaas, Joshua (Wed Jun 21 2017 - 11:06:57 CDT)
  • Radak, Brian K (Wed Jun 21 2017 - 11:01:08 CDT)
  • Giacomo Fiorin (Tue Jun 20 2017 - 21:49:26 CDT)
  • Hemanth Vemuri (Tue Jun 20 2017 - 00:25:29 CDT)
• 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)
• difference between .vel and .vel.restart
  • David Hardy (Thu Aug 17 2017 - 13:25:02 CDT)
  • t.shivam_at_iitg.ernet.in (Thu Aug 10 2017 - 04:39:49 CDT)
• difference between constraining,restraining and fixing the atoms
  • Jérôme Hénin (Sun Aug 06 2017 - 10:20:51 CDT)
  • Brian Radak (Fri Aug 04 2017 - 09:34:22 CDT)
  • Fotis Baltoumas (Thu Aug 03 2017 - 23:33:22 CDT)
  • t.shivam_at_iitg.ernet.in (Fri Aug 04 2017 - 01:25:23 CDT)
• Dihedral colvar
  • Giacomo Fiorin (Fri Sep 08 2017 - 14:54:44 CDT)
  • PRITI ROY (Fri Sep 08 2017 - 14:33:45 CDT)
  • Vermaas, Joshua (Fri Sep 08 2017 - 14:06:25 CDT)
  • PRITI ROY (Fri Sep 08 2017 - 13:55:01 CDT)
  • Jérôme Hénin (Fri Sep 08 2017 - 08:53:28 CDT)
  • PRITI ROY (Fri Sep 08 2017 - 08:44:31 CDT)
  • Jérôme Hénin (Mon Sep 04 2017 - 07:40:26 CDT)
  • PRITI ROY (Mon Sep 04 2017 - 06:08:00 CDT)
  • Stefano Guglielmo (Wed Jan 18 2017 - 01:43:48 CST)
  • Giacomo Fiorin (Tue Jan 17 2017 - 20:47:39 CST)
  • Stefano Guglielmo (Tue Jan 17 2017 - 19:11:09 CST)
• 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)
• displacement of protein
  • Ajasja LjubetiÄ� (Fri Sep 22 2017 - 02:29:00 CDT)
  • Estefanía Hugo (Thu Sep 21 2017 - 09:08:19 CDT)
• DNA capping
  • Strahs, Dr. Daniel Bernard (Fri Jun 02 2017 - 10:01:52 CDT)
  • Nicholus Bhattacharjee (Fri Jun 02 2017 - 09:57:41 CDT)
  • Lennart Nilsson (Fri Jun 02 2017 - 09:10:04 CDT)
  • Nicholus Bhattacharjee (Fri Jun 02 2017 - 07:38:24 CDT)
  • Strahs, Dr. Daniel Bernard (Fri Jun 02 2017 - 07:30:57 CDT)
  • Nicholus Bhattacharjee (Fri Jun 02 2017 - 07:09:08 CDT)
  • Nicholus Bhattacharjee (Thu Jun 01 2017 - 04:11:48 CDT)
• DNA not translocating under electric field
  • Athreya, Nagendra Bala Murali (Wed Nov 30 2016 - 21:20:55 CST)
• Does FEP really run on Knights Landing?
  • Francesco Pietra (Thu Jul 27 2017 - 11:44:13 CDT)
• download stmv files for benchmarking
  • Bennion, Brian (Wed Jun 01 2016 - 14:29:22 CDT)
• Downloads are .tar files but have .tar.gz extension
  • Toon Verstraelen (Thu Nov 09 2017 - 05:07:26 CST)
• Drude minimization does not converge
  • Christian Jorgensen (Fri Jan 13 2017 - 10:16:08 CST)
  • Christian Jorgensen (Fri Jan 13 2017 - 13:21:39 CST)
  • Christian Jorgensen (Fri Jan 13 2017 - 11:26:39 CST)
  • salehesam_at_gmail.com (Fri Jan 13 2017 - 10:36:41 CST)
  • Christian Jorgensen (Fri Jan 13 2017 - 10:19:03 CST)
• Drude Prepper error in genic
  • Francesco Pietra (Mon Jun 13 2016 - 01:33:15 CDT)
• 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)
• eABF - Fullsamples and windows merging
  • philippe Bourly (Fri Jul 21 2017 - 12:54:03 CDT)
  • yjcoshc_at_gmail.com (Wed Jul 19 2017 - 09:01:40 CDT)
  • philippe Bourly (Wed Jul 19 2017 - 08:41:56 CDT)
• Early bird extended! ISQBP2016 meeting - Bergen Norway
  • Vlad Cojocaru (Mon Apr 18 2016 - 14:35:38 CDT)
• Electric field simulation: eFieldNormalized
  • Giacomo Fiorin (Wed Nov 29 2017 - 08:48:05 CST)
  • Carlo Guardiani (Tue Nov 28 2017 - 13:53:57 CST)
• 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 difference between HSE and HSD
  • Jérôme Hénin (Tue May 09 2017 - 11:28:52 CDT)
  • Radak, Brian K (Tue May 09 2017 - 11:12:14 CDT)
  • Jérôme Hénin (Tue May 09 2017 - 10:51:00 CDT)
  • Radak, Brian K (Tue May 09 2017 - 10:43:49 CDT)
  • Hao Dong (Mon May 08 2017 - 23:48:48 CDT)
• 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 Gradient Plotting
  • Radak, Brian K (Wed Jan 18 2017 - 11:19:04 CST)
  • Zeki Zeybek (Wed Jan 18 2017 - 02:19:03 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)
• 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)
• Energy output values
  • Brian Radak (Tue Dec 06 2016 - 13:35:47 CST)
  • matthew reeves (Tue Dec 06 2016 - 13:16:00 CST)
• Energy values
  • Vermaas, Joshua (Fri Apr 14 2017 - 17:57:56 CDT)
  • matthew reeves (Fri Apr 14 2017 - 16:49:54 CDT)
• Enhanced sampling methods for oligomers
  • Jacob Usadi (Fri Oct 20 2017 - 15:33:34 CDT)
• Enhanced sampling of domain motion and gsafold
  • dhirajks_at_gmail.com (Mon Jul 03 2017 - 19:18:38 CDT)
• enhanced sampling of domain motion, GSAfold
  • Dhiraj Srivastava (Sat Jul 01 2017 - 23:49:00 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 using NPT and Production run using NVE ensemble
  • Akshay Bhatnagar (Thu Apr 27 2017 - 07:47:29 CDT)
• Equilibrium Energies
  • Brian Radak (Tue May 23 2017 - 15:18:59 CDT)
  • Theodora Teddy (Tue May 23 2017 - 11:10:19 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 - atom type not in psf
  • Vermaas, Joshua (Fri Sep 01 2017 - 16:06:53 CDT)
  • Vermaas, Joshua (Fri Sep 01 2017 - 11:36:19 CDT)
  • Natasha Gupta (Fri Sep 01 2017 - 02:28:46 CDT)
  • Vermaas, Joshua (Thu Aug 31 2017 - 17:49:48 CDT)
  • Vermaas, Joshua (Thu Aug 31 2017 - 11:25:10 CDT)
  • Natasha Gupta (Thu Aug 31 2017 - 05:56:15 CDT)
• error - parameter file for fluorine on a benzene ring
  • Kowsar Khajeh (Wed Aug 23 2017 - 17:38:42 CDT)
  • Natasha Gupta (Wed Aug 23 2017 - 15:07:08 CDT)
• Error : components of colvar "alpha" does not support system force calculation
  • Jérôme Hénin (Fri Apr 07 2017 - 07:06:36 CDT)
  • Souvik Sinha (Fri Apr 07 2017 - 03:47:11 CDT)
• Error associated with protected variable initialization: Nightly Build version
  • Sourav Ray (Tue May 17 2016 - 13:50:54 CDT)
• error during minimization
  • Lara rajam (Mon Feb 27 2017 - 13:07:44 CST)
• Error in thermodynamic integration for calculating ligand absolute binding free energy
  • Brian Radak (Mon Jul 17 2017 - 15:55:21 CDT)
  • Marawan Hussien (Mon Jul 17 2017 - 11:45:22 CDT)
• Error on Settle.C when compiling NAMD with Intel Compiler
  • Giacomo Fiorin (Thu Nov 09 2017 - 16:12:41 CST)
  • Florian Blanc (Thu Nov 09 2017 - 11:00:09 CST)
  • Giacomo Fiorin (Thu Oct 26 2017 - 13:56:26 CDT)
  • Florian Blanc (Thu Oct 26 2017 - 12:34:06 CDT)
  • Vermaas, Joshua (Wed Oct 25 2017 - 16:01:57 CDT)
  • Victor Ovchinnikov (Wed Oct 25 2017 - 15:59:42 CDT)
  • Florian Blanc (Wed Oct 25 2017 - 15:26:57 CDT)
• Error regarding missing angles between perturbed groups for fep calculation
  • Vermaas, Joshua (Fri May 26 2017 - 17:09:53 CDT)
  • Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Fri May 26 2017 - 17:03:36 CDT)
  • Vermaas, Joshua (Thu May 25 2017 - 17:29:59 CDT)
  • Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Thu May 25 2017 - 16:24:08 CDT)
  • Jeff Comer (Thu May 25 2017 - 16:16:18 CDT)
  • Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Thu May 25 2017 - 10:49:32 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 ions based on mass
  • Olya Kravchenko (Wed Oct 04 2017 - 14:38:44 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)
• Explanation of parameters for NBTABLE's tabulated external file?
  • Wasut Pornpatcharapong (Wed Mar 22 2017 - 16:59:19 CDT)
  • David Hardy (Wed Mar 22 2017 - 14:17:09 CDT)
  • David Hardy (Wed Mar 22 2017 - 14:09:17 CDT)
  • Wasut Pornpatcharapong (Wed Mar 22 2017 - 13:56:15 CDT)
  • Vermaas, Joshua (Wed Mar 22 2017 - 13:09:02 CDT)
  • Wasut Pornpatcharapong (Wed Mar 22 2017 - 12:55:12 CDT)
• 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)
• extracting avarage pdb from dcd file
  • Souvik Sinha (Mon Sep 11 2017 - 10:19:51 CDT)
  • Srijita Paul (Mon Sep 11 2017 - 00:48:06 CDT)
• extracting force on a single atom
  • Jérôme Hénin (Thu Aug 31 2017 - 10:25:18 CDT)
  • Ben Adams (Thu Aug 31 2017 - 10:11:19 CDT)
  • Florian Blanc (Thu Aug 31 2017 - 10:07:59 CDT)
  • Ben Adams (Thu Aug 31 2017 - 10:03:04 CDT)
  • Jérôme Hénin (Thu Aug 31 2017 - 08:46:28 CDT)
  • Ben Adams (Thu Aug 31 2017 - 08:38:05 CDT)
  • Jérôme Hénin (Thu Aug 31 2017 - 05:37:13 CDT)
  • Ben Adams (Wed Aug 30 2017 - 19:18:49 CDT)
• facing problem while downloading NAMD
  • Roshan Shrestha (Fri Dec 22 2017 - 03:40:20 CST)
  • Jyoti Sharma (Fri Dec 22 2017 - 03:20:26 CST)
• FAD parameter and topology files
  • Peter Freddolino (Tue Sep 19 2017 - 23:41:42 CDT)
  • amit kumar (Tue Sep 19 2017 - 23:12:39 CDT)
• FATAL ERROR CUDA error during equilibration using NAMD
  • Abraham A. Gutierrez Hernandez (Tue Aug 30 2016 - 18:27:38 CDT)
• Fatal Error in NAMD
  • Faramarz Joodaki (Thu Mar 30 2017 - 12:54:13 CDT)
  • Faramarz Joodaki (Thu Mar 30 2017 - 12:24:20 CDT)
  • Giacomo Fiorin (Thu Mar 30 2017 - 12:20:26 CDT)
  • Faramarz Joodaki (Thu Mar 30 2017 - 12:14:51 CDT)
• fatal error in running namd/2.12
  • sunyeping (Wed Jan 11 2017 - 07:46:01 CST)
• Fatal error in the simulation of a water box
  • Brian Radak (Wed May 31 2017 - 08:33:47 CDT)
  • M. Wong (Wed May 31 2017 - 04:04:38 CDT)
• FATAL ERROR running apoa1 with NAMD 2.12
  • Tim.Ho_at_csiro.au (Wed Apr 05 2017 - 01:53:26 CDT)
• FATAL ERROR: Bad global improper count!
  • Nehad Elsalamouny (Fri Dec 15 2017 - 23:53:33 CST)
• FATAL ERROR: cuda_check_progress polled 1000000 times over ...
