NAMD-L: By Subject

NAMD

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NAMD-L: By Subject

By Subject

1662 messages sorted by: [ author ] [ date ] [ thread ] [ attachment ]
About this archive

Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Fri Dec 31 2004 - 13:16:29 CST

JÃ©rÃ´me HÃ©nin (Thu Jul 01 2004 - 04:47:55 CDT)

Cable, Sam B ERDC-ITL-MS Contractor (Thu Apr 15 2004 - 15:44:57 CDT)

Gengbin Zheng (Thu Apr 15 2004 - 12:14:36 CDT)

Jim Phillips (Mon Jan 26 2004 - 17:51:12 CST)

james tomomi macdonald (Mon Dec 08 2003 - 08:46:54 CST)

Jim Phillips (Wed Dec 03 2003 - 15:03:46 CST)

Cesar Delgado (Wed Dec 03 2003 - 08:46:12 CST)

Fangqiang Zhu (Sat Nov 29 2003 - 00:41:44 CST)

Ioana Cozmuta (Mon Oct 20 2003 - 12:32:02 CDT)

Cesar Delgado (Mon Oct 20 2003 - 01:13:08 CDT)

"Constrain failure" in NAMD
- Brian Bennion (Mon May 10 2004 - 10:47:29 CDT)
- Edward Patrick Obrien (Fri May 07 2004 - 17:59:05 CDT)
- Michael Chen (Fri May 07 2004 - 14:43:41 CDT)
"GRADIENT TOLERANCE: nan", Why?
- Zhong Wenyu (Thu Jun 03 2004 - 09:02:01 CDT)
- Brian Bennion (Wed Jun 02 2004 - 16:04:15 CDT)
- Zhong Wenyu (Wed Jun 02 2004 - 07:42:50 CDT)
# of processors
- Gengbin Zheng (Mon Apr 05 2004 - 00:41:44 CDT)
- Neema Salimi (Mon Mar 29 2004 - 13:02:30 CST)
(no subject)
- mdcooper (Fri Sep 24 2004 - 14:32:46 CDT)
- ying xiong (Thu Jul 01 2004 - 01:57:18 CDT)
- Mauricio Carrillo Tripp (Mon Jun 07 2004 - 11:46:18 CDT)
- Cable, Sam B ERDC-ITL-MS Contractor (Thu Apr 15 2004 - 11:17:53 CDT)
- yu275197_at_yorku.ca (Sun Feb 22 2004 - 00:37:27 CST)
- Michael Grabe (Thu Feb 19 2004 - 14:29:21 CST)
- Michael Grabe (Fri Jan 23 2004 - 17:22:54 CST)
- li (Mon Dec 29 2008 - 16:46:32 CST)
- Alexandre Vakhrouchev (Sun Dec 07 2003 - 01:47:07 CST)
- Alexandre Vakhrouchev (Wed Dec 03 2003 - 02:57:04 CST)
- yxiong_at_mail.ccnu.edu.cn (Fri Nov 28 2003 - 20:35:59 CST)
- Alexandre Vakhrouchev (Thu Nov 06 2003 - 02:18:39 CST)
- Peter Jones (Sun Oct 19 2003 - 23:56:25 CDT)
***** SPAM POSSIBLE ***** Warning: Not all atoms have unique coordinates.
- Jérôme Hénin (Thu Jul 08 2004 - 11:01:54 CDT)
,log and .out files with namd running on mac os x (panther)
- Brian Bennion (Fri May 07 2004 - 10:51:14 CDT)
- Arieana Moore (Wed May 05 2004 - 17:30:28 CDT)
- Arieana Moore (Wed May 05 2004 - 14:37:19 CDT)
.psf and .params files for IMD
- Harit Jani (Wed Dec 10 2003 - 19:08:54 CST)
1QSU
- Tim Isgro (Thu Jan 15 2004 - 15:32:22 CST)
- Uday Chippada (Thu Jan 15 2004 - 13:45:03 CST)
2 domains rigid body rotation with IMD
- Matteo Cattaneo (Sun Dec 07 2003 - 14:33:47 CST)
- Matteo Cattaneo (Fri Dec 05 2003 - 08:28:22 CST)
32 vs. 64 bits
- Leandro Martinez (Fri May 14 2004 - 08:07:14 CDT)
64 bit G5 plans for NAMD
- Jim Phillips (Wed Oct 08 2003 - 17:14:27 CDT)
- Ken Sale (Wed Oct 08 2003 - 14:01:39 CDT)
64 nodes behaviour
- Gengbin Zheng (Fri Sep 03 2004 - 14:37:05 CDT)
- Alexandre Chauvin (Fri Sep 03 2004 - 02:52:30 CDT)
- Gengbin Zheng (Thu Sep 02 2004 - 13:19:03 CDT)
- Alexandre Chauvin (Thu Sep 02 2004 - 12:53:23 CDT)
<no subject>
- Brian Bennion (Thu Feb 26 2004 - 14:44:07 CST)
- klsale (Thu Feb 26 2004 - 13:02:36 CST)
> 10000 ato
- Brian Bennion (Fri Aug 13 2004 - 15:14:05 CDT)
> 10000 atoms
- Jhih-Wei Chu (Fri Aug 13 2004 - 13:32:25 CDT)
[Fwd: counterion software]
- bora erdemli (Mon Oct 11 2004 - 02:03:05 CDT)
- Cetin Baloglu (Sun Oct 10 2004 - 23:55:20 CDT)
[Fwd: total energy stuck between two levels]
- Amit Paliwal (Wed Jan 07 2004 - 05:10:03 CST)
[Periodic Boundary]: from charmm to namd
- Sascha Tayefeh (Tue Nov 02 2004 - 12:46:02 CST)
- Charles Danko (Tue Nov 02 2004 - 11:35:23 CST)
- Sascha Tayefeh (Tue Nov 02 2004 - 09:08:42 CST)
_alloca undefined symbol (OS X/XL compiler)
- Gengbin Zheng (Mon Apr 05 2004 - 00:20:45 CDT)
- Mike McCallum (Fri Apr 02 2004 - 18:29:26 CST)
A confused question on amber param and in charmm form~
- Îº¿ (Fri Nov 26 2004 - 07:41:55 CST)
a different bug alert
- Meric Ayse Ovacik (Sun Oct 17 2004 - 09:27:23 CDT)
- Meric Ayse Ovacik (Sun Oct 17 2004 - 09:21:47 CDT)
A problem with intermediate files
- J. Rui Rodrigues (Tue Nov 11 2003 - 07:46:33 CST)
- Ioana Cozmuta (Mon Nov 10 2003 - 22:12:05 CST)
- Ioana Cozmuta (Mon Nov 10 2003 - 22:09:20 CST)
- Zhilei Chen (Mon Nov 10 2003 - 21:52:57 CST)
A question about RMSD calculation
- Chen Yongzhi (Thu Mar 04 2004 - 22:54:08 CST)
- Chen Yongzhi (Thu Mar 04 2004 - 21:07:52 CST)
A strange thing about psfgen~
- Îº¿ (Sat Nov 13 2004 - 06:21:35 CST)
A tool to set up alchemical FEP transformations
- Jérôme Hénin (Mon Mar 29 2004 - 10:27:12 CST)
about charmm topology file
- Jim Phillips (Wed Nov 05 2003 - 13:15:48 CST)
- Brian Bennion (Wed Nov 05 2003 - 10:27:51 CST)
- Zhilei Chen (Wed Nov 05 2003 - 10:00:56 CST)
about delta-G in PMF calculation
- Hyonseok Hwang (Thu Apr 01 2004 - 22:36:27 CST)
about ExcludeFromPressure
- mashaojie163 (Tue Oct 26 2004 - 21:59:50 CDT)
- mashaojie163 (Fri Oct 22 2004 - 03:52:15 CDT)
about guesscoord
- mashaojie (Wed Mar 03 2004 - 21:31:05 CST)
about HIS residue
- J. Rui Rodrigues (Sun Dec 21 2003 - 13:47:28 CST)
- yxiong_at_mail.ccnu.edu.cn (Fri Dec 19 2003 - 20:40:35 CST)
about internal coordinate IC statement of CHARMM force field
- Brian Bennion (Tue Nov 25 2003 - 13:09:41 CST)
- yxiong_at_mail.ccnu.edu.cn (Tue Nov 25 2003 - 01:24:23 CST)
about MCTI output
- mashaojie163 (Mon Dec 27 2004 - 01:29:36 CST)
about membrane protein
- mashaojie163 (Mon Jun 14 2004 - 09:39:41 CDT)
about pmf
- mashaojie163 (Sun Jun 20 2004 - 21:10:00 CDT)
about psf file
- Kamp, Marc vander (Wed Jun 16 2004 - 11:34:51 CDT)
- mashaojie163 (Wed Jun 16 2004 - 09:33:07 CDT)
about symmetry operations
- mashaojie163 (Wed Jul 07 2004 - 10:23:45 CDT)
about temperature reassign?
- yxiong_at_mail.ccnu.edu.cn (Sat Dec 06 2003 - 03:42:30 CST)
About the SMD output file
- Ioana Cozmuta (Fri Dec 05 2003 - 16:47:31 CST)
- zhilei chen (Fri Dec 05 2003 - 16:17:41 CST)
about this bug alert
- jz7_at_duke.edu (Thu Jun 03 2004 - 09:46:54 CDT)
adding ions
- Michael Grabe (Mon Mar 22 2004 - 14:36:35 CST)
- Brian Bennion (Mon Mar 22 2004 - 14:11:46 CST)
- Amarda Shehu (Mon Mar 22 2004 - 13:30:09 CST)
ADP again
- Brian Bennion (Wed Nov 19 2003 - 11:00:40 CST)
- Fangqiang Zhu (Tue Nov 18 2003 - 18:44:24 CST)
- Brian Bennion (Tue Nov 18 2003 - 10:24:33 CST)
- Fangqiang Zhu (Mon Nov 17 2003 - 18:47:59 CST)
- Brian Bennion (Mon Nov 17 2003 - 12:58:56 CST)
- Brian Bennion (Mon Nov 17 2003 - 11:18:09 CST)
- Brian Bennion (Sun Nov 16 2003 - 00:26:00 CST)
- himanshu chandola (Mon Nov 17 2003 - 02:13:25 CST)
- himanshu chandola (Sun Nov 16 2003 - 04:27:48 CST)
Alchemical FEP calculations in NAMD
- Satyavani Vemparala (Fri Feb 20 2004 - 22:09:43 CST)
alchemical free energy perturbation
- by way of Jérôme Hénin (Mon Jan 05 2004 - 09:10:52 CST)
- AMIT PALIWAL (Mon Jan 05 2004 - 00:37:05 CST)
AMBER FF and pmf
- Fangqiang Zhu (Thu May 06 2004 - 18:18:58 CDT)
- ladam (Thu May 06 2004 - 03:33:34 CDT)
Amber on with H-bond
- Fangqiang Zhu (Thu Mar 04 2004 - 01:00:31 CST)
