NAMD-L: By Subject

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NAMD-L: By Subject

By Subject

4497 messages sorted by: [ author ] [ date ] [ thread ] [ attachment ]
About this archive

Starting: Sat Jan 01 2011 - 12:21:40 CST
Ending: Mon Dec 31 2012 - 14:36:03 CST

Axel Kohlmeyer (Sat Nov 24 2012 - 06:17:07 CST)

Chris Harrison (Thu Aug 30 2012 - 03:25:09 CDT)

Norman Geist (Thu Aug 30 2012 - 02:32:29 CDT)

Jacqueline Schmidt (Wed Aug 29 2012 - 12:48:52 CDT)

Aron Broom (Tue Jul 31 2012 - 19:35:32 CDT)

ÖÓË´ (Fri Jul 20 2012 - 02:38:00 CDT)

Aron Broom (Sun Apr 22 2012 - 16:07:24 CDT)

Axel Kohlmeyer (Sun Apr 22 2012 - 12:49:15 CDT)

forough askari (Sun Mar 11 2012 - 11:54:25 CDT)

Ajasja LjubetiÄ (Wed Jan 25 2012 - 12:05:49 CST)

Chris Harrison (Mon Oct 31 2011 - 15:24:19 CDT)

Anna James (Tue Aug 16 2011 - 12:23:05 CDT)

Jeffrey Potoff (Tue Aug 16 2011 - 09:45:33 CDT)

Babban Mia (Tue Aug 16 2011 - 09:41:58 CDT)

Jeffrey J. Potoff (Tue Aug 16 2011 - 09:35:20 CDT)

Anna James (Tue Aug 16 2011 - 09:20:49 CDT)

Anna James (Tue Aug 16 2011 - 08:48:51 CDT)

Axel Kohlmeyer (Tue Aug 16 2011 - 08:43:00 CDT)

Jim Phillips (Wed Apr 13 2011 - 10:19:45 CDT)

Jérôme Hénin (Thu Feb 03 2011 - 11:13:22 CST)

Giacomo Fiorin (Thu Feb 03 2011 - 10:49:22 CST)