  • Abhishek TYAGI (Tue Oct 24 2017 - 06:42:32 CDT)
  • Zahra Mohammadi (Tue Oct 24 2017 - 06:12:55 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: Duplicate bond
  • PRITI ROY (Tue Mar 21 2017 - 08:25:08 CDT)
• FATAL ERROR: Duplicate bond when going from nvt to npt
  • Marlon Sidore (Mon Oct 09 2017 - 04:04:17 CDT)
  • Radak, Brian K (Mon Dec 12 2016 - 09:33:46 CST)
  • Marlon Sidore (Mon Dec 12 2016 - 04:02:17 CST)
• FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
  • The Cromicus Productions (Thu Feb 09 2017 - 12:01:55 CST)
  • The Cromicus Productions (Tue Feb 07 2017 - 17:43:40 CST)
• FATAL ERROR: Singular matrix in routine ludcmp
  • Natasha Gupta (Fri Sep 01 2017 - 18:41:24 CDT)
• FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG321 CTL3 (ATOMS 8773 8776)
  • Arthur Vale (Thu Jul 20 2017 - 20:08:28 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)
• FEP double annihilation
  • Carlo Guardiani (Fri Sep 23 2016 - 13:28:30 CDT)
• FEP with ExtraBonds
  • Radak, Brian K (Mon Jun 12 2017 - 16:13:31 CDT)
  • Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Mon Jun 12 2017 - 15:30:59 CDT)
• 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 Determination of Dihedrals to be Scanned
  • Zeki Zeybek (Sun Feb 26 2017 - 08:20:30 CST)
• ffTK fitting dihedrals
  • Seth Axen (Tue May 17 2016 - 01:36:02 CDT)
• finding atoms in protein-lipid system having electrostatic interaction
  • Giacomo Fiorin (Wed Aug 09 2017 - 14:19:26 CDT)
  • Rabeta Yeasmin (Wed Aug 09 2017 - 13:32:35 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)
• Fixing COM of one atom in selection and letting the other move
  • Vermaas, Joshua (Thu Feb 16 2017 - 10:58:32 CST)
  • Vermaas, Joshua (Tue Feb 14 2017 - 18:12:38 CST)
  • Life Sciences Inc (Tue Feb 14 2017 - 12:15:00 CST)
• flat and smooth energy?
  • Brian Radak (Mon Oct 23 2017 - 14:07:13 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)
• Free energy (eABF): negative RMSD and harmonic restraints.
  • philippe Bourly (Wed Aug 02 2017 - 11:45:56 CDT)
• Free energy calculation under external bias, (e)ABF/US/etc
  • Jérôme Hénin (Fri Jul 28 2017 - 12:17:05 CDT)
  • Jérôme Hénin (Tue May 02 2017 - 05:07:29 CDT)
  • yjcoshc_at_gmail.com (Tue May 02 2017 - 04:15:21 CDT)
  • Giacomo Fiorin (Mon May 01 2017 - 10:10:18 CDT)
  • Jim (Fri Apr 28 2017 - 20:25:57 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 did not converge by using ABF
  • Nielsen, Steven (Fri Dec 08 2017 - 15:01:55 CST)
  • Jeffrey Potoff (Fri Dec 08 2017 - 13:22:44 CST)
  • Giacomo Fiorin (Fri Dec 08 2017 - 09:27:21 CST)
  • Yaxin An (Fri Dec 08 2017 - 08:57:01 CST)
  • Jérôme Hénin (Fri Dec 08 2017 - 06:39:06 CST)
  • Vermaas, Joshua (Thu Dec 07 2017 - 19:23:53 CST)
  • Yaxin An (Thu Dec 07 2017 - 17:22:31 CST)
• Free MD simulation (Production run)
  • Roshan Shrestha (Fri Sep 08 2017 - 02:36:04 CDT)
  • Roshan Shrestha (Fri Sep 08 2017 - 02:32:50 CDT)
• Functional role of the internal water channel within the receptor
  • James Starlight (Tue Aug 08 2017 - 07:42:07 CDT)
• Fw (5): zmhoseyni
  • zmhoseyni (Mon Dec 19 2016 - 13:47:30 CST)
• Fwd: (1) Failure running QM-MM with ORCA and (2) problems preparing input with transition metals
  • Francesco Pietra (Mon Jan 02 2017 - 04:54:19 CST)
• Fwd: ABF FEP with multichain receptor
  • Francesco Pietra (Tue Jul 11 2017 - 01:20:12 CDT)
  • Francesco Pietra (Mon Jul 10 2017 - 05:25:30 CDT)
• Fwd: About the robustness of ABF and FEB protein-ligand
  • Francesco Pietra (Wed Jun 28 2017 - 09:47:59 CDT)
• Fwd: About wall clock time
  • Giacomo Fiorin (Fri Oct 27 2017 - 08:39:25 CDT)
  • Rik Chakraborty (Thu Oct 26 2017 - 23:09:27 CDT)
  • Giacomo Fiorin (Tue Oct 17 2017 - 09:25:13 CDT)
  • Giacomo Fiorin (Mon Oct 16 2017 - 12:16:29 CDT)
  • Chitrak Gupta (Mon Oct 16 2017 - 08:48:38 CDT)
  • Renfro, Michael (Mon Oct 16 2017 - 08:18:27 CDT)
  • Rik Chakraborty (Mon Oct 16 2017 - 01:20:40 CDT)
• Fwd: Appropriate FF for a specific solvent
  • faride badalkhani (Fri Mar 18 2016 - 10:53:15 CDT)
• Fwd: Are KNL a good choice for classical MD?
  • Francesco Pietra (Sat Aug 05 2017 - 02:42:31 CDT)
• Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand
  • Francesco Pietra (Thu Jul 06 2017 - 01:15:50 CDT)
  • Giacomo Fiorin (Wed Jul 05 2017 - 11:30:59 CDT)
  • Francesco Pietra (Wed Jul 05 2017 - 11:03:05 CDT)
  • Francesco Pietra (Thu Jun 29 2017 - 08:47:59 CDT)
  • Giacomo Fiorin (Wed Jun 28 2017 - 11:35:19 CDT)
  • Francesco Pietra (Tue Jun 27 2017 - 02:46:38 CDT)
  • Giacomo Fiorin (Mon Jun 26 2017 - 11:32:58 CDT)
  • Francesco Pietra (Mon Jun 26 2017 - 11:24:59 CDT)
  • Francesco Pietra (Mon Jun 26 2017 - 05:28:49 CDT)
• Fwd: colvars to restrain peptide close to lipid
  • Chitrak Gupta (Wed Apr 26 2017 - 17:22:37 CDT)
• Fwd: enhanced sampling of domain motion, GSAfold
  • Dhiraj Srivastava (Mon Jul 03 2017 - 16:33:17 CDT)
• Fwd: facing problem while downloading NAMD
  • Jyoti Sharma (Fri Dec 22 2017 - 03:24:19 CST)
• Fwd: H-bonds in charmm36 with namd2.11
  • Francesco Pietra (Sun May 22 2016 - 01:46:52 CDT)
• Fwd: ISQBP 2016 meeting - registration opened!
  • Vlad Cojocaru (Mon Mar 14 2016 - 03:13:10 CDT)
• Fwd: Klaus Schulten Memorial Symposium, registration and accommodation
  • David Hardy (Thu Oct 05 2017 - 15:29:08 CDT)
• Fwd: measuring Euler angles and polar angles
  • Francesco Pietra (Sat Jun 24 2017 - 01:22:17 CDT)
• 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 2.12 released
  • Francesco Pietra (Wed Dec 28 2016 - 02:12:14 CST)
  • Francesco Pietra (Wed Dec 28 2016 - 02:10:55 CST)
• Fwd: namd on Windows 10
  • Branko (Fri Feb 05 2016 - 08:13:51 CST)
• Fwd: problem with angle parameters
  • faride badalkhani (Wed Mar 30 2016 - 10:01:22 CDT)
• Fwd: Problems running NAMD QM-MM with ORCA 3.0.3
  • Francesco Pietra (Fri Dec 30 2016 - 03:51:10 CST)
• Fwd: Regarding system forces in NAMD
  • sruthi c k (Fri Jan 08 2016 - 03:38:26 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)
• GAAMP
  • Stefano Guglielmo (Mon Jul 10 2017 - 06:55:21 CDT)
• GaMD in NAMD
  • Chitrak Gupta (Mon Jun 19 2017 - 08:43:37 CDT)
  • Francesco Pietra (Mon Jun 19 2017 - 00:36:19 CDT)
  • Chitrak Gupta (Sun Jun 18 2017 - 14:57:20 CDT)
  • David Hardy (Sun Jun 18 2017 - 11:02:19 CDT)
  • jeevan gc (Sun Jun 18 2017 - 10:49:40 CDT)
  • Chitrak Gupta (Sun Jun 18 2017 - 09:20:11 CDT)
  • Francesco Pietra (Sun Jun 18 2017 - 01:04:59 CDT)
  • Chitrak Gupta (Sat Jun 17 2017 - 15:16:18 CDT)
• GBIS error
  • sunyeping (Sat Jan 02 2016 - 22:55:10 CST)
• gbis for acetonitrile
  • hem_chandra_at_iitg.ernet.in (Sat Mar 11 2017 - 00:40:15 CST)
• GBIS intrinsic radii set from aber parm7
  • Norman Geist (Fri Dec 16 2016 - 02:04:15 CST)
• gbsa
  • Stefano Guglielmo (Wed Dec 20 2017 - 15:57:21 CST)
  • Brian Radak (Wed Dec 20 2017 - 11:57:24 CST)
  • Stefano Guglielmo (Tue Dec 19 2017 - 19:55:21 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 nodelist and error
  • Hyun (Thu Mar 16 2017 - 10:10:19 CDT)
• generating topology file
  • Nehir NALINCI (Mon Apr 24 2017 - 07:25:06 CDT)
  • Nehir NALINCI (Sat Apr 15 2017 - 03:09:07 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)
• 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)
• Gradual cooling of the system
  • Natalia Ostrowska (Mon Dec 25 2017 - 02:23:11 CST)
  • Monika Madhavi (Sun Dec 24 2017 - 22:27:27 CST)
• 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)
• group selection in TCL script for use in NAMD
  • Allen, Caley R (Wed Jul 27 2016 - 13:35:05 CDT)
• Gyration in colvars doesn't work with eABF.
  • Haohao Fu (Thu Jun 15 2017 - 02:17:55 CDT)
  • yjcoshc (Wed Jun 14 2017 - 06:49:51 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)
• Hands-On Workshop on Computational Biophysics: April 17-21 in Urbana, IL
  • João Ribeiro KS (Fri Feb 24 2017 - 09:11:34 CST)
  • João Ribeiro KS (Fri Feb 17 2017 - 16:57:13 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: May 30 - June 2 in Pittsburgh, PA
  • João Ribeiro KS (Wed Mar 22 2017 - 10:15:40 CDT)
• 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)
• Harmonic force Keyword "centers" significance
  • Vermaas, Joshua (Wed Jun 21 2017 - 17:49:20 CDT)
  • Rabeta Yeasmin (Wed Jun 21 2017 - 17:40:43 CDT)
• Have GPU-accelerated NAMD Questions? Join us for a Live Webinar
  • MARK (Fri May 20 2016 - 13:07:08 CDT)
• Having problem with restarting colvar distance,
  • Aliasghar Alizadeh-Mojarad (Fri Dec 29 2017 - 14:46:29 CST)
  • Jérôme Hénin (Fri Dec 29 2017 - 04:34:56 CST)
  • Aliasghar Alizadeh-Mojarad (Fri Dec 29 2017 - 02:10:07 CST)
• 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)
• Hi All
  • msa5 (Tue Nov 01 2016 - 22:06:01 CDT)
• High pressure calculations
  • faride badalkhani (Fri Feb 03 2017 - 13:23:34 CST)
  • Vermaas, Joshua (Fri Feb 03 2017 - 11:15:04 CST)
  • faride badalkhani (Fri Feb 03 2017 - 10:10:39 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 do I restart umbrella sampling calculations?
  • Olya Kravchenko (Wed Jan 25 2017 - 09:19:10 CST)
  • Vermaas, Joshua (Tue Jan 24 2017 - 16:26:39 CST)
  • Olya Kravchenko (Tue Jan 24 2017 - 16:11:17 CST)
  • Giacomo Fiorin (Tue Jan 24 2017 - 16:09:13 CST)
  • Olya Kravchenko (Tue Jan 24 2017 - 15:44:32 CST)
  • Giacomo Fiorin (Tue Jan 24 2017 - 15:20:38 CST)
  • Olya Kravchenko (Tue Jan 24 2017 - 15:14:55 CST)
  • Vermaas, Joshua (Tue Jan 24 2017 - 14:57:36 CST)
  • Giacomo Fiorin (Tue Jan 24 2017 - 14:50:41 CST)
  • Olya Kravchenko (Tue Jan 24 2017 - 14:39:12 CST)
• How to calculate 2d surface energy surface on segmented adaptive biased force (ABF) simulations
  • Jérôme Hénin (Tue Apr 18 2017 - 04:47:22 CDT)
  • sunyeping (Mon Apr 17 2017 - 21:06:19 CDT)
  • Jérôme Hénin (Mon Apr 17 2017 - 15:22:36 CDT)
  • sunyeping (Mon Apr 17 2017 - 05:54:46 CDT)
• How to calculate free energy to unbias colvars restraint?
  • Giacomo Fiorin (Sat Jul 29 2017 - 09:51:01 CDT)
  • Victoria Lim (Fri Jul 28 2017 - 19:17:33 CDT)
  • Giacomo Fiorin (Fri Jul 28 2017 - 19:10:59 CDT)
  • Victoria Lim (Fri Jul 28 2017 - 18:56:44 CDT)
• How to calculate the number of solvent molecules for simulations in a specified pressure
  • faride badalkhani (Wed Feb 01 2017 - 04:33:55 CST)
• 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 define spheres of different sizes and their spatial constrains using NAMD?
