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NAMD-L: By Subject

By Subject

3174 messages sorted by: [ author ] [ date ] [ thread ] [ attachment ]
About this archive

Starting: Wed Jan 01 2014 - 05:18:45 CST
Ending: Tue Dec 29 2015 - 07:12:19 CST

• Zhe Wu (Wed Oct 21 2015 - 14:16:02 CDT)
• Norman Geist (Thu Feb 05 2015 - 07:55:53 CST)
• Gianluca Interlandi (Thu Aug 28 2014 - 00:16:37 CDT)
• Jim Phillips (Tue Aug 26 2014 - 10:38:36 CDT)
• Ajasja LjubetiÄ� (Tue Jul 22 2014 - 13:18:02 CDT)
• Aron Broom (Tue Jul 22 2014 - 12:36:33 CDT)
• Jérôme Hénin (Tue Jul 22 2014 - 12:21:26 CDT)
• Jason Swails (Tue Jul 22 2014 - 12:06:31 CDT)
• Kenno Vanommeslaeghe (Tue Jul 22 2014 - 11:58:25 CDT)
• Jérôme Hénin (Tue Jul 22 2014 - 11:57:54 CDT)
• Aaron Larsen (Tue Jul 22 2014 - 11:38:27 CDT)
• Kenno Vanommeslaeghe (Mon Jul 14 2014 - 15:58:25 CDT)
• Gianluca Interlandi (Mon Jul 14 2014 - 13:26:57 CDT)
• Branko (Mon Jul 14 2014 - 13:24:43 CDT)
• Aron Broom (Mon Jul 14 2014 - 13:18:14 CDT)
• manish kesherwani (Wed Apr 16 2014 - 13:21:34 CDT)
• Aron Broom (Tue Apr 15 2014 - 13:47:48 CDT)
• Kenno Vanommeslaeghe (Tue Apr 15 2014 - 12:14:07 CDT)
• Boyang Wang (Thu Feb 20 2014 - 00:53:46 CST)
• "BAK" format files
  • Ramin Ekhteiari (Mon Nov 24 2014 - 06:52:20 CST)
• "Beefier" benchmark
  • Phil Greer (Tue Aug 19 2014 - 11:30:38 CDT)
  • Aron Broom (Tue Aug 19 2014 - 11:15:29 CDT)
  • Maxime Boissonneault (Tue Aug 19 2014 - 11:14:31 CDT)
  • Phil Greer (Tue Aug 19 2014 - 11:10:28 CDT)
  • Maxime Boissonneault (Tue Aug 19 2014 - 10:48:30 CDT)
• "Hands-on" Workshop on Computational Biophysics at Lake Tahoe, August 4-8, 2014
  • David Brandon (Thu Apr 03 2014 - 11:17:33 CDT)
• "implausibly old time stamp" for charm++ 6.7 in CVS
  • Jim Phillips (Mon Dec 21 2015 - 10:04:11 CST)
  • Brian Radak (Wed Dec 16 2015 - 11:42:29 CST)
• "missing operator at _@_ in expression" for if statement
  • Norman Geist (Tue Jul 28 2015 - 01:33:01 CDT)
  • Simon Kit Sang Chu (Mon Jul 27 2015 - 19:39:51 CDT)
• "UNABLE TO FIND BOND PARAMETERS" but bond is defined in stream file
  • Josh Vermaas (Fri Sep 04 2015 - 10:29:38 CDT)
  • Bryan Roessler (Fri Sep 04 2015 - 00:07:49 CDT)
• "Unknown command-line option +replicas"
  • Norman Geist (Tue Mar 03 2015 - 08:35:47 CST)
  • Mitul Saha (Mon Mar 02 2015 - 23:33:11 CST)
• (no subject)
  • Srijita Paul (Tue Dec 22 2015 - 00:06:49 CST)
  • Mattia Felice Palermo (Wed Oct 21 2015 - 04:07:03 CDT)
  • Ma'Mon Hatmal (Thu Feb 05 2015 - 06:32:09 CST)
  • tillmann.utesch_at_mailbox.tu-berlin.de (Wed Nov 26 2014 - 03:20:51 CST)
  • flavio seixas (Tue Nov 25 2014 - 19:13:24 CST)
  • BIPLAB NANDI (Wed Aug 27 2014 - 22:13:06 CDT)
  • ukulililixl (Tue Aug 26 2014 - 01:22:20 CDT)
  • Shalton Evans (Sat Aug 09 2014 - 23:00:48 CDT)
  • sudipta.mml (Sat Aug 02 2014 - 20:01:46 CDT)
  • Carlos Navarrro Retamal (Tue Jul 22 2014 - 11:43:10 CDT)
  • Mitul Saha (Tue Jul 22 2014 - 11:27:04 CDT)
  • Eifler, Jay Q. (UMKC-Student) (Mon Jul 14 2014 - 13:05:36 CDT)
  • sudipta.mml (Mon Jul 07 2014 - 01:08:12 CDT)
  • zmhoseyni (Thu Jul 03 2014 - 22:36:44 CDT)
  • zmhoseyni (Wed Jul 02 2014 - 00:25:31 CDT)
  • zmhoseyni (Wed May 21 2014 - 04:48:25 CDT)
  • zmhoseyni (Mon May 19 2014 - 04:18:48 CDT)
  • Boshra Moradi (Tue May 06 2014 - 16:35:44 CDT)
  • manish kesherwani (Tue Apr 15 2014 - 00:02:12 CDT)
  • Boyang Wang (Thu Feb 20 2014 - 00:05:03 CST)
• *** glibc detected *** namd2: invalid fastbin entry (free)
  • Wesley Lay (Thu May 22 2014 - 15:19:11 CDT)
• +p option on Windows 7
  • Jim Phillips (Wed May 20 2015 - 11:58:13 CDT)
  • Norman Geist (Mon May 18 2015 - 02:39:30 CDT)
  • Kukol, Andreas (Fri May 15 2015 - 05:07:55 CDT)
  • Kukol, Andreas (Wed Jul 30 2014 - 09:56:28 CDT)
• -xHost
  • Gianluca Interlandi (Mon Jul 06 2015 - 13:08:37 CDT)
• .inpcrd to .pdb
  • Jason Swails (Sun Dec 21 2014 - 20:04:39 CST)
  • Shalton Evans (Sun Dec 21 2014 - 13:56:30 CST)
• 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD
  • Lachele Foley (Tue Mar 17 2015 - 21:46:19 CDT)
  • clarkzhy (Tue Mar 17 2015 - 21:18:48 CDT)
  • Lachele Foley (Tue Mar 17 2015 - 21:15:41 CDT)
  • clarkzhy (Tue Mar 17 2015 - 20:33:41 CDT)
• 1-5 Intramolecular repulsions
  • cuiyoutian_at_163.com (Wed Nov 05 2014 - 15:12:43 CST)
  • Axel Kohlmeyer (Wed Nov 05 2014 - 15:12:43 CST)
  • rocwhite168 (Wed Nov 05 2014 - 14:55:05 CST)
  • Rebecca Lindsey (Wed Nov 05 2014 - 13:07:49 CST)
  • rocwhite168 (Wed Nov 05 2014 - 13:02:55 CST)
  • Jeffrey Potoff (Wed Nov 05 2014 - 12:51:02 CST)
  • Kenno Vanommeslaeghe (Wed Nov 05 2014 - 12:33:12 CST)
  • Rebecca Lindsey (Wed Nov 05 2014 - 11:54:40 CST)
• 11/22/2014 6:32:52 PM
  • jeremy adler (Sat Nov 22 2014 - 00:32:52 CST)
• 16 total processes killed (some possibly by mpirun during cleanup)
  • Shalton Evans (Mon Nov 02 2015 - 14:34:13 CST)
• 2-residue patch for Asn-Lys side chain amide bond
  • Kenno Vanommeslaeghe (Fri Jul 25 2014 - 12:20:46 CDT)
• 2-residue patch for hydrocarbon staple
  • Kenno Vanommeslaeghe (Thu Jul 24 2014 - 15:48:52 CDT)
• 6 equilibration steps at charmm gui server
  • Sunhwan Jo (Thu Apr 03 2014 - 09:34:23 CDT)
  • Ramin Ekhteiari (Thu Apr 03 2014 - 04:32:58 CDT)
• [ANN] MDTraj 1.0: Trajectory Analysis in Python
  • Ivan Gregoretti (Tue Sep 09 2014 - 12:09:49 CDT)
  • Robert McGibbon (Mon Sep 08 2014 - 17:19:00 CDT)
• [External] Boost value in aMD simulation
  • James Starlight (Fri Aug 22 2014 - 11:54:05 CDT)
  • James Starlight (Tue Aug 19 2014 - 13:45:58 CDT)
  • James Starlight (Tue Aug 19 2014 - 04:56:58 CDT)
  • Thomas Evangelidis (Mon Aug 18 2014 - 04:21:25 CDT)
  • James Starlight (Mon Aug 18 2014 - 03:25:53 CDT)
  • James Starlight (Thu Jul 24 2014 - 01:13:09 CDT)
  • Thomas Evangelidis (Wed Jul 23 2014 - 16:37:47 CDT)
  • James Starlight (Wed Jul 23 2014 - 15:32:53 CDT)
  • Thomas Evangelidis (Wed Jul 23 2014 - 15:02:25 CDT)
  • James Starlight (Wed Jul 23 2014 - 14:24:45 CDT)
• A problem in ABF simulations
  • Jeff Comer (Mon Nov 24 2014 - 11:44:45 CST)
  • Azadeh Alavi (Sat Nov 22 2014 - 05:50:03 CST)
• aa_ref-monomer-noh.dcd file in the tutorial of shape-based coarse grained (SBCG) simulation
  • sunyeping (Mon Mar 10 2014 - 20:01:13 CDT)
• aa_ref-monomer-noh.dcd in shape-based coarse grained simulation
  • sunyeping (Sat Mar 08 2014 - 20:09:26 CST)
• ABF calculations - reaction coordinate
  • Giacomo Fiorin (Mon Nov 16 2015 - 20:30:56 CST)
  • Mohan maruthi sena (Mon Nov 16 2015 - 19:15:15 CST)
• ABF error on NAMD 2.10
  • Giacomo Fiorin (Mon Nov 02 2015 - 08:51:52 CST)
  • Haleh a (Mon Nov 02 2015 - 08:45:29 CST)
  • Giacomo Fiorin (Mon Nov 02 2015 - 07:49:46 CST)
  • Jérôme Hénin (Mon Nov 02 2015 - 07:47:25 CST)
  • Haleh a (Mon Nov 02 2015 - 05:55:59 CST)
• ABF force distribution
  • Kasra Fattah (Sat Mar 01 2014 - 18:20:11 CST)
  • Jérôme Hénin (Thu Feb 27 2014 - 06:59:48 CST)
  • MEHRAN MB (Tue Feb 18 2014 - 10:50:59 CST)
  • Kasra Fattah (Thu Feb 13 2014 - 14:56:42 CST)
• ABF hBond
  • Giacomo Fiorin (Mon Aug 25 2014 - 10:18:12 CDT)
  • Charles Whidborne (Mon Aug 25 2014 - 02:52:45 CDT)
• ABF simulation fails with "FATAL ERROR: Low global exclusion count!"
  • Maria Pikoula (Fri Feb 28 2014 - 12:50:27 CST)
  • Jérôme Hénin (Fri Feb 28 2014 - 11:58:59 CST)
  • Maria Pikoula (Fri Feb 28 2014 - 11:42:47 CST)
  • Giacomo Fiorin (Tue Feb 25 2014 - 20:19:28 CST)
  • Maria Pikoula (Tue Feb 25 2014 - 11:02:24 CST)
• ABF simulation, free energy to remove a DNA strand
  • Thomas C. Bishop (Tue Aug 05 2014 - 10:17:07 CDT)
  • Jérôme Hénin (Tue Aug 05 2014 - 03:15:46 CDT)
  • Charles Whidborne (Tue Aug 05 2014 - 01:54:14 CDT)
• ABF simulations
  • MEHRAN MB (Tue Feb 18 2014 - 10:38:25 CST)
  • Aron Broom (Fri Feb 14 2014 - 07:34:46 CST)
  • Abir Ganguly (Thu Feb 13 2014 - 22:50:10 CST)
  • Aron Broom (Mon Feb 10 2014 - 11:20:54 CST)
  • Abir Ganguly (Sat Feb 08 2014 - 15:38:01 CST)
• ABF with external electric field
  • Giacomo Fiorin (Tue Mar 31 2015 - 13:16:15 CDT)
  • Jeff Comer (Tue Mar 31 2015 - 11:41:35 CDT)
  • Bala subramanian (Tue Mar 31 2015 - 10:42:24 CDT)
• ABF with the RMSD colvar
  • George Patargias (Mon Sep 29 2014 - 05:25:01 CDT)
  • Jérôme Hénin (Mon Sep 22 2014 - 08:37:00 CDT)
  • George Patargias (Mon Sep 22 2014 - 06:21:45 CDT)
  • Jérôme Hénin (Fri Sep 19 2014 - 10:46:45 CDT)
  • George Patargias (Fri Sep 19 2014 - 10:12:40 CDT)
  • Jérôme Hénin (Wed Sep 17 2014 - 07:13:05 CDT)
  • George Patargias (Wed Sep 17 2014 - 06:43:44 CDT)
  • Giacomo Fiorin (Fri Apr 25 2014 - 09:41:54 CDT)
  • George Patargias (Fri Apr 25 2014 - 05:20:31 CDT)
  • Giacomo Fiorin (Wed Apr 16 2014 - 13:41:54 CDT)
  • George Patargias (Wed Apr 16 2014 - 05:14:05 CDT)
  • Giacomo Fiorin (Tue Apr 15 2014 - 10:06:44 CDT)
  • George Patargias (Tue Apr 15 2014 - 05:22:46 CDT)
• ABF/colvar error in NAMD2.9
  • Harish Vashisth (Tue Jul 22 2014 - 14:39:15 CDT)
  • Niklaus Johner (Tue Jul 22 2014 - 13:32:12 CDT)
  • Aron Broom (Tue Jul 22 2014 - 13:08:48 CDT)
  • Harish Vashisth (Tue Jul 22 2014 - 13:00:04 CDT)
  • Aron Broom (Tue Jul 22 2014 - 12:32:06 CDT)
  • Jérôme Hénin (Tue Jul 22 2014 - 11:56:06 CDT)
  • Aron Broom (Tue Jul 22 2014 - 11:30:49 CDT)
  • Jérôme Hénin (Tue Jul 22 2014 - 11:29:47 CDT)
  • Harish Vashisth (Tue Jul 22 2014 - 11:23:13 CDT)
• about "small molecules" in OPLS-AAM FF
  • Francesco Pietra (Wed Oct 07 2015 - 16:14:12 CDT)
• about angles in coordination complexes
  • luca belmonte (Wed Feb 04 2015 - 04:37:28 CST)
  • luca belmonte (Mon Jan 26 2015 - 11:51:11 CST)
  • luca belmonte (Mon Jan 26 2015 - 10:55:10 CST)
  • Jérôme Hénin (Mon Jan 26 2015 - 10:50:35 CST)
  • luca belmonte (Mon Jan 26 2015 - 10:28:17 CST)
  • Jérôme Hénin (Mon Jan 26 2015 - 10:20:37 CST)
  • luca belmonte (Mon Jan 26 2015 - 10:02:27 CST)
  • Jérôme Hénin (Mon Jan 26 2015 - 09:56:07 CST)
  • luca belmonte (Mon Jan 26 2015 - 09:28:16 CST)
  • luca belmonte (Mon Jan 26 2015 - 08:39:17 CST)
• About asterisk in IC statements in topology files
  • Kevin C Chan (Tue Jul 08 2014 - 02:30:25 CDT)
• about command replicaRecv and replicaSend
  • jc guo (Mon Oct 19 2015 - 02:09:43 CDT)
• about compiling NAMD using intel icc and impi
  • XSC (Fri Jan 23 2015 - 04:00:29 CST)
• About converting NAMD dcd file into CHARMM dcd file
  • Kenno Vanommeslaeghe (Fri Jun 13 2014 - 21:18:52 CDT)
  • Mo Chen (Fri Jun 13 2014 - 18:41:30 CDT)
• about deca alanine tutorial setup
  • Branko (Mon Nov 02 2015 - 16:26:57 CST)
  • Ajasja LjubetiÄ� (Mon Nov 02 2015 - 16:14:28 CST)
  • Jessen Lucas (Mon Nov 02 2015 - 15:22:16 CST)
• About electrostatic treatment
  • David Hardy (Sat May 31 2014 - 12:01:34 CDT)
  • Mo Chen (Fri May 30 2014 - 19:39:31 CDT)
  • Mo Chen (Fri May 30 2014 - 19:35:50 CDT)
• about hydrogen bond analysis
  • Mo Chen (Tue Mar 24 2015 - 16:19:37 CDT)
  • Hasan haska (Tue Mar 24 2015 - 16:07:08 CDT)
• About keep_water_out.tcl
  • zeynab mohamad hoseyni (Thu Feb 20 2014 - 05:21:23 CST)
• about langevin dynamics
  • Norman Geist (Mon Mar 09 2015 - 01:44:18 CDT)
  • Gisella Alfonsino (Sun Mar 08 2015 - 05:36:28 CDT)
• About NAMD
  • Douglas Houston (Tue Nov 18 2014 - 09:32:59 CST)
• About Number of atoms in fixed atoms PDB doesn't match coordinate PDB
  • Sridhar Kumar Kannam (Sat Jan 25 2014 - 23:49:47 CST)
  • Vidhya Sankar (Sat Jan 25 2014 - 21:01:01 CST)
• About Psfgen error for Lipid molecules
  • Vidhya Sankar (Sun Jan 19 2014 - 07:29:51 CST)
• about re install
  • sunyeping (Tue Oct 20 2015 - 02:09:33 CDT)
  • jc guo (Tue Oct 20 2015 - 01:20:08 CDT)
• about replica exchange
  • Jeff Comer (Fri Oct 16 2015 - 16:17:13 CDT)
  • jc guo (Fri Oct 16 2015 - 10:43:23 CDT)
• about replica exchange example in lib of 2.10 NAMD
  • Jeff Comer (Tue Oct 20 2015 - 20:10:00 CDT)
  • jc guo (Fri Oct 16 2015 - 00:11:18 CDT)
• About Tcl8.3 error in namd2.8
  • Phil Miller (Wed Jan 01 2014 - 09:33:57 CST)
  • Vidhya Sankar (Wed Jan 01 2014 - 08:20:20 CST)
• About the TMDInitialRMSD parameter in targeted molecular dynamics
  • sunyeping (Tue Oct 20 2015 - 12:06:22 CDT)
• about the vdw Interpolation calculation in NAMD source code
  • ¬Óíï¿ (Thu Nov 20 2014 - 20:35:48 CST)
  • Jim Phillips (Thu Nov 20 2014 - 16:00:29 CST)
  • ¬Óíï¿ (Thu Nov 20 2014 - 09:32:10 CST)
  • Jim Phillips (Thu Nov 20 2014 - 08:29:27 CST)
  • Jeff Comer (Thu Nov 20 2014 - 08:20:54 CST)
  • ¬Óíï¿ (Thu Nov 20 2014 - 02:44:40 CST)
• About Warning in compilation of Namd
  • Axel Kohlmeyer (Sat Jan 04 2014 - 06:21:55 CST)
  • Vidhya Sankar (Sat Jan 04 2014 - 03:41:57 CST)
• Accelerated MD (aMD)
  • Thomas Evangelidis (Sat Jul 26 2014 - 06:38:20 CDT)
  • Ramin Ekhteiari (Sat Jul 26 2014 - 06:06:25 CDT)
• accelerated MD as the engine for loop refirement
  • Gianluca Interlandi (Tue Jul 15 2014 - 02:05:30 CDT)
  • Ramin Ekhteiari (Tue Jul 15 2014 - 01:30:12 CDT)
  • Tristan Croll (Mon Jul 14 2014 - 18:18:05 CDT)
  • Chris Ing (Mon Jul 14 2014 - 16:53:07 CDT)
  • James Starlight (Mon Jul 14 2014 - 05:16:46 CDT)
  • Tristan Croll (Mon Jul 14 2014 - 00:40:11 CDT)
  • James Starlight (Sun Jul 13 2014 - 14:05:10 CDT)
  • James Starlight (Sat Jul 12 2014 - 09:28:21 CDT)
  • Gianluca Interlandi (Thu Jul 10 2014 - 17:59:24 CDT)
  • Kenno Vanommeslaeghe (Thu Jul 10 2014 - 17:32:38 CDT)
  • James Starlight (Thu Jul 10 2014 - 04:39:17 CDT)
  • Ajasja LjubetiÄ� (Wed Jul 09 2014 - 15:22:15 CDT)
  • Gianluca Interlandi (Wed Jul 09 2014 - 15:08:17 CDT)
  • James Starlight (Wed Jul 09 2014 - 14:39:08 CDT)
• Accelerated MD in NAMD
  • James Starlight (Sat Mar 08 2014 - 09:24:47 CST)
• accelerated MD log
  • Felipe Merino (Mon Mar 31 2014 - 03:57:30 CDT)
• accelerated MD new variant
  • Brian Radak (Mon Nov 30 2015 - 09:48:36 CST)
  • Vlad Cojocaru (Mon Nov 30 2015 - 10:00:35 CST)
  • Vlad Cojocaru (Sun Nov 29 2015 - 03:53:20 CST)
• Accelerated MD with transmembrane protein
  • Francesco Pietra (Sat Apr 12 2014 - 08:24:00 CDT)
  • Kevin Kastner (Fri Apr 11 2014 - 13:06:28 CDT)
  • Francesco Pietra (Fri Apr 11 2014 - 12:16:40 CDT)
  • Jeff Wereszczynski (Fri Apr 11 2014 - 11:50:20 CDT)
  • Francesco Pietra (Fri Apr 11 2014 - 11:39:10 CDT)
  • Jeff Wereszczynski (Fri Apr 11 2014 - 07:19:20 CDT)
  • Felipe Merino (Fri Apr 11 2014 - 03:27:09 CDT)
  • Kevin Kastner (Thu Apr 10 2014 - 13:40:26 CDT)
• Accelerated Molecular Dynamics logs
  • Johny Telecaster (Sat Mar 08 2014 - 09:37:05 CST)
• Accelerated molecular dynamics: Energy value in output file
  • Kapil jain (Tue Aug 19 2014 - 23:53:20 CDT)
• accelMD and GBIS?
  • Brian Radak (Fri Feb 27 2015 - 18:15:13 CST)
• accelMD on GPUs
  • Francesco Pietra (Sat Mar 29 2014 - 02:38:58 CDT)
• Adaptive Tempering - Velocity Rescaling
  • Sachin Natesh (Mon Aug 31 2015 - 09:45:16 CDT)
• Adaptive tempering implementation in NAMD differs
  • Nicholas M Glykos (Fri Sep 25 2015 - 04:36:52 CDT)
  • Sachin Natesh (Thu Sep 24 2015 - 20:28:36 CDT)
  • Sachin Natesh (Wed Sep 23 2015 - 10:28:05 CDT)
  • Nicholas M. Glykos (Wed Sep 23 2015 - 05:45:40 CDT)
• Adaptive tempering implementation in NAMD differs from original paper?
  • Sachin Natesh (Tue Sep 22 2015 - 19:45:22 CDT)
• Add ions/molecules different from Autoionize defaults
  • Tristan Croll (Tue Dec 29 2015 - 07:12:10 CST)
  • Peter Freddolino (Sun Dec 27 2015 - 22:04:00 CST)
  • Josh Vermaas (Sun Dec 27 2015 - 06:25:50 CST)
  • Peter Freddolino (Sat Dec 26 2015 - 21:12:23 CST)
  • Ardavan Mehdizadeh (Fri Dec 25 2015 - 12:28:43 CST)
  • amin_at_imtech.res.in (Fri Dec 25 2015 - 07:16:46 CST)
  • Peter Freddolino (Thu Dec 24 2015 - 08:45:43 CST)
  • Ardavan Mehdizadeh (Thu Dec 24 2015 - 07:37:39 CST)
  • Ardavan Mehdizadeh (Thu Dec 24 2015 - 07:37:01 CST)
  • Ardavan Mehdizadeh (Wed Dec 23 2015 - 12:05:36 CST)
• Adding hydrogen atoms to the crystall structure
  • Thomas Evangelidis (Tue Feb 18 2014 - 16:04:23 CST)
  • MEHRAN MB (Tue Feb 18 2014 - 15:54:55 CST)
  • Thomas Evangelidis (Tue Feb 18 2014 - 14:56:21 CST)
  • zeynab mohamad hoseyni (Tue Feb 18 2014 - 14:30:00 CST)
  • Thomas Evangelidis (Tue Feb 18 2014 - 10:44:56 CST)
  • MEHRAN MB (Tue Feb 18 2014 - 10:10:53 CST)
  • zeynab mohamad hoseyni (Sun Feb 16 2014 - 09:54:40 CST)
• adjust water box size in RBCG
  • Yongcheng Zhou (Sun Feb 01 2015 - 16:03:54 CST)
• Aggregation related analysis scripts
  • Aditya Ranganathan (Wed Feb 25 2015 - 01:13:42 CST)
  • Jeff Comer (Tue Feb 24 2015 - 15:39:12 CST)
  • Jérôme Hénin (Tue Feb 24 2015 - 09:39:01 CST)
  • Aditya Ranganathan (Tue Feb 24 2015 - 02:28:10 CST)
• alchElecLambdaStart (Thermodynamic Integration)
  • Javad Noroozi (Fri Jun 06 2014 - 13:55:28 CDT)
• Alchemical FEP calculation involving glycine
  • Jérôme Hénin (Thu Mar 12 2015 - 04:26:18 CDT)
  • jostmey . (Wed Mar 11 2015 - 17:57:02 CDT)
  • Chris Chipot (Tue Mar 10 2015 - 05:59:57 CDT)
  • jostmey . (Mon Mar 09 2015 - 23:58:31 CDT)
• Alchemical FEP calculations in Implicit Solvent
  • jostmey . (Mon Feb 23 2015 - 14:45:13 CST)
  • jostmey . (Mon Feb 23 2015 - 13:21:57 CST)
  • MEHRAN MB (Mon Feb 23 2015 - 13:08:56 CST)
  • jostmey . (Mon Feb 23 2015 - 13:04:15 CST)
• alchemical free energy simulations with parmtop
  • Jim Phillips (Fri Dec 05 2014 - 14:49:55 CST)
  • hannes.loeffler_at_stfc.ac.uk (Thu Dec 04 2014 - 11:52:49 CST)
  • Jim Phillips (Thu Dec 04 2014 - 11:09:22 CST)
  • hannes.loeffler_at_stfc.ac.uk (Tue Dec 02 2014 - 12:39:41 CST)
  • Jim Phillips (Tue Dec 02 2014 - 12:06:40 CST)
  • Hannes Loeffler (Mon Dec 01 2014 - 03:20:17 CST)
  • Hannes Loeffler (Tue Jun 17 2014 - 04:35:59 CDT)
• Alchemy Shift Coefficient at Low Density Regime (TI)
  • Brian Radak (Thu Feb 05 2015 - 13:44:14 CST)
  • JAVAD NOROOZI (Wed Feb 04 2015 - 02:58:15 CST)
• Algorithm used by NAMD
  • David Hardy (Fri Apr 03 2015 - 11:18:46 CDT)
  • Gurpreet Kaur Dhindsa (Thu Apr 02 2015 - 09:55:36 CDT)
• Alignment
  • Axel Kohlmeyer (Thu Sep 04 2014 - 07:53:23 CDT)
  • Zeinab Emami (Thu Sep 04 2014 - 07:12:14 CDT)
• Altering extrabonds forces during MD
  • Bryan Roessler (Tue Apr 15 2014 - 09:53:02 CDT)
• aMD and GPU acceleration
  • Thomas Albers (Thu Oct 22 2015 - 13:53:09 CDT)
• Analysis plugins for Martini Coarse Grained protein simulations
  • Fotis Baltoumas (Sat Feb 07 2015 - 05:25:50 CST)
  • Aditya Ranganathan (Sat Feb 07 2015 - 03:55:33 CST)
• Analysis problem (Data vector empty)
  • Stephan Grein (Tue Jul 29 2014 - 04:06:27 CDT)
• angle between 2 vectors as collective variable
  • Vlad Cojocaru (Thu Mar 26 2015 - 11:04:09 CDT)
  • Giacomo Fiorin (Thu Mar 26 2015 - 10:16:25 CDT)
  • Vlad Cojocaru (Thu Mar 26 2015 - 10:03:36 CDT)
  • Giacomo Fiorin (Thu Mar 26 2015 - 09:58:26 CDT)
  • Vlad Cojocaru (Thu Mar 26 2015 - 09:17:41 CDT)
• ANGLE PARAMETERS FOR NH3 HC NH3
  • Francesco Pietra (Tue Oct 27 2015 - 11:12:20 CDT)
• angles between residues
  • luca belmonte (Tue Dec 30 2014 - 07:38:14 CST)
• anionic cysteine
  • Tristan Croll (Wed Dec 09 2015 - 04:23:03 CST)
  • Francesco Pietra (Wed Dec 09 2015 - 04:13:54 CST)
  • Tristan Croll (Tue Dec 08 2015 - 22:00:12 CST)
  • Francesco Pietra (Tue Dec 08 2015 - 08:50:19 CST)
• anisotropic pressure control
  • Maxim Igaev (Wed Nov 26 2014 - 05:10:09 CST)
  • Maxim Igaev (Wed Nov 26 2014 - 04:04:49 CST)
  • Maxim Igaev (Wed Nov 26 2014 - 03:47:41 CST)
  • Maxim Igaev (Wed Nov 26 2014 - 02:48:51 CST)
• Annealing process of silica with excluded block
  • Marzieh Alishahi (Mon Sep 15 2014 - 09:40:21 CDT)
  • Jeff Comer (Mon Sep 15 2014 - 09:30:57 CDT)
  • Marzieh Alishahi (Fri Sep 12 2014 - 10:22:51 CDT)
• Announcement: "Hands-On" Workshop on Computational Biophysics in Urbana, IL (April 6-10,2015)
  • Lela Vukovic (Mon Feb 16 2015 - 14:44:55 CST)
• Announcement: 'Hands On' Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015)
  • Emad Tajkhorshid (Wed May 20 2015 - 00:43:55 CDT)
  • Sourav Ray (Wed May 20 2015 - 00:33:00 CDT)
• Announcement: Hands-On Workshop On Computational Biophysics
  • Danielle Chandler (Wed Jan 07 2015 - 12:30:35 CST)
  • Danielle Chandler (Wed Dec 17 2014 - 10:24:50 CST)
  • Danielle Chandler (Tue Oct 07 2014 - 11:30:07 CDT)
  • Danielle Chandler (Wed Aug 27 2014 - 13:05:05 CDT)
  • Danielle Chandler (Tue Aug 12 2014 - 09:31:17 CDT)
• Announcement: Workshop on Simulation Based Drug Discovery (San Diego, CA, Sept 21-25, 2015)
  • Lela Vukovic (Fri Jun 12 2015 - 21:06:22 CDT)
• Announcement: ‘Hands On’ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015)
  • Lela Vukovic (Wed May 20 2015 - 00:06:46 CDT)
• Announcement: ‘Hands On’ Workshop on Computational Biophysics (Lake Tahoe, CA, Aug 3-7, 2015)
  • Lela Vukovic (Tue Mar 24 2015 - 15:50:58 CDT)
• Announcement: ‘Hands On’ Workshop on Computational Biophysics (Odense, Denmark, Oct 12-16, 2015)
  • Lela Vukovic (Wed May 06 2015 - 01:39:55 CDT)
• Announcement: ‘Hands On’ Workshop on Computational Biophysics (Pittsburgh, PA, June 1-5, 2015)
  • Lela Vukovic (Wed Mar 04 2015 - 13:07:25 CST)
• ApoA1 simulation
  • Kostas Malavazos (Wed Oct 21 2015 - 05:21:28 CDT)
• APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
  • Jim Phillips (Thu Nov 13 2014 - 15:47:52 CST)
  • Bin He (Thu Nov 13 2014 - 01:53:42 CST)
• Apply magnetic field through TCLBC
  • Hongbo Du (Mon Mar 03 2014 - 16:23:55 CST)
  • Axel Kohlmeyer (Mon Mar 03 2014 - 11:46:25 CST)
  • Kenno Vanommeslaeghe (Mon Mar 03 2014 - 11:33:06 CST)
  • Hongbo Du (Fri Feb 28 2014 - 11:22:04 CST)
• applying a force to some atoms
  • Jérôme Hénin (Sun Jun 28 2015 - 15:54:42 CDT)
  • jing liang (Sat Jun 27 2015 - 06:22:02 CDT)
• Asking help on results of our GPU benchmark
  • Axel Kohlmeyer (Mon Jan 05 2015 - 10:36:24 CST)
  • 周文昌 (Tue Dec 23 2014 - 14:05:30 CST)
  • 周文昌 (Mon Dec 22 2014 - 12:11:18 CST)
  • 周文昌 (Fri Dec 19 2014 - 16:06:33 CST)
  • 周文昌 (Thu Dec 18 2014 - 13:24:59 CST)
  • 周文昌 (Wed Dec 17 2014 - 15:13:24 CST)
• Assessing convergence in FEP calculations
  • Gianluca Interlandi (Thu Aug 28 2014 - 14:00:08 CDT)
• Assigning different temperatures to simulation
  • Jhonatam Cordeiro Rodrigues (Thu Apr 03 2014 - 15:24:09 CDT)
  • Jérôme Hénin (Wed Apr 02 2014 - 03:16:30 CDT)
  • Jérôme Hénin (Wed Apr 02 2014 - 02:35:40 CDT)
  • Jhonatam Cordeiro Rodrigues (Wed Apr 02 2014 - 00:42:17 CDT)
  • Jhonatam Cordeiro Rodrigues (Tue Apr 01 2014 - 15:29:36 CDT)
• atom ID in VMD and NAMD
  • Axel Kohlmeyer (Mon May 04 2015 - 07:25:49 CDT)
  • Maxim Igaev (Mon May 04 2015 - 07:18:38 CDT)
  • Axel Kohlmeyer (Mon May 04 2015 - 07:04:22 CDT)
  • Maxim Igaev (Mon May 04 2015 - 06:47:09 CDT)
  • Jérôme Hénin (Mon May 04 2015 - 04:52:06 CDT)
  • Maxim Igaev (Mon May 04 2015 - 03:16:09 CDT)
• Atom selection in Tcl Force script with Amber partop file
  • Daniel Torrente (Fri Aug 15 2014 - 18:21:23 CDT)
  • Daniel Torrente (Fri Aug 15 2014 - 19:01:23 CDT)
  • Maxim Belkin (Fri Aug 15 2014 - 18:33:18 CDT)
  • Daniel Torrente (Fri Aug 15 2014 - 18:25:23 CDT)
  • Maxim Belkin (Fri Aug 15 2014 - 16:48:12 CDT)
  • Daniel Torrente (Fri Aug 15 2014 - 12:25:49 CDT)
• atom types in PSF/PRM/RTF
  • hannes.loeffler_at_stfc.ac.uk (Sun May 31 2015 - 07:43:34 CDT)
  • Jason Swails (Thu May 28 2015 - 13:55:44 CDT)
  • Hannes Loeffler (Thu May 28 2015 - 13:19:14 CDT)
  • Josh Vermaas (Fri May 22 2015 - 09:55:44 CDT)
  • Aaron Larsen (Fri May 22 2015 - 07:34:37 CDT)
  • Hannes Loeffler (Fri May 22 2015 - 04:42:45 CDT)
• Atoms moving too fast; simulation has become unstable
  • Peter Freddolino (Mon Sep 21 2015 - 07:53:14 CDT)
  • Monika Madhavi (Mon Sep 21 2015 - 00:58:32 CDT)
  • Peter Freddolino (Thu Sep 17 2015 - 23:01:32 CDT)
  • Monika Madhavi (Thu Sep 17 2015 - 22:58:12 CDT)
  • Peter Freddolino (Thu Sep 17 2015 - 21:44:09 CDT)
  • Monika Madhavi (Thu Sep 17 2015 - 04:42:40 CDT)
  • Peter Freddolino (Mon Aug 31 2015 - 08:30:48 CDT)
  • Sourav Ray (Mon Aug 31 2015 - 06:29:30 CDT)
  • farzad kiani (Mon Aug 31 2015 - 06:17:38 CDT)
  • Monika Madhavi (Mon Aug 31 2015 - 05:42:48 CDT)
• atoms sequence in improper, OPLS, TOPOTOOLS, CHARMM
  • AnkiReddy katha (Thu May 07 2015 - 06:17:27 CDT)
• Atomselect for coor, vel, xsc
  • Kevin C Chan (Fri Nov 21 2014 - 04:20:16 CST)
  • Axel Kohlmeyer (Fri Nov 14 2014 - 09:02:47 CST)
  • Josh Vermaas (Fri Nov 14 2014 - 08:58:29 CST)
  • Kevin C Chan (Thu Nov 13 2014 - 22:49:02 CST)
• atomselect option for extracting protein-ligand complex
  • Axel Kohlmeyer (Mon Feb 17 2014 - 16:22:38 CST)
  • KK R (Mon Feb 17 2014 - 16:16:43 CST)
• Atomselect within radial pair distribution function g(r)
  • Chitrak Gupta (Wed Sep 30 2015 - 08:09:16 CDT)
  • Aditya Ranganathan (Wed Sep 30 2015 - 03:55:37 CDT)
• Attempting modification to accumulate "Langevin heat"
  • Brian Radak (Tue Jun 30 2015 - 10:43:40 CDT)
• automatic extraction of RMSD values of the heavy atoms of residues from NAMD output?