"Constraint failure in RATTLE algorithm" when restart FEP
- Dong Luo (Mon Aug 01 2011 - 10:50:27 CDT)
- Dong Luo (Fri Jul 29 2011 - 14:36:44 CDT)
- Dong Luo (Thu Jul 28 2011 - 12:21:28 CDT)
"FATAL ERROR: Bad global improper count" revisited
- johan strumpfer (Tue Mar 22 2011 - 12:41:42 CDT)
- Markus K. Dahlgren (Tue Mar 22 2011 - 10:42:49 CDT)
"Warning" meaning
- Salvatore Mario Cosseddu (Thu Mar 01 2012 - 04:27:12 CST)
- Chris Harrison (Thu Mar 01 2012 - 00:23:26 CST)
- Cosseddu, Salvatore (Mon Feb 27 2012 - 13:55:50 CST)
'cutting' colvars.traj file
- Bjoern Olausson (Tue May 03 2011 - 08:34:21 CDT)
- Branko (Tue May 03 2011 - 06:41:34 CDT)
- Branko (Tue May 03 2011 - 05:55:42 CDT)
- Bjoern Olausson (Tue May 03 2011 - 05:45:23 CDT)
- Bjoern Olausson (Wed Apr 27 2011 - 05:53:41 CDT)
- Branko (Sat Apr 23 2011 - 13:07:20 CDT)
- Wang Yi (Sat Apr 23 2011 - 12:54:15 CDT)
- Branko (Sat Apr 23 2011 - 12:28:58 CDT)
'firsttimestep' treated as signed integer ?
- Nicholas M Glykos (Mon Aug 22 2011 - 12:01:26 CDT)
'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, February 11-15, 2012 in Urbana, Illinois
- David Brandon (Thu Nov 17 2011 - 13:46:56 CST)
'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 17-21, 2011, Bremen, Germany
- David Brandon (Fri Jul 29 2011 - 14:13:05 CDT)
'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 22-26, 2012 in Urbana, Illinois
- David Brandon (Mon Jul 09 2012 - 14:29:08 CDT)
(NAMD2.7b1) loadtotalforces gives output even when there are no forces in system
- Aoife Fogarty (Tue Mar 15 2011 - 13:15:04 CDT)
- Hugh Heldenbrand (Mon Mar 07 2011 - 07:10:09 CST)
- Aoife Fogarty (Mon Mar 07 2011 - 03:43:14 CST)
(no subject)
- Steven W Rick (Fri Nov 23 2012 - 14:29:17 CST)
- saman amiri (Fri Nov 16 2012 - 08:05:21 CST)
- Suranga Edirisinghe (Wed Aug 29 2012 - 16:13:55 CDT)
- Jacqueline Schmidt (Wed Aug 29 2012 - 11:06:10 CDT)
- ¼¿ëÀÏ (Sun Aug 26 2012 - 22:55:40 CDT)
- Sean T Kigerl (Tue Jul 31 2012 - 18:27:12 CDT)
- ÖÓË´ (Mon Jul 16 2012 - 08:59:14 CDT)
- Francesco Pietra (Sun Jun 10 2012 - 12:45:22 CDT)
- Marc Charendoff (Thu May 31 2012 - 12:09:43 CDT)
- Puspita Halder (Wed May 23 2012 - 07:45:48 CDT)
- Taruna Gupta (Sun Apr 22 2012 - 12:37:42 CDT)
- David Rogers (Wed Apr 18 2012 - 23:21:43 CDT)
- Hannes Loeffler (Mon Apr 16 2012 - 03:34:41 CDT)
- Vidhya Sankar (Sat Apr 14 2012 - 01:26:21 CDT)
- Madhulika Gupta (Tue Jan 24 2012 - 23:08:52 CST)
- Basak Isin (Mon Jan 23 2012 - 01:16:45 CST)
- ÐìÖÓºÓ (Mon Jan 02 2012 - 03:03:31 CST)
- Chandra Ramananjara (Tue Nov 22 2011 - 12:31:08 CST)
- Gabriel Jara (Tue Nov 22 2011 - 06:59:12 CST)
- Chandra Ramananjara (Tue Nov 22 2011 - 06:53:15 CST)
- Gurunath Katagi (Thu Nov 03 2011 - 03:01:19 CDT)
- Gurunath Katagi (Thu Nov 03 2011 - 03:00:22 CDT)
- Buddhadev Maiti (Fri Oct 28 2011 - 22:14:30 CDT)
- Axel Kohlmeyer (Tue Aug 23 2011 - 09:37:15 CDT)
- David Rogers (Mon Aug 22 2011 - 20:25:04 CDT)
- Andrea Holfelder (Thu Aug 18 2011 - 04:59:05 CDT)
- Anna James (Tue Aug 16 2011 - 08:38:14 CDT)
- Chandra Ramananjara (Sun May 15 2011 - 12:32:07 CDT)
- Chandra Ramananjara (Thu May 12 2011 - 19:58:21 CDT)
- Chandra Ramananjara (Sun May 08 2011 - 09:37:04 CDT)
- Chandra Ramananjara (Sat May 07 2011 - 14:00:37 CDT)
- Nicolas Sapay (Tue May 03 2011 - 11:51:42 CDT)
- David Rogers (Mon Apr 11 2011 - 22:26:09 CDT)
- Erik Nordgren (Mon Apr 11 2011 - 21:38:33 CDT)
- Buddhadev Maiti (Mon Apr 11 2011 - 14:27:13 CDT)
- Buddhadev Maiti (Fri Apr 08 2011 - 10:45:19 CDT)
- Alexandra Nemkevich (Thu Feb 03 2011 - 04:30:50 CST)
- Chen, Zhihong (chenz2) (Wed Jan 05 2011 - 18:43:15 CST)
(solved) charmrun: ssh_exchange_identification: Connection closed by remote host
- Leandro Martínez (Fri Sep 02 2011 - 14:44:24 CDT)
* CGtool force field *
- HAMID - (Wed Oct 26 2011 - 08:47:39 CDT)
- Axel Kohlmeyer (Sun Oct 23 2011 - 16:16:47 CDT)
- HAMID - (Sun Oct 23 2011 - 03:09:03 CDT)
- Chris Harrison (Sat Oct 22 2011 - 17:02:37 CDT)
- Axel Kohlmeyer (Sat Oct 22 2011 - 14:36:38 CDT)
- HAMID - (Sat Oct 22 2011 - 14:11:14 CDT)
- Axel Kohlmeyer (Sat Oct 22 2011 - 12:47:47 CDT)
- HAMID - (Sat Oct 22 2011 - 12:00:19 CDT)
.colvars.state file in ABF
- Jérôme Hénin (Wed Jan 05 2011 - 07:15:45 CST)
- Parisa Akhski (Tue Jan 04 2011 - 15:51:09 CST)
- Alex Liu (Mon Jan 03 2011 - 15:53:45 CST)
.COOR TO PDB FILE
- Ehsan Ban (Sat Aug 13 2011 - 02:47:27 CDT)
- JC Gumbart (Sat Aug 13 2011 - 01:29:04 CDT)
- Babban Mia (Sat Aug 13 2011 - 01:11:48 CDT)
1-4 tabulated potentials?
- Jorge Hernandez Cobos (Tue Oct 16 2012 - 15:04:57 CDT)
1-4 vdw scaling?
- Axel Kohlmeyer (Sat Aug 11 2012 - 14:49:03 CDT)
- Jacqueline Schmidt (Sat Aug 11 2012 - 14:41:20 CDT)
2.9b1 and GPU accelerated GB implicit solvent
- David Tanner (Wed Mar 21 2012 - 12:41:23 CDT)
- Aron Broom (Tue Mar 20 2012 - 23:16:57 CDT)
2.9b1 crashes
- Chris Harrison (Wed Mar 28 2012 - 15:41:39 CDT)
- Chris Harrison (Tue Mar 27 2012 - 20:33:25 CDT)
- Chris Harrison (Tue Mar 27 2012 - 10:15:36 CDT)
- Francesco Pietra (Tue Mar 27 2012 - 09:56:15 CDT)
2CPU+1GPU vs 1CPU+2GPU
- Ajasja LjubetiÄ (Mon Feb 13 2012 - 09:08:30 CST)
- Aron Broom (Mon Feb 13 2012 - 08:26:30 CST)
- Nicholas M Glykos (Mon Feb 13 2012 - 05:44:59 CST)
- Marcel UJI (IMAP) (Mon Feb 13 2012 - 05:21:18 CST)
4 x Opteron 12-core or 4 x Xeon 8-core ?
- David McGiven (Thu Jan 20 2011 - 05:59:13 CST)
??: compilation of namd
- TAO WANG (Fri May 06 2011 - 00:56:41 CDT)
[MetaD; namd 2.9] Pmf output file problem once the CV boundaries are reached, even using "expandBoundaries on"
- Giacomo Fiorin (Tue Nov 20 2012 - 18:41:02 CST)
- Robert Elder (Sun Nov 18 2012 - 15:53:46 CST)
- Giacomo Fiorin (Fri Sep 07 2012 - 11:38:08 CDT)
- Salvatore Mario Cosseddu (Fri Sep 07 2012 - 07:49:36 CDT)
[ppl] Compliling NAMD in RedHat
- Phil Miller (Tue Aug 02 2011 - 10:10:18 CDT)
[ppl] Help Regarding NAMD Application Testing
- Phil Miller (Mon Mar 21 2011 - 09:00:13 CDT)
[ppl] NAMD at linux on sparc
- Phil Miller (Sun Feb 06 2011 - 21:18:32 CST)
[ppl] Regarding Compiling in Redhat linux.
- Phil Miller (Wed Aug 03 2011 - 09:30:01 CDT)
A "strange" observation during ColVar calculations
- Jérôme Hénin (Mon Mar 28 2011 - 09:51:21 CDT)
- Jérôme Hénin (Mon Mar 28 2011 - 08:33:42 CDT)
- Wang Yi (Mon Mar 28 2011 - 08:40:51 CDT)
- Wang Yi (Tue Mar 22 2011 - 12:54:29 CDT)
- Jérôme Hénin (Tue Mar 22 2011 - 11:30:56 CDT)
- Wang Yi (Mon Mar 21 2011 - 15:58:17 CDT)
- Giacomo Fiorin (Mon Mar 21 2011 - 15:46:27 CDT)
- Wang Yi (Mon Mar 21 2011 - 13:49:45 CDT)
A bug in replica.namd?
- Ada Zhan (Thu Nov 08 2012 - 13:32:39 CST)
- Ada Zhan (Wed Nov 07 2012 - 16:37:13 CST)
a bundle of coor files
- Massimiliano Porrini (Tue Jul 05 2011 - 10:34:16 CDT)
- Massimiliano Porrini (Sat Jul 02 2011 - 20:16:05 CDT)
- Rajan Vatassery (Sat Jul 02 2011 - 16:26:32 CDT)
- Massimiliano Porrini (Sat Jul 02 2011 - 13:21:56 CDT)
A namd2.8b1 bug ?
- Jim Phillips (Tue May 10 2011 - 21:02:49 CDT)
- charlie (Wed Apr 27 2011 - 02:23:56 CDT)
A newer version of win32 libraries
- Ajasja LjubetiÄ (Tue May 10 2011 - 15:55:06 CDT)
- Jim Phillips (Tue May 10 2011 - 14:39:25 CDT)
- Ajasja LjubetiÄ (Mon May 09 2011 - 07:35:47 CDT)
a question about ensemble
- Albert (Thu May 03 2012 - 01:04:58 CDT)
A question about the CHARMM force field
- Hall McDull (Fri May 04 2012 - 03:32:30 CDT)
- Axel Kohlmeyer (Fri May 04 2012 - 08:12:26 CDT)
- Hall McDull (Fri May 04 2012 - 07:33:48 CDT)
A question on Jarkynski equation
- Jun Zhang (Wed Jun 15 2011 - 00:25:17 CDT)
- Jun Zhang (Tue Jun 14 2011 - 23:03:53 CDT)
- johan strumpfer (Tue Jun 14 2011 - 09:51:22 CDT)
- Jérôme Hénin (Tue Jun 14 2011 - 09:09:13 CDT)
- Wang Yi (Tue Jun 14 2011 - 08:11:46 CDT)
- Jérôme Hénin (Tue Jun 14 2011 - 03:43:55 CDT)
- Jun Zhang (Mon Jun 13 2011 - 22:01:59 CDT)
a question on version nightly build flatforms
- Hyonseok Hwang (Sun Oct 07 2012 - 01:26:26 CDT)
ABACAVIR parameters
- Athanassios Stavrakoudis (Mon Nov 19 2012 - 08:38:12 CST)
Abe versus Lincoln
- Gianluca Interlandi (Thu Apr 07 2011 - 16:55:51 CDT)
- johan strumpfer (Thu Apr 07 2011 - 16:23:16 CDT)
- Axel Kohlmeyer (Thu Apr 07 2011 - 16:18:09 CDT)
- Gianluca Interlandi (Thu Apr 07 2011 - 15:40:11 CDT)
- Axel Kohlmeyer (Thu Apr 07 2011 - 14:21:33 CDT)
- Gianluca Interlandi (Thu Apr 07 2011 - 13:57:41 CDT)
- Gianluca Interlandi (Thu Apr 07 2011 - 13:50:45 CDT)
- Axel Kohlmeyer (Thu Apr 07 2011 - 13:46:34 CDT)
- johan strumpfer (Thu Apr 07 2011 - 13:40:13 CDT)
- Gianluca Interlandi (Thu Apr 07 2011 - 13:22:37 CDT)
ABF & distanceZ projection axis
- HAMID - (Thu Sep 22 2011 - 01:20:02 CDT)
- Giacomo Fiorin (Wed Sep 21 2011 - 19:22:36 CDT)
- HAMID - (Wed Sep 21 2011 - 16:15:45 CDT)
ABF & distanceZ projection axis more
- HAMID - (Thu Sep 22 2011 - 05:36:32 CDT)
- Jérôme Hénin (Thu Sep 22 2011 - 04:33:02 CDT)
- HAMID - (Thu Sep 22 2011 - 03:05:07 CDT)
ABF - coordNum collective variable
- Jérôme Hénin (Mon Mar 19 2012 - 10:47:45 CDT)
- Giacomo Fiorin (Fri Mar 16 2012 - 10:59:38 CDT)
- Adam Skelton (Thu Mar 15 2012 - 15:27:07 CDT)
ABF atom selection
- Jérôme Hénin (Tue May 10 2011 - 09:59:08 CDT)
- Parisa Akhski (Tue May 10 2011 - 09:16:29 CDT)
- Jérôme Hénin (Sun May 08 2011 - 11:41:09 CDT)
- Parisa Akhski (Sat May 07 2011 - 18:14:24 CDT)
ABF atom selection question
- Parisa Akhski (Thu May 05 2011 - 21:50:00 CDT)
ABF calculation using RMSD
- Giacomo Fiorin (Mon Apr 25 2011 - 22:26:54 CDT)
- Buddhadev Maiti (Mon Apr 25 2011 - 22:14:39 CDT)
- JC Gumbart (Wed Feb 16 2011 - 21:24:01 CST)
- Buddhadev Maiti (Wed Feb 16 2011 - 21:04:11 CST)
- Jérôme Hénin (Tue Feb 15 2011 - 04:46:25 CST)
- Buddhadev Maiti (Mon Feb 14 2011 - 19:08:32 CST)
ABF colvar error-capped nanotube interaction
- Axel Kohlmeyer (Sun Mar 20 2011 - 12:13:43 CDT)
- sakthi kumaran (Sun Mar 20 2011 - 11:26:04 CDT)
- sakthi kumaran (Sun Mar 20 2011 - 01:55:30 CDT)
- Giacomo Fiorin (Sat Mar 19 2011 - 13:54:37 CDT)
- Axel Kohlmeyer (Sat Mar 19 2011 - 12:02:53 CDT)
- sakthi kumaran (Sat Mar 19 2011 - 11:12:57 CDT)
Abf force output
- Jérôme Hénin (Wed Feb 09 2011 - 07:30:16 CST)
- stefhoor (Wed Feb 09 2011 - 04:12:50 CST)
- Jérôme Hénin (Wed Feb 09 2011 - 03:25:59 CST)
- stefhoor (Tue Feb 08 2011 - 20:58:39 CST)
ABF question
- Jérôme Hénin (Wed Sep 21 2011 - 07:01:50 CDT)
ABF question (sampling and colvars output file)
- Parisa Akhski (Mon Feb 07 2011 - 14:27:03 CST)
- Jérôme Hénin (Mon Feb 07 2011 - 11:16:28 CST)
- Jérôme Hénin (Mon Feb 07 2011 - 04:20:28 CST)
- Parisa Akhski (Sun Feb 06 2011 - 15:20:47 CST)
- Parisa Akhski (Tue Feb 01 2011 - 10:27:43 CST)
ABF reproducibility
- Jérôme Hénin (Mon Feb 14 2011 - 06:29:40 CST)
- Parisa Akhski (Sun Feb 13 2011 - 15:08:26 CST)
ABF Restart
- Jérôme Hénin (Fri Mar 18 2011 - 04:08:34 CDT)
- Buddhadev Maiti (Thu Mar 17 2011 - 21:46:37 CDT)
ABF results interpretation
- HAMID - (Wed Sep 21 2011 - 10:22:38 CDT)
ABF simulation
- Jérôme Hénin (Sat Jan 07 2012 - 05:16:24 CST)
- Tugba Nogay (Fri Jan 06 2012 - 10:53:36 CST)
ABF simulation with extendedLagrangian on keeps crashing
- Jérôme Hénin (Thu May 12 2011 - 04:36:20 CDT)
- Ajasja LjubetiÄ (Thu May 12 2011 - 03:55:03 CDT)
- Jérôme Hénin (Thu May 05 2011 - 17:02:56 CDT)
- Giacomo Fiorin (Thu May 05 2011 - 16:22:09 CDT)
- Ajasja LjubetiÄ (Thu May 05 2011 - 15:50:34 CDT)
- Jérôme Hénin (Thu May 05 2011 - 10:23:23 CDT)
- Ajasja LjubetiÄ (Thu May 05 2011 - 03:38:16 CDT)
- Ajasja LjubetiÄ (Wed May 04 2011 - 06:31:58 CDT)
- Ajasja LjubetiÄ (Tue May 03 2011 - 11:02:12 CDT)
- Jérôme Hénin (Tue May 03 2011 - 10:23:17 CDT)
- Ajasja LjubetiÄ (Tue May 03 2011 - 08:11:26 CDT)
- Jérôme Hénin (Fri Apr 22 2011 - 15:38:07 CDT)
- Ajasja LjubetiÄ (Fri Apr 22 2011 - 09:27:24 CDT)
- Ajasja LjubetiÄ (Fri Apr 22 2011 - 03:34:29 CDT)
- Jérôme Hénin (Thu Apr 21 2011 - 09:43:21 CDT)
- Ajasja LjubetiÄ (Thu Apr 21 2011 - 06:30:47 CDT)
- Giacomo Fiorin (Wed Apr 20 2011 - 11:22:37 CDT)
- Ajasja Ljubetiè (Wed Apr 20 2011 - 09:22:21 CDT)
- Ajasja Ljubetiè (Tue Apr 19 2011 - 12:43:12 CDT)
- Ajasja LjubetiÄ (Tue Apr 19 2011 - 12:05:23 CDT)
- Giacomo Fiorin (Tue Apr 19 2011 - 11:41:55 CDT)
- Ajasja LjubetiÄ (Tue Apr 19 2011 - 11:05:09 CDT)
- Ajasja LjubetiÄ (Tue Apr 19 2011 - 10:55:57 CDT)
ABF with Alpha colvar can't be used on supercomputer?
- Yun Luo (Thu Sep 29 2011 - 14:25:57 CDT)
- Chris Harrison (Thu Sep 29 2011 - 10:11:32 CDT)
- Jérôme Hénin (Thu Sep 29 2011 - 09:56:46 CDT)
- JC Gumbart (Thu Sep 29 2011 - 08:05:19 CDT)
- Jérôme Hénin (Thu Sep 29 2011 - 05:04:42 CDT)
- JC Gumbart (Thu Sep 29 2011 - 01:05:53 CDT)
- Yun Luo (Wed Sep 28 2011 - 15:38:02 CDT)
ABF/Steered MD for DNA Hybridization on Carbon Nanotubes
- Robert Johnson (Fri Jul 13 2012 - 13:35:46 CDT)
- Robert Johnson (Thu Jul 12 2012 - 14:47:49 CDT)
- Jérôme Hénin (Thu Jul 05 2012 - 05:24:31 CDT)
- Robert Johnson (Tue Jul 03 2012 - 13:47:38 CDT)
- Jérôme Hénin (Thu Jun 21 2012 - 09:47:28 CDT)
- Robert Johnson (Wed Jun 20 2012 - 11:30:29 CDT)
- Jérôme Hénin (Wed Jun 20 2012 - 06:25:36 CDT)
- Aron Broom (Tue Jun 19 2012 - 16:56:51 CDT)
- Robert Johnson (Tue Jun 19 2012 - 15:43:26 CDT)
Abnormal EOF Error in Extra Bonds File
- Jim Phillips (Tue May 10 2011 - 20:15:18 CDT)
- Eli Fine (Tue Apr 26 2011 - 14:22:11 CDT)
Abouf Psfgen error
- Syed Kashif Zafar (Sat Apr 14 2012 - 14:50:37 CDT)
About "alchDecouple" in FEP
- wenhao_at_uchicago.edu (Sun Oct 23 2011 - 07:47:26 CDT)
- Jérôme Hénin (Sat Oct 22 2011 - 11:51:27 CDT)
- wenhao_at_uchicago.edu (Sat Oct 22 2011 - 10:47:14 CDT)
about charmm force field
- oguz gurbulak (Fri Jun 10 2011 - 09:55:26 CDT)
About Columb energy of 2 ions in Vacuum
- Jérôme Hénin (Fri Aug 26 2011 - 04:30:54 CDT)
- wenhao_at_uchicago.edu (Fri Aug 26 2011 - 02:30:48 CDT)
- JC Gumbart (Fri Aug 26 2011 - 01:37:05 CDT)
- wenhao_at_uchicago.edu (Thu Aug 25 2011 - 18:02:04 CDT)
- wenhao_at_uchicago.edu (Tue Aug 23 2011 - 22:32:08 CDT)
- wenhao_at_uchicago.edu (Tue Aug 23 2011 - 22:30:29 CDT)
- Edward Lyman (Tue Aug 23 2011 - 19:47:25 CDT)
- wenhao_at_uchicago.edu (Tue Aug 23 2011 - 17:28:04 CDT)
about conf file
- Jim Phillips (Thu May 26 2011 - 09:55:14 CDT)
- oguz gurbulak (Thu May 26 2011 - 09:11:29 CDT)
about D amino acid
- Eduard Schreiner (Fri Jul 29 2011 - 04:27:39 CDT)
- AB (Fri Jul 29 2011 - 03:50:16 CDT)
about dcd files
- Axel Kohlmeyer (Mon Jul 02 2012 - 09:00:43 CDT)
- Namd Namd (Mon Jul 02 2012 - 08:30:17 CDT)
About error during creation of psf file
- flavio seixas (Thu Apr 19 2012 - 13:48:42 CDT)
- Vidhya Sankar (Sat Apr 14 2012 - 01:28:27 CDT)
About error in .pgn error in vmd cmd prompt
- Vidhya Sankar (Wed Apr 25 2012 - 03:00:33 CDT)
about extrabonds restrain
- JC Gumbart (Tue Aug 30 2011 - 08:41:35 CDT)
- Axel Kohlmeyer (Tue Aug 30 2011 - 08:06:04 CDT)
- Ling Wu (Mon Aug 29 2011 - 16:22:53 CDT)
About fastest CUDA cards
- Francesco Pietra (Fri Jul 29 2011 - 04:09:37 CDT)
about log file
- Bjoern Olausson (Thu Jun 09 2011 - 05:02:36 CDT)
- Molecular Dynamics (Thu Jun 09 2011 - 04:30:30 CDT)
about long namd trajectory and pbc effect
- Liqun Zhang (Mon Dec 03 2012 - 14:00:50 CST)
- Thomas Evangelidis (Sun Dec 02 2012 - 15:39:36 CST)
- Liqun Zhang (Sun Dec 02 2012 - 14:53:24 CST)
about md in npt
- Joshua Adelman (Wed Dec 28 2011 - 07:55:02 CST)
- Hasan haska (Wed Dec 28 2011 - 02:18:30 CST)
about molecular axis
- Namd Namd (Wed Apr 11 2012 - 05:40:30 CDT)
About psfgen error
- Vidhya Sankar (Sat Apr 14 2012 - 11:15:01 CDT)
about rigid bonds
- Axel Kohlmeyer (Wed Apr 13 2011 - 10:38:19 CDT)
- Jim Phillips (Wed Apr 13 2011 - 10:32:07 CDT)
- oguz gurbulak (Wed Apr 13 2011 - 03:39:34 CDT)
About the correction of charging two ion water box by using FEP
- JC Gumbart (Sat Jun 02 2012 - 07:43:15 CDT)
- Win Liu (Sat Jun 02 2012 - 03:34:28 CDT)
- JC Gumbart (Mon May 28 2012 - 17:15:35 CDT)
- Win Liu (Mon May 28 2012 - 11:59:33 CDT)
- JC Gumbart (Mon May 28 2012 - 08:41:56 CDT)
- Win Liu (Mon May 28 2012 - 02:06:09 CDT)
about trajectory analysis
- Nicholas M Glykos (Wed May 30 2012 - 02:06:56 CDT)
- oguz gurbulak (Wed May 30 2012 - 01:43:42 CDT)
Accelerated MD
- Felipe Merino (Wed Nov 07 2012 - 10:08:15 CST)
- Chris Harrison (Wed Aug 29 2012 - 23:49:03 CDT)
- Chris Harrison (Wed Aug 29 2012 - 23:19:27 CDT)
- Jeff Wereszczynski (Wed Aug 29 2012 - 23:19:39 CDT)
- Thomas Albers (Wed Aug 29 2012 - 21:38:20 CDT)
- Thomas Albers (Wed Aug 29 2012 - 16:20:50 CDT)
- Thomas Albers (Wed Aug 29 2012 - 15:53:43 CDT)
- Jeff Wereszczynski (Wed Aug 29 2012 - 15:47:31 CDT)
- Chris Harrison (Wed Aug 29 2012 - 15:37:06 CDT)
- Thomas Albers (Wed Aug 29 2012 - 15:06:04 CDT)
accelerated MD (aMD) with GPU
- Jiyong Park (Fri Aug 03 2012 - 17:48:42 CDT)
Accelerated MD documentation?
- Chris Harrison (Sat Mar 19 2011 - 00:15:15 CDT)
- Bjoern Olausson (Tue Mar 15 2011 - 10:47:21 CDT)
- Francesco Pietra (Tue Mar 15 2011 - 10:20:18 CDT)
- Chris Harrison (Tue Mar 15 2011 - 09:28:35 CDT)
- Chris Harrison (Tue Mar 15 2011 - 09:22:55 CDT)
- Bjoern Olausson (Tue Mar 15 2011 - 08:59:48 CDT)
- patrick wintrode (Tue Mar 15 2011 - 08:05:19 CDT)
Accelerated MD with membrane embedded proteins.
- Raul Araya (Mon Mar 28 2011 - 13:45:36 CDT)
Accelerated MD: question about dual boost mode
- Bjoern Olausson (Tue May 10 2011 - 10:17:59 CDT)
- Bjoern Olausson (Tue May 10 2011 - 07:32:13 CDT)
- Jeff Wereszczynski (Thu Mar 31 2011 - 17:07:07 CDT)
- patrick wintrode (Thu Mar 31 2011 - 15:01:49 CDT)
Accelerated Molecular Dynamics
- Vijay Vammi (Wed Nov 02 2011 - 20:42:07 CDT)
- Vijay Vammi (Tue Oct 25 2011 - 23:45:32 CDT)
- Vijay Vammi (Tue Oct 25 2011 - 21:04:49 CDT)
- Yi Wang (Tue Oct 25 2011 - 18:03:33 CDT)
- Vijay Vammi (Tue Oct 25 2011 - 16:11:54 CDT)
AccelMD + GBIS
- Thomas Evangelidis (Sat Dec 01 2012 - 12:09:03 CST)
- Thomas Evangelidis (Sat Dec 01 2012 - 12:06:55 CST)
- Thomas Evangelidis (Sat Dec 01 2012 - 12:03:53 CST)
- Thomas Evangelidis (Sat Dec 01 2012 - 12:00:44 CST)
- Thomas Evangelidis (Sat Dec 01 2012 - 08:39:09 CST)
- Felipe Merino (Fri Nov 30 2012 - 04:26:21 CST)
- Jeff Wereszczynski (Thu Nov 29 2012 - 16:57:24 CST)
- Felipe Merino (Thu Nov 29 2012 - 09:39:18 CST)
accelMD parameter choice
- Chris Harrison (Sat Mar 24 2012 - 17:23:50 CDT)
- Grant Schauer (Sat Mar 24 2012 - 17:08:55 CDT)
Accessing Colvars Within NAMD TCL
- Jérôme Hénin (Thu Jun 30 2011 - 12:05:01 CDT)
- David Rogers (Thu Jun 30 2011 - 10:28:33 CDT)
accuracy of measurement
- Gianluca Interlandi (Mon Feb 21 2011 - 22:11:43 CST)
- Pletezhov Alexandr (Mon Feb 21 2011 - 17:14:16 CST)
acylated and amidated parameters.
- JC Gumbart (Wed Nov 14 2012 - 17:20:55 CST)
- Martin, Erik W (Wed Nov 14 2012 - 11:45:32 CST)
Adaptive Tempering "OPENING EXTENDED SYSTEM TRAJECTORY FILE" error
- Siri Søndergaard (Sun Dec 16 2012 - 22:53:31 CST)
Add bonds and topology file problem
- Edroaldo Lummertz da Rocha (Sun May 01 2011 - 16:57:16 CDT)
- Axel Kohlmeyer (Sun May 01 2011 - 15:52:30 CDT)
- Edroaldo Lummertz da Rocha (Sun May 01 2011 - 15:20:01 CDT)
Advertisement Workshop Aspen Center for Physics
- MARK PLUMMER (Thu May 24 2012 - 16:04:35 CDT)
Advice on buying GPUs
- Axel Kohlmeyer (Mon Jun 06 2011 - 06:50:16 CDT)
- Ajasja LjubetiÄ (Mon Jun 06 2011 - 06:39:31 CDT)
- Ajasja Ljubetiè (Thu Jun 02 2011 - 09:46:55 CDT)
- Axel Kohlmeyer (Thu Jun 02 2011 - 09:06:08 CDT)
- Ajasja Ljubetiè (Thu Jun 02 2011 - 08:27:47 CDT)
- Axel Kohlmeyer (Thu Jun 02 2011 - 06:17:14 CDT)
- Ajasja LjubetiÄ (Thu Jun 02 2011 - 03:13:10 CDT)
- Ajasja LjubetiÄ (Wed Jun 01 2011 - 09:43:24 CDT)
Advice on how to perform multiple copy ligand simulation
- Vijay Vammi (Thu Jun 14 2012 - 08:09:19 CDT)
Advisable limit on the number of quadrants a 2D ABF simulation can be split.
- Jérôme Hénin (Mon Mar 28 2011 - 09:42:33 CDT)
- Ajasja LjubetiÄ (Mon Mar 28 2011 - 09:06:40 CDT)
- Jérôme Hénin (Fri Mar 25 2011 - 06:25:30 CDT)
- Ajasja LjubetiÄ (Fri Mar 25 2011 - 04:52:09 CDT)
alchDecouple
- Jérôme Hénin (Mon Jul 25 2011 - 15:19:14 CDT)
- Jérôme Hénin (Sat Jul 23 2011 - 02:44:36 CDT)
- esmael (Fri Jul 22 2011 - 19:10:59 CDT)
Alchemical free-energy methods and electroneutrality
- JC Gumbart (Sat Jan 28 2012 - 15:47:54 CST)
- Rajan Vatassery (Sat Jan 28 2012 - 15:31:18 CST)
- Thomas Albers (Sat Jan 28 2012 - 13:35:27 CST)
Alchemical protein transformation with a group of (non proteic) atoms bound to two amino acids
- Francesco Pietra (Mon Aug 06 2012 - 02:36:47 CDT)
Alchemical transformations and DDG of point mutations
- Gianluca Interlandi (Tue Dec 18 2012 - 12:53:21 CST)
- JÃ©rÃ´me HÃ©nin (Tue Dec 18 2012 - 07:57:33 CST)
- Gianluca Interlandi (Mon Dec 17 2012 - 18:11:01 CST)
- JC Gumbart (Mon Dec 17 2012 - 17:18:44 CST)
- Gianluca Interlandi (Thu Dec 13 2012 - 16:10:45 CST)
- JÃ©rÃ´me HÃ©nin (Mon Dec 17 2012 - 03:06:19 CST)
- JC Gumbart (Sun Dec 16 2012 - 19:24:25 CST)
- Gianluca Interlandi (Fri Dec 14 2012 - 19:07:00 CST)
- JÃ©rÃ´me HÃ©nin (Fri Dec 14 2012 - 02:38:45 CST)
- JC Gumbart (Thu Dec 13 2012 - 15:47:14 CST)
- Gianluca Interlandi (Thu Dec 13 2012 - 13:22:47 CST)
- Chris Chipot (Thu Dec 13 2012 - 12:47:46 CST)
- Gianluca Interlandi (Wed Dec 12 2012 - 16:24:09 CST)
- Chris Chipot (Wed Dec 12 2012 - 15:02:02 CST)
- Gianluca Interlandi (Wed Dec 12 2012 - 14:22:55 CST)
- Gianluca Interlandi (Tue Dec 11 2012 - 15:22:37 CST)
Alchemical with parm7 ff
- Francesco Pietra (Wed Jul 11 2012 - 03:39:30 CDT)
aligning two molecules by principal axes of inertia using measure.c
- Ajasja LjubetiÄ (Mon Jun 20 2011 - 09:40:20 CDT)
- Ada Sedova (Mon Jun 20 2011 - 08:18:41 CDT)
Alpha P.M.F. with NAMD 2.8
- Prathit Chatterjee (Fri Jun 03 2011 - 07:55:52 CDT)
- Giacomo Fiorin (Fri Jun 03 2011 - 07:16:05 CDT)
- Ajasja LjubetiÄ (Fri Jun 03 2011 - 07:05:47 CDT)
- Prathit Chatterjee (Fri Jun 03 2011 - 06:21:46 CDT)
alpha pmf
- Jérôme Hénin (Tue May 10 2011 - 03:37:24 CDT)
- Giacomo Fiorin (Mon May 09 2011 - 16:05:19 CDT)
- Prathit Chatterjee (Sat May 07 2011 - 00:33:28 CDT)
- Jérôme Hénin (Fri May 06 2011 - 07:58:37 CDT)
- Prathit Chatterjee (Fri May 06 2011 - 05:54:55 CDT)
- Giacomo Fiorin (Thu May 05 2011 - 09:31:51 CDT)
- Prathit Chatterjee (Thu May 05 2011 - 01:21:02 CDT)
- Jérôme Hénin (Wed May 04 2011 - 04:17:16 CDT)
- Ajasja LjubetiÄ (Wed May 04 2011 - 03:04:14 CDT)
- felmerino_at_uchile.cl (Wed May 04 2011 - 02:37:06 CDT)
- Prathit Chatterjee (Wed May 04 2011 - 00:55:40 CDT)
Am I doing the Right Thing?
- Aron Broom (Thu Jul 12 2012 - 22:44:49 CDT)
- Roy Fernando (Thu Jul 12 2012 - 18:00:49 CDT)
- Aron Broom (Thu Jul 12 2012 - 12:36:06 CDT)
- Roy Fernando (Thu Jul 12 2012 - 12:31:36 CDT)
- Aron Broom (Thu Jul 12 2012 - 12:10:43 CDT)
- Roy Fernando (Thu Jul 12 2012 - 12:02:05 CDT)
Am I using the right version for accelerated MD?
- Chris Harrison (Tue Mar 22 2011 - 16:11:35 CDT)
- patrick wintrode (Tue Mar 22 2011 - 15:34:29 CDT)
AMBER in NAMD
- Aron Broom (Thu Sep 20 2012 - 12:35:58 CDT)
- George M Giambasu (Thu Sep 20 2012 - 12:07:13 CDT)
- Axel Kohlmeyer (Thu Sep 20 2012 - 11:26:05 CDT)
- Shomesankar Bhunia (Thu Sep 20 2012 - 11:12:26 CDT)
Amber topology
- felmerino_at_uchile.cl (Mon Apr 16 2012 - 16:13:54 CDT)
AMD Multicore + CUDA Benchmarks, are them ok ?
- Axel Kohlmeyer (Thu May 05 2011 - 08:57:18 CDT)
- Axel Kohlmeyer (Thu May 05 2011 - 08:47:56 CDT)
- Nicholas M Glykos (Thu May 05 2011 - 04:31:52 CDT)
- David McGiven (Thu May 05 2011 - 04:08:30 CDT)
aMD with implicit solvent - Segmentation fault
- Thomas Evangelidis (Wed Dec 05 2012 - 10:43:57 CST)
AMD-PhenomII-1075_GTX470 NAMD-CUDA performance
- Axel Kohlmeyer (Mon Jun 06 2011 - 06:57:35 CDT)
- Axel Kohlmeyer (Mon Jun 06 2011 - 06:29:38 CDT)
- Axel Kohlmeyer (Mon Jun 06 2011 - 05:50:24 CDT)
- Francesco Pietra (Mon Jun 06 2011 - 02:54:52 CDT)
an error when merge pdb and psf files in vmd for big model
- Chris Harrison (Sun Sep 09 2012 - 09:16:28 CDT)
- farzad kiani (Sun Sep 09 2012 - 08:45:58 CDT)
an important question for equilibration script
- Jernej Zidar (Thu Sep 29 2011 - 18:42:58 CDT)
- matziast_at_med.uth.gr (Thu Sep 29 2011 - 15:44:58 CDT)
Analysis of FEP output file
- Chris Chipot (Thu Feb 16 2012 - 07:35:12 CST)
- Chris Harrison (Wed Feb 15 2012 - 15:29:59 CST)
- sudipta (Tue Jan 31 2012 - 11:41:33 CST)
analysis question
- Bjoern Olausson (Tue Jul 19 2011 - 05:43:34 CDT)
- Namd Namd (Tue Jul 19 2011 - 04:32:06 CDT)
angles
- Giacomo Fiorin (Thu Mar 31 2011 - 18:05:28 CDT)
- flavio seixas (Thu Mar 31 2011 - 15:57:33 CDT)
Announcement: Large biomolecule benchmark report
- Hannes Loeffler (Thu Mar 15 2012 - 07:51:36 CDT)
Another PSF question...
- Richard Wood (Tue Feb 15 2011 - 16:13:13 CST)
Apply two Different eFeild on the same Direction
- Mohammad Jomah Ibraheem Ali Abu Saude (mbusaude) (Thu Mar 15 2012 - 02:34:46 CDT)
Applying TclBC script every x steps Error
- Maria Pikoula (Fri May 04 2012 - 16:46:03 CDT)
Area per lipid error
- Andres Morales N (Mon Oct 17 2011 - 21:12:33 CDT)
ask for new toppar files for drude in NAMD2.9
- Huihui Liu (Thu Dec 06 2012 - 05:30:25 CST)
Aspirin charmm ff
- Ramin Ekhteiari (Tue Jul 17 2012 - 10:21:13 CDT)
Assertion failed in file @ KRAKEN
- Axel Kohlmeyer (Wed Nov 09 2011 - 11:00:04 CST)
- PAUL NEWMAN (Wed Nov 09 2011 - 10:07:07 CST)
atom select within hbond analysis
- sajad falsafi (Tue Jun 07 2011 - 09:21:09 CDT)
- Branko (Tue Jun 07 2011 - 07:40:09 CDT)
Atomic Radii for GB Implicit Solvent
- Aron Broom (Fri May 11 2012 - 14:40:12 CDT)
Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration
- Aron Broom (Mon Jul 16 2012 - 16:59:22 CDT)
- Roy Fernando (Mon Jul 16 2012 - 16:43:04 CDT)
- Aron Broom (Mon Jul 16 2012 - 16:27:34 CDT)
- Axel Kohlmeyer (Mon Jul 16 2012 - 15:46:51 CDT)
- Roy Fernando (Mon Jul 16 2012 - 15:03:53 CDT)
- Ajasja LjubetiÄ (Mon Jul 16 2012 - 01:25:10 CDT)
- Aron Broom (Sun Jul 15 2012 - 20:31:26 CDT)
- Roy Fernando (Sun Jul 15 2012 - 17:13:22 CDT)
Atoms moving too fast only with CUDA version.
- amin_at_imtech.res.in (Wed Jun 27 2012 - 01:34:28 CDT)
- Aron Broom (Wed Jun 27 2012 - 00:51:33 CDT)
- amin_at_imtech.res.in (Wed Jun 27 2012 - 00:37:55 CDT)
Atoms moving too fast with NAMD/Amber
- Francesco Pietra (Thu Jul 26 2012 - 00:48:46 CDT)
ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing
- Axel Kohlmeyer (Tue Jan 10 2012 - 14:21:26 CST)
- Bennion, Brian (Tue Jan 10 2012 - 14:18:06 CST)
- Gurunath Katagi (Tue Jan 10 2012 - 14:03:03 CST)
Automatic GPU selection in NAMD ?
- David McGiven (Thu May 19 2011 - 04:42:39 CDT)
- Jim Phillips (Wed May 18 2011 - 13:22:57 CDT)
- David McGiven (Tue May 17 2011 - 09:35:57 CDT)
- Axel Kohlmeyer (Tue May 17 2011 - 07:19:44 CDT)
- Jesper Sørensen (Tue May 17 2011 - 06:17:43 CDT)
- David McGiven (Tue May 17 2011 - 06:02:29 CDT)
- Jesper Sørensen (Tue May 17 2011 - 05:41:03 CDT)
- David McGiven (Tue May 17 2011 - 05:34:21 CDT)
- Jesper Sørensen (Tue May 17 2011 - 05:05:27 CDT)
- David McGiven (Tue May 17 2011 - 04:58:56 CDT)
Automatic PSF Builder Problem
- ehenriques_at_qui.uc.pt (Sat Mar 12 2011 - 10:49:05 CST)
- Marc Charendoff (Fri Mar 11 2011 - 10:43:15 CST)
AW:
- Norman Geist (Fri Jul 20 2012 - 07:47:21 CDT)
- Norman Geist (Tue Jul 17 2012 - 00:35:19 CDT)
- Norman Geist (Wed Nov 23 2011 - 00:01:50 CST)
AW: "Warning" meaning
- Salvatore Mario Cosseddu (Fri Mar 02 2012 - 04:53:19 CST)
- Norman Geist (Fri Mar 02 2012 - 01:03:10 CST)
AW: .COOR TO PDB FILE
- Norman Geist (Mon Aug 15 2011 - 00:34:58 CDT)
AW: 2CPU+1GPU vs 1CPU+2GPU
- Marcel UJI (IMAP) (Tue Feb 14 2012 - 05:07:26 CST)
- Axel Kohlmeyer (Tue Feb 14 2012 - 08:24:53 CST)
- Axel Kohlmeyer (Tue Feb 14 2012 - 08:19:59 CST)
- Nicholas M Glykos (Tue Feb 14 2012 - 04:04:20 CST)
- Marcel UJI (IMAP) (Tue Feb 14 2012 - 03:26:50 CST)
- Norman Geist (Tue Feb 14 2012 - 01:18:44 CST)
AW: about extrabonds restrain
- Ling Wu (Tue Aug 30 2011 - 07:58:25 CDT)
- Norman Geist (Tue Aug 30 2011 - 01:18:37 CDT)
AW: about long namd trajectory and pbc effect
- Norman Geist (Mon Dec 03 2012 - 00:44:31 CST)
AW: about trajectory analysis
- Norman Geist (Wed May 30 2012 - 02:18:25 CDT)
AW: aligning two molecules by principal axes of inertia using measure.c
- Norman Geist (Mon Jun 20 2011 - 09:30:02 CDT)
AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance
- Norman Geist (Mon Jun 06 2011 - 06:49:06 CDT)
- Norman Geist (Mon Jun 06 2011 - 07:22:45 CDT)
- Norman Geist (Mon Jun 06 2011 - 06:11:18 CDT)
- Norman Geist (Mon Jun 06 2011 - 04:51:31 CDT)
AW: Atoms moving too fast only with CUDA version.
- Aron Broom (Wed Jun 27 2012 - 02:12:40 CDT)
- amin_at_imtech.res.in (Wed Jun 27 2012 - 02:10:04 CDT)
- Norman Geist (Wed Jun 27 2012 - 01:43:14 CDT)
AW: Atoms moving too fast with NAMD/Amber
- Norman Geist (Fri Jul 27 2012 - 03:39:33 CDT)
- Norman Geist (Thu Jul 26 2012 - 01:42:42 CDT)
AW: Automatic GPU selection in NAMD ?
- Norman Geist (Wed May 18 2011 - 00:24:45 CDT)
AW: AW:
- Norman Geist (Wed Nov 23 2011 - 01:25:12 CST)
- Norman Geist (Wed Nov 23 2011 - 00:59:15 CST)
- Norman Geist (Wed Nov 23 2011 - 01:00:42 CST)
AW: AW: 2CPU+1GPU vs 1CPU+2GPU
- Nicholas M Glykos (Wed Feb 15 2012 - 03:22:43 CST)
- Norman Geist (Wed Feb 15 2012 - 01:45:32 CST)
- Norman Geist (Tue Feb 14 2012 - 06:14:22 CST)
AW: AW: about extrabonds restrain
- Norman Geist (Wed Aug 31 2011 - 00:05:47 CDT)
AW: AW: Atoms moving too fast only with CUDA version.
- amin_at_imtech.res.in (Wed Jun 27 2012 - 09:40:38 CDT)
- Norman Geist (Wed Jun 27 2012 - 03:23:23 CDT)
- Norman Geist (Wed Jun 27 2012 - 03:28:33 CDT)
AW: AW: Automatic GPU selection in NAMD ?
- Norman Geist (Thu May 19 2011 - 01:41:37 CDT)
AW: AW: AW: 2CPU+1GPU vs 1CPU+2GPU
- Nicholas M Glykos (Wed Feb 15 2012 - 03:55:01 CST)
- Norman Geist (Wed Feb 15 2012 - 03:46:09 CST)
AW: AW: AW: Atoms moving too fast only with CUDA version.
- amin_at_imtech.res.in (Thu Jun 28 2012 - 01:13:07 CDT)
- Norman Geist (Thu Jun 28 2012 - 00:21:11 CDT)
AW: AW: AW: AW: Atoms moving too fast only with CUDA version.
- Norman Geist (Thu Jun 28 2012 - 02:05:11 CDT)
AW: AW: AW: AW: Error in membrane protein simulation
- amin_at_imtech.res.in (Tue Sep 04 2012 - 02:12:37 CDT)
- Norman Geist (Tue Sep 04 2012 - 01:53:15 CDT)
AW: AW: AW: AW: namd-ibverbs fails to start
- Norman Geist (Thu Nov 24 2011 - 00:15:52 CST)
AW: AW: AW: AW: tclBC incorrect output
- P.-L. Chau (Mon May 07 2012 - 20:59:14 CDT)
- Norman Geist (Mon May 07 2012 - 00:26:11 CDT)
AW: AW: AW: CUDA problem?
- Norman Geist (Wed Apr 11 2012 - 01:07:16 CDT)
- Norman Geist (Wed Apr 11 2012 - 01:04:08 CDT)
AW: AW: AW: Error in membrane protein simulation
- Axel Kohlmeyer (Mon Sep 03 2012 - 15:28:20 CDT)
- Rajan Vatassery (Mon Sep 03 2012 - 15:15:28 CDT)
- Axel Kohlmeyer (Mon Sep 03 2012 - 15:13:39 CDT)
- Rajan Vatassery (Mon Sep 03 2012 - 15:03:21 CDT)
- amin_at_imtech.res.in (Mon Sep 03 2012 - 11:50:08 CDT)
- Norman Geist (Mon Sep 03 2012 - 10:33:31 CDT)
AW: AW: AW: libcudart.so.4 error
- Norman Geist (Mon Nov 26 2012 - 00:11:25 CST)
AW: AW: AW: NAMD crashes with OpenMPI/OpenMX
- Jim Phillips (Wed Jun 15 2011 - 11:17:47 CDT)
- Norman Geist (Wed Jun 15 2011 - 10:37:47 CDT)
AW: AW: AW: NAMD feature request Hydrogenscale
- Norman Geist (Fri Jun 01 2012 - 01:33:48 CDT)
AW: AW: AW: namd-ibverbs fails to start
- Norman Geist (Wed Nov 23 2011 - 00:09:41 CST)
AW: AW: AW: question about wrap atoms to its original coordinates
- Norman Geist (Mon May 23 2011 - 01:03:53 CDT)
AW: AW: AW: Running NAMD on Forge (CUDA)
- Norman Geist (Mon Jul 16 2012 - 02:11:45 CDT)
AW: AW: AW: Sudden energy drop after minimization
- Norman Geist (Tue Jun 26 2012 - 04:31:42 CDT)
AW: AW: AW: tclBC incorrect output
- Cruz-Chu Eduardo Roberto (Fri May 04 2012 - 02:43:20 CDT)
- P.-L. Chau (Fri May 04 2012 - 03:33:57 CDT)
- P.-L. Chau (Fri May 04 2012 - 02:19:02 CDT)
- Norman Geist (Fri May 04 2012 - 02:03:02 CDT)
AW: AW: center of mass movement removal throughout simulation?
- Norman Geist (Wed Mar 14 2012 - 01:49:39 CDT)
AW: AW: compress PSF into INTER
- Norman Geist (Thu Jun 07 2012 - 08:25:10 CDT)
AW: AW: conf file question
- Norman Geist (Mon Mar 26 2012 - 00:39:38 CDT)
AW: AW: Consistent temperature increase in CUDA runs
- Norman Geist (Wed Feb 29 2012 - 00:17:26 CST)
AW: AW: CUDA problem?
- Francesco Pietra (Sat Apr 07 2012 - 00:40:04 CDT)
- Jim Phillips (Fri Apr 06 2012 - 08:26:18 CDT)
- Jim Phillips (Fri Apr 06 2012 - 08:10:47 CDT)
- Albert (Fri Apr 06 2012 - 07:39:09 CDT)
- Francesco Pietra (Fri Apr 06 2012 - 02:59:59 CDT)
- Albert (Fri Apr 06 2012 - 00:07:53 CDT)
- Jim Phillips (Thu Apr 05 2012 - 22:37:53 CDT)
- Norman Geist (Thu Apr 05 2012 - 01:22:38 CDT)
AW: AW: Energy minimization of membrane
- Norman Geist (Mon Feb 06 2012 - 01:01:41 CST)
- Norman Geist (Fri Feb 03 2012 - 06:02:39 CST)
- Norman Geist (Fri Feb 03 2012 - 05:54:19 CST)
AW: AW: Error in membrane protein simulation
- amin_at_imtech.res.in (Mon Sep 03 2012 - 06:27:14 CDT)
- Norman Geist (Mon Sep 03 2012 - 04:45:25 CDT)
AW: AW: Generating force field for novel molecules
- Mayne, Christopher G (Fri May 25 2012 - 12:07:43 CDT)
- Jeffrey Potoff (Fri May 25 2012 - 09:34:11 CDT)
- Axel Kohlmeyer (Fri May 25 2012 - 05:44:42 CDT)
- Sajad Falsafi-Zadeh (Fri May 25 2012 - 01:50:35 CDT)
- Norman Geist (Fri May 25 2012 - 00:56:07 CDT)
AW: AW: libcudart.so.4 error
- Norman Geist (Fri Nov 23 2012 - 07:43:50 CST)
AW: AW: Low CPU usage with NAMD running on linux cluster
- amin_at_imtech.res.in (Wed Aug 01 2012 - 00:16:30 CDT)
- Norman Geist (Tue Jul 31 2012 - 01:06:32 CDT)
AW: AW: namd 2.9 ibverbs issues
- Norman Geist (Mon Sep 10 2012 - 10:52:43 CDT)
AW: AW: namd 2.9 not going so well
- Michael Galloway (Tue Sep 18 2012 - 09:47:20 CDT)
- Norman Geist (Mon Sep 17 2012 - 09:23:36 CDT)
AW: AW: namd 2.9 run instability (segfaults)
- Norman Geist (Mon Sep 10 2012 - 02:09:43 CDT)
AW: AW: NAMD crashes with OpenMPI/OpenMX
- Jim Phillips (Wed Jun 15 2011 - 11:25:34 CDT)
- Thomas Albers (Wed Jun 15 2011 - 10:01:00 CDT)
- Norman Geist (Wed Jun 15 2011 - 09:37:40 CDT)
- Norman Geist (Wed Jun 15 2011 - 01:01:25 CDT)
AW: AW: NAMD feature request Hydrogenscale
- Vincent Leroux (Thu May 31 2012 - 10:40:32 CDT)
- Norman Geist (Thu May 31 2012 - 01:06:29 CDT)
AW: AW: namd-ibverbs fails to start
- Norman Geist (Wed Nov 23 2011 - 00:16:28 CST)
- Norman Geist (Tue Nov 22 2011 - 00:47:00 CST)
- Norman Geist (Tue Nov 22 2011 - 00:49:46 CST)
AW: AW: No output after "scheduler running in netpoll mode"
- Norman Geist (Wed Aug 22 2012 - 01:35:50 CDT)
AW: AW: Only one process running on cluster
- Norman Geist (Wed Jun 13 2012 - 05:13:45 CDT)
AW: AW: problem with pdb psf files!
- Axel Kohlmeyer (Tue Sep 04 2012 - 06:15:27 CDT)
- Jacqueline Schmidt (Tue Sep 04 2012 - 06:06:06 CDT)
- Norman Geist (Tue Sep 04 2012 - 01:59:41 CDT)
AW: AW: question about wrap atoms to its original coordinates
- Norman Geist (Fri May 20 2011 - 00:04:48 CDT)
AW: AW: Running NAMD on Forge (CUDA)
- Axel Kohlmeyer (Mon Jul 16 2012 - 02:28:25 CDT)
- Gianluca Interlandi (Sat Jul 14 2012 - 20:59:05 CDT)
- Gianluca Interlandi (Fri Jul 13 2012 - 14:08:57 CDT)
- Norman Geist (Fri Jul 13 2012 - 02:09:04 CDT)
AW: AW: Running NAMD parallel on two machines with 3 CUDAs
- Norman Geist (Fri May 06 2011 - 01:36:20 CDT)
AW: AW: save the last frame as a pdb file using dcd file
- Norman Geist (Thu Sep 22 2011 - 04:33:07 CDT)
AW: AW: Set up NPT simulation in cubic PBC-box
- Norman Geist (Mon Apr 30 2012 - 00:29:21 CDT)
- Norman Geist (Mon Apr 30 2012 - 00:21:02 CDT)
AW: AW: simulation:protein,ligand,lipid,water and ions
- Norman Geist (Fri Aug 31 2012 - 00:47:21 CDT)
AW: AW: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA)
- Norman Geist (Tue May 29 2012 - 00:59:55 CDT)
AW: AW: Sudden energy drop after minimization
- tillmann.utesch_at_mail.tu-berlin.de (Tue Jun 26 2012 - 03:03:34 CDT)
- Hyuntae Na (Tue Jun 26 2012 - 01:56:00 CDT)
- Norman Geist (Tue Jun 26 2012 - 01:40:39 CDT)
AW: AW: tclBC incorrect output
- P.-L. Chau (Fri May 04 2012 - 01:26:49 CDT)
- Norman Geist (Fri May 04 2012 - 01:10:57 CDT)
AW: Batch Mode MD simulation Script for NAMD
- Norman Geist (Mon Aug 15 2011 - 00:29:43 CDT)
- Norman Geist (Mon Aug 15 2011 - 00:34:15 CDT)
- Norman Geist (Fri Aug 12 2011 - 07:02:29 CDT)
- Norman Geist (Fri Aug 12 2011 - 00:47:19 CDT)
AW: Benchmarks for GTX 690's and 590's
- Norman Geist (Wed Nov 28 2012 - 10:04:50 CST)
AW: Bond Breaking in Polymer Networks - United Atom Forcefield
- Norman Geist (Tue Nov 13 2012 - 10:40:42 CST)
AW: box dimension for unwrapped boxes?
- Norman Geist (Thu Oct 04 2012 - 01:05:47 CDT)
AW: cell size
- Norman Geist (Thu Dec 15 2011 - 00:16:59 CST)
AW: center of mass movement removal throughout simulation?
- Aron Broom (Tue Mar 13 2012 - 11:30:38 CDT)
- Markus K. Dahlgren (Tue Mar 13 2012 - 09:50:37 CDT)
- Norman Geist (Tue Mar 13 2012 - 01:36:16 CDT)
- Norman Geist (Tue Mar 13 2012 - 01:32:45 CDT)
AW: compilation of namd
- Norman Geist (Fri May 06 2011 - 01:16:56 CDT)
- Norman Geist (Fri May 06 2011 - 00:46:01 CDT)
AW: compilation with CUDA error
- Norman Geist (Tue Oct 30 2012 - 02:19:22 CDT)
AW: compiling charm++ Error: can not find mpi library
- Norman Geist (Thu Sep 27 2012 - 08:14:57 CDT)
- Norman Geist (Thu Sep 27 2012 - 01:46:23 CDT)
AW: compress PSF into INTER
- Chris Harrison (Thu Jun 07 2012 - 10:40:35 CDT)
- JC Gumbart (Thu Jun 07 2012 - 08:11:49 CDT)
- Cruz-Chu Eduardo Roberto (Thu Jun 07 2012 - 07:02:35 CDT)
- JC Gumbart (Thu Jun 07 2012 - 05:26:58 CDT)
- Norman Geist (Thu Jun 07 2012 - 05:15:09 CDT)
- Norman Geist (Thu Jun 07 2012 - 05:11:54 CDT)
- Norman Geist (Thu Jun 07 2012 - 01:24:31 CDT)
AW: conf file question
- Norman Geist (Fri Mar 23 2012 - 06:09:41 CDT)
- Norman Geist (Wed Mar 21 2012 - 10:27:19 CDT)
AW: Consistent temperature increase in CUDA runs
- Vlad Cojocaru (Tue Feb 28 2012 - 03:24:30 CST)
- Nicholas M Glykos (Tue Feb 28 2012 - 08:40:29 CST)
- Axel Kohlmeyer (Tue Feb 28 2012 - 06:14:18 CST)
- JC Gumbart (Tue Feb 28 2012 - 02:57:30 CST)
- Norman Geist (Tue Feb 28 2012 - 00:19:29 CST)
- Norman Geist (Mon Feb 27 2012 - 00:28:03 CST)
AW: Constraint failure during equalibration
- Norman Geist (Wed Sep 14 2011 - 00:31:59 CDT)
AW: Corrupt dcd files
- Marc Baaden (Sun May 15 2011 - 06:28:38 CDT)
- Marc Baaden (Sat May 14 2011 - 16:23:30 CDT)
- Jim Phillips (Thu May 12 2011 - 17:20:36 CDT)
- Norman Geist (Thu May 12 2011 - 01:53:23 CDT)
- Norman Geist (Thu May 12 2011 - 01:51:56 CDT)
- Norman Geist (Thu May 12 2011 - 01:46:51 CDT)
AW: crossing the border by protein/ion complex
- Norman Geist (Wed Feb 08 2012 - 00:54:30 CST)
AW: CUDA error on Pe 4: device cannot map host memory
- Vignesh (Wed Jun 13 2012 - 02:16:24 CDT)
- Norman Geist (Wed Jun 13 2012 - 00:58:11 CDT)
AW: Cuda errors in Ubuntu12amd64
- Norman Geist (Thu Oct 04 2012 - 00:51:13 CDT)
AW: CUDA on GPU Cluster
- Norman Geist (Mon Aug 22 2011 - 00:47:16 CDT)
AW: CUDA problem?
- Albert (Thu Apr 05 2012 - 01:15:52 CDT)
- Norman Geist (Thu Apr 05 2012 - 01:12:24 CDT)
AW: CUDA simulation memory usage
- Norman Geist (Wed May 18 2011 - 07:10:58 CDT)
AW: cuda_check_local_progress polled 1000000 times
- Norman Geist (Wed Jun 06 2012 - 00:38:05 CDT)
- Norman Geist (Tue Jun 05 2012 - 06:42:24 CDT)
- Norman Geist (Tue Jun 05 2012 - 00:29:17 CDT)
AW: deca-Ala simulations with different cutoff produce different results
- Norman Geist (Mon May 16 2011 - 04:20:58 CDT)
AW: efield energies incorrect in analysis mode (run 0) ?
- Norman Geist (Thu Jun 28 2012 - 00:29:32 CDT)
AW: energy minimization
- Norman Geist (Tue Aug 21 2012 - 01:24:22 CDT)
AW: Energy minimization of membrane
- Chris Harrison (Thu Feb 09 2012 - 01:28:36 CST)
- Chris Harrison (Thu Feb 09 2012 - 01:25:56 CST)
- R. Charbel Maroun (Fri Feb 03 2012 - 08:53:37 CST)
- Ajasja LjubetiÄ (Fri Feb 03 2012 - 05:25:01 CST)
- kanchi subbarao rao (Fri Feb 03 2012 - 05:20:29 CST)
- R. Charbel Maroun (Fri Feb 03 2012 - 04:58:17 CST)
- Norman Geist (Fri Feb 03 2012 - 01:14:50 CST)
AW: Error in membrane protein simulation
- Ajasja LjubetiÄ (Mon Sep 03 2012 - 04:16:11 CDT)
- amin_at_imtech.res.in (Mon Sep 03 2012 - 03:41:25 CDT)
- Norman Geist (Mon Sep 03 2012 - 01:52:45 CDT)
AW: Error with "namd"
- Norman Geist (Wed Oct 26 2011 - 02:05:17 CDT)
AW: execute vs. config directory
- Norman Geist (Mon Sep 17 2012 - 01:47:22 CDT)
- Norman Geist (Mon Sep 17 2012 - 01:43:57 CDT)
AW: extract velocities
- Norman Geist (Wed Oct 24 2012 - 00:34:56 CDT)
AW: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version
- Norman Geist (Tue Oct 23 2012 - 01:04:04 CDT)
- Norman Geist (Tue Oct 23 2012 - 00:37:16 CDT)
- Norman Geist (Mon Oct 22 2012 - 01:01:02 CDT)
AW: FEP - Dynamic charges