  • Sahoo, Dushyant (Tue Feb 21 2017 - 02:40:33 CST)
• How to get 3D figure of solvent accessible surface area from APBS output
  • Rabeta Yeasmin (Fri Aug 11 2017 - 17:18:54 CDT)
• How to get ideal alpha-helical, ω-shaped γ-turn, and turn/310-helix conformations
  • Jérôme Hénin (Tue Feb 07 2017 - 10:43:53 CST)
  • Jessen Lucas (Tue Feb 07 2017 - 10:58:22 CST)
  • Jessen Lucas (Tue Feb 07 2017 - 09:28:21 CST)
  • Jérôme Hénin (Fri Jan 13 2017 - 02:57:13 CST)
  • Jessen Lucas (Thu Jan 12 2017 - 20:09:30 CST)
• How to get the right density of a methane system
  • Monika Madhavi (Fri Aug 25 2017 - 03:29:17 CDT)
  • Francesco Pietra (Sat Aug 12 2017 - 01:07:54 CDT)
  • Nielsen, Steven (Fri Aug 11 2017 - 23:38:18 CDT)
  • Monika Madhavi (Fri Aug 11 2017 - 21:56:51 CDT)
• how to have large coordinate values in the "coordinates PDB" file
  • Giacomo Fiorin (Mon Apr 17 2017 - 14:05:40 CDT)
  • Vermaas, Joshua (Mon Apr 17 2017 - 14:03:15 CDT)
  • Nielsen, Steven (Mon Apr 17 2017 - 13:33:37 CDT)
• how to not overwrite a modified file? (while producing coordinates for ABF/US windows)
  • Olya Kravchenko (Sat Aug 06 2016 - 07:18:56 CDT)
• How to perform REMD of a system a membrane-protein system?
  • Giacomo Fiorin (Tue Jan 10 2017 - 10:09:04 CST)
  • Panagiota Kyriakou (Mon Jan 09 2017 - 16:34:03 CST)
  • Giacomo Fiorin (Wed Jan 04 2017 - 08:24:18 CST)
  • Panagiota Kyriakou (Tue Jan 03 2017 - 18:38:54 CST)
• How to pull protein-Monomer from DNA using ABF without any force on DNA?
  • Jeff Comer (Tue Jun 13 2017 - 13:37:05 CDT)
  • Mehdi Bagherpour (Tue Jun 13 2017 - 12:30:29 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 restart metadynamics in namd
  • Giacomo Fiorin (Mon Jan 09 2017 - 00:11:17 CST)
  • Giacomo Fiorin (Sun Jan 08 2017 - 23:59:54 CST)
  • Wang, X. Y. (Sun Jan 08 2017 - 22:29:41 CST)
• How to sample pressure from NAMD log file.
  • Daipayan Sarkar (Thu Sep 21 2017 - 22:16:54 CDT)
• How to set setting periodic boundary condition
  • Chitrak Gupta (Fri Jul 07 2017 - 09:54:54 CDT)
  • Vidhya Sankar (Thu Jul 06 2017 - 07:43:56 CDT)
• How to set the configuration file for a NVE simulation
  • Roshan Shrestha (Mon Sep 04 2017 - 19:59:40 CDT)
  • Monika Madhavi (Mon Sep 04 2017 - 19:02:29 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)
• Howto gaussian accelerated MD
  • Francesco Pietra (Tue May 16 2017 - 09:34:11 CDT)
• Hybrid QM/MM in NAMD 2.12 with Gaussian
  • Stober, Spencer T (Wed Apr 19 2017 - 10:44:18 CDT)
  • Stober, Spencer T (Tue Apr 18 2017 - 10:24:03 CDT)
• Hybrid QM/MM NAMD: Problem Reading Extended psf files -- But some good news too
  • Angelo Rossi (Wed Apr 26 2017 - 11:00:24 CDT)
  • Marcelo C. R. Melo (Wed Apr 26 2017 - 09:32:15 CDT)
  • Angelo Rossi (Wed Apr 26 2017 - 08:06:03 CDT)
• hyper-branched polymers
  • faride badalkhani (Tue May 24 2016 - 09:24:41 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)
• I don't have any eabf output file.
  • fhh2626_at_gmail.com (Wed Jul 26 2017 - 01:47:09 CDT)
  • philippe Bourly (Tue Jul 25 2017 - 07:23:34 CDT)
  • Haohao (Tue Jul 25 2017 - 06:20:33 CDT)
  • Haohao (Tue Jul 25 2017 - 06:14:48 CDT)
  • philippe Bourly (Tue Jul 25 2017 - 05:20:51 CDT)
  • yjcoshc_at_gmail.com (Tue Jul 25 2017 - 05:06:44 CDT)
  • philippe Bourly (Fri Jul 21 2017 - 13:46:39 CDT)
• Implementation of sortreplicas executable for restarted REST2 simulations
  • Bhati, Agastya (Thu Oct 12 2017 - 09:00:27 CDT)
  • Chitrak Gupta (Thu Oct 12 2017 - 08:21:09 CDT)
  • Bhati, Agastya (Thu Oct 12 2017 - 06:50:40 CDT)
  • Chitrak Gupta (Wed Oct 11 2017 - 20:20:24 CDT)
  • Bhati, Agastya (Wed Oct 11 2017 - 14:50:46 CDT)
  • Chitrak Gupta (Wed Oct 11 2017 - 14:32:54 CDT)
  • Bhati, Agastya (Wed Oct 11 2017 - 14:12:44 CDT)
• Implicit solvent no non-bonded pairing
  • Eric Pederson (Thu Mar 16 2017 - 19:41:51 CDT)
• Improper section for parameterization
  • Jérôme Hénin (Tue Nov 21 2017 - 07:26:17 CST)
  • Theodora Teddy (Tue Nov 21 2017 - 07:20:59 CST)
• Inconsistency between NAMD 2.11 and NAMD 2.12
  • Bryan Roessler (Fri Feb 03 2017 - 14:47:27 CST)
  • Bryan Roessler (Fri Feb 03 2017 - 14:17:51 CST)
  • Bryan Roessler (Tue Jan 31 2017 - 10:12:07 CST)
  • Bryan Roessler (Tue Jan 31 2017 - 09:47:30 CST)
  • Bryan Roessler (Tue Jan 31 2017 - 00:52:22 CST)
• Inconsistent atom count
  • Laura Joana (Tue Jul 05 2016 - 12:04:44 CDT)
• Incorporate aluminum oxide monolayer
  • Seibold, Steve Allan (Wed Apr 12 2017 - 09:47:43 CDT)
  • The Cromicus Productions (Tue Apr 11 2017 - 14:50:37 CDT)
• initial structure
  • faride badalkhani (Mon Apr 18 2016 - 10:17:30 CDT)
  • faride badalkhani (Fri Apr 15 2016 - 14:18:03 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)
• 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)
• introduction to research on free energies
  • asaffarhi_at_post.tau.ac.il (Fri Jan 20 2017 - 09:34:05 CST)
• 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)
• ion moving laterally during Umbrella Sampling?
  • Giacomo Fiorin (Wed Oct 04 2017 - 12:05:39 CDT)
  • Olya Kravchenko (Wed Oct 04 2017 - 11:48:43 CDT)
  • Giacomo Fiorin (Tue Oct 03 2017 - 15:16:01 CDT)
  • Olya Kravchenko (Tue Oct 03 2017 - 12:45:09 CDT)
• Ion type in NAMD Implicit solvent model for ionizing the system
  • Brian Radak (Wed Sep 13 2017 - 09:59:27 CDT)
  • Chitrak Gupta (Wed Sep 13 2017 - 09:26:11 CDT)
  • Roshan Shrestha (Wed Sep 13 2017 - 00:49:39 CDT)
  • Susmita Ghosh (Wed Sep 13 2017 - 00:31:50 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 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 NVE ensemble for production run justified?
  • Brian Radak (Tue Mar 21 2017 - 09:44:52 CDT)
  • Akshay Bhatnagar (Tue Mar 21 2017 - 00:13:19 CDT)
• is there a way to prevent ions from entering the channel?
  • Olya Kravchenko (Thu Jul 21 2016 - 12:56:57 CDT)
• Issues about Keep_water_out.tcl acript
  • Vidhya Sankar (Fri Aug 18 2017 - 10:25:55 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)
• Keeping potassium ions out of an area during equilibration
  • Vermaas, Joshua (Wed Jun 07 2017 - 12:15:45 CDT)
  • Souvik Sinha (Wed Jun 07 2017 - 01:37:38 CDT)
  • Vermaas, Joshua (Tue Jun 06 2017 - 11:59:46 CDT)
  • Charles Hoying (Mon Jun 05 2017 - 22:57:40 CDT)
• Kinetic energy outputs
  • Giacomo Fiorin (Thu Apr 27 2017 - 08:50:37 CDT)
  • matthew reeves (Thu Apr 27 2017 - 06:29:38 CDT)
• Klaus Schulten Memorial Issue (http://pubs.acs.org/toc/jpcbfk/121/15)
  • Chris Chipot (Thu Apr 20 2017 - 12:10:34 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)
• Linux Ubuntu Workstation Networks: Charmrun> error attaching to node '192.168.1.8': Timeout waiting for node-program to connect
  • Marisol Oswald (Fri Dec 30 2016 - 18:51:28 CST)
• Lipid bilayer and ligand interactions
  • Saleh AlKhalifa (Sun Feb 26 2017 - 08:47:58 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)
• lipid centering
  • Karteek Bejagam (Tue Apr 11 2017 - 13:26:05 CDT)
  • Vermaas, Joshua (Tue Apr 11 2017 - 13:23:05 CDT)
  • Mihaela Drenscko (Tue Apr 11 2017 - 13:08:24 CDT)
• Lipid_bilayer_area_per_lipid_problem_using_NPT_CharmmForcefield
  • yousef nademi (Fri Jul 07 2017 - 17:50:40 CDT)
  • Fotis Baltoumas (Fri Jul 07 2017 - 02:22:06 CDT)
  • yousef nademi (Thu Jul 06 2017 - 20:49:48 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)
• 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)
• 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 membrane tutorial
  • Vidhya Sankar (Sat Feb 18 2017 - 23:34:54 CST)
• Maintaining PBC on Collective Variables
  • Malay Ranjan Biswal (Thu Jul 13 2017 - 11:49:15 CDT)
  • Vermaas, Joshua (Mon Jul 10 2017 - 12:49:11 CDT)
  • Jérôme Hénin (Mon Jul 10 2017 - 08:20:55 CDT)
  • Malay Ranjan Biswal (Mon Jul 10 2017 - 08:17:30 CDT)
• make psf error for ligand
  • Natasha Gupta (Fri Aug 25 2017 - 05:37:38 CDT)
  • Oscar Bastidas (Thu Aug 24 2017 - 13:26:58 CDT)
  • Nikhil Maroli (Thu Aug 24 2017 - 12:44:45 CDT)
  • Oscar Bastidas (Wed Aug 23 2017 - 17:59:27 CDT)
  • Natasha Gupta (Wed Aug 23 2017 - 17:35:34 CDT)
  • Natasha Gupta (Wed Aug 23 2017 - 16:46:55 CDT)
• making glucose chains using charmm36
  • Mohammad Hassan Khatami (Mon Jul 24 2017 - 13:29:18 CDT)
• 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)
• margin and pressure in CUDA version
  • JC Gumbart (Wed Sep 27 2017 - 12:55:49 CDT)
  • JC Gumbart (Wed Sep 27 2017 - 11:48:52 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)
• MD trajectory analysis
  • Deng, Jinxia (Nancy) (Thu Jan 28 2016 - 13:02:14 CST)
• MD using implicit solvent
  • Vermaas, Joshua (Fri Dec 30 2016 - 11:03:05 CST)
  • hem_chandra_at_iitg.ernet.in (Fri Dec 30 2016 - 05:51:58 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 simulations in membrane environment
  • Ryan McGreevy (Thu Feb 23 2017 - 08:33:24 CST)
  • Ryan McGreevy (Wed Feb 22 2017 - 09:28:04 CST)
  • Luba Simhaev (Wed Feb 22 2017 - 06:15:09 CST)
• MDFF with two symmetry groups
  • Benjamin.Haberl_at_physik.uni-muenchen.de (Tue May 17 2016 - 14:48:19 CDT)
• measuring Euler angles and polar angles
  • Francesco Pietra (Fri Jun 23 2017 - 12:06:18 CDT)
  • Jérôme Hénin (Fri Jun 23 2017 - 10:04:46 CDT)
  • Giacomo Fiorin (Fri Jun 23 2017 - 10:00:36 CDT)
  • Francesco Pietra (Fri Jun 23 2017 - 09:55:31 CDT)
  • Giacomo Fiorin (Thu Jun 22 2017 - 12:18:00 CDT)
  • Francesco Pietra (Thu Jun 22 2017 - 12:01:39 CDT)
• 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 run in NAMD or using plumed in NAMD
  • Rabeta Yeasmin (Fri Dec 08 2017 - 12:39:49 CST)
  • Giacomo Fiorin (Fri Dec 08 2017 - 12:19:43 CST)
  • Rabeta Yeasmin (Fri Dec 08 2017 - 12:14:11 CST)
  • Giacomo Fiorin (Fri Dec 08 2017 - 07:08:36 CST)
  • Rabeta Yeasmin (Fri Dec 08 2017 - 02:06:22 CST)
  • Rabeta Yeasmin (Fri Dec 08 2017 - 01:53:49 CST)
  • yjcoshc (Thu Dec 07 2017 - 19:22:06 CST)
  • Rabeta Yeasmin (Thu Dec 07 2017 - 17:49:22 CST)
• Metadynamics simulation
  • Giacomo Fiorin (Thu Jan 05 2017 - 09:51:08 CST)
  • Azadeh Alavi (Thu Jan 05 2017 - 06:39:34 CST)
  • Giacomo Fiorin (Wed Jan 04 2017 - 12:16:25 CST)
  • Azadeh Alavi (Tue Jan 03 2017 - 09:00:43 CST)
• 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 state file
  • Giacomo Fiorin (Thu Feb 23 2017 - 03:09:17 CST)
  • Carlo Guardiani (Mon Feb 20 2017 - 13:20:05 CST)
  • Giacomo Fiorin (Fri Feb 17 2017 - 12:22:05 CST)
  • Carlo Guardiani (Fri Feb 17 2017 - 06:53:31 CST)
• minimization error
  • Peter Freddolino (Sat Sep 09 2017 - 22:51:23 CDT)
  • Natasha Gupta (Fri Sep 08 2017 - 19:48:14 CDT)
  • 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, heating, equilibration and production run in one script
  • Dhiraj Srivastava (Thu Apr 28 2016 - 10:05:55 CDT)
• minimizing each structure of a DCD file
  • Giacomo Fiorin (Sun Jan 22 2017 - 11:28:05 CST)
  • saeed amini (Sun Jan 22 2017 - 07:21:23 CST)
• minimum CUDA compute capability required for NAMD2.12
  • David Hardy (Sun Sep 24 2017 - 10:31:29 CDT)
  • Albers, Thomas (Sat Sep 23 2017 - 16:03:24 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)
• missing binary operator before token "("
  • Fırat Yılmaz (Thu Jun 15 2017 - 02:30:12 CDT)
• missing parameters.