- Sichun Yang (Thu Mar 04 2004 - 00:15:56 CST)
- Fangqiang Zhu (Wed Mar 03 2004 - 21:45:15 CST)
- Sichun Yang (Wed Mar 03 2004 - 17:59:55 CST)
AMBER parameters and SMD
- Valodymyr Nechyporuk-Zloy (Mon Jul 26 2004 - 04:42:55 CDT)
Amber94 files in CHARMM format
- Kamp, Marc vander (Wed Jun 23 2004 - 10:08:47 CDT)
- Aaron Oakley (Wed Jun 23 2004 - 08:08:13 CDT)
Anyone having problems under Solaris 7?
- Charles Danko (Mon Oct 11 2004 - 11:05:33 CDT)
Argon solvent
- Jérôme Hénin (Tue Feb 17 2004 - 12:03:16 CST)
- Gianni De Fabritiis (Tue Feb 17 2004 - 09:55:02 CST)
Atom number limitations?
- Leandro Martinez (Fri Apr 30 2004 - 08:16:19 CDT)
- Hrant Gharabekyan (Thu Apr 29 2004 - 22:50:26 CDT)
atom numbers limitation
- Jim Phillips (Tue Feb 24 2004 - 15:31:06 CST)
- Wei Fu (Wed Feb 18 2004 - 14:43:27 CST)
Atom type explaination for NAMD
- myang (Wed May 26 2004 - 18:04:05 CDT)
ATOMS moving too fast
- Michael Chen (Thu May 20 2004 - 09:50:23 CDT)
- Jim Phillips (Fri Nov 07 2003 - 11:10:34 CST)
- Jim Phillips (Fri Nov 07 2003 - 10:11:43 CST)
- himanshu chandola (Fri Nov 07 2003 - 20:21:27 CST)
- Brian Bennion (Thu Nov 06 2003 - 11:16:03 CST)
- himanshu chandola (Thu Nov 06 2003 - 19:11:58 CST)
- Brian Bennion (Wed Nov 05 2003 - 17:36:51 CST)
- himanshu chandola (Thu Nov 06 2003 - 03:59:10 CST)
- Brian Bennion (Wed Nov 05 2003 - 16:50:53 CST)
- himanshu chandola (Thu Nov 06 2003 - 03:21:12 CST)
ATP fix (fwd)
- himanshu chandola (Wed Nov 19 2003 - 23:36:48 CST)
- Brian Bennion (Wed Nov 19 2003 - 11:06:19 CST)
- himanshu chandola (Wed Nov 19 2003 - 11:32:17 CST)
Autogene angles dihed / patch / psfgen problem
- Jim Phillips (Wed Oct 15 2003 - 13:53:38 CDT)
- Andersen, Kim Vilbour (KVA) (Wed Oct 15 2003 - 06:27:17 CDT)
Autoionize plugin problem
- Gaurav Sharma (Tue Dec 14 2004 - 12:52:03 CST)
autoionize script
- Olya Kravchenko (Mon May 17 2004 - 14:00:12 CDT)
- amodzelewska_at_dns.iimcb.gov.pl (Sun May 16 2004 - 13:21:58 CDT)
Bad global exclusion count
- Harindar Keer (Fri Jan 16 2004 - 14:06:28 CST)
Basic question.
- Jérôme Hénin (Tue Dec 02 2003 - 13:50:38 CST)
- Brian Bennion (Tue Dec 02 2003 - 13:30:30 CST)
- hansang bae (Tue Dec 02 2003 - 13:03:16 CST)
benchmarking mistake?
- Ioana Cozmuta (Sun May 30 2004 - 20:12:52 CDT)
Berendsen or Langevin Temp control?
- Edward Patrick Obrien (Wed Nov 10 2004 - 15:54:07 CST)
best choice of linux cluster to run NAMD
- Nikolai Skrynnikov (Thu Jul 01 2004 - 03:02:10 CDT)
big systems using namd on 700 cpus
- Brian Bennion (Mon Dec 29 2003 - 13:47:04 CST)
bigdcd
- Ioana Cozmuta (Wed Nov 05 2003 - 17:00:40 CST)
Binary conversions
- Jim Phillips (Wed Dec 03 2003 - 15:08:17 CST)
- Hua Wong (Tue Dec 02 2003 - 02:11:10 CST)
binary troubles
- Brian Bennion (Fri Dec 05 2003 - 13:40:35 CST)
- Michael Grabe (Fri Dec 05 2003 - 13:14:54 CST)
binding constant
- Jérôme Hénin (Mon Sep 20 2004 - 17:16:43 CDT)
- Oliver Hucke (Mon Sep 20 2004 - 15:23:20 CDT)
- bora erdemli (Mon Sep 20 2004 - 13:33:45 CDT)
binding energy
- bora erdemli (Tue Dec 14 2004 - 07:38:05 CST)
- Brian Bennion (Tue Mar 09 2004 - 10:42:19 CST)
- Gadi Oron (Tue Mar 09 2004 - 07:37:22 CST)
- Brian Bennion (Mon Mar 08 2004 - 13:23:38 CST)
- Ahmet Bakan (Mon Mar 08 2004 - 12:57:18 CST)
Binding energy analysis
- AHMET BAKAN (Sat Apr 24 2004 - 21:09:45 CDT)
binding free energy
- bora erdemli (Mon Dec 20 2004 - 08:39:06 CST)
Binding free energy of a protein complex
- Gadi Oron (Wed May 05 2004 - 09:31:52 CDT)
- Ahmet Bakan (Mon May 03 2004 - 06:02:29 CDT)
- Gadi Oron (Mon May 03 2004 - 02:06:05 CDT)
BOND CP2 - CT2 IN PARAMETER FILES
- Brian Bennion (Fri Oct 29 2004 - 11:32:18 CDT)
- bora erdemli (Thu Oct 28 2004 - 16:42:09 CDT)
Box Dimension
- Valodymyr Nechyporuk-Zloy (Tue Jun 29 2004 - 09:00:53 CDT)
Bringing Up To Temp
- Tim Cm (Sun Aug 15 2004 - 16:48:42 CDT)
Bug alert!!!
- bora erdemli (Fri Dec 24 2004 - 01:06:32 CST)
BUG ALERT: Bad global exclusion count!
- li (Mon Mar 03 2008 - 17:56:01 CST)
BUG ALERT: Hydrogen group error caught in rattle1
- li (Sun Oct 31 2004 - 05:44:31 CST)
BUG ALERT: Mother atom with hydrogenGroupSize of 0!
- Vani Krishna (Fri Dec 17 2004 - 11:39:30 CST)
BUG ALERT: Stray PME grid charges detected.
- li (Fri Apr 09 2004 - 22:04:45 CDT)
Bug in Pair force interaction calculation was fixed?
- Brian Bennion (Wed Oct 27 2004 - 10:19:49 CDT)
- Zhong Wenyu (Wed Oct 27 2004 - 09:26:26 CDT)
- Brian Bennion (Tue Oct 26 2004 - 12:20:36 CDT)
- Zhong Wenyu (Mon Oct 25 2004 - 22:11:12 CDT)
bug report and stray pme
- Brian Bennion (Tue Oct 19 2004 - 15:31:43 CDT)
- Cheri M Turman (Mon Oct 18 2004 - 16:23:42 CDT)
build charm on ia-64 linux
- Chris Samuel (Tue Jun 15 2004 - 18:23:17 CDT)
- Gengbin Zheng (Fri Jun 11 2004 - 21:54:20 CDT)
- Sichun Yang (Fri Jun 11 2004 - 21:44:12 CDT)
- Gengbin Zheng (Fri Jun 11 2004 - 20:57:01 CDT)
- Sichun Yang (Fri Jun 11 2004 - 19:41:26 CDT)
- Sichun Yang (Fri Jun 11 2004 - 18:40:29 CDT)
build NAMD
- bioinfo Gu (Mon Sep 08 2003 - 09:54:12 CDT)
building charm++ on macosX
- yu275197_at_yorku.ca (Sat Feb 07 2004 - 16:51:15 CST)
Building NAMD with Portland's C++ Comipler
- Suxing Hu (Thu Dec 09 2004 - 21:08:54 CST)
- Gengbin Zheng (Thu Dec 09 2004 - 12:47:54 CST)
- Suxing Hu (Thu Dec 09 2004 - 12:29:57 CST)
Bun in charmd?
- Gengbin Zheng (Sun Dec 21 2003 - 14:11:56 CST)
- Gadi Oron (Sun Dec 21 2003 - 08:53:49 CST)
calculate energy with water excluded
- li (Mon May 17 2004 - 01:04:39 CDT)
Calculate Potential Energy
- Shirley Hui (Sat May 15 2004 - 17:20:03 CDT)
calculate the binding energy or binding free energy?
- Vani Krishna (Thu Sep 02 2004 - 21:13:58 CDT)
- Blake Charlebois (Thu Sep 02 2004 - 15:31:42 CDT)
- LEWYN LI (Thu Sep 02 2004 - 14:27:03 CDT)
- ying xiong (Thu Sep 02 2004 - 03:49:40 CDT)
Calculating Free Energy Change
- Jérôme Hénin (Fri Apr 23 2004 - 16:07:52 CDT)
- Shirley Hui (Fri Apr 23 2004 - 15:30:01 CDT)
- Jérôme Hénin (Fri Apr 23 2004 - 15:00:25 CDT)
- Shirley Hui (Fri Apr 23 2004 - 13:44:17 CDT)
- Brian Bennion (Fri Apr 23 2004 - 11:08:12 CDT)
- Shirley Hui (Thu Apr 22 2004 - 13:02:07 CDT)
Calculating parameters.
- Jan Saam (Sat May 15 2004 - 10:32:36 CDT)
- Ahmet Bakan (Fri May 14 2004 - 16:59:15 CDT)
- ivan.vinogradov_at_utoronto.ca (Fri May 14 2004 - 13:29:50 CDT)
Calculation of velocities
- Eric Cyr (Fri Sep 03 2004 - 14:27:38 CDT)
- Blake Charlebois (Thu Sep 02 2004 - 08:21:34 CDT)
- Eric Cyr (Tue Aug 31 2004 - 15:44:47 CDT)
can i restrain the center of molecule in aqueous solution?
- li (Tue Apr 20 2004 - 03:43:12 CDT)
Can we fix the position of two atoms while minimization?
- Brian Bennion (Wed Sep 29 2004 - 18:00:43 CDT)
- Shahid Qamar (Wed Sep 29 2004 - 15:18:31 CDT)
capping by psfgen
- Brian Bennion (Mon Apr 05 2004 - 11:59:38 CDT)
- tsaih_at_ncifcrf.gov (Sun Apr 04 2004 - 13:36:58 CDT)
CCL:where to find the force field parameters for F and P atom?
- Joey Harriman (Fri Dec 12 2003 - 09:22:15 CST)
Cell Basis Vector.
- Pijush Ghosh (Wed Sep 08 2004 - 23:20:22 CDT)
- Edward Patrick Obrien (Tue Sep 07 2004 - 18:45:13 CDT)
- Pijush Ghosh (Tue Sep 07 2004 - 18:28:46 CDT)