  • Maxim Belkin (Mon Aug 04 2014 - 11:25:15 CDT)
  • Andras Borosy (Mon Aug 04 2014 - 05:32:53 CDT)
• Automatic PSF builder for cyclic peptide
  • Aditya Ranganathan (Sun Sep 20 2015 - 08:20:24 CDT)
  • Nikhil Maroli (Sun Sep 20 2015 - 07:04:36 CDT)
• autopsf (patch)
  • Cenk Denktas (Tue Jul 15 2014 - 12:41:48 CDT)
• AW:
  • flavio seixas (Wed Nov 26 2014 - 09:53:23 CST)
  • Norman Geist (Wed Nov 26 2014 - 02:26:35 CST)
  • Norman Geist (Thu Feb 20 2014 - 00:41:55 CST)
• AW: "Beefier" benchmark
  • Maxime Boissonneault (Wed Aug 20 2014 - 09:20:15 CDT)
  • Norman Geist (Wed Aug 20 2014 - 01:38:51 CDT)
• AW: 16 total processes killed (some possibly by mpirun during cleanup)
  • Norman Geist (Tue Nov 03 2015 - 00:25:15 CST)
• AW: about angles in coordination complexes
  • Norman Geist (Tue Jan 27 2015 - 02:23:29 CST)
  • Norman Geist (Mon Jan 26 2015 - 09:24:39 CST)
• AW: about command replicaRecv and replicaSend
  • Norman Geist (Mon Oct 19 2015 - 02:43:43 CDT)
• AW: about compiling NAMD using intel icc and impi
  • Norman Geist (Fri Jan 23 2015 - 04:59:43 CST)
• AW: About NAMD
  • Douglas Houston (Wed Nov 26 2014 - 05:28:39 CST)
  • Norman Geist (Wed Nov 19 2014 - 01:10:11 CST)
• AW: anisotropic pressure control
  • Norman Geist (Wed Nov 26 2014 - 05:04:20 CST)
  • Norman Geist (Wed Nov 26 2014 - 03:22:31 CST)
• AW: Asking help on results of our GPU benchmark
  • Norman Geist (Mon Jan 05 2015 - 00:37:40 CST)
  • Norman Geist (Tue Dec 23 2014 - 02:34:58 CST)
  • Norman Geist (Mon Dec 22 2014 - 01:16:12 CST)
  • Norman Geist (Fri Dec 19 2014 - 00:30:22 CST)
  • Norman Geist (Thu Dec 18 2014 - 02:39:51 CST)
• AW: Assigning different temperatures to simulation
  • Norman Geist (Wed Apr 02 2014 - 02:45:57 CDT)
  • Norman Geist (Wed Apr 02 2014 - 00:06:08 CDT)
  • Norman Geist (Wed Apr 02 2014 - 00:02:58 CDT)
• AW: AW: "Beefier" benchmark
  • Maxime Boissonneault (Thu Aug 21 2014 - 07:32:10 CDT)
  • Norman Geist (Thu Aug 21 2014 - 03:04:01 CDT)
• AW: AW: AW: "Beefier" benchmark
  • Maxime Boissonneault (Thu Aug 21 2014 - 09:04:42 CDT)
  • Norman Geist (Thu Aug 21 2014 - 08:43:05 CDT)
• AW: AW: AW: AW: AW: Using nodelist file causes namd to hang
  • Norman Geist (Thu Jun 19 2014 - 05:09:43 CDT)
• AW: AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process.
  • Maxime Boissonneault (Mon Aug 25 2014 - 07:34:34 CDT)
  • Norman Geist (Mon Aug 25 2014 - 01:07:21 CDT)
• AW: AW: AW: AW: Using nodelist file causes namd to hang
  • Douglas Houston (Thu Jun 19 2014 - 04:56:28 CDT)
  • Norman Geist (Thu Jun 19 2014 - 02:19:03 CDT)
• AW: AW: AW: AW: warnings while using amber files
  • Norman Geist (Mon Jan 05 2015 - 08:56:36 CST)
• AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process.
  • Maxime Boissonneault (Fri Aug 22 2014 - 08:59:26 CDT)
  • Norman Geist (Fri Aug 22 2014 - 08:56:32 CDT)
• AW: AW: AW: Hybrid MPI + Multicore + Cuda build
  • Norman Geist (Fri Aug 15 2014 - 00:39:36 CDT)
• AW: AW: AW: Using nodelist file causes namd to hang
  • Douglas Houston (Thu Aug 28 2014 - 07:54:30 CDT)
  • Norman Geist (Thu Aug 28 2014 - 06:08:47 CDT)
  • Norman Geist (Tue Jun 24 2014 - 08:50:06 CDT)
  • Norman Geist (Wed Jun 18 2014 - 07:52:29 CDT)
  • Douglas Houston (Wed Jun 18 2014 - 07:57:59 CDT)
  • Norman Geist (Wed Apr 09 2014 - 07:09:53 CDT)
  • Norman Geist (Tue Apr 08 2014 - 07:30:15 CDT)
• AW: AW: AW: warnings while using amber files
  • amin_at_imtech.res.in (Mon Jan 05 2015 - 07:34:30 CST)
  • Norman Geist (Mon Jan 05 2015 - 06:35:46 CST)
• AW: AW: benchmark info
  • Norman Geist (Fri Mar 07 2014 - 01:40:25 CST)
• AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process.
  • Maxime Boissonneault (Fri Aug 22 2014 - 08:22:43 CDT)
  • Norman Geist (Fri Aug 22 2014 - 08:21:25 CDT)
• AW: AW: How to refer to side-chain via tcl-force scripting?
  • zeynab mohamad hoseyni (Mon Jun 16 2014 - 11:20:46 CDT)
  • zeynab mohamad hoseyni (Sat Jun 14 2014 - 09:03:09 CDT)
  • Tristan Croll (Sat Jun 14 2014 - 01:09:39 CDT)
  • zeynab mohamad hoseyni (Fri Jun 13 2014 - 23:01:42 CDT)
  • Norman Geist (Fri Jun 13 2014 - 03:26:33 CDT)
• AW: AW: Hybrid MPI + Multicore + Cuda build
  • Maxime Boissonneault (Thu Aug 14 2014 - 11:53:16 CDT)
  • Norman Geist (Thu Aug 14 2014 - 08:14:30 CDT)
• AW: AW: NAMD and NUMA
  • Kenno Vanommeslaeghe (Fri May 09 2014 - 11:45:09 CDT)
  • Norman Geist (Fri May 09 2014 - 02:11:19 CDT)
• AW: AW: Periodic Box Dimension (WrapAll is on)
  • Norman Geist (Tue Jan 20 2015 - 02:07:47 CST)
• AW: AW: Question to NAMD source
  • Jim Phillips (Mon Sep 08 2014 - 08:43:00 CDT)
  • Norman Geist (Mon Sep 08 2014 - 04:40:10 CDT)
  • Norman Geist (Mon Sep 08 2014 - 01:19:49 CDT)
• AW: AW: Regarding NAMD installation
  • Norman Geist (Mon Aug 17 2015 - 05:22:11 CDT)
• AW: AW: Using nodelist file causes namd to hang
  • Douglas Houston (Thu Aug 28 2014 - 05:43:48 CDT)
  • Norman Geist (Thu Aug 28 2014 - 02:47:58 CDT)
  • Douglas Houston (Tue Jun 24 2014 - 08:42:20 CDT)
  • Norman Geist (Fri Jun 20 2014 - 05:15:02 CDT)
  • Douglas Houston (Wed Jun 18 2014 - 07:24:00 CDT)
  • Norman Geist (Mon Jun 16 2014 - 02:19:28 CDT)
  • Douglas Houston (Mon Jun 02 2014 - 04:50:40 CDT)
  • Douglas Houston (Wed Apr 09 2014 - 06:16:35 CDT)
  • Norman Geist (Wed Apr 09 2014 - 05:53:50 CDT)
  • Douglas Houston (Tue Apr 08 2014 - 07:13:42 CDT)
  • Norman Geist (Tue Apr 08 2014 - 06:22:41 CDT)
• AW: AW: warnings while using amber files
  • amin_at_imtech.res.in (Mon Jan 05 2015 - 04:39:58 CST)
  • Norman Geist (Mon Jan 05 2015 - 03:19:13 CST)
• AW: AW: Xeon vs i7 and ECC vs SDRAM
  • Norman Geist (Thu Jun 26 2014 - 00:59:13 CDT)
  • Norman Geist (Wed Jun 25 2014 - 01:47:38 CDT)
• AW: benchmark info
  • Norman Geist (Fri Feb 28 2014 - 01:18:46 CST)
• AW: Changing Boundary conditions from PBC to non-periodic
  • Norman Geist (Fri Nov 20 2015 - 01:52:26 CST)
• AW: Compilation of NAMD from Source (Cray XC40)
  • Jim Phillips (Tue Oct 13 2015 - 17:00:08 CDT)
  • Richter, Stefan (Tue Oct 13 2015 - 13:10:44 CDT)
• AW: Constraint failure in RATTLE
  • Norman Geist (Tue Apr 01 2014 - 00:11:28 CDT)
  • Norman Geist (Mon Mar 31 2014 - 00:43:09 CDT)
• AW: Constraint failure in RATTLE algorithm
  • Norman Geist (Thu Jun 19 2014 - 02:29:16 CDT)
• AW: coordinates in namd
  • Norman Geist (Tue Jun 03 2014 - 01:40:14 CDT)
• AW: CUDA error in cuda_check_local_progress
  • Norman Geist (Tue Apr 22 2014 - 00:39:49 CDT)
  • Norman Geist (Thu Apr 17 2014 - 04:50:10 CDT)
  • Norman Geist (Thu Apr 17 2014 - 03:21:44 CDT)
• AW: Dihedrals multiplicity!
  • Kenno Vanommeslaeghe (Thu Feb 20 2014 - 10:35:55 CST)
  • Kenno Vanommeslaeghe (Tue Feb 18 2014 - 20:12:14 CST)
  • Anna Borlsky (Tue Feb 18 2014 - 03:11:42 CST)
  • Kenno Vanommeslaeghe (Mon Feb 17 2014 - 12:44:19 CST)
  • hannes.loeffler_at_stfc.ac.uk (Mon Feb 17 2014 - 11:43:47 CST)
  • Kenno Vanommeslaeghe (Mon Feb 17 2014 - 10:56:29 CST)
  • Kenno Vanommeslaeghe (Sun Feb 16 2014 - 12:45:16 CST)
  • hannes.loeffler_at_stfc.ac.uk (Sun Feb 16 2014 - 02:34:16 CST)
  • Kenno Vanommeslaeghe (Sat Feb 15 2014 - 22:15:33 CST)
  • Anna Borlsky (Sat Feb 15 2014 - 11:51:16 CST)
  • Kenno Vanommeslaeghe (Sat Feb 15 2014 - 11:30:42 CST)
  • Anna Borlsky (Sat Feb 15 2014 - 04:34:49 CST)
  • Kenno Vanommeslaeghe (Thu Feb 13 2014 - 19:48:12 CST)
  • Kenno Vanommeslaeghe (Thu Feb 13 2014 - 17:53:49 CST)
  • Norman Geist (Thu Feb 13 2014 - 14:23:52 CST)
• AW: ERROR in CUDA run
  • Norman Geist (Thu Dec 17 2015 - 09:24:20 CST)
• AW: Error on write to binary file
  • Norman Geist (Tue Dec 23 2014 - 02:42:04 CST)
• AW: error parsing config file while executing
  • Norman Geist (Mon Jan 05 2015 - 00:26:37 CST)
• AW: Failure MD with par7/rst7 amber input
  • Norman Geist (Wed Jan 07 2015 - 03:28:15 CST)
• AW: Fatal error..
  • Norman Geist (Mon Jun 23 2014 - 03:33:27 CDT)
• AW: FATAL ERROR: error parsing config file while executing <feff>
  • Jim Phillips (Mon Nov 10 2014 - 16:00:19 CST)
  • Jim Phillips (Mon Nov 10 2014 - 15:44:39 CST)
  • Norman Geist (Mon Nov 10 2014 - 08:20:48 CST)
  • Norman Geist (Mon Nov 10 2014 - 00:56:24 CST)
• AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory
  • Douglas Houston (Fri Dec 19 2014 - 08:40:04 CST)
  • Maxime Boissonneault (Fri Dec 19 2014 - 08:18:38 CST)
  • Douglas Houston (Fri Dec 19 2014 - 02:12:48 CST)
  • Norman Geist (Fri Dec 19 2014 - 00:35:26 CST)
• AW: feature request: external initiated clean exit
  • Daniel Möller (Fri Aug 21 2015 - 19:21:54 CDT)
• AW: Fixing atoms while equilibration
  • Norman Geist (Mon Sep 01 2014 - 02:26:11 CDT)
• AW: global does not work in configuration and callback function
  • Norman Geist (Sat Oct 24 2015 - 08:30:48 CDT)
• AW: GPU accelerated MD
  • Norman Geist (Fri Oct 23 2015 - 05:00:05 CDT)
• AW: GPU/CPU workstation optimal simulation parameters for NAMD2.9 performance
  • Norman Geist (Wed Feb 19 2014 - 01:38:53 CST)
• AW: How to calculate the temperature for a subset of my simulation
  • Norman Geist (Wed Oct 21 2015 - 02:24:09 CDT)
  • Norman Geist (Tue Oct 20 2015 - 01:23:57 CDT)
• AW: How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory
  • Norman Geist (Tue Apr 29 2014 - 02:21:20 CDT)
  • Norman Geist (Tue Apr 29 2014 - 02:20:33 CDT)
• AW: how to get cell vectors in tcl forces script
  • Norman Geist (Thu Mar 13 2014 - 08:34:58 CDT)
  • Norman Geist (Wed Mar 12 2014 - 09:59:12 CDT)
  • Norman Geist (Wed Mar 12 2014 - 07:54:50 CDT)
  • Norman Geist (Wed Mar 12 2014 - 02:29:43 CDT)
• AW: How to refer to side-chain via tcl-force scripting?
  • zeynab mohamad hoseyni (Fri Jun 13 2014 - 03:21:08 CDT)
  • Norman Geist (Fri Jun 13 2014 - 02:56:03 CDT)
  • Norman Geist (Fri Jun 13 2014 - 02:53:41 CDT)
• AW: Hybrid MPI + Multicore + Cuda build
  • Maxime Boissonneault (Thu Aug 14 2014 - 07:19:37 CDT)
  • Norman Geist (Thu Aug 14 2014 - 02:13:32 CDT)
• AW: ibverb&&smp build NAMD
  • Norman Geist (Mon Sep 01 2014 - 02:17:13 CDT)
  • Norman Geist (Thu Aug 28 2014 - 05:25:13 CDT)
• AW: information about simulation speed
  • Norman Geist (Wed Dec 03 2014 - 02:31:26 CST)
• AW: is there a method equivalent to conformational flooding in NAMD 2.10
  • Norman Geist (Mon Jan 12 2015 - 00:53:25 CST)
• AW: Job script for multi node job
  • Norman Geist (Fri Feb 14 2014 - 06:03:47 CST)
  • Norman Geist (Fri Feb 14 2014 - 05:12:56 CST)
• AW: keeping Crystal angles constant
  • Norman Geist (Thu Jan 16 2014 - 02:36:51 CST)
  • Norman Geist (Thu Jan 16 2014 - 02:13:08 CST)
• AW: Loading Velocity DCD file
  • Norman Geist (Thu Dec 18 2014 - 02:31:16 CST)
• AW: Log file is not being updated
  • Norman Geist (Mon Feb 10 2014 - 07:32:10 CST)
  • Norman Geist (Mon Feb 10 2014 - 06:42:06 CST)
• AW: Movie of a channel trajectory
  • Norman Geist (Mon Apr 07 2014 - 02:05:25 CDT)
• AW: moving out of the box
  • Ariel Talavera Perez (Thu Feb 20 2014 - 07:48:07 CST)
  • MEHRAN MB (Mon Feb 17 2014 - 11:48:44 CST)
  • Ariel Talavera Perez (Mon Feb 17 2014 - 06:51:36 CST)
  • Ariel Talavera Perez (Mon Feb 17 2014 - 04:39:29 CST)
  • Felipe Merino (Sat Feb 15 2014 - 04:50:15 CST)
  • Aron Broom (Fri Feb 14 2014 - 13:25:54 CST)
  • Kenno Vanommeslaeghe (Fri Feb 14 2014 - 13:15:37 CST)
  • Aaron Larsen (Fri Feb 14 2014 - 09:10:36 CST)
  • Ariel Talavera Perez (Fri Feb 14 2014 - 08:38:01 CST)
  • Norman Geist (Thu Feb 13 2014 - 14:24:53 CST)
  • Norman Geist (Thu Feb 13 2014 - 14:21:26 CST)
• AW: NAMD 2.10 Manual
  • Norman Geist (Fri Aug 22 2014 - 08:46:07 CDT)
• AW: NAMD 2.10b1 CUDA PME offload
  • Norman Geist (Tue Aug 26 2014 - 10:24:50 CDT)
• AW: NAMD and NUMA
  • Kenno Vanommeslaeghe (Mon May 12 2014 - 12:06:53 CDT)
  • Norman Geist (Mon May 12 2014 - 01:12:54 CDT)
  • Joseph Farran (Thu May 08 2014 - 11:33:25 CDT)
  • Joseph Farran (Thu May 08 2014 - 11:28:46 CDT)
  • Norman Geist (Thu May 08 2014 - 01:53:12 CDT)
• AW: NAMD error LInux 3.11.10-21-desktop kernel AMD opternon 6272
  • Norman Geist (Thu Nov 06 2014 - 01:43:36 CST)
• AW: NAMD Multicore CUDA usage
  • Norman Geist (Tue Jun 10 2014 - 02:33:13 CDT)
• AW: NAMD slows at startup phase 1 smp problem
  • Norman Geist (Tue Jan 13 2015 - 05:52:43 CST)
  • Norman Geist (Tue Jan 13 2015 - 05:50:39 CST)
  • Norman Geist (Tue Jan 13 2015 - 01:22:03 CST)
• AW: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation??
  • Norman Geist (Tue Jun 10 2014 - 02:43:11 CDT)
• AW: NAMD-SMP-Ibverbs-CUDA assistance
  • Norman Geist (Wed May 14 2014 - 00:42:51 CDT)
• AW: NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults
  • Norman Geist (Wed Jun 11 2014 - 03:07:21 CDT)
• AW: On-the-fly modification of tclforces script?
  • Norman Geist (Tue Nov 10 2015 - 04:18:02 CST)
• AW: paricle type in residue based coarse graining of NAMD
  • Norman Geist (Tue Jun 24 2014 - 03:13:21 CDT)
• AW: Periodic Box Dimension (WrapAll is on)
  • JAVAD NOROOZI (Tue Jan 20 2015 - 01:37:18 CST)
  • Norman Geist (Tue Jan 20 2015 - 00:39:59 CST)
• AW: Probelm with Lone Pairs on TIP4 model
  • Norman Geist (Tue Jan 06 2015 - 05:34:59 CST)
• AW: Problem running REMD simulation
  • Norman Geist (Thu Aug 27 2015 - 03:42:10 CDT)
  • Norman Geist (Tue Aug 25 2015 - 03:50:15 CDT)
• AW: problem with water molecules angle in MD simulation
  • Norman Geist (Thu Jan 29 2015 - 01:56:18 CST)
  • Norman Geist (Wed Jan 28 2015 - 10:50:47 CST)
  • Norman Geist (Wed Jan 28 2015 - 04:08:53 CST)
  • Norman Geist (Tue Jan 27 2015 - 02:28:18 CST)
  • Norman Geist (Mon Jan 26 2015 - 02:43:41 CST)
• AW: problems compiling NAMD with mpicxx from mvapich2
  • Norman Geist (Mon Jan 26 2015 - 02:36:17 CST)
• AW: problems running amber parm7
  • Norman Geist (Tue Jan 20 2015 - 02:10:44 CST)
  • Norman Geist (Tue Jan 20 2015 - 01:38:30 CST)
  • Norman Geist (Tue Jan 20 2015 - 00:19:40 CST)
• AW: question about '+devices'
  • Norman Geist (Wed Oct 08 2014 - 02:13:08 CDT)
• AW: Question about accelerated MD
  • Ryan McGreevy (Wed Mar 26 2014 - 11:19:17 CDT)
  • Mare Libero (Wed Mar 26 2014 - 11:35:38 CDT)
  • Thomas Evangelidis (Wed Mar 26 2014 - 10:36:51 CDT)
  • Mare Libero (Wed Mar 26 2014 - 10:12:13 CDT)
  • Norman Geist (Wed Mar 26 2014 - 02:34:20 CDT)
• AW: question about CUDA-enabled
  • Norman Geist (Mon Dec 01 2014 - 02:56:08 CST)
  • Norman Geist (Mon Dec 01 2014 - 02:05:20 CST)
• AW: Question regarding reverse CG to all-atom
  • Norman Geist (Tue Jan 21 2014 - 06:18:10 CST)
• AW: Question to NAMD source
  • Jim Phillips (Fri Sep 05 2014 - 14:34:55 CDT)
  • Norman Geist (Fri Sep 05 2014 - 01:32:29 CDT)
• AW: recent comparison of NAMD to other MD engines
  • Norman Geist (Fri Jan 24 2014 - 13:22:51 CST)
  • Norman Geist (Fri Jan 24 2014 - 01:01:04 CST)
  • Norman Geist (Thu Jan 23 2014 - 01:32:54 CST)
• AW: Reducing the amount of work being done on CPU
  • Norman Geist (Tue Sep 01 2015 - 12:47:56 CDT)
• AW: Reg: deformation of water box during equilibration
  • Norman Geist (Tue Jun 10 2014 - 02:23:04 CDT)
• AW: Reg: minimization
  • Norman Geist (Thu Sep 25 2014 - 05:23:26 CDT)
• AW: Reg: movement of protein outside box
  • Norman Geist (Fri Jun 13 2014 - 03:09:20 CDT)
  • Norman Geist (Tue Jun 10 2014 - 07:26:58 CDT)
  • Norman Geist (Tue Jun 10 2014 - 02:47:32 CDT)
• AW: Reg: QM/MM calculations in NAMD
  • Norman Geist (Mon Nov 10 2014 - 08:12:44 CST)
• AW: Regarding NAMD and MD simulations
  • Joel Moniz (Tue Jul 08 2014 - 22:17:19 CDT)
  • Norman Geist (Mon Jul 07 2014 - 02:48:08 CDT)
• AW: Regarding NAMD installation
  • Pragya Priyadarshini (Mon Aug 17 2015 - 04:38:29 CDT)
  • Norman Geist (Mon Aug 17 2015 - 04:32:19 CDT)
• AW: regarding PME grid setting problem
  • Norman Geist (Mon Jan 05 2015 - 00:48:11 CST)
• AW: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark
  • Norman Geist (Tue Oct 20 2015 - 03:53:51 CDT)
  • Norman Geist (Tue Oct 20 2015 - 01:29:19 CDT)
• AW: Regarding Temperature calculation from velocity trajectory of NAMD-2.9
  • Norman Geist (Fri Jul 11 2014 - 02:51:44 CDT)
  • Norman Geist (Thu Jul 10 2014 - 05:08:50 CDT)
• AW: REMD
  • Norman Geist (Tue Feb 18 2014 - 02:59:07 CST)
• AW: remd across gpus
  • Norman Geist (Mon Mar 31 2014 - 04:13:21 CDT)
  • Norman Geist (Mon Mar 31 2014 - 00:39:03 CDT)
• AW: REMD on IBM iDataPlex DX360M3
  • Norman Geist (Wed Jul 09 2014 - 02:24:27 CDT)
  • Norman Geist (Tue Jul 08 2014 - 01:12:46 CDT)
  • Norman Geist (Thu Jul 03 2014 - 05:42:02 CDT)
  • Norman Geist (Thu Jul 03 2014 - 05:38:48 CDT)
  • Norman Geist (Thu Jul 03 2014 - 04:28:46 CDT)
• AW: replica exchange module
  • Norman Geist (Tue Oct 27 2015 - 03:08:42 CDT)
  • Norman Geist (Mon Oct 26 2015 - 03:21:01 CDT)
  • Norman Geist (Mon Oct 26 2015 - 02:11:47 CDT)
• AW: Require Suggestion
  • Norman Geist (Wed Feb 19 2014 - 01:42:09 CST)
• AW: residue_rmsd.tcl segmentation fault
  • John Xi (Fri Apr 04 2014 - 07:04:45 CDT)
  • Norman Geist (Fri Apr 04 2014 - 03:18:08 CDT)
  • Norman Geist (Fri Apr 04 2014 - 02:53:45 CDT)
• AW: Running Charmrun/NAMD with more than 10 processes fails
  • Norman Geist (Tue Dec 16 2014 - 04:06:49 CST)
• AW: Running CUDA-enabled NAMD on multiple nodes without InfiniBand?
  • Norman Geist (Thu Dec 04 2014 - 01:08:09 CST)
  • Norman Geist (Mon Dec 01 2014 - 09:19:24 CST)
• AW: Running NAMD via GROMACS topology
  • Norman Geist (Mon Aug 11 2014 - 00:33:15 CDT)
• AW: Self-Assemble Monolayer--Periodic Boundary Conditions
  • Norman Geist (Tue Sep 30 2014 - 01:38:57 CDT)
• AW: Should PME be used for electrostatic interaction energy calculations?
  • Norman Geist (Thu Jun 19 2014 - 02:46:48 CDT)
  • Norman Geist (Thu Jun 19 2014 - 02:25:49 CDT)
• AW: Simulation crash during NPT equilibration
  • Norman Geist (Fri Apr 11 2014 - 06:31:49 CDT)
• AW: slice of water box
  • Norman Geist (Thu Apr 10 2014 - 01:46:05 CDT)
• AW: stepspercycle
  • Gianluca Interlandi (Mon Oct 19 2015 - 12:31:23 CDT)
  • Norman Geist (Mon Oct 19 2015 - 01:25:18 CDT)
• AW: TclForces wrapmode FATAL ERROR: Setting parameter wrapmode from script failed
  • Norman Geist (Thu May 08 2014 - 01:54:10 CDT)
• AW: Temperature assignment REMD
  • Norman Geist (Mon Jan 05 2015 - 01:29:55 CST)
• AW: Tempreture Profile along z axis
  • Norman Geist (Fri Jan 09 2015 - 02:23:04 CST)
• AW: time per step during GPU-accelerated Implicit Solvent calculations
  • Thomas Albers (Wed Nov 18 2015 - 08:38:07 CST)
  • Jim Phillips (Mon Nov 16 2015 - 08:55:26 CST)
  • Norman Geist (Mon Nov 16 2015 - 01:52:00 CST)
• AW: Using nodelist file causes namd to hang
  • Norman Geist (Thu Sep 18 2014 - 12:32:23 CDT)
  • Douglas Houston (Thu Sep 18 2014 - 05:35:30 CDT)
  • Douglas Houston (Wed Aug 27 2014 - 12:47:24 CDT)
  • Ajasja LjubetiÄ� (Wed Aug 27 2014 - 12:32:53 CDT)
  • Douglas Houston (Wed Aug 27 2014 - 09:30:42 CDT)
  • Douglas Houston (Fri Jun 20 2014 - 05:00:05 CDT)
  • Norman Geist (Fri Jun 20 2014 - 02:25:11 CDT)
  • Douglas Houston (Fri Jun 13 2014 - 12:17:15 CDT)
  • Norman Geist (Wed Apr 09 2014 - 05:28:51 CDT)
  • Douglas Houston (Wed Apr 09 2014 - 04:28:37 CDT)
  • Norman Geist (Wed Apr 09 2014 - 00:21:40 CDT)
  • Douglas Houston (Tue Apr 08 2014 - 07:21:19 CDT)
  • Douglas Houston (Tue Apr 08 2014 - 05:52:52 CDT)
  • Norman Geist (Tue Apr 08 2014 - 05:06:03 CDT)
• AW: Various questions
  • Douglas Houston (Wed Jan 22 2014 - 04:30:17 CST)
  • Norman Geist (Wed Jan 22 2014 - 02:42:07 CST)
• AW: velocity manipulation
  • Norman Geist (Thu Oct 16 2014 - 08:26:37 CDT)
  • Norman Geist (Thu Oct 16 2014 - 08:11:59 CDT)
  • Norman Geist (Thu Oct 16 2014 - 07:27:28 CDT)
• AW: vmd-l: Stray PME grid
  • Norman Geist (Wed Oct 01 2014 - 02:27:31 CDT)
• AW: warnings while using amber files
  • amin_at_imtech.res.in (Mon Jan 05 2015 - 02:50:52 CST)
  • Norman Geist (Mon Jan 05 2015 - 00:42:51 CST)
• AW: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD
  • Norman Geist (Tue Nov 11 2014 - 07:03:53 CST)
  • Norman Geist (Tue Nov 11 2014 - 02:48:52 CST)
  • Norman Geist (Mon Nov 10 2014 - 00:53:15 CST)
• AW: Why the computational speed does not increase with the increase of GPUs?
  • Norman Geist (Fri Oct 23 2015 - 03:49:49 CDT)
  • sunyeping (Fri Oct 23 2015 - 02:57:48 CDT)
  • Norman Geist (Thu Oct 22 2015 - 02:27:54 CDT)
• AW: wrapping in two dimensions
  • Norman Geist (Mon Oct 20 2014 - 01:14:02 CDT)
  • Norman Geist (Fri Oct 17 2014 - 02:21:07 CDT)
• AW: Xeon vs i7 and ECC vs SDRAM
  • Kenno Vanommeslaeghe (Wed Jun 25 2014 - 10:26:26 CDT)
  • Gianluca Interlandi (Wed Jun 25 2014 - 01:14:48 CDT)
  • Norman Geist (Wed Jun 25 2014 - 00:31:47 CDT)
• backbone constraint
  • Josh Vermaas (Wed Jul 22 2015 - 08:59:48 CDT)
  • Urszula Uciechowska (Wed Jul 22 2015 - 02:59:37 CDT)
• Bad global crossterm count!
  • Mitul Saha (Tue Jul 08 2014 - 16:48:51 CDT)
  • Mitul Saha (Tue Jul 08 2014 - 16:46:17 CDT)
• benchmark info
  • Hassan Kianinejad (Thu Feb 27 2014 - 16:34:08 CST)
• Best Practices for Nucleobase Parameterization
  • Mayne, Christopher G (Wed May 20 2015 - 08:12:55 CDT)
  • Aaron Larsen (Mon May 18 2015 - 11:30:22 CDT)
• Bias-exchange metadynamics
  • Fidan Sumbul (Sun Oct 18 2015 - 18:16:34 CDT)
• Biasing potential of a Metadynamics Simulation
  • Giacomo Fiorin (Tue Oct 27 2015 - 15:55:13 CDT)
  • Fidan Sumbul (Tue Oct 27 2015 - 14:38:16 CDT)
  • Giacomo Fiorin (Tue Oct 27 2015 - 13:14:06 CDT)
  • Fidan Sumbul (Tue Oct 27 2015 - 13:05:02 CDT)
• bilayer simulation keeps crashing
  • Chitrak Gupta (Tue Apr 14 2015 - 10:00:27 CDT)
• bond angle and dihedral values
  • oguz gurbulak (Thu Mar 26 2015 - 03:55:03 CDT)
• bond lengths and angles constraints
  • oguz gurbulak (Tue Jun 23 2015 - 10:04:53 CDT)
• BONDS vs DOUBLE in topology file
  • Gianluca Interlandi (Fri Oct 09 2015 - 12:42:43 CDT)
  • Josh Vermaas (Fri Oct 09 2015 - 09:46:07 CDT)
  • Gianluca Interlandi (Fri Oct 09 2015 - 00:42:05 CDT)
• Boost value in aMD simulation
  • James Starlight (Wed Jul 23 2014 - 06:30:12 CDT)
• boron nitride nanotube
  • Axel Kohlmeyer (Thu Jun 12 2014 - 05:46:33 CDT)
  • Z (Thu Jun 12 2014 - 05:28:33 CDT)
  • Axel Kohlmeyer (Mon Jun 09 2014 - 04:19:24 CDT)
  • Z (Mon Jun 09 2014 - 02:58:02 CDT)
• Bubble in water during membrane simulations
  • Kevin Chan (Mon Nov 16 2015 - 10:41:21 CST)
  • Giacomo Fiorin (Mon Nov 16 2015 - 09:48:42 CST)
  • Kevin C Chan (Mon Nov 16 2015 - 02:12:29 CST)
• buffer overflow with long file paths in psfgen in NAMD 2.11b2?
  • Jim Phillips (Tue Dec 08 2015 - 16:41:22 CST)
  • Brian Radak (Tue Dec 08 2015 - 15:54:28 CST)
• BUG: NAMD-2.10 CUDA REMD segfault with TCL exec randomly
  • Norman Geist (Wed Mar 04 2015 - 04:40:07 CST)
  • Norman Geist (Wed Mar 04 2015 - 01:47:42 CST)
• building namd on a Cray XE6 with Interlagos procs
  • Giovanni Settanni (Tue May 20 2014 - 09:03:22 CDT)
• Calculating density for a molecule
  • Jeffrey Potoff (Fri Feb 07 2014 - 13:17:17 CST)
  • Research Jubilant (Fri Feb 07 2014 - 11:36:41 CST)
• calculating free energy
  • Aron Broom (Sat Jun 28 2014 - 15:53:02 CDT)
  • Alireza Mansouri (Sat Jun 28 2014 - 12:22:40 CDT)
• Calculating RMSF per residue
  • Abir Ganguly (Tue Apr 21 2015 - 02:58:40 CDT)
  • Aron Broom (Mon Apr 20 2015 - 15:59:23 CDT)
  • Abir Ganguly (Mon Apr 20 2015 - 12:58:24 CDT)
• Calculating the force needed to constrain a protein
  • Maxim Belkin (Fri Jul 18 2014 - 11:43:27 CDT)
  • Shane.OMahony (Fri Jul 18 2014 - 11:18:05 CDT)
• Calculating the spin angle collective variable value
  • Marlon SIDORE (Mon May 11 2015 - 09:06:46 CDT)
  • Giacomo Fiorin (Mon May 11 2015 - 08:57:41 CDT)
  • Marlon SIDORE (Mon May 11 2015 - 08:48:51 CDT)
  • Giacomo Fiorin (Mon May 11 2015 - 08:40:34 CDT)
  • Marlon SIDORE (Mon May 11 2015 - 03:51:38 CDT)
• Calculation of PMF between protein domains NAMD
  • Chola Regmi (Wed May 13 2015 - 18:14:49 CDT)
  • Chola Regmi (Fri Apr 17 2015 - 18:50:25 CDT)
  • Jeff Comer (Fri Apr 17 2015 - 18:22:17 CDT)
  • Aron Broom (Fri Apr 17 2015 - 18:00:09 CDT)
  • Aron Broom (Fri Apr 17 2015 - 17:57:48 CDT)
  • Josh Vermaas (Fri Apr 17 2015 - 17:54:37 CDT)
  • Giacomo Fiorin (Fri Apr 17 2015 - 17:48:33 CDT)
  • Josh Vermaas (Fri Apr 17 2015 - 17:43:49 CDT)
  • Chola Regmi (Fri Apr 17 2015 - 17:26:03 CDT)
• Calculation of the water inside of protein during trajectory
  • James Starlight (Tue Feb 03 2015 - 09:51:07 CST)
• call "NAMD" from another program
  • bay__gulf618_at_sina.com (Sat Jul 11 2015 - 22:21:09 CDT)
  • Ajasja LjubetiÄ� (Fri Jul 10 2015 - 02:50:31 CDT)
  • Thomas C Bishop (Fri Jul 10 2015 - 02:38:00 CDT)
  • Aron Broom (Thu Jul 09 2015 - 17:59:08 CDT)
  • Ma'Mon Hatmal (Thu Jul 09 2015 - 17:53:24 CDT)
• Call for participation: ISQBP Meeting, Telluride 15-19.06.2014
  • Vlad Cojocaru (Mon Mar 10 2014 - 11:38:09 CDT)
• Can 'nonbonded interaction parameters' be ignored in the parameter file?
  • ¶¡êÏ (Tue May 26 2015 - 20:43:52 CDT)
• Can NAMD does Langevin Dynamics Simulation
  • Jeff Comer (Thu Nov 13 2014 - 15:11:10 CST)
  • Jeff Comer (Thu Nov 13 2014 - 14:37:13 CST)
  • Fidan Sumbul (Thu Nov 13 2014 - 10:41:39 CST)
  • Jeff Comer (Wed Nov 12 2014 - 16:37:31 CST)
  • Fidan Sumbul (Wed Nov 12 2014 - 14:48:25 CST)
• Can NAMD handle two different LJ cutoffs in a single simulation?
  • Lewis Martin (Mon Sep 14 2015 - 23:17:36 CDT)
• Can NAMD simulation solve the problem of coordinate clash in a structural model?
  • Tristan Croll (Fri Apr 17 2015 - 16:50:07 CDT)
  • sunyeping (Sun Apr 12 2015 - 21:19:18 CDT)
  • sunyeping (Sun Apr 12 2015 - 21:18:30 CDT)
• CAN'T FIND DIHEDRAL PARAMETERS FOR CPH1 NR2 FE NPH
  • Roy Fernando (Tue Jan 07 2014 - 08:05:22 CST)
  • Katherine Parra Pulido (Mon Jan 06 2014 - 23:33:49 CST)
• Can't find documentation of known bug in NAMD 2.9
  • Klas Karis (Mon Apr 13 2015 - 12:02:25 CDT)
• Can't start SMP NAMD - Problem clearly is in front of the monitor
  • Jim Phillips (Tue Nov 17 2015 - 12:45:51 CST)
  • Vogel, Alexander (Tue Nov 17 2015 - 03:18:05 CST)
• Cannot find colvar dih1 (dih colvars)
  • Francesco Pietra (Tue Dec 23 2014 - 11:15:31 CST)
• carboxyl NBFIX on proteins
  • Jeff Comer (Thu Nov 20 2014 - 10:46:35 CST)
  • Giacomo Fiorin (Thu Nov 20 2014 - 10:05:10 CST)
  • Jeff Comer (Thu Nov 20 2014 - 09:18:45 CST)
• Carma v.1.4 released.
  • Nicholas M Glykos (Mon Oct 27 2014 - 06:09:24 CDT)
• CGenFF atom type N-
  • Francesco Pietra (Mon Nov 24 2014 - 02:55:04 CST)
• change in pdb..