  • Lennart Nilsson (Mon Nov 20 2017 - 11:54:32 CST)
  • Vermaas, Joshua (Mon Nov 20 2017 - 11:08:47 CST)
  • Brian Radak (Mon Nov 20 2017 - 08:33:41 CST)
  • NEHÄ°R NALINCI (Mon Nov 20 2017 - 05:32:44 CST)
  • Giacomo Fiorin (Thu Nov 16 2017 - 06:19:04 CST)
  • NEHÄ°R NALINCI (Thu Nov 16 2017 - 01:28:42 CST)
  • Brian Radak (Wed Nov 15 2017 - 08:10:46 CST)
  • NEHÄ°R NALINCI (Wed Nov 15 2017 - 06:53:06 CST)
• 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)
• 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)
• Molecule-based Electrostatics Cutoff?
  • David Hardy (Mon Sep 11 2017 - 17:21:11 CDT)
  • David Huggins (Mon Sep 11 2017 - 16:58:59 CDT)
• More FEP using separated topologies
  • David Huggins (Fri Apr 28 2017 - 03:28:55 CDT)
  • Radak, Brian K (Wed Apr 26 2017 - 09:59:47 CDT)
  • Jérôme Hénin (Wed Apr 26 2017 - 05:27:27 CDT)
  • David Huggins (Tue Apr 25 2017 - 14:10:06 CDT)
  • Jérôme Hénin (Fri May 27 2016 - 23:00:20 CDT)
  • David Huggins (Fri May 27 2016 - 15:21:01 CDT)
• Movement of chloride ions during MD
  • Luba Simhaev (Sun Oct 08 2017 - 06:21:53 CDT)
• Movie in VMD
  • Daipayan Sarkar (Sat Aug 26 2017 - 22:56:24 CDT)
• MPIRUN SLURM SCRIPT
  • Bennion, Brian (Tue May 09 2017 - 13:07:08 CDT)
  • Zeki Zeybek (Tue May 09 2017 - 11:00:07 CDT)
  • Zeki Zeybek (Tue May 09 2017 - 10:58:29 CDT)
  • Vermaas, Joshua (Tue May 09 2017 - 10:48:25 CDT)
  • Zeki Zeybek (Tue May 09 2017 - 06:02:20 CDT)
  • Susmita Ghosh (Tue May 09 2017 - 05:39:23 CDT)
  • Zeki Zeybek (Tue May 09 2017 - 05:08:22 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)
• 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 Electric Field simulation
  • Athreya, Nagendra Bala Murali (Wed Mar 01 2017 - 15:13:37 CST)
• multiple replicas metadynamics
  • Giacomo Fiorin (Tue Jan 10 2017 - 15:40:43 CST)
  • Mihaela Drenscko (Tue Jan 10 2017 - 14:57:55 CST)
  • Giacomo Fiorin (Tue Jan 10 2017 - 11:37:00 CST)
  • quo.physics_at_gmail.com (Tue Jan 10 2017 - 05:57:27 CST)
  • Ajasja LjubetiÄ� (Mon Jan 09 2017 - 23:55:38 CST)
  • Mihaela Drenscko (Mon Jan 09 2017 - 16:20:34 CST)
  • Mihaela Drenscko (Mon Jan 09 2017 - 16:02:45 CST)
  • Giacomo Fiorin (Sun Jan 08 2017 - 17:37:21 CST)
  • Mihaela Drenscko (Fri Jan 06 2017 - 20:24:46 CST)
• multiple run commands freeze when using MTS?
  • Brian Radak (Thu Nov 03 2016 - 15:45:40 CDT)
• namd "WARNING: ignoring command" problem
  • Shambo Hore (Tue May 31 2016 - 12:11:35 CDT)
• 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)
• namd 2.12 and plumed 2.3
  • vlad.cojocaru_at_mpi-muenster.mpg.de (Tue May 02 2017 - 11:50:02 CDT)
  • Vlad Cojocaru (Tue May 02 2017 - 10:33:34 CDT)
  • yjcoshc_at_gmail.com (Tue May 02 2017 - 11:02:33 CDT)
  • Vermaas, Joshua (Tue May 02 2017 - 10:22:01 CDT)
  • Giacomo Fiorin (Tue May 02 2017 - 09:45:17 CDT)
  • Vlad Cojocaru (Tue May 02 2017 - 09:00:14 CDT)
  • Giacomo Fiorin (Tue May 02 2017 - 08:38:06 CDT)
  • Vlad Cojocaru (Tue May 02 2017 - 08:12:22 CDT)
  • Giacomo Fiorin (Wed Apr 26 2017 - 12:01:51 CDT)
  • Vermaas, Joshua (Wed Apr 26 2017 - 11:43:41 CDT)
  • Vlad Cojocaru (Wed Apr 26 2017 - 11:23:54 CDT)
  • Bassam Haddad (Wed Apr 26 2017 - 10:48:55 CDT)
  • Vlad Cojocaru (Wed Apr 26 2017 - 05:20:28 CDT)
• Namd 2.12 error with Nvidia M2090 cards
  • Vermaas, Joshua (Thu Aug 03 2017 - 11:45:40 CDT)
  • Michelle Kuttel (Thu Aug 03 2017 - 03:30:21 CDT)
• NAMD 2.12 multicore CUDA on Ubuntu 16.04 with NVIDIA Tesla M10 produces segmentation fault
  • Wilson,Michael (Tue Jul 18 2017 - 15:18:28 CDT)
  • Vermaas, Joshua (Tue Jul 18 2017 - 14:10:20 CDT)
  • Wilson,Michael (Tue Jul 18 2017 - 13:57:16 CDT)
• 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 2.12 using CUDA 8.0
  • Wright, David (Thu Apr 20 2017 - 08:40:28 CDT)
• NAMD 2.12b1 released
  • Jim Phillips (Thu Nov 03 2016 - 17:06:48 CDT)
• NAMD Acceleration using P100 (GP-GPU) accelerator
  • Atanu Maity (Tue Feb 07 2017 - 03:25:52 CST)
• 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 crashes when Multilevel Summation Method (MSM) is on
  • David Hardy (Tue May 30 2017 - 11:11:07 CDT)
  • Shadrina Maria (Tue May 30 2017 - 10:12:46 CDT)
• NAMD DCD file format
  • Dmitri Priimak (Fri Jun 09 2017 - 01:47:36 CDT)
• NAMD developer workshop - Chicago, May 22-23, 2017
  • João Ribeiro (Tue Apr 25 2017 - 07:45:59 CDT)
  • João Ribeiro (Tue Apr 18 2017 - 07:45:04 CDT)
• NAMD developer workshop at Chicago IL, May 22-23, 2017
  • João Ribeiro KS (Fri Feb 24 2017 - 19:23:08 CST)
• 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 energy run in VMD
  • Peter Freddolino (Tue Nov 21 2017 - 13:02:07 CST)
  • Srijita Paul (Tue Nov 21 2017 - 09:43:08 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 for Stampede2
  • Maria Bykhovskaia (Wed Aug 09 2017 - 20:21:20 CDT)
  • Vermaas, Joshua (Wed Aug 09 2017 - 17:45:00 CDT)
  • Maria Bykhovskaia (Wed Aug 09 2017 - 10:26:57 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 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 job termination
  • Chitrak Gupta (Wed Nov 08 2017 - 21:17:25 CST)
  • Richard Overstreet (Wed Nov 08 2017 - 21:08:32 CST)
  • Amali Guruge (Wed Nov 08 2017 - 21:01:25 CST)
• namd leaves zombie processes on nodes?
  • JC Gumbart (Mon May 23 2016 - 10:01:45 CDT)
• NAMD on Stampede 2
  • Chitrak Gupta (Fri Oct 06 2017 - 11:04:16 CDT)
  • Vermaas, Joshua (Fri Oct 06 2017 - 10:43:59 CDT)
  • Giacomo Fiorin (Fri Oct 06 2017 - 09:08:35 CDT)
  • Chitrak Gupta (Fri Oct 06 2017 - 08:32:30 CDT)
  • Giacomo Fiorin (Fri Oct 06 2017 - 07:50:50 CDT)
  • Chitrak Gupta (Thu Oct 05 2017 - 18:23:05 CDT)
• NAMD on UCSD Comet
  • Alexander Adams (Mon Jul 03 2017 - 13:26:48 CDT)
• 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 performance monitor
  • Vermaas, Joshua (Tue Jan 17 2017 - 10:47:33 CST)
  • Nikhil Maroli (Tue Jan 17 2017 - 06:42:41 CST)
• NAMD QM/MM
  • Marcelo C. R. Melo (Tue Nov 14 2017 - 11:39:49 CST)
  • Constanza Galaz Araya (Tue Nov 14 2017 - 10:08:45 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 running on a Cluster of Ubuntu Linux
  • Marisol Oswald (Sun Oct 09 2016 - 18:37:55 CDT)
• NAMD survey starting
  • Jim Phillips (Tue Mar 15 2016 - 13:34:00 CDT)
• NAMD with multiple molecules
  • t.shivam_at_iitg.ernet.in (Thu Aug 17 2017 - 22:51:58 CDT)
  • Axel Kohlmeyer (Thu Aug 17 2017 - 10:15:15 CDT)
  • Benz, Max (Thu Aug 17 2017 - 10:09:17 CDT)
• NAMD-2.12 CUDA2 and PMECUDA problems
  • David Hardy (Wed Aug 30 2017 - 11:05:47 CDT)
  • Nicholas M. Glykos (Tue Aug 29 2017 - 12:54:40 CDT)
  • Norman Geist (Mon Aug 28 2017 - 05:54:58 CDT)
• NAMD-2.12 handful of issues with CUDA
  • Ajasja LjubetiÄ� (Fri Mar 10 2017 - 05:14:10 CST)
  • Norman Geist (Fri Mar 10 2017 - 03:16:13 CST)
• namd-l digest V1 #2196
  • Vermaas, Joshua (Fri Jun 09 2017 - 17:07:05 CDT)
  • Rabeta Yeasmin (Fri Jun 09 2017 - 15:40:37 CDT)
• namd-l digest V1 #2289
  • Abhishek TYAGI (Wed Oct 25 2017 - 05:42:24 CDT)
  • Zahra Mohammadi (Wed Oct 25 2017 - 02:58:36 CDT)
• namd-l digest V1 #2316
  • Yaxin An (Fri Dec 08 2017 - 09:06:19 CST)
• 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)
• NAMD2.12b1 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)
• NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom!
  • 王茜茜 (Tue Sep 05 2017 - 05:23:02 CDT)
  • Richard (Fri Aug 25 2017 - 23:03:00 CDT)
  • 王茜茜 (Fri Aug 25 2017 - 22:47:16 CDT)
  • 王茜茜 (Fri Aug 25 2017 - 22:33:43 CDT)
• namd2.exe has stopped working, NAMD Energy
  • Richard Overstreet (Thu Feb 02 2017 - 20:46:29 CST)
  • Darya Fadavi (Thu Feb 02 2017 - 19:44:09 CST)
  • Goedde, Chris (Wed Feb 01 2017 - 14:45:02 CST)
  • Darya Fadavi (Wed Feb 01 2017 - 12:31:15 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)
• NAMDEnergy with xtc file
  • Brian Radak (Thu Oct 05 2017 - 07:39:03 CDT)
  • Fotis Baltoumas (Thu Oct 05 2017 - 05:29:44 CDT)
  • Sneha M (Thu Oct 05 2017 - 05:11:37 CDT)
• nan for Drude's LP in distance-like colvars
  • Giacomo Fiorin (Fri Nov 24 2017 - 12:31:37 CST)
  • Bogdan MAREKHA (Fri Nov 24 2017 - 10:44:01 CST)
• 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)
• Neutralize a box for FEP
  • Grace Brannigan (Wed Apr 12 2017 - 13:08:16 CDT)
  • Radak, Brian K (Wed Apr 12 2017 - 13:17:46 CDT)
  • David Huggins (Wed Apr 12 2017 - 13:05:05 CDT)
  • Radak, Brian K (Wed Apr 12 2017 - 11:14:26 CDT)
  • David Huggins (Wed Apr 12 2017 - 10:30:20 CDT)
• No minimized system after running minimization in NAMD
  • Ajasja LjubetiÄ� (Thu Sep 07 2017 - 09:38:18 CDT)
  • Roshan Shrestha (Thu Sep 07 2017 - 09:17:02 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)
• 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-standard solvants
  • faride badalkhani (Wed Jun 01 2016 - 11:55:28 CDT)
• not a number error
  • Mohaddeseh Habibzadeh (Mon Jan 09 2017 - 08:07:12 CST)
  • Ajasja LjubetiÄ� (Mon Jan 09 2017 - 07:39:15 CST)
  • Mohaddeseh Habibzadeh (Mon Jan 09 2017 - 01:53:08 CST)
• not a number in NAMD log file
  • Mohaddeseh Habibzadeh (Tue Jan 17 2017 - 00:31:55 CST)
• Npt lipid simulation with electrostatics 2
  • Life Sciences Inc (Fri Feb 17 2017 - 11:04:12 CST)
  • Life Sciences Inc (Fri Feb 17 2017 - 10:52:36 CST)
  • Jeff Comer (Fri Feb 17 2017 - 10:31:43 CST)
  • Radak, Brian K (Fri Feb 17 2017 - 09:26:20 CST)
  • Life Sciences Inc (Thu Feb 16 2017 - 16:46:32 CST)
• NPT simulations with PLUMED in NAMD
  • Eric Lang (Wed Nov 15 2017 - 07:58:27 CST)
• 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)
• 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 vs nve file
  • NEHÄ°R NALINCI (Tue Dec 05 2017 - 00:42:47 CST)
  • Roshan Shrestha (Mon Dec 04 2017 - 18:20:49 CST)
  • Vermaas, Joshua (Mon Dec 04 2017 - 12:26:59 CST)
  • Giacomo Fiorin (Mon Dec 04 2017 - 12:21:34 CST)
  • NEHÄ°R NALINCI (Mon Dec 04 2017 - 12:11:27 CST)
• Occasional performance slow down using NAMD with Xeon Phi
  • Mattia Felice Palermo (Fri Apr 01 2016 - 09:53:37 CDT)
• On-the-fly eABF: Problem with the tcl script.