Cell Basis Vectors
- Kamp, Marc vander (Mon Jul 05 2004 - 09:46:24 CDT)
- Raymond C. Fort Jr. (Mon Jul 05 2004 - 07:57:53 CDT)
cellBasisVector x,y,z values
- Brian Bennion (Thu Jul 08 2004 - 10:35:11 CDT)
- p.w.fowler_at_qmul.ac.uk (Thu Jul 08 2004 - 10:30:31 CDT)
- Kamp, Marc vander (Thu Jul 08 2004 - 10:18:42 CDT)
- Edward Patrick Obrien (Thu Jul 08 2004 - 09:36:43 CDT)
- Shirley Hui (Thu Jul 08 2004 - 08:46:16 CDT)
cff91 force field in namd
- Rowan Hargreaves (Mon Aug 23 2004 - 06:35:38 CDT)
cff91 force field in namd + A Question
- Rowan Hargreaves (Wed Aug 25 2004 - 12:06:18 CDT)
- Ahmet Bakan (Wed Aug 25 2004 - 10:53:59 CDT)
Changing SMD parameters
- Gadi Oron (Mon Feb 09 2004 - 07:32:11 CST)
charamrun / Rocks distribution problem
- Mounir Tarek (Mon Oct 25 2004 - 10:20:28 CDT)
charm++ mpi-linux compilation errors
- g srinivasa murthy (Thu May 20 2004 - 09:57:55 CDT)
- ghg_at_xalt.am (Wed May 19 2004 - 11:38:28 CDT)
charm++ MPICH and Myrinet
- Mauricio Carrillo Tripp (Mon Jul 26 2004 - 17:34:53 CDT)
Charm++ nodelist commands
- Gadi Oron (Thu Jan 08 2004 - 02:40:06 CST)
- Gengbin Zheng (Sun Jan 04 2004 - 23:18:42 CST)
- Gengbin Zheng (Sun Jan 04 2004 - 16:23:27 CST)
- Gengbin Zheng (Fri Jan 02 2004 - 12:09:51 CST)
- Gengbin Zheng (Wed Dec 31 2003 - 11:59:00 CST)
- Gadi Oron (Wed Dec 31 2003 - 03:31:17 CST)
- Gengbin Zheng (Tue Dec 30 2003 - 18:05:36 CST)
- Gengbin Zheng (Tue Dec 30 2003 - 13:14:52 CST)
- Gadi Oron (Tue Dec 30 2003 - 08:10:29 CST)
- Gengbin Zheng (Tue Dec 23 2003 - 17:22:29 CST)
- Gadi Oron (Mon Dec 22 2003 - 11:30:55 CST)
- Alexandre Vakhrouchev (Thu Dec 18 2003 - 11:36:11 CST)
- Gadi Oron (Mon Dec 22 2003 - 05:10:39 CST)
- Alexandre Vakhrouchev (Thu Dec 18 2003 - 06:33:16 CST)
- Gadi Oron (Sun Dec 21 2003 - 02:38:11 CST)
- Gengbin Zheng (Thu Dec 18 2003 - 13:04:28 CST)
- Gadi Oron (Thu Dec 18 2003 - 05:48:02 CST)
Charm++ Problem
- Brian Bennion (Thu Feb 26 2004 - 12:09:18 CST)
- Ben Brooks (Thu Feb 26 2004 - 11:32:28 CST)
charm++ with gm
- Alexandre Chauvin (Mon Aug 30 2004 - 09:41:49 CDT)
Charm++ workshop webcast Oct 20-22
- Jim Phillips (Fri Oct 17 2003 - 17:41:56 CDT)
CHARMM
- Eunice Ramirez Melendez (Mon Sep 06 2004 - 21:30:50 CDT)
charmm and dihedral multiplicity
- Vani Krishna (Fri Dec 17 2004 - 18:46:04 CST)
- Brian Bennion (Fri Dec 17 2004 - 10:55:34 CST)
- mdcooper (Thu Dec 16 2004 - 13:19:02 CST)
charmm param. for ADP
- Brian Bennion (Mon Oct 27 2003 - 15:14:57 CST)
- himanshu chandola (Tue Oct 28 2003 - 01:27:28 CST)
- Cosmin ROMAN (Mon Oct 27 2003 - 11:14:08 CST)
- Brian Bennion (Mon Oct 27 2003 - 10:20:34 CST)
- himanshu chandola (Mon Oct 27 2003 - 18:45:58 CST)
charmm restart file
- Mauricio Carrillo Tripp (Wed Jun 09 2004 - 12:57:47 CDT)
charmm restart file to NAMD
- Giovanni Settanni (Mon Nov 17 2003 - 05:27:03 CST)
charmm->gromacs->charmm force field conversion
- Enrico Piccinini (Wed Dec 01 2004 - 09:36:06 CST)
charmm27
- Wei Fu (Tue Jan 13 2004 - 19:27:02 CST)
- Amit Paliwal (Tue Jan 13 2004 - 12:31:50 CST)
- Brian Bennion (Tue Jan 13 2004 - 17:24:49 CST)
- Wei Fu (Tue Jan 13 2004 - 17:15:49 CST)
Charmm27 Xplor format
- Peter Jones (Tue Nov 30 2004 - 03:56:22 CST)
charmrun vs. miprun and nature of parallelism
- Gengbin Zheng (Fri Mar 19 2004 - 02:10:26 CST)
- Stern, Julie (Thu Mar 18 2004 - 11:39:39 CST)
Chloroform Solvent Box
- alessandro.pedretti_at_unimi.it (Tue Nov 23 2004 - 14:19:11 CST)
- Harindar Keer (Tue Nov 23 2004 - 11:17:45 CST)
cluseter node freezes while running namd 2.5/2.5b1
- EPF (Esben Peter Friis) (Sun Oct 19 2003 - 14:00:00 CDT)
- Richard Brown (Sat Oct 18 2003 - 22:48:30 CDT)
clustering
- yu275197_at_yorku.ca (Fri Mar 12 2004 - 10:57:04 CST)
- Leandro Martinez (Fri Mar 12 2004 - 07:15:35 CST)
clustering - fault tolerant NAMD
- Gengbin Zheng (Fri Mar 12 2004 - 13:18:01 CST)
clustering macs
- yu275197_at_yorku.ca (Tue Feb 10 2004 - 16:04:58 CST)
clustermatic 4 and 5 Namd/charm
- Gengbin Zheng (Fri Dec 31 2004 - 12:10:17 CST)
- Rene Salmon (Fri Dec 31 2004 - 10:08:21 CST)
- Gengbin Zheng (Thu Dec 30 2004 - 18:52:47 CST)
- Rene Salmon (Thu Dec 30 2004 - 17:49:47 CST)
clustermatic 4 binaries?
- Jim Phillips (Tue Dec 16 2003 - 22:22:08 CST)
- Mike Grommet (Tue Dec 16 2003 - 01:05:59 CST)
Clustermatic 4.0
- Gengbin Zheng (Fri Mar 12 2004 - 21:36:16 CST)
- Jerry Ebalunode (Mon Mar 08 2004 - 14:16:20 CST)
Clustermatic 4: Charmrun> error 1 attaching to node:
- Roy Campbell (Fri Sep 10 2004 - 12:24:05 CDT)
Clustermatic PCI IDs
- Peter Jones (Thu Nov 11 2004 - 22:54:37 CST)
Clustermatic with SCSI
- Leandro Martinez (Thu Aug 19 2004 - 07:12:57 CDT)
- Chris Samuel (Wed Aug 18 2004 - 20:17:05 CDT)
- Leandro Martinez (Wed Aug 18 2004 - 18:15:11 CDT)
CMAP in CHARMM force field
- Jorge Pikunic (Fri Oct 08 2004 - 12:27:47 CDT)
coarse grained force field
- Giovanni (Fri Apr 02 2004 - 15:29:06 CST)
coarse grained model
- Giovanni (Fri May 07 2004 - 05:02:57 CDT)
CoM motion not removed
- Jim Phillips (Mon Feb 23 2004 - 11:01:02 CST)
- Neema Salimi (Wed Feb 18 2004 - 13:00:22 CST)
COM position
- Brian Bennion (Tue Jul 06 2004 - 12:50:52 CDT)
- Mauricio Carrillo Tripp (Tue Jul 06 2004 - 12:43:40 CDT)
- Brian Bennion (Tue Jul 06 2004 - 12:11:28 CDT)
- Mauricio Carrillo Tripp (Tue Jul 06 2004 - 12:12:49 CDT)
- Mauricio Carrillo Tripp (Tue Jul 06 2004 - 10:45:53 CDT)
- Kamp, Marc vander (Tue Jul 06 2004 - 01:40:01 CDT)
- Mauricio Carrillo Tripp (Mon Jul 05 2004 - 14:47:51 CDT)
- Mauricio Carrillo Tripp (Fri Jul 02 2004 - 16:54:01 CDT)
COM velocity
- Amit Paliwal (Thu Apr 15 2004 - 04:50:29 CDT)
Common Problem!: Periodic cell has become too small for original patch grid!
- Meric Ayse Ovacik (Mon Jul 12 2004 - 03:25:04 CDT)
- Shirley Hui (Fri Jul 09 2004 - 15:24:43 CDT)
communication with NAMD?
- Brian Bennion (Tue Oct 26 2004 - 18:10:07 CDT)
- Hui-Hsu Tsai (Tue Oct 26 2004 - 15:37:37 CDT)
Compilation on an Opteron Server SuSE Linux Enterprise System Version 8
- Marek Dynowski (Thu Oct 21 2004 - 03:03:54 CDT)
- Chris Samuel (Wed Oct 20 2004 - 18:05:49 CDT)
- Gengbin Zheng (Wed Oct 20 2004 - 10:24:09 CDT)
- Marek Dynowski (Wed Oct 20 2004 - 10:20:16 CDT)
- Leandro Martinez (Wed Oct 20 2004 - 09:30:57 CDT)
- Leandro Martinez (Wed Oct 20 2004 - 08:27:50 CDT)
- Marek Dynowski (Wed Oct 20 2004 - 07:26:14 CDT)
Compilation on Opteron
- Alexandre Chauvin (Fri Aug 27 2004 - 03:05:43 CDT)
- Gengbin Zheng (Thu Aug 26 2004 - 00:25:44 CDT)
- Chris Samuel (Thu Aug 26 2004 - 00:04:07 CDT)
- Leandro Martinez (Wed Aug 25 2004 - 13:35:13 CDT)
- Alexandre Chauvin (Wed Aug 25 2004 - 12:22:43 CDT)
compiled namd on clustermatic fails !
- Gengbin Zheng (Tue Aug 03 2004 - 11:31:31 CDT)
- Amit Paliwal (Tue Aug 03 2004 - 06:38:31 CDT)
- Gengbin Zheng (Tue Aug 03 2004 - 10:23:19 CDT)
- AMIT PALIWAL (Thu Jul 29 2004 - 19:24:52 CDT)
- Amit Paliwal (Thu Jul 29 2004 - 13:33:10 CDT)
compiler flags.
- gengbin (Wed Jul 14 2004 - 23:58:54 CDT)
- Brian Bennion (Wed Jul 14 2004 - 23:41:22 CDT)
Compiling charm on a opteron cluster
