NAMD-L: By Subject

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NAMD-L: By Subject

By Subject

3203 messages sorted by: [ author ] [ date ] [ thread ] [ attachment ]
About this archive

Starting: Sat Jan 01 2011 - 12:21:40 CST
Ending: Fri May 25 2012 - 14:53:54 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)
(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)
- 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)
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)
[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 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)
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)
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 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 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)
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 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)
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)
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)
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 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 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-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 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)
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)
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 (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: 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: 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: 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: 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: 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-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: 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: 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: 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: 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-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: question about wrap atoms to its original coordinates
- Norman Geist (Fri May 20 2011 - 00:04:48 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: 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: 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: 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 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: deca-Ala simulations with different cutoff produce different results
- Norman Geist (Mon May 16 2011 - 04:20:58 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 with "namd"
- Norman Geist (Wed Oct 26 2011 - 02:05:17 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: free energy of binding
- Norman Geist (Thu Jul 07 2011 - 05:35:07 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: 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: 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: 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: Letzte Hilfe
- Bjoern Olausson (Tue Aug 16 2011 - 06:17:36 CDT)
- Norman Geist (Mon Aug 15 2011 - 07:16:39 CDT)
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: 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: 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: 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 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 2.9b1 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-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: nvidia cuda driver version
- Norman Geist (Mon Aug 08 2011 - 00:04:40 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: Peptide planarity Dihedral angle restraints
- Norman Geist (Fri Dec 09 2011 - 00:18:47 CST)
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: 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: 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: restart a simulation
- Norman Geist (Fri Mar 16 2012 - 02:01:34 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: 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: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA)
- 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: 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: vmd-l: segmentation fault with NAMDenergy
- Norman Geist (Mon Apr 23 2012 - 00:52:17 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)
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)
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)
Benchmark for NAMD2.7 (curent version)
- Branko (Wed Jan 05 2011 - 14:19:19 CST)
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 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)
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)
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)
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)
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 for Mn 2+ ion
- Lisa Brown (Fri Mar 25 2011 - 10:43:45 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)
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)
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 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, 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)
Compiled Windows HPC version.
- Chewning, Joseph (Tue Oct 04 2011 - 07:04:31 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 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_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)
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)
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)
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)
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)
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)
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)
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)
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 compiled code for Windows HPC
- Chewning, Joseph (Wed Sep 28 2011 - 14:52:29 CDT)
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 limitations
- 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)
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)
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 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)
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)
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 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)
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
- 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 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)
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 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 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)
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)
expect NAMD survey emails this week
- Jim Phillips (Tue Jul 19 2011 - 11:51:22 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)
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 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: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE AUC
- Kiarash Hosseini (Tue Apr 10 2012 - 04:24:10 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 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)
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)
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)
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 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 group of atoms, Proper for manipualation
- M Mahjour (Wed Apr 13 2011 - 17:06:43 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 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)
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: 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: Generating .tpr file using NAMD files
- rajitha rajeshwar (Mon Dec 19 2011 - 03:05:34 CST)
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: 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: 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)
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)
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)
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-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)
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)
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)
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)
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 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)
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 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 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 convert X_PLOR to CHARMM?
- Lisa Brown (Fri Mar 25 2011 - 11:01:26 CDT)
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 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 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 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)
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)
Infiniband and commodity hardware
- Axel Kohlmeyer (Sun Sep 18 2011 - 02:38:48 CDT)
- Thomas Albers (Sat Sep 17 2011 - 14:59:20 CDT)
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)
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)
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
- 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 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)