  • Emmanuel MOUTOUSSAMY (Fri Jan 27 2017 - 02:58:38 CST)
  • Chris Chipot (Thu Jan 26 2017 - 07:20:13 CST)
  • Emmanuel MOUTOUSSAMY (Thu Jan 26 2017 - 06:06:52 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)
• Optimizing namd run
  • Vermaas, Joshua (Wed Oct 11 2017 - 14:14:01 CDT)
  • Dr. Eddie (Wed Oct 11 2017 - 13:04:29 CDT)
• Organic Solvent & Water Simulation
  • Oscar Bastidas (Tue Jun 20 2017 - 15:15:05 CDT)
• Output temperature not agreeing with tcouple temperature
  • Karson Bader (Fri May 13 2016 - 12:07:52 CDT)
• 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 CG Model
  • Giacomo Fiorin (Fri Jul 28 2017 - 13:23:43 CDT)
  • Alexander Adams (Fri Jul 28 2017 - 12:53:24 CDT)
• Packing of different system
  • Srijita Paul (Thu Apr 07 2016 - 10:51:32 CDT)
• pairInteraction and PME?
  • David Hardy (Tue Sep 12 2017 - 11:05:23 CDT)
  • Michael LeVine (Mon Sep 11 2017 - 19:20:59 CDT)
• pairInteraction commands
  • Brian Radak (Mon Feb 20 2017 - 08:19:54 CST)
  • matthew reeves (Sun Feb 19 2017 - 16:39:27 CST)
• 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 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)
• Particle Mesh Ewald with Martini
  • Sourav Ray (Mon May 16 2016 - 10:55:14 CDT)
• patch
  • Giacomo Fiorin (Fri Mar 31 2017 - 07:49:16 CDT)
  • hem_chandra_at_iitg.ernet.in (Fri Mar 31 2017 - 04:03:15 CDT)
  • hem_chandra_at_iitg.ernet.in (Mon Mar 27 2017 - 23:28:53 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 creation
  • Vermaas, Joshua (Wed Feb 08 2017 - 11:37:22 CST)
  • Chitrak Gupta (Wed Feb 08 2017 - 11:27:29 CST)
  • Bennion, Brian (Wed Feb 08 2017 - 11:23:57 CST)
  • matthew reeves (Wed Feb 08 2017 - 11:14:13 CST)
  • Chitrak Gupta (Wed Feb 08 2017 - 08:46:20 CST)
  • matthew reeves (Tue Feb 07 2017 - 17:52:08 CST)
• PDB File of Primary structure and Simulation
  • Emerson Macedo (Fri Sep 02 2016 - 11:19:18 CDT)
• performance drop during run
  • Chitrak Gupta (Fri Jul 29 2016 - 10:41:32 CDT)
• performance is more poor for namd 2.12
  • Yi Huizhan (Wed Sep 13 2017 - 22:25:13 CDT)
• performance of GPU calculations
  • Hao Dong (Sun Nov 06 2016 - 21:11:40 CST)
• performance of NAMD on KNL
  • Vermaas, Joshua (Fri Sep 29 2017 - 16:49:40 CDT)
  • jing liang (Fri Sep 29 2017 - 15:10:04 CDT)
• performance of NAMD SMP MPI version
  • Bennion, Brian (Thu May 25 2017 - 13:45:13 CDT)
  • jing liang (Thu May 25 2017 - 13:38:10 CDT)
• performance on ~1.5 million atoms system
  • Vermaas, Joshua (Mon Apr 17 2017 - 10:33:04 CDT)
  • Steven Neumann (Mon Apr 17 2017 - 00:42:12 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 cell too small with GPUs, not with pur CPUs
  • JC Gumbart (Sat Aug 26 2017 - 08:11:13 CDT)
  • David Hardy (Fri Aug 25 2017 - 21:34:38 CDT)
  • JC Gumbart (Fri Aug 25 2017 - 17:09:49 CDT)
  • David Hardy (Fri Aug 25 2017 - 14:31:31 CDT)
  • Francesco Pietra (Fri Aug 04 2017 - 06:44:37 CDT)
  • David Hardy (Tue Jul 18 2017 - 17:05:00 CDT)
  • Francesco Pietra (Mon Jul 17 2017 - 09:09:20 CDT)
  • David Hardy (Wed Jul 05 2017 - 11:02:14 CDT)
  • Joshua . (Wed Jul 05 2017 - 09:39:40 CDT)
  • Francesco Pietra (Wed Jul 05 2017 - 02:09:14 CDT)
• Periodic molecules in NAMD
  • Haohao Fu (Wed Dec 13 2017 - 22:14:16 CST)
  • Vermaas, Joshua (Wed Dec 13 2017 - 12:18:31 CST)
  • Bogdan MAREKHA (Wed Dec 13 2017 - 05:13:54 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)
• pKa calculation with thermodynamic integration (TI)
  • Sadegh Faramarzi Ganjabad (Tue May 30 2017 - 13:12:23 CDT)
  • Brian Radak (Tue May 30 2017 - 09:23:34 CDT)
  • Sadegh Faramarzi Ganjabad (Mon May 29 2017 - 15:45:10 CDT)
  • Radak, Brian K (Wed May 24 2017 - 13:29:59 CDT)
  • Sadegh Faramarzi Ganjabad (Wed May 24 2017 - 13:16:46 CDT)
  • Radak, Brian K (Wed May 24 2017 - 11:35:50 CDT)
  • Sadegh Faramarzi Ganjabad (Wed May 24 2017 - 10:48:29 CDT)
  • Brian Radak (Tue May 23 2017 - 09:32:14 CDT)
  • Sadegh Faramarzi Ganjabad (Tue May 23 2017 - 01:04:17 CDT)
  • Radak, Brian K (Wed May 17 2017 - 09:54:39 CDT)
  • Hannes Loeffler (Wed May 17 2017 - 03:37:52 CDT)
  • Sadegh Faramarzi Ganjabad (Wed May 17 2017 - 02:00:11 CDT)
  • Vermaas, Joshua (Thu May 11 2017 - 11:52:48 CDT)
  • Brian Radak (Thu May 11 2017 - 10:27:25 CDT)
  • Sadegh Faramarzi Ganjabad (Wed May 10 2017 - 19:36:16 CDT)
  • Radak, Brian K (Tue May 09 2017 - 10:41:52 CDT)
  • Vermaas, Joshua (Mon May 08 2017 - 17:01:05 CDT)
  • Sadegh Faramarzi Ganjabad (Mon May 08 2017 - 14:59:06 CDT)
• plumed
  • Stefano Guglielmo (Sun Feb 28 2016 - 10:21:32 CST)
• 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)
• 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)
• polymer
  • Giacomo Fiorin (Thu Jul 27 2017 - 08:14:01 CDT)
  • Nehir NALINCI (Thu Jul 27 2017 - 03:02:49 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)
• Positions for Ph.D. candidates in biomolecular modeling
  • Jan Brezovsky (Thu Feb 02 2017 - 05:30:48 CST)
• 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)
• Post-doc position at ALCF - HPC post-doc in Computational Materials
  • Wei Jiang (Fri Apr 07 2017 - 10:18:55 CDT)
• Postdoc position available
  • Ivaylo Nikolaev Ivanov (Tue May 17 2016 - 10:05:18 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)
• Pressure Profile.
  • msa5 (Thu Nov 17 2016 - 11:06:48 CST)
• principal axes in colvars
  • Jérôme Hénin (Wed Jun 14 2017 - 07:23:30 CDT)
  • Stefano Guglielmo (Wed Jun 14 2017 - 06:28:44 CDT)
• problem in minimization
  • Ma'Mon Hatmal (Tue Nov 08 2016 - 00:01:28 CST)
• Problem in NAMD QMMM
  • Kshatresh Dutta Dubey (Sat Mar 25 2017 - 13:37:25 CDT)
• problem in running targeted MD
  • giulia palermo (Wed Feb 24 2016 - 19:56:11 CST)
• Problem in running wham
  • Rabeta Yeasmin (Fri Aug 04 2017 - 10:41:06 CDT)
• problem in writing the coor files
  • Fidan Sumbul (Tue Nov 07 2017 - 02:55:40 CST)
  • Haohao Fu (Mon Nov 06 2017 - 23:27:01 CST)
  • Fidan Sumbul (Mon Nov 06 2017 - 11:11:28 CST)
• problem to generate LPS PSF file using PSFGEN
  • 송연호 (Mon Mar 20 2017 - 19:22:29 CDT)
  • Fotis Baltoumas (Fri Mar 17 2017 - 05:03:42 CDT)
  • 송연호 (Thu Mar 16 2017 - 23:19:36 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 minimization
  • Abhishek TYAGI (Thu Oct 27 2016 - 06:13:10 CDT)
  • Ma'Mon Hatmal (Thu Oct 27 2016 - 05:22:52 CDT)
• problem with minimization and calculation of force on a fixed atom
  • Jérôme Hénin (Fri Sep 01 2017 - 11:23:23 CDT)
  • Jérôme Hénin (Fri Sep 01 2017 - 11:02:52 CDT)
  • Ben Adams (Fri Sep 01 2017 - 11:01:49 CDT)
  • Jérôme Hénin (Fri Sep 01 2017 - 10:48:49 CDT)
  • Ben Adams (Fri Sep 01 2017 - 10:36:21 CDT)
  • Jérôme Hénin (Thu Aug 31 2017 - 17:36:54 CDT)
  • Ben Adams (Thu Aug 31 2017 - 17:03:21 CDT)
• Problem with namd2 execution on Windows GPU version
  • md_at_novamechanics.com (Fri Mar 17 2017 - 15:57:26 CDT)
• Problem with running on multiple nodes
  • Karteek Bejagam (Wed May 31 2017 - 11:33:48 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)
• 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 mutating HID to TYR for free energy calculations
  • Vermaas, Joshua (Wed Mar 08 2017 - 09:45:49 CST)
  • Nehad Elsalamouny (Tue Mar 07 2017 - 17:39:37 CST)
  • Brian Radak (Tue Mar 07 2017 - 17:02:27 CST)
  • Nehad Elsalamouny (Tue Mar 07 2017 - 16:50:32 CST)
  • Radak, Brian K (Tue Mar 07 2017 - 09:49:38 CST)
  • Nehad Elsalamouny (Tue Mar 07 2017 - 04:27:28 CST)
• Problems running FEP on Lenovo NextScale KNL
  • Brian Radak (Thu Jul 27 2017 - 15:55:21 CDT)
  • Francesco Pietra (Thu Jul 27 2017 - 01:27:24 CDT)
  • Brian Radak (Wed Jul 26 2017 - 14:45:22 CDT)
  • Francesco Pietra (Wed Jul 26 2017 - 10:27:20 CDT)
  • Brian Radak (Wed Jul 26 2017 - 10:04:22 CDT)
  • Francesco Pietra (Wed Jul 26 2017 - 09:23:19 CDT)
• Problems running NAMD QM-MM with ORCA 3.0.3
  • Francesco Pietra (Fri Dec 30 2016 - 03:24:04 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)
• Production run after equilibration
  • Brian Radak (Tue Aug 29 2017 - 10:10:44 CDT)
  • Roshan Shrestha (Tue Aug 29 2017 - 05:38:00 CDT)
• Proper combination of langevinHydrogen with rigidbonds
  • Jérôme Hénin (Thu Aug 31 2017 - 10:43:12 CDT)
  • Benjamin Rousseau (Thu Aug 31 2017 - 10:31:31 CDT)
• Protein Penetrating Water Box
  • salehesam101 . (Sun Jan 29 2017 - 20:07:08 CST)
  • Saleh AlKhalifa (Sun Jan 29 2017 - 14:02:05 CST)
  • Oscar Bastidas (Sun Jan 29 2017 - 03:15:25 CST)
• protein stability in a membrane and SMD
  • Martin, Erik W (Fri Feb 17 2017 - 17:14:31 CST)
• Protein trapped on an edge of the simulation cell using C36 force field
  • istamkos_at_auth.gr (Tue Jul 11 2017 - 03:15:51 CDT)
  • istamkos_at_auth.gr (Tue Jul 04 2017 - 01:25:13 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 file generation with Gromacs Parameters
  • Amali Guruge (Thu Nov 09 2017 - 19:45:28 CST)
  • Fotis Baltoumas (Wed Nov 08 2017 - 17:43:42 CST)
  • Amali Guruge (Wed Nov 08 2017 - 17:17:14 CST)
  • Haohao Fu (Mon Nov 06 2017 - 23:22:05 CST)
  • Amali Guruge (Mon Nov 06 2017 - 19:53:58 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 failed to guess coordinate due to bad angle CD CG HG2
  • Radak, Brian K (Fri Feb 10 2017 - 09:36:22 CST)
  • Radak, Brian K (Thu Feb 09 2017 - 10:58:59 CST)
  • Sarath Josh M.K (Thu Feb 09 2017 - 03:19:39 CST)
• psfgen giving wrong structure in the autopdb file
  • Peter Freddolino (Thu Apr 06 2017 - 19:50:01 CDT)
  • Harish Srinivasan (Thu Apr 06 2017 - 01:37:29 CDT)
• psfgen readpsf error with no more explanation
  • Vermaas, Joshua (Wed May 17 2017 - 16:12:41 CDT)
  • Sadegh Faramarzi Ganjabad (Wed May 17 2017 - 15:58:37 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)
• Pulling protein through membrane without changing the position of membrane
  • Rabeta Yeasmin (Mon May 15 2017 - 13:23:22 CDT)
  • Amy Rice (Thu May 11 2017 - 12:05:37 CDT)
  • Rabeta Yeasmin (Thu May 11 2017 - 11:51:44 CDT)
• Q=9B=9E=E5=A4=8D:__Free_energy_(eABF):_ne?= gative RMSD and harmonic restraints.