- Gianluca Interlandi (Fri Dec 03 2004 - 15:11:18 CST)
- Gianluca Interlandi (Fri Dec 03 2004 - 15:03:11 CST)
compiling linux scyld mpi 64bit
- Eric Franz (Tue Jun 29 2004 - 10:40:31 CDT)
compiling NAMD
- gzheng (Fri Jul 09 2004 - 20:52:04 CDT)
- Brian Bennion (Fri Jul 09 2004 - 12:27:28 CDT)
- Brian Bennion (Fri Jul 09 2004 - 11:56:03 CDT)
- Gengbin Zheng (Wed Apr 07 2004 - 20:10:12 CDT)
- Ken Sale (Wed Apr 07 2004 - 19:23:07 CDT)
Compiling NAMD from SRC: Tungsten@NCSA
- Vani Krishna (Fri Sep 10 2004 - 19:54:55 CDT)
compiling namd on amd opteron arch : TCL problems (fwd)
- Jerry Ebalunode (Fri Apr 23 2004 - 17:07:40 CDT)
Compiling NAMD on amd64
- Wenyu Zhong (Thu Apr 15 2004 - 06:35:08 CDT)
- Wenyu Zhong (Thu Apr 15 2004 - 01:42:17 CDT)
Compiling NAMD on IA64 cluter
- li (Thu Nov 04 2004 - 05:48:16 CST)
- Gengbin Zheng (Wed Nov 03 2004 - 11:24:27 CST)
- Brian Bennion (Wed Nov 03 2004 - 10:39:23 CST)
- Brian Bennion (Wed Oct 27 2004 - 10:19:16 CDT)
- li (Tue Oct 26 2004 - 19:28:34 CDT)
Compiling NAMD on Linux cluster
- Gengbin Zheng (Fri May 28 2004 - 15:48:41 CDT)
- Xin Chen (Fri May 28 2004 - 15:14:12 CDT)
compiling NAMD on OSC P4 cluster
- Amit Paliwal (Fri Sep 03 2004 - 12:11:51 CDT)
Compiling NAMD on Tungsten.ncsa
- Jim Phillips (Fri Feb 13 2004 - 17:35:20 CST)
- Satyavani Vemparala (Wed Feb 11 2004 - 20:18:12 CST)
Compiling on G5 using xlC
- klsale (Thu Feb 26 2004 - 15:38:47 CST)
- Gengbin Zheng (Thu Feb 26 2004 - 15:40:59 CST)
concatenating two DCD files
- J. Rui Rodrigues (Tue Feb 10 2004 - 18:01:10 CST)
- Satyavani Vemparala (Tue Feb 10 2004 - 17:28:27 CST)
configuration files
- Michael Grabe (Wed Nov 19 2003 - 16:38:24 CST)
constant angle NPT simulation
- Joseph E. Curtis, Ph. D. (Thu Nov 04 2004 - 12:16:21 CST)
Constant pressure contril
- Sichun Yang (Sun Feb 29 2004 - 22:48:15 CST)
- Jérôme Hénin (Sun Feb 29 2004 - 02:41:07 CST)
- Sichun Yang (Sat Feb 28 2004 - 20:39:58 CST)
- Juan Alfredo Freites (Sat Feb 28 2004 - 20:18:51 CST)
- Sichun Yang (Sat Feb 28 2004 - 18:32:31 CST)
- Jérôme Hénin (Sat Feb 28 2004 - 17:50:46 CST)
- Sichun Yang (Sat Feb 28 2004 - 17:05:03 CST)
constant velocity smd with distance restraints
- Gilbert G.Feng (Fri Dec 03 2004 - 14:22:50 CST)
constraining movement of atoms
- himanshu chandola (Thu Oct 16 2003 - 02:49:01 CDT)
Constraint failure in RATTLE again
- li (Sat Nov 06 2004 - 20:13:26 CST)
Constraint failure in RATTLE algorithm
- Zhong Wenyu (Sun Sep 19 2004 - 02:14:27 CDT)
- bora erdemli (Wed Jul 28 2004 - 15:05:47 CDT)
constraintScaling parameter
- Peter Jones (Sun Mar 14 2004 - 10:33:40 CST)
construct a protein surrounded by membrane
- mashaojie (Fri Mar 19 2004 - 08:41:20 CST)
- mashaojie (Fri Mar 19 2004 - 01:52:37 CST)
contraint failure in RATTLE algorithm
- Jim Phillips (Fri Nov 07 2003 - 10:33:01 CST)
- ELENA JEAN LEVIN (Thu Nov 06 2003 - 16:01:07 CST)
- Brian Bennion (Thu Nov 06 2003 - 14:10:49 CST)
- ELENA JEAN LEVIN (Thu Nov 06 2003 - 13:45:19 CST)
convert DCD files to GROMACS .XTC format
- Vani Krishna (Sat Aug 28 2004 - 17:43:11 CDT)
Converting Gromacs OPLS parameters to Charmm format
- David Chalmers (Mon Mar 01 2004 - 17:41:57 CST)
Converting Gromacs parameters to Charmm format
- Ben Roberts (Mon Sep 27 2004 - 01:35:23 CDT)
Converting PSF TYPES: from XPLOr to CHARMM
- Mike McCallum (Tue Apr 13 2004 - 09:08:04 CDT)
- Eric Hajjar (Tue Apr 13 2004 - 07:15:58 CDT)
coorfile
- Shunzhou Wan (Wed Dec 10 2003 - 11:23:46 CST)
coorfile command fail
- Jim Phillips (Tue Sep 23 2003 - 11:20:13 CDT)
- Liu, Zhanwu (Mon Sep 22 2003 - 20:53:13 CDT)
counterion software
- mashaojie163 (Mon Oct 11 2004 - 01:46:24 CDT)
- Cetin Baloglu (Sun Oct 10 2004 - 23:51:56 CDT)
counterions
- David Chalmers (Tue Mar 30 2004 - 23:12:17 CST)
- himanshu chandola (Wed Mar 31 2004 - 03:13:51 CST)
- Brian Bennion (Tue Mar 30 2004 - 12:41:03 CST)
- himanshu chandola (Tue Mar 30 2004 - 02:53:19 CST)
covalent bonds across periodic boundaries
- Philip Blood (Sat Nov 27 2004 - 11:39:33 CST)
CP3-NH3 error
- Han Choe (Thu Mar 04 2004 - 16:48:46 CST)
- Tim Isgro (Thu Mar 04 2004 - 13:56:44 CST)
- Tim Isgro (Tue Mar 02 2004 - 17:31:08 CST)
- Han Choe (Mon Mar 01 2004 - 21:36:44 CST)
crash in FFT optimizing...
- Brian Bennion (Thu Feb 19 2004 - 15:44:28 CST)
creating Charmm psf from Xplor format
- EPF (Esben Peter Friis) (Wed Feb 04 2004 - 07:40:50 CST)
- Shunzhou Wan (Wed Feb 04 2004 - 06:32:42 CST)
Creating Parmtop files for NAMD
- Edward Patrick Obrien (Tue Apr 13 2004 - 19:42:25 CDT)
cylindrical boundary conditions
- Jim Phillips (Mon Oct 27 2003 - 13:40:51 CST)
- Ioana Cozmuta (Wed Oct 15 2003 - 16:48:08 CDT)
D-amino acids
- Aaron Oakley (Tue Oct 26 2004 - 03:05:28 CDT)
- Giovanni Bellesia (Mon Oct 25 2004 - 07:00:46 CDT)
dcd files
- Jim Phillips (Fri Nov 14 2003 - 14:36:29 CST)
- Juan Alfredo Freites (Tue Nov 11 2003 - 15:50:11 CST)
- himanshu chandola (Tue Nov 11 2003 - 23:52:13 CST)
- Brian Bennion (Tue Nov 11 2003 - 10:27:42 CST)
- himanshu chandola (Tue Nov 11 2003 - 09:44:21 CST)
dcd files generated with catdcd
- J. Rui Rodrigues (Fri Apr 30 2004 - 14:02:49 CDT)
- Giovanni (Fri Apr 30 2004 - 13:08:33 CDT)
- J. Rui Rodrigues (Fri Apr 30 2004 - 10:51:27 CDT)
- Giovanni (Fri Apr 30 2004 - 04:11:00 CDT)
dcd format
- himanshu chandola (Fri Jan 30 2004 - 14:10:21 CST)
- Brian Bennion (Thu Jan 29 2004 - 17:11:37 CST)
- himanshu chandola (Fri Jan 30 2004 - 04:25:28 CST)
Dealing with hyperthreading
- Gadi Oron (Sun Mar 07 2004 - 04:43:09 CST)
Density
- AHMET BAKAN (Tue Dec 16 2003 - 12:45:26 CST)
dielectric
- Michael Grabe (Wed Dec 17 2003 - 11:30:59 CST)
different dielectric constant during simulation
- Liu, Zhanwu (Wed Dec 17 2003 - 10:24:30 CST)
different result when I run the same *.conf file many times.
- yxiong_at_mail.ccnu.edu.cn (Sat Jan 03 2004 - 05:18:48 CST)
DIHEDral drift ?
- Nicholas M Glykos (Thu Jun 10 2004 - 13:15:09 CDT)
DIHEDral drift [2] ?
- Brian Bennion (Wed Jun 30 2004 - 17:16:39 CDT)
- Nicholas M Glykos (Wed Jun 30 2004 - 13:08:14 CDT)
- Brian Bennion (Wed Jun 30 2004 - 12:30:15 CDT)
- Nicholas M Glykos (Wed Jun 30 2004 - 09:26:43 CDT)
Dihedral restraint
- Jérôme Hénin (Sun Jan 11 2004 - 13:08:05 CST)
Dihedral restraint : question closed
- Jérôme Hénin (Mon Jan 12 2004 - 05:04:49 CST)
dimer minimisation and psfgen problem
- Brian Bennion (Thu Mar 18 2004 - 17:24:45 CST)
- Uday Chippada (Thu Mar 18 2004 - 14:44:35 CST)
- Brian Bennion (Wed Mar 17 2004 - 10:18:12 CST)
- Hua Wong (Wed Mar 17 2004 - 03:17:57 CST)
Direction of SMD force
- aida_at_mit.edu (Tue Feb 17 2004 - 09:06:16 CST)
Direction of the force in Pair interactions
- Kamp, Marc vander (Wed Aug 25 2004 - 01:29:18 CDT)
- Jim Phillips (Tue Aug 24 2004 - 11:06:52 CDT)
- Jérôme Hénin (Tue Aug 24 2004 - 03:46:33 CDT)
Discrepency in cell volume? Cell origin can move in NPT?
- Edward Patrick Obrien (Mon Apr 26 2004 - 09:11:34 CDT)
- Edward Patrick Obrien (Sun Apr 25 2004 - 12:56:36 CDT)
distance constraint
- Jim Phillips (Fri Feb 06 2004 - 14:34:50 CST)
- Hyonseok Hwang (Wed Feb 04 2004 - 17:56:20 CST)