- Norman Geist (Wed May 16 2012 - 00:48:20 CDT)
AW: ffTK in the just released VMD 1.9.1
- Norman Geist (Mon Feb 06 2012 - 01:04:05 CST)
AW: fixed bond length
- Norman Geist (Mon May 14 2012 - 01:23:05 CDT)
AW: Fixing bonds in dihydrogen phosphate to save computation time
- Norman Geist (Tue Jul 10 2012 - 05:36:15 CDT)
- Norman Geist (Tue Jul 10 2012 - 00:44:57 CDT)
AW: Force Field Topology and Parameter Files
- Norman Geist (Wed Nov 14 2012 - 00:15:42 CST)
AW: free energy of binding
- Norman Geist (Thu Jul 07 2011 - 05:35:07 CDT)
AW: Fwd: Fwd: namd on gtx-680
- Norman Geist (Thu Jun 21 2012 - 00:49:23 CDT)
AW: Generating force field for novel molecules
- Norman Geist (Thu May 24 2012 - 00:15:11 CDT)
AW: Glycosaminoglycan sulfate group with CHARMM
- Norman Geist (Thu Mar 29 2012 - 00:58:54 CDT)
- Norman Geist (Fri Mar 23 2012 - 01:48:05 CDT)
AW: glycosaminoglycan with GLYCAM06 in amber format
- Massimiliano Porrini (Thu Dec 22 2011 - 11:12:10 CST)
- felmerino_at_uchile.cl (Wed Dec 21 2011 - 12:44:08 CST)
- Norman Geist (Wed Dec 21 2011 - 00:51:03 CST)
- Norman Geist (Wed Dec 21 2011 - 00:54:50 CST)
- Norman Geist (Tue Dec 20 2011 - 06:45:32 CST)
- Norman Geist (Mon Dec 19 2011 - 07:35:58 CST)
- Norman Geist (Mon Dec 19 2011 - 00:45:19 CST)
AW: GPU cluster
- Norman Geist (Thu Jun 21 2012 - 05:43:56 CDT)
- Norman Geist (Thu Jun 21 2012 - 00:45:48 CDT)
AW: GPU workstation build
- Norman Geist (Tue Aug 21 2012 - 09:33:48 CDT)
- Norman Geist (Tue Aug 21 2012 - 01:22:49 CDT)
AW: GTX-660 Ti benchmark
- Norman Geist (Wed Sep 19 2012 - 01:50:58 CDT)
- Norman Geist (Tue Sep 18 2012 - 01:36:06 CDT)
- Norman Geist (Mon Sep 17 2012 - 01:31:12 CDT)
AW: How can I write a log file on my cluster?
- Norman Geist (Wed Oct 24 2012 - 00:42:06 CDT)
- Norman Geist (Tue Oct 23 2012 - 00:30:44 CDT)
- Norman Geist (Mon Oct 22 2012 - 09:04:29 CDT)
AW: how to calculate the box size
- Norman Geist (Wed Mar 07 2012 - 01:01:31 CST)
AW: how to edit restart.coor
- Norman Geist (Thu Apr 05 2012 - 01:18:58 CDT)
AW: How to Get Bonded Pair Force Calculation with NAMD
- Norman Geist (Wed Mar 28 2012 - 01:11:34 CDT)
- Norman Geist (Tue Mar 27 2012 - 01:16:10 CDT)
AW: how to run NAMD-CUDA on multiple nodes
- Norman Geist (Wed Nov 28 2012 - 03:45:53 CST)
- Norman Geist (Wed Nov 28 2012 - 01:29:58 CST)
- Norman Geist (Tue Nov 27 2012 - 08:57:08 CST)
- Norman Geist (Tue Nov 27 2012 - 02:09:01 CST)
AW: IB fabrics
- Norman Geist (Mon Jan 09 2012 - 00:49:02 CST)
AW: Ib version and nodelist
- Norman Geist (Mon Aug 22 2011 - 00:50:56 CDT)
AW: increment torsion restrain before minimization
- Norman Geist (Mon Nov 05 2012 - 01:32:39 CST)
AW: Infiniband and commodity hardware
- Norman Geist (Mon Sep 19 2011 - 01:03:41 CDT)
AW: Installing NAMD on a 64-bit linux (NVIDIA CUDA)
- Norman Geist (Tue Jan 31 2012 - 00:53:47 CST)
AW: installing namd on ibm cluster (powerpc)
- Norman Geist (Mon Dec 05 2011 - 03:30:48 CST)
- Norman Geist (Mon Dec 05 2011 - 00:29:43 CST)
AW: Keep PBC box size in Z-direction constant?
- Norman Geist (Wed Feb 22 2012 - 00:24:02 CST)
- Norman Geist (Tue Feb 21 2012 - 00:27:45 CST)
AW: keeping a protein in a solvation box
- Norman Geist (Wed Jun 13 2012 - 01:17:06 CDT)
AW: Letzte Hilfe
- Bjoern Olausson (Tue Aug 16 2011 - 06:17:36 CDT)
- Norman Geist (Mon Aug 15 2011 - 07:16:39 CDT)
AW: libcudart.so.4 error
- flavio seixas (Fri Nov 23 2012 - 04:47:36 CST)
- Norman Geist (Fri Nov 23 2012 - 00:50:54 CST)
AW: Line minimizerfailure because of IMPR?
- Norman Geist (Thu Apr 05 2012 - 03:28:14 CDT)
- Norman Geist (Thu Apr 05 2012 - 03:24:12 CDT)
- Norman Geist (Thu Apr 05 2012 - 01:08:31 CDT)
AW: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue?
- Norman Geist (Mon Mar 26 2012 - 00:43:17 CDT)
- Norman Geist (Fri Mar 23 2012 - 02:09:28 CDT)
- Norman Geist (Wed Mar 21 2012 - 02:02:41 CDT)
- Norman Geist (Tue Mar 20 2012 - 01:36:34 CDT)
AW: Low CPU usage with NAMD running on linux cluster
- amin_at_imtech.res.in (Tue Jul 31 2012 - 00:01:02 CDT)
- Norman Geist (Mon Jul 30 2012 - 11:01:37 CDT)
AW: malloc memory error using CUDA devices
- Norman Geist (Thu Nov 01 2012 - 02:01:50 CDT)
AW: max number of CPU PEs per GPU?
- Norman Geist (Fri Jun 10 2011 - 06:25:45 CDT)
- Norman Geist (Fri Jun 10 2011 - 02:56:30 CDT)
AW: memory-optimized version binary coordinates?
- Norman Geist (Thu Jun 21 2012 - 00:39:57 CDT)
AW: minimization and water bubbles
- Norman Geist (Fri Jun 15 2012 - 01:34:42 CDT)
AW: Minimization doesn't stop when converged
- Norman Geist (Fri Oct 07 2011 - 04:54:47 CDT)
AW: Minimization is taking a lot of computing time.
- Norman Geist (Wed Aug 10 2011 - 01:21:10 CDT)
- Norman Geist (Wed Aug 10 2011 - 00:44:55 CDT)
- Norman Geist (Fri Aug 05 2011 - 05:54:49 CDT)
AW: Multi core problem
- Norman Geist (Tue Jul 10 2012 - 00:38:51 CDT)
AW: multicore versus net-linux
- Norman Geist (Wed Apr 11 2012 - 01:05:33 CDT)
AW: Multinode NAMD CUDA GPU Selection
- Axel Kohlmeyer (Fri Aug 19 2011 - 06:33:28 CDT)
- Norman Geist (Fri Aug 19 2011 - 00:53:31 CDT)
- Norman Geist (Fri Aug 19 2011 - 00:22:56 CDT)
AW: Multiple gpu cards
- Norman Geist (Wed Aug 15 2012 - 09:58:14 CDT)
AW: Multiple Runs in a Single Conf File
- Norman Geist (Thu Jun 09 2011 - 00:40:18 CDT)
- Norman Geist (Wed Jun 08 2011 - 03:27:54 CDT)
AW: NAMD 2.8 and PLUMED 1.3
- Norman Geist (Mon Sep 03 2012 - 01:34:07 CDT)
AW: namd 2.9 ibverbs issues
- Michael Galloway (Mon Sep 10 2012 - 08:55:42 CDT)
- Norman Geist (Mon Sep 10 2012 - 02:22:52 CDT)
AW: namd 2.9 not going so well
- Michael Galloway (Mon Sep 17 2012 - 07:16:59 CDT)
- Norman Geist (Mon Sep 17 2012 - 01:00:51 CDT)
AW: namd 2.9 run instability (segfaults)
- Michael Galloway (Fri Sep 07 2012 - 09:28:36 CDT)
- Norman Geist (Fri Sep 07 2012 - 01:10:23 CDT)
AW: NAMD 2.9 Windows CUDA build?
- Norman Geist (Mon Nov 05 2012 - 01:27:43 CST)
AW: NAMD 2.9 with CUDA runs
- Norman Geist (Mon Sep 03 2012 - 01:30:46 CDT)
AW: NAMD 2.9: Segmentation fault?
- Maria Antonieta Sanchez Farran (Wed Aug 01 2012 - 15:25:15 CDT)
- Norman Geist (Wed Aug 01 2012 - 01:20:53 CDT)
AW: NAMD 2.9b1 crashes during minimization
- Norman Geist (Fri Mar 23 2012 - 01:58:15 CDT)
AW: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8
- Norman Geist (Tue Apr 03 2012 - 02:10:08 CDT)
- Norman Geist (Tue Apr 03 2012 - 02:03:48 CDT)
- Norman Geist (Mon Apr 02 2012 - 01:43:07 CDT)
AW: NAMD crashes with OpenMPI/OpenMX
- Norman Geist (Mon Jun 20 2011 - 00:36:54 CDT)
- Thomas Albers (Wed Jun 15 2011 - 09:10:28 CDT)
AW: NAMD failed to read AMBER parm file
- Norman Geist (Fri Nov 09 2012 - 01:37:25 CST)
AW: NAMD feature request Hydrogenscale
- Norman Geist (Thu May 31 2012 - 01:09:59 CDT)
- Vincent Leroux (Wed May 30 2012 - 10:27:47 CDT)
- Norman Geist (Wed May 30 2012 - 09:17:48 CDT)
AW: Namd list: "Size cell" for restart
- Norman Geist (Thu Aug 30 2012 - 01:59:07 CDT)
AW: NAMD SGE Job Script Scale Up issues!
- Norman Geist (Fri Oct 19 2012 - 00:41:54 CDT)
AW: namd simulation:protein,ligand,lipid,water and ions
- Norman Geist (Fri Jun 15 2012 - 01:20:45 CDT)
- Norman Geist (Thu Jun 14 2012 - 01:50:39 CDT)
AW: namd simulationâ€‹:protein,lâ€‹igand,lipiâ€‹d,water and ions
- Norman Geist (Thu Aug 30 2012 - 02:06:14 CDT)
AW: Namd-I: namd compiling problem
- Norman Geist (Thu Aug 04 2011 - 00:33:59 CDT)
- Norman Geist (Wed Aug 03 2011 - 00:23:52 CDT)
AW: namd-ibverbs fails to start
- Axel Kohlmeyer (Tue Nov 22 2011 - 08:02:12 CST)
AW: NAMDenergy plugin_van der Waal interactions
- Norman Geist (Wed Feb 22 2012 - 00:20:15 CST)
- Norman Geist (Tue Feb 21 2012 - 00:16:40 CST)
AW: NAMDEnergy: run with XSC file or not?
- Norman Geist (Thu Nov 22 2012 - 00:40:21 CST)
- Norman Geist (Thu Nov 22 2012 - 00:43:49 CST)
AW: Newbie's question
- Norman Geist (Tue Aug 07 2012 - 00:25:25 CDT)
AW: No output after "scheduler running in netpoll mode"
- amin_at_imtech.res.in (Tue Aug 21 2012 - 11:43:20 CDT)
- Norman Geist (Tue Aug 21 2012 - 09:39:35 CDT)
AW: no. of CPUs for optimal GTX-690 performance
- Norman Geist (Wed Nov 07 2012 - 01:56:25 CST)
AW: nvidia cuda driver version
- Norman Geist (Mon Aug 08 2011 - 00:04:40 CDT)
AW: Only one process running on cluster
- amin_at_imtech.res.in (Wed Jun 13 2012 - 04:02:40 CDT)
- Norman Geist (Wed Jun 13 2012 - 03:35:49 CDT)
AW: outputting atom coordinated
- Norman Geist (Mon Sep 17 2012 - 01:52:28 CDT)
AW: patch becoming too small
- Norman Geist (Tue Aug 09 2011 - 02:41:19 CDT)
AW: PDB sugar unit residue name
- Norman Geist (Fri Mar 30 2012 - 01:25:16 CDT)
AW: peculiar scaling on the GPU
- Norman Geist (Wed Aug 01 2012 - 01:14:26 CDT)
AW: Peptide planarity Dihedral angle restraints
- Norman Geist (Fri Dec 09 2011 - 00:18:47 CST)
AW: performance variation during run time
- Norman Geist (Thu Nov 29 2012 - 01:26:31 CST)
AW: periodic boundaries
- Norman Geist (Tue Jul 10 2012 - 00:30:50 CDT)
AW: periodicity error
- Norman Geist (Tue Sep 18 2012 - 08:58:27 CDT)
- Norman Geist (Mon Sep 17 2012 - 09:15:29 CDT)
AW: Please read: fatal error namd 2.7b1 for Win32 Memory allocation failed on processor > 0
- Norman Geist (Tue Aug 28 2012 - 02:00:12 CDT)
AW: Problem running NAMD 2.8 with ibverbs
- Norman Geist (Thu Jan 12 2012 - 07:34:31 CST)
- Norman Geist (Mon Jan 09 2012 - 00:32:06 CST)
AW: problem with gpu namd 2.9b3
- Norman Geist (Mon Apr 23 2012 - 00:45:58 CDT)
- Norman Geist (Fri Apr 20 2012 - 00:45:50 CDT)
AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..."
- Norman Geist (Thu Jun 09 2011 - 00:44:01 CDT)
- Norman Geist (Thu Jun 09 2011 - 00:36:44 CDT)
- Norman Geist (Thu Jun 09 2011 - 00:26:13 CDT)
AW: Problem with parameter file in Pair Interaction Calculation
- M Mahjour (Tue Jan 10 2012 - 10:48:33 CST)
- Kovacs, Sandor (Tue Jan 10 2012 - 01:14:04 CST)
- Norman Geist (Tue Jan 10 2012 - 00:41:23 CST)
AW: problem with paramters?
- Norman Geist (Thu Mar 22 2012 - 02:08:44 CDT)
AW: problem with pdb psf files!
- Axel Kohlmeyer (Mon Sep 03 2012 - 11:20:45 CDT)
- Jacqueline Schmidt (Mon Sep 03 2012 - 11:01:17 CDT)
- Norman Geist (Mon Sep 03 2012 - 02:18:08 CDT)
AW: queries about "Tclforces" utility in NAMD
- Norman Geist (Fri May 25 2012 - 01:11:47 CDT)
AW: Question about GPUs hardware.
- Norman Geist (Tue Apr 24 2012 - 01:11:01 CDT)
AW: question about wrap atoms to its original coordinates
- jnsong (Thu May 19 2011 - 21:31:54 CDT)
- Norman Geist (Wed May 18 2011 - 00:34:33 CDT)
AW: question and NAMD operation
- Norman Geist (Thu Aug 30 2012 - 02:16:40 CDT)
AW: question regarding simulated annealing
- Norman Geist (Thu Aug 30 2012 - 02:56:04 CDT)
- Norman Geist (Thu Aug 30 2012 - 01:50:11 CDT)
AW: Random seed and equilibrated structure
- Norman Geist (Fri Jul 27 2012 - 01:50:17 CDT)
AW: Reading files for multiple threaded simulations
- Norman Geist (Fri Nov 04 2011 - 02:28:50 CDT)
- Norman Geist (Thu Nov 03 2011 - 02:26:05 CDT)
- Norman Geist (Wed Nov 02 2011 - 01:45:32 CDT)
AW: Reflecting boundary z axis in NAMD
- Norman Geist (Wed Sep 05 2012 - 01:38:44 CDT)
AW: Replica-exchange MD on a single node / SMP workstation
- Norman Geist (Mon Nov 12 2012 - 00:33:23 CST)
AW: residue_rmsd.tcl via
- Norman Geist (Thu Aug 09 2012 - 09:44:28 CDT)
AW: restart a simulation
- Norman Geist (Fri Mar 16 2012 - 02:01:34 CDT)
AW: restraining
- Jeffrey Potoff (Fri Aug 24 2012 - 09:37:49 CDT)
- Axel Kohlmeyer (Fri Aug 24 2012 - 08:25:22 CDT)
- Christopher Rowley (Fri Aug 24 2012 - 08:08:42 CDT)
- Norman Geist (Fri Aug 24 2012 - 01:42:27 CDT)
AW: Running NAMD on Forge (CUDA)
- Gianluca Interlandi (Fri Jul 13 2012 - 01:35:49 CDT)
- Norman Geist (Fri Jul 13 2012 - 01:28:49 CDT)
AW: Running NAMD parallel on two machines with 3 CUDAs
- Norman Geist (Fri May 06 2011 - 00:41:11 CDT)
- Norman Geist (Fri May 06 2011 - 00:36:27 CDT)
AW: save the last frame as a pdb file using dcd file
- Norman Geist (Thu Sep 22 2011 - 03:15:43 CDT)
AW: scaling
- Norman Geist (Mon Jan 02 2012 - 00:44:13 CST)
AW: scnb value to prevent VDWs scaling
- Norman Geist (Thu Sep 06 2012 - 08:09:22 CDT)
AW: script for equilibration
- Norman Geist (Tue Oct 04 2011 - 00:18:04 CDT)
AW: segmentation fault with NAMDenergy
- Norman Geist (Fri Apr 20 2012 - 01:00:23 CDT)
AW: Set up NPT simulation in cubic PBC-box
- Aron Broom (Mon Apr 30 2012 - 01:40:35 CDT)
- Xi Cheng (Fri Apr 27 2012 - 10:22:56 CDT)
- Norman Geist (Fri Apr 27 2012 - 00:42:29 CDT)
AW: SHAKE Tolerance and Performance
- Norman Geist (Fri Mar 02 2012 - 04:47:02 CST)
- Norman Geist (Fri Mar 02 2012 - 01:14:57 CST)
AW: Simulation Box Deformation
- Axel Kohlmeyer (Tue Dec 04 2012 - 11:40:26 CST)
- John Doe (Tue Dec 04 2012 - 06:24:09 CST)
- Norman Geist (Tue Dec 04 2012 - 00:57:13 CST)
AW: simulation:protein,ligand,lipid,water and ions
- Norman Geist (Thu Aug 30 2012 - 09:47:47 CDT)
AW: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA)
- Norman Geist (Tue May 29 2012 - 01:05:16 CDT)
- Benjamin Merget (Sun May 27 2012 - 09:04:48 CDT)
- Norman Geist (Fri May 25 2012 - 01:10:17 CDT)
AW: stereo-chemical inversion during MD
- Branko (Tue May 08 2012 - 15:03:08 CDT)
- Branko (Tue May 08 2012 - 10:51:46 CDT)
- Axel Kohlmeyer (Tue May 08 2012 - 08:33:03 CDT)
- Branko (Tue May 08 2012 - 03:26:25 CDT)
- Norman Geist (Tue May 08 2012 - 01:01:05 CDT)
AW: Sticking TIP4P water molecules AMBER
- Norman Geist (Tue Dec 20 2011 - 00:33:08 CST)
AW: stochastical boundary conditions in NAMD
- Norman Geist (Wed Dec 07 2011 - 00:38:58 CST)
AW: Sudden energy drop after minimization
- Aron Broom (Mon Jun 25 2012 - 22:05:39 CDT)
- Hyuntae Na (Mon Jun 25 2012 - 00:59:18 CDT)
- Norman Geist (Mon Jun 25 2012 - 00:37:43 CDT)
AW: system splitted
- Norman Geist (Mon Mar 05 2012 - 00:59:23 CST)
AW: tclBC incorrect output
- P.-L. Chau (Thu May 03 2012 - 01:44:17 CDT)
- Norman Geist (Thu May 03 2012 - 00:55:58 CDT)
AW: temperature-TS with NAMDplot
- Norman Geist (Fri Jul 08 2011 - 06:02:14 CDT)
AW: The size of a periodic cell in NAMD operation
- Norman Geist (Mon Sep 03 2012 - 01:45:48 CDT)
AW: The structure files for the second turn of simulation
- Norman Geist (Tue Aug 28 2012 - 02:10:17 CDT)
AW: Three GPU cards on shared-mem motherboard
- Norman Geist (Wed May 30 2012 - 01:55:50 CDT)
- Norman Geist (Tue May 29 2012 - 01:24:34 CDT)
AW: Trying to run a setup with amber force field in NAMD
- Norman Geist (Thu Jun 14 2012 - 01:41:15 CDT)
- Norman Geist (Wed Jun 13 2012 - 00:50:10 CDT)
AW: Unexplained segmentation faults in NAMD 2.9 using CUDA and GBIS
- Norman Geist (Fri Nov 30 2012 - 00:32:14 CST)
AW: vmd-l: segmentation fault with NAMDenergy
- Norman Geist (Mon Apr 23 2012 - 00:52:17 CDT)
AW: VMD_waterbox
- Norman Geist (Mon Sep 17 2012 - 02:18:29 CDT)
AW: Warning: Not all atoms have unique coordinates
- Norman Geist (Thu Aug 30 2012 - 01:54:20 CDT)
AW: Water bubbles in NVT equilibration dynamics
- Norman Geist (Tue Aug 28 2012 - 01:26:25 CDT)
AW: water equilibration
- Narasimhan LOGANATHAN (Fri Aug 05 2011 - 07:53:22 CDT)
- Norman Geist (Fri Aug 05 2011 - 05:56:04 CDT)
AW: water is forming bonds between oxigens
- Norman Geist (Wed Jun 15 2011 - 01:05:35 CDT)
AW: water molecules
- Norman Geist (Tue Jan 03 2012 - 00:34:15 CST)
AW: what restraint can I use to prevent membrane diffusion on the Z-axis?
- Norman Geist (Tue Feb 28 2012 - 00:42:24 CST)
AW: Win64-MPI
- Norman Geist (Tue Jul 12 2011 - 08:20:11 CDT)
AW: wrap dcd files
- Namd Namd (Thu Jun 28 2012 - 07:25:22 CDT)
- Norman Geist (Thu Jun 28 2012 - 06:10:17 CDT)
AW: Writing an output file into pdb format in a simulation.
- Norman Geist (Fri Jun 01 2012 - 02:39:56 CDT)
Bactenecine
- Branko (Wed Mar 16 2011 - 16:35:57 CDT)
- johan strumpfer (Wed Mar 16 2011 - 15:54:46 CDT)
- Andres Morales N (Wed Mar 16 2011 - 14:22:09 CDT)
- Andres Morales N (Mon Mar 14 2011 - 23:11:05 CDT)
Basic question on fixed atom
- Ganesh Kamath (Thu Oct 11 2012 - 09:08:37 CDT)
Batch Mode MD simulation Script for NAMD
- JC Gumbart (Sat Aug 13 2011 - 08:45:56 CDT)
- Babban Mia (Sat Aug 13 2011 - 07:36:56 CDT)
- Ismail, Mohd F. (Fri Aug 12 2011 - 14:40:31 CDT)
- Babban Mia (Fri Aug 12 2011 - 13:55:03 CDT)
- Ismail, Mohd F. (Fri Aug 12 2011 - 13:07:59 CDT)
- Babban Mia (Fri Aug 12 2011 - 12:59:45 CDT)
- Babban Mia (Fri Aug 12 2011 - 12:06:28 CDT)
- Jernej Zidar (Fri Aug 12 2011 - 08:03:21 CDT)
- Axel Kohlmeyer (Fri Aug 12 2011 - 07:53:13 CDT)
- Jeffrey Potoff (Fri Aug 12 2011 - 06:45:12 CDT)
- Babban Mia (Fri Aug 12 2011 - 05:46:32 CDT)
- Babban Mia (Thu Aug 11 2011 - 18:56:19 CDT)
Behavior of explicit water beyond periodic boundaries
- Aron Broom (Thu Dec 20 2012 - 11:56:30 CST)
- Aron Broom (Thu Dec 20 2012 - 11:56:11 CST)
- Dr. Eddie (Thu Dec 20 2012 - 11:42:31 CST)
- Dr. Eddie (Thu Dec 20 2012 - 11:03:02 CST)
Benchmark for NAMD2.7 (curent version)
- Branko (Wed Jan 05 2011 - 14:19:19 CST)
Benchmarks for GTX 690's and 590's
- Dr. Eddie (Wed Nov 28 2012 - 10:35:53 CST)
- Axel Kohlmeyer (Wed Nov 28 2012 - 10:11:27 CST)
- Dr. Eddie (Wed Nov 28 2012 - 09:12:12 CST)
- Dr. Eddie (Sun Nov 25 2012 - 20:11:47 CST)
- Aron Broom (Sun Nov 25 2012 - 13:25:19 CST)
- Dr. Eddie (Sun Nov 25 2012 - 11:41:46 CST)
Benefits of SandyBridge EP in NAMD2.9
- Axel Kohlmeyer (Fri Jun 01 2012 - 09:19:50 CDT)
- Axel Kohlmeyer (Fri Jun 01 2012 - 09:04:52 CDT)
- Jérôme Hénin (Fri Jun 01 2012 - 08:57:23 CDT)
- Axel Kohlmeyer (Fri Jun 01 2012 - 08:35:37 CDT)
- Florian Mrugalla (Fri Jun 01 2012 - 06:52:19 CDT)
bigdcd file help
- Nicholas M Glykos (Tue Jul 05 2011 - 13:35:43 CDT)
- snoze pa (Tue Jul 05 2011 - 13:19:06 CDT)
- snoze pa (Tue Jul 05 2011 - 09:56:15 CDT)
- sajad falsafi (Mon Jul 04 2011 - 08:52:36 CDT)
- Cosseddu, Salvatore (Mon Jul 04 2011 - 04:11:55 CDT)
- snoze pa (Mon Jul 04 2011 - 01:29:23 CDT)
binaryrestart/binaryoutput problem
- Francesco Pietra (Tue Mar 01 2011 - 02:54:26 CST)
Blue Waters
- Andy Somogyi (Tue Aug 09 2011 - 10:18:49 CDT)
Bond Breaking in Polymer Networks - United Atom Forcefield
- Axel Kohlmeyer (Tue Nov 13 2012 - 10:53:11 CST)
- Stefanos Anogiannakis (Tue Nov 13 2012 - 04:14:38 CST)
bond lengths angles in namd
- Ajasja LjubetiÄ (Thu Jan 27 2011 - 07:14:26 CST)
- Jérôme Hénin (Thu Jan 27 2011 - 06:55:28 CST)
- oguz gurbulak (Thu Jan 27 2011 - 06:35:34 CST)
- oguz gurbulak (Thu Jan 27 2011 - 05:43:09 CST)
Bonds are too long after simulation
- Anthony Rey (Wed Sep 07 2011 - 22:48:37 CDT)
- Axel Kohlmeyer (Wed Sep 07 2011 - 13:18:26 CDT)
- flavio seixas (Wed Sep 07 2011 - 13:10:13 CDT)
- Markus K. Dahlgren (Wed Sep 07 2011 - 12:54:16 CDT)
- Anthony Rey (Wed Sep 07 2011 - 10:32:11 CDT)
BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars)
- Francesco Pietra (Fri Mar 11 2011 - 11:46:30 CST)
Boundary potential of colvar alpha not working?
- Jérôme Hénin (Thu Oct 13 2011 - 10:23:41 CDT)
- Yun Luo (Thu Oct 13 2011 - 08:21:15 CDT)
- Yun Luo (Thu Oct 13 2011 - 09:03:46 CDT)
- Jérôme Hénin (Thu Oct 13 2011 - 08:54:35 CDT)
- Jérôme Hénin (Thu Oct 13 2011 - 07:14:53 CDT)
- Yun Luo (Wed Oct 12 2011 - 09:34:27 CDT)
box dimension for unwrapped boxes?
- Jacqueline Schmidt (Wed Oct 03 2012 - 10:32:37 CDT)
- Aron Broom (Wed Oct 03 2012 - 10:19:05 CDT)
- Jacqueline Schmidt (Wed Oct 03 2012 - 10:14:09 CDT)
Breaking of Disulfide Bonds
- JC Gumbart (Wed May 30 2012 - 23:29:53 CDT)
- Gianluca Interlandi (Wed May 30 2012 - 23:29:16 CDT)
- Gianluca Interlandi (Wed May 30 2012 - 23:27:20 CDT)
- Aron Broom (Wed May 30 2012 - 23:14:21 CDT)
- Kapil jain (Wed May 30 2012 - 23:09:25 CDT)
Buffer Underflow in Multiple Walker MetaDynamics
- Giacomo Fiorin (Thu Jul 05 2012 - 18:07:46 CDT)
- Aron Broom (Thu Jul 05 2012 - 18:01:04 CDT)
- Giacomo Fiorin (Thu Jul 05 2012 - 17:25:02 CDT)
- Aron Broom (Tue Jul 03 2012 - 20:04:09 CDT)
- Giacomo Fiorin (Thu Jun 14 2012 - 17:25:26 CDT)
- Aron Broom (Thu Jun 14 2012 - 17:12:45 CDT)
- Giacomo Fiorin (Thu Jun 14 2012 - 15:54:17 CDT)
- Aron Broom (Thu Jun 14 2012 - 15:47:10 CDT)
- Giacomo Fiorin (Thu Jun 14 2012 - 15:20:04 CDT)
- Aron Broom (Thu Jun 14 2012 - 14:56:30 CDT)
- Giacomo Fiorin (Thu Jun 14 2012 - 13:48:07 CDT)
- Aron Broom (Thu Jun 14 2012 - 13:26:03 CDT)
Bug in SASA for alanin example
- John Jumper (Fri Mar 30 2012 - 15:10:44 CDT)
Bug with BOUNDARY energy in postprocessing?
- Chris Harrison (Fri Apr 20 2012 - 19:41:37 CDT)
- David Minh (Fri Apr 20 2012 - 13:10:29 CDT)
- David Minh (Fri Apr 20 2012 - 13:03:31 CDT)
Build .pdb and .psf after coarse graining results in errors
- Edroaldo Lummertz da Rocha (Thu May 19 2011 - 13:37:15 CDT)
calculating energy term from extrabonds
- Segun Jung (Mon Feb 07 2011 - 23:50:43 CST)
- Segun Jung (Mon Feb 07 2011 - 20:08:33 CST)
Calculating Potential Energy for an atom selection
- Aron Broom (Sun Aug 19 2012 - 20:03:19 CDT)
- Axel Kohlmeyer (Fri Aug 17 2012 - 15:57:41 CDT)
- Aron Broom (Fri Aug 17 2012 - 15:49:38 CDT)
Calculation of distance traveled by an atom
- Aron Broom (Tue Dec 06 2011 - 02:43:34 CST)
- M.Raviprasad (Mon Dec 05 2011 - 23:11:19 CST)
- M.Raviprasad (Mon Dec 05 2011 - 23:19:54 CST)
- Axel Kohlmeyer (Mon Dec 05 2011 - 23:22:53 CST)
- Aron Broom (Mon Dec 05 2011 - 17:38:33 CST)
- Axel Kohlmeyer (Mon Dec 05 2011 - 17:36:58 CST)
- M.Raviprasad (Mon Dec 05 2011 - 14:54:27 CST)
Calculation of IR spectra using VMD IRspec Plug-in
- Axel Kohlmeyer (Sun Feb 20 2011 - 12:40:41 CST)
- Branko (Sat Feb 19 2011 - 11:54:48 CST)
- Mikhail Suyetin (Thu Feb 17 2011 - 01:22:00 CST)
Can DCD trajectory files contain only protein but water surround
- Axel Kohlmeyer (Thu Jan 13 2011 - 19:57:05 CST)
- yandongÂ Huang (Thu Jan 13 2011 - 08:44:10 CST)
Can I do protein-ligand docking using NAMD?
- JC Gumbart (Wed Feb 16 2011 - 01:08:36 CST)
- Bo Liu (Wed Feb 16 2011 - 00:30:54 CST)
- Àî¼Ñ¼ü (Tue Feb 15 2011 - 23:32:03 CST)
Can I set a range to limit the ABF
- Giacomo Fiorin (Wed Apr 20 2011 - 11:25:44 CDT)
- Shen, Han (Wed Apr 20 2011 - 10:24:46 CDT)
Can paratools really parametrize a structure? Is it really finished?
- JC Gumbart (Mon Feb 28 2011 - 13:31:16 CST)
- Ranyere Deyler (Mon Feb 28 2011 - 13:28:30 CST)
- JC Gumbart (Mon Feb 28 2011 - 11:23:54 CST)
- Ranyere Deyler (Mon Feb 28 2011 - 10:56:35 CST)
can RHDO crystal shape works in NAMD
- pxq_at_dicp.ac.cn (Fri Jul 01 2011 - 01:33:14 CDT)
can TMD alignment prior to force calculation be turned off?
- Jérôme Hénin (Sun Jan 08 2012 - 17:18:28 CST)
- Michael Zimmermann (Sun Jan 08 2012 - 17:03:41 CST)
- Axel Kohlmeyer (Sun Jan 08 2012 - 15:19:55 CST)
- Michael Zimmermann (Sun Jan 08 2012 - 15:04:15 CST)
can we run FEP calculation in water sphere?
- wenhao_at_uchicago.edu (Fri Sep 09 2011 - 03:21:01 CDT)
Cannot find bond parameters
- Axel Kohlmeyer (Tue Jun 28 2011 - 11:09:12 CDT)
- Gayatri Rathod (Tue Jun 28 2011 - 11:03:45 CDT)
Carma v.1.1 released.
- Nicholas M Glykos (Thu Oct 27 2011 - 12:54:24 CDT)
Carma v.1.2 released.
- Nicholas M Glykos (Thu Nov 15 2012 - 04:22:25 CST)
cell shape after increasing margin (parm7 ff)
- Francesco Pietra (Thu Jun 07 2012 - 01:26:35 CDT)
cell size
- Hasan haska (Wed Dec 14 2011 - 06:41:10 CST)
- Aron Broom (Tue Dec 13 2011 - 10:03:58 CST)
- Axel Kohlmeyer (Tue Dec 13 2011 - 10:00:43 CST)
- Hasan haska (Tue Dec 13 2011 - 09:47:50 CST)
- Axel Kohlmeyer (Tue Dec 13 2011 - 08:21:18 CST)
- Hasan haska (Tue Dec 13 2011 - 08:10:49 CST)
cellBasisvectors/.xsc fixing/colvars while running amber ff
- Giacomo Fiorin (Fri Oct 21 2011 - 17:06:43 CDT)
- Francesco Pietra (Fri Oct 21 2011 - 13:13:57 CDT)
center of mass movement removal throughout simulation?
- Markus K. Dahlgren (Mon Mar 12 2012 - 18:53:53 CDT)
CG parameterization problem
- Stefan Franzen (Tue Apr 26 2011 - 05:07:32 CDT)
CG parameters from dcd file for protein CG modelling
- Nicolás Pérez (Sun Feb 27 2011 - 13:32:18 CST)
CG-MD high electrostatic energy values
- sibel.cakan (Fri Jun 24 2011 - 03:40:32 CDT)
CG_MD temperature
- Sibel Cakan (Fri Jan 28 2011 - 07:52:15 CST)
changing harmonic restraints (colvars)
- Jérôme Hénin (Thu Apr 05 2012 - 11:17:56 CDT)
- Aron Broom (Thu Apr 05 2012 - 10:01:16 CDT)
- Jon Phillips (Thu Apr 05 2012 - 06:52:46 CDT)
changing solventDielectric in GBIS
- Andres Colubri (Mon Jun 13 2011 - 08:17:36 CDT)
- Ajasja LjubetiÄ (Mon Jun 13 2011 - 07:50:42 CDT)
- Andres Colubri (Mon Jun 13 2011 - 07:36:41 CDT)
Channel flow equilibration
- Jim Phillips (Wed Jun 15 2011 - 17:02:10 CDT)
- Mao Mao (Wed Jun 15 2011 - 11:46:26 CDT)
charging free energies with alchdecouple
- Harris, Robert C. (Fri Dec 21 2012 - 12:44:42 CST)
- JÃ©rÃ´me HÃ©nin (Thu Dec 20 2012 - 03:06:05 CST)
- Ali Khanlarkhani (Wed Dec 19 2012 - 13:06:40 CST)
- Harris, Robert C. (Wed Dec 19 2012 - 11:29:08 CST)
charmm 19 parameters
- Hasan haska (Fri Mar 25 2011 - 09:49:24 CDT)
- Hasan haska (Fri Mar 25 2011 - 09:38:41 CDT)
charmm force field
- Swarna M Patra (Thu Feb 03 2011 - 21:55:22 CST)
CHARMM General Force Field (CGENFF)
- Gianluca Interlandi (Wed Feb 16 2011 - 18:56:33 CST)
charmm param ... wrong charges
- Aron Broom (Thu Mar 08 2012 - 18:58:01 CST)
- Raghav (Thu Mar 08 2012 - 17:31:24 CST)
- Aron Broom (Thu Mar 08 2012 - 13:27:49 CST)
- Cristhian Boetsch (Thu Mar 08 2012 - 12:49:35 CST)
- raghav singh (Wed Mar 07 2012 - 08:44:50 CST)
Charmm parameter for H2 gas
- Mikhail Suyetin (Wed Jun 29 2011 - 05:00:05 CDT)
- Zhao Lina (Wed Jun 29 2011 - 04:41:15 CDT)
CHARMM parameters and topology for YO-PRO and/or Lucyfer Yellow
- Raul Araya (Wed Sep 12 2012 - 09:58:18 CDT)
CHARMM parameters for Mn 2+ ion
- Lisa Brown (Fri Mar 25 2011 - 10:43:45 CDT)
charmm to namd conversion
- Felipe Merino (Wed Jun 06 2012 - 16:36:34 CDT)
- Matthew B. Roark (Wed Jun 06 2012 - 15:40:23 CDT)
- Felipe Merino (Mon Jun 04 2012 - 16:39:55 CDT)
- Felipe Merino (Mon Jun 04 2012 - 13:37:53 CDT)
- Matthew B. Roark (Mon Jun 04 2012 - 12:29:55 CDT)
charmm toppar in namd
- Matthew B. Roark (Thu May 31 2012 - 14:04:18 CDT)
CHARMM-GUI running error for ligand
- Hannes Loeffler (Fri Mar 30 2012 - 05:50:58 CDT)
- Albert (Fri Mar 30 2012 - 05:48:12 CDT)
- Hannes Loeffler (Fri Mar 30 2012 - 05:39:17 CDT)
- Albert (Fri Mar 30 2012 - 05:27:35 CDT)
- Chiara Cosenza unina (Fri Mar 30 2012 - 05:05:58 CDT)
- Albert (Fri Mar 30 2012 - 02:37:10 CDT)
charmrun constantly hanging
- Axel Kohlmeyer (Sat Nov 26 2011 - 10:06:22 CST)
- jani vinod (Sat Nov 26 2011 - 01:06:22 CST)
- Axel Kohlmeyer (Fri Nov 25 2011 - 08:27:08 CST)
- jani vinod (Fri Nov 25 2011 - 00:59:35 CST)
charmrun setup
- Norman Geist (Mon May 07 2012 - 00:49:22 CDT)
- Branko (Sat May 05 2012 - 13:37:05 CDT)
- Pedro Armando Ojeda May (Sat May 05 2012 - 13:14:12 CDT)
checkpoint and revert
- Dr. Eddie (Wed Dec 12 2012 - 15:04:14 CST)
Cluster on commodity hardware
- Thomas Albers (Mon Oct 31 2011 - 12:37:30 CDT)
clustering of trajectory
- Jun Zhang (Tue Jul 05 2011 - 20:18:16 CDT)
- Nicholas M Glykos (Tue Jul 05 2011 - 09:57:50 CDT)
- Bala subramanian (Tue Jul 05 2011 - 09:46:24 CDT)
CNT builder
- farzad kiani (Tue Jul 24 2012 - 09:25:23 CDT)
Coarse Graining problem resolved
- Stefan Franzen (Tue Apr 26 2011 - 05:32:21 CDT)
Coarse Graining setup question
- Stefan Franzen (Tue Apr 26 2011 - 05:13:23 CDT)
coarse-grained MD
- Demet Akten (Fri Feb 11 2011 - 03:34:56 CST)
Coarse-Graining MD don't work perfect as expected
- Boyang Wang (Fri Dec 30 2011 - 03:57:44 CST)
- ÐìÖÓºÓ (Thu Dec 29 2011 - 00:50:31 CST)
Coarse_Graining tempetrature
- Sibel Cakan (Fri Jan 28 2011 - 09:12:43 CST)
- Sibel Cakan (Fri Jan 28 2011 - 08:31:02 CST)
collective variable calculation from dcd file
- Jérôme Hénin (Thu Dec 22 2011 - 05:20:15 CST)
- Branko (Wed Dec 21 2011 - 15:38:39 CST)
- Giovanni Bellesia (Wed Dec 21 2011 - 15:20:27 CST)
- Branko (Wed Dec 21 2011 - 15:15:06 CST)
- Giovanni Bellesia (Wed Dec 21 2011 - 14:44:47 CST)
collective variable component -- eigenvector usage
- Giacomo Fiorin (Tue Mar 27 2012 - 21:13:00 CDT)
- chang (Tue Mar 27 2012 - 19:46:04 CDT)
Collective variable on COM instead of COG
- Jérôme Hénin (Tue Mar 20 2012 - 08:14:04 CDT)
- poker_at_physics.usyd.edu.au (Mon Mar 19 2012 - 20:47:53 CDT)
coloring method in VMD
- Axel Kohlmeyer (Thu Oct 20 2011 - 18:21:30 CDT)
- lam nguyen (Thu Oct 20 2011 - 18:19:14 CDT)
colvar and tclForces with CUDA
- Jiyong Park (Sun Sep 25 2011 - 02:02:29 CDT)
colvar restrain of water in lipid system
- Jérôme Hénin (Mon Aug 29 2011 - 11:17:47 CDT)
- Giacomo Fiorin (Mon Aug 29 2011 - 11:06:44 CDT)
- Ling Wu (Mon Aug 29 2011 - 09:55:45 CDT)
- Giacomo Fiorin (Mon Aug 29 2011 - 09:36:39 CDT)
- Ling Wu (Mon Aug 29 2011 - 09:13:58 CDT)
- Ling Wu (Fri Aug 26 2011 - 14:44:21 CDT)
Colvars "tilt" component force constant units for WHAM
- Robert Elder (Fri Jul 22 2011 - 11:06:16 CDT)
- Robert Elder (Tue Jul 12 2011 - 16:36:55 CDT)
- Giacomo Fiorin (Tue Jul 12 2011 - 23:19:31 CDT)
- Robert Elder (Tue Jul 12 2011 - 16:48:48 CDT)
Colvars Error?
- David Minh (Fri Oct 26 2012 - 22:02:12 CDT)
- JC Gumbart (Fri Oct 26 2012 - 21:26:42 CDT)
- David Minh (Fri Oct 26 2012 - 13:20:21 CDT)
- Giacomo Fiorin (Fri Oct 26 2012 - 12:56:33 CDT)
- David Minh (Fri Oct 26 2012 - 11:13:21 CDT)
colvars orientation problem appears in 2.8 only?
- Jérôme Hénin (Fri Apr 29 2011 - 06:16:55 CDT)
- JC Gumbart (Thu Apr 28 2011 - 18:41:17 CDT)
colvars PMF history problem
- Ajasja LjubetiÄ (Wed Mar 09 2011 - 03:40:18 CST)
- Jérôme Hénin (Tue Mar 08 2011 - 22:55:42 CST)
- Axel Kohlmeyer (Mon Mar 07 2011 - 17:56:05 CST)
- Nikolaos Glykos (Mon Mar 07 2011 - 16:54:35 CST)
- Ajasja LjubetiÄ (Mon Mar 07 2011 - 15:01:08 CST)
- Ajasja LjubetiÄ (Mon Mar 07 2011 - 14:50:06 CST)
- Nicholas M Glykos (Mon Mar 07 2011 - 11:14:40 CST)
- Axel Kohlmeyer (Mon Mar 07 2011 - 10:03:24 CST)
- Ajasja Ljubetiè (Mon Mar 07 2011 - 09:43:02 CST)
- Axel Kohlmeyer (Mon Mar 07 2011 - 09:27:19 CST)
- Ajasja LjubetiÄ (Mon Mar 07 2011 - 08:43:08 CST)
Colvars value is out of boundary
- Giacomo Fiorin (Mon Dec 10 2012 - 16:29:52 CST)
- Aron Broom (Mon Dec 10 2012 - 16:29:18 CST)
- DAI, JIAN (Mon Dec 10 2012 - 16:15:45 CST)
colvars, discontinuous rotation
- JC Gumbart (Wed Jul 27 2011 - 23:27:23 CDT)
- Giacomo Fiorin (Wed Jul 27 2011 - 21:20:41 CDT)
- JC Gumbart (Wed Jul 27 2011 - 20:41:30 CDT)
combining metadynamics simulations
- Giacomo Fiorin (Fri Aug 26 2011 - 09:18:01 CDT)
- Giovanni Bellesia (Fri Aug 26 2011 - 08:40:29 CDT)
combining thermodynamic integration with replica exchange in NAMD
- Hugh Heldenbrand (Mon Jul 25 2011 - 10:05:50 CDT)
compilation of namd
- johan strumpfer (Fri May 06 2011 - 09:09:35 CDT)
- TAO WANG (Thu May 05 2011 - 21:08:37 CDT)
compilation with CUDA error
- Martin, Erik W (Fri Nov 09 2012 - 14:06:52 CST)
- Thomas Evangelidis (Fri Nov 09 2012 - 11:05:54 CST)
- Martin, Erik W (Fri Nov 09 2012 - 10:49:29 CST)
- Thomas Evangelidis (Tue Oct 30 2012 - 02:59:41 CDT)
- Aron Broom (Mon Oct 29 2012 - 12:43:44 CDT)
- Thomas Evangelidis (Mon Oct 29 2012 - 08:44:23 CDT)
Compiled Windows HPC version.
- Chewning, Joseph (Tue Oct 04 2011 - 07:04:31 CDT)
Compiling and running NAMD on multiple nodes of SDSC Trestles
- Gianluca Interlandi (Tue Jul 03 2012 - 16:22:21 CDT)
- Gianluca Interlandi (Tue Jul 03 2012 - 13:28:36 CDT)
compiling charm++ Error: can not find mpi library
- Thomas Evangelidis (Thu Sep 27 2012 - 08:24:57 CDT)
- Thomas Evangelidis (Thu Sep 27 2012 - 02:00:24 CDT)
- Thomas Evangelidis (Wed Sep 26 2012 - 17:15:00 CDT)
Compiling NAMD
- Marcel UJI (IMAP) (Fri Mar 09 2012 - 06:49:34 CST)
Compiling NAMD 2.7 with the PLUMED patch
- Davide Branduardi (Thu Jan 06 2011 - 17:42:56 CST)
- Gianluca Interlandi (Thu Jan 06 2011 - 17:41:23 CST)
- Gianluca Interlandi (Thu Jan 06 2011 - 16:55:03 CST)
Compiling NAMD 2.9 on BlueGene/Q
- Vasudevan V (Wed Dec 26 2012 - 17:11:17 CST)
Compiling NAMD for CUDA
- Thomas Albers (Sat Jun 11 2011 - 21:53:56 CDT)
- Axel Kohlmeyer (Sat Jun 11 2011 - 16:43:28 CDT)
- Thomas Albers (Sat Jun 11 2011 - 16:23:01 CDT)
Compiling NAMD on Cray XE6
- Jeff Wereszczynski (Mon Feb 28 2011 - 11:38:48 CST)
Compiling Namd on MAC with Cuda
- Stan Skafidas (Wed Aug 10 2011 - 07:16:49 CDT)
Compiling NAMD on NICS Kraken
- Alexander Predeus (Fri Mar 09 2012 - 11:45:11 CST)
- Jernej Zidar (Thu Mar 08 2012 - 23:42:09 CST)
- Alexander Predeus (Thu Mar 08 2012 - 22:39:05 CST)
Compiling NAMD with CUDA on MacOSX Mountain Lion
- Maximilian Ebert (Sat Nov 17 2012 - 18:38:51 CST)
- Maximilian Ebert (Sat Nov 17 2012 - 18:39:25 CST)
compiling namd-2.9 on bluegeneQ
- Zhuyi Xue (Mon Oct 15 2012 - 15:46:40 CDT)
Compiling NAMD_2.9b2_Source with GCC 4.7.0
- Jim Phillips (Fri Mar 30 2012 - 10:21:21 CDT)
- Axel Kohlmeyer (Fri Mar 30 2012 - 08:32:19 CDT)
- Fabien Archambault (Fri Mar 30 2012 - 08:25:18 CDT)
Component distanceZ-ABF
- Jérôme Hénin (Tue Sep 06 2011 - 04:27:44 CDT)
- Parisa Akhski (Mon Sep 05 2011 - 13:07:26 CDT)
- Jérôme Hénin (Mon Sep 05 2011 - 10:56:06 CDT)
- Parisa Akhski (Mon Sep 05 2011 - 09:42:17 CDT)
- Jérôme Hénin (Fri Sep 02 2011 - 16:19:53 CDT)
- Parisa Akhski (Fri Sep 02 2011 - 11:21:56 CDT)
compress PSF into INTER
- Cruz-Chu Eduardo Roberto (Thu Jun 07 2012 - 04:20:56 CDT)
- Cruz-Chu Eduardo Roberto (Wed Jun 06 2012 - 13:37:34 CDT)
Computing interaction energies in namd
- Jérôme Hénin (Wed Feb 23 2011 - 03:42:14 CST)
- Axel Kohlmeyer (Tue Feb 22 2011 - 19:07:11 CST)
- Samy Hamdouche (Tue Feb 22 2011 - 18:21:46 CST)
- JC Gumbart (Tue Feb 22 2011 - 14:48:51 CST)
- Samy Hamdouche (Tue Feb 22 2011 - 14:40:31 CST)
Computing several pair interactions
- Samy Hamdouche (Tue Feb 15 2011 - 18:11:25 CST)
concatenate pmf files in colvars
- Parisa Akhski (Sat Jan 01 2011 - 12:23:06 CST)
Concerning Restarting Multiple Walkers MetaDynamics
- Aron Broom (Fri May 04 2012 - 16:33:39 CDT)
- Giacomo Fiorin (Fri May 04 2012 - 16:30:26 CDT)
- Aron Broom (Fri May 04 2012 - 15:54:28 CDT)
- Aron Broom (Fri May 04 2012 - 15:52:41 CDT)
conf file question
- Molecular Dynamics (Wed Mar 21 2012 - 04:19:57 CDT)
conf file script ( help needed )
- flavio seixas (Mon Jun 06 2011 - 07:02:41 CDT)
- flavio seixas (Sat Jun 04 2011 - 07:53:08 CDT)
- Axel Kohlmeyer (Fri Jun 03 2011 - 08:45:27 CDT)
- Molecular Dynamics (Fri Jun 03 2011 - 08:37:57 CDT)
Conflict between CUDA NAMD and PMEMD
- Martin, Erik W (Thu Nov 15 2012 - 18:38:55 CST)
connect a spring between all the atoms present in pdb structure
- Axel Kohlmeyer (Sat Aug 04 2012 - 13:21:27 CDT)
- SONY kaur (Sat Aug 04 2012 - 04:31:42 CDT)
Consistent temperature increase in CUDA runs
- Aron Broom (Mon Feb 27 2012 - 08:31:46 CST)
- Aron Broom (Fri Feb 24 2012 - 19:53:08 CST)
- Aron Broom (Fri Feb 24 2012 - 14:49:28 CST)
- Norman Geist (Fri Feb 24 2012 - 00:51:38 CST)
Constant Pull Velocity
- ishiikai08_at_yahoo.co.jp (Mon Mar 05 2012 - 21:39:29 CST)
- Wang Yi (Mon Mar 05 2012 - 09:59:28 CST)
- ishiikai08_at_yahoo.co.jp (Mon Mar 05 2012 - 09:11:28 CST)
constant pulling velocity in SMD
- tillmann.utesch_at_mail.tu-berlin.de (Mon Apr 30 2012 - 03:12:07 CDT)
- JC Gumbart (Fri Apr 27 2012 - 12:30:53 CDT)
- JC Gumbart (Thu Apr 26 2012 - 23:21:25 CDT)
- Jiao, Dian NMN (-EXP) (Thu Apr 26 2012 - 23:10:55 CDT)
- JC Gumbart (Thu Apr 26 2012 - 18:15:42 CDT)
- Jiao, Dian NMN (-EXP) (Thu Apr 26 2012 - 11:33:07 CDT)
- Axel Kohlmeyer (Wed Apr 25 2012 - 17:16:15 CDT)
- Jiao, Dian NMN (-EXP) (Wed Apr 25 2012 - 14:41:06 CDT)
constant velocity of carbon nanotube through water
- Cruz-Chu Eduardo Roberto (Fri Jul 20 2012 - 05:46:13 CDT)
- bond.james (Fri Jul 20 2012 - 05:41:56 CDT)
- Cruz-Chu Eduardo Roberto (Fri Jul 20 2012 - 03:25:11 CDT)
- Axel Kohlmeyer (Fri Jul 20 2012 - 01:42:11 CDT)
- bond.james (Fri Jul 20 2012 - 00:11:27 CDT)
Constraint failure during equalibration
- Jiao, Dian NMN (-EXP) (Tue Sep 13 2011 - 12:45:50 CDT)
- Jiao, Dian NMN (-EXP) (Tue Sep 13 2011 - 12:55:22 CDT)
Constraint failure; simulation has become unstable
- Axel Kohlmeyer (Mon Jan 10 2011 - 08:49:07 CST)
- Joshua Adelman (Sat Jan 08 2011 - 09:49:18 CST)
- Wendy González (Sat Jan 08 2011 - 08:29:37 CST)
- Athanassios Stavrakoudis (Sat Jan 08 2011 - 08:05:15 CST)
- Wendy González (Sat Jan 08 2011 - 07:53:11 CST)
- Joshua Adelman (Fri Jan 07 2011 - 18:18:05 CST)
- Wendy González (Fri Jan 07 2011 - 14:42:46 CST)
- Wendy González (Fri Jan 07 2011 - 15:18:20 CST)
- Wendy González (Fri Jan 07 2011 - 15:25:23 CST)
- Athanassios Stavrakoudis (Fri Jan 07 2011 - 15:04:08 CST)
control distance between solvent and solute
- Jim Phillips (Wed Jul 20 2011 - 11:57:16 CDT)
- Kang Hee Cho (Fri Jul 15 2011 - 20:07:56 CDT)
Controlling fans on a GTX 560 ti
- Ajasja LjubetiÄ (Tue Jan 17 2012 - 09:10:51 CST)
- Axel Kohlmeyer (Tue Jan 17 2012 - 08:35:42 CST)
- Ajasja LjubetiÄ (Tue Jan 17 2012 - 08:25:29 CST)
- Axel Kohlmeyer (Mon Jan 16 2012 - 19:29:26 CST)
- Axel Kohlmeyer (Fri Jul 22 2011 - 09:19:59 CDT)
- Ajasja LjubetiÄ (Fri Jul 22 2011 - 09:12:29 CDT)
- Axel Kohlmeyer (Fri Jul 22 2011 - 08:56:17 CDT)
- Ajasja LjubetiÄ (Fri Jul 22 2011 - 05:24:26 CDT)
convergence and stability of simulation
- Jorgen Simonsen (Mon Aug 15 2011 - 14:08:29 CDT)
convergence of FEP calculation.
- dbaogen (Mon Dec 10 2012 - 21:16:09 CST)
Convergence of the Gram-Charlier expansion
- Ali Khanlarkhani (Sun Sep 30 2012 - 12:32:29 CDT)
- Chris Chipot (Sun Sep 30 2012 - 11:46:58 CDT)
- Ali Khanlarkhani (Sun Sep 30 2012 - 10:34:56 CDT)
convert pdb format to normal pdb format
- flavio seixas (Wed Aug 24 2011 - 18:05:18 CDT)
- hamze rahimi (Wed Aug 24 2011 - 04:48:09 CDT)
coordNum colvar with dummyAtom
- Giacomo Fiorin (Thu Dec 22 2011 - 17:41:20 CST)
- Ernesto Vargas (Mon Dec 19 2011 - 18:56:40 CST)
Copper ion moving out of the protein towards bulk solvent
- poker_at_physics.usyd.edu.au (Wed Feb 08 2012 - 18:24:50 CST)
- SUBHA KALYAANAMOORTHY (Tue Feb 07 2012 - 19:16:26 CST)
correlation functions
- Thomas Bishop (Mon Dec 12 2011 - 07:54:06 CST)
- Boyang Wang (Sat Dec 10 2011 - 18:03:53 CST)
- Aron Broom (Sat Dec 10 2011 - 08:54:56 CST)
- Molecular Dynamics (Sat Dec 10 2011 - 05:18:50 CST)
Corrupt dcd files
- Marc Baaden (Wed May 11 2011 - 11:15:55 CDT)
could acpype output file be used for NAMD CHARMM FF?
- Albert (Thu Jun 14 2012 - 13:29:06 CDT)
Coulomb 1-4 interactions
- Axel Kohlmeyer (Fri Dec 02 2011 - 10:21:36 CST)
- oguz gurbulak (Fri Dec 02 2011 - 10:11:24 CST)
Coulombic component of configurational energy
- divya nayar (Tue May 24 2011 - 03:12:24 CDT)
cpu-gpu vs cpu
- Axel Kohlmeyer (Tue Nov 29 2011 - 10:19:50 CST)
- Nicholas M Glykos (Tue Nov 29 2011 - 09:28:34 CST)
- Axel Kohlmeyer (Tue Nov 29 2011 - 07:41:51 CST)
- Francesco Pietra (Tue Nov 29 2011 - 00:44:10 CST)
create junction between nanotubes
- farzad kiani (Fri Nov 09 2012 - 06:13:59 CST)
creating .psf file for a nanotube
- Axel Kohlmeyer (Fri Mar 11 2011 - 08:26:58 CST)
- sakthi kumaran (Fri Mar 11 2011 - 06:34:36 CST)
- Axel Kohlmeyer (Fri Mar 11 2011 - 05:18:57 CST)
- sakthi kumaran (Fri Mar 11 2011 - 05:13:34 CST)
- sakthi kumaran (Fri Mar 11 2011 - 02:36:02 CST)
creating a protonated cytidine entry
- raghav singh (Mon Apr 16 2012 - 06:35:15 CDT)
cross terms
- JC Gumbart (Mon Nov 19 2012 - 23:45:27 CST)
- Dr. Eddie (Mon Nov 19 2012 - 21:38:38 CST)
- JC Gumbart (Sun Nov 18 2012 - 14:41:26 CST)
- Dr. Eddie (Sun Nov 18 2012 - 10:20:01 CST)
- JC Gumbart (Sat Nov 17 2012 - 16:24:49 CST)
- JC Gumbart (Fri Nov 16 2012 - 14:26:56 CST)
- Dr. Eddie (Fri Nov 16 2012 - 13:51:19 CST)
- JC Gumbart (Fri Nov 16 2012 - 13:48:37 CST)
- Dr. Eddie (Fri Nov 16 2012 - 13:15:59 CST)
crossing the border by protein/ion complex
- Axel Kohlmeyer (Tue Feb 07 2012 - 17:33:08 CST)
- Maria Bykhovskaia (Tue Feb 07 2012 - 17:16:30 CST)
crossterm error
- Dr. Eddie (Thu Jul 26 2012 - 15:56:46 CDT)
- Cristhian Boetsch (Fri Jul 20 2012 - 13:06:04 CDT)
CT1 terminal patch for THR
- GONZALEZ NOYA, EVA (Mon Mar 07 2011 - 14:47:57 CST)
CthCreate failed to create fiber
- Ajasja LjubetiÄ (Thu Jun 09 2011 - 15:29:25 CDT)
- Jim Phillips (Tue Jun 07 2011 - 18:02:21 CDT)
- Ajasja LjubetiÄ (Tue Jun 07 2011 - 13:57:00 CDT)
- Jim Phillips (Fri Jun 03 2011 - 11:42:44 CDT)
- Patriche Simona (Fri Jun 03 2011 - 08:52:28 CDT)
Cu+2 parameters
- jose correa (Wed Jan 26 2011 - 07:36:59 CST)
CUDA - OwnerBox::close failure
- Vlastimil ZÃma (Wed Oct 24 2012 - 05:21:43 CDT)
CUDA compiled code for Windows HPC
- Chewning, Joseph (Wed Sep 28 2011 - 14:52:29 CDT)
Cuda error
- Aron Broom (Mon Jul 16 2012 - 13:30:57 CDT)
- Dr. Eddie (Mon Jul 16 2012 - 13:19:19 CDT)
CUDA error (as a misleding error message)
- Aron Broom (Wed Nov 07 2012 - 10:01:51 CST)
- Francesco Pietra (Wed Nov 07 2012 - 05:33:41 CST)
CUDA error 0 attaching to node
- Francesco Pietra (Fri Mar 09 2012 - 09:12:19 CST)
cuda error cudastreamcreate