  • yjcoshc_at_gmail.com (Wed Aug 02 2017 - 20:00:22 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)
• QM atoms outside the PBC boundary in QM/MM calculation
  • Haohao Fu (Sun Sep 03 2017 - 08:56:44 CDT)
  • Haohao Fu (Sat Sep 02 2017 - 21:55:26 CDT)
• QM-MM flooding potential
  • Francesco Pietra (Tue Jan 03 2017 - 01:40:20 CST)
• QM-MM ORCA Charm++ error Could not find QM output file
  • Marcelo C. R. Melo (Fri Jan 20 2017 - 08:33:18 CST)
  • Francesco Pietra (Thu Jan 19 2017 - 11:56:20 CST)
  • Marcelo C. R. Melo (Tue Jan 17 2017 - 15:58:58 CST)
  • Francesco Pietra (Tue Jan 17 2017 - 12:10:52 CST)
  • Marcelo C. R. Melo (Mon Jan 16 2017 - 16:17:19 CST)
  • Francesco Pietra (Mon Jan 16 2017 - 01:55:38 CST)
• QM/MM Parallel Computing With Orca
  • Nisler, Collin R. (Tue Sep 12 2017 - 11:08:47 CDT)
  • Marcelo C. R. Melo (Tue Sep 12 2017 - 09:45:08 CDT)
  • Nisler, Collin R. (Tue Sep 12 2017 - 09:12:59 CDT)
• QM/MM With Mopac Error
  • Marcelo C. R. Melo (Fri Sep 15 2017 - 07:36:26 CDT)
  • Nisler, Collin R. (Wed Sep 13 2017 - 15:27:19 CDT)
• Queries regarding metadynamics and .pmf visualization
  • Giacomo Fiorin (Tue Nov 15 2016 - 10:40:15 CST)
• Querries on eABF
  • Souvik Sinha (Sat Jul 15 2017 - 07:39:34 CDT)
  • Souvik Sinha (Wed Jul 12 2017 - 07:34:46 CDT)
  • Jérôme Hénin (Wed Jul 12 2017 - 07:24:14 CDT)
  • Souvik Sinha (Wed Jul 12 2017 - 07:15:51 CDT)
  • Jérôme Hénin (Tue May 30 2017 - 23:10:42 CDT)
  • yjcoshc_at_gmail.com (Tue May 30 2017 - 20:18:40 CDT)
  • Souvik Sinha (Tue May 30 2017 - 11:01:09 CDT)
  • Giacomo Fiorin (Tue May 30 2017 - 08:12:30 CDT)
  • Jérôme Hénin (Tue May 30 2017 - 07:54:55 CDT)
  • Souvik Sinha (Tue May 30 2017 - 07:37:19 CDT)
  • Souvik Sinha (Tue May 30 2017 - 02:51:31 CDT)
  • Souvik Sinha (Fri May 26 2017 - 10:53:04 CDT)
  • Jérôme Hénin (Fri May 26 2017 - 10:30:46 CDT)
  • Souvik Sinha (Fri May 26 2017 - 00:45:37 CDT)
  • Jeff Comer (Thu May 25 2017 - 16:06:33 CDT)
  • Souvik Sinha (Thu May 25 2017 - 05:02:32 CDT)
  • Jérôme Hénin (Thu Apr 27 2017 - 16:00:31 CDT)
  • Souvik Sinha (Wed Apr 26 2017 - 06:17:03 CDT)
  • Souvik Sinha (Wed Apr 26 2017 - 01:40:21 CDT)
• 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 applying external force
  • The Cromicus Productions (Mon Mar 06 2017 - 18:27:20 CST)
  • Giacomo Fiorin (Mon Mar 06 2017 - 16:23:57 CST)
  • The Cromicus Productions (Mon Mar 06 2017 - 15:59:25 CST)
  • Giacomo Fiorin (Mon Mar 06 2017 - 15:40:38 CST)
  • The Cromicus Productions (Mon Mar 06 2017 - 15:32:36 CST)
  • Jérôme Hénin (Mon Mar 06 2017 - 14:23:24 CST)
  • The Cromicus Productions (Mon Mar 06 2017 - 13:56:30 CST)
• question about GPU
  • parinaz bashirbanaem (Mon Feb 06 2017 - 09:00:53 CST)
• Question about new NAMD QM/MM code
  • Eric Smoll (Sun May 07 2017 - 22:08:08 CDT)
• question about point substitution A→U
  • parinaz bashirbanaem (Sat Dec 30 2017 - 12:47:43 CST)
• question about Steered Molecular Dynamics
  • Jérôme Hénin (Wed Feb 15 2017 - 17:11:42 CST)
  • Oleksii Zdorevskyi (Wed Feb 15 2017 - 08:38:22 CST)
• 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 on creating constraints in NAMD
  • Randy J. Zauhar (Sat Mar 11 2017 - 13:01:17 CST)
  • Randy J. Zauhar (Tue Feb 21 2017 - 10:07:18 CST)
  • Jérôme Hénin (Tue Feb 21 2017 - 09:51:20 CST)
  • Randy J. Zauhar (Tue Feb 21 2017 - 09:03:21 CST)
• Questions on implementing new collective variable in colvars.
  • Jérôme Hénin (Wed Jun 14 2017 - 07:26:16 CDT)
  • yjcoshc (Tue Jun 13 2017 - 20:36:32 CDT)
  • Jérôme Hénin (Tue Jun 13 2017 - 10:32:23 CDT)
  • yjcoshc (Mon Jun 12 2017 - 22:48:26 CDT)
  • Axel Kohlmeyer (Mon Jun 12 2017 - 22:38:48 CDT)
  • yjcoshc (Mon Jun 12 2017 - 22:14:35 CDT)
• Radial pair distribution function for internal water analysis
  • James Starlight (Thu Aug 31 2017 - 05:49:39 CDT)
• raising temperature after equiliobration
  • Brian Radak (Mon Aug 28 2017 - 09:12:40 CDT)
  • t.shivam_at_iitg.ernet.in (Sat Aug 26 2017 - 02:20:20 CDT)
• RATTLE error with lipid bilayer system
  • Vermaas, Joshua (Tue Nov 21 2017 - 14:22:05 CST)
  • Ahmad Kiani Karanji (Tue Nov 21 2017 - 13:08:46 CST)
• readable output of gbis.coor
  • Harish Srinivasan (Sat Jan 07 2017 - 01:58:23 CST)
  • hem_chandra_at_iitg.ernet.in (Sat Jan 07 2017 - 00:43:19 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)
• reconstructing pmf
  • Stefano Guglielmo (Wed Dec 20 2017 - 01:55:15 CST)
  • Giacomo Fiorin (Tue Dec 19 2017 - 18:24:46 CST)
  • Stefano Guglielmo (Tue Dec 19 2017 - 18:17:35 CST)
  • Jeff Comer (Tue Dec 19 2017 - 12:52:21 CST)
  • Giacomo Fiorin (Tue Dec 19 2017 - 10:27:09 CST)
  • Jeff Comer (Tue Dec 19 2017 - 09:20:57 CST)
  • Giacomo Fiorin (Tue Dec 19 2017 - 08:08:03 CST)
  • Stefano Guglielmo (Tue Dec 19 2017 - 02:48:53 CST)
  • Giacomo Fiorin (Mon Dec 18 2017 - 19:40:03 CST)
  • Vermaas, Joshua (Mon Dec 18 2017 - 18:35:31 CST)
  • Stefano Guglielmo (Mon Dec 18 2017 - 18:24:15 CST)
• 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)
• reg diffusion of water molecules
  • Vidhya Sankar (Sat Aug 12 2017 - 23:51:25 CDT)
• Reg membrane assembly
  • Vidhya Sankar (Thu Aug 17 2017 - 00:37:42 CDT)
• REG Protein inserion in to membrane bi layear
  • Vermaas, Joshua (Thu Jun 22 2017 - 12:25:00 CDT)
  • Arthur Oliveira Vale (Thu Jun 22 2017 - 10:27:47 CDT)
  • Vermaas, Joshua (Tue Jun 20 2017 - 10:49:51 CDT)
  • Vidhya Sankar (Tue Jun 20 2017 - 05:05:39 CDT)
• Reg seeting of periodic boundary condition
  • Vidhya Sankar (Tue Jun 20 2017 - 11:56:59 CDT)
  • Vidhya Sankar (Wed Jun 14 2017 - 21:59:27 CDT)
• Regarding Bionanotechnology tutorial
  • arpita agarwal (Wed Apr 13 2016 - 20:07:26 CDT)
• regarding constant velocity steered molecular dynamics
  • Radak, Brian K (Wed Feb 08 2017 - 11:48:09 CST)
  • mrinal patel (Wed Feb 08 2017 - 04:07:24 CST)
• Regarding Error on HB2
  • Vermaas, Joshua (Tue Feb 21 2017 - 11:28:49 CST)
  • Obayed Ullah (Mon Feb 20 2017 - 18:48:56 CST)
• 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 radial distribution function graph
  • siddharth kamal (Thu Jun 16 2016 - 08:31:23 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)
• Regarding: Free energy of alchemical transformation of K + and Na +
  • B.W.J. Irwin (Fri Jan 06 2017 - 08:50:24 CST)
  • Amit Kumar (Fri Jan 06 2017 - 05:09:35 CST)
• Regular vs US sampling runs.
  • jeevan gc (Fri Sep 01 2017 - 16:32:20 CDT)
  • Vermaas, Joshua (Fri Sep 01 2017 - 11:53:11 CDT)
  • jeevan gc (Fri Sep 01 2017 - 11:32:27 CDT)
  • Giacomo Fiorin (Thu Aug 31 2017 - 21:34:56 CDT)
  • jeevan gc (Thu Aug 31 2017 - 20:13:38 CDT)
  • Vermaas, Joshua (Thu Aug 31 2017 - 18:56:17 CDT)
  • jeevan gc (Thu Aug 31 2017 - 18:23:43 CDT)
• 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 HPC
  • HOUSTON Douglas (Mon Mar 06 2017 - 08:15:25 CST)
• REMD using NAMD 2.13
  • Aliasghar Alizadeh-Mojarad (Wed Nov 22 2017 - 17:14:40 CST)
  • Brian Radak (Mon Nov 20 2017 - 08:29:29 CST)
  • Aliasghar Alizadeh-Mojarad (Sat Nov 18 2017 - 18:03:41 CST)
  • Chitrak Gupta (Sat Nov 18 2017 - 17:58:53 CST)
  • Vermaas, Joshua (Fri Nov 17 2017 - 18:16:43 CST)
  • Aliasghar Alizadeh-Mojarad (Fri Nov 17 2017 - 18:02:46 CST)
• Remembering Klaus Schulten
  • Thomas C. Bishop (Tue Nov 01 2016 - 09:33:31 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 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)
• replica_bias and colvars
  • Giacomo Fiorin (Sat Aug 12 2017 - 13:29:48 CDT)
  • JC Gumbart (Sat Aug 12 2017 - 06:49:35 CDT)
  • Giacomo Fiorin (Thu Aug 10 2017 - 21:10:21 CDT)
  • JC Gumbart (Thu Aug 10 2017 - 16:17:21 CDT)
  • Giacomo Fiorin (Thu Aug 10 2017 - 15:25:35 CDT)
  • Vermaas, Joshua (Thu Aug 10 2017 - 12:58:27 CDT)
  • Giacomo Fiorin (Thu Aug 10 2017 - 12:51:26 CDT)
  • JC Gumbart (Thu Aug 10 2017 - 12:07:45 CDT)
• Repulsion of lipid bilayer during equilibration
  • Mahrukh Imtiaz (Fri Jul 22 2016 - 05:00:41 CDT)
• REST2 patch for NAMD 2.12
  • Chitrak Gupta (Fri Feb 17 2017 - 14:49:07 CST)
• REST2 simulations: Corecting shifted dcd files!