distance constraints in NAMD
- tsaih_at_ncifcrf.gov (Fri Mar 19 2004 - 07:06:34 CST)
distance dependant dielectric constant
- Wagener, M. (Markus) (Fri Feb 27 2004 - 06:58:43 CST)
Distance-dependent dielectrics in NAMD
- Jim Phillips (Thu Nov 13 2003 - 15:52:31 CST)
- Sarah Harris (Mon Nov 10 2003 - 05:05:36 CST)
Does anybody have gromacs topology example, which works OK using NAMD??
- Armen Poghosyan (Tue Jun 01 2004 - 14:24:00 CDT)
DOWSER
- Peter Jones (Mon Dec 08 2003 - 02:26:35 CST)
DPPC
- Jérôme Hénin (Mon Aug 30 2004 - 11:48:39 CDT)
- Eunice Ramirez Melendez (Mon Aug 30 2004 - 02:28:55 CDT)
Dynamically resizing waterbox
- Edward Patrick Obrien (Wed Jul 14 2004 - 15:01:00 CDT)
- Nur Aida Abdul Rahim (Wed Jul 14 2004 - 14:22:26 CDT)
Edge Water in PBC
- Brian Bennion (Wed Nov 03 2004 - 10:32:58 CST)
- Cetin Baloglu (Wed Nov 03 2004 - 05:01:40 CST)
Effect of FullDirect electrostatics
- Ben Roberts (Mon May 31 2004 - 18:22:45 CDT)
eigenvector projections
- Peter Jones (Mon Nov 08 2004 - 23:41:36 CST)
electron density calculations of lipid bilayers
- Jérôme Hénin (Mon Feb 23 2004 - 01:47:11 CST)
- Satyavani Vemparala (Sun Feb 22 2004 - 17:45:58 CST)
Electrostatics energy calculation
- Ben Roberts (Wed May 26 2004 - 20:09:43 CDT)
Energy Determination
- mdcooper (Wed Sep 15 2004 - 17:48:11 CDT)
Energy minimization at NAMD
- Michael Grabe (Tue Jun 15 2004 - 16:55:01 CDT)
- Edward Patrick Obrien (Tue Jun 15 2004 - 16:07:06 CDT)
- Xin Chen (Tue Jun 15 2004 - 15:25:38 CDT)
Energy problem after restart
- Fangqiang Zhu (Tue Nov 25 2003 - 09:47:30 CST)
- Fangqiang Zhu (Mon Nov 24 2003 - 15:15:56 CST)
- Alessandro Pedretti (Mon Nov 24 2003 - 03:00:11 CST)
- Fangqiang Zhu (Thu Nov 20 2003 - 17:15:11 CST)
- Alessandro Pedretti (Thu Nov 20 2003 - 07:13:56 CST)
Energy units
- Brian Bennion (Tue Dec 30 2003 - 13:53:17 CST)
- Sundaramoorthy, Munirathinam (Tue Dec 30 2003 - 12:21:59 CST)
entropy calculations
- Ioana Cozmuta (Mon Feb 23 2004 - 17:41:54 CST)
equilibration of protein in water box
- Valodymyr Nechyporuk-Zloy (Tue Jun 29 2004 - 09:08:01 CDT)
error
- Amit Paliwal (Mon May 24 2004 - 04:29:43 CDT)
error codes in charmrun/namd?
- J. Rui Rodrigues (Wed Feb 25 2004 - 14:02:43 CST)
error in notes on compiling namd2.5b2 with plugins
- Jerry Ebalunode (Tue Sep 16 2003 - 13:06:20 CDT)
error in starting the minimization
- Jim Phillips (Fri Nov 14 2003 - 14:41:35 CST)
- Ruxandra Dima (Wed Nov 12 2003 - 18:20:53 CST)
- Brian Bennion (Wed Nov 12 2003 - 18:11:42 CST)
- Ruxandra Dima (Wed Nov 12 2003 - 17:06:44 CST)
Error in temperature calculation
- Raymond C. Fort Jr. (Fri Sep 24 2004 - 13:57:08 CDT)
Error opening XSC output file...Invalid argument
- Randy Crawford (Thu Aug 26 2004 - 13:48:38 CDT)
Error Running NAMD
- Jim Phillips (Wed Oct 08 2003 - 11:04:41 CDT)
- Raymond C. Fort Jr. (Wed Oct 08 2003 - 08:18:00 CDT)
Error Running ubq-get-energy.conf
- Jim Phillips (Wed Oct 22 2003 - 18:50:49 CDT)
- Raymond C. Fort Jr. (Thu Oct 16 2003 - 12:13:35 CDT)
Error when running NAMD_2.5 on mytinet
- Cesar Delgado (Sat Oct 04 2003 - 18:20:13 CDT)
error: Number of atoms in fixed atoms PDB doesn't match coordinate PDB
- Olya Kravchenko (Tue May 11 2004 - 17:43:22 CDT)
- Tim Isgro (Tue May 11 2004 - 00:01:55 CDT)
- Olya Kravchenko (Thu May 06 2004 - 19:03:49 CDT)
errors building charm on ia64
- Gianluca Interlandi (Thu Jun 17 2004 - 11:31:42 CDT)
- Allison Heath (Thu Jun 17 2004 - 11:18:29 CDT)
essential dynamics analysis
- Armen Nalian (Mon Nov 22 2004 - 15:58:10 CST)
estradiol
- lc_at_chem.au.dk (Tue Aug 31 2004 - 06:56:44 CDT)
Euro QSAR 2004
- Ahmet Bakan (Sun Sep 05 2004 - 15:42:27 CDT)
excluding water in dcd files
- Jim Phillips (Wed Nov 05 2003 - 13:36:37 CST)
- Brian Bennion (Tue Nov 04 2003 - 10:35:55 CST)
- himanshu chandola (Tue Nov 04 2003 - 11:45:28 CST)
- Jim Phillips (Mon Nov 03 2003 - 17:21:00 CST)
- himanshu chandola (Tue Nov 04 2003 - 02:00:18 CST)
- Jerry Ebalunode (Mon Nov 03 2003 - 06:42:28 CST)
- Brian Bennion (Mon Nov 03 2003 - 11:23:38 CST)
- himanshu chandola (Mon Nov 03 2003 - 02:31:41 CST)
Failed to set coordinate for atom errors!
- Shirley Hui (Mon Dec 20 2004 - 21:39:30 CST)
- Blake Charlebois (Mon Dec 20 2004 - 19:27:51 CST)
- Shirley Hui (Mon Dec 20 2004 - 16:32:10 CST)
fatal error
- vivek sharma (Wed Dec 15 2004 - 04:11:45 CST)
- Gengbin Zheng (Tue Dec 14 2004 - 12:14:28 CST)
- Brian Bennion (Tue Dec 14 2004 - 12:01:25 CST)
- vivek sharma (Tue Dec 14 2004 - 00:49:59 CST)
- Fangqiang Zhu (Thu Nov 27 2003 - 23:47:41 CST)
- Hua Wong (Thu Nov 27 2003 - 08:32:15 CST)
fatal error running namd
- Brian Bennion (Mon Nov 15 2004 - 10:52:34 CST)
- Enrico Piccinini (Mon Nov 15 2004 - 04:30:06 CST)
FATAL ERROR: Asymmetric water molecule ?
- bora erdemli (Wed Dec 22 2004 - 02:26:19 CST)
- Gaurav Sharma (Tue Dec 21 2004 - 14:58:11 CST)
FATAL ERROR: Patch needed for tuple is missing.
- Armen Poghosyan (Thu May 06 2004 - 07:21:57 CDT)
Fatal Socket error
- Gengbin Zheng (Thu Apr 08 2004 - 16:16:35 CDT)
- Juan Carlos Mobarec (Thu Apr 08 2004 - 11:05:30 CDT)
Fatal Socket error: code 93523-Error in accept
- Armen Nalian (Wed Aug 04 2004 - 15:05:17 CDT)
Feedback on "alchemify" tool
- Jérôme Hénin (Thu Apr 08 2004 - 10:52:31 CDT)
FEP and restraints
- Jérôme Hénin (Tue Mar 23 2004 - 14:42:12 CST)
- Michael Grabe (Tue Mar 23 2004 - 13:45:32 CST)
FEP calculations: defining hybrid residues
- Jérôme Hénin (Wed Mar 24 2004 - 11:55:54 CST)
- Satyavani Vemparala (Wed Mar 24 2004 - 10:04:53 CST)
Finished install
- beckloni_at_umdnj.edu (Tue Apr 20 2004 - 00:53:09 CDT)
firsttimestep
- Jim Phillips (Tue Feb 24 2004 - 15:22:27 CST)
- Ekta Khurana (Tue Feb 17 2004 - 18:50:30 CST)
FIRSTTIMESTEP in config file
- Gadi Oron (Mon Mar 15 2004 - 04:02:07 CST)
- Satyavani Vemparala (Wed Mar 10 2004 - 05:49:55 CST)
firsttimestep: simple question
- Brian Bennion (Fri Oct 29 2004 - 17:34:53 CDT)
- Sascha Tayefeh (Fri Oct 29 2004 - 16:16:56 CDT)
fix or Harmonic constraint ?
- li (Wed Apr 14 2004 - 02:05:19 CDT)
fixed atoms parameters
- Jérôme Hénin (Fri Nov 07 2003 - 16:17:48 CST)
- himanshu chandola (Fri Nov 07 2003 - 23:54:04 CST)
fixed particles
- Kamp, Marc vander (Sat Jul 17 2004 - 03:20:33 CDT)
- AMIT PALIWAL (Fri Jul 16 2004 - 18:22:23 CDT)
Fixing position of COM
- Mauricio Carrillo Tripp (Wed Jun 30 2004 - 10:42:10 CDT)
FK506 ligand topology file(1FKF)
- MERIC AYSE OVACIK (Thu Oct 28 2004 - 05:29:21 CDT)
flexible cell
- AMIT PALIWAL (Tue May 18 2004 - 17:08:41 CDT)
- Juan Alfredo Freites (Sat Jan 03 2004 - 21:44:05 CST)
- Juan Alfredo Freites (Mon Dec 22 2003 - 12:10:32 CST)
for help from all!
- Lv Shouqin (Sat Feb 14 2004 - 23:14:38 CST)
Force Calculation in NAMD
- Gadi Oron (Sun May 23 2004 - 02:37:27 CDT)
- Xin Chen (Fri May 21 2004 - 13:02:09 CDT)
forces during SMD
- zhilei chen (Sun Dec 07 2003 - 10:16:43 CST)
Free energy constraints and logfile
- David Chalmers (Mon Dec 01 2003 - 22:54:01 CST)
Fwd: missing atom prob
- surendra negi (Mon Nov 01 2004 - 17:58:33 CST)
Fwd: PSFgen error
- Brian Bennion (Tue Nov 02 2004 - 10:14:50 CST)