- Jim Phillips (Tue Jun 14 2011 - 11:02:33 CDT)
- Ajasja LjubetiÄ (Tue Jun 14 2011 - 08:23:23 CDT)
- Francesco Pietra (Tue Jun 14 2011 - 00:45:37 CDT)
cuda error cudastreamcreate. SOLVED (probably)
- Axel Kohlmeyer (Thu Jun 16 2011 - 04:40:03 CDT)
- Francesco Pietra (Thu Jun 16 2011 - 00:57:15 CDT)
- Axel Kohlmeyer (Wed Jun 15 2011 - 09:51:33 CDT)
CUDA error on Pe 4: device cannot map host memory
- Vignesh (Tue Jun 12 2012 - 18:57:14 CDT)
CUDA error vs clashes
- Francesco Pietra (Fri Nov 09 2012 - 01:52:32 CST)
- Francesco Pietra (Thu Nov 08 2012 - 11:42:09 CST)
Cuda errors in Ubuntu12amd64
- ´ÞÓ×Ìñ (Tue Oct 02 2012 - 22:33:49 CDT)
CUDA limitations
- Ajasja LjubetiÄ (Thu Sep 06 2012 - 08:47:40 CDT)
- Ajasja LjubetiÄ (Fri Jun 24 2011 - 07:37:13 CDT)
- Ajasja LjubetiÄ (Thu Jun 09 2011 - 15:32:09 CDT)
- Jim Phillips (Fri May 13 2011 - 09:02:36 CDT)
- Ajasja LjubetiÄ (Fri May 13 2011 - 07:00:49 CDT)
- Jim Phillips (Thu May 12 2011 - 12:45:44 CDT)
- Ajasja LjubetiÄ (Thu May 12 2011 - 03:07:02 CDT)
CUDA on GPU Cluster
- Arvind Kannan (Fri Aug 19 2011 - 17:31:06 CDT)
CUDA problem with 2.9b2
- Albert (Thu Apr 05 2012 - 00:51:05 CDT)
CUDA problem?
- Albert (Wed Apr 04 2012 - 14:02:49 CDT)
CUDA simulation memory usage
- Jesper SÃ¸rensen (Thu May 19 2011 - 03:11:41 CDT)
- Jim Phillips (Wed May 18 2011 - 17:37:45 CDT)
- Jesper Sørensen (Wed May 18 2011 - 08:41:34 CDT)
- Axel Kohlmeyer (Wed May 18 2011 - 08:29:18 CDT)
- Jesper SÃ¸rensen (Wed May 18 2011 - 07:23:28 CDT)
- Jesper SÃ¸rensen (Wed May 18 2011 - 06:14:51 CDT)
- Jesper SÃ¸rensen (Wed May 18 2011 - 05:55:59 CDT)
- Jesper SÃ¸rensen (Wed May 18 2011 - 05:03:17 CDT)
CUDA workstation
- Arturas (Sat Sep 08 2012 - 11:22:49 CDT)
cuda_check_local_progress polled 1000000 times
- Francesco Pietra (Wed Jun 06 2012 - 02:29:18 CDT)
- Francesco Pietra (Tue Jun 05 2012 - 08:34:47 CDT)
- Francesco Pietra (Tue Jun 05 2012 - 02:28:30 CDT)
- Francesco Pietra (Mon Jun 04 2012 - 12:20:56 CDT)
- Francesco Pietra (Sat Jun 02 2012 - 14:06:49 CDT)
Current status of polarizable force fields in NAMD
- lucie delemotte (Wed Feb 16 2011 - 04:37:03 CST)
Custom CHARMM forcefield usage problem
- JC Gumbart (Wed Aug 10 2011 - 00:00:55 CDT)
- Jernej Zidar (Tue Aug 09 2011 - 23:47:30 CDT)
- Jernej Zidar (Tue Aug 09 2011 - 23:12:04 CDT)
cylinder constraint with colvar
- Aron Broom (Tue Dec 18 2012 - 23:19:54 CST)
- Aron Broom (Tue Dec 18 2012 - 15:31:25 CST)
- Wang (Tue Dec 18 2012 - 11:42:28 CST)
Dangling Bonds?
- atsuiai_at_aim.com (Thu Sep 29 2011 - 08:45:39 CDT)
- atsuiai_at_aim.com (Thu Sep 29 2011 - 06:23:55 CDT)
- Axel Kohlmeyer (Wed Sep 28 2011 - 17:58:18 CDT)
- atsuiai_at_aim.com (Wed Sep 28 2011 - 17:35:12 CDT)
DCD
- Nicholas M Glykos (Fri Apr 06 2012 - 02:37:50 CDT)
- Buddhadev Maiti (Thu Apr 05 2012 - 22:29:13 CDT)
- Gianluca Interlandi (Thu Apr 05 2012 - 17:04:15 CDT)
- Gianluca Interlandi (Thu Apr 05 2012 - 16:30:29 CDT)
- Axel Kohlmeyer (Thu Apr 05 2012 - 16:27:30 CDT)
- Ernesto Vargas (Thu Apr 05 2012 - 16:21:19 CDT)
- Buddhadev Maiti (Thu Apr 05 2012 - 16:22:52 CDT)
- Gianluca Interlandi (Thu Apr 05 2012 - 16:04:41 CDT)
- Buddhadev Maiti (Thu Apr 05 2012 - 15:44:43 CDT)
dcd files
- Artem Zhmurov (Sun May 22 2011 - 16:52:19 CDT)
- grazia cottone (Sun May 22 2011 - 15:14:41 CDT)
- Jim Phillips (Sun May 22 2011 - 14:53:45 CDT)
- PAUL NEWMAN (Sun May 22 2011 - 14:46:57 CDT)
- Jim Phillips (Sun May 22 2011 - 14:38:55 CDT)
- Axel Kohlmeyer (Sun May 22 2011 - 09:15:48 CDT)
- Axel Kohlmeyer (Sun May 22 2011 - 09:10:29 CDT)
- PAUL NEWMAN (Sun May 22 2011 - 08:24:15 CDT)
- Molecular Dynamics (Sun May 22 2011 - 08:02:48 CDT)
dcd to trr using catdcd
- Anurag Sethi (Tue Mar 22 2011 - 02:03:56 CDT)
- Neelanjana Sengupta (Tue Mar 22 2011 - 00:11:33 CDT)
- Neelanjana Sengupta (Mon Mar 21 2011 - 05:44:39 CDT)
Dear friend
- Niraj kumar (Sun May 22 2011 - 20:29:53 CDT)
deca-Ala simulations with different cutoff produce different results
- Jun Zhang (Mon May 16 2011 - 03:47:44 CDT)
- Norman Geist (Mon May 16 2011 - 02:12:40 CDT)
- Jun Zhang (Mon May 16 2011 - 00:48:36 CDT)
Denaturation via increased temperature
- Bjoern Olausson (Mon Aug 15 2011 - 06:11:17 CDT)
- Jernej Zidar (Mon Aug 15 2011 - 04:38:55 CDT)
- Bjoern Olausson (Mon Aug 15 2011 - 04:31:25 CDT)
- Bjoern Olausson (Mon Aug 15 2011 - 04:11:06 CDT)
Density Profile in VMD
- oguz gurbulak (Mon Sep 05 2011 - 02:30:50 CDT)
determining force constant in exterbonds (harmonic potential)
- Segun Jung (Sat Feb 05 2011 - 10:09:50 CST)
Development plan of NAMD?
- Jim Phillips (Tue May 24 2011 - 13:54:09 CDT)
- Norman Geist (Tue May 24 2011 - 02:03:37 CDT)
dextran and or poly-D-glucosamine topology
- Raul Araya (Fri Nov 04 2011 - 16:58:34 CDT)
Dielectric constant for MDFF of a membrane protein.
- JC Gumbart (Fri Mar 30 2012 - 13:55:56 CDT)
- Raul Araya (Fri Mar 30 2012 - 09:18:22 CDT)
Difference between cwd and cd
- Ajasja LjubetiÄ (Wed Jul 06 2011 - 08:59:30 CDT)
- Axel Kohlmeyer (Wed Jul 06 2011 - 07:49:18 CDT)
- Ajasja LjubetiÄ (Wed Jul 06 2011 - 04:43:43 CDT)
difference between run and minimize
- snoze pa (Wed Sep 14 2011 - 10:05:56 CDT)
- snoze pa (Wed Sep 14 2011 - 10:02:03 CDT)
- snoze pa (Fri Sep 09 2011 - 16:01:55 CDT)
Differences between ABF and metadynamics
- Jérôme Hénin (Tue Sep 13 2011 - 08:45:17 CDT)
- Jérôme Hénin (Tue Sep 13 2011 - 05:43:39 CDT)
- Alex (Tue Sep 13 2011 - 05:13:34 CDT)
differences in multiprocessor energy minimization results
- Markus Metz (Wed Aug 17 2011 - 11:44:19 CDT)
different seeds and protein behavior
- Aron Broom (Fri Jul 20 2012 - 11:58:13 CDT)
- Ajasja LjubetiÄ (Fri Jul 20 2012 - 09:06:58 CDT)
- Aron Broom (Fri Jul 20 2012 - 08:50:40 CDT)
- Dr. Eddie (Fri Jul 20 2012 - 07:56:44 CDT)
- Nicholas M Glykos (Fri Jul 20 2012 - 03:14:17 CDT)
- amin_at_imtech.res.in (Thu Jul 19 2012 - 21:36:23 CDT)
- Aron Broom (Thu Jul 19 2012 - 20:21:44 CDT)
- Dr. Eddie (Thu Jul 19 2012 - 18:29:21 CDT)
different velocities problem
- Jérôme Hénin (Tue Oct 25 2011 - 02:10:14 CDT)
- Hasan haska (Tue Oct 25 2011 - 01:28:22 CDT)
dihedral rotation with ABF
- kakali sen (Sun Apr 10 2011 - 12:48:17 CDT)
discrepancy in results from different machines!
- Thomas Evangelidis (Tue Dec 25 2012 - 17:56:16 CST)
- Jacqueline Schmidt (Tue Dec 25 2012 - 17:29:05 CST)
discrete energy value after restart
- Chris Harrison (Sun Jan 23 2011 - 10:00:07 CST)
- Kang Hee Cho (Thu Jan 20 2011 - 21:25:46 CST)
Displaying the gradient tolerance in the output
- Chris Harrison (Thu Aug 23 2012 - 22:52:31 CDT)
- Webber (Tue Aug 21 2012 - 03:46:25 CDT)
Displaying the gradient tolerance in the output as the example output from tutorial 1-2 Water Sphere
- Webber (Tue Aug 21 2012 - 01:57:53 CDT)
- Webber (Sun Aug 19 2012 - 19:02:29 CDT)
distance calculation between atoms of two segments
- Ajasja LjubetiÄ (Sat Jan 22 2011 - 13:48:54 CST)
- mjyang (Sat Jan 22 2011 - 10:51:00 CST)
Distance XY-colvars
- Giacomo Fiorin (Wed Jan 05 2011 - 16:12:32 CST)
- Alex Liu (Tue Jan 04 2011 - 15:56:56 CST)
distanceXY colvar-ABF
- Giacomo Fiorin (Sun Aug 21 2011 - 12:28:07 CDT)
- Parisa Akhski (Sun Aug 21 2011 - 09:05:16 CDT)
distortion of some bonds during structure preparation
- bharat gupta (Mon Jul 04 2011 - 03:36:39 CDT)
Dividing a 2D ABF simulations into regions (on nodes with different speeds)
- Ajasja LjubetiÄ (Fri Jul 29 2011 - 11:56:17 CDT)
- Axel Kohlmeyer (Fri Jul 29 2011 - 08:34:33 CDT)
- Ajasja LjubetiÄ (Fri Jul 29 2011 - 04:44:38 CDT)
DNA system and PH control
- Aron Broom (Mon Mar 19 2012 - 12:54:11 CDT)
- raghav singh (Mon Mar 19 2012 - 12:42:31 CDT)
DNA terminal Patch / How could I retain the primes in DNA
- raghav singh (Tue Jul 05 2011 - 03:23:21 CDT)
Dock a metal ion into a peptide/protein
- Branko (Thu Sep 01 2011 - 04:09:16 CDT)
- Andrea Holfelder (Wed Aug 31 2011 - 21:51:27 CDT)
- Branko (Wed Aug 31 2011 - 15:28:17 CDT)
- Andrea Holfelder (Wed Aug 31 2011 - 14:29:39 CDT)
does any body have the parameter file for aldehyde group?
- felmerino_at_uchile.cl (Fri Jul 08 2011 - 01:44:15 CDT)
- AlbertAlbert (Fri Jul 08 2011 - 01:34:22 CDT)
Does GB Implicit Solvent handle explicit ions?
- Gianluca Interlandi (Sun Apr 17 2011 - 22:43:37 CDT)
- David Tanner (Sun Apr 17 2011 - 06:39:19 CDT)
Domain error ParseFEP
- Christian Jorgensen (Fri Mar 25 2011 - 09:42:29 CDT)
- Chris Chipot (Fri Mar 25 2011 - 09:57:19 CDT)
- Chris Chipot (Fri Mar 25 2011 - 09:41:25 CDT)
- Christian Jorgensen (Fri Mar 25 2011 - 09:14:02 CDT)
DPPC membrane
- Andres Morales N (Fri Jul 29 2011 - 03:16:50 CDT)
- Ajasja LjubetiÄ (Thu Jul 28 2011 - 05:21:10 CDT)
- Andres Morales N (Thu Jul 28 2011 - 01:29:36 CDT)
Drude polarizable models with namd
- Ana Celia Vila Verde (Thu Aug 02 2012 - 11:11:08 CDT)
drude water in namd
- David Hardy (Tue Jul 24 2012 - 16:22:57 CDT)
- Sandeep Patel (Tue Jul 24 2012 - 16:07:50 CDT)
drude water simulation bug ?
- Sergey (Tue Feb 28 2012 - 14:35:26 CST)
drude water simulation bug ? radial distrubuion function
- Sergey (Wed Feb 29 2012 - 01:22:30 CST)
Drug design issue.
- Branko (Tue Feb 28 2012 - 05:39:26 CST)
- Boyang Wang (Tue Feb 28 2012 - 02:08:07 CST)
dummyAtom-ABF
- Jérôme Hénin (Fri Aug 26 2011 - 10:32:20 CDT)
- Parisa Akhski (Fri Aug 26 2011 - 09:57:13 CDT)
dump specific atom positions into a txt file during the simulation
- Jacqueline Schmidt (Fri Aug 31 2012 - 07:33:40 CDT)
- Ajasja LjubetiÄ (Fri Aug 31 2012 - 03:44:42 CDT)
- Jacqueline Schmidt (Fri Aug 31 2012 - 03:15:56 CDT)
- Jacqueline Schmidt (Fri Aug 31 2012 - 01:14:09 CDT)
duplicate residue key
- Katrin Stöbener (Fri Oct 19 2012 - 02:30:19 CDT)
efield energies incorrect in analysis mode (run 0) ?
- Mark Triger (Thu Jun 28 2012 - 14:22:18 CDT)
- Mark Triger (Wed Jun 27 2012 - 16:25:04 CDT)
- Mark Triger (Wed Jun 27 2012 - 13:19:48 CDT)
energy jump between minimization and simulation
- Eva Gonzalez Noya (Wed Feb 16 2011 - 13:15:01 CST)
- Bennion, Brian (Wed Feb 16 2011 - 10:58:33 CST)
- Eva Gonzalez Noya (Wed Feb 16 2011 - 10:14:45 CST)
- Ajasja LjubetiÄ (Wed Feb 16 2011 - 03:27:53 CST)
- Eva Gonzalez Noya (Tue Feb 15 2011 - 18:06:25 CST)
energy jump running a simulation after minimization
- Eva Gonzalez Noya (Tue Feb 15 2011 - 17:23:07 CST)
- Eva Gonzalez Noya (Tue Feb 15 2011 - 16:37:59 CST)
energy minimization
- Aron Broom (Tue Aug 21 2012 - 00:47:47 CDT)
- Aaron Oakley (Mon Aug 20 2012 - 23:45:51 CDT)
- yandong Huang (Mon Aug 20 2012 - 23:24:30 CDT)
- bharat gupta (Tue Jun 28 2011 - 18:49:01 CDT)
Energy minimization of membrane
- Boyang Wang (Thu Feb 02 2012 - 23:31:28 CST)
- R. Charbel Maroun (Thu Feb 02 2012 - 06:37:42 CST)
Epsilon, Rmin for copper ions
- Francesco Pietra (Sat Sep 24 2011 - 03:55:34 CDT)
equilibrate conf file
- Axel Kohlmeyer (Thu Aug 16 2012 - 03:54:48 CDT)
- Namd Namd (Thu Aug 16 2012 - 02:56:30 CDT)
equilibrate glycerol molecules
- Axel Kohlmeyer (Thu Aug 23 2012 - 04:04:34 CDT)
- Namd Namd (Thu Aug 23 2012 - 03:45:32 CDT)
equilibrate the system in NPT
- Hasan haska (Mon Dec 26 2011 - 13:57:37 CST)
equilibrate water molecules
- Hasan haska (Thu Nov 24 2011 - 01:43:38 CST)
Equilibration
- Erik Nordgren (Thu Jul 21 2011 - 20:44:38 CDT)
- Chris Harrison (Tue Jul 19 2011 - 14:42:06 CDT)
- Andres Morales N (Tue Jul 19 2011 - 13:39:37 CDT)
- Jim Phillips (Mon Jul 18 2011 - 16:01:26 CDT)
- saman amiri (Thu Jun 30 2011 - 02:53:42 CDT)
- snoze pa (Wed Jun 29 2011 - 18:00:48 CDT)
- saman amiri (Wed Jun 29 2011 - 16:05:11 CDT)
- johan strumpfer (Wed Jun 29 2011 - 01:25:35 CDT)
- Norman Geist (Wed Jun 29 2011 - 04:08:26 CDT)
- Norman Geist (Wed Jun 29 2011 - 04:04:42 CDT)
- Norman Geist (Wed Jun 29 2011 - 01:39:13 CDT)
- bharat gupta (Wed Jun 29 2011 - 01:06:10 CDT)
Equilibration - NVT & NPT
- bharat gupta (Thu Jun 30 2011 - 01:36:56 CDT)
Equilibration when splitting an ABF calculation
- Jérôme Hénin (Fri Jan 28 2011 - 06:44:32 CST)
- Ajasja LjubetiÄ (Fri Jan 28 2011 - 06:26:58 CST)
- Ajasja LjubetiÄ (Thu Jan 27 2011 - 08:48:48 CST)
- Jérôme Hénin (Thu Jan 27 2011 - 08:08:12 CST)
- Ajasja LjubetiÄ (Thu Jan 27 2011 - 06:25:04 CST)
Erratic pressure values during equilibration of water box
- Axel Kohlmeyer (Sun Jun 17 2012 - 09:08:31 CDT)
- Ashwin C.V. (Sun Jun 17 2012 - 08:49:27 CDT)
error
- Axel Kohlmeyer (Wed Nov 28 2012 - 03:29:35 CST)
- Maria Saeed (Wed Nov 28 2012 - 03:24:50 CST)
Error in membrane protein simulation
- JC Gumbart (Mon Sep 03 2012 - 15:51:35 CDT)
- amin_at_imtech.res.in (Sat Sep 01 2012 - 01:59:27 CDT)
Error in NAMD 2.8 function
- Chris Harrison (Thu Mar 01 2012 - 00:25:22 CST)
- Sereda, Yuriy Vladimirovich (Wed Feb 22 2012 - 11:02:09 CST)
error in psf file
- farzad kiani (Mon Dec 10 2012 - 09:47:00 CST)
error in the orientationAngle
- Ajasja LjubetiÄ (Sun May 22 2011 - 05:48:29 CDT)
- Prathit Chatterjee (Sun May 22 2011 - 05:01:55 CDT)
- Giacomo Fiorin (Sat May 21 2011 - 09:47:49 CDT)
- Prathit Chatterjee (Sat May 21 2011 - 03:51:10 CDT)
Error on closing binary file
- Seren Soner (Thu Jan 13 2011 - 06:42:50 CST)
error regarding membrane embedded protein
- Axel Kohlmeyer (Wed Nov 28 2012 - 02:23:21 CST)
- Maria Saeed (Wed Nov 28 2012 - 01:58:31 CST)
Error when run Replica Exchange Method on Ranger
- Guoxiong Su (Thu May 12 2011 - 14:13:59 CDT)
Error while using larger timesteps in Coarse grained Simulation of Polymer
- rohan uttarwar (Fri Mar 04 2011 - 15:53:56 CST)
Error with "namd"
- Bob Masong (Wed Oct 26 2011 - 00:01:21 CDT)
Error with tclBC to induce shear flow
- KONG Xian (Thu Oct 20 2011 - 20:59:42 CDT)
Error with ubqp.pdb in NAMD tutorial
- Jens K. Munk (Tue Oct 25 2011 - 02:10:22 CDT)
- Bob Masong (Mon Oct 24 2011 - 22:43:46 CDT)
ERROR: 0031-250 task 0: Terminated
- Gurunath Katagi (Mon Jan 09 2012 - 23:42:53 CST)
ERROR: Atoms moving too fast;
- Chris Harrison (Fri Nov 11 2011 - 13:03:52 CST)
- Nikhil Kumar Mittal (Fri Nov 11 2011 - 12:10:52 CST)
ERROR: CUDA-enabled NAMD requires at least one patch per process
- Arash Azari (Wed Apr 27 2011 - 23:49:56 CDT)
error: expected floating-point number but got
- Axel Kohlmeyer (Thu Aug 04 2011 - 10:29:08 CDT)
- Shen, Han (Thu Aug 04 2011 - 10:21:32 CDT)
Error: keyword "group1" is not supported, or not recognized in this context.
- Giacomo Fiorin (Fri Apr 15 2011 - 11:02:03 CDT)
- Shen, Han (Fri Apr 15 2011 - 09:14:11 CDT)
Error: periodicity of dihedral zero
- Francesco Pietra (Tue Jul 24 2012 - 03:23:19 CDT)
Errors compiling namd with CUDA
- Martin, Erik W (Tue Nov 13 2012 - 10:15:53 CST)
Errors compiling namd with CUDA. .
- Martin, Erik W (Tue Nov 13 2012 - 17:43:50 CST)
Evaluate Work for Targeted Molecular Dynamics Simulations
- Mert Gür (Wed Aug 15 2012 - 16:08:52 CDT)
Evaluated heat capacities via NAMD are larger than experimental values
- Jun Zhang (Wed Oct 26 2011 - 19:00:18 CDT)
- Mert Gür (Wed Oct 26 2011 - 13:44:35 CDT)
Ewald contribution to pressure profile only working on single core
- Bjoern Olausson (Tue Feb 07 2012 - 06:59:43 CST)
ewald method
- David Hardy (Fri Mar 25 2011 - 10:27:11 CDT)
- Hasan haska (Fri Mar 25 2011 - 09:49:57 CDT)
- Hasan haska (Fri Mar 25 2011 - 09:45:45 CDT)
example psf and pdb files for simulations with tip4p
- Peter Freddolino (Wed Mar 02 2011 - 13:28:48 CST)
- Ana Celia Vila Verde (Wed Mar 02 2011 - 12:21:44 CST)
execute vs. config directory
- Aron Broom (Fri Sep 14 2012 - 15:51:17 CDT)
- Thomas C. Bishop (Fri Sep 14 2012 - 15:07:24 CDT)
expandBoundaries and multiple walker metadynamics
- Giacomo Fiorin (Mon Oct 01 2012 - 16:15:36 CDT)
- Aron Broom (Mon Oct 01 2012 - 15:54:32 CDT)
- Aron Broom (Mon Oct 01 2012 - 15:50:29 CDT)
- Jeff Wereszczynski (Mon Oct 01 2012 - 15:50:12 CDT)
- Giacomo Fiorin (Mon Oct 01 2012 - 15:44:48 CDT)
- Giacomo Fiorin (Mon Oct 01 2012 - 15:40:18 CDT)
- Aron Broom (Mon Oct 01 2012 - 15:39:41 CDT)
- Jeff Wereszczynski (Mon Oct 01 2012 - 15:24:46 CDT)
- Aron Broom (Mon Oct 01 2012 - 15:13:41 CDT)
- Jeff Wereszczynski (Mon Oct 01 2012 - 14:52:08 CDT)
- Giacomo Fiorin (Mon Oct 01 2012 - 14:21:11 CDT)
- Jeff Wereszczynski (Mon Oct 01 2012 - 13:52:53 CDT)
expect NAMD survey emails this week
- Jim Phillips (Tue Jul 19 2011 - 11:51:22 CDT)
experimental density value
- Ganesh Kamath (Thu Sep 27 2012 - 20:52:16 CDT)
- Aron Broom (Thu Sep 27 2012 - 20:13:04 CDT)
- Guanglei Cui (Thu Sep 27 2012 - 14:17:47 CDT)
- oguz gurbulak (Thu Sep 27 2012 - 07:40:35 CDT)
Explicit Solvent Sytem (40% Ethanol + 60% Water)
- Babban Mia (Wed Aug 10 2011 - 04:49:20 CDT)
- Branko (Tue Aug 09 2011 - 13:29:52 CDT)
- Ismail, Mohd F. (Tue Aug 09 2011 - 13:02:19 CDT)
- Babban Mia (Tue Aug 09 2011 - 09:42:26 CDT)
- Babban Mia (Tue Aug 09 2011 - 01:20:20 CDT)
External electric field using Grid
- Mohammad Jomah Ibraheem Ali Abu Saude (mbusaude) (Thu Mar 15 2012 - 14:47:12 CDT)
external forces
- Jim Phillips (Wed Apr 13 2011 - 09:47:03 CDT)
- johan strumpfer (Mon Apr 04 2011 - 11:07:02 CDT)
- Matteo Rotter (Mon Apr 04 2011 - 08:13:24 CDT)
Extra bonds-ABF
- Giacomo Fiorin (Mon Nov 07 2011 - 11:01:22 CST)
- Parisa Akhski (Mon Nov 07 2011 - 10:53:18 CST)
extract velocities
- Giulia (Tue Oct 23 2012 - 06:58:38 CDT)
Fail to Run VMD
- Axel Kohlmeyer (Tue May 31 2011 - 13:57:24 CDT)
- Àî¼Ñ¼ü (Tue May 31 2011 - 13:53:07 CDT)
Failure to run namd-cuda with gtx-470
- Francesco Pietra (Thu Jul 07 2011 - 01:57:25 CDT)
- Francesco Pietra (Wed Jul 06 2011 - 16:18:53 CDT)
- Francesco Pietra (Wed Jul 06 2011 - 10:44:38 CDT)
FATAL ERROR : Line too long in pdb file
- Aron Broom (Fri Jun 15 2012 - 20:10:39 CDT)
- amin_at_imtech.res.in (Fri Jun 15 2012 - 19:43:31 CDT)
FATAL ERROR : Line too long in pdb file]
- Aron Broom (Fri Jun 15 2012 - 21:24:20 CDT)
- amin_at_imtech.res.in (Fri Jun 15 2012 - 20:25:57 CDT)
Fatal Error Periodic cell has become too small for original patch grid
- bharat gupta (Fri Jul 01 2011 - 00:59:56 CDT)
fatal error running namd on Mac
- johan strumpfer (Tue Apr 10 2012 - 19:05:26 CDT)
- JC Gumbart (Tue Apr 10 2012 - 20:25:46 CDT)
- Aron Broom (Tue Apr 10 2012 - 18:04:25 CDT)
- Jiao, Dian NMN (-EXP) (Tue Apr 10 2012 - 17:53:54 CDT)
FATAL error when run Replica Exchange Method on Franklin
- Guoxiong Su (Thu May 12 2011 - 14:03:58 CDT)
FATAL ERROR: Bad global angle count!
- johan strumpfer (Sun Apr 24 2011 - 16:16:52 CDT)
- PAUL NEWMAN (Sat Apr 23 2011 - 22:04:37 CDT)
- PAUL NEWMAN (Fri Apr 22 2011 - 19:42:02 CDT)
FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version
- Thomas Evangelidis (Mon Oct 22 2012 - 16:42:57 CDT)
- David Hardy (Mon Oct 22 2012 - 12:00:48 CDT)
- Aron Broom (Mon Oct 22 2012 - 10:10:54 CDT)
- Thomas Evangelidis (Sat Oct 20 2012 - 11:46:53 CDT)
- Thomas Evangelidis (Thu Sep 27 2012 - 06:08:04 CDT)
- Norman Geist (Mon Sep 24 2012 - 00:19:08 CDT)
- Thomas Evangelidis (Sun Sep 23 2012 - 11:33:31 CDT)
- Roberts, Jason (Sat Sep 22 2012 - 20:34:50 CDT)
- Thomas Evangelidis (Sat Sep 22 2012 - 10:32:11 CDT)
- Chris Harrison (Sat Sep 22 2012 - 10:23:16 CDT)
- Thomas Evangelidis (Sat Sep 22 2012 - 10:09:11 CDT)
- Chris Harrison (Sat Sep 22 2012 - 09:03:42 CDT)
- Thomas Evangelidis (Sat Sep 22 2012 - 08:19:11 CDT)
- Chris Harrison (Sat Sep 22 2012 - 07:56:34 CDT)
- Thomas Evangelidis (Sat Sep 22 2012 - 07:41:25 CDT)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE AUC
- Kiarash Hosseini (Tue Apr 10 2012 - 04:24:10 CDT)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG2R
- Shubhra Ghosh Dastidar (Wed Oct 31 2012 - 21:55:49 CDT)
FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small.
- Chris Harrison (Mon Aug 29 2011 - 20:07:33 CDT)
- Chris Harrison (Mon Aug 29 2011 - 19:35:42 CDT)
- Massimiliano Porrini (Mon Aug 29 2011 - 14:26:06 CDT)
- Chris Harrison (Mon Aug 29 2011 - 11:50:00 CDT)
- Massimiliano Porrini (Mon Aug 29 2011 - 09:36:55 CDT)
FATAL ERROR: Setting parameter fixedAtomsFile from script failed!
- Rajan Vatassery (Fri Jul 15 2011 - 16:43:04 CDT)
- Jorgen Simonsen (Fri Jul 15 2011 - 15:55:26 CDT)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100)
- johan strumpfer (Sun Oct 23 2011 - 16:42:07 CDT)
- Jernej Zidar (Sun Oct 23 2011 - 19:45:56 CDT)
- Jens K. Munk (Sun Oct 23 2011 - 14:39:24 CDT)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
- johan strumpfer (Thu Apr 07 2011 - 09:23:02 CDT)
- Gary M. Skinner (Thu Apr 07 2011 - 07:17:14 CDT)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1)
- Ajasja LjubetiÄ (Fri Jun 24 2011 - 03:46:18 CDT)
- JC Gumbart (Thu Jun 23 2011 - 16:17:59 CDT)
- Jorgen Simonsen (Thu Jun 23 2011 - 08:51:52 CDT)
FATAL ERROR: Unable to open binary file
- sibel.cakan (Thu Jul 14 2011 - 05:34:57 CDT)
Feature request for the colvars module -- TCL syntax
- Ajasja LjubetiÄ (Mon Jan 24 2011 - 08:16:01 CST)
- Ajasja LjubetiÄ (Tue Jan 18 2011 - 11:44:54 CST)
- Axel Kohlmeyer (Tue Jan 18 2011 - 09:09:54 CST)
- Ajasja LjubetiÄ (Tue Jan 18 2011 - 07:17:54 CST)
- Chris Harrison (Mon Jan 17 2011 - 11:00:22 CST)
- Jérôme Hénin (Mon Jan 17 2011 - 11:52:23 CST)
- Ajasja LjubetiÄ (Mon Jan 17 2011 - 09:26:47 CST)
FEP - Dynamic charges
- Jérôme Hénin (Wed May 16 2012 - 03:03:54 CDT)
- John Baker (Tue May 15 2012 - 12:38:59 CDT)
FEP - Protein binding to Membrane surface
- Bjoern Olausson (Thu Feb 10 2011 - 03:50:37 CST)
FEP difficulties between two ion species
- Jérôme Hénin (Wed May 23 2012 - 13:21:26 CDT)
- Jérôme Hénin (Sat May 19 2012 - 15:11:55 CDT)
- Niklaus Johner (Fri May 18 2012 - 09:13:06 CDT)
- Jérôme Hénin (Tue Apr 24 2012 - 07:19:45 CDT)
- Jeremy Parlin (Mon Apr 23 2012 - 16:38:31 CDT)
FEP simulation using AmberFF
- Jiyong Park (Mon Dec 10 2012 - 01:41:28 CST)
FEP tutorial-my molecule doesn't show up in VMD
- Alisha \ (Mon Mar 19 2012 - 11:02:52 CDT)
- JC Gumbart (Mon Mar 19 2012 - 05:54:20 CDT)
- Chris Harrison (Mon Mar 19 2012 - 02:00:38 CDT)
- Alisha \ (Mon Mar 19 2012 - 01:56:38 CDT)
- Chris Harrison (Mon Mar 19 2012 - 01:40:57 CDT)
- Alisha \ (Mon Mar 19 2012 - 01:20:44 CDT)
FEP using amber topologies
- felmerino_at_uchile.cl (Mon Apr 23 2012 - 17:46:17 CDT)
FEP with flattened free energy surface?
- Jérôme Hénin (Sat Apr 09 2011 - 01:18:19 CDT)
- Ivan Vyalov (Fri Apr 08 2011 - 15:48:09 CDT)
- Jérôme Hénin (Fri Apr 08 2011 - 15:05:30 CDT)
- Ivan Vyalov (Fri Apr 08 2011 - 14:12:38 CDT)
- Jérôme Hénin (Wed Apr 06 2011 - 11:45:29 CDT)
- Ivan Vyalov (Wed Apr 06 2011 - 04:49:50 CDT)
fep/parm7
- Francesco Pietra (Mon Aug 06 2012 - 10:57:36 CDT)
ffTK in the just released VMD 1.9.1
- JC Gumbart (Mon Feb 06 2012 - 01:15:52 CST)
- JC Gumbart (Sat Feb 04 2012 - 15:04:05 CST)
FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?)
- Francesco Pietra (Tue Jun 05 2012 - 02:16:40 CDT)
fftw libraries for ppc
- Gurunath Katagi (Wed Oct 19 2011 - 22:04:42 CDT)
Filtered mail?
- Jérôme Hénin (Tue Jul 12 2011 - 10:19:41 CDT)
- Austin B. Yongye (Tue Jul 12 2011 - 09:04:32 CDT)
Final production run in MD
- Jérôme Hénin (Fri Jul 01 2011 - 02:31:04 CDT)
- bharat gupta (Thu Jun 30 2011 - 18:42:23 CDT)
finding water around protein
- divya nayar (Thu Jun 23 2011 - 00:59:56 CDT)
First impressions from AMBER ff12SB ?
- Nicholas M Glykos (Sun Dec 23 2012 - 10:58:36 CST)
five 'ERROR' in the log file of NAMD2.9
- ypg (Sun May 13 2012 - 09:48:18 CDT)
- JC Gumbart (Sun May 13 2012 - 09:27:26 CDT)
- Aron Broom (Sun May 13 2012 - 09:16:26 CDT)
- ypg (Sun May 13 2012 - 09:13:49 CDT)
- JC Gumbart (Sun May 13 2012 - 08:23:53 CDT)
- ypg (Sun May 13 2012 - 02:15:27 CDT)
Fix atoms-Colvars
- Jérôme Hénin (Fri Jan 07 2011 - 13:04:10 CST)
- Alex Liu (Thu Jan 06 2011 - 15:46:14 CST)
Fixed atoms in SMD
- khalil ghafarian (Tue Oct 09 2012 - 03:40:20 CDT)
- Axel Kohlmeyer (Mon Oct 08 2012 - 07:00:09 CDT)
- khalil ghafarian (Mon Oct 08 2012 - 05:22:25 CDT)
fixed bond length
- Aron Broom (Fri May 11 2012 - 13:25:14 CDT)
- Mortaza Aghtar (Fri May 11 2012 - 11:29:12 CDT)
- Ajasja LjubetiÄ (Fri May 11 2012 - 11:06:35 CDT)
- Mortaza Aghtar (Fri May 11 2012 - 10:51:01 CDT)
Fixed COM
- Ajasja LjubetiÄ (Tue Jul 12 2011 - 08:11:04 CDT)
- Ajasja LjubetiÄ (Mon Jul 11 2011 - 14:37:43 CDT)
- Parisa Akhski (Mon Jul 11 2011 - 13:52:21 CDT)
- Ali Khanlarkhani (Mon Jul 11 2011 - 13:30:32 CDT)
Fixing bonds in dihydrogen phosphate to save computation time
- Axel Kohlmeyer (Tue Jul 10 2012 - 05:21:14 CDT)
- Evgeny Bulat (Mon Jul 09 2012 - 13:55:45 CDT)
fixing group of atoms, Proper for manipualation
- M Mahjour (Wed Apr 13 2011 - 17:06:43 CDT)
flipdcd corrupting dcd files
- Joshua D. Moore (Fri Jun 15 2012 - 09:11:38 CDT)
- peter.schmidtke_at_fr.netgrs.com (Fri Jun 15 2012 - 00:58:16 CDT)
- Joshua D. Moore (Thu Jun 14 2012 - 13:39:52 CDT)
- peter.schmidtke_at_fr.netgrs.com (Thu Jun 14 2012 - 06:30:48 CDT)
Force constant for Umbrella Sampling
- Buddhadev Maiti (Mon Feb 14 2011 - 19:19:02 CST)
force field
- Namd Namd (Mon Jun 13 2011 - 03:36:04 CDT)
force field for 2-methyl-2,4-pentanediol (MPD)
- Yang Gao (Tue May 10 2011 - 10:40:40 CDT)
Force field parameter and topology for zinc finger protein
- sudipta (Mon Jun 11 2012 - 20:09:56 CDT)
force field parameters for Silicon
- farzad kiani (Tue Jul 10 2012 - 07:57:05 CDT)
Force field Parametrization
- JC Gumbart (Fri Nov 30 2012 - 10:34:05 CST)
- Thomas Evangelidis (Fri Nov 30 2012 - 09:39:49 CST)
- Dr. Eddie (Fri Nov 30 2012 - 09:09:34 CST)
Force Field Topology and Parameter Files
- Stephen Holmes (Tue Nov 13 2012 - 09:00:59 CST)
force question
- Hasan haska (Thu Sep 22 2011 - 05:36:47 CDT)
- Ehsan Ban (Thu Sep 22 2011 - 05:18:34 CDT)
- Jérôme Hénin (Thu Sep 22 2011 - 04:32:45 CDT)
- Hasan haska (Thu Sep 22 2011 - 02:50:18 CDT)
Force Vector Between Two Atoms
- Ehsan Ban (Mon Oct 10 2011 - 01:19:55 CDT)
- Bruno Luís Pinto de Oliveira (Sat Oct 08 2011 - 04:25:40 CDT)
- Ehsan Ban (Fri Oct 07 2011 - 17:14:02 CDT)
ForceConstant in Umbrella Sampling
- Chris Harrison (Fri Oct 28 2011 - 18:10:40 CDT)
- Buddhadev Maiti (Fri Oct 28 2011 - 12:38:24 CDT)
Forcefield for simulating peptide with heparin!!!!
- Aditya Ranganathan (Mon May 02 2011 - 07:24:56 CDT)
forces on fixed atoms
- Jérôme Hénin (Thu Feb 17 2011 - 03:31:32 CST)
- Bennion, Brian (Wed Feb 16 2011 - 18:04:30 CST)
- Jérôme Hénin (Wed Feb 16 2011 - 17:58:28 CST)
- Bennion, Brian (Wed Feb 16 2011 - 16:01:44 CST)
forces saved in forcedcd
- Xiaohu Li (Fri May 04 2012 - 10:31:41 CDT)
- Jérôme Hénin (Fri May 04 2012 - 09:32:29 CDT)
- Xiaohu Li (Fri May 04 2012 - 08:49:14 CDT)
- JC Gumbart (Fri May 04 2012 - 08:51:43 CDT)
- JC Gumbart (Fri May 04 2012 - 00:58:54 CDT)
- Xiaohu Li (Thu May 03 2012 - 22:45:37 CDT)
- Xiaohu Li (Thu May 03 2012 - 22:40:34 CDT)
- Chris Harrison (Thu May 03 2012 - 22:22:58 CDT)
- JC Gumbart (Thu May 03 2012 - 22:05:40 CDT)
- Xiaohu Li (Thu May 03 2012 - 21:57:20 CDT)
- JC Gumbart (Thu May 03 2012 - 20:11:32 CDT)
- Xiaohu Li (Thu May 03 2012 - 19:51:36 CDT)
- Chris Harrison (Thu May 03 2012 - 18:42:19 CDT)
- Xiaohu Li (Thu May 03 2012 - 15:43:50 CDT)
formyl and ethanolamide parameters and topology
- Branko (Fri Jun 24 2011 - 03:52:32 CDT)
- flavio seixas (Thu Jun 23 2011 - 21:58:27 CDT)
- poker_at_physics.usyd.edu.au (Thu Jun 23 2011 - 19:11:57 CDT)
- flavio seixas (Thu Jun 23 2011 - 12:08:58 CDT)
- Jorgen Simonsen (Thu Jun 23 2011 - 09:52:18 CDT)
free energy of binding
- Richard Wood (Thu Jul 07 2011 - 18:56:48 CDT)
- Jeff Wereszczynski (Thu Jul 07 2011 - 18:27:55 CDT)
- Gianluca Interlandi (Thu Jul 07 2011 - 17:29:18 CDT)
- Jeffrey Potoff (Thu Jul 07 2011 - 17:16:02 CDT)
- Chris Harrison (Thu Jul 07 2011 - 17:12:34 CDT)
- Gianluca Interlandi (Thu Jul 07 2011 - 17:08:55 CDT)
- Francesco Pietra (Thu Jul 07 2011 - 16:50:12 CDT)
- Dong Luo (Thu Jul 07 2011 - 10:50:07 CDT)
- Francesco Pietra (Thu Jul 07 2011 - 04:52:38 CDT)
free energy perturbation
- Jérôme Hénin (Wed Jan 05 2011 - 12:07:39 CST)
- Jérôme Hénin (Wed Jan 05 2011 - 07:39:37 CST)
- BIN ZHANG (Wed Jan 05 2011 - 02:07:57 CST)
freeEnergy parsing error
- Lada Biedermannová (Wed Apr 27 2011 - 09:08:46 CDT)
fullSamples in ABF: applied at restart?
- Jérôme Hénin (Mon Nov 21 2011 - 04:11:06 CST)
- Neelanjana Sengupta (Mon Nov 21 2011 - 02:51:55 CST)
- Jérôme Hénin (Mon Nov 21 2011 - 02:10:10 CST)
- Neelanjana Sengupta (Sun Nov 20 2011 - 22:19:00 CST)
- Neelanjana Sengupta (Sun Nov 20 2011 - 22:14:15 CST)
Functional form to apply constraints
- Mariana Graterol (Fri Aug 24 2012 - 18:28:43 CDT)
Functionalizing the nanopore
- Sridhar Kumar Kannam (Mon Nov 26 2012 - 23:24:19 CST)
fwd:
- sara (Fri Apr 27 2012 - 21:51:49 CDT)
- sara (Fri Apr 27 2012 - 21:51:50 CDT)
- Madhulika Gupta (Mon Jan 30 2012 - 22:10:37 CST)
Fwd: "cuda error cudastreamcreate",
- Francesco Pietra (Fri Jun 17 2011 - 02:36:49 CDT)
- John Stone (Fri Jun 17 2011 - 01:22:50 CDT)
- Francesco Pietra (Fri Jun 17 2011 - 00:50:05 CDT)
Fwd: about md in npt
- Boyang Wang (Wed Dec 28 2011 - 02:54:01 CST)
Fwd: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance
- Francesco Pietra (Mon Jun 06 2011 - 04:30:46 CDT)
- Francesco Pietra (Mon Jun 06 2011 - 04:15:44 CDT)
Fwd: AW: stereo-chemical inversion during MD
- Gordon Wells (Wed May 09 2012 - 10:04:04 CDT)
Fwd: binaryrestart/binaryoutput problem
- Francesco Pietra (Tue Mar 01 2011 - 02:56:29 CST)
Fwd: CUDA error 0 attaching to node
- Francesco Pietra (Sun Mar 11 2012 - 10:28:04 CDT)
- Francesco Pietra (Sat Mar 10 2012 - 00:32:08 CST)
Fwd: cuda error cudastreamcreate. SOLVED (probably)
- Francesco Pietra (Wed Jun 15 2011 - 09:43:28 CDT)
- Francesco Pietra (Wed Jun 15 2011 - 02:45:26 CDT)
Fwd: CUDA error vs clashes
- Francesco Pietra (Wed Nov 07 2012 - 09:26:19 CST)
Fwd: Fwd: Fwd: namd on gtx-680
- Francesco Pietra (Wed Jun 20 2012 - 12:57:06 CDT)
Fwd: Fwd: hi
- Axel Kohlmeyer (Thu Jun 02 2011 - 12:52:25 CDT)
- kanchi subbarao rao (Thu Jun 02 2011 - 12:44:27 CDT)
- kanchi subbarao rao (Wed Jun 01 2011 - 13:32:41 CDT)
Fwd: Fwd: namd on gtx-680
- Francesco Pietra (Thu Jun 21 2012 - 03:09:27 CDT)
- Francesco Pietra (Thu Jun 21 2012 - 02:10:50 CDT)
- Axel Kohlmeyer (Wed Jun 20 2012 - 13:52:21 CDT)
- Axel Kohlmeyer (Wed Jun 20 2012 - 10:11:48 CDT)
- Vincent Leroux (Wed Jun 20 2012 - 10:03:29 CDT)
- Francesco Pietra (Wed Jun 20 2012 - 09:38:32 CDT)
- Francesco Pietra (Wed Jun 20 2012 - 05:10:03 CDT)
Fwd: Generating .tpr file using NAMD files
- rajitha rajeshwar (Mon Dec 19 2011 - 03:05:34 CST)
Fwd: GPU workstation build
- Francesco Pietra (Tue Aug 21 2012 - 08:44:09 CDT)
Fwd: hBond component in colvars and patching
- Francesco Pietra (Sun Mar 06 2011 - 02:36:10 CST)
Fwd: hi
- kanchi subbarao rao (Tue May 31 2011 - 05:10:32 CDT)
Fwd: hi all
- kanchi subbarao rao (Thu Jun 16 2011 - 07:16:22 CDT)
- kanchi subbarao rao (Wed Jun 15 2011 - 11:46:09 CDT)
Fwd: Incompatibility between colvars and tclforces?
- Francesco Pietra (Wed Mar 30 2011 - 12:32:53 CDT)
- Vlad Cojocaru (Thu Mar 31 2011 - 05:12:10 CDT)
- Vlad Cojocaru (Thu Mar 31 2011 - 02:27:40 CDT)
- Jérôme Hénin (Thu Mar 31 2011 - 03:25:18 CDT)
- Francesco Pietra (Thu Mar 31 2011 - 02:45:10 CDT)
Fwd: Keyword "lower" not supported...colvars
- Francesco Pietra (Sun Mar 13 2011 - 05:37:41 CDT)
Fwd: Line minimizerfailure because of IMPR?
- Francesco Pietra (Thu Apr 05 2012 - 03:10:59 CDT)
- Francesco Pietra (Thu Apr 05 2012 - 03:02:14 CDT)
Fwd: membrane moving up in simulation box
- kanchi subbarao rao (Thu Oct 13 2011 - 06:26:12 CDT)
- kanchi subbarao rao (Thu Oct 13 2011 - 04:54:15 CDT)
Fwd: namd cuda error.
- kanchi subbarao rao (Tue Jul 03 2012 - 00:20:01 CDT)
Fwd: namd on gtx-680
- Francesco Pietra (Wed Jun 20 2012 - 09:06:26 CDT)
- Francesco Pietra (Wed Jun 20 2012 - 05:08:30 CDT)
Fwd: nvidia 275.09.07 driver. SOLVED, NO DRIVER PROBLEM
- Francesco Pietra (Thu Jun 30 2011 - 14:49:56 CDT)
Fwd: phosphotyrosine
- poker_at_physics.usyd.edu.au (Mon Jun 20 2011 - 01:42:49 CDT)
- bharat gupta (Mon Jun 20 2011 - 00:29:04 CDT)
Fwd: problem regarding charmm parameter file of carbon nano tube
- kanchi subbarao rao (Mon Nov 21 2011 - 05:07:50 CST)
Fwd: ramd firstRamdAtom
- Francesco Pietra (Mon Mar 28 2011 - 03:15:56 CDT)
Fwd: ramd seed
- Francesco Pietra (Thu Apr 07 2011 - 08:41:08 CDT)
Fwd: RAMD Setting parameter TclForces from script failed
- Cojocaru, Vlad (Mon Mar 28 2011 - 16:55:44 CDT)
- Jim Phillips (Mon Mar 28 2011 - 16:49:25 CDT)
- Francesco Pietra (Mon Mar 28 2011 - 15:37:24 CDT)
- Francesco Pietra (Mon Mar 28 2011 - 15:19:57 CDT)
Fwd: Re : Setting up a membrane simulation
- Bjoern Olausson (Tue Sep 20 2011 - 05:43:30 CDT)
- Bjoern Olausson (Tue Sep 20 2011 - 04:27:23 CDT)
Fwd: restrain on COM
- Jérôme Hénin (Sat Nov 19 2011 - 10:48:41 CST)
- Swarna M Patra (Fri Nov 18 2011 - 23:33:09 CST)
Fwd: rigid bonds
- Francesco Pietra (Fri Oct 14 2011 - 09:44:14 CDT)
Fwd: Solved stream files and paratool
- Francesco Pietra (Fri Sep 23 2011 - 10:13:06 CDT)
Fwd: SOLVED, however multiple CUDA efficiency?
- Francesco Pietra (Sun Mar 11 2012 - 11:36:55 CDT)
Fwd: stereo-chemical inversion during MD
- Francesco Pietra (Tue May 08 2012 - 01:59:49 CDT)
Fwd: Three GPU cards on shared-mem motherboard
- Francesco Pietra (Wed May 30 2012 - 12:33:47 CDT)
Fwd: what restraint can I use to prevent membrane diffusion on the Z-axis?
- kanchi subbarao rao (Tue Feb 28 2012 - 13:50:50 CST)
Fwd: Wrong exit from RAMD runs
- Vlad Cojocaru (Thu Apr 14 2011 - 03:08:54 CDT)
- Jim Phillips (Wed Apr 13 2011 - 10:02:18 CDT)
- Jim Phillips (Wed Apr 13 2011 - 09:59:25 CDT)
- Francesco Pietra (Tue Apr 05 2011 - 15:34:19 CDT)
Galilean Invariant Thermostat
- Jérôme Hénin (Mon Apr 09 2012 - 04:43:37 CDT)
- Ismail, Mohd F. (Sun Apr 08 2012 - 18:26:38 CDT)
GBIS and ABF
- Ajasja LjubetiÄ (Mon Mar 28 2011 - 11:34:07 CDT)
- Giacomo Fiorin (Mon Mar 28 2011 - 10:08:00 CDT)
- Giacomo Fiorin (Mon Mar 28 2011 - 10:09:55 CDT)
- Bjoern Olausson (Mon Mar 28 2011 - 09:56:41 CDT)
- Ajasja LjubetiÄ (Mon Mar 28 2011 - 08:37:36 CDT)
- Bjoern Olausson (Mon Mar 28 2011 - 02:45:46 CDT)
- Jérôme Hénin (Thu Mar 24 2011 - 10:01:43 CDT)
- Jérôme Hénin (Thu Mar 24 2011 - 05:39:52 CDT)
- Ajasja LjubetiÄ (Wed Mar 23 2011 - 14:17:48 CDT)
- Bjoern Olausson (Wed Mar 23 2011 - 06:57:32 CDT)
- Jérôme Hénin (Wed Mar 23 2011 - 12:10:15 CDT)
- Bjoern Olausson (Wed Mar 23 2011 - 09:32:43 CDT)
- Bjoern Olausson (Wed Mar 23 2011 - 07:04:29 CDT)
- Bjoern Olausson (Tue Mar 22 2011 - 18:13:18 CDT)
- Branko (Tue Mar 22 2011 - 17:16:54 CDT)
- Branko (Fri Mar 18 2011 - 04:53:00 CDT)
- Giacomo Fiorin (Thu Mar 17 2011 - 20:02:37 CDT)
- Branko (Thu Mar 17 2011 - 15:50:40 CDT)
GBIS and hydrophobic solvation
- Gianluca Interlandi (Wed Feb 15 2012 - 15:45:54 CST)
- David Tanner (Wed Feb 15 2012 - 15:36:31 CST)
- Gianluca Interlandi (Fri Jan 20 2012 - 18:41:27 CST)
- David Tanner (Thu Oct 13 2011 - 13:40:32 CDT)
- Branko (Mon Oct 10 2011 - 10:11:42 CDT)
- Jérôme Hénin (Mon Oct 10 2011 - 07:24:50 CDT)
GBIS and hydrophobic term, in replay to Jerome and David discussion
- Branko (Sun Oct 23 2011 - 09:55:27 CDT)
- Jérôme Hénin (Sun Oct 23 2011 - 09:43:08 CDT)
- Branko (Sun Oct 23 2011 - 09:36:17 CDT)
GBIS and thermostats
- Gianluca Interlandi (Wed Mar 28 2012 - 21:48:40 CDT)
GBIS not compatible with CUDA at this time
- David Tanner (Tue Mar 22 2011 - 14:21:09 CDT)
- Michael S. Sellers (Cont, ARL/WMRD) (Tue Mar 22 2011 - 13:27:48 CDT)
GBIS on GPU?
- Danny Xu (Thu Aug 04 2011 - 11:51:57 CDT)
GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03
- Bjoern Olausson (Wed Mar 23 2011 - 07:06:21 CDT)
- Jérôme Hénin (Wed Mar 23 2011 - 05:39:51 CDT)
- Bjoern Olausson (Wed Mar 23 2011 - 03:18:22 CDT)
- Giacomo Fiorin (Tue Mar 22 2011 - 21:07:53 CDT)
- Bjoern Olausson (Tue Mar 22 2011 - 17:56:09 CDT)
GBIS synamics
- David Tanner (Wed Mar 02 2011 - 07:56:59 CST)
- Francesco Oteri (Wed Mar 02 2011 - 05:02:29 CST)
GeForce vs Tesla GPUs for high performance computing
- Axel Kohlmeyer (Thu Apr 14 2011 - 14:57:16 CDT)
- Gianluca Interlandi (Thu Apr 14 2011 - 14:48:58 CDT)
- Axel Kohlmeyer (Thu Apr 14 2011 - 14:23:50 CDT)
- Salvador H-V (Thu Apr 14 2011 - 13:58:30 CDT)
Generalized Born calcs
- Thomas Bishop (Tue Aug 16 2011 - 14:53:17 CDT)
Generalized Born implicit solvent model in 2.8b1
- David Tanner (Wed Mar 30 2011 - 12:04:20 CDT)
- Enrico Guarnera (Wed Mar 30 2011 - 09:40:45 CDT)
Generalized Born Solvent Question
- Roy Fernando (Tue Aug 07 2012 - 16:47:01 CDT)
- Gianluca Interlandi (Tue Aug 07 2012 - 16:20:34 CDT)
- Aron Broom (Tue Aug 07 2012 - 16:10:05 CDT)
- Gianluca Interlandi (Tue Aug 07 2012 - 15:16:04 CDT)
- Roy Fernando (Tue Aug 07 2012 - 14:55:57 CDT)
- Aron Broom (Fri Aug 03 2012 - 15:21:22 CDT)
- Roy Fernando (Fri Aug 03 2012 - 14:07:26 CDT)
- Aron Broom (Mon Jul 30 2012 - 17:06:54 CDT)
- Aron Broom (Thu Jul 19 2012 - 13:34:34 CDT)
Generating .tpr file using NAMD files
- Jeffrey Potoff (Mon Dec 19 2011 - 12:05:56 CST)
- Axel Kohlmeyer (Mon Dec 19 2011 - 11:59:35 CST)
- rajitha tatikonda (Mon Dec 19 2011 - 00:32:56 CST)
Generating force field for novel molecules
- MOHAMMAD JAVAD AGHAEI (Wed May 23 2012 - 03:16:36 CDT)
gentoo ebuild
- Aron Broom (Fri Jul 13 2012 - 16:03:23 CDT)
- Dr. Eddie (Fri Jul 13 2012 - 16:01:12 CDT)
geometry deformation
- Grace Brannigan (Wed Mar 07 2012 - 15:45:36 CST)
- lecan (Wed Mar 07 2012 - 15:10:27 CST)
Get number of timesteps from DCD via script
- Bjoern Olausson (Thu Feb 10 2011 - 03:52:44 CST)
- Joshua D. Moore (Wed Feb 09 2011 - 08:40:27 CST)
- Joshua D. Moore (Wed Feb 09 2011 - 06:41:06 CST)
- Axel Kohlmeyer (Wed Feb 09 2011 - 08:43:21 CST)
- Bjoern Olausson (Wed Feb 09 2011 - 08:05:42 CST)
- Bjoern Olausson (Wed Feb 09 2011 - 08:32:13 CST)
- Axel Kohlmeyer (Wed Feb 09 2011 - 07:43:17 CST)
- Bjoern Olausson (Wed Feb 09 2011 - 06:37:20 CST)
- Joshua D. Moore (Tue Feb 08 2011 - 17:01:32 CST)
- Joshua D. Moore (Tue Feb 08 2011 - 16:56:02 CST)
- Andrew Emerson (Tue Feb 08 2011 - 08:00:07 CST)
- Bjoern Olausson (Tue Feb 08 2011 - 05:24:29 CST)
- Chris Harrison (Mon Feb 07 2011 - 12:34:25 CST)
- Bjoern Olausson (Mon Feb 07 2011 - 06:52:39 CST)
Get restart file (restart.coor) from DCD
- Joshua D. Moore (Mon Mar 28 2011 - 20:18:11 CDT)
- Ismail, Mohd F. (Mon Mar 28 2011 - 17:41:56 CDT)
Getting "nan" at ELEC energy value
- Aron Broom (Sat Dec 08 2012 - 00:22:13 CST)
- jesmin jahan (Fri Dec 07 2012 - 22:48:46 CST)
Gibbs potential
- sajad falsafi (Tue Jun 07 2011 - 02:14:40 CDT)
- Patriche Simona (Mon Jun 06 2011 - 10:10:01 CDT)
Glycosaminoglycan sulfate group with CHARMM
- Massimiliano Porrini (Wed Mar 28 2012 - 12:18:08 CDT)
- Michelle Kuttel (Fri Mar 23 2012 - 02:20:29 CDT)
- Massimiliano Porrini (Thu Mar 22 2012 - 10:09:03 CDT)
glycosaminoglycan with GLYCAM06 in amber format
- Massimiliano Porrini (Tue Dec 20 2011 - 09:46:18 CST)
- Massimiliano Porrini (Tue Dec 20 2011 - 08:55:58 CST)
- Lachele Foley (Lists) (Tue Dec 20 2011 - 08:53:59 CST)
- Massimiliano Porrini (Mon Dec 19 2011 - 05:04:40 CST)
- Massimiliano Porrini (Sun Dec 18 2011 - 10:44:48 CST)
Go model in NAMD?
- Bin Zhang (Thu Apr 26 2012 - 16:52:26 CDT)
Gold nanoparticle and 1-octanethiol
- Edroaldo Lummertz da Rocha (Thu Apr 28 2011 - 19:07:44 CDT)
- Edroaldo Lummertz da Rocha (Wed Apr 27 2011 - 07:01:52 CDT)
- Edroaldo Lummertz da Rocha (Mon Apr 25 2011 - 13:14:22 CDT)
GPCR MD Tutorial
- Anirban Ghosh (Thu Apr 26 2012 - 04:18:08 CDT)
GPRESSURE becomes nan in TIP4P simulation
- Udaysankar Midya (Sat Dec 31 2011 - 05:23:35 CST)
GPU acceleration by using ATI video card
- dongsheng lei (Fri Dec 14 2012 - 03:42:08 CST)
- Aron Broom (Fri Dec 14 2012 - 03:13:40 CST)
- Axel Kohlmeyer (Fri Dec 14 2012 - 03:11:06 CST)
- Axel Kohlmeyer (Fri Dec 14 2012 - 03:04:27 CST)
- Axel Kohlmeyer (Fri Dec 14 2012 - 02:56:14 CST)
- Aron Broom (Fri Dec 14 2012 - 02:49:04 CST)
- dongsheng lei (Fri Dec 14 2012 - 02:28:13 CST)
GPU cluster
- Axel Kohlmeyer (Tue Jun 19 2012 - 14:40:38 CDT)
- Matthew B. Roark (Tue Jun 19 2012 - 14:07:58 CDT)
GPU workstation build
- Aron Broom (Mon Aug 20 2012 - 11:21:10 CDT)
- Blake Mertz (Mon Aug 20 2012 - 10:41:13 CDT)
GPU-CPU small-scale machine for NAMD
- Jim Phillips (Wed May 18 2011 - 12:48:52 CDT)
- Darko Stefanovski (Tue May 17 2011 - 12:10:31 CDT)
- Francesco Pietra (Mon May 16 2011 - 03:45:37 CDT)
Graphene pdb/psf files cannot be read by psfgen
- Axel Kohlmeyer (Thu Feb 16 2012 - 07:39:36 CST)
- Wanzhi Qiu (Thu Feb 16 2012 - 00:36:20 CST)
- Axel Kohlmeyer (Thu Feb 16 2012 - 00:09:13 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 23:58:52 CST)
- Axel Kohlmeyer (Wed Feb 15 2012 - 23:13:47 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 23:04:53 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 22:41:23 CST)
- kanchi subbarao rao (Wed Feb 15 2012 - 21:48:00 CST)