  • Joaquim Rui de Castro Rodrigues (Wed Jun 11 2014 - 13:03:18 CDT)
  • Axel Kohlmeyer (Wed Jun 11 2014 - 20:55:34 CDT)
  • Gurpreet Kaur Dhindsa (Wed Jun 11 2014 - 20:34:29 CDT)
  • Ivan Gregoretti (Wed Jun 11 2014 - 10:29:05 CDT)
  • Gurpreet Kaur Dhindsa (Wed Jun 11 2014 - 09:39:31 CDT)
  • Gurpreet Kaur Dhindsa (Sat Jun 07 2014 - 18:37:41 CDT)
• Changing Boundary conditions from PBC to non-periodic
  • Gianluca Interlandi (Thu Nov 19 2015 - 14:30:16 CST)
  • Mahdi Tavakol (Thu Nov 19 2015 - 12:30:23 CST)
• changing damping coefficient during simulation
  • Gozde Eskici (Tue Mar 18 2014 - 10:20:25 CDT)
• Charm++ warning> fences and atomic operations not available in native assembly
  • Ern Seang Ong (Thu Aug 20 2015 - 02:56:40 CDT)
• charm36 for ATP and MG
  • Radhika Anoop (Wed Sep 09 2015 - 05:09:39 CDT)
  • Julian Gamboa (Tue Sep 08 2015 - 11:19:03 CDT)
  • Josh Vermaas (Tue Sep 08 2015 - 11:13:19 CDT)
  • Radhika Anoop (Tue Sep 08 2015 - 00:55:48 CDT)
• Charmm
  • Kenno Vanommeslaeghe (Thu Feb 20 2014 - 12:53:55 CST)
  • Gianluca Interlandi (Thu Feb 20 2014 - 12:10:22 CST)
  • Kenno Vanommeslaeghe (Thu Feb 20 2014 - 10:40:41 CST)
  • Peter Reinke (Thu Feb 20 2014 - 02:31:35 CST)
• CHARMM parameter file
  • Fransiska Kurniawan (Wed Apr 15 2015 - 04:11:00 CDT)
• CHARMM36 and NAMD
  • Kenno Vanommeslaeghe (Tue Feb 18 2014 - 20:23:37 CST)
  • Douglas Houston (Tue Feb 18 2014 - 04:02:38 CST)
• chloromethyl ketone patch?
  • Jesper Madsen (Tue Feb 11 2014 - 16:49:21 CST)
• choose the best equilibrium arrangement of water molecules
  • Boshra Moradi (Tue May 06 2014 - 16:55:17 CDT)
• Choosing of windows and width for Umbrella Sampling
  • Kevin C Chan (Mon Dec 08 2014 - 09:39:46 CST)
  • Giacomo Fiorin (Mon Dec 08 2014 - 08:29:49 CST)
  • Kevin C Chan (Mon Dec 08 2014 - 06:48:19 CST)
• Citating colvars module
  • Giacomo Fiorin (Tue Jan 21 2014 - 11:12:55 CST)
  • Salvatore Mario Cosseddu (Tue Jan 21 2014 - 11:20:50 CST)
• citing SODIUM program
  • Shyno Mathew (Sat Jan 04 2014 - 10:45:36 CST)
• Coarse grained instability: atoms moving too fast
  • Marlon Sidore (Mon Oct 05 2015 - 06:47:41 CDT)
• coarse-grained simulation: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C5M P5 (ATOMS 1 2)
  • Khaled Barakat (Sun Mar 23 2014 - 22:44:02 CDT)
• code implementation based on NAMD source code
  • Teerapong Pirojsirikul (Thu May 29 2014 - 17:39:21 CDT)
• Collective variable module
  • naresh kumar (Mon Apr 14 2014 - 10:11:37 CDT)
  • Giacomo Fiorin (Fri Apr 11 2014 - 12:49:20 CDT)
  • naresh kumar (Fri Apr 11 2014 - 12:01:32 CDT)
  • Giacomo Fiorin (Thu Apr 10 2014 - 14:06:18 CDT)
  • naresh kumar (Thu Apr 10 2014 - 12:54:02 CDT)
  • Giacomo Fiorin (Thu Apr 10 2014 - 12:03:27 CDT)
  • naresh kumar (Thu Apr 10 2014 - 11:36:07 CDT)
• Collective Variables to Restrain Ions Away From Protein
  • Aron Broom (Sun Apr 20 2014 - 00:27:37 CDT)
  • Aron Broom (Thu Apr 17 2014 - 23:15:35 CDT)
  • Chris Ing (Thu Apr 17 2014 - 18:36:06 CDT)
• colvar DistanceZ
  • Kevin C Chan (Wed Nov 26 2014 - 20:32:24 CST)
  • Jérôme Hénin (Wed Nov 26 2014 - 07:35:37 CST)
  • Kevin C Chan (Wed Nov 26 2014 - 07:25:03 CST)
  • Jérôme Hénin (Wed Nov 26 2014 - 05:07:19 CST)
  • Kevin C Chan (Tue Nov 25 2014 - 21:03:55 CST)
• COLVAR metadynamics: center of mass of atoms crossing simulation box
  • Lorenz Ripka (Fri May 23 2014 - 07:35:23 CDT)
  • Giacomo Fiorin (Tue May 20 2014 - 11:41:56 CDT)
  • Lorenz Ripka (Mon May 19 2014 - 03:44:36 CDT)
  • Lorenz Ripka (Mon May 19 2014 - 07:17:47 CDT)
• COLVAR related quesion
  • Giacomo Fiorin (Tue Mar 11 2014 - 16:19:24 CDT)
  • Abir Ganguly (Tue Mar 11 2014 - 16:06:20 CDT)
• Colvar with variable axis
  • Mitchell Gleed (Thu Mar 12 2015 - 10:49:21 CDT)
  • Jérôme Hénin (Thu Mar 12 2015 - 08:53:45 CDT)
  • Giacomo Fiorin (Thu Mar 12 2015 - 08:25:54 CDT)
  • Mitchell Gleed (Thu Mar 12 2015 - 07:59:56 CDT)
  • Giacomo Fiorin (Thu Mar 12 2015 - 06:23:31 CDT)
  • Mitchell Gleed (Thu Mar 12 2015 - 06:01:56 CDT)
• Colvar: minimal distance between 2 groups of atoms
  • Vlad Cojocaru (Tue Nov 18 2014 - 03:40:53 CST)
  • Jérôme Hénin (Mon Nov 17 2014 - 13:13:07 CST)
  • Vlad Cojocaru (Mon Nov 17 2014 - 12:12:42 CST)
  • Ajasja LjubetiÄ� (Mon Nov 17 2014 - 11:30:45 CST)
  • Vlad Cojocaru (Mon Nov 17 2014 - 10:49:57 CST)
  • Ajasja LjubetiÄ� (Mon Nov 17 2014 - 10:28:20 CST)
  • Vlad Cojocaru (Mon Nov 17 2014 - 10:14:58 CST)
  • Jérôme Hénin (Mon Nov 17 2014 - 10:07:38 CST)
  • Vlad Cojocaru (Mon Nov 17 2014 - 09:57:37 CST)
  • Giacomo Fiorin (Mon Nov 17 2014 - 08:49:18 CST)
  • Vlad Cojocaru (Mon Nov 17 2014 - 07:41:31 CST)
• colvars and drude don't play nice?
  • JC Gumbart (Sat Jan 17 2015 - 15:34:43 CST)
  • Jim Phillips (Fri Jan 16 2015 - 16:57:58 CST)
  • Giacomo Fiorin (Fri Jan 16 2015 - 11:04:44 CST)
  • Giacomo Fiorin (Wed Jan 14 2015 - 10:07:23 CST)
  • JC Gumbart (Wed Jan 14 2015 - 09:58:28 CST)
  • Giacomo Fiorin (Tue Jan 13 2015 - 18:31:38 CST)
  • JC Gumbart (Tue Jan 13 2015 - 18:08:42 CST)
• colvars angle centerReference
  • Giacomo Fiorin (Wed Jan 07 2015 - 14:00:02 CST)
  • Jeff Comer (Wed Dec 10 2014 - 09:22:10 CST)
  • Giacomo Fiorin (Wed Dec 10 2014 - 08:44:22 CST)
  • Jeff Comer (Wed Dec 10 2014 - 08:41:06 CST)
  • Jim Phillips (Wed Dec 10 2014 - 07:31:11 CST)
  • Giacomo Fiorin (Tue Dec 09 2014 - 21:54:55 CST)
  • Jeff Comer (Tue Dec 09 2014 - 21:41:26 CST)
  • Giacomo Fiorin (Tue Dec 09 2014 - 18:35:22 CST)
  • Jeff Comer (Fri Dec 05 2014 - 15:00:44 CST)
• Colvars Boundary potentials do not look harmonic
  • Panel Nicolas (M.) (Thu Jun 04 2015 - 08:08:49 CDT)
  • Jeff Comer (Wed Jun 03 2015 - 11:54:28 CDT)
  • Jérôme Hénin (Wed Jun 03 2015 - 10:15:04 CDT)
  • Panel Nicolas (M.) (Wed Jun 03 2015 - 10:00:53 CDT)
• Colvars error
  • Kevin C Chan (Tue Nov 25 2014 - 21:11:41 CST)
  • Kevin C Chan (Tue Nov 25 2014 - 05:11:55 CST)
  • Giacomo Fiorin (Tue Nov 25 2014 - 08:53:58 CST)
  • Subbarao Kanchi (Tue Nov 25 2014 - 06:30:36 CST)
  • Subbarao Kanchi (Tue Nov 25 2014 - 02:08:45 CST)
  • Kevin C Chan (Tue Nov 25 2014 - 00:57:45 CST)
  • Kevin C Chan (Tue Nov 25 2014 - 00:10:05 CST)
• colvars fatal error
  • Jérôme Hénin (Wed Nov 05 2014 - 02:54:43 CST)
  • Leili Zhang (Tue Nov 04 2014 - 22:44:05 CST)
• Colvars keyword problem
  • Jérôme Hénin (Mon May 05 2014 - 10:01:03 CDT)
  • Sofya Lushchekina (Mon May 05 2014 - 09:32:11 CDT)
• colvars replica exchange oddity
  • JC Gumbart (Tue Oct 14 2014 - 22:27:07 CDT)
• Colvars simulation running slow?
  • Ajasja LjubetiÄ� (Wed Sep 10 2014 - 19:58:48 CDT)
  • Tristan Croll (Wed Sep 10 2014 - 19:51:15 CDT)
  • Tristan Croll (Wed Sep 10 2014 - 17:15:35 CDT)
  • Jérôme Hénin (Wed Sep 10 2014 - 02:13:00 CDT)
  • Tristan Croll (Tue Sep 09 2014 - 20:31:06 CDT)
• colvars with replica exchange molecular dynamics
  • Francesco Pietra (Fri Jan 31 2014 - 01:38:21 CST)
  • Giacomo Fiorin (Thu Jan 30 2014 - 17:32:47 CST)
  • Francesco Pietra (Tue Jan 14 2014 - 02:25:19 CST)
  • Giacomo Fiorin (Mon Jan 13 2014 - 15:17:25 CST)
  • Francesco Pietra (Mon Jan 13 2014 - 14:29:41 CST)
• colvars: keyword "name" is not supported, or not recognized in this context.
  • Francesco Pietra (Thu Jan 15 2015 - 09:52:16 CST)
• Combining interleaved and top posting is considered harmful.
  • Jim Phillips (Thu Aug 28 2014 - 11:29:10 CDT)
  • Nicholas M Glykos (Thu Aug 28 2014 - 11:11:40 CDT)
• Combining parameter files from CHARMM
  • Josh Vermaas (Mon Jun 15 2015 - 11:10:43 CDT)
  • Branko (Mon Jun 15 2015 - 07:39:49 CDT)
  • Kevin C Chan (Mon Jun 15 2015 - 07:29:36 CDT)
  • Branko (Mon Jun 15 2015 - 05:12:57 CDT)
  • Kevin C Chan (Mon Jun 15 2015 - 03:08:06 CDT)
  • Branko (Fri Jun 05 2015 - 05:17:56 CDT)
  • Kevin C Chan (Fri Jun 05 2015 - 04:51:13 CDT)
• Compilation of NAMD from Source (Cray XC40)
  • Stefan Richter (Wed Oct 14 2015 - 04:38:17 CDT)
  • Vlad Cojocaru (Tue Oct 13 2015 - 15:04:02 CDT)
  • Jim Phillips (Tue Oct 13 2015 - 10:03:39 CDT)
  • Richter, Stefan (Tue Oct 13 2015 - 09:26:06 CDT)
• Compilation with OpenMPI
  • Kevin C Chan (Mon Jul 20 2015 - 05:02:10 CDT)
  • Kevin C Chan (Tue Jul 14 2015 - 00:11:38 CDT)
  • Kevin C Chan (Sun Jul 12 2015 - 01:13:30 CDT)
• Compile NAMD - Projections
  • Stefan Richter (Thu Oct 15 2015 - 04:40:44 CDT)
  • Kostas Malavazos (Wed Oct 14 2015 - 11:45:04 CDT)
• compile psfgen as shared object or Tcl package?
  • Brian Radak (Wed Feb 18 2015 - 15:47:27 CST)
• compiling namd-lite
  • Hassan Kianinejad (Thu Mar 06 2014 - 19:08:28 CST)
  • Hassan Kianinejad (Thu Mar 06 2014 - 18:55:54 CST)
• Compiling with Open64 4.5.2.1 for AMD Opteron 6378
  • David Chin (Mon Mar 24 2014 - 10:44:54 CDT)
• Compressibility of Berendesen Barostat (Simulations Near Critical Point)
  • JAVAD NOROOZI (Fri Feb 13 2015 - 00:37:42 CST)
• computing forces on atoms by postprocessing a dcd file generated with FEP enabled
  • Harris, Robert C. (Wed Sep 03 2014 - 14:05:40 CDT)
• concerning paratools
  • Mayne, Christopher G (Thu Dec 03 2015 - 14:11:52 CST)
  • luca belmonte (Thu Dec 03 2015 - 04:36:04 CST)
• configuration file question
  • Jeff Comer (Thu Feb 26 2015 - 17:34:09 CST)
  • Hasan haska (Thu Feb 26 2015 - 16:49:55 CST)
• Constant Pressure, Variable Volume, Minimization
  • Josh Vermaas (Thu Dec 18 2014 - 13:17:35 CST)
  • Miss. State (Thu Dec 18 2014 - 13:01:05 CST)
• Constant velocity SMD
  • maral hassani (Tue Jun 09 2015 - 07:14:16 CDT)
• Constraining two sets of atoms
  • Natnael Doilicho (Tue Sep 16 2014 - 12:06:38 CDT)
• Constraint failure in RATTLE
  • Massimiliano Porrini (Mon Mar 31 2014 - 11:48:38 CDT)
  • Francesco Pietra (Mon Mar 31 2014 - 02:29:48 CDT)
  • Massimiliano Porrini (Sun Mar 30 2014 - 06:49:34 CDT)
  • Francesco Pietra (Sun Mar 30 2014 - 02:31:54 CDT)
• Constraint failure in RATTLE algorithm
  • Douglas Houston (Tue Jul 01 2014 - 04:29:38 CDT)
  • Kenno Vanommeslaeghe (Fri Jun 27 2014 - 10:37:19 CDT)
  • Douglas Houston (Fri Jun 27 2014 - 09:29:42 CDT)
  • Aron Broom (Sun Jun 22 2014 - 23:02:28 CDT)
  • Tristan Croll (Sat Jun 21 2014 - 18:43:43 CDT)
  • Douglas Houston (Fri Jun 20 2014 - 08:31:56 CDT)
  • Aron Broom (Thu Jun 19 2014 - 09:15:49 CDT)
  • Aron Broom (Thu Jun 19 2014 - 10:37:59 CDT)
  • Douglas Houston (Thu Jun 19 2014 - 09:51:33 CDT)
  • Douglas Houston (Thu Jun 19 2014 - 05:26:53 CDT)
  • Tristan Croll (Wed Jun 18 2014 - 20:29:08 CDT)
  • Aron Broom (Wed Jun 18 2014 - 14:07:04 CDT)
  • Axel Kohlmeyer (Wed Jun 18 2014 - 13:23:05 CDT)
  • Douglas Houston (Wed Jun 18 2014 - 12:29:48 CDT)
• constraint failure in Rattle algorithm for atom 54134
  • Life Sciences Inc (Mon Oct 26 2015 - 13:37:42 CDT)
  • Chitrak Gupta (Mon Oct 26 2015 - 13:01:16 CDT)
  • Chitrak Gupta (Mon Oct 26 2015 - 09:10:59 CDT)
  • Tristan Croll (Mon Oct 26 2015 - 01:59:47 CDT)
  • Chitrak Gupta (Mon Oct 26 2015 - 08:31:44 CDT)
  • Life Sciences Inc (Sun Oct 25 2015 - 19:42:57 CDT)
• constraint file from amber prmtop/inpcrd
  • amin_at_imtech.res.in (Sat May 24 2014 - 14:32:55 CDT)
• Controlling water diffusion
  • Evandro Semighini (Sun Jul 19 2015 - 21:42:17 CDT)
  • Peter Freddolino (Sun Jul 19 2015 - 21:13:15 CDT)
  • Evandro Semighini (Fri Jul 17 2015 - 07:44:36 CDT)
  • Peter Freddolino (Thu Jul 16 2015 - 21:54:49 CDT)
  • Evandro Semighini (Thu Jul 16 2015 - 14:21:50 CDT)
• coordinates in namd
  • Tristan Croll (Tue Jun 03 2014 - 02:25:49 CDT)
  • Research Jubilant (Mon Jun 02 2014 - 23:34:52 CDT)
• Cost of a colvar calculation
  • Branko (Wed Jul 23 2014 - 07:45:31 CDT)
  • George Patargias (Wed Jul 23 2014 - 01:33:23 CDT)
  • Jo, Sunhwan (Tue Jul 22 2014 - 19:02:20 CDT)
  • Giacomo Fiorin (Tue Jul 22 2014 - 17:31:23 CDT)
  • Jo, Sunhwan (Tue Jul 22 2014 - 13:06:12 CDT)
  • Jérôme Hénin (Tue Jul 22 2014 - 11:20:56 CDT)
  • Axel Kohlmeyer (Tue Jul 22 2014 - 11:02:47 CDT)
  • Aron Broom (Tue Jul 22 2014 - 10:56:45 CDT)
  • Ivan Gregoretti (Tue Jul 22 2014 - 08:41:41 CDT)
  • Jérôme Hénin (Tue Jul 22 2014 - 07:43:30 CDT)
  • Branko (Tue Jul 22 2014 - 07:44:04 CDT)
  • Ivan Gregoretti (Tue Jul 22 2014 - 07:33:14 CDT)
  • Jérôme Hénin (Tue Jul 22 2014 - 06:56:42 CDT)
  • George Patargias (Tue Jul 22 2014 - 06:27:52 CDT)
• Could I run aMD in Drude force field?
  • Brian Radak (Thu Feb 05 2015 - 13:50:15 CST)
  • dream (Thu Feb 05 2015 - 02:14:04 CST)
• Crazy rigid water molecules
  • Brian Radak (Thu Nov 19 2015 - 15:40:55 CST)
• Create psf file
  • Asma el-magboub (Mon Jun 22 2015 - 18:43:13 CDT)
  • Mayne, Christopher G (Mon Jun 22 2015 - 10:01:23 CDT)
  • Raed Ahmed Abdelsalam Shalaby (Mon Jun 22 2015 - 05:54:32 CDT)
  • Fransiska Kurniawan (Sat Jun 20 2015 - 17:56:52 CDT)
• create psf file without hydrogens
  • Revthi Sanker (Fri Nov 21 2014 - 03:23:19 CST)
  • Tristan Croll (Thu Nov 20 2014 - 14:22:06 CST)
  • Revthi Sanker (Thu Nov 20 2014 - 12:26:48 CST)
• Cross-correlation analysis in multidomain proteins
  • James Starlight (Thu Mar 13 2014 - 05:32:22 CDT)
• CUDA error in cuda_check_local_progress
  • Abhishek TYAGI (Thu Apr 17 2014 - 04:23:44 CDT)
  • Abhishek TYAGI (Thu Apr 17 2014 - 04:07:36 CDT)
  • Abhishek TYAGI (Thu Apr 17 2014 - 02:41:11 CDT)
• CUDA Fatal Error While Trying to Run Under Windows 8.1
  • Jim Phillips (Thu Nov 06 2014 - 13:00:35 CST)
  • Branko (Thu Nov 06 2014 - 12:15:59 CST)
  • Justin Sanders (Thu Nov 06 2014 - 12:01:58 CST)
• Cyclic peptide Nanotube
  • Nikhil Maroli (Fri Oct 02 2015 - 08:52:59 CDT)
• Daily cron stalls running NAMD outputs
  • Jérôme Hénin (Wed Apr 08 2015 - 03:16:22 CDT)
  • Vlastimil Zíma (Wed Apr 08 2015 - 02:41:23 CDT)
  • Vlastimil Zíma (Wed Apr 01 2015 - 07:08:28 CDT)
  • Vlastimil Zíma (Wed Apr 01 2015 - 03:04:26 CDT)
• DCD Error
  • Abhishek TYAGI (Thu Mar 19 2015 - 03:59:56 CDT)
  • Atanu Maity (Wed Mar 18 2015 - 23:32:32 CDT)
  • Abhishek Tyagi (Wed Mar 18 2015 - 10:13:07 CDT)
  • Josh Vermaas (Wed Mar 18 2015 - 10:06:43 CDT)
  • Maxim Belkin (Wed Mar 18 2015 - 10:06:34 CDT)
  • btreece_at_andrew.cmu.edu (Wed Mar 18 2015 - 10:05:58 CDT)
  • Abhishek Tyagi (Wed Mar 18 2015 - 09:51:17 CDT)
  • Josh Vermaas (Wed Mar 18 2015 - 09:36:52 CDT)
  • Abhishek Tyagi (Wed Mar 18 2015 - 09:29:42 CDT)
  • btreece_at_andrew.cmu.edu (Wed Mar 18 2015 - 09:27:28 CDT)
  • manish kesherwani (Wed Mar 18 2015 - 08:10:18 CDT)
  • Abhishek TYAGI (Wed Mar 18 2015 - 06:23:58 CDT)
• Debugging and Force Checking?
  • Jérôme Hénin (Mon Jul 20 2015 - 12:42:20 CDT)
  • Brian Radak (Mon Jul 20 2015 - 09:32:44 CDT)
• Density of water box
  • Akshay Bhatnagar (Tue Jun 03 2014 - 07:26:41 CDT)
  • Ana Celia Vila Verde (Tue Jun 03 2014 - 06:29:02 CDT)
  • Akshay Bhatnagar (Tue Jun 03 2014 - 05:22:00 CDT)
• Detection of Internal water along MD trajectory
  • James Starlight (Mon Mar 17 2014 - 04:14:38 CDT)
• Determining HIS protonation state using PropKa vmd plug-in
  • zeynab mohamad hoseyni (Tue Feb 11 2014 - 06:30:09 CST)
• Determining the PMF with Adaptive Biasing Forces
  • sunyzero (Tue Dec 08 2015 - 22:00:19 CST)
  • Jérôme Hénin (Tue Dec 08 2015 - 09:09:58 CST)
  • Souvik Sinha (Tue Dec 08 2015 - 01:42:34 CST)
  • sunyzero (Mon Dec 07 2015 - 23:48:55 CST)
  • sunyzero (Mon Dec 07 2015 - 20:02:35 CST)
• DIDN'T FIND vdW PARAMETER FOR ATOM TYPE SG3O1
  • Srijita Paul (Fri Dec 25 2015 - 00:41:47 CST)
• Dielectric constant of water from MSM and PME simulations
  • Otello Maria Roscioni (Mon Oct 26 2015 - 12:29:02 CDT)
  • Zhe Wu (Fri Oct 23 2015 - 10:46:41 CDT)
  • Zhe Wu (Fri Oct 23 2015 - 10:31:04 CDT)
  • Axel Kohlmeyer (Fri Oct 23 2015 - 09:47:38 CDT)
  • Mattia Felice Palermo (Fri Oct 23 2015 - 08:57:37 CDT)
• Different trajectories with and without restarting
  • Grzegorz Nawrocki (Mon May 18 2015 - 15:04:17 CDT)
  • Axel Kohlmeyer (Sat May 16 2015 - 00:06:27 CDT)
  • Grzegorz Nawrocki (Fri May 15 2015 - 21:08:40 CDT)
  • Axel Kohlmeyer (Fri May 15 2015 - 18:26:53 CDT)
  • btreece_at_andrew.cmu.edu (Fri May 15 2015 - 18:26:09 CDT)
  • Grzegorz Nawrocki (Fri May 15 2015 - 18:09:57 CDT)
• Difficulties with using the "rescalevels" command every MD timestep
  • Spencer, Jacob (Thu Jan 09 2014 - 09:48:37 CST)
• Dihedral calculation with colvars
  • Giacomo Fiorin (Fri Mar 13 2015 - 10:05:20 CDT)
  • Jérôme Hénin (Fri Mar 13 2015 - 09:42:21 CDT)
  • Jérôme Hénin (Thu Mar 12 2015 - 06:29:22 CDT)
  • Kevin C Chan (Thu Mar 12 2015 - 06:13:00 CDT)
  • Jérôme Hénin (Thu Mar 12 2015 - 05:27:07 CDT)
  • Kevin C Chan (Thu Mar 12 2015 - 01:20:46 CDT)
  • Aron Broom (Wed Mar 11 2015 - 23:17:09 CDT)
  • Kevin C Chan (Wed Mar 11 2015 - 23:05:45 CDT)
• Dihedral definition in NAMD
  • Kevin C Chan (Wed Mar 11 2015 - 05:03:54 CDT)
  • Giacomo Fiorin (Wed Mar 11 2015 - 03:13:27 CDT)
  • Josh Vermaas (Tue Mar 10 2015 - 13:32:12 CDT)
  • Kevin C Chan (Tue Mar 10 2015 - 22:22:34 CDT)
  • Giacomo Fiorin (Tue Mar 10 2015 - 18:46:42 CDT)
  • Kevin C Chan (Tue Mar 10 2015 - 13:13:00 CDT)
  • Giacomo Fiorin (Tue Mar 10 2015 - 09:49:00 CDT)
  • Giacomo Fiorin (Tue Mar 10 2015 - 09:33:15 CDT)
  • Josh Vermaas (Tue Mar 10 2015 - 09:30:21 CDT)
  • Kevin C Chan (Tue Mar 10 2015 - 09:24:23 CDT)
  • Josh Vermaas (Tue Mar 10 2015 - 09:14:27 CDT)
  • Kevin C Chan (Tue Mar 10 2015 - 06:52:53 CDT)
  • Giacomo Fiorin (Tue Mar 10 2015 - 06:28:26 CDT)
  • Kevin C Chan (Tue Mar 10 2015 - 06:19:16 CDT)
• Dihedrals multiplicity!
  • Jeffrey Potoff (Thu Feb 13 2014 - 11:34:16 CST)
  • Jeffrey Potoff (Thu Feb 13 2014 - 10:51:12 CST)
  • Anna Borlsky (Thu Feb 13 2014 - 09:24:46 CST)
• Dioxygen atom type with CHARMM36
  • Francesco Pietra (Wed Nov 12 2014 - 01:17:44 CST)
  • Kenno Vanommeslaeghe (Tue Nov 11 2014 - 14:19:40 CST)
  • Francesco Pietra (Tue Nov 11 2014 - 13:34:13 CST)
  • Kenno Vanommeslaeghe (Tue Nov 11 2014 - 12:46:48 CST)
  • Francesco Pietra (Tue Nov 11 2014 - 11:19:17 CST)
  • Kenno Vanommeslaeghe (Tue Nov 11 2014 - 11:07:25 CST)
  • Francesco Pietra (Tue Nov 11 2014 - 10:11:00 CST)
• Dioxygen params charmm36
  • Francesco Pietra (Wed Oct 29 2014 - 16:27:17 CDT)
• Dipole Moment Watcher, Ibuprofen
  • Branko (Tue Mar 31 2015 - 04:12:14 CDT)
  • JAVAD NOROOZI (Tue Mar 31 2015 - 01:01:46 CDT)
• does fixedAtoms modify velocities?
  • Brian Radak (Tue Jul 07 2015 - 12:48:23 CDT)
  • Brian Radak (Tue Jul 07 2015 - 12:25:32 CDT)
• Does NAMD have some way to test the result?
  • Jérôme Hénin (Sat Oct 04 2014 - 04:20:57 CDT)
  • Axel Kohlmeyer (Fri Oct 03 2014 - 22:17:05 CDT)
  • ukulililixl (Fri Oct 03 2014 - 21:50:52 CDT)
• DOF during alchemical simulations
  • Brian Radak (Tue Dec 01 2015 - 10:08:08 CST)
  • Hannes Loeffler (Tue Dec 01 2015 - 08:19:00 CST)
  • Grace Brannigan (Mon Nov 30 2015 - 14:45:55 CST)
  • Brian Radak (Mon Nov 30 2015 - 12:30:33 CST)
  • Grace Brannigan (Mon Nov 30 2015 - 12:05:36 CST)
  • Brian Radak (Mon Nov 30 2015 - 09:36:55 CST)
  • Jérôme Hénin (Fri Nov 27 2015 - 03:31:25 CST)
  • Aron Broom (Thu Nov 26 2015 - 12:28:27 CST)
  • Jérôme Hénin (Thu Nov 26 2015 - 12:00:01 CST)
  • Brian Radak (Wed Nov 25 2015 - 10:31:11 CST)
• Dual boost accelerated md energy parameters?
  • Thomas Evangelidis (Mon May 12 2014 - 14:11:45 CDT)
  • Per Larsson (Mon May 12 2014 - 13:54:48 CDT)
• dual-boost aMD and the dV value in the output file
  • Ozge Sensoy (Sun Jan 18 2015 - 14:00:47 CST)
• eBiothon platform
  • eBiothon Admin Team (Mon Aug 03 2015 - 10:07:36 CDT)
• Editing Patch Grid Dimensions
  • Ryan Gordon (Thu Feb 05 2015 - 12:08:20 CST)
  • Jim Phillips (Thu Feb 05 2015 - 10:32:28 CST)
  • Ryan Gordon (Thu Feb 05 2015 - 10:00:28 CST)
• efficient way to apply time-dependent electric field
  • Jim Phillips (Thu Sep 04 2014 - 11:18:00 CDT)
  • Azadeh Alavi (Thu Sep 04 2014 - 05:38:12 CDT)
• Electronic density profile of lipid bilayer.
  • Subbarao Kanchi (Sun Apr 06 2014 - 20:32:54 CDT)
• electrostatics cutoff parameters
  • Z (Mon Jun 08 2015 - 09:06:00 CDT)
• Empirical force fields: release new version of RED Server Dev/PyRED
  • FyD (Mon May 05 2014 - 06:07:18 CDT)
• Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014
  • FyD (Tue Dec 09 2014 - 02:43:22 CST)
• Energy decomposition analyse in NAMD
  • sunyzero (Mon Dec 28 2015 - 20:23:28 CST)
• energy groups in NAMD
  • Andre Ribeiro (Fri Mar 06 2015 - 14:22:34 CST)
  • Andre Ribeiro (Fri Mar 06 2015 - 14:23:14 CST)
• energy minimization
  • Dhiraj Srivastava (Mon Apr 20 2015 - 21:57:55 CDT)
• energy minimization in namd
  • Branko (Thu Apr 23 2015 - 11:57:06 CDT)
  • Brian Radak (Thu Apr 23 2015 - 11:51:26 CDT)
  • Chitrak Gupta (Thu Apr 23 2015 - 11:44:51 CDT)
  • Hasan haska (Thu Apr 23 2015 - 11:29:43 CDT)
• energy output
  • Jeffrey Potoff (Wed Dec 09 2015 - 11:56:45 CST)
  • Deng, Jinxia (Nancy) (Wed Dec 09 2015 - 13:12:11 CST)
  • Branko (Wed Dec 09 2015 - 11:51:45 CST)
  • Chitrak Gupta (Wed Dec 09 2015 - 11:47:57 CST)
  • Deng, Jinxia (Nancy) (Wed Dec 09 2015 - 11:39:14 CST)
• Energy term in output file of Accelerated dynamics
  • Kapil jain (Sun Aug 10 2014 - 21:39:32 CDT)
  • Kapil jain (Fri Aug 08 2014 - 02:14:56 CDT)
• Enerygy Minimization of a homology modelled structure in NAMD
  • Jérôme Hénin (Wed Apr 01 2015 - 02:07:59 CDT)
  • Arijit Ghosh (Tue Mar 31 2015 - 22:46:49 CDT)
  • Arijit Ghosh (Mon Mar 30 2015 - 00:21:35 CDT)
  • Arijit Ghosh (Sun Mar 29 2015 - 21:16:03 CDT)
• equilibrate the bulk water system
  • Axel Kohlmeyer (Sun Mar 15 2015 - 21:30:06 CDT)
  • Hasan haska (Sat Mar 14 2015 - 14:38:03 CDT)
  • Abhishek Tyagi (Fri Mar 13 2015 - 09:49:20 CDT)
  • Maxim Belkin (Fri Mar 13 2015 - 11:28:35 CDT)
  • Hasan haska (Fri Mar 13 2015 - 06:57:15 CDT)
  • Norman Geist (Wed Mar 11 2015 - 02:03:46 CDT)
  • Hasan haska (Tue Mar 10 2015 - 16:51:30 CDT)
• Equilibration for a reverse FEP run
  • Matthew Ralph Adendorff (Thu Apr 23 2015 - 10:16:08 CDT)
  • Chris Chipot (Thu Apr 23 2015 - 10:04:32 CDT)
  • Matthew Ralph Adendorff (Thu Apr 23 2015 - 09:54:41 CDT)
• error : segmentation fault
  • Faezeh Mottaghitalab (Wed Jan 01 2014 - 05:18:30 CST)
• Error applying PME to simulation set up
  • Axel Kohlmeyer (Wed May 13 2015 - 08:00:00 CDT)
  • Sourav Ray (Wed May 13 2015 - 06:02:51 CDT)
  • Norman Geist (Wed May 13 2015 - 05:08:45 CDT)
  • Sourav Ray (Wed May 13 2015 - 04:24:41 CDT)
• Error compiling NAMD2.9 after patching with PLUMED2.1
  • Rubén Granero (Tue Dec 16 2014 - 12:07:45 CST)
  • Jim Phillips (Tue Dec 16 2014 - 09:22:04 CST)
  • Rubén Granero (Tue Dec 16 2014 - 07:39:02 CST)
  • Jim Phillips (Mon Dec 15 2014 - 08:37:26 CST)
  • Rubén Granero (Mon Dec 15 2014 - 06:47:27 CST)
• Error during Opt. Charges while using FF Took Kit
  • Aaron Larsen (Wed May 20 2015 - 16:38:19 CDT)
• ERROR in CUDA run
  • Jim Phillips (Thu Dec 17 2015 - 19:50:54 CST)
  • Lara rajam (Thu Dec 17 2015 - 08:50:49 CST)
• Error in Metadynamics Simulation
  • Fidan Sumbul (Fri Oct 23 2015 - 06:08:40 CDT)
  • Giacomo Fiorin (Thu Oct 22 2015 - 15:41:57 CDT)
  • Fidan Sumbul (Wed Oct 21 2015 - 16:31:30 CDT)
• Error in NAMD Controller Class Reference- Adaptive Tempering
  • Jeff Comer (Fri Sep 11 2015 - 08:12:15 CDT)
  • Jeff Comer (Fri Sep 11 2015 - 08:10:02 CDT)
  • Sachin Natesh (Thu Sep 10 2015 - 19:13:41 CDT)
• Error in TI derivatives for staggered lambda scaling?
  • Brian Radak (Tue Jul 21 2015 - 13:41:28 CDT)
• error in writing colvars state file
  • Jérôme Hénin (Fri Jun 05 2015 - 05:33:07 CDT)
  • Bennion, Brian (Thu Jun 04 2015 - 16:30:07 CDT)
  • Bennion, Brian (Thu Jun 04 2015 - 16:24:44 CDT)
• error message
  • Richard Wood (Tue Jun 03 2014 - 19:13:26 CDT)
• Error on write to binary file
  • Mihaela Drenscko (Mon Dec 22 2014 - 18:02:54 CST)
• error reading colvars.conf in REUS
  • Chitrak Gupta (Mon Nov 16 2015 - 08:42:08 CST)
  • Giacomo Fiorin (Wed Nov 11 2015 - 11:00:21 CST)
  • Chitrak Gupta (Tue Nov 10 2015 - 20:18:11 CST)
  • Giacomo Fiorin (Fri Nov 06 2015 - 14:41:42 CST)
  • Chitrak Gupta (Thu Nov 05 2015 - 16:45:48 CST)
• error running min
  • Jeff Comer (Tue Feb 03 2015 - 08:32:57 CST)
  • Urszula Uciechowska (Tue Feb 03 2015 - 08:23:28 CST)
• Error when running MIC version of namd on Stampede
  • Chen Wei (Fri Feb 21 2014 - 09:49:38 CST)
• error when use Charmm_Gui prepared *.inp for NAMD
  • Jeffrey Potoff (Thu Dec 03 2015 - 08:44:53 CST)
  • Deng, Jinxia (Nancy) (Thu Dec 03 2015 - 09:52:20 CST)
  • Josh Vermaas (Thu Dec 03 2015 - 08:50:36 CST)
  • Chitrak Gupta (Thu Dec 03 2015 - 08:49:59 CST)
  • Deng, Jinxia (Nancy) (Thu Dec 03 2015 - 08:37:14 CST)
• error while making psf file for bacteriorhodopsin system
  • Faezeh Mottaghitalab (Fri May 09 2014 - 13:10:55 CDT)
  • Kenno Vanommeslaeghe (Fri May 09 2014 - 11:38:08 CDT)
  • Kenno Vanommeslaeghe (Thu May 08 2014 - 15:57:52 CDT)
  • Faezeh Mottaghitalab (Thu May 08 2014 - 15:11:26 CDT)
• error while running namd on CRAY XC40 machine
  • Santosh Kumar Chaudhary (Fri Mar 27 2015 - 01:00:51 CDT)
  • Jim Phillips (Mon Mar 23 2015 - 13:59:47 CDT)
  • Santosh Kumar Chaudhary (Sun Mar 22 2015 - 02:40:31 CDT)
• ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG!