  • Bhati, Agastya (Wed Oct 11 2017 - 14:36:14 CDT)
• 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 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 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)
• 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 and continuing - difference
  • Giacomo Fiorin (Mon Aug 14 2017 - 09:16:24 CDT)
  • t.shivam_at_iitg.ernet.in (Mon Aug 14 2017 - 09:05:03 CDT)
• Restarting FEP calculations
  • Sadegh Faramarzi Ganjabad (Mon Oct 23 2017 - 15:10:55 CDT)
• restarting simulation
  • Francesco Pietra (Mon Mar 14 2016 - 09:45:44 CDT)
• restraining selected atom's z coordinates
  • Rabeta Yeasmin (Mon May 15 2017 - 13:19:33 CDT)
  • Vermaas, Joshua (Mon May 15 2017 - 11:30:55 CDT)
  • Ajasja LjubetiÄ� (Sun May 14 2017 - 01:51:03 CDT)
  • Rabeta Yeasmin (Sat May 13 2017 - 19:17:26 CDT)
• Restraining the mass centre coordinate during Umbrella Sampling
  • Rabeta Yeasmin (Wed Jun 07 2017 - 10:46:57 CDT)
• restraint backbone to keep secondary structure in coarse grain MD
  • Deng, Jinxia (Nancy) (Wed Nov 09 2016 - 10:42:46 CST)
• restraints and constraints in NAMD
  • Vermaas, Joshua (Wed Feb 22 2017 - 11:57:14 CST)
  • Lara rajam (Tue Feb 21 2017 - 17:42:40 CST)
• Restring the coordinate during Umbrella Sampling
  • Rabeta Yeasmin (Tue Jun 06 2017 - 16:13:08 CDT)
• 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)
• RFC: shell scripts and support functions for NAMD on Slurm (including GPU and Infiniband)
  • Renfro, Michael (Mon Sep 04 2017 - 13:57:54 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
  • Ajasja LjubetiÄ� (Fri Dec 30 2016 - 10:46:39 CST)
  • Jérôme Hénin (Fri Dec 30 2016 - 07:49:17 CST)
  • Wang, X. Y. (Fri Dec 30 2016 - 06:03:02 CST)
  • Jérôme Hénin (Thu Dec 22 2016 - 05:06:35 CST)
  • Wang, X. Y. (Thu Dec 22 2016 - 04:26:21 CST)
• RMSD colvar not working in NAMD2.12 Linux version
  • Giacomo Fiorin (Wed Nov 08 2017 - 05:40:19 CST)
  • Jérôme Hénin (Wed Nov 08 2017 - 05:12:12 CST)
  • Abhaysinh Gaikwad (Tue Nov 07 2017 - 21:46:28 CST)
• RMSD of backbone changes rapidly at the beginning of production run
  • Monika Madhavi (Fri Nov 03 2017 - 18:45:34 CDT)
  • Fidan Sumbul (Fri Nov 03 2017 - 06:27:42 CDT)
  • Peter Freddolino (Thu Nov 02 2017 - 20:25:17 CDT)
  • Vermaas, Joshua (Thu Nov 02 2017 - 17:59:45 CDT)
  • Monika Madhavi (Thu Nov 02 2017 - 17:28:24 CDT)
  • Peter Freddolino (Thu Nov 02 2017 - 09:02:13 CDT)
  • Monika Madhavi (Thu Nov 02 2017 - 04:52:11 CDT)
• 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 cuda with srun.
  • Fırat Yılmaz (Wed Jun 21 2017 - 03:36:09 CDT)
  • Fırat Yılmaz (Tue Jun 20 2017 - 16:03:29 CDT)
• Running 2.12
  • Vermaas, Joshua (Mon Oct 16 2017 - 12:07:07 CDT)
  • Dr. Eddie (Fri Oct 13 2017 - 19:56:46 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 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 IMD with TMD (domain restraints)
  • Giacomo Fiorin (Wed Jan 04 2017 - 08:36:46 CST)
  • Steven Cohen (Mon Jan 02 2017 - 10:43:09 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 multiple-replicas metadynamics
  • Giacomo Fiorin (Tue Nov 14 2017 - 09:07:43 CST)
  • Giacomo Fiorin (Thu Nov 09 2017 - 17:45:50 CST)
  • Giacomo Fiorin (Wed Nov 08 2017 - 16:50:17 CST)
  • Giacomo Fiorin (Wed Nov 08 2017 - 15:49:54 CST)
  • Prapasiri Pongprayoon (Wed Nov 08 2017 - 15:37:51 CST)
  • Giacomo Fiorin (Wed Nov 08 2017 - 05:58:38 CST)
  • Prapasiri Pongprayoon (Mon Nov 06 2017 - 16:35:51 CST)
  • Giacomo Fiorin (Sun Nov 05 2017 - 10:17:13 CST)
  • Vermaas, Joshua (Fri Nov 03 2017 - 19:05:18 CDT)
  • Prapasiri Pongprayoon (Fri Nov 03 2017 - 18:30:11 CDT)
• Running NAMD on Intel OmniPath
  • David Hardy (Fri Jul 28 2017 - 10:29:37 CDT)
  • Giacomo Fiorin (Thu Jul 27 2017 - 17:53:52 CDT)
  • David Hardy (Thu Jul 27 2017 - 16:36:47 CDT)
  • Giacomo Fiorin (Thu Jul 27 2017 - 14:33:38 CDT)
  • David Hardy (Thu Jul 27 2017 - 14:18:47 CDT)
  • Maxime Boissonneault (Thu Jul 27 2017 - 13:47:54 CDT)
  • Mauro Lapelosa (Thu Jul 27 2017 - 13:06:24 CDT)
  • Maxime Boissonneault (Thu Jul 27 2017 - 13:00:04 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)
• Sample umbrella sampling input file
  • Vermaas, Joshua (Fri Oct 06 2017 - 17:35:33 CDT)
  • Rabeta Yeasmin (Fri Oct 06 2017 - 17:14:02 CDT)
• Scaling behaviour of NAMD on hosts with GPU accelrators
  • Boonstra, S. (Fri Mar 24 2017 - 06:41:19 CDT)
  • Jeff Comer (Thu Mar 23 2017 - 12:24:23 CDT)
  • Kraus, Sebastian (Thu Mar 23 2017 - 11:18:14 CDT)
• Script for Terachem QMMM
  • Marcelo C. R. Melo (Thu Dec 14 2017 - 15:45:59 CST)
  • Haohao Fu (Thu Dec 14 2017 - 07:13:47 CST)
  • Chris Butch (Thu Dec 14 2017 - 03:29:17 CST)
• 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 during water MD
  • Kevin C Chan (Tue Apr 25 2017 - 06:59:07 CDT)
  • nikolaev_at_spbau.ru (Tue Apr 18 2017 - 09:37:10 CDT)
• Segmentation fault error with 'nan' pressure and energy
  • Sadegh Faramarzi Ganjabad (Tue Jun 06 2017 - 14:07:24 CDT)
  • Sadegh Faramarzi Ganjabad (Thu Jun 01 2017 - 13:05:09 CDT)
  • Brian Radak (Wed May 31 2017 - 18:24:19 CDT)
  • Sadegh Faramarzi Ganjabad (Wed May 31 2017 - 13:37:09 CDT)
  • Vermaas, Joshua (Tue May 30 2017 - 17:14:16 CDT)
  • Sadegh Faramarzi Ganjabad (Tue May 30 2017 - 16:48:09 CDT)
  • Richard Overstreet (Tue May 30 2017 - 16:41:33 CDT)
  • Sadegh Faramarzi Ganjabad (Tue May 30 2017 - 16:17:12 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)
• Selecting atoms in NAMD .conf file and time-varying electric field
  • Ben Lowe (Wed Mar 01 2017 - 15:42:55 CST)
• 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 softcore parameters for FEP
  • Brian Radak (Thu Aug 03 2017 - 13:03:29 CDT)
  • John Green (Thu Aug 03 2017 - 12:49:20 CDT)
  • Brian Radak (Thu Aug 03 2017 - 12:02:47 CDT)
  • John Green (Thu Aug 03 2017 - 11:38:37 CDT)
  • Brian Radak (Thu Aug 03 2017 - 08:20:36 CDT)
  • John Green (Wed Aug 02 2017 - 16:18:32 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)
• Setting up the range for movement of protein in umbrella sampling
  • Rabeta Yeasmin (Fri Jun 16 2017 - 16:21:55 CDT)
• Shear flow simulation setup
  • James Starlight (Thu Apr 27 2017 - 07:09:25 CDT)
  • Giacomo Fiorin (Wed Apr 26 2017 - 09:47:21 CDT)
  • James Starlight (Wed Apr 26 2017 - 08:51:54 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, 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 Protein Entering membrane
  • Vermaas, Joshua (Mon Jun 19 2017 - 12:01:45 CDT)
  • Arthur Oliveira Vale (Sun Jun 18 2017 - 20:14:32 CDT)
• Simulating Protein/Membrane interface with pre-equiliibrated lipid bilayer
  • Vermaas, Joshua (Wed Aug 23 2017 - 19:16:51 CDT)
  • Arthur Vale (Wed Aug 23 2017 - 18:58:59 CDT)
• Simulating SDS molecules
  • Giacomo Fiorin (Fri Jun 30 2017 - 09:27:36 CDT)
  • Ajasja LjubetiÄ� (Fri Jun 30 2017 - 09:20:08 CDT)
  • Siddharth Girdhar (Fri Jun 30 2017 - 09:11:08 CDT)
• Simulation crashes on GPU
  • Mohan maruthi sena (Tue Oct 24 2017 - 05:25:10 CDT)
• simulation crashing in 2nd stage equilibration
  • Giacomo Fiorin (Fri Aug 11 2017 - 08:31:53 CDT)
  • t.shivam_at_iitg.ernet.in (Fri Aug 11 2017 - 08:20:42 CDT)
  • Giacomo Fiorin (Fri Aug 11 2017 - 07:57:11 CDT)
  • t.shivam_at_iitg.ernet.in (Fri Aug 11 2017 - 06:32:32 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 of the mechanical stress in NAMD
  • Giacomo Fiorin (Mon Jul 17 2017 - 13:15:14 CDT)
  • Giacomo Fiorin (Mon Jul 17 2017 - 07:49:49 CDT)
  • James Starlight (Mon Jul 17 2017 - 02:55:30 CDT)
• 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)
• 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)
• Slurm Run on supercomputer
  • Marisol Oswald (Sun Jan 22 2017 - 18:21:01 CST)
• Slurm Script for Multi Node Run
  • Bennion, Brian (Mon Apr 17 2017 - 11:52:58 CDT)
  • Zeki Zeybek (Sun Apr 16 2017 - 11:42:41 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 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: constant velocity output analysis (Develop force and displacement plot)
  • Keshab Thapa (Mon Nov 13 2017 - 17:20:38 CST)
• SMP instructions for multi-node calculation on POWER 8 + P100
  • Adrien Cerdan (Wed Nov 22 2017 - 10:09:51 CST)
• Software for molecular electrostatic calculations
  • David Hardy (Thu Aug 17 2017 - 13:28:19 CDT)
  • Rabeta Yeasmin (Thu Aug 10 2017 - 10:31:58 CDT)
  • Giacomo Fiorin (Thu Aug 10 2017 - 08:15:28 CDT)
  • Rabeta Yeasmin (Wed Aug 09 2017 - 16:44:01 CDT)
  • Giacomo Fiorin (Wed Aug 09 2017 - 14:16:54 CDT)
  • Rabeta Yeasmin (Wed Aug 09 2017 - 13:03:49 CDT)
• Solvation free energy difference of alchemical transformation of K+ into Na+
  • Brian Radak (Wed Jan 11 2017 - 10:20:21 CST)
  • Abhishek Kumar Singh (Wed Jan 11 2017 - 00:39:11 CST)
  • Radak, Brian K (Tue Jan 10 2017 - 14:28:57 CST)
  • Radak, Brian K (Tue Jan 10 2017 - 12:27:07 CST)
  • Hannes Loeffler (Tue Jan 10 2017 - 09:59:35 CST)
  • B.W.J. Irwin (Tue Jan 10 2017 - 09:09:52 CST)
  • Hannes Loeffler (Tue Jan 10 2017 - 06:15:02 CST)
  • Abhishek Kumar Singh (Tue Jan 10 2017 - 05:09:01 CST)
  • Brian Radak (Mon Jan 09 2017 - 10:11:47 CST)
  • Hannes Loeffler (Mon Jan 09 2017 - 01:55:35 CST)
  • Abhishek Kumar Singh (Mon Jan 09 2017 - 00:09:32 CST)
  • Abhishek Kumar Singh (Sun Jan 08 2017 - 22:12:34 CST)
• Solvent box fluctuations
  • Vermaas, Joshua (Mon Mar 27 2017 - 12:13:37 CDT)
  • Götz, Alexander (Mon Mar 27 2017 - 11:56:09 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 about the orthogonality of colvars in ABF.