- surendra negi (Mon Nov 01 2004 - 17:58:12 CST)
Fwd: vmd-l: MOE discussion
- Mike McCallum (Wed Apr 28 2004 - 23:11:43 CDT)
G5 or P4 cluster
- Grischa R. Meyer (Tue Nov 11 2003 - 00:58:07 CST)
gcc and G5 Xserves
- Charles McCallum (Mon Nov 15 2004 - 23:07:17 CST)
- Michael Grabe (Mon Nov 15 2004 - 02:06:03 CST)
GdHCl parameters
- Brian Bennion (Thu Mar 18 2004 - 17:19:38 CST)
- Ruxandra Dima (Thu Mar 18 2004 - 16:18:16 CST)
General and specific atom types in NAMD?
- David Chalmers (Thu Mar 04 2004 - 18:21:42 CST)
Generate PSF structure
- Tim Isgro (Tue Mar 09 2004 - 10:24:01 CST)
- Peter Spijker (Mon Mar 08 2004 - 12:23:12 CST)
- Brian Bennion (Mon Mar 08 2004 - 12:17:52 CST)
- Peter Spijker (Mon Mar 08 2004 - 12:01:28 CST)
Generating novel structure
- Fangqiang Zhu (Tue Mar 02 2004 - 13:38:12 CST)
generating psf files (and more!)
- Luis Rosales (Tue Sep 14 2004 - 17:40:20 CDT)
- mdcooper (Tue Sep 14 2004 - 16:52:38 CDT)
Generating psf files for non-proteins
- Alessandro Pedretti (Fri Apr 09 2004 - 07:09:52 CDT)
- Mike McCallum (Thu Apr 08 2004 - 16:22:43 CDT)
- Scott, Greg (Thu Apr 08 2004 - 13:08:21 CDT)
generating PSF files using CHARMM for FEP calculations
- Satyavani Vemparala (Thu Mar 04 2004 - 11:56:07 CST)
generating psf for RNA using psfgen
- MinSoo Kim (Fri Jan 30 2004 - 01:53:40 CST)
Generating simulation with large conformational changes
- Shirley Hui (Sat Feb 21 2004 - 18:36:12 CST)
Generating topology file
- li (Tue Nov 16 2004 - 01:11:51 CST)
- li (Sun Nov 14 2004 - 02:45:43 CST)
- li (Thu Nov 11 2004 - 04:03:37 CST)
- ANDY NG (Thu Nov 11 2004 - 00:59:51 CST)
geometric mean
- Leandro Martinez (Thu Jan 29 2004 - 07:53:58 CST)
Getting forces: segmentation violation or illegal instruction
- Fangqiang Zhu (Mon Mar 22 2004 - 11:54:41 CST)
- Justyna Jaroniec (Mon Mar 22 2004 - 11:09:25 CST)
Gradient Tolerance
- Brian Bennion (Wed Oct 13 2004 - 14:43:04 CDT)
- mdcooper (Tue Oct 12 2004 - 18:52:43 CDT)
Gromacs force field paramets: Syntax error in ATOMS
- Sichun Yang (Wed Jun 23 2004 - 03:09:39 CDT)
GROMACS to CHARMM
- Alessandro Pedretti (Tue Nov 30 2004 - 01:47:01 CST)
- chandran karunakaran (Mon Nov 29 2004 - 11:14:48 CST)
gromacs/gromos96 force field
- Jorge Pikunic (Wed Jun 09 2004 - 11:11:30 CDT)
hanging at startup phase
- Gengbin Zheng (Fri May 21 2004 - 10:53:23 CDT)
- Allison Heath (Fri May 21 2004 - 10:29:49 CDT)
- Gengbin Zheng (Fri May 21 2004 - 00:59:55 CDT)
- allison (Wed May 19 2004 - 14:00:25 CDT)
Haptic Device
- Uday Chippada (Fri Apr 02 2004 - 13:55:42 CST)
hard sphere simulation
- Jim Phillips (Tue Sep 23 2003 - 10:52:14 CDT)
- AMIT PALIWAL (Mon Sep 22 2003 - 20:08:31 CDT)
- Jim Phillips (Mon Sep 22 2003 - 14:38:11 CDT)
- Amit Paliwal (Sat Sep 20 2003 - 11:01:18 CDT)
Harmonic constraint parameter k
- Tim Isgro (Thu Dec 11 2003 - 18:21:48 CST)
- zhilei chen (Thu Dec 11 2003 - 08:39:48 CST)
harmonic restraint
- Amit Paliwal (Tue Jun 15 2004 - 12:23:10 CDT)
Has NAMD been ported to Itanium2 + Linux?
- Gengbin Zheng (Tue Aug 10 2004 - 16:54:08 CDT)
- Shantenu Jha (Tue Aug 10 2004 - 16:25:28 CDT)
- Randy Crawford (Tue Aug 10 2004 - 10:06:44 CDT)
help needed on node list
- srinivasa murthy (Tue Sep 16 2003 - 23:36:51 CDT)
Help with NAMD + Clustermatic 4 please
- Mike Grommet (Sun Dec 14 2003 - 01:01:55 CST)
Help with: Constraint failure in RATTLE algorithm
- Jim Phillips (Fri Oct 03 2003 - 13:09:35 CDT)
- Cartailler, Jean-Philippe (Thu Oct 02 2003 - 11:17:58 CDT)
Help! There is no angle or dihedral definitions for patches in .psf!
- Brian Bennion (Thu Apr 29 2004 - 13:23:55 CDT)
- Edward Patrick Obrien (Thu Apr 29 2004 - 13:09:05 CDT)
- Edward Patrick Obrien (Thu Apr 29 2004 - 10:43:09 CDT)
Help! unstable simulation - ARG go nuts...
- Jim Phillips (Wed Dec 17 2003 - 09:23:02 CST)
- Gadi Oron (Wed Dec 17 2003 - 04:36:47 CST)
- Jim Phillips (Tue Dec 16 2003 - 22:10:31 CST)
- Gadi Oron (Tue Dec 16 2003 - 09:33:25 CST)
Help! unstable simulation.
- Alexandre Vakhrouchev (Fri Dec 12 2003 - 03:16:55 CST)
- Gadi Oron (Thu Dec 11 2003 - 01:51:14 CST)
Help, MD run errors
- Xiaobing Tian (Sun May 02 2004 - 21:06:58 CDT)
HEM residue in NAMD
- Blake Charlebois (Tue Nov 02 2004 - 04:03:00 CST)
- Peter Bazeley (Tue Nov 02 2004 - 02:23:50 CST)
Heme A topology?
- Olya Kravchenko (Thu Jan 22 2004 - 17:05:49 CST)
Hessian
- mdcooper (Mon Nov 01 2004 - 18:08:24 CST)
Heteroatom entries
- Mithun Mitra (Tue Apr 27 2004 - 10:17:00 CDT)
hexagonal unit cell
- Anna Modzelewska (Thu Jul 01 2004 - 03:49:56 CDT)
Hi
- Shirley Hui (Fri Apr 23 2004 - 16:02:54 CDT)
- Uday Chippada (Fri Apr 23 2004 - 15:20:56 CDT)
- himanshu chandola (Sat Apr 24 2004 - 02:09:57 CDT)
- Uday Chippada (Fri Apr 23 2004 - 12:57:23 CDT)
- Wang Yu (Mon Dec 29 2003 - 07:44:57 CST)
HIERARCHY OF INTERACTIONS"
- Vlad Cojocaru (Wed Oct 20 2004 - 11:10:43 CDT)
high (or low) pressure readings
- Charles Danko (Tue Dec 14 2004 - 13:31:21 CST)
- Brian Bennion (Tue Dec 14 2004 - 11:45:13 CST)
- nordgren_at_sas.upenn.edu (Mon Dec 13 2004 - 18:30:51 CST)
- carlos n. a. (Mon Dec 13 2004 - 13:36:10 CST)
- Brian Bennion (Mon Dec 13 2004 - 11:13:42 CST)
- Charles Danko (Mon Dec 13 2004 - 09:42:52 CST)
high temperature, 498K, unfolding simulations
- Michael Grabe (Thu Nov 13 2003 - 12:31:28 CST)
- Brian Bennion (Thu Nov 13 2003 - 12:23:13 CST)
- james tomomi macdonald (Thu Nov 13 2003 - 11:47:29 CST)
HIS modification
- yxiong_at_mail.ccnu.edu.cn (Wed Dec 17 2003 - 04:37:24 CST)
how can I know which type HIS belong to?(HSD,HSE,HSP)
- Jérôme Hénin (Sat Nov 29 2003 - 04:37:30 CST)
- Fangqiang Zhu (Sat Nov 29 2003 - 00:22:03 CST)
- yxiong_at_mail.ccnu.edu.cn (Fri Nov 28 2003 - 04:02:05 CST)
How can I move an atom by 10nm with a step of 0.1nm
- Brian Bennion (Tue Oct 05 2004 - 10:44:01 CDT)
- Shahid Qamar (Mon Oct 04 2004 - 17:22:36 CDT)
How do I Heat, then Switch to NPT in the same *.config?
- Jerry W. Jenkins (Fri Mar 26 2004 - 10:42:22 CST)
How do we combine chains in the end
- Jim Phillips (Mon Feb 02 2004 - 11:54:51 CST)
- Uday Chippada (Sat Jan 31 2004 - 11:37:42 CST)
How do we know the velocity?
- Leandro Martinez (Thu Jun 03 2004 - 11:47:05 CDT)
- Uday Chippada (Thu Jun 03 2004 - 10:17:10 CDT)
How do you specify which coordinates are to be fixed?
- Luis Rosales (Thu Oct 28 2004 - 18:32:28 CDT)
- Brian Bennion (Thu Oct 28 2004 - 18:08:26 CDT)
- Blake Charlebois (Thu Oct 28 2004 - 17:36:56 CDT)
- Charles Danko (Thu Oct 28 2004 - 16:44:21 CDT)
How I can get the hole program?
- mashaojie163 (Sat Sep 18 2004 - 11:08:05 CDT)
- mashaojie163 (Mon Sep 13 2004 - 19:04:36 CDT)
How I can run two simulations one after an other
- Michael Grabe (Tue Dec 14 2004 - 15:15:36 CST)
- Shahid Qamar (Tue Dec 14 2004 - 14:30:08 CST)
how many steps do we need do for energy minimization ?
- Edward Patrick Obrien (Tue May 11 2004 - 08:39:17 CDT)
- ying xiong (Tue May 11 2004 - 01:19:39 CDT)
how should I run NAMD on parallel platform?
- Jim Phillips (Thu Dec 18 2003 - 13:27:24 CST)
- yxiong_at_mail.ccnu.edu.cn (Thu Dec 18 2003 - 04:40:58 CST)