  • Axel Kohlmeyer (Mon Feb 17 2014 - 21:39:00 CST)
  • Axel Kohlmeyer (Mon Feb 17 2014 - 17:26:41 CST)
  • Miss. State (Mon Feb 17 2014 - 17:05:09 CST)
• ERROR: CALCULATED VDWA/B FORCES DOES NOT MATCH ENERGY
  • Shalton Evans (Mon Feb 03 2014 - 21:13:41 CST)
• Error: Constraint failure in RATTLE algorithm for atom 5380! in NAMD
  • Mahya Hemmat (Mon Jul 06 2015 - 11:06:39 CDT)
• ERROR: Molecule destroyed by fatal error
  • Axel Kohlmeyer (Mon Jan 27 2014 - 13:37:58 CST)
  • Marlet Martinez (Mon Jan 27 2014 - 13:31:18 CST)
• exchange force constants
  • Lu Hong (Mon Jul 21 2014 - 11:25:25 CDT)
  • Sunhwan Jo (Mon Jul 21 2014 - 09:30:08 CDT)
  • Lu Hong (Mon Jul 21 2014 - 08:50:24 CDT)
• Excluding non bonded interactions between segments
  • Fotis Baltoumas (Tue Apr 08 2014 - 07:08:40 CDT)
  • Jérôme Hénin (Tue Apr 08 2014 - 06:56:22 CDT)
  • Fotis Baltoumas (Tue Apr 08 2014 - 06:57:35 CDT)
  • Jérôme Hénin (Wed Apr 02 2014 - 08:09:21 CDT)
  • Fotis Baltoumas (Wed Apr 02 2014 - 07:40:29 CDT)
• expected speed up after fixing atoms?
  • Jose Borreguero (Wed Sep 24 2014 - 14:26:06 CDT)
  • JC Gumbart (Wed Sep 24 2014 - 14:15:54 CDT)
  • Kenno Vanommeslaeghe (Wed Sep 24 2014 - 14:06:46 CDT)
  • Aron Broom (Wed Sep 24 2014 - 14:07:32 CDT)
  • Jose Borreguero (Wed Sep 24 2014 - 13:41:02 CDT)
  • Aron Broom (Wed Sep 24 2014 - 13:10:45 CDT)
  • Jose Borreguero (Wed Sep 24 2014 - 12:44:48 CDT)
• explicit membrane in implicit solvent
  • Kenno Vanommeslaeghe (Mon Nov 03 2014 - 10:46:24 CST)
  • Gisella Alfonsino (Mon Nov 03 2014 - 05:00:36 CST)
• extendedLagrangian for non-scalar colvar
  • Jerome Karp (Thu Dec 10 2015 - 12:05:51 CST)
  • Jérôme Hénin (Thu Dec 10 2015 - 11:18:39 CST)
  • Jerome Karp (Thu Dec 10 2015 - 10:45:27 CST)
• extra bonds
  • Josh Vermaas (Fri Jul 03 2015 - 09:08:25 CDT)
  • Lara rajam (Thu Jul 02 2015 - 12:35:14 CDT)
  • Josh Vermaas (Thu Jul 02 2015 - 09:48:22 CDT)
  • Lara rajam (Thu Jul 02 2015 - 09:20:59 CDT)
• Extracting data
  • Stephan Grein (Thu Feb 05 2015 - 03:44:29 CST)
  • Jeff Comer (Wed Feb 04 2015 - 08:39:33 CST)
  • Axel Kohlmeyer (Wed Feb 04 2015 - 08:24:25 CST)
  • Jeff Comer (Wed Feb 04 2015 - 07:56:42 CST)
  • Stephan Grein (Wed Feb 04 2015 - 05:56:47 CST)
  • Stephan Grein (Wed Feb 04 2015 - 05:55:37 CST)
• Extracting Kinetic Energy of Certain Atoms
  • JAVAD NOROOZI (Wed Dec 17 2014 - 03:19:09 CST)
• FAD topology and parameters
  • Kenno Vanommeslaeghe (Tue Feb 18 2014 - 20:01:28 CST)
  • Tanner, John J. (Mon Feb 17 2014 - 10:15:52 CST)
  • flavio seixas (Mon Feb 17 2014 - 06:01:14 CST)
  • Tanner, John J. (Sun Feb 16 2014 - 15:30:38 CST)
• Failure MD with par7/rst7 amber input
  • Francesco Pietra (Fri Jan 09 2015 - 02:31:55 CST)
  • Francesco Pietra (Wed Jan 07 2015 - 02:55:16 CST)
• Failure of namd2.10 in keeping trace of cell in t-remd
  • Francesco Pietra (Tue Feb 18 2014 - 05:44:34 CST)
• Fatal error..
  • Gurpreet Kaur Dhindsa (Sun Jun 22 2014 - 17:32:16 CDT)
• FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2
  • Sadegh Faramarzi Ganjabad (Wed Mar 18 2015 - 17:50:58 CDT)
  • Josh Vermaas (Wed Mar 18 2015 - 17:42:03 CDT)
  • Jeff Comer (Wed Mar 18 2015 - 17:35:39 CDT)
  • Sadegh Faramarzi Ganjabad (Wed Mar 18 2015 - 16:47:50 CDT)
• FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE
  • zeynab mohamad hoseyni (Thu Feb 20 2014 - 13:31:50 CST)
• FATAL ERROR: error parsing config file while executing <feff>
  • Mihaela Drenscko (Sun Nov 09 2014 - 11:39:11 CST)
• FATAL ERROR: Incorrect atom count in binary file min.coor
  • Urszula Uciechowska (Fri Jul 24 2015 - 03:27:31 CDT)
• FATAL ERROR: Low global exclusion count!
  • Jeff Comer (Wed Feb 18 2015 - 18:59:28 CST)
  • Akshata Rudrapatna (Wed Feb 18 2015 - 18:32:03 CST)
  • Yongcheng Zhou (Wed Feb 18 2015 - 18:29:33 CST)
• FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small.
  • Sandhyaa Subramanian (Wed Sep 03 2014 - 02:37:32 CDT)
  • Sandhyaa Subramanian (Wed Sep 03 2014 - 02:34:06 CDT)
  • Tristan Croll (Wed Sep 03 2014 - 02:26:27 CDT)
  • Tristan Croll (Tue Sep 02 2014 - 17:27:20 CDT)
  • Sandhyaa Subramanian (Sat Aug 30 2014 - 09:06:14 CDT)
• FATAL ERROR: PME offload requires exactly one CUDA device per process.
  • Maxime Boissonneault (Fri Aug 22 2014 - 06:40:06 CDT)
• FATAL ERROR: seek failed while writing DCD file: No such file or directory
  • Douglas Houston (Fri Dec 19 2014 - 08:33:31 CST)
  • Douglas Houston (Thu Dec 18 2014 - 14:39:51 CST)
• FATAL ERROR: Setting parameter colvars from script failed!
  • Jérôme Hénin (Tue Sep 30 2014 - 13:28:48 CDT)
  • Jérôme Hénin (Tue Sep 30 2014 - 13:04:27 CDT)
  • Jérôme Hénin (Tue Sep 30 2014 - 10:17:02 CDT)
  • Mihaela Drenscko (Tue Sep 30 2014 - 09:27:18 CDT)
• FATAL ERROR: Setting parameter tclForces from script failed!
  • zeynab mohamad hoseyni (Tue Apr 22 2014 - 02:43:23 CDT)
• FATAL ERROR: Unable to access config file ubq_ws_eq.log
  • Jim Phillips (Thu Nov 12 2015 - 22:45:32 CST)
  • Hugo Siles (Thu Nov 12 2015 - 16:40:41 CST)
• FATAL ERROR: UNABLE TO FIND BOND PARAMETERS
  • Jeff Comer (Wed Jan 07 2015 - 20:15:30 CST)
  • Mihaela Drenscko (Wed Jan 07 2015 - 19:58:27 CST)
• FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C NH3 (ATOMS 105 107)
  • Kenno Vanommeslaeghe (Fri Jul 25 2014 - 16:44:15 CDT)
  • Cenk Denktas (Fri Jul 25 2014 - 15:30:40 CDT)
• FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CTL2 OC301 (ATOMS 25 45)
  • Sourav Ray (Fri Jun 12 2015 - 13:49:00 CDT)
  • Danielle Grodi (Fri Jun 12 2015 - 13:39:30 CDT)
• feature request: external initiated clean exit
  • Peter Freddolino (Fri Aug 21 2015 - 20:04:42 CDT)
  • Peter Freddolino (Fri Aug 21 2015 - 17:09:40 CDT)
  • Axel Kohlmeyer (Fri Aug 21 2015 - 17:03:32 CDT)
  • Peter Freddolino (Fri Aug 21 2015 - 16:47:55 CDT)
  • Peter Freddolino (Fri Aug 21 2015 - 16:44:27 CDT)
  • Parag Khuraswar (Fri Aug 21 2015 - 07:58:53 CDT)
  • Daniel Möller (Fri Aug 21 2015 - 07:37:02 CDT)
• FEP error using CUDA
  • Gianluca Interlandi (Sun Apr 13 2014 - 23:14:03 CDT)
  • Sadegh Faramarzi Ganjabad (Sun Apr 13 2014 - 22:42:12 CDT)
• FEP is in kj/mol
  • Javad Noroozi (Sun Apr 27 2014 - 08:32:33 CDT)
• FEP method- Free energy of solvation of ligand
  • hannes.loeffler_at_stfc.ac.uk (Wed Jul 22 2015 - 03:10:42 CDT)
  • Felipe Merino (Wed Jul 22 2015 - 03:07:32 CDT)
  • Mohan maruthi sena (Wed Jul 22 2015 - 02:25:40 CDT)
• FEP of water molecule in binding pocket
  • Monika Sharma (Wed May 28 2014 - 15:35:33 CDT)
• FEP Restart file
  • Jérôme Hénin (Wed Jan 21 2015 - 08:57:20 CST)
  • g_at_ut#@m! (Wed Jan 21 2015 - 08:26:15 CST)
• FEP result analysis
  • Javad Noroozi (Sat Mar 01 2014 - 03:37:29 CST)
• FEP using separated topologies
  • Jérôme Hénin (Thu Nov 12 2015 - 08:48:12 CST)
  • David Huggins (Thu Nov 12 2015 - 07:46:54 CST)
• FEP utility for binding estimation
  • HERBERT MAX VENTHUR PEÂ¥A (Mon Sep 14 2015 - 10:35:17 CDT)
• FEP, big variations in dG within a window
  • Felipe Merino (Mon Jan 05 2015 - 10:27:30 CST)
  • Jonasson Gabriella (Mon Jan 05 2015 - 09:44:31 CST)
• FEP, Ewald size-dependence charge correction
  • JC Gumbart (Sat Sep 13 2014 - 18:38:44 CDT)
  • Sebastian Stolzenberg (Fri Sep 12 2014 - 13:21:10 CDT)
  • Sebastian Stolzenberg (Sun Sep 07 2014 - 10:23:17 CDT)
  • Sebastian Stolzenberg (Tue Sep 02 2014 - 15:12:17 CDT)
• FFTK - error
  • Mayne, Christopher G (Mon Jun 08 2015 - 11:56:34 CDT)
  • Mohan maruthi sena (Sat Jun 06 2015 - 18:35:44 CDT)
• ffTK and phase angles
  • Kenno Vanommeslaeghe (Thu Jun 19 2014 - 20:01:05 CDT)
  • Benjamin Hill (Thu Jun 19 2014 - 17:43:28 CDT)
• ffTK problem: initial parameter fiel is viod of atoms!
  • Mayne, Christopher G (Mon Oct 20 2014 - 11:45:39 CDT)
  • Zeinab Emami (Mon Oct 20 2014 - 11:33:25 CDT)
  • Mayne, Christopher G (Mon Oct 20 2014 - 09:55:55 CDT)
  • Zeinab Emami (Wed Oct 15 2014 - 07:42:57 CDT)
• ffTK problem: initial parameter file is void of of atoms!
  • Zeinab Emami (Thu Oct 16 2014 - 04:15:55 CDT)
• ffTK problem: OPT.Charges
  • Zeinab Emami (Fri Nov 07 2014 - 09:14:15 CST)
• Fixed atoms.
  • Maxim Belkin (Thu Jun 05 2014 - 17:14:48 CDT)
  • Aron Broom (Thu Jun 05 2014 - 17:03:12 CDT)
  • Gurpreet Kaur Dhindsa (Thu Jun 05 2014 - 16:15:05 CDT)
• FixedAtoms and Reference group in spinangle colvar
  • nicolas martin (Thu May 22 2014 - 07:06:08 CDT)
  • Jérôme Hénin (Thu May 22 2014 - 07:00:25 CDT)
  • nicolas martin (Thu May 22 2014 - 06:21:02 CDT)
  • Giacomo Fiorin (Sun May 11 2014 - 17:27:29 CDT)
  • nicolas martin (Sun May 11 2014 - 16:52:42 CDT)
  • Jérôme Hénin (Fri May 09 2014 - 13:53:56 CDT)
  • nicolas martin (Fri May 09 2014 - 09:01:28 CDT)
• Fixing atoms while equilibration
  • Kenno Vanommeslaeghe (Mon Sep 01 2014 - 10:52:07 CDT)
  • Axel Kohlmeyer (Mon Sep 01 2014 - 08:14:37 CDT)
  • Siva Dasetty (Mon Sep 01 2014 - 08:07:59 CDT)
  • Axel Kohlmeyer (Mon Sep 01 2014 - 07:48:34 CDT)
  • Siva Dasetty (Mon Sep 01 2014 - 07:33:57 CDT)
  • Siva Dasetty (Fri Aug 29 2014 - 20:12:21 CDT)
• Folic acid parameters
  • Haleh a (Wed Oct 01 2014 - 01:42:20 CDT)
  • Kenno Vanommeslaeghe (Tue Sep 30 2014 - 11:37:03 CDT)
  • Kenno Vanommeslaeghe (Tue Sep 30 2014 - 10:43:21 CDT)
  • Fotis Baltoumas (Tue Sep 30 2014 - 10:06:43 CDT)
  • Haleh a (Tue Sep 30 2014 - 08:44:38 CDT)
• Force field design
  • Axel Kohlmeyer (Thu Jul 24 2014 - 14:35:11 CDT)
  • Thomas Evangelidis (Thu Jul 24 2014 - 14:31:31 CDT)
  • Gianluca Interlandi (Thu Jul 24 2014 - 14:22:41 CDT)
  • Kenno Vanommeslaeghe (Thu Jul 24 2014 - 11:12:18 CDT)
  • R.J. Swett (Wed Jul 23 2014 - 23:03:48 CDT)
  • Abhishek TYAGI (Wed Jul 23 2014 - 19:57:40 CDT)
  • Gianluca Interlandi (Wed Jul 23 2014 - 23:30:58 CDT)
  • Axel Kohlmeyer (Wed Jul 23 2014 - 22:06:21 CDT)
  • Kenno Vanommeslaeghe (Wed Jul 23 2014 - 18:20:53 CDT)
  • Abhishek TYAGI (Wed Jul 23 2014 - 00:23:36 CDT)
  • Abhishek TYAGI (Tue Jul 22 2014 - 23:04:23 CDT)
  • Axel Kohlmeyer (Wed Jul 23 2014 - 05:13:16 CDT)
  • Axel Kohlmeyer (Tue Jul 22 2014 - 23:36:30 CDT)
  • Abhishek TYAGI (Tue Jul 22 2014 - 05:40:00 CDT)
  • Axel Kohlmeyer (Tue Jul 22 2014 - 11:14:16 CDT)
  • Kenno Vanommeslaeghe (Tue Jul 22 2014 - 10:40:37 CDT)
  • Mayne, Christopher G (Tue Jul 22 2014 - 09:01:58 CDT)
  • Kenno Vanommeslaeghe (Mon Jul 21 2014 - 10:47:12 CDT)
  • Abhishek TYAGI (Sat Jul 19 2014 - 07:44:53 CDT)
  • Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:24:29 CDT)
  • Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:06:23 CDT)
  • Mayne, Christopher G (Wed Jul 16 2014 - 10:46:48 CDT)
  • Sunhwan Jo (Wed Jul 16 2014 - 07:37:19 CDT)
  • Gianluca Interlandi (Wed Jul 16 2014 - 00:32:49 CDT)
  • Gianluca Interlandi (Tue Jul 15 2014 - 22:32:35 CDT)
  • Aron Broom (Tue Jul 15 2014 - 21:58:07 CDT)
  • Abhishek TYAGI (Tue Jul 15 2014 - 11:55:35 CDT)
• Force field for sulfated tyrosines
  • Kenno Vanommeslaeghe (Mon May 05 2014 - 13:11:47 CDT)
  • Shaon Chakrabarti (Sun May 04 2014 - 21:35:38 CDT)
• force field parameter for graphene oxide
  • Kenno Vanommeslaeghe (Fri Mar 07 2014 - 11:28:50 CST)
  • Asis Jana (Fri Mar 07 2014 - 07:58:34 CST)
• Force Field Parameters for PEG
  • Axel Kohlmeyer (Mon Feb 24 2014 - 10:49:58 CST)
  • Roy Fernando (Mon Feb 24 2014 - 10:48:08 CST)
  • Aron Broom (Mon Feb 24 2014 - 10:29:42 CST)
  • Roy Fernando (Mon Feb 24 2014 - 10:22:47 CST)
• Force-field for DOPI lipid
  • Josh Vermaas (Sun May 24 2015 - 08:27:46 CDT)
  • Kevin C Chan (Sat May 23 2015 - 13:58:30 CDT)
• Format of colvars.state
  • Jérôme Hénin (Thu Aug 27 2015 - 04:27:00 CDT)
  • Hossein Mohammadiarani (Wed Aug 26 2015 - 18:05:19 CDT)
  • Jérôme Hénin (Mon Aug 24 2015 - 13:04:50 CDT)
  • Hossein Mohammadiarani (Mon Aug 24 2015 - 12:53:14 CDT)
• free energy calculation along image index in us
  • ÂÀСӨ (Wed Jun 24 2015 - 02:27:35 CDT)
• Free Energy Calculation Using Thermodynamic Integration
  • Javad Noroozi (Mon Mar 17 2014 - 02:06:08 CDT)
• free energy changes via FEP method
  • Haleh a (Thu Dec 17 2015 - 05:42:15 CST)
  • Gianluca Interlandi (Wed Dec 16 2015 - 12:49:26 CST)
  • Brian Radak (Wed Dec 16 2015 - 12:15:10 CST)
  • Haleh a (Tue Dec 15 2015 - 09:59:10 CST)
• Free Energy Perturbation
  • Jérôme Hénin (Thu Feb 27 2014 - 07:05:00 CST)
  • Javad Noroozi (Tue Feb 25 2014 - 00:36:30 CST)
• Free energy profiles in ABF tutorial
  • Giacomo Fiorin (Mon Nov 16 2015 - 07:52:31 CST)
  • Haleh a (Mon Nov 16 2015 - 06:35:30 CST)
• Free Energy Workshop, Münster, March 9-11, 2015
  • Vlad Cojocaru (Fri Jan 09 2015 - 03:19:04 CST)
• Free Energy Workshop, Münster, March 9-11Q_2015?=
  • Vlad Cojocaru (Fri Dec 19 2014 - 12:02:00 CST)
• fructose 1,6 bisphosphate forcefield parameters.
  • Dhiraj Srivastava (Wed Dec 02 2015 - 00:06:45 CST)
• full electrostatics and pairlistdist
  • Jonathan Phillips (Fri Apr 18 2014 - 05:51:02 CDT)
  • Jason Swails (Wed Apr 16 2014 - 08:27:34 CDT)
  • Jonathan Phillips (Mon Apr 14 2014 - 16:25:04 CDT)
• Fwd: [External] Boost value in aMD simulation
  • Thomas Evangelidis (Thu Aug 21 2014 - 06:05:05 CDT)
  • Thomas Evangelidis (Tue Aug 19 2014 - 05:24:17 CDT)
• Fwd: all atom equilibrium of yeast PGK simulation with NAMD
  • Qing Li (Tue Feb 03 2015 - 21:14:36 CST)
• Fwd: ANGLE PARAMETERS FOR NH3 HC NH3
  • Tristan Croll (Wed Oct 28 2015 - 20:36:08 CDT)
  • Francesco Pietra (Tue Oct 27 2015 - 13:33:59 CDT)
  • Josh Vermaas (Tue Oct 27 2015 - 11:24:47 CDT)
  • Francesco Pietra (Tue Oct 27 2015 - 11:19:48 CDT)
• Fwd: Cannot find colvar dih1 (dih colvars)
  • Francesco Pietra (Wed Dec 24 2014 - 05:53:54 CST)
  • Maxim Belkin (Tue Dec 23 2014 - 15:59:09 CST)
  • Jeff Comer (Tue Dec 23 2014 - 15:35:37 CST)
  • Francesco Pietra (Tue Dec 23 2014 - 15:01:39 CST)
  • Francesco Pietra (Tue Dec 23 2014 - 14:23:04 CST)
• Fwd: colvars with replica exchange molecular dynamics
  • Francesco Pietra (Thu Jan 30 2014 - 04:38:47 CST)
  • Francesco Pietra (Wed Jan 29 2014 - 10:40:22 CST)
• Fwd: colvars: keyword "name" is not supported, or not recognized in this context.
  • Francesco Pietra (Thu Jan 15 2015 - 10:54:47 CST)
  • Jérôme Hénin (Thu Jan 15 2015 - 10:34:22 CST)
  • Francesco Pietra (Thu Jan 15 2015 - 10:10:14 CST)
• Fwd: Constraint failure in RATTLE
  • Francesco Pietra (Sun Mar 30 2014 - 03:07:50 CDT)
• Fwd: Failure of namd2.10 in keeping trace of cell in t-remd
  • Francesco Pietra (Tue Feb 18 2014 - 12:45:35 CST)
• Fwd: Getting extra atoms by Patching!
  • Sadegh Faramarzi Ganjabad (Thu May 08 2014 - 15:49:14 CDT)
• Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech
  • JC Gumbart (Wed Sep 09 2015 - 18:15:34 CDT)
  • JC Gumbart (Wed Sep 09 2015 - 10:13:31 CDT)
• Fwd: Local minima on minimiztion with colvars
  • Francesco Pietra (Thu Jan 22 2015 - 02:55:09 CST)
  • Francesco Pietra (Wed Jan 21 2015 - 13:01:33 CST)
• Fwd: Majordomo results
  • Kuldeep Roy (Wed Jan 01 2014 - 16:33:22 CST)
  • farzad kiani (Wed Jan 01 2014 - 14:57:29 CST)
  • Faezeh Mottaghitalab (Wed Jan 01 2014 - 05:19:11 CST)
• Fwd: membrane lipid involvement of cholesterol
  • Thomas Evangelidis (Sat Jul 26 2014 - 06:39:30 CDT)
• Fwd: No steric clashes, still not minimizing
  • Francesco Pietra (Wed Mar 11 2015 - 12:28:44 CDT)
• Fwd: PCL dcd files
  • Mihaela Drenscko (Mon Sep 29 2014 - 11:38:30 CDT)
• Fwd: question about CUDA-enabled
  • maryam atabay (Mon Nov 24 2014 - 05:08:04 CST)
• Fwd: Reg: solvation in DMSO
  • Kenno Vanommeslaeghe (Wed Sep 03 2014 - 14:43:59 CDT)
  • Akshay Bhatnagar (Wed Sep 03 2014 - 02:36:04 CDT)
• Fwd: Regarding problem in generating psf file of heparin and heparan sulfate
  • siddharth kamal (Thu Jul 16 2015 - 07:44:46 CDT)
• Fwd: Regarding Temperature calculation from velocity trajectory of NAMD-2.9
  • Shailesh Pandey (Thu Jul 10 2014 - 09:31:03 CDT)
• Fwd: REMD on IBM iDataPlex DX360M3
  • Francesco Pietra (Tue Jul 08 2014 - 00:41:54 CDT)
• Fwd: TCL command "run" erratic
  • Francesco Pietra (Mon Mar 17 2014 - 02:22:26 CDT)
  • Aron Broom (Sun Mar 16 2014 - 15:58:34 CDT)
  • Francesco Pietra (Sun Mar 16 2014 - 14:57:53 CDT)
  • Francesco Pietra (Sun Mar 16 2014 - 14:48:12 CDT)
• Fwd: TIP4P and CHARMM27
  • Francesco Pietra (Thu Dec 03 2015 - 12:19:58 CST)
  • Peter Freddolino (Wed Dec 02 2015 - 12:51:43 CST)
  • Francesco Pietra (Wed Dec 02 2015 - 11:47:58 CST)
  • Francesco Pietra (Tue Dec 01 2015 - 03:22:31 CST)
  • Jim Phillips (Mon Nov 30 2015 - 16:21:44 CST)
  • Francesco Pietra (Fri Nov 27 2015 - 15:54:56 CST)
  • Peter Freddolino (Fri Nov 27 2015 - 11:37:48 CST)
  • Francesco Pietra (Fri Nov 27 2015 - 11:35:25 CST)
  • Peter Freddolino (Fri Nov 27 2015 - 10:26:05 CST)
  • Francesco Pietra (Fri Nov 27 2015 - 10:18:28 CST)
  • Peter Freddolino (Fri Nov 27 2015 - 09:41:00 CST)
  • Francesco Pietra (Fri Nov 27 2015 - 09:17:35 CST)
• GBIS CUDA not yet compatible with fixed atoms
  • Siva Dasetty (Fri Sep 05 2014 - 18:01:13 CDT)
  • Aron Broom (Fri Sep 05 2014 - 16:50:39 CDT)
  • Siva Dasetty (Fri Sep 05 2014 - 15:24:45 CDT)
  • Jim Phillips (Fri Sep 05 2014 - 15:16:04 CDT)
  • Siva Dasetty (Fri Sep 05 2014 - 10:03:12 CDT)
• GBIS in NAMD 2.10 CUDA with IMD
  • Tristan Croll (Sun Feb 15 2015 - 20:38:40 CST)
  • Jim Phillips (Sat Feb 14 2015 - 12:18:25 CST)
  • Jim Phillips (Thu Feb 12 2015 - 12:29:25 CST)
  • Tristan Croll (Wed Feb 11 2015 - 15:09:11 CST)
  • Jim Phillips (Wed Feb 11 2015 - 10:51:31 CST)
  • Tristan Croll (Wed Feb 11 2015 - 04:18:11 CST)
• GBIS using CUDA enabled NAMD
  • Siva Dasetty (Wed Sep 17 2014 - 09:36:03 CDT)
  • Jim Phillips (Wed Sep 10 2014 - 16:32:32 CDT)
  • David Hardy (Wed Sep 10 2014 - 14:46:22 CDT)
  • Siva Dasetty (Tue Sep 09 2014 - 18:59:01 CDT)
• Generalized Born Implicit solvation with implicit membrane
  • Thomas Evangelidis (Fri Mar 14 2014 - 14:22:36 CDT)
  • Fotis Baltoumas (Fri Mar 14 2014 - 08:28:45 CDT)
• Generating .psf for amorphous disaccharide
  • JC Gumbart (Sat Mar 01 2014 - 21:41:45 CST)
  • Maxwell Wesley Terban (Fri Feb 28 2014 - 13:10:56 CST)
• Generating solvent models.
  • VINAYAK BHAT (Sun Jul 05 2015 - 04:06:27 CDT)
• getting different dihedral energy with two identical backbones
  • Joyce Yang (Mon Sep 29 2014 - 21:15:54 CDT)
  • Jim Phillips (Fri Sep 26 2014 - 17:18:24 CDT)
  • Joyce Yang (Wed Sep 24 2014 - 16:45:52 CDT)
• Getting extra atoms by Patching!
  • Kenno Vanommeslaeghe (Thu May 08 2014 - 12:38:10 CDT)
  • Kenno Vanommeslaeghe (Mon May 05 2014 - 11:45:48 CDT)
  • Michelle Kuttel (Sat May 03 2014 - 01:11:50 CDT)
  • Sadegh Faramarzi Ganjabad (Fri May 02 2014 - 18:51:31 CDT)
• Getting Infinity in Calculation of Free Energy using SMD
  • Ebru Çetin (Tue Jun 23 2015 - 00:23:19 CDT)
• Getting residue mapping correpond to bead using SBCG (Shape based CG) Model in Coarse Grain Builder VMD
  • Christian Bope Domilongo (Fri Jan 09 2015 - 09:18:32 CST)
  • Jeff Comer (Fri Jan 09 2015 - 08:23:03 CST)
  • Christian Bope Domilongo (Fri Jan 09 2015 - 04:31:44 CST)
• global does not work in configuration and callback function
  • jc guo (Sat Oct 24 2015 - 08:51:33 CDT)
  • jc guo (Sat Oct 24 2015 - 01:46:21 CDT)
• GPU accelerated MD
  • Nikhil Maroli (Fri Oct 23 2015 - 04:12:24 CDT)
• GPU Multinodes problem
  • Jim Phillips (Wed Feb 18 2015 - 17:36:26 CST)
  • horacio poblete (Wed Feb 18 2015 - 15:59:07 CST)
• GPU Programming workshop @ ICTP: deadline extended for participants not requiring visa and financial support
  • Axel Kohlmeyer (Tue Mar 24 2015 - 14:17:40 CDT)
• GPU/CPU workstation optimal simulation parameters for NAMD2.9 performance
  • Pino, James Christopher (Tue Feb 18 2014 - 12:00:34 CST)
• Graphene simualtion
  • Abhishek TYAGI (Mon Oct 20 2014 - 03:28:51 CDT)
• grcarma : a graphical user interface to carma
  • Lenin Domínguez (Sun Jan 05 2014 - 18:20:50 CST)
• Grid forces visualisation
  • Jeff Comer (Wed Feb 11 2015 - 08:16:41 CST)
  • Charan Thota (Wed Feb 11 2015 - 06:13:12 CST)
• gromacs to charmm conversion
  • Francesco Pietra (Fri Oct 23 2015 - 02:34:15 CDT)
• Guideline for selecting water box size.
  • Aron Broom (Sun Feb 16 2014 - 19:12:30 CST)
  • Hyuntae Na (Sun Feb 16 2014 - 18:49:00 CST)
• H-Bond measurements
  • Stephan Grein (Thu Aug 14 2014 - 01:57:40 CDT)
• Hamiltonian Replica Exchange MD Simulation in NAMD
  • Fidan Sumbul (Tue Jan 27 2015 - 14:07:31 CST)
  • JC Gumbart (Tue Jan 27 2015 - 08:52:42 CST)
  • Fidan Sumbul (Fri Jan 23 2015 - 13:04:19 CST)
• harmonic restraints between multiple atom pairs
  • Tristan Croll (Mon Nov 03 2014 - 23:20:09 CST)
  • Neelanjana Sengupta (Mon Nov 03 2014 - 22:42:33 CST)
• Help to solve the error
  • Flora Chettiar (Thu Mar 27 2014 - 01:47:09 CDT)
  • Ivan Gregoretti (Thu Mar 27 2014 - 07:20:50 CDT)
  • Ivan Gregoretti (Wed Mar 26 2014 - 17:11:58 CDT)
  • Flora Chettiar (Wed Mar 26 2014 - 04:00:46 CDT)
• heparin
  • Lara rajam (Sat Aug 29 2015 - 18:48:08 CDT)
• Hexagonal cell instability during lipid bilayer sim in NAMD 2.9
  • Michael Bokoch (Mon Jul 07 2014 - 21:42:54 CDT)
• hey! you! why did my simulation crash?
  • Edward Lyman (Wed Mar 26 2014 - 10:42:46 CDT)
• Histidine C-H---O hydrogen bonding
  • Branko (Thu Jan 29 2015 - 12:53:52 CST)
  • Tanner, John J. (Thu Jan 29 2015 - 12:51:42 CST)
  • eprates_at_iqm.unicamp.br (Thu Jan 29 2015 - 11:39:57 CST)
  • eprates_at_iqm.unicamp.br (Thu Jan 29 2015 - 11:36:33 CST)
  • Josh Vermaas (Thu Jan 29 2015 - 09:21:27 CST)
  • eprates_at_iqm.unicamp.br (Thu Jan 29 2015 - 09:03:17 CST)
• how does NAMD calculate intramolecular electrostatic interactions between Drude pairs?
  • Ana Celia Vila Verde (Thu Nov 26 2015 - 01:13:38 CST)
  • Ana Celia Vila Verde (Mon Nov 23 2015 - 09:27:00 CST)
• How occupancy relates to force in SMD
  • daneshkaftroody_v_at_mech.sharif.ir (Mon Nov 02 2015 - 10:41:11 CST)
• How to Amend a PBD file for NAMD
  • Zeinab Emami (Wed Oct 01 2014 - 09:27:15 CDT)
• How to apply a magnetic field with NAMD
  • Faezeh Mottaghitalab (Wed Jun 25 2014 - 15:40:43 CDT)
  • Kenno Vanommeslaeghe (Wed Jun 25 2014 - 10:08:11 CDT)
  • Axel Kohlmeyer (Tue Jun 24 2014 - 19:43:42 CDT)
  • Ajasja LjubetiÄ� (Tue Jun 24 2014 - 16:52:06 CDT)
  • Faezeh Mottaghitalab (Tue Jun 24 2014 - 16:00:48 CDT)
• How to calculate the temperature for a subset of my simulation
  • Josh Vermaas (Tue Oct 20 2015 - 14:03:32 CDT)
  • Jhonatam Cordeiro Rodrigues (Tue Oct 20 2015 - 13:47:53 CDT)
  • Jhonatam Cordeiro Rodrigues (Tue Oct 20 2015 - 12:20:46 CDT)
  • Jhonatam Cordeiro Rodrigues (Mon Oct 19 2015 - 15:08:27 CDT)
• how to create two namd jobs in a single script with 2 x dual cuda gpus?
  • nam kim (Sat Aug 01 2015 - 16:36:15 CDT)
  • nam kim (Sat Aug 01 2015 - 16:33:04 CDT)
• How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory
  • zeynab mohamad hoseyni (Mon Apr 28 2014 - 23:12:57 CDT)
• how to fix the problem
  • Jeff Comer (Sat Nov 15 2014 - 08:33:54 CST)
  • Jeff Comer (Fri Nov 14 2014 - 20:02:44 CST)
  • Jeff Comer (Fri Nov 14 2014 - 20:02:09 CST)
  • Liqun Zhang (Fri Nov 14 2014 - 17:19:37 CST)
• how to get cell vectors in tcl forces script
  • Cosseddu, Salvatore (Thu Mar 13 2014 - 13:11:01 CDT)
  • Thomas Evangelidis (Thu Mar 13 2014 - 11:47:28 CDT)
  • Hongbo Du (Thu Mar 13 2014 - 11:32:32 CDT)
  • Thomas Evangelidis (Thu Mar 13 2014 - 06:11:48 CDT)
  • Thomas Evangelidis (Wed Mar 12 2014 - 09:26:46 CDT)
  • Cosseddu, Salvatore (Wed Mar 12 2014 - 09:01:35 CDT)
  • Cosseddu, Salvatore (Wed Mar 12 2014 - 07:05:43 CDT)
  • Thomas Evangelidis (Tue Mar 11 2014 - 15:14:17 CDT)
• how to get the restart files from the dcd file?
  • Azadeh Alavi (Mon Dec 21 2015 - 07:10:47 CST)
  • Azadeh Alavi (Sun Dec 20 2015 - 14:30:07 CST)
  • Jeff Comer (Sun Dec 20 2015 - 12:46:16 CST)
  • Jeff Comer (Sun Dec 20 2015 - 12:06:17 CST)
  • Azadeh Alavi (Sun Dec 20 2015 - 03:02:36 CST)
• How to let NAMD terminate automatically at a given time
  • Qing Lv (Mon Mar 02 2015 - 22:20:40 CST)
  • Norman Geist (Tue Mar 03 2015 - 02:35:36 CST)
  • hannes.loeffler_at_stfc.ac.uk (Mon Mar 02 2015 - 14:17:16 CST)
  • Jeff Comer (Mon Mar 02 2015 - 13:58:14 CST)
  • hannes.loeffler_at_stfc.ac.uk (Mon Mar 02 2015 - 13:19:08 CST)
  • Jérôme Hénin (Mon Mar 02 2015 - 11:12:40 CST)
  • Dong Luo (Mon Mar 02 2015 - 09:27:22 CST)
  • ÂÀÇç (Fri Feb 27 2015 - 20:02:18 CST)
• How to maintain Density constant?
  • Tristan Croll (Thu Mar 06 2014 - 16:30:43 CST)
  • Kenno Vanommeslaeghe (Thu Mar 06 2014 - 12:39:08 CST)
  • Morgan, Brittany (Thu Mar 06 2014 - 12:26:02 CST)
  • Roy Fernando (Thu Mar 06 2014 - 12:03:37 CST)
  • Morgan, Brittany (Thu Mar 06 2014 - 11:41:12 CST)
  • Roy Fernando (Thu Mar 06 2014 - 11:28:23 CST)
  • Kenno Vanommeslaeghe (Thu Mar 06 2014 - 10:55:28 CST)
  • Ivan Gregoretti (Thu Mar 06 2014 - 10:34:43 CST)
  • Kenno Vanommeslaeghe (Thu Mar 06 2014 - 09:57:24 CST)
  • Ivan Gregoretti (Thu Mar 06 2014 - 07:23:29 CST)
  • Kenno Vanommeslaeghe (Wed Mar 05 2014 - 16:51:30 CST)
  • Roy Fernando (Wed Mar 05 2014 - 15:43:59 CST)
• How to output CCC per residue from MDFF
  • Ryan McGreevy (Thu Apr 23 2015 - 22:15:49 CDT)
  • Michael Yuchi (Thu Apr 23 2015 - 21:48:11 CDT)
• How to parametrize new atom types in Namd
  • Dian Jiao (Fri Jan 17 2014 - 15:44:50 CST)
• how to quantify and visualize the flow of water into a protein
  • Mo Chen (Tue Jul 08 2014 - 19:43:35 CDT)
  • Joshua Adelman (Tue Jul 08 2014 - 19:36:02 CDT)
  • Maxim Belkin (Tue Jul 08 2014 - 19:20:12 CDT)
  • Thomas Evangelidis (Tue Jul 08 2014 - 19:12:40 CDT)
  • Thomas Evangelidis (Tue Jul 08 2014 - 19:04:01 CDT)
  • Maxim Belkin (Tue Jul 08 2014 - 18:40:15 CDT)
  • Thomas Evangelidis (Tue Jul 08 2014 - 18:20:48 CDT)
• How to refer to side-chain via tcl-force scripting?
  • Tristan Croll (Fri Jun 13 2014 - 02:08:51 CDT)
  • zeynab mohamad hoseyni (Fri Jun 13 2014 - 00:53:12 CDT)
• How to save a structure after minimizing for 1000 steps?