  • yjcoshc (Wed Mar 15 2017 - 08:39:58 CDT)
  • Jérôme Hénin (Wed Mar 15 2017 - 07:26:23 CDT)
  • yjcoshc (Wed Mar 15 2017 - 07:11:46 CDT)
• 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)
• Some water molecules are missing in psf
  • Giacomo Fiorin (Fri Nov 03 2017 - 08:49:48 CDT)
  • Vermaas, Joshua (Thu Nov 02 2017 - 18:13:28 CDT)
  • Amali Guruge (Thu Nov 02 2017 - 17:33:06 CDT)
• sortreplicas on Stampede 2
  • Chitrak Gupta (Mon Oct 16 2017 - 14:34:15 CDT)
• Spawning too many gpu processes on the first node
  • Robert Sawko (Thu Dec 01 2016 - 13:10:12 CST)
• specify H-bond in CGMD
  • Deng, Jinxia (Nancy) (Thu Mar 09 2017 - 08:42:14 CST)
• Specify number of water molecules:simulation set up in VMD
  • Bennion, Brian (Fri Mar 10 2017 - 13:34:56 CST)
  • Rabeta Yeasmin (Fri Mar 10 2017 - 13:21:31 CST)
• Stack Traceback problem in colvar restrain
  • PRITI ROY (Thu Oct 26 2017 - 07:35:09 CDT)
  • Giacomo Fiorin (Wed Oct 25 2017 - 12:19:16 CDT)
  • PRITI ROY (Wed Oct 25 2017 - 12:11:52 CDT)
  • Giacomo Fiorin (Wed Oct 25 2017 - 10:55:59 CDT)
  • PRITI ROY (Wed Oct 25 2017 - 07:46:57 CDT)
• Standard Output: Benchmark vs Timing
  • Vermaas, Joshua (Sun Apr 09 2017 - 20:58:47 CDT)
  • Jim (Fri Apr 07 2017 - 17:31:55 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 Molecular Dynamics
  • Abhaysinh Gaikwad (Tue Aug 29 2017 - 10:25:19 CDT)
  • Bassam Haddad (Fri Aug 25 2017 - 12:38:14 CDT)
  • Abhaysinh Gaikwad (Thu Aug 24 2017 - 13:28:49 CDT)
• strange diffs in energy output of NAMD 2.9 vs. 2.11
  • Erik Nordgren (Fri Feb 03 2017 - 14:05:23 CST)
• 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)
• 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)
• 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)
• Syntax for replicaRecv
  • Florian Blanc (Tue Aug 08 2017 - 05:13:50 CDT)
  • Florian Blanc (Mon Aug 07 2017 - 08:47:02 CDT)
  • Florian Blanc (Fri Aug 04 2017 - 10:17:27 CDT)
• System temperature check of specific atoms , sys temp of only coupled atoms?
  • Karson Bader (Thu Jul 21 2016 - 15:36:13 CDT)
• 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, "Biased atoms" and "Fitted atoms", RMSD
  • 黄å§�姮 (Wed Nov 29 2017 - 07:27:15 CST)
• TCBG Live Computational Biophysics Workshop Lectures
  • João Ribeiro (Mon Apr 17 2017 - 09:13:24 CDT)
  • João Ribeiro (Mon Apr 10 2017 - 08:24:13 CDT)
• 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)
• tcl used for binary compilation
  • Giacomo Fiorin (Mon Dec 18 2017 - 14:32:23 CST)
  • Francesco Pietra (Mon Dec 18 2017 - 14:26:30 CST)
• 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)
• 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 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 needed time for a MD simulation
  • faride badalkhani (Mon Sep 05 2016 - 10:11:08 CDT)
• The number of QM atoms received is different than expected
  • Haohao Fu (Fri Sep 08 2017 - 04:23:59 CDT)
  • Haohao Fu (Fri Sep 08 2017 - 04:01:24 CDT)
• The question about Network calculation
  • ÀîÎľê (Thu Jun 23 2016 - 03:28:47 CDT)
• The reason for the formation of bubbles in heating stage
  • Danilo Di Maio (Mon Jan 09 2017 - 09:09:58 CST)
  • Mohaddeseh Habibzadeh (Mon Jan 09 2017 - 08:16:51 CST)
• The use of NPT or NVT ensemble to observe dynamical parameters
  • Ana Celia Vila Verde (Mon Jan 02 2017 - 04:13:20 CST)
  • Harish Srinivasan (Mon Jan 02 2017 - 02:27:50 CST)
• 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)
• TMD without alignment
  • John Green (Wed Aug 09 2017 - 17:27:25 CDT)
  • Jérôme Hénin (Sun Aug 06 2017 - 04:23:42 CDT)
  • John Green (Fri Aug 04 2017 - 13:27:31 CDT)
• TMD: initial and targeted structure does not have same number of atoms
  • Rabeta Yeasmin (Wed Mar 08 2017 - 10:20:26 CST)
  • Jeff Comer (Tue Mar 07 2017 - 10:15:39 CST)
  • Rabeta Yeasmin (Tue Mar 07 2017 - 09:42:58 CST)
• Too many iterations in routine jacobi during FEP
  • Francesco Pietra (Wed Sep 06 2017 - 01:36:16 CDT)
• Too many iterations in routine jacobi.
  • Francesco Pietra (Sun Jul 23 2017 - 01:58:42 CDT)
  • Giacomo Fiorin (Fri Jul 21 2017 - 12:49:56 CDT)
  • Francesco Pietra (Fri Jul 21 2017 - 12:06:45 CDT)
• Topology and parameter files for liquid methane
  • Monika Madhavi (Wed Aug 31 2016 - 00:24:24 CDT)
• 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 file for the residue CSO
  • Radak, Brian K (Fri Jun 23 2017 - 13:10:51 CDT)
  • Hyun (Fri Jun 23 2017 - 11:43:38 CDT)
• torsional restrain
  • Lara rajam (Thu Feb 23 2017 - 15:23:31 CST)
  • Vermaas, Joshua (Thu Feb 23 2017 - 12:02:18 CST)
  • Lara rajam (Thu Feb 23 2017 - 11:56:45 CST)
  • Vermaas, Joshua (Thu Feb 23 2017 - 11:09:02 CST)
  • Lara rajam (Thu Feb 23 2017 - 10:14:21 CST)
• 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)
• 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)
• Two parameter file in NAMD configuration file
  • divyabharathi korlepara (Wed Jun 14 2017 - 00:01:04 CDT)
  • Vermaas, Joshua (Mon Jun 12 2017 - 10:20:44 CDT)
  • Vermaas, Joshua (Fri Jun 09 2017 - 12:00:01 CDT)
  • Radak, Brian K (Fri Jun 09 2017 - 09:39:46 CDT)
  • divyabharathi korlepara (Fri Jun 09 2017 - 02:58:16 CDT)
• two stage equilibration in single configuration file
  • Brian Radak (Thu Aug 03 2017 - 12:45:14 CDT)
  • Bassam Haddad (Thu Aug 03 2017 - 12:29:53 CDT)
  • Vermaas, Joshua (Thu Aug 03 2017 - 11:38:18 CDT)
  • t.shivam_at_iitg.ernet.in (Thu Aug 03 2017 - 01:03:46 CDT)
• Type of solvent water molecules
  • Boonstra, S. (Wed Apr 19 2017 - 05:20:31 CDT)
  • Brian Radak (Tue Apr 18 2017 - 16:56:02 CDT)
  • Eduard Schreiner (Tue Apr 18 2017 - 16:21:01 CDT)
  • Oscar Bastidas (Tue Apr 18 2017 - 16:05:06 CDT)
• Umbrella Sampling colvar file parameters
  • Vermaas, Joshua (Thu Jun 08 2017 - 12:32:44 CDT)
  • Rabeta Yeasmin (Thu Jun 08 2017 - 12:20:16 CDT)
• 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 run CUDA NAMD but able to run non-CUDA version on Windows
  • Chun Heung Wong (Sat Dec 16 2017 - 07:22:29 CST)
  • Chun Heung Wong (Sat Dec 16 2017 - 06:50:06 CST)
• 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)
• Urey-Bradley parameters
  • faride badalkhani (Fri Mar 11 2016 - 09:10:39 CST)
• Using 3 GPUs (but not 2) causes energy and temperatures to rise extremely fast in NAMD 2.12
  • Bryan Roessler (Thu Feb 16 2017 - 12:10:23 CST)
  • Bryan Roessler (Tue Feb 07 2017 - 19:55:59 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 Gromacs topology in NAMD
  • Amali Guruge (Sun Nov 12 2017 - 22:19:43 CST)
• Using Mergestructs
  • Eric Weine (Tue May 31 2016 - 14:09:46 CDT)
• 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)
• value of langevinTemp in case of binvelocities
  • t.shivam_at_iitg.ernet.in (Thu Aug 10 2017 - 04:41:10 CDT)
  • fhh2626_at_gmail.com (Thu Aug 10 2017 - 02:13:20 CDT)
  • t.shivam_at_iitg.ernet.in (Thu Aug 10 2017 - 02:05:43 CDT)
• 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)
• veldcdfile command
  • Laura Joana (Mon Jul 03 2017 - 06:13:06 CDT)
  • Laura Joana (Fri Jun 30 2017 - 07:38:02 CDT)
  • Jérôme Hénin (Thu Jun 29 2017 - 07:11:45 CDT)
  • Jérôme Hénin (Thu Jun 29 2017 - 05:12:26 CDT)
  • Laura Joana (Wed Jun 28 2017 - 14:26:17 CDT)
  • Laura Joana (Wed Jun 28 2017 - 14:25:35 CDT)
  • Giacomo Fiorin (Wed Jun 28 2017 - 13:36:43 CDT)
  • Laura Joana (Wed Jun 28 2017 - 13:09:28 CDT)
  • Jérôme Hénin (Wed Jun 28 2017 - 11:41:21 CDT)
  • Jérôme Hénin (Wed Jun 28 2017 - 11:05:58 CDT)
  • Laura Joana (Wed Jun 28 2017 - 09:59:45 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)
• verbs-smp on a single node
  • Jeff Comer (Mon May 01 2017 - 11:22:48 CDT)
  • Jeff Comer (Wed Apr 26 2017 - 15:13:40 CDT)
• very small cell
  • Brian Radak (Sun Jan 08 2017 - 18:59:15 CST)
  • å°�澤å�‹ (Fri Jan 06 2017 - 20:29:34 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: 780Ti and NAMD2
  • David Hardy (Wed Aug 30 2017 - 10:21:40 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: Inconsistent atom count
  • John Stone (Tue Jul 05 2016 - 12:54:26 CDT)
• Water atoms' explosion out of solvate box in my RBCG simulation on NAMD
  • Florian Blanc (Mon Oct 23 2017 - 06:03:14 CDT)
  • ThatMind TV (Mon Oct 23 2017 - 05:57:39 CDT)
• 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 aquaporin-Z
  • Isaac Twelves (Fri Jul 07 2017 - 13:04:37 CDT)
• water permeation through nanotube in lipid bilayer
  • Nikhil Maroli (Fri Jul 29 2016 - 07:18:45 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 is the exact form of the harmonic potential used by the NAMD "constraints" option?
  • Jérôme Hénin (Tue Sep 19 2017 - 13:03:04 CDT)
  • Victoria Lim (Tue Sep 19 2017 - 12:39:34 CDT)
  • Lennart Nilsson (Tue Sep 19 2017 - 12:29:33 CDT)
  • Giacomo Fiorin (Tue Sep 19 2017 - 12:23:46 CDT)
  • Brian Radak (Tue Sep 19 2017 - 11:39:05 CDT)
  • Victoria Lim (Tue Sep 19 2017 - 11:33:46 CDT)
  • Brian Radak (Tue Sep 19 2017 - 08:30:20 CDT)
  • Victoria Lim (Tue Sep 19 2017 - 01:37:21 CDT)
• What to cite for CHARMM22
  • Giacomo Fiorin (Tue Apr 18 2017 - 12:42:19 CDT)
  • Oscar Bastidas (Tue Apr 18 2017 - 12:37:04 CDT)
• Which NAMD-Build for my local HPC?
  • Giacomo Fiorin (Wed Nov 01 2017 - 08:30:27 CDT)
  • Bassam Haddad (Tue Oct 31 2017 - 15:50:19 CDT)
  • Bassam Haddad (Tue Oct 31 2017 - 13:34:12 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 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)
• Workshop on Computational Biophysics, Urbana, IL: Application Deadline March 10th
  • João Ribeiro KS (Sat Mar 04 2017 - 15:56:47 CST)
• Workshop on MD simulation software design
  • Giacomo Fiorin (Tue Mar 21 2017 - 13:42:55 CDT)
• 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 molecules in a NAMD simulation
  • Sourav Ray (Mon Apr 04 2016 - 08:23:02 CDT)
• write first point into (vel)dcd file
  • Laura Joana (Mon Jul 03 2017 - 07:11:37 CDT)
• Writing number of atoms in a specific group to a file
  • Vermaas, Joshua (Fri Dec 16 2016 - 13:12:22 CST)
  • Hamed Fadaei (Fri Dec 16 2016 - 12:52:06 CST)
  • Brian Radak (Fri Dec 16 2016 - 12:11:04 CST)
  • Hamed Fadaei (Fri Dec 16 2016 - 11:35:24 CST)
• Writing pdb file for a particular frame
  • Sourav Pal (Tue May 16 2017 - 22:18:31 CDT)
  • Rabeta Yeasmin (Tue May 16 2017 - 18:18:33 CDT)
• wrong pdb struvture generated while using patch
  • hem_chandra_at_iitg.ernet.in (Fri Apr 07 2017 - 02:06:11 CDT)
• XPLOR format PSF file for small molecules
  • Felix W.-H. Weng (Sun Apr 24 2016 - 11:21:45 CDT)
• »Ø¸´: about User-Defined Forces
  • bay__gulf618_at_sina.com (Mon Jan 18 2016 - 05:23:00 CST)
• “Cannot compile C++ programs with mpicxx" error when compiling charm-6.7
  • sunyeping (Sun Nov 20 2016 - 13:22:02 CST)
• æ�¥è‡ª"ZOU Changling" <zoucl@ihep.ac.cn>的邮件
  • Jeff Comer (Thu Mar 03 2016 - 11:22:49 CST)