Issues with 'Gyration' in Colvars module
- 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)
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 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)
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)
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)
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)
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)
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)
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 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 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)
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
- 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)
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 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)
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 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 node run causes "CUDA error cudaStreamCreate"
- 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 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 dihedral parameters in X-PLOR format
- Joe Yelk (Tue Oct 18 2011 - 17:46:57 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)
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 + 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 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 released
- Jim Phillips (Thu May 03 2012 - 10:27:09 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 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 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 error message
- JC Gumbart (Fri Jan 14 2011 - 11:46:39 CST)
- snoze pa (Fri Jan 14 2011 - 11:37:54 CST)
NAMD energy plugin
- politr_at_fh.huji.ac.il (Thu Jul 28 2011 - 04:22:42 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 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 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 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 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 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 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 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-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-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)
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_ti.pl Modification of non-creatable array value attempted, subscript -49999
- Pete Kekenes-Huskey (Tue Sep 06 2011 - 17:22:26 CDT)
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)
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)
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 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)
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)
Nice paper on MD Simulations
- pawan raghav (Sat Sep 10 2011 - 13:37:00 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)
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)
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)
online guide for using amber ff in NAMD
- George Madalin Giambasu (Wed Aug 03 2011 - 11:18:10 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)
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)
Pair interaction and thermo integration
- Courtney Taylor (Mon Aug 01 2011 - 09:32:38 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)
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 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 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)
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)
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)
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)
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)
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 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)
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)
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 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 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 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 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 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)
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 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 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)
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 (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 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 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 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 from a tutorial
- JC Gumbart (Thu Jan 20 2011 - 14:29:23 CST)
- Lisa Brown (Thu Jan 20 2011 - 14:17:29 CST)
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 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)
Questions
- Joshua Adelman (Mon Oct 10 2011 - 21:54:49 CDT)
- Kevin Littrell (Mon Oct 10 2011 - 21:20:37 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)
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)
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)
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 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)
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 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 and multiple time-stepping
- Niklaus Johner (Mon Mar 05 2012 - 10:19:10 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)
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)
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 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 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)
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 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 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 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 NAMD CUDA
- Axel Kohlmeyer (Fri Nov 04 2011 - 15:16:45 CDT)
- Steven Cox (Fri Nov 04 2011 - 15:06:31 CDT)
Running NAMD parallel on two machines with 3 CUDAs
- Darko Stefanovski (Thu May 05 2011 - 11:53:40 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)
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)
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)
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 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)
- 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)
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: 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)
Steered dynamics
- JC Gumbart (Sat Nov 12 2011 - 01:18:06 CST)
- Jacopo Sgrignani (Fri Nov 11 2011 - 04:56:32 CST)
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)
subscribe namd-l
- Michael Zimmermann (Wed Mar 23 2011 - 13:24:38 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)
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)
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
- sakthi kumaran (Thu Mar 17 2011 - 09:08:25 CDT)
- sakthi kumaran (Thu Mar 17 2011 - 01:28:59 CDT)
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)
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)
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)
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 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)
Thermodynamic integration questions
- pepe barrientos (Tue Dec 06 2011 - 10:39:38 CST)
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)
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)
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)
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 (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 by NAMD
- Jérôme Hénin (Tue Jun 14 2011 - 07:31:53 CDT)
- jafar azamat (Tue Jun 14 2011 - 06:27:45 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)
unit of force constant for dihedral angle restrain with extrabonds command
- Ling Wu (Thu Oct 13 2011 - 15:43:13 CDT)
Unpredictable crash at runtime
- pellegrini (Fri Mar 18 2011 - 03:14:22 CDT)
unsubcribe
- Charlie Forde (Wed Jan 05 2011 - 10:49:54 CST)
Unsubscribe
- 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 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)
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
- 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: 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: 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: 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)
volume calculation
- Swarna M Patra (Tue Feb 01 2011 - 04:02:48 CST)
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 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 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)
WG: Abnormal EOF Error in Extra Bonds File
- Norman Geist (Mon May 02 2011 - 06:48:41 CDT)
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 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)
where can I find parameters for t-BuO(C=O)NH-?
- AlbertAlbert (Tue Jul 12 2011 - 12:33:39 CDT)
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-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)
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)
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: Fri May 25 2012 - 14:53:54 CDT
Archived on: Fri May 25 2012 - 23:20:48 CDT

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