- Axel Kohlmeyer (Wed Feb 15 2012 - 20:57:14 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 20:50:30 CST)
- Axel Kohlmeyer (Wed Feb 15 2012 - 20:13:44 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 20:12:05 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 20:06:01 CST)
- kanchi subbarao rao (Wed Feb 15 2012 - 08:11:10 CST)
- Cruz-Chu Eduardo Roberto (Wed Feb 15 2012 - 05:06:31 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 01:14:04 CST)
Grid Forces: example code, documentation edit, and requested feature
- David Minh (Tue Oct 23 2012 - 09:49:26 CDT)
gromacs analysis tools
- Axel Kohlmeyer (Sun Apr 03 2011 - 14:28:04 CDT)
- Francesco Oteri (Sun Apr 03 2011 - 13:47:19 CDT)
- Joshua Adelman (Sun Apr 03 2011 - 10:45:16 CDT)
- Molecular Dynamics (Sun Apr 03 2011 - 04:33:14 CDT)
- Molecular Dynamics (Sun Apr 03 2011 - 04:54:35 CDT)
Gromacs analysis tools for Namd output
- Axel Kohlmeyer (Wed Feb 01 2012 - 11:48:47 CST)
- PAUL NEWMAN (Wed Feb 01 2012 - 11:41:40 CST)
GTX-660 Ti benchmark
- Guanglei Cui (Wed Sep 19 2012 - 08:32:38 CDT)
- Aron Broom (Tue Sep 18 2012 - 11:41:47 CDT)
- Michael Galloway (Tue Sep 18 2012 - 09:43:02 CDT)
- Guanglei Cui (Tue Sep 18 2012 - 09:38:39 CDT)
- Aron Broom (Mon Sep 17 2012 - 20:56:41 CDT)
- Guanglei Cui (Mon Sep 17 2012 - 15:35:34 CDT)
- Roberts, Jason (Sun Sep 16 2012 - 17:08:55 CDT)
- Thomas Albers (Sun Sep 16 2012 - 14:54:49 CDT)
- Thomas Albers (Sun Sep 16 2012 - 14:47:35 CDT)
- Guanglei Cui (Fri Sep 14 2012 - 08:50:41 CDT)
- Wenyu Zhong (Thu Sep 13 2012 - 22:10:23 CDT)
- Wenyu Zhong (Thu Sep 13 2012 - 22:02:07 CDT)
- Aron Broom (Thu Sep 13 2012 - 18:01:14 CDT)
- Thomas Albers (Thu Sep 13 2012 - 14:50:43 CDT)
gtx-680: CUDA error in cudaGetDeviceCount
- lcbllcc_at_gmail.com (Thu Jul 12 2012 - 04:28:08 CDT)
gurukatagi@gmail.com
- Marcos Sotomayor (Thu Feb 23 2012 - 16:44:47 CST)
- Aron Broom (Wed Feb 22 2012 - 12:08:08 CST)
- Ajasja LjubetiÄ (Wed Feb 22 2012 - 11:51:51 CST)
- Gurunath Katagi (Wed Feb 22 2012 - 11:22:01 CST)
- Aron Broom (Mon Feb 06 2012 - 12:09:08 CST)
- Ajasja LjubetiÄ (Mon Feb 06 2012 - 11:05:26 CST)
- Gurunath Katagi (Mon Feb 06 2012 - 10:37:49 CST)
handling buckingham potentials in NAMD - regd
- Ramesh Cheerla (Tue Oct 02 2012 - 10:17:47 CDT)
Handling torsional potentials other than CHARMM type - regd
- Jeffrey Potoff (Fri Oct 12 2012 - 15:34:01 CDT)
- Ramesh Cheerla (Fri Oct 12 2012 - 14:46:10 CDT)
Hard sphere potential
- Axel Kohlmeyer (Thu Feb 02 2012 - 22:41:22 CST)
- M.Raviprasad (Thu Feb 02 2012 - 22:18:23 CST)
- Axel Kohlmeyer (Thu Feb 02 2012 - 20:56:09 CST)
- M.Raviprasad (Thu Feb 02 2012 - 20:20:14 CST)
Harmonic Constrain like MMFP in CHARMM
- Giacomo Fiorin (Tue Jan 24 2012 - 09:40:08 CST)
- Vahid Mirjalili (Mon Jan 23 2012 - 14:56:55 CST)
- Giacomo Fiorin (Sat Jan 21 2012 - 01:24:14 CST)
- Vahid Mirjalili (Fri Jan 20 2012 - 19:41:28 CST)
- Giacomo Fiorin (Fri Jan 20 2012 - 18:42:26 CST)
- Vahid Mirjalili (Fri Jan 20 2012 - 17:52:14 CST)
has system reached a steady state condition?
- farzad kiani (Wed Aug 22 2012 - 06:14:25 CDT)
- farzad kiani (Wed Aug 22 2012 - 06:11:06 CDT)
hBond colvars and patching
- Giacomo Fiorin (Fri Mar 11 2011 - 11:40:06 CST)
- Francesco Pietra (Fri Mar 11 2011 - 09:07:20 CST)
- Peter Freddolino (Tue Mar 08 2011 - 13:48:53 CST)
- Francesco Pietra (Tue Mar 08 2011 - 00:34:36 CST)
- Peter Freddolino (Mon Mar 07 2011 - 17:08:23 CST)
- Francesco Pietra (Mon Mar 07 2011 - 10:04:37 CST)
- Peter Freddolino (Mon Mar 07 2011 - 09:19:20 CST)
- Francesco Pietra (Mon Mar 07 2011 - 00:12:54 CST)
- Giacomo Fiorin (Sun Mar 06 2011 - 22:57:04 CST)
- Francesco Pietra (Sun Mar 06 2011 - 14:05:47 CST)
hBond component in colvars and patching
- Francesco Pietra (Sat Mar 05 2011 - 14:38:45 CST)
hbonds colvar component
- Giacomo Fiorin (Thu May 24 2012 - 10:12:51 CDT)
- Vlad Cojocaru (Thu May 24 2012 - 09:47:45 CDT)
- Giacomo Fiorin (Thu May 24 2012 - 08:58:04 CDT)
- Vlad Cojocaru (Thu May 24 2012 - 02:13:29 CDT)
heat annealing conf file
- Molecular Dynamics (Fri Jun 03 2011 - 09:57:07 CDT)
- Ada Zhan (Thu Jun 02 2011 - 14:02:06 CDT)
- Molecular Dynamics (Thu Jun 02 2011 - 05:26:17 CDT)
Heating /Equilibration
- Axel Kohlmeyer (Fri Aug 26 2011 - 08:16:29 CDT)
- Babban Mia (Fri Aug 26 2011 - 05:20:23 CDT)
- Babban Mia (Wed Aug 24 2011 - 02:56:37 CDT)
Heating in NAMD
- Babban Mia (Sun Aug 21 2011 - 06:06:25 CDT)
- Babban Mia (Sat Aug 20 2011 - 05:37:53 CDT)
- Erik Nordgren (Fri Aug 19 2011 - 12:52:31 CDT)
- Babban Mia (Thu Aug 18 2011 - 10:13:08 CDT)
Heating in NPT
- Pellegrini Eric (Mon Sep 19 2011 - 07:44:04 CDT)
Hello
- imran.1.618_at_gmail.com (Sat Oct 15 2011 - 00:32:59 CDT)
- murffyp_at_gmail.com (Tue Jun 21 2011 - 07:54:59 CDT)
Help building a desktop for namd
- Axel Kohlmeyer (Thu Apr 14 2011 - 08:37:20 CDT)
- Jeffrey Potoff (Thu Apr 14 2011 - 00:07:16 CDT)
- Axel Kohlmeyer (Wed Apr 13 2011 - 17:22:03 CDT)
- Gianluca Interlandi (Wed Apr 13 2011 - 17:06:53 CDT)
- Salvador H-V (Wed Apr 13 2011 - 11:34:18 CDT)
- Jim Phillips (Wed Apr 13 2011 - 10:17:27 CDT)
- Axel Kohlmeyer (Mon Apr 11 2011 - 16:34:22 CDT)
- Gianluca Interlandi (Mon Apr 11 2011 - 16:25:26 CDT)
- Gianluca Interlandi (Mon Apr 11 2011 - 16:21:27 CDT)
- Axel Kohlmeyer (Mon Apr 11 2011 - 15:06:33 CDT)
- Gianluca Interlandi (Mon Apr 11 2011 - 14:41:28 CDT)
- Axel Kohlmeyer (Mon Apr 11 2011 - 12:55:34 CDT)
- Salvador H-V (Mon Apr 11 2011 - 12:22:01 CDT)
- Axel Kohlmeyer (Sun Apr 10 2011 - 12:52:59 CDT)
- Salvador H-V (Sun Apr 10 2011 - 12:40:05 CDT)
help in a FEP restart?
- Chris Chipot (Sat Nov 26 2011 - 10:51:57 CST)
- Bruno Luís Pinto de Oliveira (Sat Nov 26 2011 - 10:15:13 CST)
Help in FEP backward/reverse calculation
- Jérôme Hénin (Fri Sep 23 2011 - 03:22:52 CDT)
- Bruno Luís Pinto de Oliveira (Thu Sep 22 2011 - 14:36:38 CDT)
help in FEP calculations : analysis/confirmation of results
- Bruno Luís Pinto de Oliveira (Thu Sep 08 2011 - 13:59:23 CDT)
help in FEP calculations_binding free energy difference between 2 inhibitors
- Chirag Vora (Mon Sep 05 2011 - 16:36:04 CDT)
- Bruno Luís Pinto de Oliveira (Mon Sep 05 2011 - 13:08:58 CDT)
- Bruno Luís Pinto de Oliveira (Thu Sep 01 2011 - 10:04:41 CDT)
Help in reverse Free Energy perturbation - hysteresis
- Chris Chipot (Wed Oct 05 2011 - 01:10:24 CDT)
- Bruno Luís Pinto de Oliveira (Tue Oct 04 2011 - 14:29:34 CDT)
- Chris Chipot (Mon Oct 03 2011 - 07:05:16 CDT)
- Jérôme Hénin (Mon Oct 03 2011 - 06:49:46 CDT)
- Bruno Luís Pinto de Oliveira (Mon Oct 03 2011 - 05:24:58 CDT)
help needed
- harish vashisth (Tue Mar 01 2011 - 10:00:46 CST)
- Richard Wood (Tue Mar 01 2011 - 09:25:51 CST)
help on building PATCH
- Matteo Pappalardo (Fri Jun 08 2012 - 03:15:53 CDT)
Help required for nanoscale simulation
- amit banerjee (Wed Jul 13 2011 - 03:03:45 CDT)
Help With colvars/abf Please
- Angelo Rossi (Sun Jan 30 2011 - 11:00:38 CST)
- Jérôme Hénin (Sun Jan 30 2011 - 09:10:50 CST)
- Angelo Rossi (Sun Jan 30 2011 - 07:09:41 CST)
help with how pbc are defined.
- David Hardy (Thu Oct 11 2012 - 13:34:10 CDT)
- Martin, Erik W (Thu Oct 11 2012 - 12:48:27 CDT)
help with how pbc are defined.. .
- David Hardy (Fri Oct 12 2012 - 12:16:14 CDT)
- Martin, Erik W (Fri Oct 12 2012 - 09:39:34 CDT)
HEME and Cystein instead of His
- Bruno Luís Pinto de Oliveira (Wed Nov 23 2011 - 14:33:39 CST)
- Raul Araya (Wed Nov 23 2011 - 14:25:37 CST)
- Aron Broom (Wed Nov 23 2011 - 14:02:42 CST)
- Raul Araya (Wed Nov 23 2011 - 13:10:36 CST)
HETATM vs ATOM in .pdb file
- Bjoern Olausson (Wed Aug 31 2011 - 06:20:55 CDT)
- Axel Kohlmeyer (Wed Aug 31 2011 - 06:16:16 CDT)
- Andrea Holfelder (Wed Aug 31 2011 - 04:56:35 CDT)
hi
- Sándor Kovács (Thu Jul 14 2011 - 14:19:52 CDT)
- kanchi subbarao rao (Thu Jul 14 2011 - 12:31:06 CDT)
- kanchi subbarao rao (Wed Jul 13 2011 - 13:47:30 CDT)
- murffyp_at_gmail.com (Sun May 22 2011 - 23:14:11 CDT)
- Bjoern Olausson (Thu May 19 2011 - 04:29:14 CDT)
- Jim Phillips (Wed May 18 2011 - 17:52:49 CDT)
- Giacomo Fiorin (Wed May 18 2011 - 10:28:48 CDT)
- kanchi subbarao rao (Wed May 18 2011 - 03:43:25 CDT)
hi all
- Ajasja LjubetiÄ (Thu Jun 16 2011 - 07:29:53 CDT)
- kanchi subbarao rao (Wed Jun 15 2011 - 04:14:04 CDT)
Hi, I am a new user of Namd, and I met some problems using increment of temperature during simulation
- Ye Yang (Fri Feb 25 2011 - 13:40:43 CST)
Hi: some doubt about nvt and npt equilibration
- johan strumpfer (Sun Jul 03 2011 - 20:53:47 CDT)
- bharat gupta (Sun Jul 03 2011 - 20:36:19 CDT)
Hints for building namd2.8 on charm++ ibverbs layer?
- Bennion, Brian (Fri Sep 02 2011 - 18:06:15 CDT)
Hole
- Buddhadev Maiti (Fri May 04 2012 - 22:47:27 CDT)
how can i demonstrate that a chain-like molecule within a membrane.
- Chris Chipot (Wed Feb 15 2012 - 07:27:44 CST)
- superdirac (Wed Feb 15 2012 - 07:19:36 CST)
How can I write a log file on my cluster?
- äÍÉÔÒÉÊ âÅÇÏ×ÁÔÏ× (Mon Oct 22 2012 - 01:39:58 CDT)
how do I pass environmental variables to namd on BlueGene/P?
- Aaron Oakley (Thu Aug 02 2012 - 23:39:06 CDT)
how does namd handle violations of the minimum image convention?
- Boyang Wang (Tue Jan 10 2012 - 21:45:04 CST)
- Ana Celia Vila Verde (Mon Jan 09 2012 - 05:32:32 CST)
How does NAMD treat a bond across periodic boundaries
- Axel Kohlmeyer (Thu Jul 12 2012 - 01:56:00 CDT)
- mj_aghaei_at_aut.ac.ir (Wed Jul 11 2012 - 23:17:49 CDT)
how obtain .xst form .dcd file?
- Erik Santiso (Wed Mar 23 2011 - 17:24:16 CDT)
- Ajasja LjubetiÄ (Wed Mar 23 2011 - 14:11:27 CDT)
- wood irene (Wed Mar 23 2011 - 12:59:01 CDT)
- wood irene (Mon Mar 21 2011 - 09:25:47 CDT)
how to apply different temperature simultaneously to different atoms in the same system
- charlie (Wed Apr 27 2011 - 02:41:08 CDT)
How to calculate Binding Free energy in NAMD
- Chris Chipot (Sat Jun 18 2011 - 07:51:20 CDT)
- jnsong (Sat Jun 18 2011 - 01:00:49 CDT)
how to calculate partial charge for ligand based on CHARMM principle?
- Jeffrey Potoff (Thu Jul 21 2011 - 12:02:49 CDT)
- AB (Thu Jul 21 2011 - 11:49:39 CDT)
How to calculate surface tension properly
- Bjoern Olausson (Wed Feb 08 2012 - 07:59:15 CST)
how to calculate the box size
- mjyang (Wed Mar 07 2012 - 01:27:17 CST)
- Cristhian Boetsch (Tue Mar 06 2012 - 10:48:30 CST)
- Chris Harrison (Tue Mar 06 2012 - 10:11:24 CST)
- Axel Kohlmeyer (Tue Mar 06 2012 - 09:55:42 CST)
- Chris Harrison (Tue Mar 06 2012 - 09:44:47 CST)
- Ajasja LjubetiÄ (Tue Mar 06 2012 - 09:32:43 CST)
- Chris Harrison (Tue Mar 06 2012 - 09:23:01 CST)
- JC Gumbart (Tue Mar 06 2012 - 09:00:14 CST)
- Axel Kohlmeyer (Tue Mar 06 2012 - 08:52:59 CST)
- Aron Broom (Tue Mar 06 2012 - 08:44:57 CST)
- mjyang (Tue Mar 06 2012 - 01:48:45 CST)
How to compute "only the GB Energy" using NAMD?
- jesmin jahan (Thu Dec 06 2012 - 07:44:43 CST)
- jesmin jahan (Wed Dec 05 2012 - 09:52:15 CST)
- David Minh (Wed Dec 05 2012 - 09:56:09 CST)
- jesmin jahan (Mon Dec 03 2012 - 20:34:02 CST)
how to convert X_PLOR to CHARMM?
- Lisa Brown (Fri Mar 25 2011 - 11:01:26 CDT)
How to create psf for graphene
- Axel Kohlmeyer (Sat Aug 04 2012 - 13:28:04 CDT)
- Monika Madhavi (Sat Aug 04 2012 - 01:04:24 CDT)
- Monika Madhavi (Fri Aug 03 2012 - 22:35:28 CDT)
How to decide whether an ABF curve has been converged?
- Aron Broom (Thu Nov 15 2012 - 14:52:48 CST)
- Jérôme Hénin (Thu Nov 15 2012 - 04:50:00 CST)
- dream (Thu Nov 15 2012 - 03:38:39 CST)
how to define the numsteps in ABF or metadynamics simulation?
- Jérôme Hénin (Sat Jul 16 2011 - 10:57:21 CDT)
- ÕÅÓÂ (Thu Jul 14 2011 - 19:48:32 CDT)
- Giacomo Fiorin (Tue Jul 12 2011 - 15:06:17 CDT)
- Clark Zhang (Wed Jul 06 2011 - 23:08:50 CDT)
how to edit restart.coor
- Victor Ovchinnikov (Wed Apr 04 2012 - 18:37:41 CDT)
- Victor Ovchinnikov (Wed Apr 04 2012 - 18:38:09 CDT)
- Aron Broom (Wed Apr 04 2012 - 18:26:43 CDT)
- Jiao, Dian NMN (-EXP) (Wed Apr 04 2012 - 17:56:38 CDT)
- Aron Broom (Wed Apr 04 2012 - 17:47:52 CDT)
- Jiao, Dian NMN (-EXP) (Wed Apr 04 2012 - 17:29:26 CDT)
How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system?
- Salvador H-V (Thu Aug 25 2011 - 11:12:49 CDT)
- Boyang Wang (Thu Aug 25 2011 - 02:32:01 CDT)
- å¼ å‹‡ (Thu Aug 25 2011 - 02:26:50 CDT)
- Boyang Wang (Thu Aug 25 2011 - 01:41:51 CDT)
- ÕÅÓÂ (Thu Aug 25 2011 - 01:32:33 CDT)
how to find cellorigin for periodic boundary condition
- Axel Kohlmeyer (Tue Dec 04 2012 - 10:37:47 CST)
- Maria Saeed (Tue Dec 04 2012 - 10:35:39 CST)
- Maria Saeed (Tue Dec 04 2012 - 10:34:09 CST)
how to generate psf for membrane+protein
- Jiao, Dian NMN (-EXP) (Mon Apr 09 2012 - 18:16:59 CDT)
how to generate transparent figures?
- Bjoern Olausson (Mon Jul 25 2011 - 04:04:58 CDT)
- Nicholas M Glykos (Sat Jul 23 2011 - 10:47:54 CDT)
- AB (Sat Jul 23 2011 - 09:59:07 CDT)
How to Get Bonded Pair Force Calculation with NAMD
- Ehsan Ban (Tue Mar 27 2012 - 09:01:04 CDT)
- Ehsan Ban (Mon Mar 26 2012 - 07:41:01 CDT)
how to get the energy in vacuum of a molecule in NAMD
- Jim Phillips (Wed Jul 20 2011 - 11:25:59 CDT)
- jnsong (Wed Jun 22 2011 - 08:36:40 CDT)
How to improve the GPU utility in NAMD
- Thomas Evangelidis (Tue Dec 25 2012 - 04:33:56 CST)
- Íõ¾ü (Tue Dec 25 2012 - 02:35:06 CST)
How to parameterize Protein ligand complex in membrane?
- Maria Saeed (Tue Dec 18 2012 - 00:04:08 CST)
- Maria Saeed (Mon Dec 17 2012 - 22:54:06 CST)
How to restraint pairinteractions
- Giacomo Fiorin (Fri Jun 01 2012 - 00:20:05 CDT)
- Family Xu (Thu May 31 2012 - 11:29:11 CDT)
- Giacomo Fiorin (Wed May 30 2012 - 17:15:03 CDT)
- sanxing.xu_at_gmail.com (Wed May 30 2012 - 17:01:20 CDT)
how to run NAMD-CUDA on multiple nodes
- Thomas Evangelidis (Wed Nov 28 2012 - 01:45:14 CST)
- Thomas Evangelidis (Tue Nov 27 2012 - 10:13:07 CST)
- Thomas Evangelidis (Tue Nov 27 2012 - 03:20:16 CST)
- Thomas Evangelidis (Mon Nov 26 2012 - 07:57:18 CST)
How to set protonation states of certain atom in DNA with namd/vmd
- raghav singh (Wed Mar 07 2012 - 07:15:55 CST)
How to set the right PME parameters for amber's prmtop and inpcrd files?
- a a (Wed Jan 26 2011 - 04:34:33 CST)
- a a (Wed Jan 26 2011 - 04:17:32 CST)
How to simulate a charged surface
- Yingzhe Liu (Wed Jun 22 2011 - 02:53:56 CDT)
- Yingzhe Liu (Thu Jun 23 2011 - 05:43:49 CDT)
how to solve such kind of crossterm parameter problem?
- Liqun Zhang (Tue Jun 12 2012 - 10:31:09 CDT)
- Liqun Zhang (Tue Jun 12 2012 - 10:28:09 CDT)
how to understand vdwForceSwitching
- Chris Harrison (Wed Feb 15 2012 - 15:50:33 CST)
- Liqun Zhang (Sat Feb 11 2012 - 17:09:48 CST)
how to use variables in colvar configuration file
- Jérôme Hénin (Fri Sep 23 2011 - 13:23:55 CDT)
- Ling Wu (Fri Sep 23 2011 - 12:26:08 CDT)
how to visualize an alchemical FEP transformation??
- Chris Harrison (Sat Oct 22 2011 - 12:48:16 CDT)
- Bruno Luís Pinto de Oliveira (Sat Oct 22 2011 - 12:31:01 CDT)
- Axel Kohlmeyer (Sat Oct 22 2011 - 11:33:47 CDT)
- Bruno Luís Pinto de Oliveira (Sat Oct 22 2011 - 09:58:42 CDT)
- Chris Harrison (Thu Oct 20 2011 - 18:02:32 CDT)
- Axel Kohlmeyer (Thu Oct 20 2011 - 16:42:02 CDT)
- Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 16:19:38 CDT)
- Chris Harrison (Thu Oct 20 2011 - 15:21:59 CDT)
- Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 15:10:28 CDT)
- Axel Kohlmeyer (Thu Oct 20 2011 - 14:02:59 CDT)
- Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 13:28:13 CDT)
- Axel Kohlmeyer (Thu Oct 20 2011 - 09:02:34 CDT)
- Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 06:27:47 CDT)
How to write a dcd in fortran?
- Axel Kohlmeyer (Mon Oct 03 2011 - 18:13:20 CDT)
- lam nguyen (Mon Oct 03 2011 - 18:03:37 CDT)
- Joshua D. Moore (Mon Oct 03 2011 - 15:56:57 CDT)
- Axel Kohlmeyer (Mon Oct 03 2011 - 14:13:03 CDT)
- lam nguyen (Mon Oct 03 2011 - 14:07:47 CDT)
- Axel Kohlmeyer (Mon Oct 03 2011 - 13:26:54 CDT)
- lam nguyen (Mon Oct 03 2011 - 13:21:36 CDT)
How to write gradual heating config files
- Cristina Rodríguez (Mon Feb 14 2011 - 19:08:07 CST)
how to write out the dcd file by vmd python command?
- mjyang (Mon Feb 21 2011 - 08:53:58 CST)
how to write the bond across the cell boundary
- Axel Kohlmeyer (Fri Mar 25 2011 - 08:17:05 CDT)
- Ajasja LjubetiÄ (Fri Mar 25 2011 - 03:44:41 CDT)
- Íõ—² (Fri Mar 25 2011 - 01:52:15 CDT)
html manual 2.8, ref 46 and some GBIS questions
- Branko (Sun Mar 20 2011 - 09:05:27 CDT)
Hybrid Monte Carlo?
- David Minh (Tue Oct 23 2012 - 09:58:26 CDT)
I M wants to share "legis_2011" with you
- Dropbox (Fri Jun 03 2011 - 15:20:24 CDT)
I need help with this
- Chris Harrison (Fri Feb 11 2011 - 12:08:56 CST)
- Chris Harrison (Fri Feb 11 2011 - 12:44:42 CST)
- Richard Wood (Fri Feb 11 2011 - 12:39:57 CST)
- Richard Wood (Fri Feb 11 2011 - 12:00:11 CST)
- Chris Harrison (Fri Feb 11 2011 - 11:42:41 CST)
- felmerino_at_uchile.cl (Fri Feb 11 2011 - 10:35:52 CST)
- Richard Wood (Fri Feb 11 2011 - 11:07:42 CST)
- Richard Wood (Fri Feb 11 2011 - 06:07:23 CST)
- Cruz-Chu Eduardo Roberto (Thu Feb 10 2011 - 02:51:43 CST)
- Richard Wood (Wed Feb 09 2011 - 13:01:25 CST)
IB fabrics
- Bennion, Brian (Fri Jan 06 2012 - 12:58:08 CST)
- Chris Harrison (Fri Jan 06 2012 - 12:52:21 CST)
- Bennion, Brian (Fri Jan 06 2012 - 12:39:04 CST)
- Axel Kohlmeyer (Fri Jan 06 2012 - 11:58:14 CST)
- Thomas Bishop (Fri Jan 06 2012 - 11:42:53 CST)
Ib version and nodelist
- Neelanjana Sengupta (Mon Aug 22 2011 - 00:36:09 CDT)
IBverbs charmrun problem
- Seren Soner (Tue Mar 08 2011 - 05:41:33 CST)
image centering problem
- ipsita basu (Thu Aug 11 2011 - 00:41:20 CDT)
implementing RBCG
- Peter Freddolino (Wed Mar 23 2011 - 20:19:09 CDT)
- Peter Freddolino (Tue Mar 22 2011 - 21:17:32 CDT)
- Chris Harrison (Tue Mar 22 2011 - 21:25:54 CDT)
- Michael Zimmermann (Tue Mar 22 2011 - 15:11:30 CDT)
Implicit solvent
- David Tanner (Mon Jun 27 2011 - 09:04:24 CDT)
- Massimiliano Porrini (Mon Jun 27 2011 - 06:35:00 CDT)
implicit solvent and cuda
- Jim Phillips (Tue May 10 2011 - 20:24:17 CDT)
- Francesco Oteri (Mon May 02 2011 - 16:03:15 CDT)
implicit solvent job error in NAMD2.8b1
- David Tanner (Tue Apr 05 2011 - 11:35:49 CDT)
- David Tanner (Mon Apr 04 2011 - 16:34:11 CDT)
- harish vashisth (Mon Apr 04 2011 - 17:14:20 CDT)
- harish vashisth (Mon Apr 04 2011 - 15:47:33 CDT)
Implicit solvent simulation
- Bjoern Olausson (Fri Jul 08 2011 - 05:57:03 CDT)
- jaya c.jose (Fri Jul 08 2011 - 05:35:40 CDT)
Importing a DCD into Mathematica
- Ajasja LjubetiÄ (Wed Apr 11 2012 - 11:37:56 CDT)
- Joshua Adelman (Wed Apr 11 2012 - 07:36:07 CDT)
- Ajasja LjubetiÄ (Wed Apr 11 2012 - 07:20:59 CDT)
- Axel Kohlmeyer (Tue Apr 10 2012 - 16:53:26 CDT)
- Ajasja LjubetiÄ (Tue Apr 10 2012 - 16:38:24 CDT)
- Branko (Tue Apr 10 2012 - 15:09:51 CDT)
- Ajasja LjubetiÄ (Tue Apr 10 2012 - 14:58:30 CDT)
improper angle
- JC Gumbart (Sat Nov 12 2011 - 01:14:09 CST)
- johan strumpfer (Fri Nov 11 2011 - 06:21:38 CST)
- Marco Sant (Fri Nov 11 2011 - 02:34:42 CST)
Impropers in Charmm and OPLS
- johan strumpfer (Tue Jun 14 2011 - 10:01:13 CDT)
- Henriette Elisabeth Autzen (Tue Jun 14 2011 - 08:33:58 CDT)
In-Residence Training at the Theoretical & Computational Biophysics Group, July 16-27, 2012
- TCBG Workshop (Tue Apr 24 2012 - 14:06:22 CDT)
Incompatibility between colvars and tclforces?
- Francesco Pietra (Wed Mar 30 2011 - 11:29:15 CDT)
- Giacomo Fiorin (Wed Mar 30 2011 - 11:20:08 CDT)
- Jérôme Hénin (Wed Mar 30 2011 - 10:23:45 CDT)
- Wang Yi (Wed Mar 30 2011 - 09:16:25 CDT)
- Francesco Pietra (Wed Mar 30 2011 - 09:06:13 CDT)
- Jérôme Hénin (Wed Mar 30 2011 - 06:23:42 CDT)
- Ajasja LjubetiÄ (Wed Mar 30 2011 - 06:21:23 CDT)
- Francesco Pietra (Wed Mar 30 2011 - 05:04:02 CDT)
incompatibility between NAMD and amber topology files
- Osman, Roman (Tue Jan 10 2012 - 15:33:43 CST)
- Osman, Roman (Mon Jan 09 2012 - 16:13:24 CST)
increasing MAX_EXCLUSIONS
- Francesco Oteri (Thu Jan 20 2011 - 09:56:35 CST)
- Axel Kohlmeyer (Wed Jan 19 2011 - 16:42:29 CST)
- Francesco Oteri (Wed Jan 19 2011 - 16:07:05 CST)
increment torsion restrain before minimization
- Axel Kohlmeyer (Mon Nov 05 2012 - 07:53:39 CST)
- Ajasja LjubetiÄ (Mon Nov 05 2012 - 07:35:19 CST)
- Tina Stokelj (Mon Nov 05 2012 - 07:16:59 CST)
- Tina Stokelj (Mon Nov 05 2012 - 06:38:32 CST)
- Tina Stokelj (Sat Nov 03 2012 - 09:59:43 CDT)
Infiniband and commodity hardware
- Axel Kohlmeyer (Sun Sep 18 2011 - 02:38:48 CDT)
- Thomas Albers (Sat Sep 17 2011 - 14:59:20 CDT)
Information about error compiling with CUDA
- Martin, Erik W (Fri Nov 09 2012 - 14:50:44 CST)
infrequent rattle failure with charmm36
- Edward Lyman (Wed Apr 20 2011 - 09:50:37 CDT)
- Markus K. Dahlgren (Wed Apr 20 2011 - 09:30:11 CDT)
- Edward Lyman (Wed Apr 20 2011 - 08:47:59 CDT)
initial structures for md simulations
- Jeffrey J. Potoff (Wed Feb 16 2011 - 09:02:13 CST)
- oguz gurbulak (Wed Feb 16 2011 - 07:52:26 CST)
- oguz gurbulak (Wed Feb 16 2011 - 06:22:11 CST)
Input configuration files for GPU version of NAMD
- Axel Kohlmeyer (Wed Nov 07 2012 - 13:03:22 CST)
- Ganesh Kamath (Wed Nov 07 2012 - 12:56:27 CST)
inputPrefix for ABF
- Giacomo Fiorin (Sun Oct 21 2012 - 13:43:52 CDT)
- Branko (Sat Oct 20 2012 - 16:36:16 CDT)
inputPrefix in ABF
- Branko (Thu Aug 16 2012 - 04:02:32 CDT)
- Jérôme Hénin (Thu Aug 16 2012 - 01:51:44 CDT)
- Branko (Tue Aug 14 2012 - 12:04:57 CDT)
Instabilities in Minimization
- Sándor Kovács (Tue Jul 17 2012 - 19:35:35 CDT)
- JC Gumbart (Tue Jul 17 2012 - 19:17:05 CDT)
- Sándor Kovács (Tue Jul 17 2012 - 18:36:32 CDT)
- JC Gumbart (Tue Jul 17 2012 - 17:50:58 CDT)
- Aron Broom (Tue Jul 17 2012 - 17:34:38 CDT)
- Sándor Kovács (Tue Jul 17 2012 - 17:14:10 CDT)
install NAMD 2.8 v
- Namd Namd (Mon Oct 10 2011 - 05:50:53 CDT)
Installing NAMD on a 64-bit linux (NVIDIA CUDA)
- Axel Kohlmeyer (Mon Jan 30 2012 - 12:24:40 CST)
- Shyno Mathew (Mon Jan 30 2012 - 12:15:15 CST)
installing namd on ibm cluster (powerpc)
- Chris Harrison (Fri Oct 28 2011 - 17:35:07 CDT)
- Gurunath Katagi (Fri Oct 28 2011 - 15:14:02 CDT)
Interfaces in NAMD
- Hasan haska (Sat Dec 17 2011 - 14:20:25 CST)
intergation algoritm of NAMD
- Namd Namd (Mon Oct 01 2012 - 03:52:30 CDT)
intermittent non-execution of NAMD on tesla
- P.-L. Chau (Mon Nov 21 2011 - 04:09:04 CST)
Internal Unit system
- Victor Ovchinnikov (Thu Mar 01 2012 - 15:16:00 CST)
- Niklaus Johner (Thu Mar 01 2012 - 14:52:24 CST)
- Ajasja LjubetiÄ (Thu Mar 01 2012 - 12:14:21 CST)
- Niklaus Johner (Thu Mar 01 2012 - 11:21:53 CST)
interpretation of timing data in output
- Jim Phillips (Wed Jul 20 2011 - 11:47:04 CDT)
- Hannes Loeffler (Fri Jun 24 2011 - 04:29:42 CDT)
Invitation to connect on LinkedIn
- Adebayo Adeleke via LinkedIn (Wed Oct 17 2012 - 03:28:28 CDT)
- Ahlam Al-Rawi (Thu Sep 15 2011 - 16:11:12 CDT)
ion placement method vs total energy of the system
- Anurag Sethi (Mon Apr 30 2012 - 10:36:59 CDT)
- raghav singh (Mon Apr 30 2012 - 10:25:42 CDT)
Iron Oxide and Arsenic
- Axel Kohlmeyer (Sat Jun 11 2011 - 17:53:28 CDT)
- felmerino_at_uchile.cl (Sat Jun 11 2011 - 17:48:57 CDT)
- Axel Kohlmeyer (Sat Jun 11 2011 - 17:38:21 CDT)
- Salvador H-V (Sat Jun 11 2011 - 17:25:25 CDT)
- Axel Kohlmeyer (Sat Jun 11 2011 - 17:16:06 CDT)
- Salvador H-V (Sat Jun 11 2011 - 17:09:20 CDT)
iron sulphur cluster parametrization
- francesco oteri (Thu Oct 13 2011 - 09:03:43 CDT)
- francesco oteri (Thu Oct 06 2011 - 09:24:31 CDT)
Is it possible to print out the force of one specific atom?
- Ehsan Ban (Wed Nov 23 2011 - 15:45:49 CST)
- Wenhao Liu (Wed Nov 23 2011 - 08:59:10 CST)
- Michelle Kuttel (Wed Nov 23 2011 - 08:45:22 CST)
- Wenhao Liu (Wed Nov 23 2011 - 08:29:23 CST)
is it possible to strip the restrain linearly?
- Jérôme Hénin (Mon Mar 19 2012 - 11:33:16 CDT)
- Albert (Mon Mar 19 2012 - 10:33:09 CDT)
- Axel Kohlmeyer (Mon Mar 19 2012 - 08:37:10 CDT)
- Albert (Mon Mar 19 2012 - 08:29:00 CDT)
Is the TMD equation in the user manual correct?
- Jérôme Hénin (Mon Oct 08 2012 - 07:10:57 CDT)
- JC Gumbart (Fri Oct 05 2012 - 15:47:39 CDT)
- Mert Gür (Fri Oct 05 2012 - 15:01:03 CDT)
- JC Gumbart (Fri Oct 05 2012 - 13:26:56 CDT)
- Mert Gür (Tue Oct 02 2012 - 12:43:00 CDT)
is there any difference between non-constrained equilibrium and normal MD production?
- AB (Mon Jul 25 2011 - 13:04:35 CDT)
Is there any difference between SMD and tclForces?
- Axel Kohlmeyer (Wed May 18 2011 - 20:34:13 CDT)
- Jun Zhang (Wed May 18 2011 - 20:29:07 CDT)
is zeroMomentum safe in a steered MD simulation?
- Jose Borreguero (Fri Mar 09 2012 - 09:08:41 CST)
issue with solute that splits
- Aron Broom (Fri Jun 01 2012 - 14:44:37 CDT)
- Felipe Merino (Fri Jun 01 2012 - 14:20:22 CDT)
- Massimiliano Porrini (Fri Jun 01 2012 - 13:52:45 CDT)
Issues with 'Gyration' in Colvars module
- Shaon Chakrabarti (Sat Jun 02 2012 - 14:29:52 CDT)
- Jérôme Hénin (Fri May 25 2012 - 13:20:49 CDT)
- Jérôme Hénin (Fri May 25 2012 - 11:08:58 CDT)
- Aron Broom (Thu May 24 2012 - 21:37:42 CDT)
- Shaon Chakrabarti (Thu May 24 2012 - 20:53:25 CDT)
- Giacomo Fiorin (Thu May 24 2012 - 09:01:09 CDT)
- Aron Broom (Wed May 23 2012 - 18:09:29 CDT)
- Shaon Chakrabarti (Wed May 23 2012 - 17:25:09 CDT)
- Shaon Chakrabarti (Wed May 23 2012 - 17:11:13 CDT)
- Giacomo Fiorin (Wed May 23 2012 - 15:27:51 CDT)
- Aron Broom (Wed May 23 2012 - 14:56:49 CDT)
- Shaon Chakrabarti (Wed May 23 2012 - 14:48:35 CDT)
Job scheduling (managing) software recommendation
- Ajasja LjubetiÄ (Wed Mar 09 2011 - 03:15:41 CST)
- Ajasja LjubetiÄ (Mon Mar 07 2011 - 15:13:48 CST)
- Axel Kohlmeyer (Mon Mar 07 2011 - 09:16:38 CST)
- Nicholas M Glykos (Mon Mar 07 2011 - 07:50:07 CST)
- Francesco Oteri (Mon Mar 07 2011 - 06:30:53 CST)
- Ajasja LjubetiÄ (Mon Mar 07 2011 - 05:36:42 CST)
job termination
- Chris Harrison (Fri Feb 11 2011 - 11:50:20 CST)
- ipsita basu (Fri Feb 11 2011 - 00:46:17 CST)
jobs failed
- Axel Kohlmeyer (Sat Mar 17 2012 - 14:52:17 CDT)
- Albert (Sat Mar 17 2012 - 14:33:19 CDT)
jobs with Intel i7
- Neelanjana Sengupta (Wed Jun 27 2012 - 07:33:09 CDT)
Joining PSF Files
- Axel Kohlmeyer (Tue May 24 2011 - 09:08:32 CDT)
- Jeffrey Potoff (Tue May 24 2011 - 09:04:53 CDT)
- PAUL NEWMAN (Tue May 24 2011 - 09:04:24 CDT)
- Axel Kohlmeyer (Tue May 24 2011 - 09:00:57 CDT)
- PAUL NEWMAN (Tue May 24 2011 - 08:58:24 CDT)
Keep PBC box size in Z-direction constant?
- Bjoern Olausson (Wed Feb 22 2012 - 03:36:42 CST)
- Bjoern Olausson (Mon Feb 20 2012 - 06:37:05 CST)
keeping a protein in a solvation box
- Dr. Eddie (Wed Jun 13 2012 - 16:39:29 CDT)
- Eduard Schreiner (Tue Jun 12 2012 - 18:19:11 CDT)
- Aron Broom (Wed Jun 13 2012 - 10:26:14 CDT)
- Aaron Oakley (Tue Jun 12 2012 - 22:26:52 CDT)
- Axel Kohlmeyer (Tue Jun 12 2012 - 22:16:30 CDT)
- Dr. Eddie (Tue Jun 12 2012 - 22:03:43 CDT)
- Giacomo Fiorin (Tue Jun 12 2012 - 18:52:05 CDT)
- Giacomo Fiorin (Tue Jun 12 2012 - 18:50:17 CDT)
- Aaron Oakley (Tue Jun 12 2012 - 18:45:19 CDT)
- Dr. Eddie (Tue Jun 12 2012 - 17:44:26 CDT)
Keeping rigidBonds during Minimization
- Jérôme Hénin (Mon Sep 12 2011 - 18:09:58 CDT)
- David Huggins (Mon Sep 12 2011 - 12:20:28 CDT)
- David Huggins (Wed Aug 31 2011 - 19:05:05 CDT)
Keeping water out of the binding pocket with ColVar
- JC Gumbart (Fri Jul 20 2012 - 23:44:19 CDT)
- Wang Yi (Fri Jul 20 2012 - 20:21:30 CDT)
- Aron Broom (Fri Jul 20 2012 - 20:19:09 CDT)
- Wang Yi (Fri Jul 20 2012 - 20:14:41 CDT)
Keyword "lower" not supported...colvars
- Chris Harrison (Sat Mar 12 2011 - 20:52:30 CST)
- Axel Kohlmeyer (Sat Mar 12 2011 - 16:02:38 CST)
- Francesco Pietra (Sat Mar 12 2011 - 11:16:19 CST)
Langevin Buffer Region
- David Huggins (Wed Feb 16 2011 - 04:19:51 CST)
laptop GPU support
- Axel Kohlmeyer (Wed Aug 01 2012 - 06:23:32 CDT)
- Thomas Evangelidis (Wed Aug 01 2012 - 05:27:58 CDT)
large load rate using implicit solvent
- charlie (Sun May 08 2011 - 20:45:10 CDT)
last frame and restart are different
- Francesco Oteri (Thu May 19 2011 - 15:50:06 CDT)
- Jim Phillips (Thu May 19 2011 - 14:02:25 CDT)
- Francesco Oteri (Thu May 19 2011 - 11:12:22 CDT)
LCPO SASA Calculation on the GPU
- Aron Broom (Wed Aug 01 2012 - 22:44:09 CDT)
Lenard Jones coefficients for Neon atoms
- Roy Fernando (Mon Jul 23 2012 - 08:53:39 CDT)
lengthening time-step with constraints causes RMSD "jump"
- P.-L. Chau (Thu Jun 02 2011 - 16:03:53 CDT)
- Jim Phillips (Thu Jun 02 2011 - 15:36:33 CDT)
- P.-L. Chau (Thu Jun 02 2011 - 11:23:34 CDT)
- Jim Phillips (Thu Jun 02 2011 - 11:11:28 CDT)
- P.-L. Chau (Thu Jun 02 2011 - 06:53:05 CDT)
libcudart.so.4 error
- Thomas Evangelidis (Thu Nov 22 2012 - 15:33:10 CST)
- Aron Broom (Thu Nov 22 2012 - 15:17:45 CST)
- flavio seixas (Thu Nov 22 2012 - 14:26:30 CST)
- flavio seixas (Thu Nov 22 2012 - 13:57:53 CST)
- Thomas Evangelidis (Thu Nov 22 2012 - 13:50:18 CST)
- Aron Broom (Thu Nov 22 2012 - 13:25:23 CST)
- flavio seixas (Thu Nov 22 2012 - 12:42:57 CST)
Line minimizerfailure because of IMPR?
- Francesco Pietra (Thu Apr 05 2012 - 03:57:03 CDT)
- Francesco Pietra (Wed Apr 04 2012 - 10:01:45 CDT)
Lingand Unbinding using SMD
- Jian Liu (Mon Aug 15 2011 - 03:28:37 CDT)
- Jacopo Sgrignani (Mon Aug 15 2011 - 02:19:17 CDT)
Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue?
- Tru Huynh (Wed Mar 28 2012 - 09:48:15 CDT)
- Tru Huynh (Wed Mar 28 2012 - 09:10:26 CDT)
- Tru Huynh (Sat Mar 24 2012 - 18:03:28 CDT)
- Tru Huynh (Thu Mar 22 2012 - 14:28:54 CDT)
- Tru Huynh (Tue Mar 20 2012 - 08:32:49 CDT)
- Tru Huynh (Mon Mar 19 2012 - 18:31:40 CDT)
Lipid as residues topology
- Branko (Tue Nov 01 2011 - 05:59:43 CDT)
- Jens K. Munk (Tue Nov 01 2011 - 05:35:37 CDT)
Lipid bilayer equilibration: Periodic cell has become too small for original patch grid!
- Bjoern Olausson (Wed Aug 10 2011 - 02:49:01 CDT)
- Jeffrey Potoff (Mon Aug 08 2011 - 21:12:39 CDT)
- flavio seixas (Mon Aug 08 2011 - 21:12:24 CDT)
- Andres Morales N (Mon Aug 08 2011 - 17:20:56 CDT)
- Bjoern Olausson (Mon Aug 08 2011 - 02:57:08 CDT)
- Andres Morales N (Sun Aug 07 2011 - 21:00:38 CDT)
Logfile flooded with "The last position output [...]" when IMDon is used.
- Bjoern Olausson (Tue Aug 23 2011 - 04:32:47 CDT)
lookup tables
- Thomas Brian (Wed Jun 20 2012 - 23:17:11 CDT)
loop-to-helix change during SMD
- yp sun (Mon Dec 31 2012 - 05:17:53 CST)
Low CPU usage with NAMD running on linux cluster
- Aron Broom (Mon Jul 30 2012 - 18:14:44 CDT)
- amin_at_imtech.res.in (Sun Jul 29 2012 - 00:09:49 CDT)
- Jeffrey Potoff (Sat Jul 28 2012 - 21:05:53 CDT)
- Branko (Sat Jul 28 2012 - 10:29:03 CDT)
- amin_at_imtech.res.in (Sat Jul 28 2012 - 10:10:02 CDT)
- Branko (Sat Jul 28 2012 - 07:52:17 CDT)
- amin_at_imtech.res.in (Sat Jul 28 2012 - 01:33:17 CDT)
low dielectric constants in GBIS
- Branko (Tue Aug 16 2011 - 15:41:04 CDT)
Low global exclusion count
- matziast_at_med.uth.gr (Tue Nov 08 2011 - 04:23:47 CST)
- Austin B. Yongye (Tue Jul 12 2011 - 15:08:51 CDT)
Low global exclusion count errors
- Jim Phillips (Mon Jul 18 2011 - 17:00:02 CDT)
- Austin B. Yongye (Wed Jul 13 2011 - 13:10:10 CDT)
mainboard-power source for GPU
- Axel Kohlmeyer (Tue Jan 25 2011 - 06:36:57 CST)
- Francesco Pietra (Tue Jan 25 2011 - 01:47:42 CST)
making force grids
- Thomas Brian (Fri Jun 22 2012 - 15:37:14 CDT)
- Thomas Brian (Wed Jun 20 2012 - 23:08:24 CDT)
- Thomas Brian (Wed Jun 13 2012 - 18:36:00 CDT)
malloc memory error using CUDA devices
- Blake Mertz (Wed Oct 31 2012 - 07:25:11 CDT)
Margin Value in NAMD
- johan strumpfer (Thu Sep 01 2011 - 00:35:30 CDT)
- Andrea Holfelder (Thu Sep 01 2011 - 03:09:09 CDT)
- Andrea Holfelder (Wed Aug 31 2011 - 23:57:36 CDT)
- johan strumpfer (Wed Aug 31 2011 - 22:56:39 CDT)
- Andrea Holfelder (Wed Aug 31 2011 - 21:42:05 CDT)
martini force field
- Chris Harrison (Wed Feb 15 2012 - 15:09:45 CST)
- Chris Harrison (Wed Feb 15 2012 - 15:02:28 CST)
- Swarna M Patra (Tue Feb 14 2012 - 21:41:19 CST)
Martini parameter files
- Chiara Cosenza unina (Thu Apr 26 2012 - 04:45:18 CDT)
MARTINI parameters and Bead definitions
- Edroaldo Lummertz da Rocha (Fri Jun 03 2011 - 18:56:49 CDT)
max number of CPU PEs per GPU?
- Jim Phillips (Sat Jun 11 2011 - 14:12:35 CDT)
- Danny Xu (Sat Jun 11 2011 - 00:49:10 CDT)
- Danny Xu (Fri Jun 10 2011 - 22:34:34 CDT)
- Jim Phillips (Fri Jun 10 2011 - 15:15:19 CDT)
- Ajasja LjubetiÄ (Fri Jun 10 2011 - 15:17:43 CDT)
- Danny Xu (Fri Jun 10 2011 - 11:20:13 CDT)
- Ajasja LjubetiÄ (Fri Jun 10 2011 - 06:50:44 CDT)
- Danny Xu (Fri Jun 10 2011 - 01:17:53 CDT)
maximum number of atoms per patch
- JC Gumbart (Sun Feb 27 2011 - 12:34:36 CST)
- Branko (Sun Feb 27 2011 - 12:21:56 CST)
MD condition
- hamze rahimi (Sun Aug 14 2011 - 05:02:36 CDT)
mdff energy calculation
- snoze pa (Mon Apr 02 2012 - 10:56:28 CDT)
mdff error
- Hamze Rahimi (Mon Jun 18 2012 - 09:41:08 CDT)
MDFF for huge trajectories
- Samuel Flores (Wed May 16 2012 - 17:20:29 CDT)
- Samuel Flores (Wed May 16 2012 - 17:54:56 CDT)
- Ajasja LjubetiÄ (Wed May 16 2012 - 16:36:41 CDT)
- Samuel Flores (Wed May 16 2012 - 14:31:53 CDT)
MDFF for protein complex
- Hamze Rahimi (Mon May 14 2012 - 09:22:42 CDT)
mean square displacement
- Axel Kohlmeyer (Mon Sep 05 2011 - 08:42:03 CDT)
- Ajasja LjubetiÄ (Mon Sep 05 2011 - 08:22:55 CDT)
- Molecular Dynamics (Mon Sep 05 2011 - 08:15:28 CDT)
membrane equilibration
- Ajasja LjubetiÄ (Fri Mar 04 2011 - 05:09:19 CST)
- Axel Kohlmeyer (Thu Mar 03 2011 - 20:42:59 CST)
- Jeffrey Potoff (Thu Mar 03 2011 - 19:58:11 CST)
- jeremy adler (Thu Mar 03 2011 - 18:30:46 CST)
- Chris Harrison (Thu Mar 03 2011 - 18:10:06 CST)
- jeremy adler (Thu Mar 03 2011 - 17:03:18 CST)
- Axel Kohlmeyer (Thu Mar 03 2011 - 13:43:48 CST)
- jeremy adler (Thu Mar 03 2011 - 13:02:57 CST)
membrane GPCR-ligands simulations
- Aron Broom (Fri Jun 08 2012 - 21:10:04 CDT)
- Axel Kohlmeyer (Fri Jun 08 2012 - 20:58:52 CDT)
- jose correa (Fri Jun 08 2012 - 20:23:46 CDT)
membrane moving up in simulation box
- Marcos Sotomayor (Mon Oct 17 2011 - 01:58:17 CDT)
- kanchi subbarao rao (Mon Oct 17 2011 - 01:09:17 CDT)
- kanchi subbarao rao (Thu Oct 13 2011 - 01:54:32 CDT)
Membrane protein simulaton
- Eduard Schreiner (Fri Jan 14 2011 - 19:08:43 CST)
- snoze pa (Fri Jan 14 2011 - 18:19:24 CST)
membrane simulation and mobility of lipids - blocking ion channel
- HAMID - (Thu Sep 29 2011 - 04:57:10 CDT)
- HAMID - (Thu Sep 29 2011 - 04:33:48 CDT)
- Jorgen Simonsen (Wed Sep 28 2011 - 09:07:50 CDT)
membrane simulation at high Temp
- Axel Kohlmeyer (Fri Nov 04 2011 - 19:08:22 CDT)
- Chris Harrison (Fri Nov 04 2011 - 19:01:07 CDT)
- Chris Harrison (Fri Nov 04 2011 - 18:58:11 CDT)
- Jiao, Dian NMN (-EXP) (Fri Nov 04 2011 - 17:38:56 CDT)
- Giacomo Fiorin (Fri Nov 04 2011 - 16:56:12 CDT)
- Jiao, Dian NMN (-EXP) (Fri Nov 04 2011 - 16:50:20 CDT)
membrane simulation Constraint failure in RATTLE algorithm
- snoze pa (Thu Feb 17 2011 - 10:00:44 CST)
- Jeffrey Potoff (Wed Feb 16 2011 - 22:18:57 CST)
- snoze pa (Wed Feb 16 2011 - 17:51:32 CST)
- Jeffrey Potoff (Wed Feb 16 2011 - 14:58:38 CST)
- snoze pa (Wed Feb 16 2011 - 14:43:06 CST)
- snoze pa (Wed Feb 16 2011 - 12:15:11 CST)
membrane simulation ERROR rattle algorithm
- snoze pa (Wed Jul 06 2011 - 10:06:03 CDT)
- Ajasja LjubetiÄ (Wed Jul 06 2011 - 06:37:10 CDT)
- Salvatore Mario Cosseddu (Wed Jul 06 2011 - 06:15:46 CDT)
- Jorgen Simonsen (Wed Jul 06 2011 - 03:36:22 CDT)
- Ajasja LjubetiÄ (Tue Jul 05 2011 - 13:40:44 CDT)
- Axel Kohlmeyer (Tue Jul 05 2011 - 13:05:18 CDT)
- Ajasja LjubetiÄ (Tue Jul 05 2011 - 12:54:40 CDT)
- Jorgen Simonsen (Tue Jul 05 2011 - 12:41:49 CDT)
- Ajasja LjubetiÄ (Tue Jul 05 2011 - 12:01:53 CDT)
- sajad falsafi (Tue Jul 05 2011 - 11:44:10 CDT)
- Jorgen Simonsen (Tue Jul 05 2011 - 10:13:57 CDT)
Membrane simulation, Box X,Y enlarge, Z shrink and membrane thickness shrink
- juan du (Tue Jun 07 2011 - 18:27:25 CDT)
membrane system
- Bjoern Olausson (Thu Sep 22 2011 - 03:10:00 CDT)
- Bjoern Olausson (Wed Sep 21 2011 - 05:02:08 CDT)
- Jérôme Hénin (Wed Sep 21 2011 - 03:47:16 CDT)
- Jérôme Hénin (Wed Sep 21 2011 - 02:44:42 CDT)
- ipsita basu (Wed Sep 21 2011 - 01:30:00 CDT)
Membranes
- Erik Nordgren (Thu Jul 21 2011 - 20:54:46 CDT)
- Andres Morales N (Tue Jul 19 2011 - 15:46:54 CDT)
Memory leak and crash before first step
- Jim Phillips (Mon Jul 18 2011 - 16:26:38 CDT)
- Pedro Gonnet (Tue Jul 12 2011 - 15:00:45 CDT)
- Erik Nordgren (Sun Jul 10 2011 - 04:02:05 CDT)
- Pedro Gonnet (Tue Jul 05 2011 - 08:25:34 CDT)
- Pedro Gonnet (Fri Jun 24 2011 - 14:28:08 CDT)
Memory leak patch
- Andy Somogyi (Tue Aug 23 2011 - 09:20:09 CDT)
memory-optimized version binary coordinates?
- Carlos Sosa (Mon Jun 25 2012 - 15:06:19 CDT)
- Aron Broom (Sun Jun 17 2012 - 11:34:48 CDT)
- Carlos Sosa (Sun Jun 17 2012 - 11:24:50 CDT)
- Aron Broom (Sun Jun 17 2012 - 11:10:31 CDT)
- Carlos Sosa (Sun Jun 17 2012 - 10:20:38 CDT)
- Aron Broom (Sat Jun 16 2012 - 21:22:29 CDT)
- Carlos Sosa (Sat Jun 16 2012 - 19:33:36 CDT)
- Aron Broom (Fri Jun 15 2012 - 16:18:22 CDT)
- Carlos Sosa (Fri Jun 15 2012 - 15:43:58 CDT)
merge pdb/psf files by psfgen - sets coordinates to zero
- Chris Harrison (Fri Sep 07 2012 - 13:57:32 CDT)
- Jacqueline Schmidt (Fri Sep 07 2012 - 13:44:49 CDT)
Metadynamics and Colvar Width
- Aron Broom (Mon Oct 29 2012 - 12:53:22 CDT)
- Marc Gordon (Mon Oct 29 2012 - 09:19:45 CDT)
metadynamics combined with PCV
- Anurag Sethi (Fri Jun 03 2011 - 14:11:54 CDT)
- Giacomo Fiorin (Fri Jun 03 2011 - 12:28:53 CDT)
- Anurag Sethi (Fri Jun 03 2011 - 12:14:18 CDT)
MetaDynamics in 2.9b2 Question
- Giacomo Fiorin (Fri Nov 09 2012 - 11:38:10 CST)
- Aron Broom (Fri Nov 09 2012 - 11:32:53 CST)
- Robert Elder (Fri Nov 09 2012 - 11:17:41 CST)
- Aron Broom (Wed Apr 04 2012 - 20:24:56 CDT)
- Giacomo Fiorin (Wed Apr 04 2012 - 19:32:41 CDT)
- Aron Broom (Wed Apr 04 2012 - 14:54:39 CDT)
Metadynamics Problems
- Aron Broom (Mon Mar 12 2012 - 16:30:16 CDT)
- Giacomo Fiorin (Thu Mar 08 2012 - 13:15:33 CST)
- Aron Broom (Wed Mar 07 2012 - 23:59:28 CST)
- Giacomo Fiorin (Wed Mar 07 2012 - 18:02:59 CST)
- Aron Broom (Wed Mar 07 2012 - 17:29:38 CST)
- Axel Kohlmeyer (Wed Mar 07 2012 - 17:22:46 CST)
- Aron Broom (Wed Mar 07 2012 - 17:13:23 CST)
metadynamics/ABF simulations using collective variables - issues with restarting the calculations
- Giacomo Fiorin (Wed Nov 14 2012 - 18:26:29 CST)
- Marimuthu Krishnan (Wed Nov 14 2012 - 18:22:48 CST)
- Giacomo Fiorin (Tue Nov 13 2012 - 14:11:05 CST)
- Aron Broom (Tue Nov 13 2012 - 13:58:29 CST)
- Marimuthu Krishnan (Tue Nov 13 2012 - 13:47:41 CST)
- Marimuthu Krishnan (Tue Nov 13 2012 - 13:22:57 CST)
- Aron Broom (Tue Nov 13 2012 - 10:47:52 CST)
- Jérôme Hénin (Tue Nov 13 2012 - 10:21:19 CST)
- Marimuthu Krishnan (Tue Nov 13 2012 - 08:42:43 CST)
Methanol - Autocorrelation of total dipole moment
- Chathurika Abeyrathne (Sat Jun 25 2011 - 03:36:06 CDT)
Minimisation algorithm
- Jim Phillips (Sun May 22 2011 - 14:49:16 CDT)
- Christian Jorgensen (Thu May 19 2011 - 18:31:03 CDT)
minimization and gradient trend
- Francesco Pietra (Mon Oct 31 2011 - 03:57:10 CDT)
minimization and water bubbles
- Axel Kohlmeyer (Thu Jun 14 2012 - 21:49:40 CDT)
- Dr. Eddie (Thu Jun 14 2012 - 21:33:27 CDT)
Minimization doesn't stop when converged
- Boyang Wang (Sat Oct 08 2011 - 01:25:24 CDT)
- Jérôme Hénin (Fri Oct 07 2011 - 05:27:13 CDT)
- Boyang Wang (Fri Oct 07 2011 - 03:56:01 CDT)
- Norman Geist (Fri Oct 07 2011 - 03:48:36 CDT)
Minimization is taking a lot of computing time.
- JC Gumbart (Wed Aug 10 2011 - 00:52:16 CDT)
- Branko (Tue Aug 09 2011 - 12:42:17 CDT)
- Kartheek (Tue Aug 09 2011 - 06:06:57 CDT)
- Kartheek (Fri Aug 05 2011 - 04:53:42 CDT)
minimization problem
- Narasimhan LOGANATHAN (Tue Aug 09 2011 - 08:21:37 CDT)
- Jeffrey Potoff (Tue Aug 09 2011 - 07:16:08 CDT)
- Narasimhan LOGANATHAN (Tue Aug 09 2011 - 07:00:28 CDT)
minimization, slow heating and then Langevin free runs
- Rajan Vatassery (Fri Dec 14 2012 - 13:38:02 CST)
- Dr. Eddie (Mon Dec 10 2012 - 15:00:56 CST)
- Rajan Vatassery (Mon Dec 10 2012 - 13:33:08 CST)
- Dr. Eddie (Mon Dec 10 2012 - 12:20:07 CST)
- Rajan Vatassery (Mon Dec 10 2012 - 11:00:40 CST)
- Dr. Eddie (Mon Dec 10 2012 - 09:08:05 CST)
- Rajan Vatassery (Sun Dec 09 2012 - 17:02:10 CST)
- Dr. Eddie (Sun Dec 09 2012 - 10:16:21 CST)
Mirror Image Energy Discrepency
- Jérôme Hénin (Thu Feb 10 2011 - 13:01:33 CST)
- Richard Wood (Wed Feb 09 2011 - 16:42:18 CST)
- Jérôme Hénin (Wed Feb 09 2011 - 14:40:06 CST)
- Keith Battle (Wed Feb 09 2011 - 13:23:28 CST)
Missing angle parameters in the ffTK
- Mayne, Christopher G (Fri Mar 09 2012 - 09:17:06 CST)
- ¼¿ëÀÏ (Fri Mar 09 2012 - 01:38:08 CST)
Missing angle parameters NH1 CT1 NH1
- Jérôme Hénin (Fri Jan 21 2011 - 11:01:56 CST)
- Christian Jorgensen (Fri Jan 21 2011 - 12:01:09 CST)