  • Chitrak Gupta (Thu Apr 23 2015 - 16:35:58 CDT)
  • Aron Broom (Thu Apr 23 2015 - 16:28:47 CDT)
  • Arijit Ghosh (Thu Apr 23 2015 - 16:15:40 CDT)
• How to setup a system with two pulling directions
  • John Xi (Thu Apr 17 2014 - 19:48:39 CDT)
  • Felipe Merino (Thu Apr 17 2014 - 10:38:06 CDT)
  • John Xi (Wed Apr 16 2014 - 19:32:27 CDT)
• How to solvate a protein using C36 and not C27
  • zeynab mohamad hoseyni (Sat Jan 25 2014 - 11:08:14 CST)
  • zeynab mohamad hoseyni (Sat Jan 25 2014 - 10:48:31 CST)
• How to stop omega trans-cis switching
  • Kenno Vanommeslaeghe (Mon Mar 03 2014 - 13:01:10 CST)
  • Alex Utev (CMP) (Mon Mar 03 2014 - 12:11:25 CST)
  • Alex Utev (CMP) (Mon Mar 03 2014 - 12:10:08 CST)
• Hwo to switch from NPT to NVT
  • Zeinab Emami (Fri Aug 15 2014 - 07:14:05 CDT)
  • Zeinab Emami (Fri Aug 15 2014 - 07:12:39 CDT)
• Hybrid coarse-grained/all-atom simulation
  • Mahya Hemmat (Mon Sep 28 2015 - 14:25:24 CDT)
• Hybrid MPI + Multicore + Cuda build
  • Maxime Boissonneault (Wed Aug 13 2014 - 11:46:59 CDT)
• Hydration of protein-lipid interface
  • zeynab mohamad hoseyni (Mon Feb 03 2014 - 10:27:20 CST)
• I can not run fixed protein in membrane with NAMD
  • Chitrak Gupta (Mon Jun 29 2015 - 14:41:11 CDT)
  • R.L. Ma (Sat Jun 27 2015 - 21:27:18 CDT)
• I would like to unsubscribe
  • Ajasja LjubetiÄ� (Wed Sep 10 2014 - 10:03:21 CDT)
  • Giacomo Fiorin (Wed Sep 10 2014 - 09:21:11 CDT)
  • MEHRAN MB (Wed Sep 10 2014 - 09:19:54 CDT)
  • Maria Kopp (Wed Sep 10 2014 - 09:04:54 CDT)
• ibverb&&smp build NAMD
  • ukulililixl (Fri Aug 29 2014 - 06:41:21 CDT)
  • ukulililixl (Thu Aug 28 2014 - 04:30:47 CDT)
• iDataPlex
  • Francesco Pietra (Tue Mar 18 2014 - 04:03:29 CDT)
  • Andrew Emerson (Tue Mar 18 2014 - 03:15:30 CDT)
  • Francesco Pietra (Mon Mar 17 2014 - 13:12:32 CDT)
• Immediate PhD Opening Computational Structural Biology Of Membrane Proteins
  • Marawan Hussien (Thu Apr 09 2015 - 19:18:53 CDT)
• Immediate Postdoctoral Position Opening
  • Marawan Hussien (Thu Apr 09 2015 - 18:10:32 CDT)
  • Marawan Hussien (Sun Mar 22 2015 - 16:08:16 CDT)
• Implementing the Virtual Bond Algorithm Using Colvars
  • Giacomo Fiorin (Thu Dec 18 2014 - 19:37:06 CST)
  • David Huggins (Wed Dec 17 2014 - 06:25:33 CST)
• Implicit solvent lipid bilayer simulation in NAMD.
  • Kenno Vanommeslaeghe (Thu Sep 18 2014 - 15:39:49 CDT)
  • Subbarao Kanchi (Wed Sep 17 2014 - 14:27:10 CDT)
  • Aron Broom (Wed Sep 17 2014 - 13:54:57 CDT)
  • Jason Swails (Wed Sep 17 2014 - 13:47:53 CDT)
  • Subbarao Kanchi (Wed Sep 17 2014 - 13:41:34 CDT)
  • Siva Dasetty (Wed Sep 17 2014 - 13:23:53 CDT)
  • Subbarao Kanchi (Wed Sep 17 2014 - 12:04:44 CDT)
• IMPROPER PARAMETERS FOR CA CA CA CA
  • Axel Kohlmeyer (Mon May 26 2014 - 16:47:44 CDT)
  • Kenno Vanommeslaeghe (Mon May 26 2014 - 16:42:29 CDT)
  • Z (Sat May 24 2014 - 10:50:49 CDT)
• Improve scaling for large amount of fixed atoms
  • Tristan Croll (Wed Mar 19 2014 - 21:15:40 CDT)
  • Norman Geist (Wed Mar 19 2014 - 03:19:38 CDT)
• Improving MDFF results
  • Kevin Chun Chan (Tue Oct 21 2014 - 10:56:00 CDT)
  • Tristan Croll (Tue Oct 21 2014 - 14:22:31 CDT)
  • Tristan Croll (Tue Oct 21 2014 - 00:36:21 CDT)
  • Kevin C Chan (Mon Oct 20 2014 - 22:15:59 CDT)
• improving tclforce efficiency, getting "Signal: segmentation violation" error
  • zeynab mohamad hoseyni (Sun Jun 15 2014 - 20:18:11 CDT)
• Including two parameters for protein-ligand simulation
  • Payal Chatterjee (Wed Oct 28 2015 - 03:08:16 CDT)
  • Abhishek TYAGI (Wed Oct 28 2015 - 01:59:21 CDT)
  • Nikhil Maroli (Wed Oct 28 2015 - 01:52:30 CDT)
• inconsistency in ABF results for helix unfolding
  • JC Gumbart (Wed Jan 28 2015 - 15:40:30 CST)
  • Giacomo Fiorin (Wed Jan 28 2015 - 14:52:54 CST)
  • MEHRAN MB (Wed Jan 28 2015 - 14:50:14 CST)
  • Ajasja LjubetiÄ� (Wed Jan 28 2015 - 04:05:37 CST)
  • gmail (Wed Jan 28 2015 - 03:49:54 CST)
  • MEHRAN MB (Tue Jan 27 2015 - 17:09:19 CST)
• INCONSISTENCY messages and minimization in toturial 1-2-sphere
  • Yan Zhou (Wed Sep 03 2014 - 03:14:30 CDT)
• Incorrect atom count in binary file
  • Mihaela Drenscko (Wed Feb 18 2015 - 07:34:15 CST)
  • Norman Geist (Wed Feb 18 2015 - 03:13:52 CST)
  • Mihaela Drenscko (Tue Feb 17 2015 - 18:59:43 CST)
• Info: Pairlistdist is too small for 3 computes during timestep 115001
  • Subbarao Kanchi (Fri Dec 12 2014 - 16:26:26 CST)
  • Jim Phillips (Fri Dec 12 2014 - 15:49:06 CST)
  • Santosh Kumar Chaudhary (Fri Dec 12 2014 - 10:34:41 CST)
• information about simulation speed
  • Jeff Comer (Tue Dec 02 2014 - 18:09:54 CST)
  • Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:45:32 CST)
  • Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:35:14 CST)
  • Josh Vermaas (Tue Dec 02 2014 - 17:08:55 CST)
  • Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:22:28 CST)
  • Axel Kohlmeyer (Tue Dec 02 2014 - 17:07:15 CST)
  • Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:04:31 CST)
  • Axel Kohlmeyer (Tue Dec 02 2014 - 16:53:44 CST)
  • Kshatresh Dutta Dubey (Tue Dec 02 2014 - 16:50:11 CST)
• Inquiry about forceConstant
  • Jérôme Hénin (Tue Jul 22 2014 - 04:37:30 CDT)
  • Mo Chen (Mon Jul 21 2014 - 16:57:15 CDT)
  • Mo Chen (Mon Jul 21 2014 - 15:23:06 CDT)
  • Aron Broom (Mon Jul 21 2014 - 15:12:06 CDT)
  • Mo Chen (Mon Jul 21 2014 - 15:03:30 CDT)
• Inquiry about lipid membrane simulation
  • JC Gumbart (Wed Jun 18 2014 - 19:48:17 CDT)
  • Wonpil Im (Wed Jun 18 2014 - 14:53:31 CDT)
  • Sunhwan Jo (Wed Jun 18 2014 - 14:46:56 CDT)
  • Mo Chen (Wed Jun 18 2014 - 14:25:16 CDT)
  • Kenno Vanommeslaeghe (Wed Jun 18 2014 - 14:02:52 CDT)
  • Kenno Vanommeslaeghe (Wed Jun 18 2014 - 10:20:24 CDT)
  • Mo Chen (Tue Jun 17 2014 - 20:57:59 CDT)
• Inspiration for most efficient implementation of coarse grained forcefield.
  • Jim Phillips (Tue Dec 16 2014 - 09:30:40 CST)
  • Jérôme Hénin (Mon Dec 15 2014 - 15:41:22 CST)
  • Ajasja LjubetiÄ� (Mon Dec 15 2014 - 12:08:03 CST)
• Instability in harmonic restraints when equilibrating large systems
  • Tristan Croll (Fri Jul 24 2015 - 16:52:05 CDT)
• Instability in thermodynamic integration
  • Maryam Sayadi (Sun Feb 16 2014 - 14:04:12 CST)
• Installation Protocol of NAMD on Linux Cluster
  • Viswanath Pasumarthi (Thu Aug 21 2014 - 14:46:27 CDT)
• Interactive molecular dynamics question
  • Axel Kohlmeyer (Sun Feb 09 2014 - 17:13:15 CST)
  • Chris Harrison (Sun Feb 09 2014 - 17:00:27 CST)
  • Mare Libero (Sun Feb 09 2014 - 15:05:51 CST)
• Intermolecular potential energy function in NAMD
  • Kenno Vanommeslaeghe (Fri Aug 01 2014 - 11:41:46 CDT)
  • Viswanath Pasumarthi (Fri Aug 01 2014 - 06:31:21 CDT)
• Interrupted Molecular Dynamics Simulation
  • Daniela Rivas (Wed Jul 29 2015 - 10:25:29 CDT)
  • Axel Kohlmeyer (Tue Jul 28 2015 - 10:53:28 CDT)
  • Felipe Merino (Tue Jul 28 2015 - 10:34:17 CDT)
  • Purushottam Dixit (Tue Jul 28 2015 - 09:51:22 CDT)
  • Daniela Rivas (Tue Jul 28 2015 - 09:45:07 CDT)
  • Chitrak Gupta (Tue Jul 28 2015 - 09:34:21 CDT)
  • Felipe Merino (Tue Jul 28 2015 - 02:03:00 CDT)
  • Daniela Rivas (Mon Jul 27 2015 - 19:21:00 CDT)
  • Chitrak Gupta (Mon Jul 27 2015 - 12:29:25 CDT)
  • Daniela Rivas (Mon Jul 27 2015 - 10:32:29 CDT)
• Invalid command error
  • Axel Kohlmeyer (Mon Jun 30 2014 - 07:44:41 CDT)
  • Adam Kells (Mon Jun 30 2014 - 06:49:07 CDT)
• Invitation to Submit Review Article Current Protein & Peptide Science (IF: 2.326)
  • Prija Ponnan (Fri Jun 27 2014 - 06:40:43 CDT)
• Ion Au+3 simulation
  • Kenno Vanommeslaeghe (Thu Jun 05 2014 - 17:27:37 CDT)
  • Aron Broom (Wed Jun 04 2014 - 16:00:23 CDT)
  • Kenno Vanommeslaeghe (Wed Jun 04 2014 - 10:32:46 CDT)
  • Daniel Torrente (Tue Jun 03 2014 - 16:17:38 CDT)
  • Aron Broom (Tue Jun 03 2014 - 16:21:52 CDT)
  • Axel Kohlmeyer (Tue Jun 03 2014 - 15:49:35 CDT)
  • Daniel Torrente (Tue Jun 03 2014 - 15:17:15 CDT)
  • Axel Kohlmeyer (Tue Jun 03 2014 - 14:38:35 CDT)
  • Daniel Torrente (Tue Jun 03 2014 - 13:31:40 CDT)
• Is it possible to rename atoms with psfgen?
  • Brian Radak (Fri Jan 30 2015 - 10:35:43 CST)
  • Jim Phillips (Thu Jan 29 2015 - 13:11:46 CST)
  • Brian Radak (Wed Jan 28 2015 - 09:54:16 CST)
• Is it so different when setting reinitvels or not?
  • Zhao Lina (Wed Dec 17 2014 - 19:31:49 CST)
  • Jeff Comer (Wed Dec 17 2014 - 05:45:09 CST)
  • Zhao Lina (Wed Dec 17 2014 - 00:03:25 CST)
• is the aMD implementation compatible with AMBER force fields
  • Thomas Evangelidis (Wed Jun 18 2014 - 18:20:00 CDT)
  • Jeff Wereszczynski (Wed Jun 18 2014 - 13:14:11 CDT)
  • Thomas Evangelidis (Wed Jun 18 2014 - 06:20:06 CDT)
• is there a method equivalent to conformational flooding in NAMD 2.10
  • Jérôme Hénin (Mon Jan 12 2015 - 04:44:58 CST)
  • Thomas Evangelidis (Mon Jan 12 2015 - 04:32:17 CST)
  • Thomas Evangelidis (Sun Jan 11 2015 - 07:43:36 CST)
• Is there any point in running NAMD over an ethernet-linked cluster?
  • Norman Geist (Thu Apr 16 2015 - 10:39:38 CDT)
  • Douglas Houston (Thu Apr 16 2015 - 05:10:12 CDT)
  • Nicholas M Glykos (Mon Sep 22 2014 - 03:40:59 CDT)
  • Axel Kohlmeyer (Mon Sep 22 2014 - 01:22:11 CDT)
  • Douglas Houston (Mon Sep 22 2014 - 00:23:41 CDT)
  • Nicholas M Glykos (Sun Sep 21 2014 - 13:21:53 CDT)
  • Douglas Houston (Sat Sep 20 2014 - 06:18:25 CDT)
• Ispopetide bond
  • Milica UtjeÅ¡anović (Fri Oct 02 2015 - 14:30:04 CDT)
• jeremy adler
  • jeremy adler (Thu Oct 23 2014 - 06:21:43 CDT)
• Job script for multi node job
  • Phil Greer (Fri Feb 14 2014 - 09:04:37 CST)
  • Subbarao Kanchi (Fri Feb 14 2014 - 08:24:13 CST)
  • Subbarao Kanchi (Fri Feb 14 2014 - 05:22:55 CST)
  • Subbarao Kanchi (Fri Feb 14 2014 - 04:20:16 CST)
• Kb, Ktheta values for TIP3P water model
  • Viswanath Pasumarthi (Wed Aug 13 2014 - 02:27:24 CDT)
  • Maxim Belkin (Tue Aug 12 2014 - 23:11:43 CDT)
  • Axel Kohlmeyer (Tue Aug 12 2014 - 14:26:05 CDT)
  • Viswanath Pasumarthi (Tue Aug 12 2014 - 14:11:40 CDT)
  • Kenno Vanommeslaeghe (Tue Aug 12 2014 - 13:31:04 CDT)
  • Axel Kohlmeyer (Tue Aug 12 2014 - 12:27:25 CDT)
  • Viswanath Pasumarthi (Tue Aug 12 2014 - 12:19:00 CDT)
  • Maxim Belkin (Mon Aug 11 2014 - 18:05:41 CDT)
  • Kenno Vanommeslaeghe (Mon Aug 11 2014 - 14:08:41 CDT)
  • Viswanath Pasumarthi (Mon Aug 11 2014 - 12:56:00 CDT)
  • Axel Kohlmeyer (Mon Aug 11 2014 - 06:40:43 CDT)
  • Kenno Vanommeslaeghe (Sun Aug 10 2014 - 23:16:19 CDT)
  • Hadi (Sun Aug 10 2014 - 22:29:55 CDT)
  • Kenno Vanommeslaeghe (Sun Aug 10 2014 - 22:10:43 CDT)
  • Hadi (Sun Aug 10 2014 - 20:59:58 CDT)
  • Kenno Vanommeslaeghe (Sun Aug 10 2014 - 17:49:01 CDT)
  • Hadi (Thu Aug 07 2014 - 17:15:09 CDT)
  • Kenno Vanommeslaeghe (Thu Aug 07 2014 - 15:08:39 CDT)
  • Hadi (Thu Aug 07 2014 - 12:36:33 CDT)
  • Kenno Vanommeslaeghe (Thu Aug 07 2014 - 10:50:24 CDT)
  • Hadi (Wed Aug 06 2014 - 17:39:50 CDT)
  • Kenno Vanommeslaeghe (Wed Aug 06 2014 - 17:28:12 CDT)
  • Hadi (Wed Aug 06 2014 - 16:07:27 CDT)
  • Axel Kohlmeyer (Wed Aug 06 2014 - 15:48:57 CDT)
  • Hadi (Wed Aug 06 2014 - 15:40:22 CDT)
  • Axel Kohlmeyer (Wed Aug 06 2014 - 15:28:23 CDT)
  • Hadi (Wed Aug 06 2014 - 14:41:58 CDT)
  • Axel Kohlmeyer (Wed Aug 06 2014 - 14:11:01 CDT)
  • Hadi (Wed Aug 06 2014 - 13:57:26 CDT)
  • Kenno Vanommeslaeghe (Tue Aug 05 2014 - 15:00:49 CDT)
  • Axel Kohlmeyer (Tue Aug 05 2014 - 14:59:14 CDT)
  • Hadi (Tue Aug 05 2014 - 14:49:48 CDT)
  • Kenno Vanommeslaeghe (Tue Aug 05 2014 - 14:29:22 CDT)
  • Axel Kohlmeyer (Tue Aug 05 2014 - 14:28:04 CDT)
  • Hadi (Tue Aug 05 2014 - 14:10:14 CDT)
  • Kenno Vanommeslaeghe (Tue Aug 05 2014 - 13:41:12 CDT)
  • Hadi Dinpajooh (Tue Aug 05 2014 - 11:52:44 CDT)
  • Kenno Vanommeslaeghe (Tue Aug 05 2014 - 09:54:35 CDT)
  • Hadi (Tue Aug 05 2014 - 02:14:00 CDT)
  • Kenno Vanommeslaeghe (Thu Jul 31 2014 - 17:28:09 CDT)
  • JC Gumbart (Thu Jul 31 2014 - 16:24:06 CDT)
  • Axel Kohlmeyer (Thu Jul 31 2014 - 14:14:43 CDT)
  • Kenno Vanommeslaeghe (Thu Jul 31 2014 - 14:03:00 CDT)
  • JC Gumbart (Wed Jul 30 2014 - 10:27:16 CDT)
  • Kenno Vanommeslaeghe (Tue Jul 29 2014 - 23:21:58 CDT)
  • Hadi (Tue Jul 29 2014 - 17:59:19 CDT)
  • Viswanath Pasumarthi (Tue Jul 29 2014 - 16:38:28 CDT)
• keeping Crystal angles constant
  • Mohan maruthi sena (Wed Jan 15 2014 - 12:03:58 CST)
• keyword "outputaccumulatedwork" is not supported, or not recognized in this context.
  • Sridhar Kumar Kannam (Thu Oct 15 2015 - 02:24:52 CDT)
  • Jérôme Hénin (Thu Oct 15 2015 - 01:43:25 CDT)
  • Sridhar Kumar Kannam (Thu Oct 15 2015 - 00:54:00 CDT)
  • Giacomo Fiorin (Wed Oct 14 2015 - 06:33:28 CDT)
  • Sridhar Kumar Kannam (Wed Oct 14 2015 - 05:41:58 CDT)
  • Jérôme Hénin (Wed Oct 14 2015 - 05:14:41 CDT)
  • Marlon Sidore (Wed Oct 14 2015 - 05:12:16 CDT)
  • Jérôme Hénin (Wed Oct 14 2015 - 05:05:54 CDT)
  • Sridhar Kumar Kannam (Tue Oct 13 2015 - 23:39:14 CDT)
• Lambda-exchange multiple-copy alchemical free energy calculations
  • 岡部篤俊 (Tue Aug 18 2015 - 09:54:40 CDT)
• LangevinDamping Coefficient for MARTINI
  • Mahdi Tavakol (Wed Dec 23 2015 - 05:33:48 CST)
• LangevinPistonPeriod (Simulation Near Critical Point)
  • JAVAD NOROOZI (Tue Feb 10 2015 - 03:15:23 CST)
• LAST CALL: Free Energy Workshop, Münster, March 9-11, 2015
  • Vlad Cojocaru (Tue Feb 03 2015 - 14:34:42 CST)
• LCPO parameters P1-P4
  • yandong Huang (Sat Jan 31 2015 - 13:24:55 CST)
  • yandong Huang (Mon Jan 26 2015 - 12:30:21 CST)
• Lennard-Jones and Electrostatic Forces and Energies
  • Brian Radak (Tue Oct 27 2015 - 08:50:27 CDT)
  • Kostas Malavazos (Mon Oct 26 2015 - 13:54:28 CDT)
• Liquid Simulation Failure
  • Roy Fernando (Fri Jan 24 2014 - 18:54:44 CST)
• LJ Parameters on hydrogen for TIP4P water models
  • Shayon Bhattacharya (Wed Sep 30 2015 - 16:39:45 CDT)
  • Peter Freddolino (Wed Sep 30 2015 - 08:14:45 CDT)
  • Brian Radak (Tue Sep 29 2015 - 14:52:44 CDT)
  • Shayon Bhattacharya (Tue Sep 29 2015 - 14:04:44 CDT)
  • Peter Freddolino (Tue Sep 29 2015 - 13:25:07 CDT)
  • Shayon Bhattacharya (Tue Sep 29 2015 - 10:20:36 CDT)
• LJcorrection + switching?
  • Peter Freddolino (Tue Sep 15 2015 - 20:11:32 CDT)
  • Brian Radak (Tue Sep 01 2015 - 09:31:34 CDT)
• LJcorrection and alchemy?
  • Brian Radak (Fri Jan 30 2015 - 14:15:01 CST)
  • Brian Radak (Fri Jan 30 2015 - 12:10:53 CST)
• Loading and analysis of DCD file (~300 MB)
  • tillmann.utesch_at_mailbox.tu-berlin.de (Thu Jul 24 2014 - 07:00:09 CDT)
  • Ajasja LjubetiÄ� (Thu Jul 24 2014 - 09:30:12 CDT)
  • Stephan Grein (Thu Jul 24 2014 - 07:02:53 CDT)
  • Stephan Grein (Thu Jul 24 2014 - 06:45:54 CDT)
  • Stephan Grein (Thu Jul 24 2014 - 06:18:45 CDT)
• Loading Velocity DCD file
  • JAVAD NOROOZI (Wed Dec 17 2014 - 13:23:20 CST)
• Local minima on minimiztion with colvars
  • Francesco Pietra (Wed Jan 21 2015 - 12:45:14 CST)
• Log file is not being updated
  • BATUHAN KAV (Thu Feb 13 2014 - 11:05:13 CST)
  • BATUHAN KAV (Mon Feb 10 2014 - 06:44:08 CST)
  • BATUHAN KAV (Mon Feb 10 2014 - 06:01:41 CST)
  • Ajasja LjubetiÄ� (Mon Feb 10 2014 - 05:53:39 CST)
  • BATUHAN KAV (Mon Feb 10 2014 - 05:41:07 CST)
• Lone Pair on H2S
  • JAVAD NOROOZI (Tue Dec 30 2014 - 06:05:39 CST)
  • JAVAD NOROOZI (Tue Dec 30 2014 - 06:05:40 CST)
  • JAVAD NOROOZI (Sat Dec 27 2014 - 09:42:25 CST)
• long running sim dies
  • ransun (Mon Oct 13 2014 - 09:12:33 CDT)
  • Tristan Croll (Mon Oct 13 2014 - 14:36:37 CDT)
  • Thomas C. Bishop (Mon Oct 13 2014 - 08:29:43 CDT)
• Looking for benchmarks on k80's
  • rswett_at_chem.wayne.edu (Thu Aug 13 2015 - 10:40:45 CDT)
• Loss of Translational entropy calculation in FEP
  • Daniel Torrente (Wed Jul 30 2014 - 16:57:08 CDT)
• mail reg DCD error
  • Vidhya Sankar (Sun May 03 2015 - 09:44:50 CDT)
• Mail reg Parameter file
  • Fotis Baltoumas (Mon Apr 20 2015 - 08:48:36 CDT)
  • Vidhya Sankar (Mon Apr 20 2015 - 07:57:34 CDT)
• mail reg parameters
  • sena (Fri Dec 25 2015 - 22:29:17 CST)
  • Vidhya Sankar (Fri Dec 25 2015 - 20:51:57 CST)
• making dipeptides with psfgen - CMAP terms?
  • Brian Radak (Tue Feb 17 2015 - 16:10:49 CST)
  • Jim Phillips (Tue Feb 17 2015 - 13:53:04 CST)
  • Brian Radak (Tue Feb 17 2015 - 12:06:54 CST)
  • Brian Radak (Tue Feb 17 2015 - 09:42:59 CST)
• Martini forcefield RBCG and ENM
  • Raul Araya (Fri Aug 15 2014 - 10:05:01 CDT)
• Maximum limit for "run" parameter
  • Jim Phillips (Wed Feb 18 2015 - 17:49:41 CST)
  • Axel Kohlmeyer (Wed Feb 18 2015 - 17:15:30 CST)
  • Jim Phillips (Wed Feb 18 2015 - 17:10:36 CST)
  • Mitul Saha (Tue Feb 17 2015 - 18:50:38 CST)
• MD Simulation of accelerated MD using GPU
  • jeevan gc (Fri Oct 16 2015 - 08:25:29 CDT)
  • jeevan gc (Wed Oct 14 2015 - 16:21:36 CDT)
  • Kenneth Huang (Mon Oct 12 2015 - 20:09:26 CDT)
  • Brian Radak (Mon Oct 12 2015 - 20:01:24 CDT)
  • jeevan gc (Mon Oct 12 2015 - 17:19:15 CDT)
  • jeevan gc (Mon Oct 12 2015 - 17:07:39 CDT)
• MD simulation of Linear Molecules (like 2-butyne£©
  • ԬС¾§ (Mon Dec 21 2015 - 20:30:09 CST)
  • Jim Phillips (Sat Dec 19 2015 - 21:53:01 CST)
  • ԬС¾§ (Fri Dec 18 2015 - 20:26:26 CST)
• MD simulation Patch grid errors
  • Thomas Evangelidis (Tue Jan 14 2014 - 02:19:55 CST)
  • Jeffrey Potoff (Mon Jan 13 2014 - 22:34:42 CST)
  • Jiann George Pazhamalil (Mon Jan 13 2014 - 21:37:41 CST)
  • Jeffrey Potoff (Tue Jan 07 2014 - 18:03:29 CST)
  • Thomas Evangelidis (Tue Jan 07 2014 - 17:56:32 CST)
  • Jiann George Pazhamalil (Tue Jan 07 2014 - 17:33:06 CST)
• Mechanical Properties of protein
  • Maxim Belkin (Thu Oct 30 2014 - 20:27:58 CDT)
  • chin chun (Thu Oct 30 2014 - 19:18:11 CDT)
• medwater config
  • Hassan Kianinejad (Fri Apr 04 2014 - 19:15:32 CDT)
• Membrane and NPAT
  • hannes.loeffler_at_stfc.ac.uk (Mon Feb 17 2014 - 10:53:49 CST)
  • Kenno Vanommeslaeghe (Mon Feb 17 2014 - 10:43:03 CST)
  • José Villalaín (Mon Feb 17 2014 - 04:49:08 CST)
• membrane lipid involvement of cholesterol
  • Ramin Ekhteiari (Sat Jul 26 2014 - 03:14:38 CDT)
• memory problem
  • Adam Moser (Fri Jun 20 2014 - 15:01:30 CDT)
• Merging the two files......
  • Aron Broom (Tue Jun 17 2014 - 10:58:22 CDT)
  • Aron Broom (Tue Jun 17 2014 - 10:44:36 CDT)
  • Gurpreet Kaur Dhindsa (Tue Jun 17 2014 - 10:00:09 CDT)
• Message about timing in *log file.
  • Jim Phillips (Mon Feb 02 2015 - 00:15:09 CST)
  • Dawid das (Sun Feb 01 2015 - 05:05:39 CST)
• Metadynamics test along eigenvector
  • Giacomo Fiorin (Tue Aug 26 2014 - 10:07:34 CDT)
  • Floquet Nicolas (Tue Aug 26 2014 - 02:58:00 CDT)
• Metadynamics with eigenvector
  • Giacomo Fiorin (Mon Aug 25 2014 - 10:17:22 CDT)
  • Nicolas Floquet (Mon Aug 25 2014 - 09:40:06 CDT)
• Metadynamics: writeHillsTrajectory
  • Chola Regmi (Thu Jul 30 2015 - 16:48:15 CDT)
  • Chola Regmi (Thu Jul 30 2015 - 16:37:53 CDT)
• Minimisation goes to several values
  • Kevin C Chan (Thu Jun 25 2015 - 11:32:10 CDT)
• Minimisation not converged
  • Jérôme Hénin (Thu Apr 02 2015 - 06:52:36 CDT)
  • Kevin C Chan (Wed Apr 01 2015 - 22:26:19 CDT)
  • Jérôme Hénin (Wed Apr 01 2015 - 02:14:12 CDT)
  • Kevin C Chan (Wed Apr 01 2015 - 01:20:37 CDT)
• Minimization without MD
  • Ajasja LjubetiÄ� (Thu Jul 16 2015 - 17:18:20 CDT)
  • Simon Kit Sang Chu (Thu Jul 16 2015 - 15:37:39 CDT)
  • Simon Kit Sang Chu (Thu Jul 16 2015 - 16:21:40 CDT)
• Misleading failure of VMD with charge/CGenFF from waterbox
  • Francesco Pietra (Sun Nov 23 2014 - 03:21:38 CST)
• MMPBSA Energy Calculations using VMD (Post-Processing)
  • James Starlight (Mon Apr 21 2014 - 14:27:38 CDT)
  • Jason Swails (Mon Apr 14 2014 - 13:02:08 CDT)
  • Kenno Vanommeslaeghe (Mon Apr 14 2014 - 12:24:33 CDT)
  • Jason Swails (Mon Apr 14 2014 - 07:31:05 CDT)
  • Jason Swails (Mon Apr 14 2014 - 07:26:59 CDT)
  • James Starlight (Mon Apr 14 2014 - 04:23:01 CDT)
  • James Starlight (Mon Apr 14 2014 - 00:56:50 CDT)
  • Jason Swails (Sat Apr 12 2014 - 06:53:32 CDT)
  • Vlad Cojocaru (Sat Apr 12 2014 - 03:46:19 CDT)
  • James Starlight (Sat Apr 12 2014 - 01:53:35 CDT)
  • Fotis Baltoumas (Thu Apr 10 2014 - 10:09:00 CDT)
  • Aditya Ranganathan (Thu Apr 10 2014 - 08:25:41 CDT)
• model.conf
  • Mai Aamer (Thu Jul 09 2015 - 17:09:01 CDT)
• modify input file for production phase MD
  • Branko (Fri Dec 04 2015 - 11:50:53 CST)
  • Deng, Jinxia (Nancy) (Fri Dec 04 2015 - 11:31:26 CST)
• Molecular Dynamics of Rigid Linear Molecules in NAMD.
  • Kenno Vanommeslaeghe (Sun Sep 28 2014 - 14:00:43 CDT)
  • Axel Kohlmeyer (Sun Sep 28 2014 - 13:31:59 CDT)
  • Kenno Vanommeslaeghe (Sun Sep 28 2014 - 13:06:06 CDT)
  • Aron Broom (Sun Sep 28 2014 - 10:25:13 CDT)
  • Mike Makowski (Sun Sep 28 2014 - 06:50:36 CDT)
  • Mike Makowski (Sun Sep 28 2014 - 03:03:10 CDT)
  • Javad Noroozi (Sun Sep 28 2014 - 00:44:28 CDT)
• Monitoring progress of an ongoing molecular dynamics simulation
  • Bennion, Brian (Fri Mar 07 2014 - 11:44:01 CST)
  • Ivan Gregoretti (Fri Mar 07 2014 - 10:57:31 CST)
  • Cosseddu, Salvatore (Fri Mar 07 2014 - 10:57:59 CST)
  • Axel Kohlmeyer (Fri Mar 07 2014 - 10:49:34 CST)
  • Cosseddu, Salvatore (Fri Mar 07 2014 - 10:43:29 CST)
  • Ivan Gregoretti (Fri Mar 07 2014 - 09:08:44 CST)
  • Douglas Houston (Fri Mar 07 2014 - 08:55:47 CST)
  • Ivan Gregoretti (Fri Mar 07 2014 - 08:52:43 CST)
  • Cosseddu, Salvatore (Fri Mar 07 2014 - 08:21:35 CST)
  • Ivan Gregoretti (Fri Mar 07 2014 - 08:08:11 CST)
• Movie of a channel trajectory
  • Javier Cáceres Delpiano (Sat Apr 05 2014 - 22:26:21 CDT)
• moving out of the box
  • Aaron Larsen (Thu Feb 13 2014 - 14:39:04 CST)
  • Ajasja LjubetiÄ� (Thu Feb 13 2014 - 10:08:36 CST)
  • Ariel Talavera Perez (Thu Feb 13 2014 - 09:57:16 CST)
• MPICH 3 with Namd2/Charm
  • Daniel Strahs (Mon Oct 13 2014 - 18:04:45 CDT)
• multicore vs ibverbs
  • Gianluca Interlandi (Sat Jul 04 2015 - 12:52:40 CDT)
• Multicore-CUDA NAMD output hangs
  • Mitchell Gleed (Tue Mar 03 2015 - 10:34:20 CST)
  • Mitchell Gleed (Wed Feb 18 2015 - 15:12:21 CST)
• Multiple Dihedral in CHARMM parameters
  • Jérôme Hénin (Mon Jan 19 2015 - 04:57:07 CST)
  • JAVAD NOROOZI (Mon Jan 19 2015 - 01:19:37 CST)
• Multiple dihedral with multiplicity of 7 greater than max of 6
  • Kenno Vanommeslaeghe (Wed Apr 02 2014 - 14:05:49 CDT)
  • Axel Kohlmeyer (Wed Apr 02 2014 - 13:52:18 CDT)
  • Rawan Al Nsour (Wed Apr 02 2014 - 13:44:33 CDT)
  • Rawan Al Nsour (Wed Apr 02 2014 - 13:38:53 CDT)
• multiple harmonic constrains
  • Jeff Comer (Sat Nov 08 2014 - 14:54:50 CST)
  • Azadeh Alavi (Sat Nov 08 2014 - 01:36:16 CST)
• Multiple input and output files
  • Jim Phillips (Thu Nov 06 2014 - 12:50:36 CST)
  • Josh Vermaas (Wed Nov 05 2014 - 20:54:02 CST)
  • Axel Kohlmeyer (Wed Nov 05 2014 - 21:51:44 CST)
  • Debashis Kundu (Wed Nov 05 2014 - 20:20:37 CST)
• Multiple NAMD calculations on windows
  • Mai Aamer (Mon Nov 02 2015 - 16:40:06 CST)
• multiple output .dcd files??
  • Deng, Jinxia (Nancy) (Tue Dec 08 2015 - 08:43:02 CST)
  • Jim Phillips (Mon Dec 07 2015 - 16:43:12 CST)
  • Deng, Jinxia (Nancy) (Mon Dec 07 2015 - 14:56:53 CST)
• Multiple Tcouple
  • JAVAD NOROOZI (Mon Jan 12 2015 - 03:35:01 CST)
• Multiple tcouple (Nonequilbirium molecular dynamics)
  • JAVAD NOROOZI (Tue Jan 06 2015 - 03:51:07 CST)
• multiple thermostats in adaptive tempering
  • Igaev, Maxim (Wed Feb 18 2015 - 11:20:52 CST)
• Multiple-replicas metadynamics / Well-tempered metadynamics
  • Giacomo Fiorin (Fri Jun 12 2015 - 14:21:15 CDT)
  • Yerko Escalona (Fri Jun 12 2015 - 14:15:39 CDT)
• My Plight
  • Syed Kashif Zafar (Wed Feb 18 2015 - 18:28:19 CST)
• NADH topology file
  • Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:39:02 CDT)
  • Kevin C Chan (Wed Jul 16 2014 - 01:51:22 CDT)
  • Kenno Vanommeslaeghe (Tue Jul 15 2014 - 09:44:10 CDT)
  • Kevin C Chan (Tue Jul 15 2014 - 05:41:51 CDT)
• NAMD
  • Brian Radak (Wed Mar 25 2015 - 11:35:27 CDT)
  • Subbarao Kanchi (Tue Mar 24 2015 - 01:48:39 CDT)
• NAMD "unable to find improper parameters"
  • Asma El-Magboub (Thu Jan 22 2015 - 21:32:09 CST)
• NAMD - wrap atoms, not center of mass
  • Josh Vermaas (Fri Oct 16 2015 - 10:48:35 CDT)
  • Sourav Ray (Fri Oct 16 2015 - 10:27:09 CDT)
  • Stanislav Q=A0imko?= (Fri Oct 16 2015 - 10:20:28 CDT)
• NAMD 2.10 Building from Source
  • Giacomo Fiorin (Thu Jul 09 2015 - 16:05:02 CDT)
  • Kumar, Amit (Thu Jul 09 2015 - 16:02:07 CDT)
  • Giacomo Fiorin (Thu Jul 09 2015 - 15:45:32 CDT)
  • Kumar, Amit (Thu Jul 09 2015 - 15:28:07 CDT)
• namd 2.10 crashes when using more than 1 CPU for FEP simulation
  • Tien Huynh (Tue Oct 27 2015 - 21:58:14 CDT)
• NAMD 2.10 Manual
  • Ajasja LjubetiÄ� (Fri Aug 22 2014 - 03:30:05 CDT)
  • Norman Geist (Fri Aug 22 2014 - 03:14:47 CDT)
• NAMD 2.10 on IBM POWER(8) machines
  • Baker D.J. (Thu Jun 25 2015 - 07:00:49 CDT)
• NAMD 2.10 released
  • Jim Phillips (Fri Dec 12 2014 - 16:35:38 CST)
• NAMD 2.10 with multiple-replica support
  • Jim Phillips (Mon Feb 02 2015 - 00:11:26 CST)
  • Branko (Sat Jan 31 2015 - 14:06:06 CST)
• NAMD 2.10 with MVAPICH2-GDR?