- Gengbin Zheng (Thu Dec 18 2003 - 02:40:16 CST)
- yxiong_at_mail.ccnu.edu.cn (Thu Dec 18 2003 - 01:33:14 CST)
how should I set those PMEGridSizeX,Y,Z?
- Tim Isgro (Thu Dec 11 2003 - 18:00:13 CST)
- yxiong_at_mail.ccnu.edu.cn (Wed Dec 10 2003 - 18:51:51 CST)
- Tim Isgro (Wed Dec 10 2003 - 14:18:37 CST)
- yxiong_at_mail.ccnu.edu.cn (Wed Dec 10 2003 - 00:13:55 CST)
how the charges of those residues of protein(for example LYS) are determined in CHARMM topology file
- yxiong_at_mail.ccnu.edu.cn (Mon Dec 01 2003 - 04:27:52 CST)
how to add counterions ?
- Fangqiang Zhu (Tue Dec 02 2003 - 18:19:19 CST)
- Alessandro Pedretti (Tue Dec 02 2003 - 06:18:58 CST)
- yxiong_at_mail.ccnu.edu.cn (Tue Dec 02 2003 - 01:54:09 CST)
- Fangqiang Zhu (Tue Dec 02 2003 - 00:24:16 CST)
- yxiong_at_mail.ccnu.edu.cn (Sun Nov 30 2003 - 04:59:36 CST)
How to calculate specific heat capacity in NAMD?
- Brian Bennion (Wed Jul 07 2004 - 11:28:40 CDT)
- Edward Patrick Obrien (Wed Jul 07 2004 - 10:39:38 CDT)
- Xin Chen (Wed Jul 07 2004 - 10:02:02 CDT)
How to chech the harmonic constraint work normally~
- Îº¿ (Thu Dec 16 2004 - 03:21:17 CST)
How to create a substrate parameter file ?
- Davit Hakobyan (Thu May 06 2004 - 15:09:00 CDT)
How to decide the protonation of some residues??
- Brian Bennion (Wed Nov 03 2004 - 10:35:07 CST)
- mashaojie163 (Wed Nov 03 2004 - 07:05:19 CST)
how to disable NTER and CTER patches?
- Olya Kravchenko (Wed Apr 07 2004 - 16:12:19 CDT)
- Brian Bennion (Wed Apr 07 2004 - 15:56:44 CDT)
- Olya Kravchenko (Wed Apr 07 2004 - 15:18:54 CDT)
How to do FEP simulations to calculate the absolute free energy of solvation?
- Jérôme Hénin (Sat Nov 15 2003 - 08:30:50 CST)
- PQCHEN (Sat Nov 15 2003 - 05:43:48 CST)
- Jérôme Hénin (Sat Nov 15 2003 - 04:27:35 CST)
- PQCHEN (Fri Nov 14 2003 - 22:24:01 CST)
How to do pH simulation on NAMD?
- Jérôme Hénin (Fri Jul 16 2004 - 05:00:03 CDT)
- Xin Chen (Thu Jul 15 2004 - 15:28:50 CDT)
how to fix some atoms?
- yingxiong (Mon Mar 08 2004 - 03:55:35 CST)
how to fix the atoms of backbone ?
- ying xiong (Fri Jul 30 2004 - 19:48:23 CDT)
how to generate your own pdb file
- Josef Scheiber (Sat May 15 2004 - 04:28:47 CDT)
- Ahmet Bakan (Fri May 14 2004 - 21:55:28 CDT)
- Tim Isgro (Fri May 14 2004 - 17:26:00 CDT)
- myang (Thu May 13 2004 - 00:12:45 CDT)
how to get "the rms force and maximum force" of energy minimization ?
- yxiong_at_mail.ccnu.edu.cn (Mon Jan 05 2004 - 23:45:18 CST)
how to get Charge of new residue?
- yxiong_at_mail.ccnu.edu.cn (Sun Nov 30 2003 - 03:51:26 CST)
- Fangqiang Zhu (Sat Nov 29 2003 - 01:03:31 CST)
- yxiong_at_mail.ccnu.edu.cn (Fri Nov 28 2003 - 23:29:34 CST)
how to get hydrogen-bond energy?
- Lv Shouqin (Tue Aug 17 2004 - 21:34:17 CDT)
how to get the plot of selected bond over time?
- Alessandro Pedretti (Fri Dec 05 2003 - 07:19:45 CST)
- yxiong_at_mail.ccnu.edu.cn (Thu Dec 04 2003 - 21:38:16 CST)
How to make a negatively charged surface
- Charles Danko (Mon Nov 08 2004 - 15:26:53 CST)
- Shahid Qamar (Mon Nov 08 2004 - 14:25:30 CST)
How to make a surface
- Shahid Qamar (Wed Nov 17 2004 - 14:08:06 CST)
How to move COM during minimization?
- Shahid Qamar (Wed Dec 15 2004 - 12:03:12 CST)
how to read amino acid such as 27, 27A,27B,27C in pdb file?
- yxiong_at_mail.ccnu.edu.cn (Mon Jul 19 2004 - 20:45:45 CDT)
how to remove all hydrogen atoms from PDB file?
- Olya Kravchenko (Wed Apr 21 2004 - 16:34:41 CDT)
- J. Rui Rodrigues (Tue Apr 20 2004 - 09:04:46 CDT)
- J. Rui Rodrigues (Tue Apr 20 2004 - 09:01:20 CDT)
- Olya Kravchenko (Mon Apr 19 2004 - 17:41:22 CDT)
how to set harmonic constraints to alpha carbon
- Jim Phillips (Fri Nov 07 2003 - 10:37:51 CST)
- Brian Bennion (Thu Nov 06 2003 - 16:34:53 CST)
- Zhilei Chen (Thu Nov 06 2003 - 15:07:05 CST)
How to treat the terminal residue psfgen in NAMD~
- Îº¿ (Mon Nov 29 2004 - 20:11:37 CST)
How to use GROMACS force field in NAMD?
- Armen Poghosyan (Mon May 31 2004 - 02:34:06 CDT)
how to use restrain command in configuration file in NAMD.
- debashis.sikdar_at_ndsu.edu (Fri Dec 17 2004 - 23:10:34 CST)
How to use restrin command in NAMD configuration file
- Charles Danko (Mon Dec 20 2004 - 10:40:30 CST)
- debashis.sikdar_at_ndsu.edu (Mon Dec 20 2004 - 09:35:28 CST)
Hybond calulator and display
- John Stone (Fri Jan 16 2004 - 13:07:09 CST)
- Jerry Ebalunode (Fri Jan 16 2004 - 12:24:30 CST)
hydrogen bonds during MD
- yu275197_at_yorku.ca (Sat Mar 06 2004 - 11:03:49 CST)
hydrogen bonds in NAMD
- Tim Isgro (Fri Mar 19 2004 - 11:25:47 CST)
- Ioana Cozmuta (Fri Mar 19 2004 - 01:02:25 CST)
Hydrogen cut off distance
- Brian Bennion (Tue Oct 26 2004 - 12:38:20 CDT)
- Uday Chippada (Mon Oct 25 2004 - 16:16:46 CDT)
hydrogengroupsize of 0!
- Brian Bennion (Thu Dec 18 2003 - 13:03:01 CST)
- Jan Saam (Thu Nov 27 2003 - 02:43:26 CST)
- Brian Bennion (Wed Nov 26 2003 - 17:57:28 CST)
Hydroxyprolin force field.
- Jim Phillips (Mon Jan 26 2004 - 17:44:10 CST)
- Brian Bennion (Fri Jan 23 2004 - 11:15:30 CST)
- ivan.vinogradov_at_utoronto.ca (Fri Jan 23 2004 - 11:01:36 CST)
HYP files
- Ivan Vinogradov (Tue Aug 03 2004 - 12:55:52 CDT)
HYP parameters
- Ivan Vinogradov (Thu Jul 29 2004 - 07:44:27 CDT)
- Valodymyr Nechyporuk-Zloy (Thu Jul 29 2004 - 03:59:44 CDT)
HYP residue and unknown residue type NH2
- Valodymyr Nechyporuk-Zloy (Wed Aug 04 2004 - 07:06:47 CDT)
I have known how to do a constrained MD before a normal MD
- yxiong_at_mail.ccnu.edu.cn (Sat Dec 06 2003 - 02:58:36 CST)
I have known how to find and click the atoms accurately and easily.
- nathalie reuter (Fri Dec 05 2003 - 02:16:29 CST)
- yxiong_at_mail.ccnu.edu.cn (Fri Dec 05 2003 - 01:30:48 CST)
IA64 and MPICH and mpiexec runtime shmem errors
- Randy Crawford (Thu Aug 05 2004 - 14:38:06 CDT)
IBM SP build
- Jim Phillips (Thu Nov 13 2003 - 14:57:20 CST)
- David Skinner (Sun Nov 09 2003 - 00:21:31 CST)
icc compilation problem
- Chris Samuel (Sun Jul 04 2004 - 20:41:14 CDT)
- Brian Bennion (Fri Jul 02 2004 - 11:05:29 CDT)
- Sean Michael Whipkey (Fri Jul 02 2004 - 09:27:55 CDT)
- Chris Samuel (Thu Jul 01 2004 - 18:11:57 CDT)
- Sean Michael Whipkey (Thu Jul 01 2004 - 16:19:55 CDT)
Illegal instruction signal at startup. (with net-rs6k smp)
- Hansang Bae (Tue Apr 13 2004 - 22:00:48 CDT)
- Gengbin Zheng (Fri Apr 09 2004 - 18:36:19 CDT)
- Hansang Bae (Fri Apr 09 2004 - 16:20:20 CDT)
- Brian Bennion (Fri Apr 09 2004 - 15:14:55 CDT)
- Hansang Bae (Fri Apr 09 2004 - 14:21:52 CDT)
- Gengbin Zheng (Thu Apr 08 2004 - 17:36:49 CDT)
- Hansang Bae (Thu Apr 08 2004 - 16:26:37 CDT)
- Gengbin Zheng (Thu Apr 08 2004 - 16:31:27 CDT)
- Gengbin Zheng (Thu Apr 08 2004 - 16:21:29 CDT)
- Hansang Bae (Tue Apr 06 2004 - 22:08:02 CDT)
IMD forces and corresponding energies ..
- Jim Phillips (Wed Oct 22 2003 - 18:16:05 CDT)
- Marc Baaden (Wed Oct 22 2003 - 16:36:35 CDT)
IMD on MPI versions of NAMD
- Jim Phillips (Wed Dec 03 2003 - 15:38:04 CST)
- Brian Bennion (Mon Dec 01 2003 - 16:58:16 CST)
- Cesar Delgado (Mon Dec 01 2003 - 16:44:05 CST)
- Brian Bennion (Mon Dec 01 2003 - 12:19:28 CST)