- Jérôme Hénin (Fri Jan 21 2011 - 06:44:14 CST)
- Christian Jorgensen (Fri Jan 21 2011 - 04:39:07 CST)
Mixed TIP3/TIP4 Waters
- Jernej Zidar (Thu Aug 11 2011 - 07:28:29 CDT)
- Keith Battle (Thu Aug 11 2011 - 06:29:18 CDT)
MMTools
- Boyang Wang (Thu Aug 18 2011 - 00:15:02 CDT)
- Chathurika Abeyrathne (Wed Aug 17 2011 - 21:07:21 CDT)
- Axel Kohlmeyer (Wed Aug 17 2011 - 20:28:28 CDT)
- Chathurika Abeyrathne (Wed Aug 17 2011 - 19:02:46 CDT)
- Axel Kohlmeyer (Wed Aug 17 2011 - 10:15:50 CDT)
- Chathurika Abeyrathne (Tue Aug 16 2011 - 20:03:45 CDT)
MMTools for analysis
- Branko (Sat Dec 10 2011 - 10:21:06 CST)
- Namd Namd (Sat Dec 10 2011 - 05:07:19 CST)
mmView - a tool for mmCIF exploration
- Daniel Svozil (Tue Dec 06 2011 - 05:38:35 CST)
Model system spherical sieve
- Francesco Pietra (Fri Mar 04 2011 - 14:28:32 CST)
modify NAMD code for Lee-Edwards boundary conditions and compute stress tensor
- Van Ngo (Tue Apr 26 2011 - 19:17:47 CDT)
Molecule2.C
- Jim Phillips (Tue Jul 26 2011 - 11:36:33 CDT)
- Andy Somogyi (Thu Jul 21 2011 - 11:45:11 CDT)
Moving an atom 1A0 in one timestep then running MD for 10,000 timesteps while holding that one atom fixed
- Ehsan Ban (Mon Aug 15 2011 - 00:01:22 CDT)
- Ehsan Ban (Fri Jul 29 2011 - 12:40:27 CDT)
Moving atoms with bad contacts followed by CUDA error
- Francesco Pietra (Thu Nov 08 2012 - 09:45:00 CST)
moving inner wall of nanotube with outer wall fixed
- johan strumpfer (Tue Mar 15 2011 - 12:01:36 CDT)
- sakthi kumaran (Tue Mar 15 2011 - 04:29:02 CDT)
msd calculation for lipid bilayers
- cnu gromacs (Thu May 05 2011 - 14:22:24 CDT)
Multi core problem
- Axel Kohlmeyer (Tue Jul 10 2012 - 05:18:28 CDT)
- flavio seixas (Sun Jul 08 2012 - 14:48:04 CDT)
Multi node run causes "CUDA error cudaStreamCreate"
- Sergei (Fri Jun 22 2012 - 04:36:20 CDT)
- Sergei (Tue Jun 19 2012 - 08:32:39 CDT)
- Jim Phillips (Wed Apr 06 2011 - 16:17:02 CDT)
- Michael S. Sellers (Cont, ARL/WMRD) (Fri Apr 01 2011 - 16:27:08 CDT)
- Axel Kohlmeyer (Fri Apr 01 2011 - 16:10:00 CDT)
- Michael S. Sellers (Cont, ARL/WMRD) (Fri Apr 01 2011 - 15:46:21 CDT)
- Axel Kohlmeyer (Fri Apr 01 2011 - 15:02:18 CDT)
- Michael S. Sellers (Cont, ARL/WMRD) (Fri Apr 01 2011 - 12:32:35 CDT)
Multicore executable error
- Chris Harrison (Wed May 09 2012 - 16:21:02 CDT)
- Caitlin Scott (Wed May 09 2012 - 13:05:20 CDT)
Multicore executable error with hydrogens
- Caitlin Scott (Tue Dec 11 2012 - 20:55:36 CST)
multicore versus net-linux
- Chris Harrison (Fri Apr 20 2012 - 19:46:56 CDT)
- Jim Phillips (Thu Apr 05 2012 - 22:40:09 CDT)
- Gianluca Interlandi (Thu Apr 05 2012 - 20:04:57 CDT)
multilevel summation in NAMD
- Chris Harrison (Wed Apr 06 2011 - 21:56:19 CDT)
- Francesco Oteri (Wed Apr 06 2011 - 17:32:49 CDT)
Multinode NAMD CUDA GPU Selection
- Axel Kohlmeyer (Thu Aug 18 2011 - 10:39:18 CDT)
- Norman Geist (Thu Aug 18 2011 - 01:25:00 CDT)
Multiple copy ligand simulations
- Vijay Vammi (Thu Jun 14 2012 - 13:48:00 CDT)
- JC Gumbart (Thu Jun 14 2012 - 13:42:16 CDT)
- Vijay Vammi (Thu Jun 14 2012 - 13:32:43 CDT)
Multiple dihedral parameters in X-PLOR format
- Joe Yelk (Tue Oct 18 2011 - 17:46:57 CDT)
multiple dynamic sections in the config file?
- Chris Harrison (Thu Aug 23 2012 - 22:55:50 CDT)
- Jacqueline Schmidt (Thu Aug 16 2012 - 19:03:44 CDT)
Multiple gpu cards
- Axel Kohlmeyer (Wed Aug 15 2012 - 09:54:10 CDT)
- Dr. Eddie (Wed Aug 15 2012 - 09:24:46 CDT)
Multiple Runs in a Single Conf File
- Rajan Vatassery (Wed Jun 08 2011 - 09:53:55 CDT)
- Rajan Vatassery (Wed Jun 08 2011 - 03:00:55 CDT)
Multiple runs of NAMD highly take fluctuating times
- yashodhan karandikar (Wed Mar 16 2011 - 00:48:27 CDT)
- Axel Kohlmeyer (Wed Mar 16 2011 - 00:36:28 CDT)
- yashodhan karandikar (Tue Mar 15 2011 - 23:06:59 CDT)
My benchmark results with TeslaC2050
- Norman Geist (Fri May 20 2011 - 01:02:36 CDT)
n-terminus in my psfgen created pdb/psf file is missing
- Jacqueline Schmidt (Sun Sep 16 2012 - 12:09:15 CDT)
- Jacqueline Schmidt (Sun Sep 16 2012 - 11:15:41 CDT)
Na ion, Cl ion in TIP4P
- divya nayar (Thu Sep 15 2011 - 02:42:54 CDT)
NADPH topology
- flavio seixas (Fri May 27 2011 - 08:58:17 CDT)
NAG simulation problem with CPS
- JC Gumbart (Wed Jan 05 2011 - 08:04:24 CST)
- Adrian Jasiñski (Wed Jan 05 2011 - 05:36:00 CST)
namd ( please help me!!! )
- snoze pa (Mon Jun 13 2011 - 15:12:19 CDT)
- Axel Kohlmeyer (Mon Jun 13 2011 - 14:36:24 CDT)
- Namd Namd (Mon Jun 13 2011 - 14:29:40 CDT)
NAMD (and VMD) fail to read simple AMBER prmtop file (and it's not the SCEE and SCNB flags)
- Aron Broom (Sun Oct 21 2012 - 18:37:56 CDT)
- Jose Borreguero (Sat Oct 20 2012 - 15:55:51 CDT)
NAMD + Plumed on Abe
- Gianluca Interlandi (Fri Feb 25 2011 - 00:03:17 CST)
Namd / gromacs
- Sara baretller (Tue Aug 16 2011 - 09:17:41 CDT)
NAMD 2.7 released
- Gianluca Interlandi (Thu Mar 17 2011 - 17:58:46 CDT)
NAMD 2.7/2.8b1 and BlueGeneL
- Dong Luo (Wed Apr 13 2011 - 16:46:00 CDT)
- Jim Phillips (Wed Apr 13 2011 - 08:46:26 CDT)
- Dong Luo (Tue Mar 29 2011 - 11:00:22 CDT)
NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0
- Bjoern Olausson (Thu May 19 2011 - 04:00:33 CDT)
- Jim Phillips (Wed May 18 2011 - 17:58:16 CDT)
- Bjoern Olausson (Wed May 18 2011 - 08:44:48 CDT)
- Jim Phillips (Tue May 17 2011 - 13:21:49 CDT)
- Bjoern Olausson (Mon May 16 2011 - 13:45:14 CDT)
- Bjoern Olausson (Mon May 16 2011 - 04:02:51 CDT)
- Bjoern Olausson (Sat May 14 2011 - 01:12:57 CDT)
- Jim Phillips (Fri May 13 2011 - 14:52:53 CDT)
- Bjoern Olausson (Fri May 13 2011 - 13:10:46 CDT)
- Bjoern Olausson (Thu May 12 2011 - 17:20:09 CDT)
NAMD 2.8 and PLUMED 1.3
- Buddhadev Maiti (Fri Aug 31 2012 - 22:40:11 CDT)
- Aron Broom (Fri Aug 31 2012 - 13:57:31 CDT)
- candy deck (Thu Aug 30 2012 - 07:59:41 CDT)
NAMD 2.8 job submission script for queenbee
- Jim Phillips (Tue Jul 26 2011 - 11:13:57 CDT)
- cnu gromacs (Mon Jul 25 2011 - 18:29:51 CDT)
NAMD 2.8 job submission script for queenbee: ManyJobs
- Thomas Bishop (Tue Jul 26 2011 - 08:46:29 CDT)
namd 2.8 new feature
- Hasan haska (Thu Sep 22 2011 - 08:37:27 CDT)
NAMD 2.8 on Cray XE6 segfaulting
- Jim Phillips (Tue Jul 26 2011 - 16:14:34 CDT)
- Jim Phillips (Tue Jul 26 2011 - 11:58:34 CDT)
- Jim Phillips (Tue Jul 26 2011 - 11:05:30 CDT)
- Tim Robinson (Tue Jul 26 2011 - 05:46:01 CDT)
NAMD 2.8 released
- Jim Phillips (Tue May 31 2011 - 14:55:34 CDT)
NAMD 2.8b1 released
- Jim Phillips (Sun Mar 27 2011 - 12:25:13 CDT)
NAMD 2.8b2 released
- Jim Phillips (Wed May 11 2011 - 17:15:43 CDT)
NAMD 2.8b3 released
- Jim Phillips (Thu May 19 2011 - 16:28:04 CDT)
namd 2.9 and plumed
- Vlad Cojocaru (Wed Oct 31 2012 - 07:24:07 CDT)
NAMD 2.9 CUDA multicore, single machine
- Aron Broom (Fri Jun 22 2012 - 13:49:57 CDT)
- Aron Broom (Fri Jun 22 2012 - 13:49:30 CDT)
- Brett T. Hannigan (Fri Jun 22 2012 - 13:04:34 CDT)
namd 2.9 ibverbs issues
- Michael Galloway (Sat Sep 08 2012 - 12:29:12 CDT)
namd 2.9 not going so well
- Michael Galloway (Thu Sep 13 2012 - 10:30:09 CDT)
NAMD 2.9 not migrating to computing nodes on Windows Server 2008 R2 HPC MPI
- Alex Smith (Thu Nov 22 2012 - 05:44:28 CST)
Namd 2.9 on a BlueGene/Q machine
- Vasudevan V (Wed Dec 26 2012 - 17:29:34 CST)
NAMD 2.9 released
- Jim Phillips (Thu May 03 2012 - 10:27:09 CDT)
NAMD 2.9 Replica Exchange (+replicas error)
- Cade Markegard (Fri Jul 06 2012 - 13:56:42 CDT)
- Robert Elder (Fri Jul 06 2012 - 13:40:23 CDT)
- Cade Markegard (Mon Jun 04 2012 - 16:57:06 CDT)
namd 2.9 Replica Exchange with colvar
- Ada Zhan (Mon Nov 05 2012 - 13:11:30 CST)
namd 2.9 run instability (segfaults)
- Michael Galloway (Thu Sep 06 2012 - 09:19:05 CDT)
NAMD 2.9 Windows CUDA build?
- Ajasja LjubetiÄ (Thu Nov 08 2012 - 03:47:01 CST)
- Frederik Heurlin Aidt (Thu Nov 08 2012 - 02:51:33 CST)
- Axel Kohlmeyer (Mon Nov 05 2012 - 02:01:30 CST)
- Frederik Heurlin Aidt (Fri Nov 02 2012 - 05:30:54 CDT)
NAMD 2.9 with CUDA runs
- Ashley Chew (Sun Sep 02 2012 - 20:37:30 CDT)
- Chris Harrison (Sat Sep 01 2012 - 20:02:28 CDT)
- Peter Jones (Fri Aug 31 2012 - 21:41:25 CDT)
- Chris Harrison (Fri Aug 31 2012 - 13:14:02 CDT)
- Ashley Chew (Fri Aug 31 2012 - 04:02:48 CDT)
NAMD 2.9: Segmentation fault?
- Maria Antonieta Sanchez Farran (Tue Jul 31 2012 - 14:52:10 CDT)
- Aron Broom (Tue Jul 31 2012 - 14:14:55 CDT)
- María Antonieta Sánchez Farrán (Tue Jul 31 2012 - 13:47:05 CDT)
- Branko (Tue Jul 31 2012 - 13:42:34 CDT)
- María Antonieta Sánchez Farrán (Tue Jul 31 2012 - 13:39:33 CDT)
- Aron Broom (Tue Jul 31 2012 - 13:17:38 CDT)
- María Antonieta Sánchez Farrán (Tue Jul 31 2012 - 13:13:03 CDT)
- Branko (Tue Jul 31 2012 - 13:04:59 CDT)
- Aron Broom (Tue Jul 31 2012 - 12:52:37 CDT)
- María Antonieta Sánchez Farrán (Tue Jul 31 2012 - 12:44:09 CDT)
NAMD 2.9b1 crashes during minimization
- Francesco Pietra (Thu Mar 22 2012 - 10:28:04 CDT)
NAMD 2.9b1 released
- Jim Phillips (Tue Mar 20 2012 - 20:35:59 CDT)
NAMD 2.9b2 released
- Jim Phillips (Tue Mar 27 2012 - 15:17:30 CDT)
NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8
- Thomas Albers (Tue Apr 03 2012 - 07:37:54 CDT)
- Thomas Albers (Mon Apr 02 2012 - 14:17:13 CDT)
- Nicholas M Glykos (Sun Apr 01 2012 - 03:41:08 CDT)
- Thomas Albers (Sat Mar 31 2012 - 18:00:06 CDT)
NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 (solved)
- Thomas Albers (Sun Apr 29 2012 - 08:33:54 CDT)
- Jim Phillips (Fri Apr 27 2012 - 14:10:20 CDT)
- Thomas Albers (Sat Apr 07 2012 - 16:44:35 CDT)
NAMD 2.9b3 colvars oddity
- Giacomo Fiorin (Tue Apr 10 2012 - 16:54:39 CDT)
- Aron Broom (Mon Apr 09 2012 - 20:48:32 CDT)
NAMD 2.9b3 released
- Jim Phillips (Fri Apr 06 2012 - 08:38:23 CDT)
namd and Fedora14
- Chris Harrison (Tue Mar 29 2011 - 04:36:36 CDT)
- Chris Harrison (Tue Mar 29 2011 - 04:33:39 CDT)
- Michael S. Sellers (Cont, ARL/WMRD) (Mon Mar 28 2011 - 09:12:47 CDT)
- Michael S. Sellers (Cont, ARL/WMRD) (Mon Mar 28 2011 - 09:16:51 CDT)
- flavio seixas (Mon Mar 28 2011 - 08:55:57 CDT)
- Michael S. Sellers (Cont, ARL/WMRD) (Tue Mar 22 2011 - 10:10:02 CDT)
- Axel Kohlmeyer (Tue Mar 22 2011 - 08:44:21 CDT)
- Chris Harrison (Tue Mar 22 2011 - 08:08:28 CDT)
- flavio seixas (Tue Mar 22 2011 - 07:28:27 CDT)
NAMD and new FF CHARMM36
- Evgeny Bulat (Wed Dec 12 2012 - 15:24:58 CST)
- Jeffrey Potoff (Wed Dec 12 2012 - 15:22:03 CST)
- JC Gumbart (Wed Dec 12 2012 - 14:53:19 CST)
- Gianluca Interlandi (Wed Dec 12 2012 - 14:49:46 CST)
- Evgeny Bulat (Wed Dec 12 2012 - 14:39:48 CST)
- Gianluca Interlandi (Wed Dec 12 2012 - 14:26:07 CST)
namd and x-plor
- Jernej Zidar (Sat Apr 14 2012 - 08:16:08 CDT)
- Hasan haska (Sat Apr 14 2012 - 06:19:57 CDT)
namd at ranger(tacc)
- Peter Freddolino (Thu Feb 24 2011 - 17:02:27 CST)
- Sándor Kovács (Thu Feb 24 2011 - 16:46:41 CST)
- Jim Phillips (Thu Feb 24 2011 - 15:36:18 CST)
- Axel Kohlmeyer (Thu Feb 24 2011 - 15:20:02 CST)
- Lei Shi (Thu Feb 24 2011 - 12:56:29 CST)
NAMD cell dimension increasing in Z direction, problem with periodic cell
- snoze pa (Fri Apr 15 2011 - 13:23:53 CDT)
NAMD chares
- Jim Phillips (Mon Jul 18 2011 - 16:47:44 CDT)
- Andy Somogyi (Mon Jul 11 2011 - 10:35:17 CDT)
NAMD compilation -- compiler issue
- Dmitry Osolodkin (Fri Oct 26 2012 - 03:33:15 CDT)
- Sergey (Thu Oct 25 2012 - 09:46:10 CDT)
- Dmitry Osolodkin (Thu Oct 25 2012 - 09:02:22 CDT)
namd crashes after 300K steps
- Peter Jones (Thu Jul 26 2012 - 03:06:17 CDT)
NAMD crashes when writing restart file and dcdfreq is 1
- Jim Phillips (Thu May 26 2011 - 09:12:02 CDT)
- Jim Phillips (Tue May 24 2011 - 13:39:51 CDT)
- Ajasja LjubetiÄ (Tue May 24 2011 - 07:25:25 CDT)
- Jim Phillips (Fri May 20 2011 - 17:06:32 CDT)
- Jim Phillips (Fri May 20 2011 - 08:45:46 CDT)
- Ajasja LjubetiÄ (Fri May 20 2011 - 05:25:31 CDT)
- Ajasja LjubetiÄ (Fri May 20 2011 - 05:16:30 CDT)
NAMD crashes with OpenMPI/OpenMX
- Thomas Albers (Sun Jun 19 2011 - 21:32:42 CDT)
- Ajasja LjubetiÄ (Fri Jun 17 2011 - 05:10:06 CDT)
- Bjoern Olausson (Thu Jun 16 2011 - 07:40:07 CDT)
- Ajasja LjubetiÄ (Thu Jun 16 2011 - 06:23:36 CDT)
- Axel Kohlmeyer (Tue Jun 14 2011 - 13:25:23 CDT)
- Thomas Albers (Tue Jun 14 2011 - 13:04:29 CDT)
- Jim Phillips (Tue Jun 14 2011 - 11:33:35 CDT)
- Thomas Albers (Mon Jun 13 2011 - 11:50:35 CDT)
NAMD CUDA 2.9 Performance drop compared to 2.8
- Norman Geist (Fri Dec 07 2012 - 05:37:20 CST)
NAMD CUDA error message
- JC Gumbart (Fri Jan 14 2011 - 11:46:39 CST)
- snoze pa (Fri Jan 14 2011 - 11:37:54 CST)
namd cuda error.
- kanchi subbarao rao (Tue Jul 03 2012 - 10:03:59 CDT)
- kanchi subbarao rao (Thu Jun 28 2012 - 11:13:43 CDT)
NAMD does not exit simulation on satisfying condition in the tclforces script
- Mithun Biswas (Thu Jul 26 2012 - 08:21:23 CDT)
- Mithun Biswas (Thu Jul 19 2012 - 10:26:01 CDT)
NAMD energy plugin
- politr_at_fh.huji.ac.il (Thu Jul 28 2011 - 04:22:42 CDT)
NAMD failed to read AMBER parm file
- Felipe Merino (Sat Nov 17 2012 - 10:48:12 CST)
- Sneha Menon (Sat Nov 17 2012 - 03:44:08 CST)
- Sneha Menon (Thu Nov 08 2012 - 23:19:00 CST)
NAMD feature request Hydrogenscale
- Vincent Leroux (Wed May 30 2012 - 08:04:01 CDT)
- Axel Kohlmeyer (Wed May 30 2012 - 07:14:40 CDT)
- Jérôme Hénin (Wed May 30 2012 - 06:51:47 CDT)
- Ajasja LjubetiÄ (Wed May 30 2012 - 06:16:46 CDT)
- Axel Kohlmeyer (Wed May 30 2012 - 04:20:03 CDT)
- Norman Geist (Wed May 30 2012 - 02:36:16 CDT)
NAMD FEP - Bad Hydrogen group size
- Jérôme Hénin (Wed Dec 07 2011 - 06:54:01 CST)
- John Baker (Wed Dec 07 2011 - 05:38:11 CST)
NAMD feture request
- Thomas Evangelidis (Wed Apr 13 2011 - 12:06:57 CDT)
- Giacomo Fiorin (Wed Apr 13 2011 - 10:17:27 CDT)
- Ajasja LjubetiÄ (Wed Apr 13 2011 - 09:46:07 CDT)
namd files
- Axel Kohlmeyer (Wed Jul 20 2011 - 08:48:08 CDT)
- Hasan haska (Wed Jul 20 2011 - 08:17:34 CDT)
NAMD fixes for dummy atoms & parameters for divalent metal ions
- Francesco Pietra (Fri Jun 01 2012 - 03:15:21 CDT)
NAMD for windows cannot run correctly according to namd tutorials
- sciencekey (Tue Apr 05 2011 - 04:00:11 CDT)
namd force field
- felmerino_at_uchile.cl (Tue Nov 22 2011 - 12:14:28 CST)
- Axel Kohlmeyer (Tue Nov 22 2011 - 08:05:08 CST)
- Molecular Dynamics (Tue Nov 22 2011 - 06:21:16 CST)
NAMD in parallel on CPUs of different type
- Thomas Albers (Fri Oct 19 2012 - 21:51:47 CDT)
- Chris Harrison (Fri Oct 19 2012 - 21:29:05 CDT)
- Thomas Albers (Fri Oct 19 2012 - 21:03:08 CDT)
NAMD initial coordinate file
- Mohd Farid Ismail (Thu Jan 13 2011 - 12:40:03 CST)
- Chris Harrison (Mon Jan 10 2011 - 06:27:07 CST)
- Ismail, Mohd F. (Fri Jan 07 2011 - 00:10:47 CST)
Namd list: "Size cell" for restart
- Suranga Edirisinghe (Tue Aug 28 2012 - 13:45:03 CDT)
- Axel Kohlmeyer (Tue Aug 28 2012 - 11:01:51 CDT)
- Mariana Graterol (Tue Aug 28 2012 - 08:07:03 CDT)
Namd list: Problem in equilibration stage
- Aron Broom (Thu Sep 27 2012 - 11:31:18 CDT)
- Mariana Graterol (Thu Sep 27 2012 - 08:35:31 CDT)
namd log file
- Jian Liu (Fri Oct 07 2011 - 19:14:39 CDT)
- Namd Namd (Fri Oct 07 2011 - 07:20:02 CDT)
NAMD on Bluegene
- Axel Kohlmeyer (Sat Mar 17 2012 - 15:27:40 CDT)
- Thomas Lemmin (Fri Mar 16 2012 - 12:39:16 CDT)
NAMD on GPU
- Jun Zhang (Mon Mar 21 2011 - 19:45:10 CDT)
- Ismail, Mohd F. (Sun Mar 20 2011 - 21:24:09 CDT)
NAMD on KRAKEN
- Axel Kohlmeyer (Fri Oct 28 2011 - 08:03:35 CDT)
- PAUL NEWMAN (Fri Oct 28 2011 - 07:55:01 CDT)
- Axel Kohlmeyer (Fri Oct 28 2011 - 04:43:59 CDT)
- PAUL NEWMAN (Fri Oct 28 2011 - 02:04:00 CDT)
namd on nvidia 302.17
- Aron Broom (Thu Sep 27 2012 - 12:56:23 CDT)
- Francesco Pietra (Thu Sep 27 2012 - 12:39:30 CDT)
- Francesco Pietra (Thu Sep 27 2012 - 08:54:10 CDT)
- Aron Broom (Thu Sep 27 2012 - 07:58:40 CDT)
- Francesco Pietra (Thu Sep 27 2012 - 02:52:11 CDT)
- Aron Broom (Wed Sep 26 2012 - 09:05:07 CDT)
- Francesco Pietra (Wed Sep 26 2012 - 08:58:45 CDT)
NAMD on Peta-Scale Machines
- Iyer, Ravishankar K (Sun Sep 02 2012 - 11:07:32 CDT)
- Axel Kohlmeyer (Sun Sep 02 2012 - 07:19:02 CDT)
- Wang Yi (Sat Sep 01 2012 - 12:18:12 CDT)
- Yim, Keun Soo (Fri Aug 31 2012 - 18:08:13 CDT)
- Yim, Keun Soo (Thu Aug 30 2012 - 13:19:10 CDT)
NAMD on PS3
- Andy Somogyi (Sat Aug 06 2011 - 13:16:20 CDT)
- Ali Khanlarkhani (Sat Aug 06 2011 - 11:02:22 CDT)
NAMD on ranger.tacc
- Jesper Sørensen (Tue Jan 24 2012 - 14:35:39 CST)
- George M Giambasu (Tue Jan 24 2012 - 12:22:42 CST)
- Jesper Sørensen (Tue Jan 24 2012 - 11:46:11 CST)
- George M Giambasu (Mon Jan 23 2012 - 11:26:26 CST)
- Jesper Sørensen (Mon Jan 23 2012 - 10:28:33 CST)
NAMD parameters +mergegrids +ignoresharing
- Norman Geist (Tue Dec 04 2012 - 01:04:09 CST)
- Aron Broom (Fri Nov 30 2012 - 09:41:04 CST)
- Norman Geist (Fri Nov 30 2012 - 00:49:17 CST)
NAMD pulling one domain
- Wang Yi (Wed Aug 29 2012 - 10:05:44 CDT)
- snoze pa (Wed Aug 29 2012 - 09:58:49 CDT)
- Wang Yi (Mon Aug 27 2012 - 14:40:22 CDT)
- snoze pa (Mon Aug 27 2012 - 14:36:34 CDT)
NAMD question
- snoze pa (Fri May 13 2011 - 16:34:16 CDT)
namd question in parameter conversion
- Boyang Wang (Thu Jan 19 2012 - 02:08:46 CST)
- Aron Broom (Wed Jan 18 2012 - 12:35:01 CST)
- Liqun Zhang (Wed Jan 18 2012 - 10:27:12 CST)
NAMD Run Instabilities
- Axel Kohlmeyer (Mon Sep 10 2012 - 08:54:50 CDT)
- Marc Gordon (Mon Sep 10 2012 - 08:39:55 CDT)
- Axel Kohlmeyer (Mon Sep 10 2012 - 08:28:17 CDT)
- Marc Gordon (Mon Sep 10 2012 - 08:19:18 CDT)
- Chris Harrison (Thu Sep 06 2012 - 08:57:41 CDT)
- Ajasja LjubetiÄ (Thu Sep 06 2012 - 08:44:30 CDT)
- Axel Kohlmeyer (Thu Sep 06 2012 - 08:27:08 CDT)
- Marc Gordon (Thu Sep 06 2012 - 08:15:58 CDT)
NAMD running on windows HPC question
- Axel Kohlmeyer (Tue Sep 20 2011 - 11:27:23 CDT)
- johan strumpfer (Tue Sep 20 2011 - 08:30:51 CDT)
- johan strumpfer (Tue Sep 20 2011 - 08:46:51 CDT)
- Chewning, Joseph (Tue Sep 20 2011 - 08:34:51 CDT)
- Nikolaos Glykos (Tue Sep 20 2011 - 08:23:34 CDT)
- Chewning, Joseph (Tue Sep 20 2011 - 07:58:43 CDT)
namd runs on compute nodes but not update files in the head node
- Ada Zhan (Fri Nov 30 2012 - 16:34:01 CST)
NAMD SGE Job Script Scale Up issues!
- Aditya Ranganathan (Fri Oct 19 2012 - 02:29:07 CDT)
- Aditya Ranganathan (Thu Oct 18 2012 - 08:04:53 CDT)
namd simulation:protein,ligand,lipid,water and ions
- Marlet Martinez (Thu Jun 14 2012 - 12:29:15 CDT)
- Marlet Martinez (Wed Jun 13 2012 - 18:44:40 CDT)
namd simulationâ€‹:protein,lâ€‹igand,lipiâ€‹d,water and ions
- Marlet Martinez (Tue Aug 28 2012 - 12:30:04 CDT)
- Marlet Martinez (Thu Jun 21 2012 - 09:59:09 CDT)
- Aron Broom (Tue Jun 19 2012 - 12:37:13 CDT)
- Marlet Martinez (Tue Jun 19 2012 - 12:33:13 CDT)
NAMD speed on MPICH2 Ubuntu 64 bit Cluster
- Norman Geist (Fri Apr 15 2011 - 07:46:00 CDT)
- Robert McCarrick (Thu Apr 07 2011 - 09:06:03 CDT)
- Jim Phillips (Wed Apr 06 2011 - 17:01:31 CDT)
- Axel Kohlmeyer (Wed Apr 06 2011 - 16:22:48 CDT)
- Robert McCarrick (Wed Apr 06 2011 - 15:50:11 CDT)
- Axel Kohlmeyer (Wed Apr 06 2011 - 12:06:41 CDT)
- Robert McCarrick (Wed Apr 06 2011 - 11:19:16 CDT)
- Robert McCarrick (Tue Apr 05 2011 - 13:51:55 CDT)
NAMD Tutorial Problem
- Jane Ren (Thu Jan 06 2011 - 13:19:50 CST)
NAMD with GPU error : "Number of VDW types exceeds CUDA LJ_TABLE_SIZE"
- David McGiven (Fri May 27 2011 - 06:12:42 CDT)
NAMD with TIP5P water
- David Huggins (Tue Jun 21 2011 - 13:24:49 CDT)
Namd, lammps comparing energies
- Axel Kohlmeyer (Fri Aug 10 2012 - 15:56:18 CDT)
- Giacomo Fiorin (Fri Aug 10 2012 - 13:20:21 CDT)
- Jacqueline Schmidt (Fri Aug 10 2012 - 12:44:05 CDT)
NAMD- molecular dynamics
- Aron Broom (Thu Sep 13 2012 - 17:46:17 CDT)
- Shomesankar Bhunia (Thu Sep 13 2012 - 14:55:14 CDT)
Namd-1: problems using increment of temperature during simulation
- Ye Yang (Sun Feb 27 2011 - 14:27:16 CST)
Namd-I: A question about constant force pulling of a group of atoms
- Ye Yang (Thu Sep 01 2011 - 10:16:18 CDT)
namd-I: cionize problem in vmd
- Ye Yang (Mon Aug 01 2011 - 11:36:26 CDT)
- Axel Kohlmeyer (Fri Jul 29 2011 - 11:23:56 CDT)
- Ye Yang (Fri Jul 29 2011 - 11:17:10 CDT)
Namd-I: Implicit solvent problem
- Matteo Rotter (Wed Jul 20 2011 - 16:06:29 CDT)
- Enrico Guarnera (Wed Jul 20 2011 - 11:22:46 CDT)
- Matteo Rotter (Wed Jul 20 2011 - 11:04:03 CDT)
- Giovanni Settanni (Thu Jun 30 2011 - 01:56:13 CDT)
- Gianluca Interlandi (Wed Jun 29 2011 - 17:49:51 CDT)
- Ye Yang (Wed Jun 29 2011 - 17:44:55 CDT)
- Ye Yang (Wed Jun 29 2011 - 17:38:54 CDT)
- Gianluca Interlandi (Wed Jun 29 2011 - 16:31:49 CDT)
- Francesco Oteri (Wed Jun 29 2011 - 16:17:21 CDT)
- Ye Yang (Wed Jun 29 2011 - 16:07:55 CDT)
Namd-I: namd compiling problem
- Ye Yang (Wed Aug 03 2011 - 10:46:13 CDT)
- Ye Yang (Tue Aug 02 2011 - 22:28:05 CDT)
namd-I: Problems with Namd coarsegrain and Gromacs top file
- Ye Yang (Wed Jun 15 2011 - 14:50:23 CDT)
namd-ibverbs fails to start
- David Hemmendinger (Fri Nov 18 2011 - 21:39:20 CST)
NAMD-INCONSISTENCY IN SCOR
- jose correa (Tue Jun 12 2012 - 17:23:00 CDT)
namd-l digest V1 #787
- Hyuntae Na (Wed Jun 27 2012 - 20:22:15 CDT)
namd-l digest V1 #918
- Aaron Cann (Tue Nov 20 2012 - 13:10:24 CST)
namd-l digest V1 #949
- Nicholas M Glykos (Mon Dec 17 2012 - 04:06:22 CST)
NAMD-l: energy jump between minimization and simulation
- Eva Gonzalez Noya (Wed Feb 16 2011 - 16:37:09 CST)
- Bennion, Brian (Wed Feb 16 2011 - 13:48:34 CST)
NAMD-l: Get the PDB file from Steered Molecular Dynamics output files
- Jim Phillips (Fri Jun 17 2011 - 13:14:11 CDT)
- albus hawking (Tue Jun 14 2011 - 22:56:55 CDT)
namd/vmd support to GTX-6## series
- Francesco Pietra (Wed Jun 06 2012 - 03:43:38 CDT)
NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..."
- Jim Phillips (Fri May 13 2011 - 08:18:37 CDT)
- Bjoern Olausson (Fri May 13 2011 - 02:47:16 CDT)
- Jim Phillips (Wed Apr 13 2011 - 10:39:41 CDT)
- Dong Luo (Tue Apr 12 2011 - 09:44:09 CDT)
- Dong Luo (Fri Mar 04 2011 - 10:40:54 CST)
- Dong Luo (Fri Mar 04 2011 - 08:08:38 CST)
- Chris Harrison (Thu Mar 03 2011 - 20:08:20 CST)
- Dong Luo (Thu Mar 03 2011 - 19:59:10 CST)
- Chris Harrison (Thu Mar 03 2011 - 00:41:50 CST)
- Axel Kohlmeyer (Wed Mar 02 2011 - 22:32:28 CST)
- Dong Luo (Wed Mar 02 2011 - 21:42:57 CST)
NAMD2.9 Release and Multi-GPU Minimization Errors
- c jepson (Thu Jul 19 2012 - 15:15:32 CDT)
namd2_ti.pl Modification of non-creatable array value attempted, subscript -49999
- Pete Kekenes-Huskey (Tue Sep 06 2011 - 17:22:26 CDT)
Namd: nohup: ignoring input and redirecting stderr to stdout
- Axel Kohlmeyer (Mon Dec 24 2012 - 01:18:10 CST)
- Maria Saeed (Mon Dec 24 2012 - 00:30:32 CST)
NAMD_2.7_AIX-POWER-MPI
- Buddhadev Maiti (Sun May 01 2011 - 21:28:41 CDT)
NAMD_CVS_Source
- Axel Kohlmeyer (Wed Mar 30 2011 - 17:27:04 CDT)
- Leonardo Herrera (Wed Mar 30 2011 - 16:43:52 CDT)
NAMDenergy calculations for nucleic acid systems
- mon_sharma_at_research.iiit.ac.in (Sat Apr 16 2011 - 08:18:17 CDT)
- Peter Freddolino (Sat Apr 16 2011 - 05:48:31 CDT)
- mon_sharma_at_research.iiit.ac.in (Sat Apr 16 2011 - 03:22:37 CDT)
NAMDenergy electrostatic energies
- Sebastian Maximilian Wilhelm (Mon Feb 28 2011 - 10:41:03 CST)
NAMDEnergy Plugin - setting PMEGridSize / mesh density
- Michael S. Sellers (Cont, ARL/WMRD) (Wed May 11 2011 - 15:29:25 CDT)
- Lela Vukovic (Wed May 11 2011 - 14:48:51 CDT)
NAMDenergy plugin_van der Waal interactions
- Axel Kohlmeyer (Tue Feb 21 2012 - 18:19:26 CST)
- Bruno Luís Pinto de Oliveira (Tue Feb 21 2012 - 18:05:44 CST)
- Bruno Luís Pinto de Oliveira (Mon Feb 20 2012 - 07:01:14 CST)
- Chris Harrison (Wed Feb 15 2012 - 15:27:12 CST)
- Bruno Luís Pinto de Oliveira (Thu Feb 02 2012 - 11:06:20 CST)
NAMDEnergy: run with XSC file or not?
- Evgeny Bulat (Wed Nov 21 2012 - 13:27:23 CST)
Namdstats.tcl
- flavio seixas (Tue May 10 2011 - 14:51:13 CDT)
NBFIX for carbonyl atoms and potassium ions -- User Defined Force -- CUDA
- Burgess, Don E (Mon Jan 17 2011 - 15:35:28 CST)
NBFIX support in CUDA NAMD
- Burgess, Don E (Mon Jan 24 2011 - 20:41:26 CST)
NBTABLE issue
- Arturas (Thu Aug 30 2012 - 13:45:14 CDT)
NCS
- flavio seixas (Wed Feb 16 2011 - 18:42:38 CST)
- Nicholas M Glykos (Wed Feb 16 2011 - 03:18:29 CST)
- Joshua Adelman (Tue Feb 15 2011 - 20:28:36 CST)
- felmerino_at_uchile.cl (Tue Feb 15 2011 - 20:22:38 CST)
- flavio seixas (Tue Feb 15 2011 - 17:20:49 CST)
- Nikolaos Glykos (Tue Feb 15 2011 - 13:59:45 CST)
- Joshua Adelman (Tue Feb 15 2011 - 11:51:46 CST)
- Jérôme Hénin (Tue Feb 15 2011 - 12:27:12 CST)
- flavio seixas (Tue Feb 15 2011 - 05:04:33 CST)
- snoze pa (Mon Feb 14 2011 - 15:09:33 CST)
- flavio seixas (Mon Feb 14 2011 - 14:09:35 CST)
need help in using colvars option
- Aron Broom (Tue Aug 28 2012 - 12:17:20 CDT)
- Giacomo Fiorin (Mon Aug 27 2012 - 17:54:09 CDT)
- sudipta (Mon Aug 27 2012 - 17:41:51 CDT)
Need help preventing hydration of the lipid-protein interface in my system
- Chris Harrison (Thu May 03 2012 - 18:31:50 CDT)
- Syed Kashif Zafar (Thu May 03 2012 - 05:48:48 CDT)
Negative surface area?
- David Minh (Tue Jul 24 2012 - 10:36:23 CDT)
- David Minh (Fri Jun 15 2012 - 09:08:12 CDT)
Net forces on each atom can be written to PDB in NAMD 2.8b1
- Jim Phillips (Mon Mar 28 2011 - 12:00:59 CDT)
- oguz gurbulak (Mon Mar 28 2011 - 04:53:55 CDT)
- oguz gurbulak (Mon Mar 28 2011 - 04:06:05 CDT)
Network version gives inconsistent wall clock timings
- Jim Phillips (Wed Apr 13 2011 - 09:04:46 CDT)
- yashodhan karandikar (Wed Mar 30 2011 - 08:39:15 CDT)
New collective variable: biolRel
- Jérôme Hénin (Fri Apr 01 2011 - 09:01:53 CDT)
New colvar feature request -- angleXY
- Giacomo Fiorin (Mon Feb 14 2011 - 17:07:05 CST)
- Ajasja Ljubetiè (Mon Feb 14 2011 - 16:04:27 CST)
- Ajasja Ljubetiè (Mon Feb 14 2011 - 10:13:28 CST)
- Jérôme Hénin (Mon Feb 14 2011 - 10:06:45 CST)
- Giacomo Fiorin (Mon Feb 14 2011 - 09:43:33 CST)
- Ajasja LjubetiÄ (Mon Feb 14 2011 - 07:19:46 CST)
new error in NAMD2.8b1 with fixedAtoms
- alex digenova bravo (Fri May 13 2011 - 23:19:54 CDT)
- Jim Phillips (Tue May 10 2011 - 20:01:25 CDT)
- dklose_at_uni-osnabrueck.de (Tue Apr 19 2011 - 11:45:25 CDT)
New NAMD version 2011-03-03 uses
- Chris Harrison (Thu Mar 17 2011 - 13:53:08 CDT)
- Chris Chipot (Thu Mar 17 2011 - 13:43:44 CDT)
- Christian Jorgensen (Thu Mar 17 2011 - 13:34:44 CDT)
- Chris Chipot (Thu Mar 17 2011 - 13:09:30 CDT)
- Christian Jorgensen (Thu Mar 17 2011 - 12:58:03 CDT)
- Chris Chipot (Tue Mar 15 2011 - 17:37:15 CDT)
- Jeff Wereszczynski (Tue Mar 15 2011 - 11:49:28 CDT)
- Chris Harrison (Tue Mar 15 2011 - 13:18:56 CDT)
- Chris Harrison (Tue Mar 15 2011 - 10:48:04 CDT)
- Chris Chipot (Tue Mar 15 2011 - 10:00:17 CDT)
- Christian Jorgensen (Tue Mar 15 2011 - 09:52:27 CDT)
New physical understanding.
- Boyang Wang (Sat Dec 17 2011 - 21:24:21 CST)
- Axel Kohlmeyer (Sat Dec 17 2011 - 13:42:31 CST)
- Boyang Wang (Sat Dec 17 2011 - 08:52:28 CST)
- Chris Harrison (Fri Dec 16 2011 - 09:20:53 CST)
- Boyang Wang (Fri Dec 16 2011 - 06:56:42 CST)
- Axel Kohlmeyer (Fri Dec 16 2011 - 05:47:48 CST)
- Boyang Wang (Fri Dec 16 2011 - 00:39:27 CST)
Newbie's question
- Axel Kohlmeyer (Tue Aug 07 2012 - 03:38:50 CDT)
- Theresa H (Mon Aug 06 2012 - 12:41:18 CDT)
- Theresa H (Mon Aug 06 2012 - 09:46:49 CDT)
Nice paper on MD Simulations
- pawan raghav (Sat Sep 10 2011 - 13:37:00 CDT)
Nicolas te ha dejado un mensaje...
- Badoo (Sun Jun 24 2012 - 16:13:10 CDT)
nitrogen in namd
- Marco Sant (Sun Jul 31 2011 - 05:47:18 CDT)
- Jim Phillips (Thu Jul 28 2011 - 11:57:05 CDT)
- Jeffrey Potoff (Wed Jul 27 2011 - 15:51:57 CDT)
- Erik Nordgren (Wed Jul 27 2011 - 14:49:04 CDT)
- Jim Phillips (Wed Jul 27 2011 - 15:07:25 CDT)
- Marco Sant (Wed Jul 27 2011 - 04:47:15 CDT)
no CUDA-capable device is detected
- Damián Montaldo (Thu Jul 19 2012 - 14:12:06 CDT)
No output after "scheduler running in netpoll mode"
- amin_at_imtech.res.in (Tue Aug 21 2012 - 08:58:40 CDT)
no output for corrfunc
- Robert Elder (Thu Nov 01 2012 - 18:26:23 CDT)
- Rui Zhang (Tue Aug 07 2012 - 18:11:32 CDT)
- Giacomo Fiorin (Mon Aug 06 2012 - 11:20:37 CDT)
- Rui Zhang (Fri Aug 03 2012 - 16:28:35 CDT)
- Giacomo Fiorin (Fri Aug 03 2012 - 16:01:59 CDT)
- Rui Zhang (Fri Aug 03 2012 - 15:53:47 CDT)
- Giacomo Fiorin (Fri Aug 03 2012 - 15:16:46 CDT)
- Rui Zhang (Fri Aug 03 2012 - 10:30:49 CDT)
- Giacomo Fiorin (Thu Aug 02 2012 - 19:15:51 CDT)
- Rui Zhang (Thu Aug 02 2012 - 19:06:25 CDT)
no. of CPUs for optimal GTX-690 performance
- Axel Kohlmeyer (Wed Nov 07 2012 - 11:05:48 CST)
- Aron Broom (Wed Nov 07 2012 - 10:23:21 CST)
- Michael Purdy (Wed Nov 07 2012 - 08:45:13 CST)
- Ajasja LjubetiÄ (Wed Nov 07 2012 - 04:57:11 CST)
- Ajasja LjubetiÄ (Wed Nov 07 2012 - 04:34:10 CST)
- Axel Kohlmeyer (Wed Nov 07 2012 - 02:45:29 CST)
- Aron Broom (Wed Nov 07 2012 - 02:16:46 CST)
- Giacomo Fiorin (Tue Nov 06 2012 - 14:46:02 CST)
- Aron Broom (Tue Nov 06 2012 - 13:44:06 CST)
- Ajasja LjubetiÄ (Tue Nov 06 2012 - 13:43:28 CST)
- Michael Purdy (Tue Nov 06 2012 - 13:01:41 CST)
NOE
- Jérôme Hénin (Tue Sep 20 2011 - 08:17:30 CDT)
- Jacopo Sgrignani (Tue Sep 20 2011 - 07:27:09 CDT)
non integer total charge
- Chris Harrison (Sat Apr 28 2012 - 21:23:42 CDT)
- raghav singh (Sat Apr 28 2012 - 21:16:02 CDT)
non integral charges
- Branko (Mon Apr 30 2012 - 08:24:29 CDT)
- raghav singh (Mon Apr 30 2012 - 08:06:15 CDT)
non-bonded potential in NAMD
- Jérôme Hénin (Sat Apr 30 2011 - 17:28:14 CDT)
- Molecular Dynamics (Sat Apr 30 2011 - 15:06:58 CDT)
non-zero charge
- Chris Harrison (Wed Jan 19 2011 - 21:08:22 CST)
- Bo Liu (Wed Jan 19 2011 - 16:31:22 CST)
- Kwee Hong (Wed Jan 19 2011 - 10:17:45 CST)
Nonbonded 3-body potential
- Axel Kohlmeyer (Fri Mar 23 2012 - 06:39:52 CDT)
- Xavier Bidault (Fri Mar 23 2012 - 05:44:59 CDT)
Nonzero BOUNDARY ENERGY without periodic boundary conditions
- David Minh (Tue Apr 10 2012 - 08:35:37 CDT)
- JC Gumbart (Mon Apr 09 2012 - 18:27:33 CDT)
- David Minh (Mon Apr 09 2012 - 12:36:25 CDT)
NOTICE: mail delivery status
- Jim Phillips (Sun Jun 03 2012 - 23:52:37 CDT)
NPT at 100 bar
- Axel Kohlmeyer (Wed Aug 22 2012 - 04:53:31 CDT)
- Francesco Pietra (Wed Aug 22 2012 - 04:37:57 CDT)
- Jernej Zidar (Wed Aug 22 2012 - 03:05:52 CDT)
- Francesco Pietra (Wed Aug 22 2012 - 03:02:03 CDT)
NPT equilibration
- Norman Geist (Fri Jul 01 2011 - 05:50:23 CDT)
- Norman Geist (Fri Jul 01 2011 - 05:49:38 CDT)
- bharat gupta (Fri Jul 01 2011 - 04:04:56 CDT)
NPT simulations in NAMD
- Axel Kohlmeyer (Tue Apr 05 2011 - 08:09:26 CDT)
- Hasan haska (Tue Apr 05 2011 - 07:31:52 CDT)
nucleic acids - total charge
- JC Gumbart (Tue May 01 2012 - 11:34:48 CDT)
- Raghav (Tue May 01 2012 - 11:18:22 CDT)
- JC Gumbart (Tue May 01 2012 - 10:48:19 CDT)
- Axel Kohlmeyer (Tue May 01 2012 - 07:37:18 CDT)
- Boyang Wang (Tue May 01 2012 - 02:50:35 CDT)
- raghav singh (Mon Apr 30 2012 - 04:55:38 CDT)
nvidia 275.09.07 driver
- Francesco Pietra (Thu Jun 30 2011 - 03:24:48 CDT)
nvidia cuda driver version
- Francesco Pietra (Fri Aug 05 2011 - 08:44:44 CDT)
NVT setup for monolayer
- Bjoern Olausson (Thu Apr 14 2011 - 02:17:35 CDT)
- Jim Phillips (Wed Apr 13 2011 - 10:09:49 CDT)
- Bjoern Olausson (Thu Apr 07 2011 - 08:24:32 CDT)
Oh dear, 'namd2 invoked oom-killer' ...
- Nicholas M Glykos (Fri Apr 15 2011 - 12:16:06 CDT)
- Jim Phillips (Fri Apr 15 2011 - 11:34:14 CDT)
- Nicholas M Glykos (Fri Apr 15 2011 - 09:55:35 CDT)
one question about gtp flipping in namd simulation
- Chris Harrison (Thu Feb 02 2012 - 13:49:56 CST)
- Liqun Zhang (Thu Feb 02 2012 - 13:42:27 CST)
one-sided harmonic restraint potential
- Giacomo Fiorin (Mon Jul 02 2012 - 21:59:42 CDT)
- Sandeep Patel (Mon Jul 02 2012 - 21:51:21 CDT)
online guide for using amber ff in NAMD
- George Madalin Giambasu (Wed Aug 03 2011 - 11:18:10 CDT)
Only one process running on cluster
- amin_at_imtech.res.in (Wed Jun 13 2012 - 02:25:14 CDT)
openAtom/NAMD2.9 implementation
- Bennion, Brian (Thu Aug 09 2012 - 12:17:57 CDT)
- Bennion, Brian (Mon Jul 30 2012 - 11:59:29 CDT)
OpenCL and AMD GPUs
- Aron Broom (Thu Nov 24 2011 - 15:53:33 CST)
- Axel Kohlmeyer (Wed Nov 23 2011 - 10:23:06 CST)
- Thomas Bishop (Wed Nov 23 2011 - 10:09:43 CST)
- Axel Kohlmeyer (Wed Nov 23 2011 - 09:52:47 CST)
- Aron Broom (Wed Nov 23 2011 - 09:06:13 CST)
- Axel Kohlmeyer (Wed Nov 23 2011 - 05:07:52 CST)
- Nicholas M Glykos (Wed Nov 23 2011 - 01:01:20 CST)
- Aron Broom (Tue Nov 22 2011 - 22:04:13 CST)
optimal CPU number for parallel MD of a small system
- Mert Gür (Fri Oct 19 2012 - 08:49:43 CDT)
- Isaure Chauvot de Beauchêne (Fri Oct 19 2012 - 08:32:57 CDT)
Oscillating Electric Field
- Cruz-Chu Eduardo Roberto (Fri Aug 31 2012 - 11:45:42 CDT)
- Quick, Ross (Fri Aug 31 2012 - 11:26:39 CDT)
output forces with tclBC
- Eduardo Cruz-Chu (Mon Mar 28 2011 - 04:33:15 CDT)
output nonbonded and bonded terms separately
- chris liopiri (Wed Mar 28 2012 - 04:59:36 CDT)
Output of thermodynamic integration
- Chris Harrison (Sun Jan 29 2012 - 16:08:41 CST)
- Okazaki, Keiichi (NIH/NIDDK) [F] (Sun Jan 29 2012 - 14:22:26 CST)
- Jérôme Hénin (Sat Jan 28 2012 - 12:52:45 CST)
- Okazaki, Keiichi (NIH/NIDDK) [F] (Sat Jan 28 2012 - 10:31:35 CST)
- Jérôme Hénin (Sat Jan 28 2012 - 04:25:19 CST)
- Kei-ichi Okazaki (Fri Jan 27 2012 - 18:16:47 CST)
outputting atom coordinated
- Ehsan Ban (Sun Sep 16 2012 - 20:01:45 CDT)
- Jacqueline Schmidt (Sun Sep 16 2012 - 16:17:25 CDT)
Pair interaction and thermo integration
- Courtney Taylor (Mon Aug 01 2011 - 09:32:38 CDT)
pairlist violations
- Thomas Brian (Tue Jul 10 2012 - 15:15:07 CDT)
- JC Gumbart (Tue Jul 10 2012 - 12:25:08 CDT)
- Axel Kohlmeyer (Tue Jul 10 2012 - 05:24:01 CDT)
- francesco oteri (Tue Jul 10 2012 - 03:40:42 CDT)
- Thomas Brian (Mon Jul 09 2012 - 18:44:55 CDT)
paper/articule on colvars module
- Leonardo Herrera (Tue Nov 29 2011 - 13:59:02 CST)
- Branko (Tue Nov 29 2011 - 04:16:42 CST)
- Giacomo Fiorin (Tue Nov 29 2011 - 01:12:39 CST)
- Leonardo Herrera (Mon Nov 28 2011 - 19:35:37 CST)
Parametarization and geometry optimization
- Dhiraj Srivastava (Tue Nov 20 2012 - 07:26:35 CST)
Parametarization and geometry optimization. .
- Ajasja LjubetiÄ (Tue Nov 20 2012 - 08:25:34 CST)
- Martin, Erik W (Tue Nov 20 2012 - 08:14:11 CST)
parameter file for DMPC lipid and protein system but with CHARMM36 lipids
- Prathit Chatterjee (Tue Jan 04 2011 - 01:14:10 CST)
- JC Gumbart (Mon Jan 03 2011 - 23:34:18 CST)
- Erica Smith (Mon Jan 03 2011 - 21:53:59 CST)
parameter file for POPC (RBCG model)
- Swarna M Patra (Thu Feb 09 2012 - 22:29:21 CST)
parameter for TFA (trifluoroacetic acid)
- liupeng012_at_mail.nankai.edu.cn (Fri May 13 2011 - 03:36:55 CDT)
Parameter in configuration NVE or NPT
- David Tanner (Wed Feb 16 2011 - 08:37:31 CST)
- snoze pa (Tue Feb 15 2011 - 11:17:03 CST)
Parameters for 3 methyl histidine.
- amin_at_imtech.res.in (Wed Sep 26 2012 - 09:13:34 CDT)
Parameters for Cesium
- Burgess, Don E (Thu May 17 2012 - 11:43:44 CDT)
Paratool`s error reading single point calculation.
- Ranyere Deyler (Sat Feb 26 2011 - 00:50:59 CST)
Parse Fep plugin error
- Joseph Antoine Garate (Fri Dec 23 2011 - 08:27:39 CST)
partial charges for organic ligands
- Richard Wood (Sat Mar 26 2011 - 22:18:50 CDT)
- Branko (Sat Mar 26 2011 - 16:09:35 CDT)
- Francesco Pietra (Sat Mar 26 2011 - 15:23:05 CDT)
- Branko (Sat Mar 26 2011 - 12:42:32 CDT)
- johan strumpfer (Sat Mar 26 2011 - 12:40:48 CDT)
- Francesco Pietra (Sat Mar 26 2011 - 11:45:26 CDT)
Patch at AutoPsfBuilder
- flavio seixas (Sun Sep 04 2011 - 14:17:38 CDT)
patch becoming too small
- Jorgen Simonsen (Tue Aug 09 2011 - 01:14:33 CDT)
patch for phosphotyrosine residue
- Jim Phillips (Wed Jun 22 2011 - 10:46:17 CDT)
- bharat gupta (Tue Jun 21 2011 - 20:53:38 CDT)
Patch link
- flavio seixas (Mon Jul 11 2011 - 10:16:54 CDT)
- Erik Nordgren (Sun Jul 10 2011 - 03:27:51 CDT)
- flavio seixas (Fri Jul 08 2011 - 14:11:38 CDT)
patch needed for tuple is missing
- Jim Phillips (Mon Jul 18 2011 - 15:35:28 CDT)
- JC Gumbart (Sat Jun 18 2011 - 23:49:47 CDT)
PBB File Format/Setup for PBC
- johan strumpfer (Fri Aug 19 2011 - 17:41:04 CDT)
- Anna James (Fri Aug 19 2011 - 07:24:11 CDT)
PBC
- johan strumpfer (Fri Jun 03 2011 - 12:09:55 CDT)
- Werner Crous (Thu Jun 02 2011 - 04:18:38 CDT)
- Werner Crous (Thu Jun 02 2011 - 04:05:41 CDT)
- johan strumpfer (Wed Jun 01 2011 - 12:19:04 CDT)
- johan strumpfer (Wed Jun 01 2011 - 11:03:04 CDT)
- Werner Crous (Wed Jun 01 2011 - 05:09:27 CDT)
pbc precision
- Thomas Brian (Thu Jun 28 2012 - 15:18:10 CDT)
PBC Wrap + TMD
- Gianluca Interlandi (Mon Oct 10 2011 - 14:02:58 CDT)
pbc wrap option for x,y,z lengths
- Axel Kohlmeyer (Mon Apr 25 2011 - 09:22:29 CDT)
- Zumot, Elia Nabil (Sun Apr 24 2011 - 19:38:43 CDT)
- Axel Kohlmeyer (Sun Apr 24 2011 - 14:53:20 CDT)
- Zumot, Elia Nabil (Sun Apr 24 2011 - 14:44:06 CDT)
- Axel Kohlmeyer (Sun Apr 24 2011 - 13:00:10 CDT)
- Zumot, Elia Nabil (Sun Apr 24 2011 - 12:51:16 CDT)
- Axel Kohlmeyer (Sat Apr 23 2011 - 03:37:20 CDT)
- Zumot, Elia Nabil (Fri Apr 22 2011 - 22:52:11 CDT)
- Axel Kohlmeyer (Fri Apr 22 2011 - 22:21:56 CDT)
- Zumot, Elia Nabil (Fri Apr 22 2011 - 14:03:29 CDT)
PDB sugar unit residue name
- Jim Phillips (Fri Mar 30 2012 - 11:30:08 CDT)
- Massimiliano Porrini (Fri Mar 30 2012 - 08:20:33 CDT)
- Massimiliano Porrini (Fri Mar 30 2012 - 07:06:15 CDT)
- Massimiliano Porrini (Fri Mar 30 2012 - 07:03:27 CDT)
- Massimiliano Porrini (Fri Mar 30 2012 - 04:57:14 CDT)
- Jim Phillips (Thu Mar 29 2012 - 17:09:39 CDT)
- Massimiliano Porrini (Thu Mar 29 2012 - 14:05:04 CDT)
- Olgun Guvench (Thu Mar 29 2012 - 11:14:52 CDT)
- Michelle Kuttel (Thu Mar 29 2012 - 09:30:25 CDT)
- Aron Broom (Thu Mar 29 2012 - 07:52:20 CDT)
- Massimiliano Porrini (Thu Mar 29 2012 - 06:03:40 CDT)
peculiar scaling on the GPU
- Axel Kohlmeyer (Wed Aug 01 2012 - 01:40:56 CDT)
- Ajasja LjubetiÄ (Tue Jul 31 2012 - 09:06:50 CDT)
pentacoordinate heme
- grazia cottone (Tue Mar 08 2011 - 16:58:27 CST)
- grazia cottone (Sun Mar 06 2011 - 09:43:02 CST)
Peptide planarity Dihedral angle restraints
- Vijay Vammi (Fri Dec 09 2011 - 00:47:00 CST)
- Chris Harrison (Fri Dec 09 2011 - 00:27:29 CST)
- Vijay Vammi (Thu Dec 08 2011 - 21:20:23 CST)
- Aron Broom (Thu Dec 08 2011 - 21:11:20 CST)
- Boyang Wang (Thu Dec 08 2011 - 20:17:02 CST)
- Vijay Vammi (Thu Dec 08 2011 - 20:07:12 CST)
peptide structure
- ipsita basu (Thu Jan 27 2011 - 02:29:21 CST)
- Chris Harrison (Sun Jan 23 2011 - 10:10:08 CST)
- ipsita basu (Tue Jan 18 2011 - 23:05:34 CST)
performance loss on GPUs
- Thomas Evangelidis (Wed Nov 28 2012 - 16:44:36 CST)
- Thomas Evangelidis (Wed Nov 28 2012 - 16:09:10 CST)
- Aron Broom (Wed Nov 28 2012 - 10:40:11 CST)
- Axel Kohlmeyer (Wed Nov 28 2012 - 10:07:02 CST)
- Aron Broom (Wed Nov 28 2012 - 09:57:06 CST)
- Axel Kohlmeyer (Wed Nov 28 2012 - 02:21:14 CST)
- Aron Broom (Wed Nov 28 2012 - 01:31:12 CST)
- Thomas Evangelidis (Wed Nov 28 2012 - 01:13:53 CST)
performance variation during run time
- Thomas C. Bishop (Wed Nov 28 2012 - 18:53:10 CST)
periodic boundaries
- farzad kiani (Sat Jul 07 2012 - 05:51:22 CDT)
Periodic Boundary Condition for a 630 Amino Acid Protein
- Babban Mia (Sun Aug 14 2011 - 09:19:18 CDT)
- Joshua Adelman (Sun Aug 14 2011 - 08:46:11 CDT)
- Babban Mia (Sun Aug 14 2011 - 08:15:28 CDT)
Periodic Boundary Condition in NAMD
- Jim Phillips (Fri Jun 03 2011 - 09:57:38 CDT)
- Van Ngo (Thu Jun 02 2011 - 23:55:08 CDT)
Periodic Boundary conditions
- ishiikai08_at_yahoo.co.jp (Mon Jun 20 2011 - 06:11:49 CDT)
- Axel Kohlmeyer (Thu Jun 02 2011 - 06:19:54 CDT)
- ishiikai08_at_yahoo.co.jp (Thu Jun 02 2011 - 03:14:12 CDT)
- Jim Phillips (Wed Jun 01 2011 - 13:08:55 CDT)
- ishiikai08_at_yahoo.co.jp (Tue May 31 2011 - 21:57:03 CDT)
Periodic cell has become too small
- lecan (Fri May 04 2012 - 00:19:38 CDT)
Periodic cell has become too small for original patch grid!â€
- Axel Kohlmeyer (Fri Sep 30 2011 - 08:06:26 CDT)
- Andres Morales N (Thu Sep 29 2011 - 23:52:39 CDT)
periodicity error
- Shomesankar Bhunia (Mon Sep 17 2012 - 04:33:50 CDT)
PhD position in Computational Structural Biology at MPI Muenster
- Vlad Cojocaru (Fri May 13 2011 - 04:47:24 CDT)
phosphorilated serine
- Branko (Sat Sep 17 2011 - 11:01:42 CDT)
phosphotyrosine
- johan strumpfer (Mon Jun 20 2011 - 06:30:03 CDT)
- bharat gupta (Sun Jun 19 2011 - 19:26:37 CDT)
Pico scale to nanoscale simulation....alteration if .conf files required
- Erik Nordgren (Tue Jul 26 2011 - 20:54:30 CDT)
- amit banerjee (Mon Jul 25 2011 - 07:42:35 CDT)
- Erik Nordgren (Thu Jul 21 2011 - 20:22:25 CDT)
- amit banerjee (Sun Jul 17 2011 - 21:28:43 CDT)
please help
- Aron Broom (Fri Jun 08 2012 - 21:13:16 CDT)
- Adeleke Adebayo Abayomi (Fri Jun 08 2012 - 14:38:18 CDT)
Please read: fatal error namd 2.7b1 for Win32 Memory allocation failed on processor > 0