  • Jim Phillips (Fri Jan 16 2015 - 16:54:35 CST)
  • David Chin (Thu Jan 15 2015 - 08:41:04 CST)
• NAMD 2.10b1 CUDA PME offload
  • Jim Phillips (Tue Aug 26 2014 - 10:22:48 CDT)
  • Norman Geist (Tue Aug 26 2014 - 09:25:48 CDT)
• NAMD 2.10b1 released
  • Jim Phillips (Mon Aug 25 2014 - 07:49:51 CDT)
• NAMD 2.10b1: occasional corrupted frame in binary dcd output
  • Tristan Croll (Tue Dec 23 2014 - 16:39:46 CST)
• NAMD 2.10b2 released
  • Jim Phillips (Mon Nov 17 2014 - 14:22:52 CST)
• NAMD 2.11 CUDA forces IBverbs
  • Jim Phillips (Fri Nov 13 2015 - 08:31:50 CST)
  • Norman Geist (Fri Nov 13 2015 - 06:00:18 CST)
• NAMD 2.11 released
  • Ajasja LjubetiÄ� (Thu Dec 24 2015 - 02:35:34 CST)
  • Francesco Pietra (Thu Dec 24 2015 - 01:22:37 CST)
  • Jeff Comer (Wed Dec 23 2015 - 19:38:21 CST)
  • Jim Phillips (Tue Dec 22 2015 - 21:37:31 CST)
  • Branko (Tue Dec 22 2015 - 16:19:37 CST)
  • Jim Phillips (Tue Dec 22 2015 - 10:38:50 CST)
• NAMD 2.11b1 multicore CUDA: Incorrect number of exclusions
  • Jim Phillips (Fri Dec 04 2015 - 16:52:30 CST)
  • Jeff Comer (Thu Dec 03 2015 - 14:20:42 CST)
• NAMD 2.11b1 released
  • Jim Phillips (Fri Nov 27 2015 - 20:10:42 CST)
  • Norman Geist (Fri Nov 27 2015 - 01:22:44 CST)
  • sunyeping (Thu Nov 26 2015 - 23:26:33 CST)
  • Jim Phillips (Thu Nov 12 2015 - 22:41:32 CST)
  • sunyeping (Thu Nov 12 2015 - 20:29:18 CST)
  • Tien Huynh (Thu Nov 12 2015 - 11:24:00 CST)
  • Jim Phillips (Thu Nov 12 2015 - 11:15:27 CST)
  • Jim Phillips (Thu Nov 12 2015 - 06:55:42 CST)
  • sunyeping (Thu Nov 12 2015 - 02:39:43 CST)
  • Tristan Croll (Wed Nov 11 2015 - 20:11:00 CST)
  • Jeff Comer (Tue Nov 10 2015 - 13:18:06 CST)
  • Tien Huynh (Tue Nov 10 2015 - 11:10:25 CST)
  • Jim Phillips (Tue Nov 10 2015 - 09:39:44 CST)
• NAMD 2.11b2 released
  • Jim Phillips (Sun Dec 06 2015 - 22:01:09 CST)
• NAMD 2.9 Changing/Replacing atoms in multiple molecules
  • Tristan Croll (Fri Feb 21 2014 - 16:04:43 CST)
  • Kenno Vanommeslaeghe (Fri Feb 21 2014 - 12:38:25 CST)
  • Axel Kohlmeyer (Fri Feb 21 2014 - 08:11:33 CST)
  • Michal Skoczek (Fri Feb 21 2014 - 08:02:41 CST)
• NAMD 2.9 quits early without error message.
  • Ivan Gregoretti (Mon Mar 10 2014 - 18:45:17 CDT)
  • Roy Fernando (Sat Mar 08 2014 - 10:03:21 CST)
  • Aron Broom (Fri Mar 07 2014 - 17:31:37 CST)
  • Morgan, Brittany (Fri Mar 07 2014 - 11:45:15 CST)
  • Ivan Gregoretti (Fri Mar 07 2014 - 11:46:54 CST)
  • Ivan Gregoretti (Fri Mar 07 2014 - 11:36:17 CST)
• NAMD and NUMA
  • Brunner, Robert Kraemer (Fri May 09 2014 - 12:03:53 CDT)
  • Joseph Farran (Wed May 07 2014 - 13:54:51 CDT)
• NAMD and usable FFs
  • Kenno Vanommeslaeghe (Fri Oct 17 2014 - 11:15:18 CDT)
  • Francesco Pietra (Fri Oct 17 2014 - 03:12:48 CDT)
  • Kenno Vanommeslaeghe (Thu Oct 16 2014 - 17:53:13 CDT)
  • Francesco Pietra (Thu Oct 16 2014 - 16:41:59 CDT)
  • Kenno Vanommeslaeghe (Thu Oct 16 2014 - 13:45:05 CDT)
  • Kenno Vanommeslaeghe (Thu Oct 16 2014 - 13:37:11 CDT)
  • Josh Vermaas (Thu Oct 16 2014 - 13:05:27 CDT)
  • Francesco Pietra (Thu Oct 16 2014 - 12:59:10 CDT)
  • Josh Vermaas (Wed Oct 15 2014 - 09:20:08 CDT)
  • Francesco Pietra (Wed Oct 15 2014 - 04:34:31 CDT)
• NAMD Anisotropic pressure control
  • Mahdi Tavakol (Fri Sep 18 2015 - 11:51:29 CDT)
  • Fotis Baltoumas (Fri Sep 18 2015 - 09:50:14 CDT)
  • Jérôme Hénin (Fri Sep 18 2015 - 09:44:50 CDT)
  • Mahdi Tavakol (Fri Sep 18 2015 - 08:50:04 CDT)
• namd coulomb conversion factor
  • Mohan maruthi sena (Sat Sep 27 2014 - 01:09:43 CDT)
• NAMD CVS_CUDA ERROR: "all CUDA-capable devices are busy or unavailable"
  • Samuel Bowerman (Mon Aug 11 2014 - 11:50:45 CDT)
• NAMD energy calculation
  • Ramin Ekhteiari (Wed Jun 25 2014 - 11:45:33 CDT)
• NAMD energy minimization
  • Axel Kohlmeyer (Sun Aug 31 2014 - 14:51:10 CDT)
  • Siva Dasetty (Sun Aug 31 2014 - 14:30:56 CDT)
• NAMD energy plugin
  • MEHRAN MB (Wed Jun 04 2014 - 15:16:09 CDT)
  • Kenno Vanommeslaeghe (Wed Jun 04 2014 - 14:16:48 CDT)
  • Kenno Vanommeslaeghe (Wed Jun 04 2014 - 14:10:39 CDT)
  • Ramin Ekhteiari (Wed Jun 04 2014 - 13:55:23 CDT)
  • Aron Broom (Wed Jun 04 2014 - 13:34:51 CDT)
  • Ramin Ekhteiari (Wed Jun 04 2014 - 12:45:36 CDT)
• NAMD energy plugin - dielectric constant
  • Ramin Ekhteiari (Mon Jul 07 2014 - 14:59:42 CDT)
• NAMD error LInux 3.11.10-21-desktop kernel AMD opternon 6272
  • Thomas C. Bishop (Tue Nov 11 2014 - 12:41:11 CST)
  • Thomas C. Bishop (Wed Nov 05 2014 - 09:48:15 CST)
• Namd grid forces -distance between molecule and surface
  • Mohan maruthi sena (Fri Jun 27 2014 - 05:20:29 CDT)
• NAMD hybrid configuration: Atoms moving too fast error
  • Puneet Singh (Mon Jul 27 2015 - 06:41:38 CDT)
• namd ibverbs
  • Kevin C Chan (Thu Jul 23 2015 - 05:38:49 CDT)
  • Gianluca Interlandi (Thu Jul 16 2015 - 17:09:40 CDT)
  • Maxime Boissonneault (Thu Jul 16 2015 - 16:43:06 CDT)
  • Gianluca Interlandi (Thu Jul 16 2015 - 16:20:34 CDT)
  • Gianluca Interlandi (Thu Jul 16 2015 - 16:06:37 CDT)
  • Maxime Boissonneault (Thu Jul 16 2015 - 15:59:19 CDT)
  • Gianluca Interlandi (Thu Jul 16 2015 - 15:56:14 CDT)
  • Maxime Boissonneault (Thu Jul 16 2015 - 15:50:36 CDT)
  • Gianluca Interlandi (Thu Jul 16 2015 - 15:31:34 CDT)
  • Maxime Boissonneault (Thu Jul 16 2015 - 12:59:50 CDT)
• namd ibverbs compile target
  • Bennion, Brian (Tue Oct 28 2014 - 18:04:52 CDT)
• NAMD Multicore CUDA usage
  • Ravi Abrol (Fri Jun 06 2014 - 14:20:10 CDT)
• NAMD nightly build compilation
  • Vlad Cojocaru (Fri May 08 2015 - 04:11:52 CDT)
  • Vlad Cojocaru (Fri May 08 2015 - 03:12:16 CDT)
  • Jérôme Hénin (Thu May 07 2015 - 09:11:53 CDT)
  • Vlad Cojocaru (Thu May 07 2015 - 08:40:00 CDT)
  • Vlad Cojocaru (Tue Mar 24 2015 - 12:51:47 CDT)
  • Vlad Cojocaru (Tue Mar 24 2015 - 12:07:03 CDT)
• NAMD Non-features
  • Axel Kohlmeyer (Wed Jan 21 2015 - 15:54:49 CST)
  • JAVAD NOROOZI (Wed Jan 21 2015 - 15:24:43 CST)
  • Jeff Comer (Wed Jan 21 2015 - 09:35:27 CST)
  • Axel Kohlmeyer (Wed Jan 21 2015 - 05:31:57 CST)
  • Axel Kohlmeyer (Wed Jan 21 2015 - 05:24:41 CST)
  • Jérôme Hénin (Wed Jan 21 2015 - 04:38:17 CST)
  • JAVAD NOROOZI (Wed Jan 21 2015 - 01:54:50 CST)
• NAMD on CRAY XE6m-200: dynamic linking in tcl not working
  • Harish Vashisth (Fri Jun 20 2014 - 18:49:59 CDT)
  • Harish Vashisth (Fri Jun 20 2014 - 15:17:34 CDT)
  • Axel Kohlmeyer (Fri Jun 20 2014 - 14:36:37 CDT)
  • Harish Vashisth (Fri Jun 20 2014 - 14:07:31 CDT)
• NAMD on Rescale
  • Istvan Jonyer (Mon Mar 10 2014 - 20:22:10 CDT)
• NAMD on SLURM
  • Abhishek TYAGI (Wed Nov 12 2014 - 21:07:16 CST)
  • Mitchell Gleed (Wed Nov 12 2014 - 12:57:16 CST)
  • Abhishek TYAGI (Wed Nov 05 2014 - 23:30:20 CST)
• NAMD on TACC (Darter)
  • Chitrak Gupta (Thu Dec 10 2015 - 17:35:15 CST)
  • Jim Phillips (Thu Dec 10 2015 - 10:03:56 CST)
  • Chitrak Gupta (Wed Dec 09 2015 - 07:49:53 CST)
  • Jim Phillips (Tue Dec 08 2015 - 22:41:19 CST)
  • Chitrak Gupta (Tue Dec 08 2015 - 22:19:12 CST)
  • Jim Phillips (Tue Dec 08 2015 - 22:15:15 CST)
  • Chitrak Gupta (Tue Dec 08 2015 - 18:16:29 CST)
• NAMD Pressure profile calculations
  • Tao Qu (Wed Apr 02 2014 - 15:43:59 CDT)
• NAMD Repeated failures launching tasks
  • Kumar, Amit (Mon May 11 2015 - 13:47:40 CDT)
• namd simulation
  • Abhishek TYAGI (Thu Mar 05 2015 - 04:46:29 CST)
  • Urszula Uciechowska (Tue Mar 03 2015 - 08:20:25 CST)
• namd simulation for solids withoy solvation
  • Subbusinger N (Fri Nov 14 2014 - 00:20:24 CST)
  • Kenno Vanommeslaeghe (Thu Nov 13 2014 - 11:50:51 CST)
  • Subbusinger N (Thu Nov 13 2014 - 00:02:42 CST)
• namd simulation with TIP5P
  • Monika Madhavi (Fri Oct 02 2015 - 01:16:41 CDT)
  • Shanshan Wu (Tue Feb 03 2015 - 18:36:34 CST)
• NAMD slows at startup phase 1 smp problem
  • Jim Phillips (Thu Jan 15 2015 - 14:20:58 CST)
  • Alexander Tzanov (Thu Jan 15 2015 - 10:05:16 CST)
  • Jim Phillips (Wed Jan 14 2015 - 17:16:19 CST)
  • Ryan Gordon (Mon Jan 12 2015 - 12:24:31 CST)
• NAMD Source, Molecule.c , Mass Critaria
  • JAVAD NOROOZI (Wed Feb 18 2015 - 12:55:25 CST)
• NAMD warning: Randomization of stack point is turned on in kernal, thread migration may not work!
  • Axel Kohlmeyer (Thu Mar 05 2015 - 11:40:42 CST)
  • Yarrow Madrona (Thu Mar 05 2015 - 10:58:11 CST)
• namd-1: Fatal Error: Unable to Open CHARMM Parameter File
  • Akshata Rudrapatna (Thu Feb 05 2015 - 06:32:40 CST)
  • Jim Phillips (Tue Feb 03 2015 - 18:48:35 CST)
  • Branko (Tue Feb 03 2015 - 16:14:32 CST)
  • David Hardy (Tue Feb 03 2015 - 15:54:49 CST)
  • David Hardy (Tue Feb 03 2015 - 15:32:57 CST)
  • Akshata Rudrapatna (Tue Feb 03 2015 - 14:43:55 CST)
• namd-1: Simulation Terminating Early
  • Akshata Rudrapatna (Mon Feb 09 2015 - 20:54:55 CST)
  • Jim Phillips (Mon Feb 09 2015 - 13:33:09 CST)
  • Norman Geist (Mon Feb 09 2015 - 03:09:57 CST)
  • Akshata Rudrapatna (Sat Feb 07 2015 - 15:06:33 CST)
• NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation??
  • Ivan Gregoretti (Thu Jun 26 2014 - 08:34:16 CDT)
  • Shailesh Pandey (Thu Jun 26 2014 - 04:41:49 CDT)
  • Shailesh Pandey (Mon Jun 09 2014 - 12:54:03 CDT)
• NAMD-GPU
  • Aron Broom (Wed May 14 2014 - 09:54:20 CDT)
  • Axel Kohlmeyer (Wed May 14 2014 - 07:51:37 CDT)
  • Ramin Ekhteiari (Wed May 14 2014 - 07:19:10 CDT)
• namd-I: How to assume the thickness of membrane when applying external Electric field ?
  • Adelman, Joshua Lev (Tue Jan 13 2015 - 08:36:01 CST)
  • Axel Kohlmeyer (Tue Jan 13 2015 - 07:21:49 CST)
  • Vy Phan (Tue Jan 13 2015 - 00:20:31 CST)
• namd-l digest V1 #1282
  • Istvan Jonyer (Fri Jan 17 2014 - 14:04:39 CST)
• namd-l digest V1 #1668
  • Bennion, Brian (Mon May 04 2015 - 10:42:12 CDT)
  • Ern Seang Ong (Sun May 03 2015 - 23:14:28 CDT)
• namd-l digest V1 #1726
  • nader zabarjad (Sun Aug 02 2015 - 10:41:55 CDT)
• NAMD-Lite
  • Axel Kohlmeyer (Tue Apr 15 2014 - 18:22:54 CDT)
  • Gianluca Interlandi (Tue Apr 15 2014 - 18:16:50 CDT)
  • Axel Kohlmeyer (Tue Apr 15 2014 - 17:42:32 CDT)
  • Hassan Kianinejad (Tue Apr 15 2014 - 17:22:56 CDT)
• NAMD-Replica exchange
  • ZOU Changling (Wed May 27 2015 - 04:31:28 CDT)
• namd-slurm file
  • Ramin Ekhteiari (Wed Jul 02 2014 - 10:08:31 CDT)
• NAMD-SMP-Ibverbs-CUDA assistance
  • Matthew Ralph Adendorff (Tue May 13 2014 - 09:25:44 CDT)
• NAMD/MIC & CUDA on Stampede
  • Maxim Belkin (Thu Jul 17 2014 - 13:32:27 CDT)
  • Maxim Belkin (Wed Jul 16 2014 - 15:44:34 CDT)
  • Jeffery Klauda (Wed Jul 16 2014 - 13:28:27 CDT)
• NAMD/VMD: generating psf for Abeta, ACE patch
  • Tristan Croll (Tue Sep 15 2015 - 17:53:20 CDT)
  • Mona Habibi (Tue Sep 15 2015 - 15:31:37 CDT)
• NAMD2.11 source code not compiling
  • Madhulika Gupta (Fri Nov 20 2015 - 01:20:05 CST)
  • Madhulika Gupta (Wed Nov 18 2015 - 10:31:55 CST)
  • Jim Phillips (Wed Nov 18 2015 - 09:21:13 CST)
  • Madhulika Gupta (Wed Nov 18 2015 - 02:47:38 CST)
• namd2.22b CUDA Phi
  • Jim Phillips (Sat Dec 05 2015 - 08:50:57 CST)
  • Francesco Pietra (Sat Dec 05 2015 - 01:06:49 CST)
• NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults
  • Axel Kohlmeyer (Wed Jun 11 2014 - 03:13:56 CDT)
  • Axel Kohlmeyer (Wed Jun 11 2014 - 02:42:48 CDT)
  • Vlastimil Zíma (Wed Jun 11 2014 - 02:36:44 CDT)
• NAMD_energy_plot
  • Jason Swails (Tue Jul 22 2014 - 17:22:29 CDT)
  • sananda chatterjee (Tue Jul 22 2014 - 17:08:56 CDT)
• NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance
  • Axel Kohlmeyer (Sun Feb 23 2014 - 20:57:18 CST)
  • sunyeping (Sun Feb 23 2014 - 20:29:02 CST)
• Nanotube Simulation
  • Samoylova, Olga M. (Tue Apr 15 2014 - 12:50:06 CDT)
  • Kenno Vanommeslaeghe (Tue Apr 15 2014 - 12:13:14 CDT)
  • Samoylova, Olga M. (Tue Apr 15 2014 - 09:49:31 CDT)
  • Axel Kohlmeyer (Mon Apr 14 2014 - 13:53:53 CDT)
  • Kenno Vanommeslaeghe (Mon Apr 14 2014 - 12:33:58 CDT)
  • Thomas C. Bishop (Mon Apr 14 2014 - 08:24:22 CDT)
  • Axel Kohlmeyer (Fri Apr 11 2014 - 17:41:04 CDT)
  • Kenno Vanommeslaeghe (Fri Apr 11 2014 - 17:18:18 CDT)
  • Axel Kohlmeyer (Fri Apr 11 2014 - 14:55:16 CDT)
  • Thomas C. Bishop (Fri Apr 11 2014 - 14:44:08 CDT)
  • MEHRAN MB (Fri Apr 11 2014 - 13:33:31 CDT)
  • Axel Kohlmeyer (Fri Apr 11 2014 - 13:30:47 CDT)
  • Miro Hodak (Fri Apr 11 2014 - 13:13:32 CDT)
  • Axel Kohlmeyer (Fri Apr 11 2014 - 12:05:50 CDT)
  • Miro Hodak (Fri Apr 11 2014 - 11:56:59 CDT)
  • Axel Kohlmeyer (Fri Apr 11 2014 - 03:36:44 CDT)
  • Miro Hodak (Thu Apr 10 2014 - 18:02:56 CDT)
• Nanotube tutorial
  • Adam Kells (Fri Jul 04 2014 - 13:19:33 CDT)
• NetworkView plugin for the non-namd trajectories
  • Vlad Cojocaru (Tue Apr 14 2015 - 10:13:47 CDT)
  • James Starlight (Tue Apr 14 2015 - 09:34:57 CDT)
• New partial charges after patching
  • Sadegh Faramarzi Ganjabad (Tue Jul 22 2014 - 06:28:57 CDT)
  • Sadegh Faramarzi Ganjabad (Tue Jul 22 2014 - 05:04:09 CDT)
  • Tristan Croll (Wed Jul 16 2014 - 18:44:39 CDT)
  • Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:53:47 CDT)
  • Sadegh Faramarzi Ganjabad (Wed Jul 16 2014 - 01:27:52 CDT)
  • Kenno Vanommeslaeghe (Fri Jul 11 2014 - 12:19:21 CDT)
  • Kenno Vanommeslaeghe (Thu Jun 19 2014 - 10:11:28 CDT)
  • Sadegh Faramarzi Ganjabad (Thu Jun 19 2014 - 03:21:33 CDT)
  • Kenno Vanommeslaeghe (Mon Jun 16 2014 - 10:23:02 CDT)
  • Sadegh Faramarzi Ganjabad (Sat Jun 14 2014 - 04:15:47 CDT)
• New web server for setup of membrane simulation systems
  • Chen, Po-chia (Sun Feb 08 2015 - 06:17:35 CST)
• Newbie GPU user, please help with my submission line
  • Jose Borreguero (Thu Oct 02 2014 - 14:03:24 CDT)
• NH4+ params
  • Mikhail Suyetin (Sat Oct 24 2015 - 11:56:15 CDT)
  • Thomas Albers (Sat Oct 24 2015 - 09:26:17 CDT)
  • Mikhail Suyetin (Fri Oct 23 2015 - 16:38:55 CDT)
• No steric clashes, still not minimizing
  • Francesco Pietra (Wed Mar 11 2015 - 06:38:40 CDT)
• node file for NAMD
  • Sourav Ray (Sat Sep 12 2015 - 01:13:32 CDT)
  • Sourav Ray (Sat Sep 12 2015 - 01:11:30 CDT)
  • Abhishek Tyagi (Fri Sep 11 2015 - 22:55:16 CDT)
  • Parag Khuraswar (Fri Sep 11 2015 - 08:02:54 CDT)
  • Parag Khuraswar (Tue Sep 01 2015 - 23:28:06 CDT)
• Non standar solvent
  • bdrakuli (Tue Feb 18 2014 - 11:43:58 CST)
  • Roy Fernando (Tue Feb 18 2014 - 10:49:10 CST)
  • MEHRAN MB (Tue Feb 18 2014 - 10:12:26 CST)
  • Javad Noroozi (Sat Feb 15 2014 - 06:52:17 CST)
• non-bonded energy of individual atoms
  • Bärwinkel, Tom (Fri Jun 12 2015 - 09:17:46 CDT)
• non-neutralized system
  • Research Jubilant (Wed Jun 04 2014 - 10:29:47 CDT)
• non-planarity problem! NOE restraints!
  • Anna Borlsky (Thu Feb 13 2014 - 09:22:43 CST)
• not able to view trajectory in VMD
  • Axel Kohlmeyer (Fri Jun 26 2015 - 13:04:20 CDT)
  • Lara rajam (Fri Jun 26 2015 - 12:55:01 CDT)
• Nucleic acid stains parameters
  • Kenno Vanommeslaeghe (Mon Aug 25 2014 - 10:56:26 CDT)
  • Sebastián Gutiérrez (Mon Aug 25 2014 - 10:37:04 CDT)
• number of close contacts and contact area
  • Abhishek TYAGI (Sun Mar 22 2015 - 04:37:57 CDT)
• Number of pdb and psf atoms are not the same!
  • Francesco Pietra (Wed Dec 16 2015 - 09:23:41 CST)
• nvt input file
  • Branko (Fri Jul 17 2015 - 08:44:24 CDT)
  • Urszula Uciechowska (Fri Jul 17 2015 - 08:25:21 CDT)
• nvt run error
  • Felipe Merino (Tue Jul 21 2015 - 03:28:40 CDT)
  • Urszula Uciechowska (Tue Jul 21 2015 - 02:54:10 CDT)
• NVT, NPT, order & combination
  • Kenno Vanommeslaeghe (Tue Aug 19 2014 - 12:17:27 CDT)
  • Zeinab Emami (Tue Aug 19 2014 - 03:23:26 CDT)
• On-the-fly modification of tclforces script?
  • John Stone (Fri Nov 13 2015 - 20:17:53 CST)
  • Tristan Croll (Fri Nov 13 2015 - 19:28:39 CST)
  • John Stone (Fri Nov 13 2015 - 19:05:34 CST)
  • Tristan Croll (Fri Nov 13 2015 - 18:14:28 CST)
  • Tristan Croll (Fri Nov 13 2015 - 16:48:21 CST)
  • Tristan Croll (Tue Nov 10 2015 - 16:03:38 CST)
  • Jim Phillips (Tue Nov 10 2015 - 09:53:42 CST)
  • Tristan Croll (Tue Nov 10 2015 - 04:27:19 CST)
  • Tristan Croll (Tue Nov 10 2015 - 03:01:19 CST)
• on-the-fly parameter introspection
  • Jim Phillips (Mon Feb 09 2015 - 13:18:02 CST)
  • Brian Radak (Thu Feb 05 2015 - 13:54:51 CST)
• OpenGL Display Window, "Key 2", SMD with NAMD
  • Zeinab Emami (Sun Dec 20 2015 - 11:57:52 CST)
• OPLS force field in NAMD
  • Peter Freddolino (Sat Jun 20 2015 - 22:20:00 CDT)
  • AnkiReddy katha (Sat Jun 20 2015 - 16:17:31 CDT)
  • farzad kiani (Sat Jun 20 2015 - 15:28:39 CDT)
  • oguz gurbulak (Sat Jun 20 2015 - 11:43:02 CDT)
• OPLS force-field in NAMD
  • AnkiReddy katha (Thu May 07 2015 - 02:12:03 CDT)
• OPLS in NAMD
  • AnkiReddy katha (Thu May 07 2015 - 04:40:47 CDT)
  • AnkiReddy katha (Thu May 07 2015 - 04:17:23 CDT)
• OPLS/AA force field
  • oguz gurbulak (Wed Aug 05 2015 - 09:00:01 CDT)
• OPLSAA to CHARMM
  • Francesco Pietra (Fri Nov 06 2015 - 00:59:02 CST)
  • Francesco Pietra (Thu Nov 05 2015 - 10:21:42 CST)
• optimising namd ibverb runs
  • Jim Phillips (Wed May 20 2015 - 12:28:37 CDT)
  • Aaron Larsen (Mon May 18 2015 - 08:48:18 CDT)
  • Norman Geist (Mon May 18 2015 - 08:16:11 CDT)
  • Thanassis Silis (Mon May 18 2015 - 06:48:03 CDT)
• output files are not stored when running namd-2.10 ibverbs
  • Thanassis Silis (Fri May 08 2015 - 05:07:50 CDT)
  • Thanassis Silis (Thu May 07 2015 - 10:29:26 CDT)
• Output to a file
  • Mahdi Tavakol (Mon Oct 05 2015 - 01:31:55 CDT)
• OutputAccumulatedWork...where's the output?
  • Giacomo Fiorin (Mon Dec 14 2015 - 13:32:17 CST)
  • Bryan Roessler (Mon Dec 14 2015 - 12:41:08 CST)
  • Giacomo Fiorin (Mon Dec 14 2015 - 10:55:36 CST)
  • Bryan Roessler (Sun Dec 13 2015 - 19:36:26 CST)
• Outward tilting which colvar to use
  • Jérôme Hénin (Thu Oct 01 2015 - 07:11:45 CDT)
  • Nicolas Martin (Thu Oct 01 2015 - 05:13:01 CDT)
• Overflow in LJcorrection?
  • Jim Phillips (Mon Dec 07 2015 - 16:35:27 CST)
  • Peter Freddolino (Sat Dec 05 2015 - 21:15:12 CST)
  • Peter Freddolino (Sat Dec 05 2015 - 17:57:22 CST)
  • Jason Swails (Sat Dec 05 2015 - 07:54:57 CST)
  • Brian Radak (Thu Dec 03 2015 - 16:26:19 CST)
  • Jason Swails (Thu Dec 03 2015 - 16:18:40 CST)
  • Brian Radak (Thu Dec 03 2015 - 16:15:59 CST)
  • Jason Swails (Thu Dec 03 2015 - 16:15:15 CST)
  • Brian Radak (Thu Dec 03 2015 - 16:10:59 CST)
  • Jason Swails (Thu Dec 03 2015 - 16:04:28 CST)
  • Brian Radak (Thu Dec 03 2015 - 15:59:27 CST)
  • Peter Freddolino (Thu Dec 03 2015 - 15:55:49 CST)
  • Jason Swails (Thu Dec 03 2015 - 15:55:30 CST)
  • Brian Radak (Thu Dec 03 2015 - 15:45:38 CST)
• PACE Force Field and NAMD 2.10
  • Fotis Baltoumas (Thu Mar 12 2015 - 06:18:07 CDT)
• Parallelization of External Program Forces
  • btreece_at_andrew.cmu.edu (Tue Mar 24 2015 - 18:49:26 CDT)
• parameter and topology files for martini polarizable water
  • Klas Karis (Thu Jul 10 2014 - 12:11:35 CDT)
  • Fotis Baltoumas (Thu Jul 10 2014 - 04:17:31 CDT)
  • Klas Karis (Wed Jul 09 2014 - 18:30:23 CDT)
• Parameter colvars
  • Giacomo Fiorin (Tue Oct 07 2014 - 13:04:53 CDT)
  • Z (Mon Oct 06 2014 - 22:05:28 CDT)
  • Grace Brannigan (Mon Oct 06 2014 - 15:56:18 CDT)
  • Giacomo Fiorin (Mon Oct 06 2014 - 15:25:06 CDT)
  • Z (Mon Oct 06 2014 - 11:20:41 CDT)
  • Jérôme Hénin (Mon Oct 06 2014 - 10:01:52 CDT)
  • Z (Mon Oct 06 2014 - 09:47:28 CDT)
  • Giacomo Fiorin (Mon Oct 06 2014 - 07:03:38 CDT)
  • Z (Mon Oct 06 2014 - 07:02:28 CDT)
  • Z (Mon Oct 06 2014 - 06:55:44 CDT)
  • Giacomo Fiorin (Mon Oct 06 2014 - 06:27:23 CDT)
  • Z (Mon Oct 06 2014 - 05:56:07 CDT)
  • Giacomo Fiorin (Mon Oct 06 2014 - 05:45:41 CDT)
  • Z (Mon Oct 06 2014 - 05:26:21 CDT)
• Parameterizing a novel peptide
  • Bryan Roessler (Tue Sep 15 2015 - 12:06:12 CDT)
  • Bennion, Brian (Tue Sep 15 2015 - 11:15:56 CDT)
  • Peter Freddolino (Mon Sep 14 2015 - 22:00:56 CDT)
  • Mayne, Christopher G (Mon Sep 14 2015 - 21:38:04 CDT)
  • Peter Freddolino (Mon Sep 14 2015 - 21:08:55 CDT)
  • Mayne, Christopher G (Mon Sep 14 2015 - 08:48:57 CDT)
  • Tomek StÄ™pniewski (Fri Sep 11 2015 - 18:16:27 CDT)
  • Bryan Roessler (Fri Sep 11 2015 - 17:14:05 CDT)
• parameters problem in sulfated molecules
  • siddharth kamal (Wed Sep 02 2015 - 08:33:11 CDT)
  • Bennion, Brian (Tue Sep 01 2015 - 12:27:17 CDT)
  • Peter Freddolino (Tue Sep 01 2015 - 12:25:02 CDT)
  • Lara rajam (Tue Sep 01 2015 - 12:12:42 CDT)
• paricle type in residue based coarse graining of NAMD
  • Yongcheng Zhou (Mon Jun 23 2014 - 09:14:12 CDT)
  • Yongcheng Zhou (Mon Jun 23 2014 - 14:37:16 CDT)
• Patch to connect monomers code
  • Kenno Vanommeslaeghe (Tue May 06 2014 - 13:33:49 CDT)
  • Kenno Vanommeslaeghe (Mon May 05 2014 - 13:11:36 CDT)
  • Rawan Al Nsour (Sun May 04 2014 - 12:15:12 CDT)
• Patch-size Error (not like the other ones)
  • Norman Geist (Mon Jul 27 2015 - 02:32:33 CDT)
  • Jeffrey Potoff (Fri Jul 24 2015 - 13:38:52 CDT)
  • Merrill, Dante (Fri Jul 24 2015 - 13:14:28 CDT)
• Patches for namd 2.10
  • Ã…ke Sandgren (Fri Apr 24 2015 - 06:06:53 CDT)
  • Jérôme Hénin (Fri Apr 24 2015 - 04:38:39 CDT)
  • Ã…ke Sandgren (Fri Apr 24 2015 - 01:09:35 CDT)
• patching SO3 group to GAG
  • Lara rajam (Thu Sep 03 2015 - 22:45:34 CDT)
  • Peter Freddolino (Thu Sep 03 2015 - 20:36:45 CDT)
  • Lara rajam (Thu Sep 03 2015 - 19:13:21 CDT)
• PBC only along the z axis.
  • Sridhar Kumar Kannam (Sat Jan 04 2014 - 18:25:28 CST)
  • David Hardy (Fri Jan 03 2014 - 17:18:47 CST)
  • Subbarao Kanchi (Fri Jan 03 2014 - 00:18:53 CST)
  • Sridhar Kumar Kannam (Thu Jan 02 2014 - 21:46:58 CST)
• PCL dcd files
  • Niklaus Johner (Tue Sep 30 2014 - 01:15:25 CDT)
  • Giacomo Fiorin (Mon Sep 29 2014 - 12:10:07 CDT)
  • Mihaela Drenscko (Mon Sep 29 2014 - 11:09:40 CDT)
• pdb files to dcd
  • Josh Vermaas (Tue Nov 03 2015 - 14:40:53 CST)
  • Amitkumar Majhi (Tue Nov 03 2015 - 14:33:21 CST)
• peptide tends to migrate out the water box
  • Kenno Vanommeslaeghe (Fri Apr 18 2014 - 10:27:09 CDT)
  • Francesco Pietra (Fri Apr 18 2014 - 03:14:49 CDT)
  • Ana Celia Vila Verde (Fri Apr 18 2014 - 02:12:40 CDT)
  • Francesco Pietra (Thu Apr 17 2014 - 17:02:01 CDT)
• Performance difference of prcompiled binary VS source code
  • Nizar Masbukhin (Mon Oct 13 2014 - 19:23:43 CDT)
• performance question
  • Norman Geist (Wed Apr 29 2015 - 03:24:46 CDT)
  • Thomas C. Bishop (Tue Apr 28 2015 - 15:53:42 CDT)
  • Bennion, Brian (Tue Apr 28 2015 - 15:06:13 CDT)
  • Thomas C. Bishop (Tue Apr 28 2015 - 14:32:16 CDT)
  • Norman Geist (Tue Apr 28 2015 - 02:51:06 CDT)
  • Thomas C. Bishop (Mon Apr 27 2015 - 15:54:10 CDT)
• Performing MD simulations with protein and halide ions (iodide, bromide, chloride)
  • Stojanoski, Vlatko (Sat Oct 17 2015 - 15:49:19 CDT)
  • Branko (Sat Oct 17 2015 - 15:42:11 CDT)
  • Stojanoski, Vlatko (Sat Oct 17 2015 - 15:31:43 CDT)
  • Branko (Sat Oct 17 2015 - 14:35:37 CDT)
  • Stojanoski, Vlatko (Sat Oct 17 2015 - 14:05:29 CDT)
• periodic boundary conditions
  • Anna Borlsky (Fri Jan 10 2014 - 15:27:34 CST)
• Periodic Box Dimension (WrapAll is on)
  • JAVAD NOROOZI (Mon Jan 19 2015 - 23:55:19 CST)
• Persistent margin errors
  • Norman Geist (Wed Apr 16 2014 - 07:49:47 CDT)
  • Vlastimil Zíma (Wed Apr 16 2014 - 05:28:56 CDT)
  • Vlastimil Zíma (Wed Feb 26 2014 - 06:38:23 CST)
• Phi vs GPU
  • Francesco Pietra (Wed Feb 04 2015 - 01:52:43 CST)
• PME Seg Fault
  • Vibhor Agrawal (Mon Aug 10 2015 - 11:31:56 CDT)
  • Richard Overstreet (Mon Aug 10 2015 - 09:11:27 CDT)
• PME: The Excluded Coulombic Interactions
  • Hadi (Fri Mar 21 2014 - 22:56:50 CDT)
• PMEGridSize and parameters controlling electrostatic interactions.
  • Maxim Belkin (Sun Jan 25 2015 - 21:20:58 CST)
  • Jeff Comer (Sun Jan 25 2015 - 18:11:17 CST)
  • Maxim Belkin (Sat Jan 24 2015 - 14:11:59 CST)
  • Dawid das (Sat Jan 24 2015 - 13:48:44 CST)
• PMEGridSizeX (number of grid points) is very small.
  • Aron Broom (Wed Feb 05 2014 - 15:10:53 CST)
  • Maxim Belkin (Wed Feb 05 2014 - 12:44:35 CST)
  • Bennion, Brian (Wed Feb 05 2014 - 12:28:37 CST)
  • Rawan Al Nsour (Wed Feb 05 2014 - 12:00:57 CST)
• PMETolerance
  • Natalie Esther Smith (Tue Apr 08 2014 - 23:07:52 CDT)
• PMF and work distribution
  • Ajasja LjubetiÄ� (Thu Jun 26 2014 - 08:05:48 CDT)
  • Giacomo Fiorin (Wed Jun 25 2014 - 12:12:52 CDT)
  • Mustafa Tekpinar (Wed Jun 25 2014 - 05:50:30 CDT)
• PMF calculation crashes with constraint failure
  • Giacomo Fiorin (Sun Jan 26 2014 - 15:37:10 CST)
  • Magnus Andersson (Sat Jan 25 2014 - 11:02:11 CST)
• PMF calculations between membrane and nano particle simulations
  • Subbarao Kanchi (Tue Jul 08 2014 - 01:01:15 CDT)
  • Giacomo Fiorin (Mon Jul 07 2014 - 18:05:06 CDT)
  • Subbarao Kanchi (Thu Jul 03 2014 - 17:46:24 CDT)
  • Giacomo Fiorin (Thu Jul 03 2014 - 16:34:33 CDT)
  • Subbarao Kanchi (Thu Jul 03 2014 - 15:58:23 CDT)
• PMF from ABF simulation not plateauing
  • Jérôme Hénin (Thu May 08 2014 - 17:37:20 CDT)
  • Aron Broom (Thu May 08 2014 - 13:56:37 CDT)
  • Riley Workman (Thu May 08 2014 - 12:08:13 CDT)
• Point group symmetry
  • bmaiti_at_andrew.cmu.edu (Mon Apr 07 2014 - 18:20:08 CDT)
• polarizable carbon nanotubes
  • ibrahim khalil (Tue Apr 21 2015 - 11:00:36 CDT)
• Polarization effect of gold cluster
  • Zhao Lina (Fri Feb 21 2014 - 06:30:34 CST)
  • Axel Kohlmeyer (Tue Feb 18 2014 - 06:32:07 CST)
  • Zhao Lina (Tue Feb 18 2014 - 06:20:20 CST)
• Polymer Layer/ Cutoff
  • Kenno Vanommeslaeghe (Thu May 15 2014 - 18:00:42 CDT)
  • Rawan Al Nsour (Thu May 15 2014 - 16:13:58 CDT)
  • Kenno Vanommeslaeghe (Thu May 15 2014 - 14:34:00 CDT)
  • Kenno Vanommeslaeghe (Thu May 15 2014 - 11:58:43 CDT)
  • Rawan Al Nsour (Thu May 15 2014 - 11:19:21 CDT)
• polymerization simulations
  • Giacomo Fiorin (Thu Jul 09 2015 - 15:51:38 CDT)
  • L. Signorile (Thu Jul 09 2015 - 13:06:51 CDT)
• Postdoc in Theoretical and Computational Biophysics
  • Aksimentiev, Oleksii (Mon Jun 08 2015 - 11:51:11 CDT)
• Postdoc positions available at IBM (bio-molecular modeling and MD)
  • Payel Das (Mon Mar 16 2015 - 09:15:05 CDT)
• posting from Yahoo addresses disabled
  • Jim Phillips (Tue Apr 08 2014 - 17:45:15 CDT)
• PREMD in NAMD
  • Matthew Ralph Adendorff (Mon Feb 10 2014 - 09:27:15 CST)
• preparing dsDNA
  • Urszula Uciechowska (Fri Feb 06 2015 - 05:58:43 CST)
• PRES and water-ions issues with charmm36
  • Francesco Pietra (Thu Dec 10 2015 - 15:30:14 CST)
• Pressure coupling options
  • Chitrak Gupta (Sun Jun 28 2015 - 15:54:05 CDT)
  • Josh Vermaas (Sat Jun 27 2015 - 19:36:17 CDT)
  • Kevin C Chan (Fri Jun 26 2015 - 23:32:05 CDT)
• pressure value
  • Jeff Comer (Sun Mar 29 2015 - 16:54:09 CDT)
  • Brian Radak (Sun Mar 29 2015 - 15:30:42 CDT)
  • Hasan haska (Sun Mar 29 2015 - 14:23:28 CDT)
• Probelm with Lone Pairs on TIP4 model
  • JAVAD NOROOZI (Tue Jan 06 2015 - 04:07:23 CST)
• problem about namdstats.tcl
  • Hasan haska (Wed Apr 01 2015 - 01:34:32 CDT)
• problem compiling NAMD
  • Ivan Gregoretti (Tue Feb 25 2014 - 13:23:23 CST)
  • David Hardy (Tue Feb 25 2014 - 12:39:11 CST)
  • David Hardy (Mon Feb 24 2014 - 13:18:32 CST)
  • Hassan Kianinejad (Mon Feb 24 2014 - 10:48:51 CST)
• problem in calculating binding energy using MMGBSA with namd-2.9
  • Shailesh Pandey (Mon Sep 01 2014 - 07:31:34 CDT)
• problem in installation of charm-6.4.0 in bluegeneL]
  • Santosh Kumar Chaudhary (Fri Dec 19 2014 - 05:49:45 CST)
• Problem on merging multi-psf files into one
  • wliu (Sun Oct 18 2015 - 07:52:11 CDT)
• problem restarting multiple walker metadynamics
  • Amy Rice (Thu Apr 02 2015 - 14:54:56 CDT)
  • Giacomo Fiorin (Wed Apr 01 2015 - 15:05:30 CDT)
  • Amy Rice (Mon Mar 30 2015 - 13:23:24 CDT)
  • Giacomo Fiorin (Sat Mar 28 2015 - 17:50:19 CDT)
  • Amy Rice (Fri Mar 27 2015 - 11:48:02 CDT)
  • Giacomo Fiorin (Thu Mar 19 2015 - 18:39:06 CDT)
  • Amy Rice (Thu Mar 19 2015 - 17:44:25 CDT)
  • Giacomo Fiorin (Thu Mar 19 2015 - 17:26:27 CDT)
  • Amy Rice (Thu Mar 19 2015 - 17:24:29 CDT)
  • Giacomo Fiorin (Sun Mar 15 2015 - 10:47:17 CDT)
  • Giacomo Fiorin (Sun Mar 15 2015 - 10:45:14 CDT)
  • Amy Rice (Thu Mar 12 2015 - 17:26:10 CDT)
  • Amy Rice (Wed Mar 11 2015 - 22:49:51 CDT)
  • Giacomo Fiorin (Wed Mar 11 2015 - 18:29:36 CDT)
  • Amy Rice (Wed Mar 11 2015 - 14:59:46 CDT)
• Problem running REMD simulation
  • Nicholus Bhattacharjee (Thu Aug 27 2015 - 03:00:31 CDT)
  • Peter Freddolino (Wed Aug 26 2015 - 08:28:57 CDT)
  • Peter Freddolino (Tue Aug 25 2015 - 23:25:00 CDT)
  • Nicholus Bhattacharjee (Tue Aug 25 2015 - 04:59:07 CDT)
  • Douglas Houston (Tue Aug 25 2015 - 04:16:55 CDT)
  • Nicholus Bhattacharjee (Tue Aug 25 2015 - 03:01:36 CDT)
  • Nicholus Bhattacharjee (Thu Aug 20 2015 - 03:47:33 CDT)
• problem with equilibration of membrane-protein system
  • Azadeh Alavi (Sat Feb 14 2015 - 05:35:59 CST)
• Problem with iron ion (FE2+)
  • Tristan Croll (Tue Aug 25 2015 - 03:56:51 CDT)
  • Josh Vermaas (Mon Aug 24 2015 - 14:17:20 CDT)
  • Branko (Mon Aug 24 2015 - 13:40:17 CDT)
  • Daniela Rivas (Mon Aug 24 2015 - 13:16:15 CDT)
  • Branko (Mon Aug 24 2015 - 13:09:01 CDT)
  • Daniela Rivas (Mon Aug 24 2015 - 12:51:59 CDT)
• Problem with Kinetic Energy of Atomselection
  • JAVAD NOROOZI (Wed Jan 07 2015 - 00:53:38 CST)
• Problem with running namdenergy plugin from text interface
  • zeynab mohamad hoseyni (Mon Sep 22 2014 - 22:29:26 CDT)
  • Josh Vermaas (Mon Sep 22 2014 - 15:09:10 CDT)
  • zeynab mohamad hoseyni (Mon Sep 22 2014 - 14:53:04 CDT)
• Problem with tcl intepreter
  • Belkin, Maxim (Tue Nov 03 2015 - 10:53:53 CST)
  • Bryan Roessler (Thu Oct 29 2015 - 20:06:58 CDT)
  • Bryan Roessler (Thu Oct 29 2015 - 20:00:31 CDT)
  • Axel Kohlmeyer (Thu Oct 29 2015 - 19:54:34 CDT)
  • Josh Vermaas (Thu Oct 29 2015 - 19:45:12 CDT)
  • Bryan Roessler (Thu Oct 29 2015 - 19:24:53 CDT)
• problem with water molecules angle in MD simulation
  • Axel Kohlmeyer (Fri Jan 30 2015 - 05:32:06 CST)
  • Tristan Croll (Fri Jan 30 2015 - 02:43:42 CST)
  • Shoresh Shafei (Fri Jan 30 2015 - 02:28:17 CST)
  • Tristan Croll (Fri Jan 30 2015 - 02:25:32 CST)
  • Shoresh (Tue Jan 27 2015 - 10:30:54 CST)
  • Shoresh Shafei (Sun Jan 25 2015 - 19:06:23 CST)
• problems about new molecule parameterization
  • Tian Li (Thu Jan 30 2014 - 22:28:36 CST)
• problems compiling NAMD with mpicxx from mvapich2
  • Jose Borreguero (Mon Jan 26 2015 - 08:27:41 CST)
  • Jose Borreguero (Sat Jan 24 2015 - 11:49:02 CST)
• Problems in running AutoIMD
  • Bennion, Brian (Fri May 01 2015 - 11:00:35 CDT)
  • Ern Seang Ong (Thu Apr 30 2015 - 23:33:47 CDT)
• problems running ABF simulation
  • Giacomo Fiorin (Tue Sep 02 2014 - 02:45:26 CDT)
  • Charles Whidborne (Tue Sep 02 2014 - 00:37:40 CDT)
• problems running amber parm7
  • Francesco Pietra (Tue Jan 20 2015 - 01:56:02 CST)
  • Francesco Pietra (Tue Jan 20 2015 - 01:25:17 CST)
  • Francesco Pietra (Mon Jan 19 2015 - 13:03:44 CST)
• Problems to parametrize molecules
  • Evandro Semighini (Fri Apr 24 2015 - 14:26:50 CDT)
  • Mayne, Christopher G (Fri Apr 24 2015 - 14:22:55 CDT)
  • Bennion, Brian (Fri Apr 24 2015 - 14:02:59 CDT)
  • Evandro Semighini (Fri Apr 24 2015 - 13:58:25 CDT)
  • Evandro Semighini (Fri Apr 24 2015 - 13:54:33 CDT)
  • Mayne, Christopher G (Fri Apr 24 2015 - 13:53:01 CDT)
  • Bennion, Brian (Fri Apr 24 2015 - 13:46:52 CDT)
  • Evandro Semighini (Fri Apr 24 2015 - 12:49:31 CDT)
  • Bennion, Brian (Fri Apr 24 2015 - 12:27:51 CDT)
  • Evandro Semighini (Fri Apr 24 2015 - 10:04:37 CDT)
  • Mayne, Christopher G (Sun Apr 19 2015 - 18:59:20 CDT)
  • Evandro Semighini (Sun Apr 19 2015 - 18:47:21 CDT)
  • Mayne, Christopher G (Fri Apr 17 2015 - 11:16:16 CDT)
  • Evandro Semighini (Thu Apr 16 2015 - 15:28:23 CDT)
  • Evandro Semighini (Thu Apr 16 2015 - 14:53:54 CDT)
  • Bennion, Brian (Wed Apr 15 2015 - 15:44:53 CDT)
  • Evandro Semighini (Wed Apr 15 2015 - 15:37:12 CDT)
  • Bennion, Brian (Wed Apr 15 2015 - 13:04:21 CDT)
  • Bennion, Brian (Tue Apr 14 2015 - 15:57:28 CDT)
  • Evandro Semighini (Tue Apr 14 2015 - 15:51:17 CDT)
  • Bennion, Brian (Tue Apr 14 2015 - 15:45:41 CDT)
  • Evandro Semighini (Tue Apr 14 2015 - 15:30:03 CDT)
• Problems when running FEP for mutation ASP to GLY
  • Yunhui Peng (Fri Apr 17 2015 - 13:53:03 CDT)
• Problems with energy minimization
  • James Starlight (Thu Apr 10 2014 - 05:32:48 CDT)
  • Hongbo Du (Wed Apr 09 2014 - 10:17:08 CDT)
  • Morgan, Brittany (Wed Apr 09 2014 - 10:20:05 CDT)
  • James Starlight (Wed Apr 09 2014 - 09:38:21 CDT)
  • Subbarao Kanchi (Wed Apr 09 2014 - 09:14:55 CDT)
  • James Starlight (Wed Apr 09 2014 - 09:07:28 CDT)
• Problems with GLUP and ASPP with CHARMM36
  • Francesco Pietra (Fri Dec 11 2015 - 09:35:48 CST)
  • Josh Vermaas (Fri Dec 11 2015 - 09:25:11 CST)
  • Francesco Pietra (Fri Dec 11 2015 - 09:21:34 CST)
  • Josh Vermaas (Fri Dec 11 2015 - 08:45:00 CST)
  • Francesco Pietra (Fri Dec 11 2015 - 05:07:03 CST)
• problems with in text mode towards pdf and pdb files
  • Francesco Pietra (Sat Nov 22 2014 - 02:45:10 CST)
  • Jim Phillips (Fri Nov 21 2014 - 12:50:22 CST)
  • Josh Vermaas (Fri Nov 21 2014 - 10:54:56 CST)
  • Jim Phillips (Fri Nov 21 2014 - 10:54:20 CST)
  • Francesco Pietra (Fri Nov 21 2014 - 10:42:05 CST)
  • Francesco Pietra (Fri Nov 21 2014 - 10:06:28 CST)
  • Jim Phillips (Fri Nov 21 2014 - 09:56:11 CST)
  • Francesco Pietra (Fri Nov 21 2014 - 09:39:56 CST)
  • Jim Phillips (Fri Nov 21 2014 - 09:29:35 CST)
  • Francesco Pietra (Fri Nov 21 2014 - 09:09:52 CST)
• Processing 64-window FEP
  • Matthew Ralph Adendorff (Sun May 10 2015 - 08:44:08 CDT)
• proper order for par files in namd
  • Mayne, Christopher G (Fri May 01 2015 - 09:21:11 CDT)
  • Bennion, Brian (Fri Apr 24 2015 - 17:05:16 CDT)
• proper order for par files in namd (solved)
  • Bennion, Brian (Fri Apr 24 2015 - 18:21:22 CDT)
• Protein solvation
  • Kipp Johnson (Sat May 10 2014 - 15:38:26 CDT)
  • farzad kiani (Sat May 10 2014 - 12:28:26 CDT)
• protein-DNA complex
  • Vlad Cojocaru (Thu Jul 16 2015 - 10:59:19 CDT)
  • Urszula Uciechowska (Thu Jul 16 2015 - 09:40:25 CDT)
• protein-membrane interface hydration
  • zeynab mohamad hoseyni (Tue Feb 18 2014 - 13:37:30 CST)
• psf file does not contain cross-terms
  • Axel Kohlmeyer (Sun Feb 16 2014 - 12:10:01 CST)
  • zeynab mohamad hoseyni (Sun Feb 16 2014 - 12:00:30 CST)
• PSF for CYCLIC PEPTIDE :
  • bay__gulf618_at_sina.com (Sat Sep 26 2015 - 21:26:01 CDT)
  • Nikhil Maroli (Sat Sep 26 2015 - 05:45:17 CDT)
• PSF for cyclic peptide nanotube
  • Nikhil Maroli (Fri Oct 02 2015 - 08:36:47 CDT)
• psf for cyclic peptide nanotube:psf ready for one ring but required for 8 ring
  • Nikhil Maroli (Sat Sep 26 2015 - 06:50:31 CDT)
• PSF generated with PSFGEN [problem in CP2K] - Problem with CGenFF naming?
  • Christian Jorgensen (Thu Feb 12 2015 - 13:01:13 CST)
  • Jim Phillips (Thu Feb 12 2015 - 12:32:42 CST)
  • Christian Jorgensen (Thu Feb 12 2015 - 10:16:00 CST)
• PSFgen with RNA-like nucleotide monophosphates
  • Aaron Larsen (Wed May 06 2015 - 11:01:26 CDT)
• pThr topology
  • ÂÀСӨ (Tue Feb 18 2014 - 21:05:27 CST)
• Putting multiple copies of peptide in a box
  • Aditya Ranganathan (Tue Feb 17 2015 - 03:39:14 CST)
• Q=B4=D7=D4"=C2=C0=D0=A1=D3=A8"_<lv-xy11@mail?= s.tsinghua.edu.cn>µÄÓʼþ
  • ÂÀСӨ (Fri Sep 25 2015 - 09:19:53 CDT)
• Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?=
  • ZOU Changling (Wed Nov 25 2015 - 06:39:26 CST)
  • ZOU Changling (Wed Nov 18 2015 - 00:25:35 CST)
• Qh
  • Lurong Pan (Thu Sep 11 2014 - 08:22:22 CDT)
• query about the cross term in psf
  • Josh Vermaas (Sat Dec 06 2014 - 14:22:32 CST)
  • Kshatresh Dutta Dubey (Sat Dec 06 2014 - 14:12:31 CST)
  • Josh Vermaas (Sat Dec 06 2014 - 13:49:06 CST)
  • Kshatresh Dutta Dubey (Sat Dec 06 2014 - 13:31:42 CST)
• query for system size in pmf calculation
  • Giacomo Fiorin (Fri Nov 20 2015 - 08:52:35 CST)
  • Atanu Maity (Fri Nov 20 2015 - 05:24:47 CST)
• question
  • Jérôme Hénin (Mon Mar 31 2014 - 12:26:01 CDT)
  • Eifler, Jay Q. (UMKC-Student) (Mon Mar 31 2014 - 11:47:16 CDT)
• question about '+devices'
  • ukulililixl (Wed Oct 08 2014 - 01:06:50 CDT)
• Question about accelerated MD
  • Mare Libero (Tue Mar 25 2014 - 17:14:27 CDT)
• question about CUDA-enabled
  • Abhishek TYAGI (Sun Nov 30 2014 - 02:57:53 CST)
  • Axel Kohlmeyer (Sat Nov 29 2014 - 19:22:55 CST)
  • Abhishek Tyagi (Sat Nov 29 2014 - 11:04:55 CST)
  • maryam atabay (Sat Nov 29 2014 - 10:19:49 CST)
  • maryam atabay (Tue Nov 25 2014 - 01:05:32 CST)
• question about FEP for amphiphile in lipid bilayer
  • Leonardo Darre (Wed Dec 10 2014 - 09:20:51 CST)
  • Giacomo Fiorin (Wed Dec 10 2014 - 08:41:25 CST)
  • Leonardo Darre (Wed Dec 10 2014 - 08:08:27 CST)
• question about force constant
  • Lurong Pan (Fri Jan 03 2014 - 09:02:13 CST)
• question about restart conf file
  • oguz gurbulak (Sun Apr 26 2015 - 07:10:44 CDT)
• question in NAMD with icc & cuda
  • ukulililixl (Mon Aug 25 2014 - 06:40:48 CDT)
• Question regarding loss of translational entropy calculation in FEP tutorial
  • Sunhwan Jo (Tue Feb 04 2014 - 14:47:17 CST)
  • Aron Broom (Tue Feb 04 2014 - 14:22:31 CST)
  • Monika Sharma (Tue Feb 04 2014 - 14:05:49 CST)
  • Monika Sharma (Sun Jan 19 2014 - 11:32:02 CST)
• Question regarding reverse CG to all-atom
  • parikshit moitra (Tue Jan 21 2014 - 04:42:04 CST)
• Question to NAMD source
  • Jim Phillips (Thu Sep 04 2014 - 11:25:48 CDT)
  • Norman Geist (Thu Sep 04 2014 - 08:02:31 CDT)
• Questions about lambda scheme in free energy perturbation
  • Jérôme Hénin (Tue Feb 24 2015 - 16:18:21 CST)
  • Jian Dai (Tue Feb 24 2015 - 08:59:57 CST)
• Questions on calling external program to calculate force with NAMD
  • Wasut Pornpatcharapong (Mon Feb 10 2014 - 15:41:48 CST)
• Random segfault for MPI based REMD at startup
  • Norman Geist (Wed Apr 02 2014 - 00:34:20 CDT)
• Rapid and accurate parameterization of new molecules in CHARMM
  • Kenno Vanommeslaeghe (Wed May 28 2014 - 10:35:07 CDT)
  • Aaron Larsen (Tue May 27 2014 - 19:22:22 CDT)
  • Kenno Vanommeslaeghe (Tue May 27 2014 - 17:58:42 CDT)
  • Tristan Croll (Tue May 27 2014 - 17:23:07 CDT)
  • JC Gumbart (Tue May 27 2014 - 09:19:40 CDT)
  • Aaron Larsen (Tue May 27 2014 - 08:21:06 CDT)
• RATTLE Error During Minimization of Charmm Gui Generated Bilayer
  • Chitrak Gupta (Fri Dec 18 2015 - 09:08:27 CST)
  • Jim Phillips (Thu Dec 17 2015 - 19:49:32 CST)
  • Chitrak Gupta (Wed Dec 16 2015 - 11:23:39 CST)
  • begüm alaybeyoÄŸlu (Wed Dec 16 2015 - 10:21:17 CST)
  • Chitrak Gupta (Wed Dec 16 2015 - 09:21:07 CST)
  • begüm alaybeyoÄŸlu (Wed Dec 16 2015 - 03:46:10 CST)
  • Chitrak Gupta (Tue Dec 15 2015 - 12:46:36 CST)
  • begüm alaybeyoÄŸlu (Tue Dec 15 2015 - 10:27:48 CST)
• RBCG and NAMD 2.9
  • Ramya Gamini (Wed Apr 16 2014 - 14:49:54 CDT)
  • Raul Araya (Wed Apr 16 2014 - 13:21:43 CDT)
• RDF calculation of crystal system
  • Axel Kohlmeyer (Sat Aug 30 2014 - 01:49:16 CDT)
  • Fatemeh Omidbeygi (Sat Aug 30 2014 - 00:41:02 CDT)
• RDF calculation with NAMD
  • Ana Celia Vila Verde (Tue Jan 21 2014 - 11:23:57 CST)
  • Dian Jiao (Tue Jan 14 2014 - 15:05:32 CST)
• Reassure fluctuations in course of simulation
  • James Starlight (Mon Jan 20 2014 - 03:19:51 CST)
• recent comparison of NAMD to other MD engines
  • Bennion, Brian (Fri Jan 24 2014 - 12:59:21 CST)
  • Tristan Croll (Fri Jan 24 2014 - 02:44:05 CST)
  • JC Gumbart (Thu Jan 23 2014 - 11:14:22 CST)
  • Hannes Loeffler (Thu Jan 23 2014 - 04:05:18 CST)
  • Giacomo Fiorin (Wed Jan 22 2014 - 20:38:29 CST)
  • Bennion, Brian (Wed Jan 22 2014 - 18:22:03 CST)
• recommendations for a fast multicore workstation
  • Jeff Comer (Tue Nov 24 2015 - 11:56:54 CST)
• Recomposing the system splitted by periodicity
  • Tristan Croll (Thu Jun 11 2015 - 23:22:50 CDT)
  • Francesco Pietra (Thu Jun 11 2015 - 04:34:57 CDT)
• Reducing the amount of work being done on CPU
  • Maxime Boissonneault (Tue Sep 01 2015 - 09:48:24 CDT)
• Reg : MD simulation with DMSO instead of water
  • Kenno Vanommeslaeghe (Tue Jun 17 2014 - 13:13:02 CDT)
  • Axel Kohlmeyer (Tue Jun 17 2014 - 06:12:55 CDT)
  • Akshay Bhatnagar (Tue Jun 17 2014 - 06:04:58 CDT)
• Reg. restarting a Thermodynamic Integration Run
  • Aditya Chattopadhyay (Mon Jan 12 2015 - 09:32:26 CST)
• Reg: deciding cell basis vector
  • Aron Broom (Mon Jul 21 2014 - 12:39:39 CDT)
  • Akshay Bhatnagar (Mon Jul 21 2014 - 08:57:57 CDT)
• Reg: deformation of water box during equilibration
  • Branko (Sat Jun 07 2014 - 05:05:35 CDT)
  • Aron Broom (Fri Jun 06 2014 - 22:28:02 CDT)
  • Akshay Bhatnagar (Fri Jun 06 2014 - 21:15:30 CDT)
  • Aron Broom (Fri Jun 06 2014 - 12:37:30 CDT)
  • Akshay Bhatnagar (Fri Jun 06 2014 - 11:35:34 CDT)
• Reg: dielectric constant calculations in NAMD
  • Akshay Bhatnagar (Fri Oct 31 2014 - 00:51:24 CDT)
• Reg: error in log file
  • Jim Phillips (Thu Oct 30 2014 - 10:46:01 CDT)
  • Akshay Bhatnagar (Tue Oct 21 2014 - 20:36:48 CDT)
• Reg: LangevinPistonDecay and LangevinPistonPeriod
  • Akshay Bhatnagar (Thu Jul 24 2014 - 02:04:25 CDT)
• Reg: minimization
  • Akshay Bhatnagar (Thu Sep 25 2014 - 04:52:40 CDT)
  • Akshay Bhatnagar (Thu Sep 25 2014 - 04:51:52 CDT)
  • Axel Kohlmeyer (Wed Sep 24 2014 - 23:44:35 CDT)
  • Akshay Bhatnagar (Wed Sep 24 2014 - 23:35:16 CDT)
• Reg: movement of protein outside box
  • Aron Broom (Mon Jun 09 2014 - 22:09:28 CDT)
  • Akshay Bhatnagar (Mon Jun 09 2014 - 20:46:56 CDT)
• Reg: QM/MM calculations in NAMD
  • Akshay Bhatnagar (Mon Nov 10 2014 - 07:05:40 CST)
• Reg: simulating an amino acid in dichloromethane
  • Akshay Bhatnagar (Mon Jan 05 2015 - 06:46:07 CST)
  • Branko (Mon Jan 05 2015 - 05:39:13 CST)
  • Jeff Comer (Sat Jan 03 2015 - 00:34:17 CST)
  • Akshay Bhatnagar (Fri Jan 02 2015 - 23:18:45 CST)
• Reg: solvating in a non-standard solvent
  • Akshay Bhatnagar (Wed Mar 25 2015 - 02:38:00 CDT)
  • Akshay Bhatnagar (Thu Mar 19 2015 - 23:38:24 CDT)
  • Maxim Belkin (Thu Mar 19 2015 - 12:06:38 CDT)
  • Maxim Belkin (Thu Mar 19 2015 - 11:59:28 CDT)
  • Jeff Comer (Thu Mar 19 2015 - 09:02:10 CDT)
  • Akshay Bhatnagar (Thu Mar 19 2015 - 01:40:55 CDT)
  • Jeff Comer (Wed Mar 18 2015 - 09:44:12 CDT)
  • Josh Vermaas (Wed Mar 18 2015 - 09:08:24 CDT)
  • Branko (Wed Mar 18 2015 - 07:19:45 CDT)
  • Akshay Bhatnagar (Wed Mar 18 2015 - 01:29:20 CDT)
• Reg: solvation in DMSO
  • Akshay Bhatnagar (Mon Sep 01 2014 - 00:01:44 CDT)
• Reg: topology file amidated and acetylated disulfide bridged Cystine
  • Akshay Bhatnagar (Fri Apr 10 2015 - 05:05:42 CDT)
• Regarding biasTemperature used in Well-tempered metadynamics
  • Giacomo Fiorin (Tue Oct 06 2015 - 09:01:52 CDT)
  • Vijay L. Roy (Tue Oct 06 2015 - 01:49:12 CDT)
• Regarding colvar distancez
  • Cosseddu, Salvatore (Sat Mar 08 2014 - 07:44:39 CST)
  • Subbarao Kanchi (Sat Mar 08 2014 - 05:00:28 CST)
• Regarding FFTW routines usage in NAMD
  • Axel Kohlmeyer (Tue Oct 20 2015 - 08:10:09 CDT)
  • Puneet Singh (Tue Oct 20 2015 - 07:39:50 CDT)
• Regarding free energy cost incurred by using pseudo bonds
  • Sharmon (Thu Jul 10 2014 - 13:29:29 CDT)
• Regarding NAMD and MD simulations
  • Joel Moniz (Mon Jul 07 2014 - 01:42:04 CDT)
• Regarding NAMD installation
  • Sourav Ray (Mon Aug 17 2015 - 02:53:00 CDT)
  • Pragya Priyadarshini (Mon Aug 17 2015 - 02:45:13 CDT)
• regarding PME grid setting problem
  • amit banerjee (Sun Jan 04 2015 - 18:31:44 CST)
• Regarding problem in psfgen of heparin
  • Tristan Croll (Tue Oct 06 2015 - 18:44:21 CDT)
  • Tristan Croll (Mon Oct 05 2015 - 23:00:32 CDT)
  • siddharth kamal (Fri Oct 02 2015 - 14:20:15 CDT)
• Regarding significance of days per ns (days/ns) parameter in NAMD benchmark
  • Brian Radak (Tue Oct 20 2015 - 09:46:32 CDT)
  • Puneet Singh (Tue Oct 20 2015 - 01:01:24 CDT)
• Regarding Temperature calculation from velocity trajectory of NAMD-2.9
  • Shailesh Pandey (Fri Jul 11 2014 - 06:14:59 CDT)
  • Shailesh Pandey (Thu Jul 10 2014 - 04:30:20 CDT)
• REMD
  • Boshra Moradi (Tue Feb 18 2014 - 02:08:53 CST)
• remd across gpus
  • Francesco Pietra (Mon Mar 31 2014 - 02:41:24 CDT)
  • Francesco Pietra (Sat Mar 29 2014 - 02:29:12 CDT)
• REMD on GPU cluster
  • Norman Geist (Tue Apr 14 2015 - 11:01:49 CDT)
  • Michael Feig (Tue Apr 14 2015 - 08:00:16 CDT)
  • Norman Geist (Tue Apr 14 2015 - 02:10:03 CDT)
  • Michael Feig (Mon Apr 13 2015 - 17:09:05 CDT)
• REMD on IBM iDataPlex DX360M3
  • Francesco Pietra (Tue Jul 08 2014 - 12:14:10 CDT)
  • Francesco Pietra (Thu Jul 03 2014 - 09:42:41 CDT)
  • Francesco Pietra (Thu Jul 03 2014 - 04:53:32 CDT)
  • Francesco Pietra (Thu Jul 03 2014 - 01:15:21 CDT)
• Remembering resid
  • Kevin C Chan (Thu Jun 18 2015 - 11:48:50 CDT)
  • Chitrak Gupta (Thu Jun 18 2015 - 08:52:08 CDT)
  • Branko (Thu Jun 18 2015 - 08:54:40 CDT)
  • Kevin C Chan (Thu Jun 18 2015 - 08:42:34 CDT)
• replica exchange and GPU acceleration
  • Mitchell Gleed (Mon Jul 13 2015 - 01:32:14 CDT)
  • Norman Geist (Mon Jul 13 2015 - 00:51:11 CDT)
  • Mitchell Gleed (Sun Jul 12 2015 - 22:36:54 CDT)
  • Norman Geist (Mon Jul 06 2015 - 01:38:11 CDT)
  • Mitchell Gleed (Sat Jul 04 2015 - 10:49:22 CDT)
  • Norman Geist (Fri Jul 03 2015 - 03:16:17 CDT)
  • Mitchell Gleed (Wed Jul 01 2015 - 11:01:50 CDT)
  • Norman Geist (Wed Jul 01 2015 - 02:13:56 CDT)
  • Mitchell Gleed (Tue Jun 30 2015 - 18:09:27 CDT)
• replica exchange module
  • Jessen Lucas (Tue Oct 27 2015 - 03:42:23 CDT)
  • Jessen Lucas (Mon Oct 26 2015 - 22:49:20 CDT)
  • Jessen Lucas (Mon Oct 26 2015 - 03:25:46 CDT)
  • Jessen Lucas (Mon Oct 26 2015 - 02:25:49 CDT)
  • Jessen Lucas (Mon Oct 26 2015 - 01:29:43 CDT)
• Replica Exchange Simulation in NAMD Precompiled binary in single node.
  • Nizar Masbukhin (Thu Oct 16 2014 - 17:09:05 CDT)
• Require Suggestion
  • amit banerjee (Tue Feb 18 2014 - 23:39:40 CST)
• Residue number changed to hexadecimal string
  • Jim Phillips (Fri Feb 06 2015 - 00:38:00 CST)
  • K Miura (Thu Feb 05 2015 - 23:34:24 CST)
• residue_rmsd.tcl segmentation fault
  • Axel Kohlmeyer (Fri Apr 04 2014 - 04:12:38 CDT)
  • Axel Kohlmeyer (Fri Apr 04 2014 - 03:03:55 CDT)
  • John Xi (Thu Apr 03 2014 - 21:49:05 CDT)
• restart error
  • Lara rajam (Mon Jul 20 2015 - 10:15:23 CDT)
• Restart heating
  • Fotis Baltoumas (Fri Jan 16 2015 - 12:26:09 CST)
  • Francesco Pietra (Fri Jan 16 2015 - 12:04:33 CST)
• restart simulation
  • oguz gurbulak (Thu Apr 23 2015 - 09:22:38 CDT)
• Restarting an abruptly interrupted simulation
  • Prathit Chatterjee (Tue Mar 17 2015 - 02:03:52 CDT)
  • Sourav Ray (Tue Mar 17 2015 - 01:30:21 CDT)
• Restarting an FEP simulation
  • Shyno Mathew (Sat Mar 22 2014 - 14:00:06 CDT)
  • Shyno Mathew (Mon Mar 10 2014 - 11:58:02 CDT)
  • Shyno Mathew (Wed Mar 05 2014 - 12:43:48 CST)
• Restarting NAMD simulation
  • Sourav Ray (Thu Mar 12 2015 - 09:16:26 CDT)
  • Norman Geist (Thu Mar 12 2015 - 09:13:14 CDT)
  • Sourav Ray (Thu Mar 12 2015 - 08:30:27 CDT)
• Restarting trajectories
  • Grzegorz Nawrocki (Thu May 21 2015 - 09:10:28 CDT)
  • Bennion, Brian (Wed May 20 2015 - 14:38:43 CDT)
  • Grzegorz Nawrocki (Wed May 20 2015 - 14:24:08 CDT)
  • Emad Tajkhorshid (Wed May 20 2015 - 12:32:12 CDT)
  • Michael Feig (Wed May 20 2015 - 11:18:12 CDT)
  • Maxim Belkin (Wed May 20 2015 - 11:11:33 CDT)
  • Josh Vermaas (Wed May 20 2015 - 11:07:42 CDT)
  • Axel Kohlmeyer (Wed May 20 2015 - 11:07:56 CDT)
  • Michael Feig (Wed May 20 2015 - 10:59:07 CDT)
  • Axel Kohlmeyer (Wed May 20 2015 - 10:49:11 CDT)
  • Bennion, Brian (Wed May 20 2015 - 10:42:46 CDT)
  • Michael Feig (Wed May 20 2015 - 02:47:08 CDT)
  • Michael Feig (Wed May 20 2015 - 03:01:37 CDT)
• Restoring simulation from the previous run
  • James Starlight (Wed Mar 19 2014 - 09:38:18 CDT)
  • James Starlight (Wed Mar 19 2014 - 03:32:31 CDT)
• Restraining angle between bond vector and coordinate vector
  • Seth Axen (Wed Mar 25 2015 - 19:01:40 CDT)
  • Jeff Comer (Mon Mar 23 2015 - 18:17:18 CDT)
  • Jérôme Hénin (Mon Mar 23 2015 - 15:45:02 CDT)
  • Seth Axen (Mon Mar 23 2015 - 15:26:37 CDT)
• restraining bonds
  • Kenno Vanommeslaeghe (Tue Sep 02 2014 - 11:04:37 CDT)
  • Kenno Vanommeslaeghe (Mon Sep 01 2014 - 10:37:17 CDT)
  • Tristan Croll (Mon Sep 01 2014 - 01:09:05 CDT)
  • Tristan Croll (Mon Sep 01 2014 - 00:57:28 CDT)
  • Tristan Croll (Mon Sep 01 2014 - 00:45:22 CDT)
  • Neelanjana Sengupta (Sun Aug 31 2014 - 23:50:24 CDT)
• Restraints between ion and small molecule
  • Daniel Torrente (Mon Jul 14 2014 - 20:51:55 CDT)
  • Aron Broom (Mon Jul 14 2014 - 21:13:44 CDT)
  • Kenno Vanommeslaeghe (Thu Jun 26 2014 - 14:43:47 CDT)
  • Aron Broom (Thu Jun 26 2014 - 13:55:13 CDT)
  • Kenno Vanommeslaeghe (Thu Jun 26 2014 - 13:21:42 CDT)
  • Kenno Vanommeslaeghe (Thu Jun 26 2014 - 13:16:31 CDT)
  • Daniel Torrente (Thu Jun 26 2014 - 11:53:49 CDT)
• Restraints on the outer solutes
  • Vibhor Agrawal (Mon Dec 28 2015 - 03:50:57 CST)
  • Diksha Dubey (Mon Dec 28 2015 - 03:39:00 CST)
• Reverse Coarse Graining using VMD CG Builder
  • Peter Freddolino (Wed Oct 21 2015 - 11:25:44 CDT)
  • Peter Freddolino (Wed Oct 21 2015 - 10:49:38 CDT)
  • Ardavan Mehdizadeh (Wed Oct 21 2015 - 10:41:55 CDT)
  • Peter Freddolino (Wed Oct 21 2015 - 07:29:13 CDT)
  • Ardavan Mehdizadeh (Wed Oct 21 2015 - 03:15:35 CDT)
• Reverse osmosis simulation
  • Z (Thu Jan 22 2015 - 05:09:24 CST)
• RE£º NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance
  • Axel Kohlmeyer (Sun Feb 23 2014 - 21:26:40 CST)
• RE： NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance
  • sunyeping (Wed Mar 12 2014 - 09:42:34 CDT)
  • sunyeping (Mon Feb 24 2014 - 03:32:06 CST)
  • sunyeping (Sun Feb 23 2014 - 21:13:52 CST)
• RE： The water box shrinks at the start of the MD simulation
  • sunyeping (Sun Jul 27 2014 - 19:19:15 CDT)
• Re：tutorial-l: Protein structure distorted after Energy minimization with NAMD
  • sunyeping (Wed Oct 08 2014 - 21:58:02 CDT)
• Rigid bonds and non-bonded energy
  • Grzegorz Nawrocki (Wed Oct 21 2015 - 08:29:22 CDT)
  • Grzegorz Nawrocki (Tue Oct 20 2015 - 11:09:20 CDT)
  • Brian Radak (Tue Oct 20 2015 - 12:52:34 CDT)
  • Grzegorz Nawrocki (Tue Oct 20 2015 - 10:11:42 CDT)
  • Brian Radak (Tue Oct 20 2015 - 10:33:51 CDT)
  • Brian Radak (Mon Oct 19 2015 - 14:40:51 CDT)
  • Brian Radak (Fri Oct 16 2015 - 17:42:34 CDT)
  • Grzegorz Nawrocki (Fri Oct 16 2015 - 16:39:48 CDT)
• Root mean square deviation..........