- subbarao kanchi (Mon Aug 27 2012 - 13:59:03 CDT)
- Suranga Edirisinghe (Mon Aug 27 2012 - 12:28:30 CDT)
- Mariana Graterol (Sun Aug 26 2012 - 14:07:17 CDT)
PLUMED release 1.3 available
- Massimiliano Bonomi (Wed Nov 09 2011 - 09:05:09 CST)
PME and net charge in the system
- Salvatore Mario Cosseddu (Thu Oct 27 2011 - 12:20:26 CDT)
- Chris Harrison (Thu Oct 27 2011 - 12:12:46 CDT)
- Salvatore Mario Cosseddu (Thu Oct 27 2011 - 12:00:12 CDT)
PME for electrostatics and cutoff for vdW?
- Christian Jorgensen (Thu Feb 10 2011 - 11:07:53 CST)
PME Grid Settings and its significance relative to a cutoff value
- Axel Kohlmeyer (Fri Aug 19 2011 - 13:05:26 CDT)
- Erik Nordgren (Fri Aug 19 2011 - 12:38:34 CDT)
- Andrea Holfelder (Tue Aug 16 2011 - 15:07:14 CDT)
PME or not PME? What happens if PME is turned off?
- Chris Harrison (Wed Aug 03 2011 - 14:48:12 CDT)
- esmael (Tue Aug 02 2011 - 18:54:03 CDT)
- Bjoern Olausson (Wed Jul 20 2011 - 03:03:10 CDT)
- Chris Harrison (Tue Jul 19 2011 - 14:45:48 CDT)
- Bjoern Olausson (Tue Jul 19 2011 - 01:48:50 CDT)
- Jérôme Hénin (Mon Jul 18 2011 - 15:27:09 CDT)
- Bjoern Olausson (Mon Jul 18 2011 - 04:10:08 CDT)
PMF
- Axel Kohlmeyer (Tue Oct 25 2011 - 07:23:21 CDT)
- jafar azamat (Tue Oct 25 2011 - 06:52:28 CDT)
- jafar azamat (Tue May 24 2011 - 00:47:30 CDT)
PMF calculation
- jafar azamat (Mon May 23 2011 - 07:31:13 CDT)
POPC membrane model in pH 4
- zhjpan_at_mail.ustc.edu.cn (Sat Sep 03 2011 - 10:12:06 CDT)
- Axel Kohlmeyer (Sat Sep 03 2011 - 09:50:08 CDT)
- zhjpan_at_mail.ustc.edu.cn (Sat Sep 03 2011 - 09:36:58 CDT)
Positional restraints - Dielectric constant
- Giacomo Fiorin (Wed Mar 02 2011 - 13:42:33 CST)
- Axel Kohlmeyer (Wed Mar 02 2011 - 11:39:39 CST)
- Francesco Pietra (Wed Mar 02 2011 - 10:56:18 CST)
Possibility of modifying the non-bonded terms of the potential
- Jérôme Hénin (Sat Jul 09 2011 - 03:34:36 CDT)
- Ali Emileh (Fri Jul 08 2011 - 16:58:44 CDT)
Possible bug or inconvenience
- Chris Harrison (Wed Feb 15 2012 - 15:12:03 CST)
- Norman Geist (Wed Feb 15 2012 - 04:06:34 CST)
postdoc position available
- JC Gumbart (Tue Oct 16 2012 - 00:47:41 CDT)
postdoctoral position available in simulations of ionic liquids at NASA Ames
- Lawson, John W. (ARC-TSM) (Mon Jul 16 2012 - 00:35:46 CDT)
Predicting the binding affinity and anion
- Aron Broom (Wed Nov 23 2011 - 12:46:33 CST)
- Axel Kohlmeyer (Wed Nov 23 2011 - 07:37:19 CST)
- bharat gupta (Wed Nov 23 2011 - 07:23:29 CST)
Pressure Calculation
- Priyan Amaras (Fri Sep 02 2011 - 12:43:25 CDT)
Pressure in equilibration stage of MD
- Mariana Graterol (Fri Oct 19 2012 - 08:42:24 CDT)
- Aron Broom (Thu Oct 18 2012 - 17:34:02 CDT)
- Mariana Graterol (Thu Oct 18 2012 - 16:52:05 CDT)
Pressure problem to equilibrate NPT
- Aron Broom (Mon Oct 22 2012 - 21:14:42 CDT)
- Mariana Graterol (Mon Oct 22 2012 - 17:28:55 CDT)
Pressure Problems, Excessively High Readings
- Rajan Vatassery (Mon Nov 14 2011 - 01:14:41 CST)
- johan strumpfer (Tue Nov 08 2011 - 21:13:23 CST)
- Jeffrey Potoff (Wed Nov 09 2011 - 04:02:30 CST)
- Rajan Vatassery (Tue Nov 08 2011 - 20:43:10 CST)
pressure profile calculations
- upayan baul (Sat Nov 17 2012 - 04:55:59 CST)
- JC Gumbart (Mon Aug 20 2012 - 20:58:53 CDT)
- Grace Brannigan (Mon Aug 20 2012 - 11:22:12 CDT)
- JC Gumbart (Sat Aug 18 2012 - 18:24:08 CDT)
- Grace Brannigan (Fri Aug 17 2012 - 06:16:21 CDT)
- Grace Brannigan (Thu Aug 16 2012 - 14:33:21 CDT)
- JC Gumbart (Mon Aug 13 2012 - 21:11:20 CDT)
print center of mass
- Ajasja LjubetiÄ (Tue May 10 2011 - 11:10:48 CDT)
- Axel Kohlmeyer (Tue May 10 2011 - 11:01:35 CDT)
- Jacopo Sgrignani (Tue May 10 2011 - 10:54:09 CDT)
Printing energy of selected atoms in NAMD
- Aron Broom (Mon Sep 24 2012 - 14:06:40 CDT)
- Ganesh Kamath (Mon Sep 24 2012 - 13:59:33 CDT)
prm and top files for charmm19 force field
- oguz gurbulak (Fri Jun 03 2011 - 09:22:47 CDT)
Problem building NAMD (multiple definitions)
- Miroslav Hodak (Mon May 23 2011 - 18:14:35 CDT)
- Jim Phillips (Mon May 23 2011 - 17:57:27 CDT)
- Miroslav Hodak (Mon May 23 2011 - 17:49:59 CDT)
- Axel Kohlmeyer (Mon May 23 2011 - 17:41:37 CDT)
- Miroslav Hodak (Mon May 23 2011 - 17:38:47 CDT)
- Axel Kohlmeyer (Mon May 23 2011 - 17:12:21 CDT)
- Jim Phillips (Mon May 23 2011 - 17:08:21 CDT)
- Miroslav Hodak (Mon May 23 2011 - 05:47:08 CDT)
problem for simulation of membrane protein system
- Giacomo Fiorin (Tue Apr 12 2011 - 11:30:39 CDT)
- Jeffrey Potoff (Tue Apr 12 2011 - 11:29:25 CDT)
- Buddhadev Maiti (Tue Apr 12 2011 - 11:06:30 CDT)
problem in accelerated MD with NAMD-GPU
- Thomas Evangelidis (Mon Nov 19 2012 - 11:19:56 CST)
problem in distance.tcl
- amit banerjee (Wed Jun 01 2011 - 22:37:42 CDT)
problem in restarting
- Jim Phillips (Fri Apr 15 2011 - 08:06:56 CDT)
- Axel Kohlmeyer (Thu Apr 14 2011 - 11:42:59 CDT)
- Ajasja LjubetiÄ (Thu Apr 14 2011 - 10:28:19 CDT)
- Jérôme Hénin (Thu Apr 14 2011 - 09:52:59 CDT)
- Axel Kohlmeyer (Thu Apr 14 2011 - 08:29:24 CDT)
- ipsita basu (Thu Apr 14 2011 - 02:11:24 CDT)
Problem of 'missing stage' in colvars.state file
- Jérôme Hénin (Wed Jun 20 2012 - 15:59:20 CDT)
- Jérôme Hénin (Wed Jun 20 2012 - 06:32:28 CDT)
- Shaon Chakrabarti (Tue Jun 19 2012 - 12:15:51 CDT)
problem regarding charmm parameter file of carbon nano tube
- kanchi subbarao rao (Mon Nov 21 2011 - 09:52:36 CST)
- kanchi subbarao rao (Sun Nov 20 2011 - 16:43:01 CST)
Problem running NAMD
- Nicholas M Glykos (Mon Jun 18 2012 - 02:16:27 CDT)
- mpahleva_at_abo.fi (Mon Jun 18 2012 - 01:56:37 CDT)
Problem running NAMD 2.8 with ibverbs
- Moritz Schlarb (Wed Jan 11 2012 - 04:20:57 CST)
- Moritz Schlarb (Fri Jan 06 2012 - 09:41:49 CST)
- Moritz Schlarb (Fri Jan 06 2012 - 09:29:18 CST)
problem to analyze the output of FEP file using vmd plugin
- sudipta (Mon Jan 30 2012 - 15:58:41 CST)
Problem while using MARTINI force field with NAMD 2.8
- rohan uttarwar (Tue Jul 12 2011 - 11:42:14 CDT)
problem with gpu namd 2.9b3
- Peter Jones (Mon Apr 23 2012 - 01:00:11 CDT)
- Aron Broom (Fri Apr 20 2012 - 09:25:40 CDT)
- Peter Jones (Thu Apr 19 2012 - 04:30:42 CDT)
problem with installing NAMD in Linux Red Hat
- Axel Kohlmeyer (Mon Mar 05 2012 - 08:57:35 CST)
- Aron Broom (Mon Mar 05 2012 - 08:33:01 CST)
- rukman kesh (Mon Mar 05 2012 - 08:24:16 CST)
- Andreas Förster (Mon Mar 05 2012 - 03:20:03 CST)
- Aron Broom (Mon Mar 05 2012 - 01:50:12 CST)
- rukman kesh (Mon Mar 05 2012 - 01:39:38 CST)
- Chris Harrison (Thu Mar 01 2012 - 00:17:28 CST)
- rukman kesh (Wed Feb 29 2012 - 00:40:12 CST)
problem with MD
- hamze rahimi (Tue Feb 15 2011 - 00:25:25 CST)
Problem with Methane-Methane PMF
- Shaon Chakrabarti (Sat May 12 2012 - 13:46:01 CDT)
- Giacomo Fiorin (Fri May 11 2012 - 16:40:03 CDT)
- Aron Broom (Fri May 11 2012 - 16:38:03 CDT)
- Shaon Chakrabarti (Fri May 11 2012 - 16:08:23 CDT)
Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..."
- Jim Phillips (Thu Jun 09 2011 - 10:53:46 CDT)
- David McGiven (Wed Jun 08 2011 - 09:00:34 CDT)
problem with NAMD surface area calculation (LCPO) -- fixed
- Clayton (Mon Jul 23 2012 - 10:08:35 CDT)
Problem with NAMD2.8 & prmtop files made with AMBER11/AmberTools1.5
- George Madalin Giambasu (Wed Sep 28 2011 - 19:04:22 CDT)
- Irene Newhouse (Wed Sep 28 2011 - 15:40:24 CDT)
Problem with NVE simulation
- Axel Kohlmeyer (Thu Jan 05 2012 - 16:48:47 CST)
- gaborekt_at_duq.edu (Thu Jan 05 2012 - 15:42:10 CST)
Problem with parameter file in Pair Interaction Calculation
- Boyang Wang (Mon Jan 09 2012 - 08:27:02 CST)
- M Mahjour (Mon Jan 09 2012 - 05:47:20 CST)
- M Mahjour (Sun Jan 08 2012 - 00:14:50 CST)
problem with paramters?
- Albert (Thu Mar 22 2012 - 00:25:27 CDT)
problem with pdb pdf!
- Jacqueline Schmidt (Sun Sep 02 2012 - 21:36:17 CDT)
problem with pdb psf files!
- Jacqueline Schmidt (Sun Sep 02 2012 - 21:44:59 CDT)
Problem with SPC/E water simulation
- Joshua D. Moore (Fri Mar 04 2011 - 17:54:20 CST)
- Axel Kohlmeyer (Fri Mar 04 2011 - 15:50:13 CST)
- Davide Vanzo/FS/VCU (Fri Mar 04 2011 - 15:07:42 CST)
Problems Bionanotechnology Tutorial
- Salvador H-V (Fri Oct 21 2011 - 22:19:01 CDT)
Problems compiling NAMD on 8-core Mac
- Minh, David D. (Tue Feb 01 2011 - 11:28:43 CST)
- Minh, David D. (Tue Feb 01 2011 - 00:23:07 CST)
- Jim Phillips (Tue Feb 01 2011 - 09:26:54 CST)
- Chris Harrison (Mon Jan 31 2011 - 22:49:39 CST)
- Minh, David D. (Mon Jan 31 2011 - 17:44:01 CST)
- Chris Harrison (Mon Jan 31 2011 - 16:44:23 CST)
- Jim Phillips (Mon Jan 31 2011 - 16:39:49 CST)
- Minh, David D. (Mon Jan 31 2011 - 12:25:40 CST)
Problems in setting up low pH systems
- Giacomo Fiorin (Wed Jan 11 2012 - 10:03:34 CST)
- Sheng, Zi-Zhang (Wed Jan 11 2012 - 09:43:31 CST)
problems with auto-psf gen and autoionize for ligand with atomtypes of more than 4 characters
- Raul Araya (Wed Sep 12 2012 - 16:34:57 CDT)
problems with simulation of LJ fluid
- Rajan Vatassery (Mon Dec 03 2012 - 12:35:42 CST)
- Jeffrey Potoff (Mon Dec 03 2012 - 12:09:01 CST)
- Axel Kohlmeyer (Mon Dec 03 2012 - 11:20:58 CST)
- ç¿æž—å²½ (Sat Dec 01 2012 - 17:30:28 CST)
Proposed Feature in Targeted MD
- Ryan McGreevy (Wed Feb 02 2011 - 12:48:58 CST)
- felmerino_at_uchile.cl (Mon Jan 31 2011 - 20:20:04 CST)
- Jérôme Hénin (Mon Jan 31 2011 - 16:39:37 CST)
- Minh, David D. (Mon Jan 31 2011 - 15:34:48 CST)
- Minh, David D. (Mon Jan 31 2011 - 15:33:42 CST)
- V.Ovchinnikov (Mon Jan 31 2011 - 15:53:38 CST)
- V.Ovchinnikov (Mon Jan 31 2011 - 15:14:15 CST)
- Minh, David D. (Mon Jan 31 2011 - 13:12:38 CST)
Protein distort during equilibration
- snoze pa (Mon Jun 13 2011 - 10:22:10 CDT)
protein folding by simulated annealing method
- Puspita Halder (Thu May 24 2012 - 00:01:25 CDT)
protein folding by simulated anneling
- Aron Broom (Mon May 28 2012 - 08:55:11 CDT)
- Puspita Halder (Mon May 28 2012 - 01:11:53 CDT)
Protein ligand simulation Tutorial
- poker_at_physics.usyd.edu.au (Wed Feb 29 2012 - 17:01:06 CST)
- Chris Chipot (Wed Feb 29 2012 - 08:07:08 CST)
- sai nitin (Wed Feb 29 2012 - 06:47:38 CST)
protein moving out during npt equilibration
- Giacomo Fiorin (Wed Jul 13 2011 - 10:54:10 CDT)
- bharat gupta (Wed Jul 13 2011 - 10:48:48 CDT)
Protein moving out of box during npt simulation
- Bjoern Olausson (Fri Jul 08 2011 - 02:50:29 CDT)
- snoze pa (Thu Jul 07 2011 - 10:02:09 CDT)
- bharat gupta (Tue Jul 05 2011 - 21:25:04 CDT)
- snoze pa (Tue Jul 05 2011 - 10:00:23 CDT)
- Bjoern Olausson (Tue Jul 05 2011 - 04:22:50 CDT)
- bharat gupta (Tue Jul 05 2011 - 03:40:59 CDT)
- Norman Geist (Tue Jul 05 2011 - 01:15:20 CDT)
- bharat gupta (Tue Jul 05 2011 - 00:33:30 CDT)
protein on solid surface
- Giovanni Bellesia (Fri Apr 08 2011 - 13:45:31 CDT)
- Giacomo Fiorin (Fri Apr 08 2011 - 11:21:33 CDT)
- Giovanni Bellesia (Fri Apr 08 2011 - 09:48:50 CDT)
Protein-DNA simulations
- Chris Harrison (Wed Jan 19 2011 - 21:24:43 CST)
- S.Archana (Mon Jan 17 2011 - 04:41:27 CST)
Protonated nucleotides
- Zack Scholl (Wed Apr 04 2012 - 16:02:22 CDT)
- Aksimentiev, Oleksii (Mon Apr 02 2012 - 13:45:27 CDT)
- johan strumpfer (Mon Apr 02 2012 - 11:15:50 CDT)
- Zack Scholl (Mon Apr 02 2012 - 07:49:53 CDT)
PSF and PDB file for SWM4 water models
- Jim Phillips (Thu May 26 2011 - 09:39:22 CDT)
- saman amiri (Thu May 26 2011 - 07:37:04 CDT)
psf problem
- ipsita basu (Sat Mar 12 2011 - 04:33:39 CST)
- ipsita basu (Fri Mar 11 2011 - 08:24:10 CST)
psfgen - ACE cap on PRO
- Peter Freddolino (Thu Mar 10 2011 - 19:59:14 CST)
- Marc Charendoff (Thu Mar 10 2011 - 19:07:33 CST)
psfgen - any version capable of reading extended PSF files?
- Bjoern Olausson (Fri Feb 11 2011 - 05:47:05 CST)
psfgen and CHARMM19 explicit exclusions
- Andrey (Sat Sep 29 2012 - 13:04:37 CDT)
- Chris Harrison (Fri Sep 28 2012 - 21:24:17 CDT)
- Andrey (Thu Sep 27 2012 - 22:48:29 CDT)
- Andrey (Mon Sep 17 2012 - 22:38:24 CDT)
- Andrey (Tue Sep 11 2012 - 21:10:20 CDT)
Psfgen CTER issues
- Evgeny Bulat (Tue Jun 05 2012 - 13:00:52 CDT)
Psfgen Errors for C-type Heme
- Thomas Freeman (Tue Mar 01 2011 - 14:15:56 CST)
- Thomas Freeman (Mon Feb 28 2011 - 13:46:04 CST)
psfgen tyrosine anion-Fe bond
- Francesco Pietra (Sun Apr 01 2012 - 12:14:27 CDT)
- Francesco Pietra (Sun Apr 01 2012 - 12:03:17 CDT)
- Francesco Pietra (Sun Apr 01 2012 - 09:53:13 CDT)
psfgen warnings
- hannes.loeffler_at_stfc.ac.uk (Mon Apr 16 2012 - 02:35:35 CDT)
- Syed Kashif Zafar (Sun Apr 15 2012 - 23:28:49 CDT)
- Vidhya Sankar (Sun Apr 15 2012 - 01:27:14 CDT)
pulling constant verocity
- ishiikai08_at_yahoo.co.jp (Tue Oct 16 2012 - 02:13:22 CDT)
pulling force didn't drop to zero in SMD
- Luthur Cheung (Wed Jun 06 2012 - 16:52:50 CDT)
- Eric H. Lee (Wed Jun 06 2012 - 11:28:19 CDT)
- johan strumpfer (Wed Jun 06 2012 - 09:21:23 CDT)
- Luthur Cheung (Wed Jun 06 2012 - 10:27:58 CDT)
- Ajasja LjubetiÄ (Wed Jun 06 2012 - 08:47:35 CDT)
- Luthur Cheung (Wed Jun 06 2012 - 08:31:43 CDT)
pulling force doesn't drop to zero in SMD
- Luthur Cheung (Tue Jun 05 2012 - 19:06:17 CDT)
Q=AD=94=E5=A4=8D:_=E7=AD=94=E5=A4=8D:__compilation_of_n?= amd
- TAO WANG (Tue May 10 2011 - 20:42:49 CDT)
Q=AD=94=E5=A4=8D:__compilation_of_namd?=
- Jim Phillips (Tue May 10 2011 - 20:32:27 CDT)
- TAO WANG (Mon May 09 2011 - 01:27:12 CDT)
- TAO WANG (Sun May 08 2011 - 19:34:03 CDT)
q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd
- Bjoern Olausson (Thu May 12 2011 - 11:13:21 CDT)
- Bjoern Olausson (Thu May 12 2011 - 09:58:47 CDT)
- Bjoern Olausson (Thu May 12 2011 - 08:11:57 CDT)
- Bjoern Olausson (Thu May 12 2011 - 02:45:49 CDT)
QM/MM
- QFrank_X=2E_V=E1zquez=22?= (Mon Apr 11 2011 - 18:23:26 CDT)
Quartz modelling
- Cruz-Chu Eduardo Roberto (Thu Jul 28 2011 - 03:20:53 CDT)
- Nikita Vakula (Thu Jul 28 2011 - 00:46:05 CDT)
queries about "Tclforces" utility in NAMD
- harish vashisth (Sun May 27 2012 - 17:39:01 CDT)
- harish vashisth (Fri May 25 2012 - 12:43:50 CDT)
- Jérôme Hénin (Fri May 25 2012 - 12:17:14 CDT)
- harish vashisth (Fri May 25 2012 - 11:25:10 CDT)
- Jérôme Hénin (Fri May 25 2012 - 11:11:23 CDT)
- harish vashisth (Fri May 25 2012 - 10:06:39 CDT)
- harish vashisth (Fri May 25 2012 - 09:57:43 CDT)
- Axel Kohlmeyer (Fri May 25 2012 - 05:54:27 CDT)
- Jérôme Hénin (Fri May 25 2012 - 02:48:01 CDT)
- harish vashisth (Fri May 25 2012 - 00:06:28 CDT)
Query about compressing PSF files
- Seetha Pothapragada (Fri Jun 08 2012 - 15:44:22 CDT)
Query about switch function using AMBER ff99SB forcefield and NAMD simulation code
- Madhurima Jana (Tue Jul 19 2011 - 06:41:25 CDT)
Question about "Free Energy of Conformational Change Calculations"
- Giacomo Fiorin (Mon Feb 06 2012 - 11:13:21 CST)
- Shen, Han (Mon Feb 06 2012 - 11:03:44 CST)
question about "useflexiblecell' command in NAMD operation
- Aron Broom (Fri Sep 07 2012 - 15:39:38 CDT)
- Patrick Chiu (Fri Sep 07 2012 - 14:05:32 CDT)
question about dcd file
- Chiara Cosenza unina (Wed May 30 2012 - 07:40:27 CDT)
- Cesar Millan (Wed May 30 2012 - 07:39:21 CDT)
- Hasan haska (Wed May 30 2012 - 07:22:11 CDT)
question about Distance XY
- Song, Hyundeok (songhk) (Tue Sep 13 2011 - 09:10:07 CDT)
- Jérôme Hénin (Tue Sep 13 2011 - 02:50:13 CDT)
- Song, Hyundeok (songhk) (Mon Sep 12 2011 - 23:27:05 CDT)
Question about end of log file
- Azat Mukhametov (Mon May 30 2011 - 21:53:50 CDT)
- Jim Phillips (Sun May 29 2011 - 22:37:30 CDT)
- Rajan Vatassery (Sun May 29 2011 - 14:14:34 CDT)
Question about equilibration
- snoze pa (Thu Jun 16 2011 - 17:33:37 CDT)
- johan strumpfer (Wed Jun 15 2011 - 13:22:56 CDT)
- johan strumpfer (Wed Jun 15 2011 - 13:10:10 CDT)
- Reichert, David (Wed Jun 15 2011 - 14:21:33 CDT)
- Gianluca Interlandi (Wed Jun 15 2011 - 14:18:43 CDT)
- Richard Wood (Wed Jun 15 2011 - 14:12:14 CDT)
- Gianluca Interlandi (Wed Jun 15 2011 - 14:03:57 CDT)
- Richard Wood (Wed Jun 15 2011 - 13:47:59 CDT)
- Richard Wood (Wed Jun 15 2011 - 13:16:00 CDT)
- Richard Wood (Wed Jun 15 2011 - 12:35:44 CDT)
- snoze pa (Wed Jun 15 2011 - 12:06:57 CDT)
- johan strumpfer (Wed Jun 15 2011 - 11:27:45 CDT)
- johan strumpfer (Wed Jun 15 2011 - 11:48:06 CDT)
- snoze pa (Wed Jun 15 2011 - 11:38:17 CDT)
- johan strumpfer (Wed Jun 15 2011 - 11:19:17 CDT)
- snoze pa (Wed Jun 15 2011 - 11:20:04 CDT)
- snoze pa (Wed Jun 15 2011 - 11:07:51 CDT)
- snoze pa (Wed Jun 15 2011 - 11:02:53 CDT)
question about force information
- Ajasja LjubetiÄ (Thu Mar 24 2011 - 14:22:10 CDT)
- Osman Yogurtcu (Thu Mar 24 2011 - 09:56:25 CDT)
- oguz gurbulak (Thu Mar 24 2011 - 06:02:14 CDT)
- oguz gurbulak (Thu Mar 24 2011 - 04:43:20 CDT)
Question about GPUs hardware.
- Aron Broom (Mon Apr 23 2012 - 19:51:44 CDT)
- Aron Broom (Mon Apr 23 2012 - 17:57:56 CDT)
- Cesar Millan (Mon Apr 23 2012 - 17:32:01 CDT)
question about namd simulation on protein in tip4p water box
- Chris Harrison (Fri Oct 28 2011 - 13:43:51 CDT)
- Liqun Zhang (Fri Oct 28 2011 - 13:14:36 CDT)
question about NPT
- Boyang Wang (Thu Jan 19 2012 - 08:18:54 CST)
- Axel Kohlmeyer (Thu Jan 19 2012 - 08:12:54 CST)
- Boyang Wang (Thu Jan 19 2012 - 05:55:23 CST)
- Axel Kohlmeyer (Thu Jan 19 2012 - 05:14:04 CST)
- Boyang Wang (Thu Jan 19 2012 - 04:03:21 CST)
- oguz gurbulak (Thu Jan 19 2012 - 03:51:42 CST)
- Boyang Wang (Thu Jan 19 2012 - 02:16:03 CST)
- JC Gumbart (Wed Jan 18 2012 - 12:36:43 CST)
- oguz gurbulak (Wed Jan 18 2012 - 02:06:19 CST)
Question about optmem input files
- Carlos Sosa (Thu Jun 14 2012 - 10:33:50 CDT)
question about relative binding free energy calculation method using FEP
- JC Gumbart (Sun Nov 25 2012 - 00:46:48 CST)
- dbaogen (Sat Nov 24 2012 - 21:50:05 CST)
- Chris Chipot (Sat Nov 24 2012 - 09:54:46 CST)
- dbaogen (Sat Nov 24 2012 - 05:58:55 CST)
question about rotation force in SMD
- Giacomo Fiorin (Wed Apr 27 2011 - 10:00:33 CDT)
- jnsong (Wed Apr 27 2011 - 09:34:09 CDT)
Question about silver nanoparticle simulation
- Axel Kohlmeyer (Wed Oct 19 2011 - 09:26:27 CDT)
- Yao Xiao (Wed Oct 19 2011 - 08:37:23 CDT)
Question about targetsNumSteps in ColVar
- Wang Yi (Wed May 02 2012 - 12:05:16 CDT)
- Giacomo Fiorin (Wed May 02 2012 - 11:57:34 CDT)
- Wang Yi (Wed May 02 2012 - 11:54:20 CDT)
- Giacomo Fiorin (Wed May 02 2012 - 11:38:18 CDT)
- Wang Yi (Wed May 02 2012 - 08:52:26 CDT)
question about v2.8
- sibel.cakan (Tue Jun 07 2011 - 09:01:58 CDT)
question about wrap atoms to its original coordinates
- jnsong (Wed May 18 2011 - 00:06:20 CDT)
question and NAMD operation
- Chris Harrison (Wed Aug 29 2012 - 15:45:39 CDT)
- snoze pa (Wed Aug 29 2012 - 15:33:48 CDT)
- Patrick Chiu (Wed Aug 29 2012 - 15:19:36 CDT)
question from a tutorial
- JC Gumbart (Thu Jan 20 2011 - 14:29:23 CST)
- Lisa Brown (Thu Jan 20 2011 - 14:17:29 CST)
question of MMPBSA calculation combined NAMD and APBS software
- Aron Broom (Thu Oct 11 2012 - 22:18:13 CDT)
- baogen duan (Thu Oct 11 2012 - 20:52:22 CDT)
Question of using deuterated water in NAMD
- Jérôme Hénin (Tue Sep 04 2012 - 14:25:57 CDT)
- Ganesh Kamath (Tue Sep 04 2012 - 13:13:27 CDT)
question on modifyAppliedForces()
- Jim Phillips (Tue May 10 2011 - 21:31:42 CDT)
- Bennion, Brian (Fri Apr 22 2011 - 12:11:27 CDT)
question on residue rmsd.tcl
- Ada Zhan (Mon Jun 06 2011 - 14:25:36 CDT)
- amit banerjee (Mon Jun 06 2011 - 00:18:48 CDT)
- Ada Zhan (Thu Jun 02 2011 - 14:06:00 CDT)
- amit banerjee (Wed Jun 01 2011 - 22:49:17 CDT)
question on the center of mass calculation in colvar
- Jérôme Hénin (Sat Apr 16 2011 - 10:55:11 CDT)
- Giacomo Fiorin (Sat Apr 16 2011 - 10:33:23 CDT)
- Hyonseok Hwang (Sat Apr 16 2011 - 09:57:16 CDT)
Question regarding FEP parameters
- Chris Harrison (Fri Aug 31 2012 - 20:06:54 CDT)
- snoze pa (Fri Aug 31 2012 - 12:06:48 CDT)
- Chris Harrison (Wed Aug 29 2012 - 15:32:52 CDT)
- snoze pa (Wed Aug 29 2012 - 13:47:31 CDT)
- snoze pa (Wed Aug 29 2012 - 13:05:15 CDT)
Question regarding NAMD membrane tutorial
- Chris Harrison (Thu Feb 03 2011 - 18:32:04 CST)
- snoze pa (Wed Feb 02 2011 - 13:03:38 CST)
- Chris Harrison (Mon Jan 31 2011 - 11:11:43 CST)
- snoze pa (Mon Jan 31 2011 - 10:49:07 CST)
question regarding simulated annealing
- Chris Harrison (Mon Sep 10 2012 - 23:17:47 CDT)
- Puspita Halder (Fri Aug 31 2012 - 00:46:05 CDT)
- Puspita Halder (Thu Aug 30 2012 - 08:15:51 CDT)
- Chris Harrison (Thu Aug 30 2012 - 02:28:00 CDT)
- Puspita Halder (Tue Aug 28 2012 - 07:03:39 CDT)
Questions
- Joshua Adelman (Mon Oct 10 2011 - 21:54:49 CDT)
- Kevin Littrell (Mon Oct 10 2011 - 21:20:37 CDT)
questions about accelerated MD
- Thomas Evangelidis (Mon Sep 24 2012 - 09:46:30 CDT)
questions about the heat diffusion calculation in the tutorial
- charlie (Sun May 22 2011 - 11:57:56 CDT)
questions regarding ABF sampling in a DMPC bilayer
- Ajasja LjubetiÄ (Mon Jan 30 2012 - 06:49:52 CST)
- Jérôme Hénin (Fri Jan 27 2012 - 09:10:44 CST)
- Ajasja LjubetiÄ (Fri Jan 27 2012 - 08:03:54 CST)
- Giacomo Fiorin (Wed Jan 18 2012 - 13:13:50 CST)
- felmerino_at_uchile.cl (Wed Jan 18 2012 - 12:27:31 CST)
- Giacomo Fiorin (Wed Jan 18 2012 - 12:05:02 CST)
- Jérôme Hénin (Wed Jan 18 2012 - 12:00:28 CST)
- Ajasja LjubetiÄ (Wed Jan 18 2012 - 08:12:20 CST)
Quick TCl scripting question
- Axel Kohlmeyer (Wed Sep 21 2011 - 21:09:50 CDT)
- Anthony Rey (Wed Sep 21 2011 - 20:57:07 CDT)
R: restart file
- Namd Namd (Mon Feb 27 2012 - 01:57:04 CST)
- Namd Namd (Mon Feb 27 2012 - 02:42:32 CST)
- Chris Harrison (Sat Feb 25 2012 - 11:50:08 CST)
- Aron Broom (Sat Feb 25 2012 - 11:00:24 CST)
- Nicholas M Glykos (Sat Feb 25 2012 - 09:38:27 CST)
- Chiara.cosenza (Sat Feb 25 2012 - 09:16:29 CST)
ramd firstRamdAtom
- Francesco Pietra (Mon Mar 28 2011 - 02:22:20 CDT)
RAMD Setting parameter TclForces from script failed
- Jim Phillips (Wed Apr 13 2011 - 08:33:57 CDT)
- Francesco Pietra (Tue Mar 29 2011 - 06:09:40 CDT)
- Vlad Cojocaru (Tue Mar 29 2011 - 04:59:25 CDT)
- Francesco Pietra (Tue Mar 29 2011 - 02:51:19 CDT)
- Cojocaru, Vlad (Mon Mar 28 2011 - 16:55:14 CDT)
- Francesco Pietra (Mon Mar 28 2011 - 16:09:55 CDT)
- Francesco Pietra (Mon Mar 28 2011 - 14:43:34 CDT)
- Jim Phillips (Mon Mar 28 2011 - 14:33:32 CDT)
- Cojocaru, Vlad (Mon Mar 28 2011 - 14:20:56 CDT)
- Francesco Pietra (Mon Mar 28 2011 - 09:50:31 CDT)
- Vlad Cojocaru (Mon Mar 28 2011 - 08:45:49 CDT)
- Francesco Pietra (Mon Mar 28 2011 - 05:26:21 CDT)
Random seed and equilibrated structure
- Axel Kohlmeyer (Fri Jul 27 2012 - 03:52:15 CDT)
- Dr. Eddie (Thu Jul 26 2012 - 16:40:05 CDT)
- Aron Broom (Thu Jul 26 2012 - 16:07:32 CDT)
- Dr. Eddie (Thu Jul 26 2012 - 15:55:13 CDT)
RBCG electrostatic term
- HAMID - (Thu Oct 20 2011 - 12:43:33 CDT)
RBCG water
- HAMID - (Thu Oct 13 2011 - 17:45:14 CDT)
RBCG water simulation
- Cristhian Boetsch (Fri Jun 03 2011 - 07:22:38 CDT)
- Chris Harrison (Fri May 27 2011 - 12:49:08 CDT)
- Cristhian Boetsch (Fri May 27 2011 - 12:17:38 CDT)
RBCG-configuration file
- Swarna M Patra (Thu Feb 09 2012 - 05:53:15 CST)
Re : AW: save the last frame as a pdb file using dcd file
- Namd Namd (Thu Sep 22 2011 - 03:33:05 CDT)
Re : Setting up a membrane simulation
- Pellegrini Eric (Mon Sep 19 2011 - 02:09:58 CDT)
Re PMF
- Branko (Sat May 28 2011 - 12:18:22 CDT)
Reading files for multiple threaded simulations
- Yi He (Wed Nov 02 2011 - 11:00:11 CDT)
- Chris Harrison (Wed Nov 02 2011 - 01:57:36 CDT)
- Yi He (Tue Nov 01 2011 - 12:16:52 CDT)
reassignFreq expression and relation with SMD
- Kang Hee Cho (Thu Mar 31 2011 - 10:56:47 CDT)
reassigning temperatures
- Martin, Erik W (Thu Dec 20 2012 - 11:40:36 CST)
ReaxFF and REBO
- Axel Kohlmeyer (Thu Sep 13 2012 - 12:02:28 CDT)
- Mikhail Suyetin (Wed Sep 12 2012 - 04:46:44 CDT)
Recent Geforce Cuda GPU cards(GT 440, GTX 560ti)
- Axel Kohlmeyer (Wed Apr 13 2011 - 09:25:58 CDT)
- Burgess, Don E (Wed Apr 13 2011 - 08:21:15 CDT)
Reduce the frequency of load balancer output
- Jim Phillips (Tue May 10 2011 - 19:12:30 CDT)
- Ajasja LjubetiÄ (Tue Apr 19 2011 - 09:23:04 CDT)
Reflecting boundary z axis in NAMD
- Ganesh Kamath (Tue Sep 04 2012 - 14:11:22 CDT)
refphrasing of the question for equilibration script
- matziast_at_med.uth.gr (Fri Sep 30 2011 - 04:16:27 CDT)
- Jernej Zidar (Fri Sep 30 2011 - 03:50:35 CDT)
- matziast_at_med.uth.gr (Fri Sep 30 2011 - 03:43:13 CDT)
Regarding Delta Delta G in FEP calculation
- snoze pa (Thu Sep 20 2012 - 13:09:57 CDT)
Regarding Installing NAMD in Ubuntu
- Axel Kohlmeyer (Mon Mar 12 2012 - 11:52:53 CDT)
- amit majhi (Mon Mar 12 2012 - 11:44:48 CDT)
regarding ion concentration in implicit solvent
- Aron Broom (Wed Feb 29 2012 - 08:31:53 CST)
- Nicholas M Glykos (Wed Feb 29 2012 - 08:29:40 CST)
- Prathit Chatterjee (Wed Feb 29 2012 - 08:04:08 CST)
- Prathit Chatterjee (Fri Feb 24 2012 - 05:19:51 CST)
Regarding thermostats
- Marcos Sotomayor (Thu Feb 23 2012 - 16:37:03 CST)
- Gianluca Interlandi (Mon Feb 13 2012 - 09:59:18 CST)
- felmerino_at_uchile.cl (Mon Feb 13 2012 - 09:21:33 CST)
regarding vmd
- scott stensland (Thu Jun 02 2011 - 08:59:15 CDT)
- kamal Kishor Thakur (Thu Jun 02 2011 - 01:28:36 CDT)
Relationship between High temperature and the boiling point of water
- Jeffrey Potoff (Thu Aug 18 2011 - 09:22:36 CDT)
- albus hawking (Wed Aug 17 2011 - 13:29:56 CDT)
Relative RMSD constraint
- Alexander Predeus (Wed Aug 17 2011 - 02:31:56 CDT)
- jiyong (Wed Aug 17 2011 - 02:00:57 CDT)
Release of the R.E.D.-III.5 tools
- FyD (Wed Feb 22 2012 - 05:00:23 CST)
release the memory taking by the aotmselects/vars
- Jacqueline Schmidt (Wed Oct 03 2012 - 10:45:48 CDT)
REMD across gpus
- Axel Kohlmeyer (Tue May 10 2011 - 15:52:42 CDT)
- Massimiliano Porrini (Tue May 10 2011 - 15:29:36 CDT)
- Axel Kohlmeyer (Tue May 10 2011 - 15:05:06 CDT)
- Massimiliano Porrini (Sun May 08 2011 - 06:02:19 CDT)
- Massimiliano Porrini (Mon May 09 2011 - 09:28:51 CDT)
- Massimiliano Porrini (Fri May 06 2011 - 07:39:56 CDT)
REMD and NAMD options
- Martin, Erik W (Fri Oct 19 2012 - 09:36:38 CDT)
REMD exchange ratios
- Jim Phillips (Fri Jun 17 2011 - 12:43:19 CDT)
- Massimiliano Porrini (Fri Jun 17 2011 - 08:47:48 CDT)
REMD segmentation fault
- Jim Phillips (Fri May 13 2011 - 08:52:47 CDT)
- Massimiliano Porrini (Fri May 13 2011 - 08:41:09 CDT)
- Jim Phillips (Fri May 13 2011 - 08:30:08 CDT)
- Massimiliano Porrini (Fri May 13 2011 - 07:58:45 CDT)
REMD with IBM SP6 LoadLeveler
- Andrew Emerson (Mon Jan 24 2011 - 02:24:58 CST)
- Luca Bellucci (Sat Jan 22 2011 - 11:45:31 CST)
remove translation of protein under spherical boundary conditions
- kakali sen (Fri Aug 19 2011 - 04:39:24 CDT)
Replica Exchange
- Jim Phillips (Tue May 10 2011 - 18:59:03 CDT)
- alamng_at_uci.edu (Fri Apr 15 2011 - 04:35:47 CDT)
Replica exchange - Temperatures and number of replicas
- Aron Broom (Sun Nov 25 2012 - 19:27:42 CST)
- Siri Søndergaard (Sun Nov 25 2012 - 17:06:44 CST)
Replica exchange and multiple time-stepping
- Niklaus Johner (Mon Mar 05 2012 - 10:19:10 CST)
replica exchange and replica.namd
- Siri Søndergaard (Tue Nov 06 2012 - 20:57:18 CST)
Replica Exchange Discrete Molecular Dynamics for structure based models
- bharat gupta (Tue Jan 03 2012 - 00:48:16 CST)
Replica exchange MD with NAMD with SGE....
- Guoxiong Su (Wed Jul 13 2011 - 17:50:57 CDT)
- Raul Araya (Fri Feb 25 2011 - 15:14:19 CST)
Replica Exchange Simulations on Blue Gene/P
- Axel Kohlmeyer (Tue Apr 12 2011 - 10:03:16 CDT)
- Dong Luo (Tue Apr 12 2011 - 09:54:31 CDT)
- Jan H. Meinke (Tue Apr 12 2011 - 07:09:32 CDT)
Replica-exchange MD on a single node / SMP workstation
- Zachary Ulissi (Fri Nov 09 2012 - 17:57:26 CST)
Replica-exchange metadynamics scripts
- Aron Broom (Sat Nov 17 2012 - 10:52:33 CST)
- Robert Elder (Tue Nov 13 2012 - 12:12:39 CST)
rescaling and reassignment parameter
- Kang Hee Cho (Mon Feb 07 2011 - 22:35:44 CST)
rescaling velocity
- Jim Phillips (Fri Jun 17 2011 - 13:16:44 CDT)
- Ajasja LjubetiÄ (Fri Jun 17 2011 - 13:14:32 CDT)
- esmael (Fri Jun 17 2011 - 13:04:10 CDT)
- Jim Phillips (Fri Jun 17 2011 - 12:45:44 CDT)
- esmael (Wed Jun 15 2011 - 18:17:58 CDT)
Resend - ERROR: Atoms moving too fast;
- Nikhil Kumar Mittal (Fri Nov 11 2011 - 20:02:51 CST)
- Nikhil Kumar Mittal (Fri Nov 11 2011 - 19:56:39 CST)
residue_rmsd.tcl via
- Branko (Thu Aug 09 2012 - 08:38:14 CDT)
- Michel Espinoza-Fonseca (Thu Aug 09 2012 - 08:18:40 CDT)
- Branko (Thu Aug 09 2012 - 07:50:56 CDT)
REST or RESTMD in NAMD?
- francesco oteri (Tue Dec 11 2012 - 12:22:47 CST)
- Gareth Shannon (Tue Dec 11 2012 - 12:08:21 CST)
restart a simulation
- upayan baul (Fri Mar 16 2012 - 06:51:28 CDT)
- Aron Broom (Thu Mar 15 2012 - 09:19:20 CDT)
- upayan baul (Thu Mar 15 2012 - 07:20:42 CDT)
- Jim Phillips (Tue May 31 2011 - 15:00:23 CDT)
- Mao Mao (Tue May 31 2011 - 14:50:22 CDT)
restart file
- Aron Broom (Sat Feb 25 2012 - 08:43:56 CST)
- Namd Namd (Sat Feb 25 2012 - 07:31:18 CST)
Restart from anywhere in DCD trajectory
- johan strumpfer (Mon Oct 03 2011 - 17:16:57 CDT)
- Zack Scholl (Mon Oct 03 2011 - 13:19:41 CDT)
restart problem
- JC Gumbart (Wed Jan 05 2011 - 14:23:32 CST)
- charlie (Wed Jan 05 2011 - 02:07:48 CST)
restart simulation writing in the same .dcd file.
- saman amiri (Sat Jul 02 2011 - 10:00:29 CDT)
- Ranyere Deyler (Sat Jul 02 2011 - 02:25:51 CDT)
restart with constraints causes RMSD "jump"
- Jim Phillips (Wed May 25 2011 - 13:40:21 CDT)
- P.-L. Chau (Wed May 25 2011 - 12:56:41 CDT)
- Jim Phillips (Wed May 25 2011 - 11:31:29 CDT)
- P.-L. Chau (Wed May 25 2011 - 07:24:11 CDT)
restarting ABF
- Jérôme Hénin (Wed Aug 01 2012 - 11:20:23 CDT)
- Giacomo Fiorin (Wed Aug 01 2012 - 10:53:56 CDT)
- Giacomo Fiorin (Wed Aug 01 2012 - 10:23:30 CDT)
- Branko (Wed Aug 01 2012 - 10:13:29 CDT)
Restarting an alchemic FEP calculation
- Jérôme Hénin (Mon Jun 27 2011 - 11:03:55 CDT)
- Giovanni Bellesia (Mon Jun 27 2011 - 09:32:25 CDT)
Restarting MD (Disabling Checklist)
- Joshua Adelman (Fri Aug 19 2011 - 07:18:17 CDT)
- Babban Mia (Fri Aug 19 2011 - 06:50:04 CDT)
- Babban Mia (Thu Aug 18 2011 - 10:58:55 CDT)
Restarting Multiple Walker/Well Tempered Metadynamics
- Giacomo Fiorin (Thu Oct 25 2012 - 16:18:49 CDT)
- Jeff Wereszczynski (Thu Oct 25 2012 - 13:17:27 CDT)
Restarting protein system simulation using different ligand
- Chris Harrison (Sun Oct 16 2011 - 18:41:55 CDT)
- Kevin Kastner (Thu Oct 13 2011 - 12:22:41 CDT)
restarting umbrella sampling simulation.
- ipsita basu (Wed Sep 12 2012 - 04:32:46 CDT)
- Aron Broom (Tue Sep 11 2012 - 08:54:27 CDT)
- Jérôme Hénin (Tue Sep 11 2012 - 07:02:02 CDT)
- ipsita basu (Tue Sep 11 2012 - 06:12:22 CDT)
- ipsita basu (Mon Sep 10 2012 - 01:48:44 CDT)
- Jérôme Hénin (Wed Sep 05 2012 - 09:00:57 CDT)
- ipsita basu (Wed Sep 05 2012 - 02:34:34 CDT)
- ipsita basu (Tue Sep 04 2012 - 07:18:02 CDT)
- Jérôme Hénin (Tue Sep 04 2012 - 04:31:05 CDT)
- Jérôme Hénin (Tue Sep 04 2012 - 02:48:15 CDT)
- ipsita basu (Tue Sep 04 2012 - 00:42:09 CDT)
restraining
- Axel Kohlmeyer (Fri Aug 24 2012 - 03:09:54 CDT)
- Chris Harrison (Thu Aug 23 2012 - 22:29:54 CDT)
- Christopher Rowley (Thu Aug 23 2012 - 22:20:55 CDT)
- Chris Harrison (Thu Aug 23 2012 - 22:08:49 CDT)
- Christopher Rowley (Thu Aug 23 2012 - 13:55:59 CDT)
restraining groups of atoms
- Wang Yi (Mon Jun 20 2011 - 08:54:13 CDT)
- Jérôme Hénin (Mon Jun 20 2011 - 07:56:06 CDT)
- Massimiliano Porrini (Mon Jun 20 2011 - 07:03:09 CDT)
restraining residues in NAMD
- johan strumpfer (Wed Sep 28 2011 - 19:44:34 CDT)
- flavio seixas (Wed Sep 28 2011 - 17:32:27 CDT)
- Haydee Valdes (Wed Sep 28 2011 - 10:59:20 CDT)
restraint with colvars mocule
- Giacomo Fiorin (Mon Sep 12 2011 - 11:23:57 CDT)
- Jérôme Hénin (Mon Sep 12 2011 - 10:08:47 CDT)
- Ling Wu (Mon Sep 12 2011 - 09:53:21 CDT)
- Jérôme Hénin (Mon Sep 12 2011 - 04:48:33 CDT)
- Ling Wu (Sun Sep 11 2011 - 16:25:39 CDT)
Reverse Mapping of RBCG Model
- Sibel Cakan (Thu Mar 31 2011 - 06:20:08 CDT)
- Sibel Cakan (Thu Mar 31 2011 - 03:51:57 CDT)
Re£º Can DCD trajectory files contain only protein but water surround
- Jun Zhang (Thu Jan 13 2011 - 19:22:10 CST)
RHDO lattice as a PBC unit Cell in NAMD
- Andrea Holfelder (Thu Aug 18 2011 - 04:59:59 CDT)
rigid body
- Dimitrios Tragoudaras (Thu Oct 20 2011 - 12:33:45 CDT)
rigid bonds
- Axel Kohlmeyer (Fri Oct 14 2011 - 09:27:34 CDT)
- Francesco Pietra (Fri Oct 14 2011 - 09:24:41 CDT)
rigidBonds water and langevinHydrogen off (no problem!)
- Aron Broom (Fri Mar 02 2012 - 10:49:34 CST)
- Aron Broom (Thu Mar 01 2012 - 14:32:20 CST)
- Victor Ovchinnikov (Thu Mar 01 2012 - 13:56:41 CST)
- Aron Broom (Thu Mar 01 2012 - 13:27:59 CST)
- JC Gumbart (Thu Mar 01 2012 - 12:49:09 CST)
rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens
- Aron Broom (Fri Mar 02 2012 - 10:51:16 CST)
- Aron Broom (Thu Mar 01 2012 - 15:06:29 CST)
- Jim Phillips (Thu Mar 01 2012 - 14:47:48 CST)
- Aron Broom (Tue Feb 28 2012 - 21:58:25 CST)
rigidBonds water option
- Chris Harrison (Thu Feb 02 2012 - 14:02:37 CST)
- Hasan haska (Thu Feb 02 2012 - 01:48:22 CST)
rmsd calculation in namd
- Guanglei Cui (Tue Sep 11 2012 - 10:29:53 CDT)
- Niklaus Johner (Fri Sep 07 2012 - 15:53:16 CDT)
- Giacomo Fiorin (Fri Sep 07 2012 - 15:36:59 CDT)
- Guanglei Cui (Fri Sep 07 2012 - 14:57:59 CDT)
RMSD collective variable - Different atons to align and to calculate RMSD
- Branko (Tue Feb 07 2012 - 12:49:37 CST)
- Paulo Cesar Telles de Souza (Tue Feb 07 2012 - 11:53:47 CST)
- Paulo Cesar Telles de Souza (Mon Feb 06 2012 - 08:39:02 CST)
- Jérôme Hénin (Thu Feb 02 2012 - 15:40:47 CST)
- Davide Branduardi (Thu Feb 02 2012 - 14:27:18 CST)
- Chris Harrison (Thu Feb 02 2012 - 13:54:55 CST)
- Giacomo Fiorin (Thu Feb 02 2012 - 13:52:49 CST)
- Paulo Cesar Telles de Souza (Thu Feb 02 2012 - 12:19:10 CST)
RMSD difference on alignment of two states of protein in VMD and NAMD TMD
- Nikita chopra (Thu Aug 02 2012 - 15:27:36 CDT)
RMSD metadynamics
- Jérôme Hénin (Thu Feb 16 2012 - 02:39:04 CST)
- Giacomo Fiorin (Wed Feb 15 2012 - 16:38:03 CST)
- simone bardwell (Wed Feb 15 2012 - 15:59:20 CST)
- Giacomo Fiorin (Wed Feb 15 2012 - 13:48:50 CST)
- simone bardwell (Wed Feb 15 2012 - 13:25:16 CST)
RMSD trajectory
- flavio seixas (Sat Nov 19 2011 - 08:44:40 CST)
- Nikolaos Glykos (Fri Nov 18 2011 - 14:32:41 CST)
- Joshua Adelman (Fri Nov 18 2011 - 14:21:46 CST)
- flavio seixas (Fri Nov 18 2011 - 14:09:15 CST)
RNA simulation
- Chris Harrison (Mon Aug 29 2011 - 19:23:07 CDT)
- Juan Antonio Raygoza Garay (Fri Aug 26 2011 - 15:38:38 CDT)
Rotate two linked proteins against each other and calculate energy profile
- Bjoern Olausson (Tue Mar 29 2011 - 10:16:12 CDT)
- Jérôme Hénin (Tue Mar 29 2011 - 07:03:14 CDT)
- Bjoern Olausson (Mon Mar 28 2011 - 16:46:29 CDT)
- Bjoern Olausson (Mon Mar 28 2011 - 16:00:25 CDT)
- Jérôme Hénin (Mon Mar 28 2011 - 15:50:44 CDT)
- Jérôme Hénin (Mon Mar 28 2011 - 15:43:46 CDT)
- Bjoern Olausson (Mon Mar 28 2011 - 11:36:13 CDT)
- Bjoern Olausson (Mon Mar 28 2011 - 11:18:09 CDT)
- Jérôme Hénin (Mon Mar 28 2011 - 11:07:43 CDT)
- Ajasja LjubetiÄ (Mon Mar 28 2011 - 09:30:28 CDT)
- Bjoern Olausson (Mon Mar 28 2011 - 07:49:23 CDT)
- Ajasja LjubetiÄ (Mon Mar 21 2011 - 03:43:55 CDT)
- Bjoern Olausson (Sun Mar 20 2011 - 11:03:32 CDT)
- Ajasja LjubetiÄ (Tue Mar 15 2011 - 16:56:39 CDT)
- Bjoern Olausson (Tue Mar 15 2011 - 14:20:00 CDT)
rsh not working
- Chris Harrison (Wed Oct 12 2011 - 10:08:27 CDT)
- Neelanjana Sengupta (Wed Oct 12 2011 - 02:29:16 CDT)
- Matteo Rotter (Tue Oct 11 2011 - 13:37:26 CDT)
- Neelanjana Sengupta (Tue Oct 11 2011 - 00:58:27 CDT)
rule of thumb for dcd sampling frequency?
- Michael S. Sellers (Cont, ARL/WMRD) (Tue Mar 22 2011 - 15:56:17 CDT)
- Irene Newhouse (Tue Mar 22 2011 - 13:00:28 CDT)
- Branko (Tue Mar 22 2011 - 04:47:29 CDT)
- Richard Wood (Mon Mar 21 2011 - 18:43:30 CDT)
- Nikolaos Glykos (Mon Mar 21 2011 - 14:51:09 CDT)
- Axel Kohlmeyer (Mon Mar 21 2011 - 14:12:00 CDT)
- Branko (Mon Mar 21 2011 - 14:13:51 CDT)
- Irene Newhouse (Mon Mar 21 2011 - 13:26:25 CDT)
Run NAMD binaries
- Suranga Edirisinghe (Wed Aug 29 2012 - 09:26:39 CDT)
- Axel Kohlmeyer (Wed Aug 29 2012 - 04:30:20 CDT)
- Monika Madhavi (Wed Aug 29 2012 - 03:58:12 CDT)
run tests with CUDA
- Massimiliano Porrini (Wed May 04 2011 - 11:45:09 CDT)
- Nicholas M Glykos (Tue May 03 2011 - 03:09:12 CDT)
- Axel Kohlmeyer (Mon May 02 2011 - 16:55:18 CDT)
- Massimiliano Porrini (Mon May 02 2011 - 16:25:17 CDT)
Running AMBER FF with NAMD 2.8-CUDA
- Nicholas M Glykos (Wed Oct 19 2011 - 10:06:08 CDT)
- Francesco Pietra (Wed Oct 19 2011 - 09:23:32 CDT)
- Nicholas M Glykos (Wed Oct 19 2011 - 08:37:15 CDT)
- Francesco Pietra (Wed Oct 19 2011 - 08:14:59 CDT)
Running bias exchange metadynamics simulations with NAMD
- Jérôme Hénin (Mon Jan 17 2011 - 10:35:20 CST)
- Ajasja LjubetiÄ (Mon Jan 17 2011 - 08:40:11 CST)
- Jérôme Hénin (Fri Jan 14 2011 - 10:37:17 CST)
- Ajasja LjubetiÄ (Fri Jan 14 2011 - 09:31:49 CST)
- Giacomo Fiorin (Mon Jan 03 2011 - 18:13:21 CST)
- Ajasja LjubetiÄ (Sun Jan 02 2011 - 15:03:48 CST)
- Jérôme Hénin (Sat Jan 01 2011 - 15:48:06 CST)
Running fulldirect in parallel
- Aron Broom (Sun Oct 07 2012 - 15:43:54 CDT)
- Tom Coles (Sun Oct 07 2012 - 15:21:32 CDT)
- Aron Broom (Sun Oct 07 2012 - 15:14:10 CDT)
- Tom Coles (Sun Oct 07 2012 - 15:08:11 CDT)
Running NAMD CUDA
- Axel Kohlmeyer (Fri Nov 04 2011 - 15:16:45 CDT)
- Steven Cox (Fri Nov 04 2011 - 15:06:31 CDT)
Running NAMD on Forge (CUDA)
- Gianluca Interlandi (Thu Jul 12 2012 - 17:25:52 CDT)
- Aron Broom (Thu Jul 12 2012 - 16:12:39 CDT)
- Gianluca Interlandi (Thu Jul 12 2012 - 15:58:42 CDT)
- Aron Broom (Thu Jul 12 2012 - 15:05:59 CDT)
- Gianluca Interlandi (Thu Jul 12 2012 - 14:53:44 CDT)
- Aron Broom (Thu Jul 12 2012 - 14:28:33 CDT)
- Gianluca Interlandi (Thu Jul 12 2012 - 14:21:38 CDT)
- Aron Broom (Thu Jul 12 2012 - 13:50:59 CDT)
- Gianluca Interlandi (Thu Jul 12 2012 - 13:41:16 CDT)
- Aron Broom (Tue Jul 10 2012 - 12:21:45 CDT)
- Gianluca Interlandi (Tue Jul 10 2012 - 12:14:52 CDT)
Running NAMD parallel on two machines with 3 CUDAs
- Darko Stefanovski (Thu May 05 2011 - 11:53:40 CDT)
Running Parallel Jobs Simultaneously with MPIRUN
- Rajan Vatassery (Thu Jul 19 2012 - 01:59:55 CDT)
- Hugh Heldenbrand (Wed Jul 18 2012 - 16:29:27 CDT)
- Axel Kohlmeyer (Wed Jul 18 2012 - 15:47:40 CDT)
- Aron Broom (Wed Jul 18 2012 - 15:30:56 CDT)
- Rajan Vatassery (Wed Jul 18 2012 - 14:28:07 CDT)
- Axel Kohlmeyer (Wed Jul 18 2012 - 11:33:46 CDT)
- Rajan Vatassery (Wed Jul 18 2012 - 10:36:04 CDT)
running simulations on different machines with different versions of NAMD
- Aron Broom (Fri Jun 15 2012 - 05:38:20 CDT)
- Puspita Halder (Fri Jun 15 2012 - 01:29:59 CDT)
Rückruf: scnb value to prevent VDWs scaling
- Norman Geist (Thu Sep 06 2012 - 08:10:22 CDT)
Sampling schemes with FEP
- Chris Chipot (Thu Oct 20 2011 - 09:16:34 CDT)
- Patargias, George (Thu Oct 20 2011 - 08:13:19 CDT)
SASA of PBD files
- David Tanner (Thu Aug 25 2011 - 08:47:31 CDT)
- Andrea Holfelder (Sat Aug 20 2011 - 04:11:25 CDT)
save the last frame as a pdb file using dcd file
- Nicholas M Glykos (Thu Sep 22 2011 - 03:10:21 CDT)
- HAMID - (Thu Sep 22 2011 - 03:08:25 CDT)
- Namd Namd (Thu Sep 22 2011 - 02:02:53 CDT)
Scaled forces, colvars and harmonic con/restraints
- Michelle Kuttel (Thu Nov 24 2011 - 09:39:56 CST)
- Jérôme Hénin (Thu Nov 24 2011 - 08:18:07 CST)
- Michelle Kuttel (Thu Nov 24 2011 - 07:24:58 CST)
- Jérôme Hénin (Thu Nov 24 2011 - 06:33:58 CST)
- Jérôme Hénin (Thu Nov 24 2011 - 03:51:51 CST)
- Michelle Kuttel (Wed Nov 23 2011 - 23:31:14 CST)
- Michelle Kuttel (Wed Nov 23 2011 - 23:33:26 CST)
- Giacomo Fiorin (Wed Nov 23 2011 - 14:40:34 CST)
- Aron Broom (Wed Nov 23 2011 - 14:36:42 CST)
- Michelle Kuttel (Wed Nov 23 2011 - 14:03:22 CST)
- Jérôme Hénin (Wed Nov 23 2011 - 10:41:58 CST)
- Giacomo Fiorin (Wed Nov 23 2011 - 09:28:50 CST)
- Michelle Kuttel (Wed Nov 23 2011 - 08:16:58 CST)
- Michelle Kuttel (Mon Nov 21 2011 - 04:45:39 CST)
scaling
- Boyang Wang (Fri Dec 30 2011 - 03:56:03 CST)
- Neelanjana Sengupta (Wed Dec 28 2011 - 22:56:45 CST)
scnb value to prevent VDWs scaling
- Marc Gordon (Mon Sep 10 2012 - 08:45:24 CDT)
- Axel Kohlmeyer (Mon Sep 10 2012 - 08:33:05 CDT)
- Marc Gordon (Mon Sep 10 2012 - 08:28:25 CDT)
- Axel Kohlmeyer (Mon Sep 10 2012 - 08:02:18 CDT)
- Marc Gordon (Mon Sep 10 2012 - 07:56:44 CDT)
- Axel Kohlmeyer (Sat Sep 08 2012 - 06:04:23 CDT)
- Marc Gordon (Sat Sep 08 2012 - 05:21:49 CDT)
- Marc Gordon (Thu Sep 06 2012 - 07:26:55 CDT)
- Marc Gordon (Mon Aug 13 2012 - 08:40:13 CDT)
script for equilibration
- matziast_at_med.uth.gr (Sun Oct 02 2011 - 04:19:19 CDT)
Script Help
- Axel Kohlmeyer (Sun May 29 2011 - 18:58:44 CDT)
- flavio seixas (Sun May 29 2011 - 18:16:51 CDT)
secondary structure restraints in coarse grain
- Jesper Sørensen (Tue Jul 24 2012 - 16:35:37 CDT)