  • Gurpreet Kaur Dhindsa (Tue Aug 12 2014 - 12:58:38 CDT)
• Rotating Constraints
  • Sourav Purohit (Tue Feb 24 2015 - 14:23:26 CST)
• RSMDTT keyword for nucleic acids
  • Aaron Larsen (Wed Feb 05 2014 - 14:43:13 CST)
• Rule of thumb for equilibration
  • Aron Broom (Mon Jul 28 2014 - 09:59:04 CDT)
  • Stephan Grein (Mon Jul 28 2014 - 09:45:43 CDT)
• run NAMD 2.10 on Xeon Phi machine
  • Xiaoge Wang (Tue Jul 28 2015 - 12:50:23 CDT)
• run on sungle node
  • Alexander Tzanov (Wed Jun 24 2015 - 13:37:01 CDT)
  • Axel Kohlmeyer (Wed Jun 24 2015 - 11:16:34 CDT)
  • Josh Vermaas (Wed Jun 24 2015 - 11:14:16 CDT)
  • Alexander Tzanov (Wed Jun 24 2015 - 11:03:24 CDT)
  • Alexander Tzanov (Wed Jun 24 2015 - 09:56:18 CDT)
• runaway minimizations
  • Bennion, Brian (Thu Feb 20 2014 - 12:06:54 CST)
• Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations)
  • Tristan Croll (Fri Feb 21 2014 - 01:44:39 CST)
  • Norman Geist (Fri Feb 21 2014 - 01:34:55 CST)
  • Tristan Croll (Thu Feb 20 2014 - 17:52:22 CST)
  • Bennion, Brian (Thu Feb 20 2014 - 11:53:31 CST)
  • Tristan Croll (Wed Feb 19 2014 - 17:53:43 CST)
  • Tristan Croll (Wed Feb 12 2014 - 17:51:13 CST)
  • Bennion, Brian (Wed Feb 12 2014 - 10:57:12 CST)
  • Tristan Croll (Tue Feb 11 2014 - 20:07:59 CST)
• running a calculation during simulation
  • Jérôme Hénin (Tue Oct 21 2014 - 04:03:13 CDT)
  • Ajasja LjubetiÄ� (Tue Oct 21 2014 - 02:52:21 CDT)
  • Maxim Belkin (Mon Oct 20 2014 - 18:00:03 CDT)
  • Josh Vermaas (Mon Oct 20 2014 - 16:38:57 CDT)
  • btreece_at_andrew.cmu.edu (Mon Oct 20 2014 - 16:08:12 CDT)
• running benchmarks on NAMD-Lite
  • Hassan Kianinejad (Fri Mar 14 2014 - 17:35:21 CDT)
• Running Charmrun/NAMD with more than 10 processes fails
  • K Miura (Tue Dec 16 2014 - 02:53:36 CST)
• Running constant pH molecular dynamics (CpHMD)
  • Jason Swails (Thu Jul 09 2015 - 20:05:36 CDT)
  • Leonardo Herrera (Thu Jul 09 2015 - 19:00:02 CDT)
• Running CUDA on a laptop
  • Tristan Croll (Tue Jan 13 2015 - 19:14:31 CST)
  • Tristan Croll (Tue Jan 13 2015 - 18:29:59 CST)
• Running CUDA-enabled NAMD on multiple nodes without InfiniBand?
  • Michel van der List (Wed Dec 03 2014 - 12:06:03 CST)
  • Michel van der List (Mon Dec 01 2014 - 08:40:46 CST)
• running Linux-x86_64-multicore precompiled version at 2 hexa-core CPUs?
  • Axel Kohlmeyer (Thu Jul 17 2014 - 09:35:59 CDT)
  • Andras Borosy (Thu Jul 17 2014 - 09:27:46 CDT)
• running multicore version on a 2-CPU node
  • Gianluca Interlandi (Sat Jul 04 2015 - 15:33:25 CDT)
• running Multiple-replicas metadynamics
  • Osvalds Verners (Fri May 16 2014 - 14:21:28 CDT)
  • Giacomo Fiorin (Fri May 16 2014 - 14:00:41 CDT)
  • Osvalds Verners (Fri May 16 2014 - 13:01:08 CDT)
• running namd gpu version
  • Sanjana Anil Kumar Nair (Sat Aug 29 2015 - 05:21:41 CDT)
• running NAMD in parallel
  • Jim Phillips (Sat Nov 29 2014 - 16:51:06 CST)
  • Kshatresh Dutta Dubey (Fri Nov 28 2014 - 19:29:43 CST)
• Running NAMD via GROMACS topology
  • Mike Makowski (Sun Aug 10 2014 - 18:05:21 CDT)
  • Mike Makowski (Sun Aug 10 2014 - 17:44:35 CDT)
• Running two molecule coarse-grained simulation
  • Prathit Chatterjee (Thu Apr 16 2015 - 11:37:21 CDT)
  • Sourav Ray (Thu Apr 16 2015 - 06:27:30 CDT)
  • Prathit Chatterjee (Wed Apr 15 2015 - 09:24:32 CDT)
  • Sourav Ray (Wed Apr 15 2015 - 09:05:43 CDT)
  • Sourav Ray (Wed Apr 15 2015 - 05:51:29 CDT)
  • Sourav Ray (Wed Apr 15 2015 - 05:39:18 CDT)
• running with replica exchange on stampede
  • Peter Freddolino (Sun May 24 2015 - 21:40:09 CDT)
• Sampling frequency
  • Jeff Comer (Tue Sep 01 2015 - 08:40:14 CDT)
  • Dr. Eddie (Mon Aug 31 2015 - 14:02:46 CDT)
• SASA calculation
  • Siva Dasetty (Thu Sep 04 2014 - 09:03:56 CDT)
• sausage plot for a namd trajectory in vmd
  • Thomas C. Bishop (Tue Aug 11 2015 - 10:30:23 CDT)
  • Aaron Larsen (Fri Jul 31 2015 - 05:44:17 CDT)
  • luca belmonte (Fri Jul 31 2015 - 05:01:02 CDT)
• scaling non-bonded interactiion parameter for specific pairs
  • MEHRAN MB (Fri Feb 27 2015 - 14:01:29 CST)
  • Jeff Comer (Fri Feb 27 2015 - 13:58:31 CST)
  • MEHRAN MB (Fri Feb 27 2015 - 13:15:11 CST)
• Scaling solvent-solute intermolecular interactions
  • Jason Swails (Wed May 14 2014 - 10:20:57 CDT)
  • Michael Bellucci (Wed May 14 2014 - 08:50:36 CDT)
  • Jason Swails (Tue May 13 2014 - 16:57:14 CDT)
  • Axel Kohlmeyer (Tue May 13 2014 - 15:17:53 CDT)
  • Michael Bellucci (Tue May 13 2014 - 15:09:06 CDT)
  • Axel Kohlmeyer (Tue May 13 2014 - 13:56:02 CDT)
  • Michael Bellucci (Tue May 13 2014 - 13:34:13 CDT)
• School on Molecular Dynamics and Enhanced Sampling Methods @ Temple University July 6-10, 2015
  • Axel Kohlmeyer (Fri May 08 2015 - 11:28:54 CDT)
• School on Molecular Dynamics with NAMD and LAMMPS in Philadelphia, August 18-22 2014
  • Axel Kohlmeyer (Thu Jul 17 2014 - 14:48:33 CDT)
• script error
  • Nikhil Maroli (Fri Oct 02 2015 - 08:44:13 CDT)
• Second Announcement: ‘Hands On’ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015)
  • Lela Vukovic (Tue Jun 16 2015 - 12:04:27 CDT)
• Segmentation Fault - Debug
  • Kumar, Amit (Mon Oct 05 2015 - 09:13:14 CDT)
• segmentation fault in accelMD
  • Anna Modzelewska (Mon Jul 28 2014 - 05:56:05 CDT)
• segmentation fault when running with mpirun
  • Puneet Singh (Fri Jul 24 2015 - 08:05:23 CDT)
• Self-Assemble Monolayer--Periodic Boundary Conditions
  • Natnael Doilicho (Wed Oct 01 2014 - 16:14:52 CDT)
  • Natnael Doilicho (Mon Sep 29 2014 - 18:03:18 CDT)
• Set exact molarity in cell
  • Stephan Grein (Thu Aug 28 2014 - 09:08:42 CDT)
• Setting constraints for SMD simulation
  • Charles Whidborne (Mon Sep 15 2014 - 20:20:39 CDT)
• Setting up membrane protein simulation from existing conformation?
  • Per Larsson (Wed May 07 2014 - 15:12:53 CDT)
  • Kenno Vanommeslaeghe (Wed May 07 2014 - 14:44:00 CDT)
  • Per Larsson (Wed May 07 2014 - 14:17:41 CDT)
• setting up namd simulation in IBM Blue Gene/L
  • Santosh Kumar Chaudhary (Sat Dec 20 2014 - 01:53:14 CST)
  • Jim Phillips (Fri Dec 19 2014 - 12:55:33 CST)
  • hannes.loeffler_at_stfc.ac.uk (Thu Dec 18 2014 - 01:43:11 CST)
  • hannes.loeffler_at_stfc.ac.uk (Thu Dec 18 2014 - 01:36:36 CST)
  • Santosh Kumar Chaudhary (Thu Dec 18 2014 - 00:09:48 CST)
  • hannes.loeffler_at_stfc.ac.uk (Wed Dec 17 2014 - 07:07:23 CST)
  • Santosh Kumar Chaudhary (Wed Dec 17 2014 - 06:21:17 CST)
• Several questions about targeted molecular dynamics
  • sunyeping (Mon Oct 19 2015 - 04:54:09 CDT)
• SHAKE or RATTLE algorithm
  • David Hardy (Fri Apr 04 2014 - 16:28:54 CDT)
  • Axel Kohlmeyer (Fri Apr 04 2014 - 15:44:45 CDT)
  • Ramin Ekhteiari (Fri Apr 04 2014 - 15:08:04 CDT)
• Should PME be used for electrostatic interaction energy calculations?
  • Thomas Evangelidis (Thu Jun 19 2014 - 02:38:50 CDT)
  • Fotis Baltoumas (Wed Jun 18 2014 - 12:59:16 CDT)
• Siginificant speedup by updating nvidia driver
  • Norman Geist (Mon Aug 25 2014 - 11:06:38 CDT)
• Silent crash NAMD-multicore-CUDA
  • Aron Broom (Tue Aug 19 2014 - 11:17:04 CDT)
  • MEHRAN MB (Tue Aug 19 2014 - 11:06:34 CDT)
  • MEHRAN MB (Thu Jul 31 2014 - 18:27:55 CDT)
  • Aron Broom (Wed Jul 30 2014 - 17:50:54 CDT)
  • MEHRAN MB (Wed Jul 30 2014 - 17:23:10 CDT)
• Simulated Annealing with many frequent restarts
  • Maxim Belkin (Fri May 01 2015 - 11:49:41 CDT)
  • Phillips, Carolyn L. (Fri May 01 2015 - 11:24:13 CDT)
  • Maxim Belkin (Fri May 01 2015 - 11:18:21 CDT)
  • Phillips, Carolyn L. (Fri May 01 2015 - 10:16:43 CDT)
  • Maxim Belkin (Fri May 01 2015 - 09:46:21 CDT)
  • Francesco Pietra (Fri May 01 2015 - 01:21:28 CDT)
  • Phillips, Carolyn L. (Thu Apr 30 2015 - 18:51:19 CDT)
• simulating graphene sheets (with bonds across boundaries) with water
  • upayan baul (Wed Sep 16 2015 - 05:40:38 CDT)
  • Axel Kohlmeyer (Tue Sep 15 2015 - 19:22:27 CDT)
  • Abhishek TYAGI (Tue Sep 15 2015 - 18:58:52 CDT)
  • upayan baul (Tue Sep 15 2015 - 06:57:20 CDT)
  • Abhishek TYAGI (Mon Sep 14 2015 - 19:28:04 CDT)
  • upayan baul (Mon Sep 14 2015 - 06:59:00 CDT)
• simulating TIP5P water
  • Monika Madhavi (Mon Oct 12 2015 - 05:10:35 CDT)
  • Monika Madhavi (Mon Oct 12 2015 - 03:44:50 CDT)
  • Peter Freddolino (Sat Oct 10 2015 - 21:33:50 CDT)
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• Simulation Box Rescaling
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• Simulation crash during NPT equilibration
  • James Starlight (Fri Apr 11 2014 - 05:58:17 CDT)
• Simulation Do not Run in the Cluster
  • Roy Fernando (Sun Sep 21 2014 - 12:16:44 CDT)
• Simulation of a membrane protein with large extracellular domains
  • Jim Phillips (Thu Nov 13 2014 - 16:05:08 CST)
  • Josh Vermaas (Thu Nov 13 2014 - 08:35:43 CST)
  • Fotis Baltoumas (Thu Nov 13 2014 - 07:30:54 CST)
• simulation options available with GPU
  • Ana Celia Vila Verde (Tue Sep 16 2014 - 02:52:51 CDT)
  • Ana Celia Vila Verde (Tue Sep 16 2014 - 02:58:28 CDT)
• single strand DNA in hairpin conformation
  • Urszula Uciechowska (Thu Feb 12 2015 - 03:14:55 CST)
• slice of water box
  • Hongbo Du (Wed Apr 09 2014 - 20:22:04 CDT)
  • Boshra Moradi (Wed Apr 09 2014 - 17:13:12 CDT)
• slow heating of system
  • Maxim Belkin (Sun Apr 19 2015 - 04:08:03 CDT)
  • Dhiraj Srivastava (Sun Apr 19 2015 - 00:55:58 CDT)
• SMD constant velocity not constant
  • Axel Kohlmeyer (Wed Oct 29 2014 - 20:04:28 CDT)
  • Charles Whidborne (Wed Oct 29 2014 - 19:25:08 CDT)
• SMD or moving contraints
  • Kevin C Chan (Thu Oct 15 2015 - 21:50:20 CDT)
• SMD pulling speed
  • Giacomo Fiorin (Sat Sep 27 2014 - 21:16:15 CDT)
  • Charles Whidborne (Sat Sep 27 2014 - 20:45:48 CDT)
• SMD with PBC
  • Mahdi Tavakol (Thu Dec 24 2015 - 00:22:36 CST)
• SMP NAMD reports threads greater than physical cores, even when distributed to other nodes
  • Jim Phillips (Sat Dec 19 2015 - 21:39:50 CST)
  • Tom Coles (Fri Dec 18 2015 - 15:16:01 CST)
  • Jim Phillips (Fri Dec 18 2015 - 09:38:15 CST)
  • Tom Coles (Thu Dec 17 2015 - 10:26:20 CST)
• SMP vs Multicore
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• SOD topology with CHARMM36
  • Kenno Vanommeslaeghe (Tue Nov 11 2014 - 12:27:08 CST)
  • Josh Vermaas (Tue Nov 11 2014 - 11:08:26 CST)
  • Francesco Pietra (Tue Nov 11 2014 - 11:02:22 CST)
• solvate plugin watsize value
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• Solvation free energy calculation with MM/GBSA
  • Neelanjana Sengupta (Fri Sep 25 2015 - 07:36:50 CDT)
  • Jeff Comer (Thu Sep 24 2015 - 08:27:26 CDT)
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  • Neelanjana Sengupta (Wed Sep 23 2015 - 06:51:28 CDT)
• Solvation in non standard solvent
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• Specific Heat Calculation
  • Rawan Al Nsour (Fri Feb 07 2014 - 20:56:14 CST)
• Spikes in the Energy Plot
  • Viswanath Pasumarthi (Mon Feb 09 2015 - 02:26:08 CST)
• Spinangle with refgroup : Warning: discontinuous rotation!
  • nicolas martin (Thu Apr 10 2014 - 09:04:21 CDT)
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• startup phase 1 for benchmark
  • Branko (Tue May 12 2015 - 09:29:28 CDT)
• statistical error of mean force in (NAMD) ABF calculations
  • Jeff Comer (Thu Jul 02 2015 - 09:09:38 CDT)
  • Branko (Wed Jul 01 2015 - 05:09:48 CDT)
• Steered MD with the RMSD colvar
  • George Patargias (Thu Jul 03 2014 - 06:26:19 CDT)
  • Giacomo Fiorin (Wed May 21 2014 - 17:52:54 CDT)
  • George Patargias (Mon May 19 2014 - 05:01:12 CDT)
• Steered NAMD using AMBER Forcefield [Config File]
  • Zeinab Emami (Sun Jan 18 2015 - 10:07:51 CST)
• Steering colvars to defined points in space
  • Tristan Croll (Sun Jan 26 2014 - 22:44:09 CST)
  • Aron Broom (Sun Jan 26 2014 - 19:23:56 CST)
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• Step size in FEP calculation
  • Javad Noroozi (Tue Apr 15 2014 - 23:21:35 CDT)
• stepspercycle
  • Gianluca Interlandi (Sun Oct 18 2015 - 20:20:26 CDT)
• strange behavior of ABF
  • Danilo Di Maio (Tue Apr 14 2015 - 12:48:13 CDT)
  • Jérôme Hénin (Tue Apr 14 2015 - 07:06:47 CDT)
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• Strange glitches when performing energy minimization in MDFF simulations
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• string method in NAMD 2.10
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  • Jerry Karp (Mon Sep 21 2015 - 10:46:45 CDT)
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• String method in NAMD 2.10b1?
  • Jenny lou (Mon Oct 06 2014 - 12:58:17 CDT)
• Structure size limitation in NAMD
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• Subscribe
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• Symmetry restraints break IMD handshaking
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• System unstable after turning electric field on.
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• TCL command "run" erratic
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• Thermodynamic integration question
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• tools for Charmm
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• topology & force field parameters for Sorbitan monooleate (span 80)
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• Topology and Parameter File
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• Topology and parameters for Sodium dodecanoate
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• Truncated octahedron : Problems in PBC when reading a dcd file with NAMD
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• Two GPU-based workstation
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• two O atoms in CTER are unusually close
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• Umbrella Sampling in NAMD
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• Umbrella Sampling of Sugar Pseudorotation
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• Umbrella sampling using colvarconfig file with dihedrals
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  • Laura (Sun Jun 15 2014 - 12:29:39 CDT)
  • Shalton Evans (Sun May 11 2014 - 19:18:39 CDT)
  • MEHRAN MB (Fri Feb 14 2014 - 11:33:01 CST)
  • Zailo Leite (Fri Feb 14 2014 - 11:20:04 CST)
• unsuscribe
  • Cat Chenal (Thu Apr 10 2014 - 09:49:18 CDT)
• Updated Link: Postdoc positions available at IBM (bio-molecular modeling and MD)
  • Sourav Ray (Mon Mar 16 2015 - 12:30:29 CDT)
  • Payel Das (Mon Mar 16 2015 - 10:50:46 CDT)
• Usage of velDCDfile and forceDCDfile keywords in viscosity calculations
  • Debashis Kundu (Mon Dec 14 2015 - 00:34:56 CST)
• useGroupPressure
  • Anna Borlsky (Fri Jan 10 2014 - 17:09:32 CST)
• Using a different potential with NAMD
  • Axel Kohlmeyer (Fri Jun 12 2015 - 09:39:47 CDT)
  • Peter Freddolino (Fri Jun 12 2015 - 09:25:32 CDT)
  • Wade, Alex (Fri Jun 12 2015 - 09:08:48 CDT)
• using CHARMM-format Amber parameters in NAMD
  • Basheer (Wed Aug 20 2014 - 22:15:22 CDT)
  • Kenno Vanommeslaeghe (Wed Aug 20 2014 - 10:27:20 CDT)
  • Mike Makowski (Tue Aug 19 2014 - 23:34:13 CDT)
  • Basheer Subei (Tue Aug 19 2014 - 19:16:43 CDT)
• Using colvars for biasing potential in Umbrella Sampling
  • Giacomo Fiorin (Wed Jan 07 2015 - 10:08:11 CST)
  • begüm alaybeyoÄŸlu (Wed Jan 07 2015 - 10:01:17 CST)
• using NAMD with CHARMM36 ff
  • Tristan Croll (Wed Jan 21 2015 - 01:37:05 CST)
  • JC Gumbart (Sun Jan 18 2015 - 12:32:35 CST)
  • Branko (Sun Jan 18 2015 - 11:46:38 CST)
  • JC Gumbart (Sat Jan 17 2015 - 19:36:55 CST)
  • Maria Bykhovskaia (Sat Jan 17 2015 - 19:26:29 CST)
• Using nodelist file causes namd to hang
  • Douglas Houston (Sat Sep 20 2014 - 06:14:29 CDT)
  • Douglas Houston (Thu Jun 19 2014 - 12:25:25 CDT)
  • Douglas Houston (Wed Apr 09 2014 - 04:49:17 CDT)
  • Douglas Houston (Tue Apr 08 2014 - 08:50:15 CDT)
  • Douglas Houston (Tue Apr 08 2014 - 04:29:34 CDT)
• Using position-dependent diffusion to simulate long colvars trajectories
  • Ajasja LjubetiÄ� (Thu Apr 03 2014 - 07:36:28 CDT)
• Using the CHARMM36 forcefield with NAMD
  • Kenno Vanommeslaeghe (Fri May 09 2014 - 11:50:45 CDT)
  • Kenno Vanommeslaeghe (Wed Apr 23 2014 - 12:28:33 CDT)
  • Alex Utev (CMP) (Wed Apr 23 2014 - 11:15:08 CDT)
• Using the multi-copy version of NAMD on a linux workstation
  • Avisek Das (Mon Jun 01 2015 - 12:22:46 CDT)
  • Norman Geist (Mon Jun 01 2015 - 02:43:36 CDT)
  • Avisek Das (Fri May 29 2015 - 14:43:18 CDT)
• Van der Waals and Electrostatic Forces - CUDA
  • Kostas Malavazos (Tue Nov 10 2015 - 11:11:37 CST)
• variable force constant
  • Aron Broom (Thu Jul 10 2014 - 13:00:32 CDT)
  • Lu Hong (Thu Jul 10 2014 - 12:34:58 CDT)
• Various questions
  • Douglas Houston (Tue Feb 04 2014 - 07:26:05 CST)
  • Norman Geist (Mon Feb 03 2014 - 04:34:48 CST)
  • Douglas Houston (Mon Feb 03 2014 - 03:52:42 CST)
  • Douglas Houston (Wed Jan 22 2014 - 08:31:03 CST)
  • Douglas Houston (Tue Jan 21 2014 - 09:42:14 CST)
• VDW energy diverged & VMD functions applied on cluster
  • Simon Kit Sang Chu (Sat Jul 18 2015 - 16:37:54 CDT)
• VDW energy: positive or negative?
  • Kenno Vanommeslaeghe (Wed Mar 05 2014 - 17:21:12 CST)
  • Jason Swails (Tue Mar 04 2014 - 20:04:38 CST)
  • Kenno Vanommeslaeghe (Tue Mar 04 2014 - 19:14:15 CST)
  • PANAGIOTA KYRIAKOU (Tue Mar 04 2014 - 18:24:54 CST)
  • Kenno Vanommeslaeghe (Tue Mar 04 2014 - 17:50:50 CST)
  • Axel Kohlmeyer (Tue Mar 04 2014 - 17:28:08 CST)
  • PANAGIOTA KYRIAKOU (Tue Mar 04 2014 - 17:20:53 CST)
• vdw parameter error | atom type <-> name problem
  • Art (Wed Mar 11 2015 - 14:03:38 CDT)
• vdW-only fep between two ions
  • Christopher Rowley (Tue Nov 04 2014 - 14:43:08 CST)
• velocity IO with psfgen?
  • John Stone (Thu Feb 26 2015 - 12:47:52 CST)
  • Maxim Belkin (Thu Feb 26 2015 - 12:14:24 CST)
  • Brian Radak (Thu Feb 26 2015 - 11:42:22 CST)
  • John Stone (Thu Feb 26 2015 - 11:03:15 CST)
  • Brian Radak (Thu Feb 26 2015 - 10:56:57 CST)
  • Ajasja LjubetiÄ� (Thu Feb 26 2015 - 10:37:55 CST)
  • Brian Radak (Thu Feb 26 2015 - 09:41:04 CST)
• velocity manipulation
  • Ajasja LjubetiÄ� (Thu Oct 16 2014 - 08:24:34 CDT)
  • Axel Kohlmeyer (Thu Oct 16 2014 - 08:21:17 CDT)
  • mostafa raeesi (Thu Oct 16 2014 - 06:37:02 CDT)
• Verification of NAMD Results
  • Kanzliersch, Lukas (Wed Aug 05 2015 - 15:32:38 CDT)
• Viscosity Calculation using EMD
  • Gaurab Sarkar (Mon Dec 14 2015 - 13:22:02 CST)
• vmd-l: Accelerated MD (aMD)
  • Juan R. Perilla (Sun Jul 27 2014 - 20:23:00 CDT)
• vmd-l: citing SODIUM program
  • John Stone (Tue Jan 14 2014 - 09:19:27 CST)
• vmd-l: ffTK problem: OPT.Charges
  • Zeinab Emami (Fri Nov 07 2014 - 11:13:04 CST)
  • Mayne, Christopher G (Fri Nov 07 2014 - 10:51:57 CST)
• vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech
  • Sourav Ray (Fri Sep 11 2015 - 11:15:47 CDT)
  • JC Gumbart (Fri Sep 11 2015 - 10:08:07 CDT)
  • Sourav Ray (Wed Sep 09 2015 - 22:51:54 CDT)
• vmd-l: GBIS in NAMD 2.10 CUDA with IMD
  • John Stone (Wed Feb 11 2015 - 10:03:39 CST)
• vmd-l: gromacs to charmm conversion
  • Ajasja LjubetiÄ� (Fri Oct 23 2015 - 03:28:28 CDT)
• vmd-l: Including two parameters for protein-ligand simulation
  • Sourav Ray (Wed Oct 28 2015 - 02:20:04 CDT)
• vmd-l: making psf files
  • Kenno Vanommeslaeghe (Mon Oct 13 2014 - 12:18:31 CDT)
  • Zeinab Emami (Mon Oct 13 2014 - 04:55:06 CDT)
• vmd-l: membrane lipid involvement of cholesterol
  • Richard Wood (Sat Jul 26 2014 - 09:07:57 CDT)
  • Richard Wood (Sat Jul 26 2014 - 06:26:59 CDT)
• vmd-l: NAMD energy calculation
  • Morgan, Brittany (Wed Jul 02 2014 - 11:58:22 CDT)
  • Ramin Ekhteiari (Tue Jul 01 2014 - 12:07:47 CDT)
  • Morgan, Brittany (Tue Jul 01 2014 - 09:26:44 CDT)
  • John Stone (Mon Jun 30 2014 - 22:59:28 CDT)
• vmd-l: Number of pdb and psf atoms are not the same!
  • Ashar Malik (Wed Dec 16 2015 - 09:57:47 CST)
  • Francesco Pietra (Wed Dec 16 2015 - 10:14:12 CST)
• vmd-l: PRES and water-ions issues with charmm36
  • Brian Radak (Thu Dec 10 2015 - 15:58:49 CST)
• vmd-l: script error
  • Nikhil Maroli (Sat Oct 03 2015 - 02:44:17 CDT)
  • John Stone (Fri Oct 02 2015 - 10:10:56 CDT)
• vmd-l: Topology for drugs to do MD after docking
  • Mayne, Christopher G (Wed Oct 21 2015 - 14:44:18 CDT)
• vmd-l: velocity IO with psfgen?
  • John Stone (Thu Feb 26 2015 - 10:24:36 CST)
• vmd-l: vmd-I: Fatal Error: Unable to Open CHARMM Parameter File
  • Ajasja LjubetiÄ� (Tue Feb 03 2015 - 07:06:43 CST)
• vmd-l: what is difference between "TOTAL", “TOTAL2" and "POTENTIAL" in the VMD plugin NAMD Plot?
  • 孙业平 (Mon Nov 09 2015 - 06:49:42 CST)
• vmd-l: Which VMD AND NAMD should install
  • John Stone (Tue Sep 22 2015 - 14:07:17 CDT)
• VMD-NAMD and PDB element column
  • Victor Ovchinnikov (Mon Dec 14 2015 - 16:27:41 CST)
  • Francesco Pietra (Mon Dec 14 2015 - 14:52:18 CST)
  • Francesco Pietra (Mon Dec 14 2015 - 14:42:21 CST)
  • Victor Ovchinnikov (Mon Dec 14 2015 - 09:47:54 CST)
  • Jim Phillips (Mon Dec 14 2015 - 09:04:21 CST)
  • Francesco Pietra (Sun Dec 13 2015 - 15:59:37 CST)
  • Jim Phillips (Sun Dec 13 2015 - 14:32:38 CST)
  • Francesco Pietra (Sun Dec 13 2015 - 13:39:11 CST)
  • Jim Phillips (Sun Dec 13 2015 - 12:17:57 CST)
  • Francesco Pietra (Sat Dec 12 2015 - 09:09:55 CST)
• Volume Entry
  • Axel Kohlmeyer (Sun Feb 16 2014 - 17:33:03 CST)
  • Rawan Al Nsour (Sun Feb 16 2014 - 16:36:04 CST)
  • Aron Broom (Sun Feb 16 2014 - 15:28:27 CST)
  • Rawan Al Nsour (Sun Feb 16 2014 - 15:16:44 CST)
  • Aron Broom (Sun Feb 16 2014 - 13:57:33 CST)
  • Axel Kohlmeyer (Sun Feb 16 2014 - 13:51:37 CST)
  • Rawan Al Nsour (Sun Feb 16 2014 - 13:08:05 CST)
  • Axel Kohlmeyer (Sun Feb 16 2014 - 10:38:13 CST)
  • Rawan Al Nsour (Sun Feb 16 2014 - 10:29:18 CST)
  • Axel Kohlmeyer (Mon Feb 10 2014 - 11:09:18 CST)
  • Rawan Al Nsour (Mon Feb 10 2014 - 11:04:06 CST)
  • Axel Kohlmeyer (Mon Feb 10 2014 - 10:45:37 CST)
  • Axel Kohlmeyer (Mon Feb 10 2014 - 10:12:49 CST)
  • Rawan Al Nsour (Mon Feb 10 2014 - 10:08:19 CST)
• VRPN cannot connect to Falcon
  • George Patargias (Wed Oct 15 2014 - 04:58:11 CDT)
• VRPN compilation error
  • Axel Kohlmeyer (Tue Oct 14 2014 - 08:54:12 CDT)
  • George Patargias (Tue Oct 14 2014 - 08:43:59 CDT)
• warnings while using amber files
  • amin_at_imtech.res.in (Thu Dec 25 2014 - 21:54:38 CST)
  • amin_at_imtech.res.in (Thu Dec 25 2014 - 05:14:20 CST)
• water-protein interation
  • Hongbo Du (Fri Nov 14 2014 - 09:03:37 CST)
  • sunyeping (Fri Nov 14 2014 - 02:32:11 CST)
• Weird Bond In Non-Polar Tail
  • Axel Kohlmeyer (Thu Jun 18 2015 - 10:45:06 CDT)
  • Danielle Grodi (Thu Jun 18 2015 - 10:15:53 CDT)
• Weird psfgen bug?
  • Tristan Croll (Fri Oct 30 2015 - 03:22:06 CDT)
• what exactly is the form of the cosine angle potential?
  • Fotis Baltoumas (Fri Jul 17 2015 - 08:47:55 CDT)
  • Charlesworth, Henry (Fri Jul 17 2015 - 08:08:50 CDT)
• where can I find the parameter file for chlorophenols?
  • Jeff Comer (Mon May 25 2015 - 14:35:46 CDT)
  • ¶¡êÏ (Sun May 24 2015 - 08:30:15 CDT)
• Which Binary to use?
  • Norman Geist (Mon Apr 27 2015 - 01:59:17 CDT)
  • Sourav Ray (Fri Apr 24 2015 - 00:45:44 CDT)
  • Arijit Ghosh (Fri Apr 24 2015 - 00:10:49 CDT)
• Which namd to use
  • Jim Phillips (Fri Nov 20 2015 - 11:11:30 CST)
  • Maxime Boissonneault (Fri Nov 20 2015 - 08:13:58 CST)
  • Jim Phillips (Fri Nov 20 2015 - 08:02:36 CST)
  • Maxime Boissonneault (Fri Nov 20 2015 - 07:29:45 CST)
• which namd versions compatible with CUDA 5.5 and other CUDA woes
  • Robert Wohlhueter (Sun Sep 28 2014 - 12:00:17 CDT)
  • Jim Phillips (Fri Sep 26 2014 - 17:25:29 CDT)
  • Robert Wohlhueter (Mon Sep 22 2014 - 13:39:19 CDT)
• WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM?
  • Jeff Comer (Mon Mar 02 2015 - 10:45:28 CST)
  • Richard Overstreet (Sun Mar 01 2015 - 16:56:39 CST)
  • Amin Dehkharghani (Sun Mar 01 2015 - 14:58:08 CST)
• Which VMD AND NAMD should install
  • Nikhil Maroli (Sat Sep 19 2015 - 01:57:30 CDT)
• whidth value of orientation in colvars
  • Giacomo Fiorin (Fri Jan 10 2014 - 16:20:45 CST)
  • ¼­¿ëÀÏ (Thu Jan 09 2014 - 18:28:22 CST)
  • Giacomo Fiorin (Thu Jan 09 2014 - 07:31:15 CST)
  • ¼­¿ëÀÏ (Thu Jan 09 2014 - 02:27:59 CST)
• Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD
  • Bin He (Tue Nov 11 2014 - 06:19:06 CST)
  • Bin He (Mon Nov 10 2014 - 13:51:15 CST)
  • Bin He (Sat Nov 08 2014 - 01:24:32 CST)
• Why RDF increases as r increase instead of constant
  • Arash Azari (Mon Nov 03 2014 - 01:32:27 CST)
  • Kenno Vanommeslaeghe (Sun Nov 02 2014 - 18:25:41 CST)
  • Kenno Vanommeslaeghe (Sun Nov 02 2014 - 12:38:04 CST)
  • Nifeng Guo hui (Sat Nov 01 2014 - 17:07:32 CDT)
• Why the computational speed does not increase with the increase of GPUs?
  • sunyeping (Wed Oct 21 2015 - 22:18:17 CDT)
• Why the Lennard−Jones parameters E for anions are usually larger than cations?
  • Axel Kohlmeyer (Mon Jun 15 2015 - 05:36:16 CDT)
  • bay__gulf618_at_sina.com (Mon Jun 15 2015 - 04:02:44 CDT)
• Widom test particle insertion in NAMD
  • Javad Noroozi (Mon Feb 17 2014 - 00:40:08 CST)
• Window for FEP calculations
  • Gianluca Interlandi (Tue Aug 26 2014 - 19:35:33 CDT)
• Workshop on GPU Programming for Molecular Modeling, in Urbana, Illinois, July 22-24, 2014
  • David Brandon (Fri Apr 18 2014 - 16:49:02 CDT)
• Workshop on Very Large System Simulation Workshop, Urbana, IL, August 11-15, 2014
  • David Brandon (Sat May 17 2014 - 18:22:07 CDT)
• Would it be possible to continue a simulation from any snapshot of a trajectory?
  • sunyeping (Thu Nov 12 2015 - 20:57:20 CST)
  • Felipe Merino (Thu Nov 12 2015 - 03:33:05 CST)
  • sunyeping (Thu Nov 12 2015 - 02:45:51 CST)
• wrapping a protein
  • Maxim Belkin (Wed Aug 20 2014 - 17:53:46 CDT)
  • Maria Bykhovskaia (Wed Aug 20 2014 - 17:40:30 CDT)
• wrapping in NVT
  • Abhishek TYAGI (Wed Jul 22 2015 - 00:27:02 CDT)
  • Richard Overstreet (Wed Jul 22 2015 - 01:05:30 CDT)
  • Abhishek TYAGI (Tue Jul 21 2015 - 22:59:52 CDT)
• wrapping in two dimensions
  • Maria Bykhovskaia (Thu Oct 16 2014 - 15:33:34 CDT)
• wrapping option in namd
  • Christian Jorgensen (Mon Jun 23 2014 - 04:59:50 CDT)
  • MEHRAN MB (Tue Apr 01 2014 - 21:44:36 CDT)
  • Research Jubilant (Wed Mar 19 2014 - 22:38:16 CDT)
  • Ivan Gregoretti (Wed Mar 19 2014 - 21:58:30 CDT)
  • Research Jubilant (Wed Mar 19 2014 - 21:34:57 CDT)
• write pdb
  • bay__gulf618_at_sina.com (Thu Feb 20 2014 - 00:31:36 CST)
• Xeon vs i7 and ECC vs SDRAM
  • Gianluca Interlandi (Tue Jun 24 2014 - 23:07:02 CDT)
  • Gianluca Interlandi (Tue Jun 24 2014 - 20:02:49 CDT)
• ´ð¸´£ºRE£º NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance
  • Axel Kohlmeyer (Mon Feb 24 2014 - 04:34:22 CST)
• À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓʼþ
  • Abhishek TYAGI (Wed Nov 25 2015 - 07:03:45 CST)
  • Abhishek TYAGI (Wed Nov 18 2015 - 20:12:47 CST)
  • ZOU Changling (Wed Nov 18 2015 - 19:34:42 CST)
  • Abhishek TYAGI (Wed Nov 18 2015 - 09:45:45 CST)
  • ZOU Changling (Wed Nov 18 2015 - 02:43:26 CST)
  • ZOU Changling (Wed Nov 18 2015 - 02:40:15 CST)
  • ZOU Changling (Wed Nov 18 2015 - 00:26:54 CST)
• 崔幼æ�¬ 自动回å¤�: Multiple input and output files
  • cuiyoutian_at_163.com (Wed Nov 05 2014 - 20:20:37 CST)
• æ�¥è‡ª"ZOU Changling" <zoucl@ihep.ac.cn>的邮件
  • Axel Kohlmeyer (Wed Nov 18 2015 - 20:15:49 CST)
• ç­”å¤�：RE： NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance
  • sunyeping (Mon Feb 24 2014 - 03:37:02 CST)