- Aron Broom (Tue Jul 24 2012 - 15:37:54 CDT)
- Eun Kim (Tue Jul 24 2012 - 13:35:00 CDT)
segmentation errors
- P Fajer (Sat Jun 16 2012 - 13:14:09 CDT)
segmentation fault with NAMDenergy
- amin_at_imtech.res.in (Thu Apr 19 2012 - 10:19:55 CDT)
Segmentation Faults on Mac OS X Lion
- Jim Phillips (Tue Jul 26 2011 - 15:46:30 CDT)
- Jesper Sørensen (Tue Jul 26 2011 - 03:40:33 CDT)
- Arvind Kannan (Mon Jul 25 2011 - 16:48:21 CDT)
- Arvind Kannan (Mon Jul 25 2011 - 16:39:31 CDT)
Segmentation violation with adaptive tempering.
- johan strumpfer (Mon Nov 21 2011 - 12:04:38 CST)
- johan strumpfer (Mon Nov 21 2011 - 12:20:28 CST)
- Nicholas M Glykos (Mon Nov 21 2011 - 12:11:45 CST)
- Nicholas M Glykos (Sun Nov 20 2011 - 05:13:02 CST)
selecting multiple fixed atom in SMD
- raghav singh (Thu Mar 15 2012 - 11:47:30 CDT)
selection of cholesterol molecules
- Chris Harrison (Wed Nov 02 2011 - 00:06:35 CDT)
- Swarna M Patra (Tue Nov 01 2011 - 23:54:06 CDT)
set dummyAtom position changing
- christos.lamprakis_at_dcb.unibe.ch (Fri Apr 01 2011 - 09:44:39 CDT)
Set up NPT simulation in cubic PBC-box
- Axel Kohlmeyer (Fri Apr 27 2012 - 11:11:30 CDT)
- Xi Cheng (Fri Apr 27 2012 - 11:08:42 CDT)
- Axel Kohlmeyer (Fri Apr 27 2012 - 10:54:15 CDT)
- Xi Cheng (Thu Apr 26 2012 - 16:22:33 CDT)
Setting integrator parameters for ABF
- Giacomo Fiorin (Wed Jul 27 2011 - 14:10:17 CDT)
- Ajasja LjubetiÄ (Wed Jul 27 2011 - 14:01:31 CDT)
- Giacomo Fiorin (Wed Jul 27 2011 - 13:12:46 CDT)
- Ajasja LjubetiÄ (Wed Jul 27 2011 - 12:49:24 CDT)
Setting PME Grid Size
- Jim Phillips (Wed Apr 13 2011 - 08:55:23 CDT)
- da xue (Tue Mar 29 2011 - 20:28:26 CDT)
Setting Up A Langevin Buffer Region
- Jérôme Hénin (Wed Feb 16 2011 - 06:34:58 CST)
- David Huggins (Wed Feb 16 2011 - 04:30:44 CST)
Setting up a membrane simulation
- Bjoern Olausson (Fri Sep 16 2011 - 07:13:56 CDT)
- Pellegrini Eric (Fri Sep 16 2011 - 02:52:05 CDT)
Setting up aMD simulation of a membrane protein
- Yi Wang (Fri Apr 01 2011 - 13:59:01 CDT)
- Jeff Wereszczynski (Fri Apr 01 2011 - 11:00:23 CDT)
- Raul Araya (Fri Apr 01 2011 - 09:05:32 CDT)
Setting up values in distance colvar
- Jérôme Hénin (Sun Mar 13 2011 - 14:45:43 CDT)
- Francesco Pietra (Sun Mar 13 2011 - 12:49:51 CDT)
SHAKE Tolerance and Performance
- Aron Broom (Fri Mar 02 2012 - 10:56:32 CST)
- Aron Broom (Fri Mar 02 2012 - 01:33:21 CST)
- Aron Broom (Thu Mar 01 2012 - 11:28:45 CST)
- Nicholas M Glykos (Thu Mar 01 2012 - 03:16:05 CST)
- Aron Broom (Thu Mar 01 2012 - 01:04:28 CST)
shift the molecules
- Chris Harrison (Thu Aug 23 2012 - 22:38:51 CDT)
- oguz gurbulak (Thu Aug 23 2012 - 03:29:53 CDT)
- Axel Kohlmeyer (Thu Aug 16 2012 - 03:56:25 CDT)
- oguz gurbulak (Thu Aug 16 2012 - 03:13:10 CDT)
Should the windows for ABF calculations be overlapped or not?
- JC Gumbart (Tue Nov 27 2012 - 09:12:48 CST)
- DAI, JIAN (Tue Nov 27 2012 - 08:38:17 CST)
simulated annealing protocol
- Massimiliano Porrini (Wed Jul 20 2011 - 12:25:18 CDT)
- Jim Phillips (Wed Jul 20 2011 - 11:31:19 CDT)
- Massimiliano Porrini (Tue Jun 21 2011 - 07:41:00 CDT)
Simulating more than 20 Million atom system
- Harshad Joshi (Mon Feb 21 2011 - 16:01:47 CST)
simulation box
- Jeffrey Potoff (Fri May 20 2011 - 11:36:57 CDT)
- Axel Kohlmeyer (Fri May 20 2011 - 11:33:20 CDT)
- PAUL NEWMAN (Fri May 20 2011 - 11:30:43 CDT)
- Axel Kohlmeyer (Fri May 20 2011 - 11:25:36 CDT)
- PAUL NEWMAN (Fri May 20 2011 - 11:11:52 CDT)
- PAUL NEWMAN (Fri May 20 2011 - 10:39:48 CDT)
Simulation Box Deformation
- John Doe (Mon Dec 03 2012 - 20:19:47 CST)
- John Doe (Mon Dec 03 2012 - 15:51:57 CST)
simulation of non-rectangular surface
- Jacqueline Schmidt (Tue Aug 28 2012 - 16:35:46 CDT)
- Axel Kohlmeyer (Tue Aug 28 2012 - 16:00:16 CDT)
- Suranga Edirisinghe (Tue Aug 28 2012 - 15:49:37 CDT)
- Jacqueline Schmidt (Tue Aug 28 2012 - 15:34:50 CDT)
- Axel Kohlmeyer (Tue Aug 28 2012 - 10:39:07 CDT)
- Jacqueline Schmidt (Tue Aug 28 2012 - 10:20:02 CDT)
Simulation Using Both NAMD and VMD
- Ajith Rathnaweera Rajapaksha Mudalige (Sat Apr 21 2012 - 00:22:33 CDT)
- Aron Broom (Fri Apr 20 2012 - 23:46:53 CDT)
- Axel Kohlmeyer (Fri Apr 20 2012 - 20:28:15 CDT)
- Ajith Rathnaweera Rajapaksha Mudalige (Fri Apr 20 2012 - 20:19:17 CDT)
- Axel Kohlmeyer (Fri Apr 20 2012 - 19:42:49 CDT)
- Axel Kohlmeyer (Fri Apr 20 2012 - 19:37:12 CDT)
- Chris Harrison (Fri Apr 20 2012 - 19:34:48 CDT)
- Axel Kohlmeyer (Fri Apr 20 2012 - 19:04:54 CDT)
- Ajith Rathnaweera Rajapaksha Mudalige (Fri Apr 20 2012 - 18:14:17 CDT)
- Aron Broom (Fri Apr 20 2012 - 17:30:14 CDT)
- Axel Kohlmeyer (Fri Apr 20 2012 - 17:10:30 CDT)
- Ajith Rathnaweera Rajapaksha Mudalige (Fri Apr 20 2012 - 17:05:28 CDT)
Simulations with alpha methylated amino acids
- amin_at_imtech.res.in (Fri Mar 16 2012 - 20:23:33 CDT)
Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA)
- Francesco Pietra (Tue May 29 2012 - 00:10:08 CDT)
- Axel Kohlmeyer (Mon May 28 2012 - 17:19:42 CDT)
- Francesco Pietra (Mon May 28 2012 - 17:11:54 CDT)
- Axel Kohlmeyer (Mon May 28 2012 - 14:58:53 CDT)
- Benjamin Merget (Sun May 27 2012 - 09:10:59 CDT)
- Axel Kohlmeyer (Fri May 25 2012 - 05:39:37 CDT)
- Benjamin Merget (Thu May 24 2012 - 04:51:06 CDT)
slow heating md
- poker_at_physics.usyd.edu.au (Thu Jun 23 2011 - 20:00:54 CDT)
- Axel Kohlmeyer (Thu Jun 23 2011 - 09:06:01 CDT)
- Grazia Cottone (Thu Jun 23 2011 - 08:33:37 CDT)
- Richard Wood (Thu Jun 23 2011 - 08:13:25 CDT)
- Ajasja LjubetiÄ (Thu Jun 23 2011 - 06:32:24 CDT)
- Hasan haska (Thu Jun 23 2011 - 06:11:51 CDT)
SMD
- Leandro Martínez (Thu Sep 15 2011 - 07:21:15 CDT)
- Jacopo Sgrignani (Thu Sep 15 2011 - 07:12:26 CDT)
- Ajasja LjubetiÄ (Mon Sep 12 2011 - 04:07:52 CDT)
- Jacopo Sgrignani (Mon Sep 12 2011 - 02:53:30 CDT)
SMD for two steered directions
- Jérôme Hénin (Sun Apr 17 2011 - 14:31:36 CDT)
- felmerino_at_uchile.cl (Sun Apr 17 2011 - 13:53:35 CDT)
- å¸¸å§—ç‡• (Sun Apr 17 2011 - 09:51:12 CDT)
SMD negative forces
- Jérôme Hénin (Fri Feb 11 2011 - 03:24:54 CST)
- S Richmond (Thu Feb 10 2011 - 15:32:35 CST)
- S Richmond (Mon Feb 07 2011 - 17:37:09 CST)
- S Richmond (Fri Feb 04 2011 - 10:39:44 CST)
SMD of three atom at a time
- snoze pa (Wed Jun 01 2011 - 08:14:39 CDT)
- Chris Harrison (Fri May 20 2011 - 12:22:09 CDT)
- snoze pa (Fri May 20 2011 - 11:32:03 CDT)
SMD simulation: stop applying force during simulation?
- Axel Kohlmeyer (Fri Apr 08 2011 - 07:46:54 CDT)
- THANH NGUYEN (Thu Apr 07 2011 - 22:05:35 CDT)
SMD under NPT ensemble
- johan strumpfer (Mon Mar 19 2012 - 11:28:25 CDT)
- johan strumpfer (Mon Mar 19 2012 - 14:35:22 CDT)
- felmerino_at_uchile.cl (Mon Mar 19 2012 - 16:11:54 CDT)
- Wang Yi (Mon Mar 19 2012 - 13:09:42 CDT)
- Wang Yi (Mon Mar 19 2012 - 10:20:07 CDT)
- raghav singh (Mon Mar 19 2012 - 10:12:17 CDT)
SMD-DNA : ABNORMAL EOF FOUND - buffer=*END*
- Chris Harrison (Mon Mar 05 2012 - 09:11:54 CST)
- Aron Broom (Mon Mar 05 2012 - 08:31:31 CST)
- raghav singh (Mon Mar 05 2012 - 08:12:33 CST)
SMD-extension
- johan strumpfer (Fri Aug 26 2011 - 07:26:18 CDT)
- Ehsan Ban (Fri Aug 26 2011 - 08:36:10 CDT)
- Axel Kohlmeyer (Fri Aug 26 2011 - 08:20:28 CDT)
- MOhan maruthi sena (Fri Aug 26 2011 - 05:18:25 CDT)
smd-tclForce intrerface
- Jacqueline Schmidt (Wed Dec 26 2012 - 12:04:23 CST)
SMD: Compressing a Molecule
- raghav singh (Thu Oct 25 2012 - 14:57:32 CDT)
sodium ion in water
- Axel Kohlmeyer (Thu Aug 11 2011 - 00:36:08 CDT)
- divya nayar (Thu Aug 11 2011 - 00:17:27 CDT)
Solvation in VMD using Non Standard Solvent System
- Axel Kohlmeyer (Wed Aug 10 2011 - 07:47:35 CDT)
- Babban Mia (Wed Aug 10 2011 - 07:35:32 CDT)
solved inputPrefix for ABF
- Branko (Sun Oct 21 2012 - 15:24:43 CDT)
SOLVED: Failure to run namd-cuda with gtx-470
- Francesco Pietra (Fri Jul 22 2011 - 09:56:34 CDT)
Specific colvar component needed.
- Giacomo Fiorin (Mon May 07 2012 - 11:05:41 CDT)
- Aron Broom (Mon May 07 2012 - 11:02:30 CDT)
- Germán Andrés Miño (Mon May 07 2012 - 10:55:14 CDT)
specify acceptance ratio in REMD
- Neelanjana Sengupta (Thu Mar 17 2011 - 01:47:32 CDT)
spinAngle
- Ajasja LjubetiÄ (Thu Jan 19 2012 - 05:13:15 CST)
- Buddhadev Maiti (Wed Jan 18 2012 - 16:28:58 CST)
- Giacomo Fiorin (Wed Jan 18 2012 - 16:34:18 CST)
- Giacomo Fiorin (Wed Jan 18 2012 - 13:41:27 CST)
- Giacomo Fiorin (Wed Jan 18 2012 - 13:06:47 CST)
- Giacomo Fiorin (Wed Jan 18 2012 - 12:32:32 CST)
Sr2+
- Maria Bykhovskaia (Wed Aug 22 2012 - 14:54:38 CDT)
src/ComputeNonbondedCUDA.C:1022: error: thread-local storage not supported for this target
- Paraskevi Gkeka (Wed Nov 21 2012 - 06:14:09 CST)
startup phase 8: not complete!
- mj_aghaei_at_aut.ac.ir (Wed Jul 25 2012 - 21:12:31 CDT)
Steered dynamics
- JC Gumbart (Sat Nov 12 2011 - 01:18:06 CST)
- Jacopo Sgrignani (Fri Nov 11 2011 - 04:56:32 CST)
steered molecular dynamics with multiple molecules
- Jérôme Hénin (Thu Jul 05 2012 - 05:10:50 CDT)
- Koivuniemi Artturi (Wed Jul 04 2012 - 05:19:15 CDT)
stereo-chemical inversion during MD
- Branko (Tue May 08 2012 - 04:53:27 CDT)
- Gordon Wells (Mon May 07 2012 - 12:01:24 CDT)
Sticking TIP4P water molecules AMBER
- George M Giambasu (Mon Dec 19 2011 - 10:16:56 CST)
- Nicholas M Glykos (Mon Dec 19 2011 - 04:58:13 CST)
- Norman Geist (Mon Dec 19 2011 - 04:33:25 CST)
stochastical boundary conditions in NAMD
- Jérôme Hénin (Wed Dec 07 2011 - 04:39:41 CST)
- mjyang (Tue Dec 06 2011 - 19:24:17 CST)
Strange (very large) atom motions
- Chris Harrison (Thu Feb 03 2011 - 18:18:24 CST)
- Craig Jolley (Thu Feb 03 2011 - 17:14:42 CST)
stream files and paratool
- Francesco Pietra (Fri Sep 23 2011 - 03:10:52 CDT)
structure changing
- Aron Broom (Thu Oct 11 2012 - 06:33:53 CDT)
- ishiikai08_at_yahoo.co.jp (Wed Oct 10 2012 - 23:51:12 CDT)
subscribe namd-l
- Michael Zimmermann (Wed Mar 23 2011 - 13:24:38 CDT)
Sudden energy drop after minimization
- Hyuntae Na (Fri Jun 22 2012 - 19:56:14 CDT)
Sufficiently large values for 'firsttimestep' can lead to immediate simulation abort.
- Nikolaos Glykos (Sun Apr 08 2012 - 13:08:59 CDT)
- Axel Kohlmeyer (Sun Apr 08 2012 - 12:38:10 CDT)
- Nikolaos Glykos (Sun Apr 08 2012 - 12:25:15 CDT)
surfaceTensionTarget - Surface Tension per interface or per bilayer
- Jérôme Hénin (Wed Jan 11 2012 - 09:18:39 CST)
- Boyang Wang (Wed Jan 11 2012 - 08:30:17 CST)
- Jon Fuller (Wed Jan 11 2012 - 04:25:24 CST)
Suspend NAMD (to RAM)
- Ajasja LjubetiÄ (Sat Jul 30 2011 - 09:44:23 CDT)
- Nicholas M Glykos (Thu Jul 21 2011 - 01:20:14 CDT)
- Giacomo Fiorin (Wed Jul 20 2011 - 20:41:27 CDT)
- Ajasja LjubetiÄ (Wed Jul 20 2011 - 17:10:06 CDT)
SV: restart simulation writing in the same .dcd file.
- Maria Musgaard (Sat Jul 02 2011 - 03:03:26 CDT)
switching function
- yandongÂ Huang (Wed Mar 23 2011 - 22:52:32 CDT)
Switching function for cut-off method
- yandongÂ Huang (Wed Mar 30 2011 - 08:54:09 CDT)
Switching function while using AMBER force field
- Sneha Menon (Thu Dec 20 2012 - 00:06:25 CST)
SWM4 water model simulation
- saman amiri (Mon Jun 27 2011 - 12:27:34 CDT)
- saman amiri (Fri Jun 17 2011 - 16:07:14 CDT)
SWM4-NDP Simulation
- David Hardy (Wed Aug 24 2011 - 18:49:22 CDT)
- David Huggins (Wed Aug 24 2011 - 14:49:33 CDT)
System net charge
- Andres Morales N (Thu Aug 04 2011 - 23:43:11 CDT)
- Cruz-Chu Eduardo Roberto (Thu Aug 04 2011 - 03:28:45 CDT)
- Andres Morales N (Tue Aug 02 2011 - 19:20:38 CDT)
- Andres Morales N (Fri Jul 29 2011 - 03:25:11 CDT)
system splitted
- Aron Broom (Fri Mar 02 2012 - 09:21:12 CST)
- lecan (Fri Mar 02 2012 - 06:54:50 CST)
tabulatd potentials
- Arturas (Thu Dec 29 2011 - 14:11:43 CST)
- Arturas (Thu Dec 29 2011 - 13:09:17 CST)
Tabulated potential
- Adam Skelton (Thu Jul 26 2012 - 13:30:54 CDT)
- Adam Skelton (Mon Jul 23 2012 - 16:17:35 CDT)
Tabulated potentials - regd
- Jérôme Hénin (Tue Oct 09 2012 - 11:29:47 CDT)
- Ramesh Cheerla (Tue Oct 09 2012 - 09:01:52 CDT)
target pressure value
- Ajasja LjubetiÄ (Tue Jan 17 2012 - 07:03:36 CST)
- Namd Namd (Tue Jan 17 2012 - 06:30:20 CST)
- Namd Namd (Tue Jan 17 2012 - 06:32:45 CST)
Targeted Molecular Dynamics
- Aron Broom (Sat Jun 30 2012 - 17:13:59 CDT)
- Thomas Albers (Sat Jun 30 2012 - 14:56:53 CDT)
- harish vashisth (Tue Jun 12 2012 - 11:22:10 CDT)
- Miguel Ángel Mompeán García (Tue Jun 12 2012 - 06:02:17 CDT)
- sakthi kumaran (Thu Mar 17 2011 - 09:08:25 CDT)
- sakthi kumaran (Thu Mar 17 2011 - 01:28:59 CDT)
TAU profiler with NAMD2.9 smp mode
- Takuro Udagawa (Tue Dec 11 2012 - 07:44:44 CST)
Tcl issue with config script
- Kristopher Opron (Fri Jun 17 2011 - 15:40:31 CDT)
- Cristhian Boetsch (Fri Jun 17 2011 - 10:13:25 CDT)
- opronkri_at_msu.edu (Fri Jun 17 2011 - 00:06:53 CDT)
tcl script for rmsd
- Aron Broom (Thu Oct 04 2012 - 11:18:29 CDT)
- yp sun (Thu Oct 04 2012 - 04:43:37 CDT)
tclBC incorrect output
- P.-L. Chau (Wed May 02 2012 - 22:18:21 CDT)
TClforce
- poker_at_physics.usyd.edu.au (Thu Oct 20 2011 - 21:22:25 CDT)
- harish vashisth (Thu Oct 20 2011 - 12:29:14 CDT)
- Swarna M Patra (Thu Oct 20 2011 - 03:11:01 CDT)
tclforces and extrabonds
- Jérôme Hénin (Mon Dec 12 2011 - 11:30:47 CST)
- Aron Broom (Mon Dec 12 2011 - 11:30:36 CST)
- Jian Dai (Mon Dec 12 2011 - 10:13:16 CST)
TclForces clearconfig cancels addforce calls?
- Niklaus Johner (Thu Mar 08 2012 - 15:32:39 CST)
tclforces- tcl extension written in c and built with swig
- Chris Harrison (Mon Oct 17 2011 - 18:46:36 CDT)
- Axel Kohlmeyer (Mon Oct 17 2011 - 18:43:08 CDT)
- Eva Gonzalez Noya (Mon Oct 17 2011 - 18:30:33 CDT)
Techinal problems with ABF simulations
- Jérôme Hénin (Wed Jun 27 2012 - 08:29:09 CDT)
Technique issue with free energy calculation on GPU
- Jun Zhang (Tue Mar 01 2011 - 08:24:59 CST)
Temperature bath
- Chathurika Abeyrathne (Mon Aug 01 2011 - 02:20:15 CDT)
Temperature during membrane equilibration
- Andres Morales N (Fri Sep 09 2011 - 20:57:36 CDT)
- Erik Nordgren (Fri Sep 09 2011 - 11:17:53 CDT)
- Andres Morales N (Thu Sep 08 2011 - 18:33:47 CDT)
- Andres Morales N (Wed Sep 07 2011 - 23:57:10 CDT)
temperature range for residue-based CG
- Demet Akten (Mon Jan 17 2011 - 08:02:59 CST)
temperature-TS with NAMDplot
- johan strumpfer (Fri Jul 08 2011 - 07:23:44 CDT)
- Bjoern Olausson (Fri Jul 08 2011 - 09:07:43 CDT)
- Axel Kohlmeyer (Fri Jul 08 2011 - 08:09:57 CDT)
- Bjoern Olausson (Fri Jul 08 2011 - 06:30:09 CDT)
- Molecular Dynamics (Fri Jul 08 2011 - 05:44:50 CDT)
tesla 2050 benchmark
- Axel Kohlmeyer (Tue Jul 12 2011 - 14:04:00 CDT)
- Burgess, Don E (Tue Jul 12 2011 - 13:56:45 CDT)
testing digest demime - please ignore
- Jim Phillips (Tue Jul 03 2012 - 17:50:18 CDT)
testing digest demime - please ignore #2
- Jim Phillips (Tue Jul 03 2012 - 19:59:09 CDT)
Tetramer protein complex
- snoze pa (Mon Feb 14 2011 - 15:01:31 CST)
- snoze pa (Sun Feb 13 2011 - 00:54:34 CST)
The biggest system simulated on one TESLA C2050 ?
- Jim Phillips (Wed Apr 13 2011 - 09:37:46 CDT)
- Axel Kohlmeyer (Wed Mar 30 2011 - 14:42:56 CDT)
- Marek Maly (Wed Mar 30 2011 - 13:30:11 CDT)
the fictitious force or the viscosity of water
- ishiikai08_at_yahoo.co.jp (Wed Oct 17 2012 - 02:44:04 CDT)
the meaning and effect of reassignFreq and reassignTemp
- Kang Hee Cho (Tue Jan 25 2011 - 08:46:39 CST)
the meaning of " 5-ZEROS" " 9-ZEROS" in the DCD file
- Bjoern Olausson (Tue May 24 2011 - 03:44:23 CDT)
- jnsong (Tue May 24 2011 - 03:12:57 CDT)
the meaning of reassignFreq and reassignTemp
- Chris Harrison (Sun Jan 23 2011 - 09:51:01 CST)
- Kang Hee Cho (Sat Jan 22 2011 - 04:28:22 CST)
The Nudged Elastic Band Approach to Find the Lowest Energy Pathway Between two States
- Buddhadev Maiti (Tue May 24 2011 - 22:14:14 CDT)
The simplest pair list generation scheme
- anaome_at_fundp.ac.be (Thu Mar 29 2012 - 14:01:45 CDT)
The size of a periodic cell in NAMD operation
- Chris Harrison (Fri Aug 31 2012 - 19:55:42 CDT)
- Patrick Chiu (Fri Aug 31 2012 - 18:45:19 CDT)
The structure files for the second turn of simulation
- yp sun (Sun Aug 26 2012 - 20:30:04 CDT)
Thermodynamic integration questions
- pepe barrientos (Tue Dec 06 2011 - 10:39:38 CST)
Three GPU cards on shared-mem motherboard
- Aron Broom (Fri Jun 01 2012 - 10:34:58 CDT)
- Francesco Pietra (Thu May 31 2012 - 00:53:33 CDT)
- Aron Broom (Wed May 30 2012 - 22:03:24 CDT)
- Axel Kohlmeyer (Wed May 30 2012 - 20:02:31 CDT)
- Aron Broom (Wed May 30 2012 - 19:50:49 CDT)
- Francesco Pietra (Wed May 30 2012 - 10:33:14 CDT)
- Aron Broom (Wed May 30 2012 - 09:14:17 CDT)
- Francesco Pietra (Wed May 30 2012 - 02:45:24 CDT)
- Francesco Pietra (Tue May 29 2012 - 16:59:32 CDT)
- Francesco Pietra (Mon May 28 2012 - 14:46:54 CDT)
- Axel Kohlmeyer (Mon May 28 2012 - 11:20:13 CDT)
- Francesco Pietra (Mon May 28 2012 - 11:03:43 CDT)
- Axel Kohlmeyer (Mon May 28 2012 - 05:35:51 CDT)
- Francesco Pietra (Mon May 28 2012 - 03:53:02 CDT)
time step and total simulation time in conf file
- Jérôme Hénin (Wed Sep 14 2011 - 10:53:43 CDT)
- Namd Namd (Wed Sep 14 2011 - 09:41:00 CDT)
timing variation during 256core run on abe.ncsa.uiuc.edu
- Axel Kohlmeyer (Tue Feb 22 2011 - 11:06:26 CST)
- Bishop, Thomas C (Tue Feb 22 2011 - 10:14:30 CST)
- Axel Kohlmeyer (Mon Feb 21 2011 - 15:07:50 CST)
- Thomas C. Bishop (Mon Feb 21 2011 - 13:52:56 CST)
TIP4P force field
- Boyang Wang (Tue Jan 03 2012 - 22:33:07 CST)
- Udaysankar Midya (Tue Jan 03 2012 - 21:46:52 CST)
TIP4P water model
- Chris Harrison (Thu Jul 21 2011 - 16:54:33 CDT)
- Molecular Dynamics (Wed Jul 20 2011 - 07:34:47 CDT)
TIP5P simulation
- Axel Kohlmeyer (Sat Jan 07 2012 - 10:18:47 CST)
- Mallajosyula, Sairam (Sat Jan 07 2012 - 09:06:14 CST)
- Boyang Wang (Fri Jan 06 2012 - 22:42:07 CST)
- Mallajosyula, Sairam (Fri Jan 06 2012 - 09:58:54 CST)
- Axel Kohlmeyer (Thu Jan 05 2012 - 21:59:12 CST)
- Mallajosyula, Sairam (Thu Jan 05 2012 - 21:41:05 CST)
TIP5P water simulation
- David Huggins (Thu May 26 2011 - 15:57:25 CDT)
TIP5P-model
- Rajan Vatassery (Thu Jul 14 2011 - 20:30:00 CDT)
- Maria Kamm (Thu Jul 14 2011 - 19:07:48 CDT)
TMD and binary coordinate files
- Bryan Roessler (Wed Sep 28 2011 - 16:40:49 CDT)
TMD output format
- JC Gumbart (Mon May 21 2012 - 11:34:17 CDT)
- Payne, Christy (Mon May 21 2012 - 10:00:24 CDT)
topology and parameter files
- Molecular Dynamics (Sat Apr 16 2011 - 07:13:28 CDT)
Topology file for ethanol
- Babban Mia (Wed Aug 10 2011 - 23:35:37 CDT)
- Babban Mia (Wed Aug 10 2011 - 22:58:19 CDT)
topology file for nanotube
- Axel Kohlmeyer (Thu Mar 10 2011 - 08:11:13 CST)
- Axel Kohlmeyer (Thu Mar 10 2011 - 04:43:37 CST)
- Axel Kohlmeyer (Thu Mar 10 2011 - 04:38:27 CST)
- Ranyere Deyler (Thu Mar 10 2011 - 02:10:13 CST)
- sakthi kumaran (Thu Mar 10 2011 - 00:57:44 CST)
topology file for nucleic acids including ammonium ion
- Alex Liu (Mon Mar 21 2011 - 16:40:55 CDT)
topology for DNA
- Eduardo Cruz-Chu (Fri Jan 28 2011 - 08:23:33 CST)
- Chris Harrison (Fri Jan 28 2011 - 07:59:06 CST)
- Neelanjana Sengupta (Fri Jan 28 2011 - 06:28:03 CST)
topology for monophosphate
- Irene Newhouse (Wed Apr 06 2011 - 14:02:30 CDT)
- Irene Newhouse (Tue Apr 05 2011 - 15:25:52 CDT)
TopoTools for tpr file
- Jeffrey Potoff (Fri Sep 09 2011 - 11:09:22 CDT)
- Daniel Aguayo (Fri Sep 09 2011 - 10:46:33 CDT)
- Axel Kohlmeyer (Fri Sep 09 2011 - 10:44:42 CDT)
- Hasan haska (Fri Sep 09 2011 - 09:01:44 CDT)
trajectory_path.tcl
- Axel Kohlmeyer (Tue May 17 2011 - 09:38:19 CDT)
- Jacopo Sgrignani (Tue May 17 2011 - 09:16:47 CDT)
Transferring environment variables when using charmrun
- Axel Kohlmeyer (Wed Jul 06 2011 - 07:47:46 CDT)
- Ajasja LjubetiÄ (Wed Jul 06 2011 - 05:08:54 CDT)
Treating Multi Chain Proteins
- Roy Fernando (Tue Sep 11 2012 - 14:58:14 CDT)
Trouble running NAMD on win7
- Jernej Zidar (Mon Sep 26 2011 - 03:42:19 CDT)
- Ajasja LjubetiÄ (Mon Sep 26 2011 - 03:09:19 CDT)
- Haque-Student,STW, Farhadul (Sun Sep 25 2011 - 23:44:14 CDT)
Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module
- Ajasja LjubetiÄ (Thu Feb 09 2012 - 12:05:19 CST)
- Giacomo Fiorin (Tue Feb 07 2012 - 16:57:33 CST)
- Ajasja LjubetiÄ (Mon Feb 06 2012 - 16:55:26 CST)
- Ajasja LjubetiÄ (Mon Feb 06 2012 - 15:04:56 CST)
- Jérôme Hénin (Fri Feb 03 2012 - 05:20:31 CST)
- Giacomo Fiorin (Thu Feb 02 2012 - 17:02:08 CST)
- Ajasja LjubetiÄ (Thu Feb 02 2012 - 09:06:37 CST)
- Giacomo Fiorin (Wed Feb 01 2012 - 19:31:53 CST)
- Ajasja LjubetiÄ (Wed Feb 01 2012 - 03:44:26 CST)
- Giacomo Fiorin (Tue Jan 31 2012 - 12:28:24 CST)
- Ajasja LjubetiÄ (Tue Jan 31 2012 - 08:30:05 CST)
Trp-cage folding simulation
- divya nayar (Thu Jul 28 2011 - 00:09:07 CDT)
Truncated octahedron - unwrapping the trajectory etc
- Alexander Predeus (Tue Aug 16 2011 - 21:46:22 CDT)
Truncated octahedron box issues (?)
- Jim Phillips (Thu May 26 2011 - 22:59:06 CDT)
- Massimiliano Porrini (Thu May 26 2011 - 14:00:49 CDT)
- Jim Phillips (Wed May 25 2011 - 13:57:05 CDT)
- Massimiliano Porrini (Wed May 25 2011 - 10:38:03 CDT)
Truncated octahedron box issues Q=3F=29?=
- Nikolaos Glykos (Wed May 25 2011 - 12:19:03 CDT)
- Nikolaos Glykos (Wed May 25 2011 - 12:15:44 CDT)
Trying to run a setup with amber force field in NAMD
- johan strumpfer (Thu Jun 14 2012 - 08:18:08 CDT)
- Eduard Schreiner (Tue Jun 12 2012 - 18:32:08 CDT)
- johan strumpfer (Tue Jun 12 2012 - 17:49:46 CDT)
- Aron Broom (Tue Jun 12 2012 - 21:34:09 CDT)
- scott davis (Tue Jun 12 2012 - 16:49:55 CDT)
Turning off Electrostatics Completely
- Daniel Aguayo (Mon Mar 07 2011 - 11:53:55 CST)
- David Tanner (Thu Feb 24 2011 - 18:50:56 CST)
- gaborekt_at_duq.edu (Thu Feb 24 2011 - 16:05:41 CST)
two NAMD questions
- sajad falsafi (Wed Nov 09 2011 - 23:16:18 CST)
- Richard Wood (Wed Nov 09 2011 - 22:31:18 CST)
Typo in NAMD 2.8b2 output for Accelerated MD
- Chris Harrison (Thu May 19 2011 - 09:32:11 CDT)
- Bjoern Olausson (Thu May 19 2011 - 07:25:51 CDT)
typo/my flawed thinking on "alchVdwLambdaEnd"?
- Jérôme Hénin (Wed Sep 05 2012 - 08:13:45 CDT)
- Sebastian Stolzenberg (Tue Sep 04 2012 - 19:20:07 CDT)
Tyrosine ligand at Fe(II)
- Francesco Pietra (Sun Mar 18 2012 - 11:34:57 CDT)
Uma wants to chat
- Uma (Thu Mar 03 2011 - 07:33:27 CST)
umbrella sampling
- Jérôme Hénin (Wed Aug 22 2012 - 05:02:11 CDT)
- Jérôme Hénin (Wed Aug 22 2012 - 03:10:17 CDT)
- ipsita basu (Wed Aug 22 2012 - 01:52:14 CDT)
- Aron Broom (Thu Jul 12 2012 - 07:46:50 CDT)
- ipsita basu (Thu Jul 12 2012 - 01:17:53 CDT)
- Jérôme Hénin (Wed Jul 11 2012 - 10:20:58 CDT)
- ipsita basu (Wed Jul 11 2012 - 06:48:16 CDT)
- ipsita basu (Tue Jun 26 2012 - 09:49:30 CDT)
- koushik.k (Tue Jun 26 2012 - 03:19:23 CDT)
- ipsita basu (Tue Jun 26 2012 - 00:13:18 CDT)
- Giacomo Fiorin (Mon Jun 25 2012 - 09:15:50 CDT)
- ipsita basu (Mon Jun 25 2012 - 02:22:21 CDT)
- Jérôme Hénin (Thu Nov 17 2011 - 03:29:23 CST)
- koushik.k (Wed Nov 16 2011 - 22:18:59 CST)
- Parisa Akhski (Wed Nov 16 2011 - 15:12:17 CST)
- Jérôme Hénin (Wed May 18 2011 - 09:40:25 CDT)
- Buddhadev Maiti (Tue May 17 2011 - 21:52:38 CDT)
Umbrella Sampling after multiple replicas metadynamics
- Aron Broom (Fri Sep 28 2012 - 16:53:09 CDT)
- Giacomo Fiorin (Fri Sep 28 2012 - 16:33:54 CDT)
- Aron Broom (Fri Sep 28 2012 - 16:23:15 CDT)
umbrella sampling by NAMD
- Jérôme Hénin (Tue Jun 14 2011 - 07:31:53 CDT)
- jafar azamat (Tue Jun 14 2011 - 06:27:45 CDT)
Umbrella Sampling plus restraints
- Aron Broom (Fri Jul 20 2012 - 08:48:00 CDT)
- felmerino_at_uchile.cl (Fri Jul 20 2012 - 04:44:48 CDT)
- Aron Broom (Wed Jul 18 2012 - 08:47:34 CDT)
- felmerino_at_uchile.cl (Wed Jul 18 2012 - 07:18:10 CDT)
Umbrella sampling using dihedral angle
- Giacomo Fiorin (Tue Jan 24 2012 - 11:21:34 CST)
- Giacomo Fiorin (Tue Jan 24 2012 - 09:38:30 CST)
- Buddhadev Maiti (Sun Jan 22 2012 - 22:17:25 CST)
Umbrella sampling with hbond
- Giacomo Fiorin (Sat Mar 24 2012 - 12:52:17 CDT)
- Payne, Christy (Thu Mar 22 2012 - 19:05:24 CDT)
Umbrella sampling-NAMD
- Aron Broom (Fri Dec 16 2011 - 09:46:39 CST)
- Parisa Akhski (Fri Dec 16 2011 - 09:29:27 CST)
- Aron Broom (Thu Dec 15 2011 - 14:14:05 CST)
- Chris Harrison (Thu Dec 15 2011 - 14:07:36 CST)
- Parisa Akhski (Thu Dec 15 2011 - 12:51:57 CST)
- Aron Broom (Thu Dec 15 2011 - 11:11:04 CST)
- Jérôme Hénin (Thu Dec 15 2011 - 11:07:04 CST)
- Parisa Akhski (Thu Dec 15 2011 - 09:24:36 CST)
Umbrella sampling-reliability of results
- Aron Broom (Fri May 04 2012 - 09:41:35 CDT)
- Parisa Akhski (Fri May 04 2012 - 09:20:17 CDT)
Unable to reproduce same results in minimization with GBIS
- Kasam, Vinod (Thu Sep 13 2012 - 13:12:24 CDT)
- Chris Harrison (Thu Sep 13 2012 - 11:50:01 CDT)
- Kasam, Vinod (Thu Sep 13 2012 - 10:52:31 CDT)
understanding the energy term in NAMD log file
- Jeffrey Potoff (Wed Dec 12 2012 - 21:46:16 CST)
- ç¿æž—å²½ (Wed Dec 12 2012 - 20:46:31 CST)
Uneven sampling in using ABF
- DAI, JIAN (Mon Jul 30 2012 - 08:17:45 CDT)
Uneven sampling when using ABF
- Aron Broom (Tue Jul 31 2012 - 07:36:22 CDT)
- JC Gumbart (Mon Jul 30 2012 - 21:36:05 CDT)
- DAI, JIAN (Mon Jul 30 2012 - 20:54:15 CDT)
- Aron Broom (Mon Jul 30 2012 - 20:33:32 CDT)
- JC Gumbart (Mon Jul 30 2012 - 20:15:02 CDT)
- Aron Broom (Mon Jul 30 2012 - 18:10:03 CDT)
- DAI, JIAN (Mon Jul 30 2012 - 12:38:12 CDT)
Unexplained segmentation faults in NAMD 2.9 using CUDA and GBIS
- Tristan Croll (Thu Nov 29 2012 - 17:42:53 CST)
- Aron Broom (Thu Nov 29 2012 - 17:01:23 CST)
- Tristan Croll (Wed Nov 28 2012 - 05:40:18 CST)
unit of force constant for dihedral angle restrain with extrabonds command
- Ling Wu (Thu Oct 13 2011 - 15:43:13 CDT)
units of pmf files
- Jérôme Hénin (Mon Oct 08 2012 - 06:12:51 CDT)
- Marc Gordon (Mon Oct 08 2012 - 05:42:37 CDT)
Unpredictable crash at runtime
- pellegrini (Fri Mar 18 2011 - 03:14:22 CDT)
unreasonably high temp/pressure
- Aron Broom (Wed Oct 24 2012 - 17:04:54 CDT)
- Martin, Erik W (Wed Oct 24 2012 - 14:33:41 CDT)
- Jesper Sørensen (Wed Oct 24 2012 - 15:00:07 CDT)
- Aron Broom (Wed Oct 24 2012 - 12:56:36 CDT)
- Martin, Erik W (Wed Oct 24 2012 - 10:34:57 CDT)
- Aron Broom (Wed Oct 24 2012 - 10:26:43 CDT)
- Martin, Erik W (Wed Oct 24 2012 - 09:55:52 CDT)
unreasonably high temp/pressure. .
- Jesper Sørensen (Wed Oct 24 2012 - 23:24:42 CDT)
- Martin, Erik W (Wed Oct 24 2012 - 17:18:06 CDT)
- Martin, Erik W (Wed Oct 24 2012 - 15:31:58 CDT)
unsubcribe
- Charlie Forde (Wed Jan 05 2011 - 10:49:54 CST)
unsubscribe
- Yuqi Liu (Mon Aug 20 2012 - 18:23:00 CDT)
- Gmail (Mon Sep 12 2011 - 14:33:58 CDT)
- Tibbitt, Jeffrey A. (Tue Jul 12 2011 - 19:32:21 CDT)
- Cole Gleason (Thu May 19 2011 - 09:37:36 CDT)
- Gary M. Skinner (Mon May 09 2011 - 03:31:45 CDT)
- Chen, Zhihong (chenz2) (Thu Mar 31 2011 - 13:02:05 CDT)
- Purushottam Dixit (Mon Jan 31 2011 - 20:59:01 CST)
Use of RBCG to convert multiple frames from atomistic trajectory to Coarse grained
- Axel Kohlmeyer (Tue Nov 01 2011 - 14:59:27 CDT)
- rohan uttarwar (Tue Nov 01 2011 - 13:13:20 CDT)
User-defined forces in NAMD
- Ali Ghaffaari (Wed Apr 11 2012 - 13:51:51 CDT)
- Axel Kohlmeyer (Wed Apr 11 2012 - 13:32:26 CDT)
- Ali Ghaffaari (Wed Apr 11 2012 - 13:12:04 CDT)
- Ehsan Ban (Tue Apr 10 2012 - 11:55:30 CDT)
- Axel Kohlmeyer (Tue Apr 10 2012 - 07:16:18 CDT)
- Ali Ghaffaari (Tue Apr 10 2012 - 06:38:13 CDT)
Using 'Alignment to principal axes '
- Andres Morales N (Mon Aug 29 2011 - 00:38:44 CDT)
Using ABF to explore the conformational space of a spin label attached to a membrane protein
- Jérôme Hénin (Thu Jan 20 2011 - 08:07:36 CST)
- Ajasja LjubetiÄ (Wed Jan 19 2011 - 10:01:42 CST)
- Jérôme Hénin (Wed Jan 19 2011 - 09:23:03 CST)
- Ajasja LjubetiÄ (Wed Jan 19 2011 - 06:53:41 CST)
- Ajasja LjubetiÄ (Tue Jan 18 2011 - 08:40:56 CST)
- Jérôme Hénin (Mon Jan 17 2011 - 11:44:24 CST)
- Ajasja LjubetiÄ (Mon Jan 17 2011 - 09:56:28 CST)
Using CHARMM Compatible Amber Parameters
- Ehsan Ban (Sun Oct 23 2011 - 12:57:03 CDT)
- Axel Kohlmeyer (Thu Oct 20 2011 - 11:34:33 CDT)
- johan strumpfer (Wed Oct 19 2011 - 22:57:48 CDT)
- Jernej Zidar (Wed Oct 19 2011 - 20:22:46 CDT)
- Ehsan Ban (Wed Oct 19 2011 - 20:10:30 CDT)
using CHARMM22STAR forcefield in NAMD
- Victor Ovchinnikov (Fri Jun 08 2012 - 09:27:46 CDT)
- Aaron Oakley (Fri Jun 08 2012 - 03:23:07 CDT)
using colvar for umbrella sampling between two carbon nanotubes in aqueous dispersion
- Aron Broom (Thu Sep 20 2012 - 12:58:35 CDT)
- Jérôme Hénin (Thu Sep 20 2012 - 12:45:49 CDT)
- nabaneeta mukhopadhyay (Thu Sep 20 2012 - 12:05:49 CDT)
- Jérôme Hénin (Thu Sep 20 2012 - 11:59:47 CDT)
- nabaneeta mukhopadhyay (Thu Sep 20 2012 - 11:21:33 CDT)
using colvars for bending modulus?
- Jérôme Hénin (Wed Jul 27 2011 - 03:12:33 CDT)
- JC Gumbart (Wed Jul 27 2011 - 01:40:24 CDT)
- Jérôme Hénin (Wed Jul 27 2011 - 01:29:59 CDT)
- JC Gumbart (Tue Jul 26 2011 - 15:43:50 CDT)
Using Measure SASA in NAMD Simulations
- Aron Broom (Tue Apr 17 2012 - 02:02:16 CDT)
- Ajith Rathnaweera Rajapaksha Mudalige (Mon Apr 16 2012 - 20:22:28 CDT)
Using RAMD for studiying conformational changes in proteins
- Vlad Cojocaru (Thu Mar 24 2011 - 17:59:22 CDT)
- Raul Araya (Thu Mar 24 2011 - 15:23:39 CDT)
Using TCLforces to rescale force(s) on particular atom(s) --- loadtotalforces, addforce and previous/current timestep issue
- Boyang Wang (Thu Jan 19 2012 - 17:45:41 CST)
- Giacomo Fiorin (Thu Jan 19 2012 - 11:56:00 CST)
- Gungor Ozer (Thu Jan 19 2012 - 11:44:29 CST)
using TIP4P 2005 in namd
- V.Ovchinnikov (Wed Feb 23 2011 - 15:54:26 CST)
- Ana Celia Vila Verde (Wed Feb 23 2011 - 11:57:03 CST)
Using VMD paratool
- æŽä½³é”® (Mon Jul 11 2011 - 16:24:12 CDT)
Vacuum simulations
- Aron Broom (Mon Oct 15 2012 - 15:14:28 CDT)
- mohan maruthi sena (Mon Oct 15 2012 - 14:16:04 CDT)
Various practical colvar module related questions
- Ajasja LjubetiÄ (Thu Jan 20 2011 - 09:12:30 CST)
- Jérôme Hénin (Wed Jan 19 2011 - 09:46:23 CST)
- Ajasja LjubetiÄ (Tue Jan 18 2011 - 11:31:46 CST)
vdw parameter of metal ion
- yandong Huang (Thu Jun 02 2011 - 07:34:20 CDT)
- yandong Huang (Thu Jun 02 2011 - 07:32:41 CDT)
- ÅÓ´ºÀö (Tue May 31 2011 - 04:49:55 CDT)
vdw value in parameter file
- ÅÓ´ºÀö (Mon Jun 20 2011 - 02:26:06 CDT)
velocity distribution
- David Hardy (Mon Oct 08 2012 - 12:54:52 CDT)
- Namd Namd (Mon Oct 08 2012 - 06:46:52 CDT)
- Jim Phillips (Wed Apr 13 2011 - 08:38:58 CDT)
- Philip Peartree (Tue Mar 29 2011 - 05:45:30 CDT)
velocity error during steered MD
- Markus K. Dahlgren (Tue Apr 26 2011 - 09:08:32 CDT)
velocity information
- Molecular Dynamics (Fri Sep 23 2011 - 08:20:29 CDT)
VMD inorganic builder plugin
- Robert Brunner (Thu Mar 17 2011 - 14:17:48 CDT)
- dota alexiou (Thu Mar 17 2011 - 05:36:31 CDT)
vmd-l: CHARMM parameters for Mn 2+ ion
- Daniel Aguayo (Fri Mar 25 2011 - 14:45:15 CDT)
- Jernej Zidar (Fri Mar 25 2011 - 12:57:00 CDT)
vmd-l: connect a spring between all the atoms present in pdb structure
- Eduard Schreiner (Sat Aug 04 2012 - 16:36:38 CDT)
- Axel Kohlmeyer (Sat Aug 04 2012 - 13:20:05 CDT)
vmd-l: FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?)
- Mayne, Christopher G (Tue Jun 05 2012 - 13:27:13 CDT)
- Francesco Pietra (Tue Jun 05 2012 - 12:54:05 CDT)
- JC Gumbart (Tue Jun 05 2012 - 09:22:10 CDT)
vmd-l: Gromacs analysis tools for Namd output
- Kei Sit (Wed Feb 01 2012 - 17:33:01 CST)
- John Stone (Wed Feb 01 2012 - 11:47:43 CST)
vmd-l: How to maximize the VMD display window
- Ajasja LjubetiÄ (Fri Mar 25 2011 - 07:48:24 CDT)
vmd-l: measure fit - wrong alignment
- Jérôme Hénin (Thu May 26 2011 - 13:09:29 CDT)
vmd-l: namd/vmd support to GTX-6## series
- Francesco Pietra (Thu Jun 21 2012 - 12:36:27 CDT)
- John Stone (Wed Jun 06 2012 - 09:13:01 CDT)
vmd-l: No APBS output: 'cannot access output file' error
- Christian Jorgensen (Mon Jul 18 2011 - 18:44:07 CDT)
vmd-l: No probability distribution plot in ParseFEP
- Christian Jorgensen (Fri Apr 01 2011 - 04:09:12 CDT)
- liupeng012_at_mail.nankai.edu.cn (Thu Mar 31 2011 - 21:08:46 CDT)
- Christian Jorgensen (Thu Mar 31 2011 - 13:24:27 CDT)
vmd-l: Parse Fep plugin error
- John Stone (Fri Dec 23 2011 - 10:47:56 CST)
vmd-l: ParseFEP output errors
- Chris Chipot (Mon Apr 11 2011 - 11:40:10 CDT)
- Christian Jorgensen (Mon Apr 11 2011 - 11:27:08 CDT)
vmd-l: protein-water RDF
- Ajasja LjubetiÄ (Mon Jun 27 2011 - 03:33:13 CDT)
- Ajasja LjubetiÄ (Mon Jun 27 2011 - 03:29:44 CDT)
vmd-l: Stand-alone VMD ?
- Mark Cunningham (Thu Feb 16 2012 - 15:45:55 CST)
vmd-l: vmd installation problem
- oguz gurbulak (Thu Jul 12 2012 - 00:59:23 CDT)
vmd: ParseFEP plot mistake
- Christian Jorgensen (Tue Mar 29 2011 - 10:08:35 CDT)
- Chris Chipot (Tue Mar 29 2011 - 07:06:46 CDT)
- Christian Jorgensen (Tue Mar 29 2011 - 04:45:07 CDT)
VMD_waterbox
- Shomesankar Bhunia (Mon Sep 17 2012 - 01:47:35 CDT)
volume calculation
- Swarna M Patra (Tue Feb 01 2011 - 04:02:48 CST)
W and S
- Axel Kohlmeyer (Tue Sep 25 2012 - 12:45:40 CDT)
- Mikhail Suyetin (Tue Sep 25 2012 - 05:24:34 CDT)
Warning & error
- Narasimhan LOGANATHAN (Wed Oct 10 2012 - 05:07:54 CDT)
- Narasimhan LOGANATHAN (Tue Oct 09 2012 - 08:48:43 CDT)
Warning: Not all atoms have unique coordinates
- Jacqueline Schmidt (Tue Aug 28 2012 - 19:17:54 CDT)
water box deformation
- felmerino_at_uchile.cl (Wed Feb 09 2011 - 12:57:23 CST)
- Jeffrey Potoff (Wed Feb 09 2011 - 10:51:41 CST)
- ais_at_fh.huji.ac.il (Wed Feb 09 2011 - 09:47:27 CST)
Water bubbles in NVT equilibration dynamics
- Jeffrey Potoff (Mon Aug 27 2012 - 10:00:39 CDT)
- Ana Celia Vila Verde (Mon Aug 27 2012 - 09:23:51 CDT)
- Mariana Graterol (Fri Aug 24 2012 - 18:52:28 CDT)
water content
- Kang Hee Cho (Thu Jan 27 2011 - 23:18:24 CST)
water equilibration
- Jeffrey Potoff (Fri Aug 05 2011 - 09:32:23 CDT)
- Narasimhan LOGANATHAN (Fri Aug 05 2011 - 05:41:27 CDT)
- Narasimhan LOGANATHAN (Thu Aug 04 2011 - 03:25:07 CDT)
- Narasimhan LOGANATHAN (Tue Aug 02 2011 - 08:42:11 CDT)
- Jim Phillips (Wed Jun 08 2011 - 14:40:03 CDT)
- Narasimhan LOGANATHAN (Wed Jun 08 2011 - 05:17:17 CDT)
- Gurunath Katagi (Tue Jun 07 2011 - 15:14:51 CDT)
- johan strumpfer (Tue Jun 07 2011 - 11:20:16 CDT)
- Narasimhan LOGANATHAN (Tue Jun 07 2011 - 11:15:10 CDT)
- johan strumpfer (Tue Jun 07 2011 - 09:44:33 CDT)
- Narasimhan LOGANATHAN (Tue Jun 07 2011 - 09:03:23 CDT)
- johan strumpfer (Mon Jun 06 2011 - 08:59:05 CDT)
- Bjoern Olausson (Mon Jun 06 2011 - 09:12:33 CDT)
- Narasimhan LOGANATHAN (Mon Jun 06 2011 - 08:55:39 CDT)
- Wang Yi (Mon Jun 06 2011 - 08:42:26 CDT)
- Narasimhan LOGANATHAN (Mon Jun 06 2011 - 08:07:38 CDT)
water is forming bonds between oxigens
- PAUL NEWMAN (Tue Jun 14 2011 - 16:36:33 CDT)
water molecules
- oguz gurbulak (Tue Jan 03 2012 - 03:08:58 CST)
- Boyang Wang (Tue Jan 03 2012 - 02:51:56 CST)
- Nicholas M Glykos (Mon Jan 02 2012 - 07:35:19 CST)
- oguz gurbulak (Mon Jan 02 2012 - 06:04:08 CST)
water parameters
- Mark Abraham (Mon Aug 27 2012 - 18:29:25 CDT)
water sphere
- Axel Kohlmeyer (Thu Jan 06 2011 - 08:18:57 CST)
- sara (Thu Jan 06 2011 - 03:14:01 CST)
water sphere plus dielectric
- esmael (Wed Jul 27 2011 - 14:11:20 CDT)
weird energy values of LJ fluids
- Lindong Weng (Tue Dec 11 2012 - 16:15:55 CST)
Weird energy values of LJ fluids simulation
- Lindong Weng (Tue Dec 11 2012 - 13:43:16 CST)
WG: Abnormal EOF Error in Extra Bonds File
- Norman Geist (Mon May 02 2011 - 06:48:41 CDT)
WHAM in the NPT ensemble
- Shaon Chakrabarti (Mon Dec 31 2012 - 14:35:50 CST)
what does .inp do from CHARMM GUI?
- Bjoern Olausson (Mon Mar 19 2012 - 07:42:46 CDT)
- Albert (Sun Mar 18 2012 - 07:19:22 CDT)
What is a good (small) test system for NAMD
- Roy Fernando (Tue Jul 10 2012 - 15:43:20 CDT)
- Aron Broom (Tue Jul 10 2012 - 15:19:01 CDT)
- Roy Fernando (Tue Jul 10 2012 - 15:07:05 CDT)
- Roy Fernando (Tue Jul 10 2012 - 14:34:40 CDT)
- Aron Broom (Tue Jul 10 2012 - 14:23:47 CDT)
- Giacomo Fiorin (Tue Jul 10 2012 - 14:17:41 CDT)
- Roy Fernando (Tue Jul 10 2012 - 14:13:01 CDT)
what is fullSamples?
- Jérôme Hénin (Tue Aug 28 2012 - 06:25:52 CDT)
- ¼¿ëÀÏ (Sun Aug 26 2012 - 22:56:59 CDT)
What is the means of system-min.conf in the Residue-Based Coarse tutorial?
- Ramya Gamini (Fri Apr 20 2012 - 14:32:41 CDT)
- javacfish (Fri Apr 20 2012 - 01:17:57 CDT)
What is the proper value of TMDk in TMD simulations?
- Gianluca Interlandi (Mon Oct 24 2011 - 11:03:37 CDT)
- Jérôme Hénin (Mon Oct 24 2011 - 03:02:43 CDT)
- å¸¸å§—ç‡• (Sun Oct 23 2011 - 23:21:19 CDT)
what is wrong with this pdb to simulate with NAMD
- raghav singh (Fri Oct 14 2011 - 12:04:20 CDT)
what restraint can I use to prevent membrane diffusion on the Z-axis?
- Axel Kohlmeyer (Wed Feb 29 2012 - 16:53:59 CST)
- Aron Broom (Wed Feb 29 2012 - 16:46:05 CST)
- Jose Borreguero (Wed Feb 29 2012 - 16:38:44 CST)
- Aron Broom (Tue Feb 28 2012 - 16:46:23 CST)
- Jose Borreguero (Tue Feb 28 2012 - 13:30:16 CST)
- kanchi subbarao rao (Tue Feb 28 2012 - 11:58:49 CST)
- Aron Broom (Mon Feb 27 2012 - 23:15:41 CST)
- kanchi subbarao rao (Mon Feb 27 2012 - 22:49:02 CST)
- kanchi subbarao rao (Sun Feb 26 2012 - 10:39:42 CST)
- Chris Harrison (Sat Feb 25 2012 - 11:59:43 CST)
- Jose Borreguero (Wed Feb 22 2012 - 14:07:30 CST)
what will be the best way to simulate substrate interaction only within a binding pocket of a large protein.
- Ajasja LjubetiÄ (Tue May 10 2011 - 15:57:58 CDT)
- Giacomo Fiorin (Tue May 10 2011 - 15:20:18 CDT)
- Arun Kumar Subramanian (Sat May 07 2011 - 21:20:29 CDT)
What's the difference between upperboundary and upperwall?
- Giacomo Fiorin (Mon Dec 03 2012 - 16:38:07 CST)
- DAI, JIAN (Mon Dec 03 2012 - 16:34:32 CST)
where can I find parameters for t-BuO(C=O)NH-?
- AlbertAlbert (Tue Jul 12 2011 - 12:33:39 CDT)
where does the second boost in accelMDdual mode refer to
- Thomas Evangelidis (Sun Nov 18 2012 - 16:25:50 CST)
where is psf develop in ffTK
- Chris Harrison (Wed Feb 15 2012 - 15:21:27 CST)
- ¼¿ëÀÏ (Mon Feb 13 2012 - 06:55:37 CST)
Why are the pressures in my box of water systematically off?
- Tom Sisan (Thu Mar 31 2011 - 17:04:03 CDT)
- Tom Sisan (Wed Mar 30 2011 - 12:40:58 CDT)
- Jim Phillips (Sun Mar 27 2011 - 10:04:35 CDT)
- Tom Sisan (Thu Mar 24 2011 - 18:33:39 CDT)
Why NAMD writes colvars step by step
- Leonardo Herrera (Sat Apr 02 2011 - 19:22:23 CDT)
- Giacomo Fiorin (Sat Apr 02 2011 - 19:38:26 CDT)
- Jérôme Hénin (Sat Apr 02 2011 - 02:34:02 CDT)
- Giacomo Fiorin (Fri Apr 01 2011 - 21:10:15 CDT)
- Leonardo Herrera (Fri Apr 01 2011 - 19:04:21 CDT)
- Leonardo Herrera (Fri Apr 01 2011 - 17:06:03 CDT)
will Jaguar enough for NAMD partial charge?
- Albert (Tue Mar 20 2012 - 02:18:54 CDT)
win64 namd cuda: compile?
- Axel Kohlmeyer (Tue Aug 07 2012 - 03:46:35 CDT)
- Aaron Cann (Tue Aug 07 2012 - 00:09:36 CDT)
Win64-MPI
- Ajasja LjubetiÄ (Tue Jul 12 2011 - 08:24:28 CDT)
- Patriche Simona (Tue Jul 12 2011 - 08:08:14 CDT)
- Ajasja LjubetiÄ (Tue Jul 05 2011 - 02:11:25 CDT)
- Patriche Simona (Tue Jul 05 2011 - 02:04:17 CDT)
Workshop - Computational Molecular Physics of Non-Bonded Bio-Molecular Interactions
- MARK PLUMMER (Mon Jun 11 2012 - 17:14:51 CDT)
Workshop for Computational Chemistry & Physics
- MARK PLUMMER (Wed Jun 20 2012 - 15:17:27 CDT)
Workshop In Aspen Colorado - Molecular Physics of Non-Bonded Biomolecular Interactions
- MARK PLUMMER (Mon Jun 04 2012 - 15:06:18 CDT)
wrap dcd files
- Namd Namd (Thu Jun 28 2012 - 05:03:10 CDT)
Wrapping
- Norman Geist (Mon Sep 17 2012 - 01:08:36 CDT)
- Norman Geist (Mon Sep 10 2012 - 02:27:54 CDT)
- Cruz-Chu Eduardo Roberto (Sat Sep 08 2012 - 14:15:05 CDT)
- Buddhadev Maiti (Fri Sep 07 2012 - 22:35:10 CDT)
Writing an output file into pdb format in a simulation.
- Nicholas M Glykos (Fri Jun 01 2012 - 02:18:01 CDT)
- JC Gumbart (Thu May 31 2012 - 16:10:38 CDT)
- Axel Kohlmeyer (Thu May 31 2012 - 15:57:33 CDT)
- Ajith Rathnaweera Rajapaksha Mudalige (Thu May 31 2012 - 15:20:58 CDT)
Wrong exit from RAMD runs
- Francesco Pietra (Tue Apr 05 2011 - 03:11:29 CDT)
xplor-formated parameters
- Chris Harrison (Tue Dec 06 2011 - 12:41:05 CST)
Yan: analysis question
- Bjoern Olausson (Fri Jul 22 2011 - 03:01:05 CDT)
zero mass particles in NAMD
- Jérôme Hénin (Wed Sep 19 2012 - 08:55:16 CDT)
- Markus Dahlgren (Wed Sep 19 2012 - 08:32:02 CDT)
zinc-finger protein simulation
- hamze rahimi (Mon Jul 18 2011 - 06:55:08 CDT)
ç”å¤: compilation of namd
- Jim Phillips (Thu May 12 2011 - 12:32:28 CDT)
- Axel Kohlmeyer (Thu May 12 2011 - 08:34:14 CDT)
- Axel Kohlmeyer (Thu May 12 2011 - 04:53:58 CDT)
- Axel Kohlmeyer (Wed May 11 2011 - 11:16:29 CDT)
- Jim Phillips (Wed May 11 2011 - 10:53:59 CDT)
- Axel Kohlmeyer (Tue May 10 2011 - 22:14:26 CDT)

Last message date: Mon Dec 31 2012 - 14:36:03 CST
Archived on: Mon Dec 31 2012 - 23:22:24 CST

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