implementing angle dependent non-bonded interaction?
- Brian Bennion (Mon May 10 2004 - 14:51:26 CDT)
- Julius Su (Mon May 10 2004 - 13:09:14 CDT)
implicit solvent model
- Frances Leung (Mon Jan 19 2004 - 20:10:59 CST)
implicit solvent models
- Jim Phillips (Wed Sep 24 2003 - 14:09:14 CDT)
- james tomomi macdonald (Wed Sep 24 2003 - 12:53:28 CDT)
Implicit water dielectric constant.
- Blake Charlebois (Tue Nov 16 2004 - 15:06:50 CST)
- Ivan Vinogradov (Wed Nov 10 2004 - 10:16:57 CST)
improving parallel on mac cluster
- David E. Konerding (Tue Feb 10 2004 - 18:21:32 CST)
- yu275197_at_yorku.ca (Tue Feb 10 2004 - 18:23:39 CST)
- yu275197_at_yorku.ca (Tue Feb 10 2004 - 16:47:34 CST)
- Brian Bennion (Mon Feb 09 2004 - 12:05:09 CST)
- yu275197_at_yorku.ca (Mon Feb 09 2004 - 11:44:31 CST)
incompatibility between VMD & NAMD for reading Amber crd files
- Kamp, Marc vander (Mon Jun 21 2004 - 07:33:11 CDT)
Infiniband and PME gridsize
- Gengbin Zheng (Tue Dec 14 2004 - 13:05:45 CST)
- Gianluca Interlandi (Tue Dec 14 2004 - 12:54:55 CST)
- Gengbin Zheng (Tue Dec 14 2004 - 12:16:55 CST)
- Brian Bennion (Tue Dec 14 2004 - 12:06:36 CST)
- Gianluca Interlandi (Tue Dec 14 2004 - 06:06:03 CST)
Info about forces on atoms
- g srinivasa murthy (Fri May 28 2004 - 03:27:23 CDT)
- Vani Krishna (Thu May 27 2004 - 11:58:32 CDT)
initial temp of simulation
- Tim Isgro (Fri Mar 26 2004 - 10:46:49 CST)
- yxiong_at_mail.ccnu.edu.cn (Thu Mar 25 2004 - 19:47:01 CST)
- Tim Isgro (Thu Mar 25 2004 - 11:11:07 CST)
- mashaojie (Thu Mar 25 2004 - 07:39:17 CST)
- Streiff, John H. (Fri Mar 19 2004 - 11:35:10 CST)
initial translation of the system
- Satyavani Vemparala (Fri Apr 09 2004 - 14:17:09 CDT)
Installing NAMD
- Brian Bennion (Wed Apr 07 2004 - 16:56:14 CDT)
- beckloni_at_umdnj.edu (Wed Apr 07 2004 - 15:56:21 CDT)
installing on beowulf cluster
- Cheri M Turman (Sun May 09 2004 - 19:58:25 CDT)
- Brian Bennion (Thu May 06 2004 - 14:41:08 CDT)
- Jerry Ebalunode (Thu May 06 2004 - 14:17:01 CDT)
- Cheri M Turman (Thu May 06 2004 - 13:38:16 CDT)
INTEL 8.0 optimization flags
- Brian Bennion (Tue Jul 13 2004 - 14:22:05 CDT)
Intel C/C++ compiler Version 8 for compiling NAMD on IA64
- Gengbin Zheng (Fri Jan 02 2004 - 12:16:32 CST)
- Jerry Ebalunode (Fri Jan 02 2004 - 12:04:41 CST)
- Gengbin Zheng (Wed Dec 31 2003 - 13:25:53 CST)
- Jerry Ebalunode (Wed Dec 31 2003 - 12:57:53 CST)
interaction energy
- vivek sharma (Thu Dec 23 2004 - 05:36:35 CST)
- zhilei chen (Tue Jan 06 2004 - 13:26:47 CST)
Interaction energy between fixed atoms
- Amit Paliwal (Wed Jan 07 2004 - 08:03:12 CST)
Interaction energy for fixed atoms
- AMIT PALIWAL (Fri Jan 09 2004 - 17:35:13 CST)
IO error when running NAMD on new cluster
- Edward Patrick Obrien (Mon Jun 07 2004 - 09:21:44 CDT)
- Alex V. (Sat Jun 05 2004 - 23:07:22 CDT)
- Edward Patrick Obrien (Sat Jun 05 2004 - 14:44:10 CDT)
Is it necessary to neutralize the system with NAMD program?
- Jérôme Hénin (Fri Mar 19 2004 - 04:39:06 CST)
- Brian Bennion (Tue Mar 16 2004 - 16:58:52 CST)
- Aaron Oakley (Tue Mar 16 2004 - 16:18:00 CST)
- Brian Bennion (Tue Mar 16 2004 - 13:07:07 CST)
- yxiong_at_mail.ccnu.edu.cn (Sun Mar 14 2004 - 02:56:41 CST)
Issues with SMD
- Tim Isgro (Mon May 10 2004 - 23:53:13 CDT)
- Brian Bennion (Mon May 10 2004 - 11:04:13 CDT)
- Gadi Oron (Mon Apr 26 2004 - 07:05:26 CDT)
Job is terminated in the middle
- Shahid Qamar (Fri Nov 19 2004 - 11:23:15 CST)
langevin coupling coefficient
- Hyonseok Hwang (Mon Feb 23 2004 - 14:39:47 CST)
Langevin dynamics
- Jérôme Hénin (Thu Feb 19 2004 - 15:33:20 CST)
- Wei Fu (Thu Feb 19 2004 - 14:26:13 CST)
- Wei Fu (Sun Jan 11 2004 - 15:04:41 CST)
Langevin Dynamics again
- Wei Fu (Thu Feb 19 2004 - 15:23:22 CST)
langevin with waterbox ?
- Lei Guo (Thu Feb 19 2004 - 13:48:36 CST)
- Jérôme Hénin (Thu Feb 19 2004 - 13:43:04 CST)
- Lei Guo (Thu Feb 19 2004 - 13:12:01 CST)
- Jérôme Hénin (Thu Feb 19 2004 - 11:48:13 CST)
- Manali Mehendale (Thu Feb 19 2004 - 10:41:16 CST)
large increase in pressure after minimization
- Satyavani Vemparala (Sun Mar 21 2004 - 20:23:33 CST)
Launching namd with PBS
- Juan Alfredo Freites (Wed Sep 24 2003 - 20:03:09 CDT)
- Jim Phillips (Wed Sep 24 2003 - 19:58:59 CDT)
- Brian Bennion (Wed Sep 24 2003 - 19:15:49 CDT)
- Scott Stagg (Wed Sep 24 2003 - 19:12:14 CDT)
Layers
- LEWYN LI (Tue Nov 16 2004 - 13:38:13 CST)
- Laura De Luca (Tue Nov 16 2004 - 10:00:07 CST)
LDB questions/problems
- Brian Bennion (Thu Dec 18 2003 - 10:23:25 CST)
- Jim Phillips (Tue Dec 16 2003 - 22:44:32 CST)
- Brian Bennion (Tue Dec 16 2003 - 15:32:51 CST)
- Gengbin Zheng (Tue Dec 16 2003 - 02:33:09 CST)
- Brian Bennion (Mon Dec 15 2003 - 15:41:32 CST)
- himanshu chandola (Tue Dec 16 2003 - 00:29:26 CST)
- Brian Bennion (Mon Dec 15 2003 - 12:58:15 CST)
libc6 on debian x86
- Grischa R. Meyer (Thu Sep 11 2003 - 22:42:17 CDT)
limit on the number of residues in each segment
- Brian Bennion (Fri Jan 09 2004 - 16:53:20 CST)
- junxie_at_uwm.edu (Fri Jan 09 2004 - 16:45:31 CST)
linux cluster trouble
- max (Fri Nov 19 2004 - 03:47:01 CST)
- Gengbin Zheng (Fri Nov 19 2004 - 09:18:28 CST)
- Gengbin Zheng (Thu Nov 18 2004 - 13:20:46 CST)
- Gengbin Zheng (Thu Nov 18 2004 - 13:01:25 CST)
- Brian Bennion (Thu Nov 18 2004 - 10:56:17 CST)
- max (Tue Nov 16 2004 - 04:44:36 CST)
- Brian Bennion (Tue Nov 16 2004 - 10:40:57 CST)
- Brian Bennion (Wed Nov 10 2004 - 11:26:36 CST)
- max (Wed Nov 10 2004 - 03:00:42 CST)
- Mounir Tarek (Tue Nov 09 2004 - 08:43:03 CST)
- Gengbin Zheng (Tue Nov 09 2004 - 08:19:10 CST)
- Mounir Tarek (Tue Nov 09 2004 - 06:27:55 CST)
- mpappala_at_unict.it (Tue Nov 09 2004 - 05:47:48 CST)
lipids
- Michael Grabe (Fri Nov 14 2003 - 02:07:21 CST)
Lithium
- Scott, Greg (Thu Apr 29 2004 - 22:01:52 CDT)
- Ahmet Bakan (Thu Apr 29 2004 - 11:14:56 CDT)
- Scott, Greg (Wed Apr 28 2004 - 23:30:08 CDT)
- Brian Bennion (Wed Apr 28 2004 - 22:59:38 CDT)
- Scott, Greg (Wed Apr 28 2004 - 22:04:14 CDT)
Load balance strategy
- Gengbin Zheng (Fri Mar 19 2004 - 01:41:44 CST)
- Alex V. (Thu Mar 18 2004 - 00:03:19 CST)
- Gengbin Zheng (Wed Mar 17 2004 - 11:31:03 CST)
- Gadi Oron (Tue Mar 16 2004 - 15:44:03 CST)
- Brian Bennion (Tue Mar 16 2004 - 11:31:15 CST)
- Alex V. (Tue Mar 16 2004 - 09:23:28 CST)
loadtotalforces: 1000+ pN per atom!
- LEWYN LI (Thu Nov 04 2004 - 20:10:07 CST)
Locally Enhanced Sampling
- Fangqiang Zhu (Tue Mar 02 2004 - 11:51:09 CST)
- Vlad Cojocaru (Tue Mar 02 2004 - 07:46:01 CST)
LYC Parameter-Topology ?
- Harindar Keer (Wed Nov 19 2003 - 13:01:55 CST)
mac clustering
- Gengbin Zheng (Sat Feb 07 2004 - 00:10:28 CST)
- yu275197_at_yorku.ca (Fri Feb 06 2004 - 23:34:41 CST)
Making PSF file
- Shahid Qamar (Wed Jul 21 2004 - 16:36:35 CDT)
margin errors
- Stern, Julie (Fri Jun 18 2004 - 14:48:36 CDT)
Margin violation
- Leandro Martinez (Tue Jun 01 2004 - 08:10:20 CDT)
mean square displacemente and diffusion of water at T=298 K
- Maira Aguilar (Thu Aug 12 2004 - 18:44:16 CDT)
Methane residue file
- Edward Patrick Obrien (Wed Oct 27 2004 - 19:19:28 CDT)
mimization warnings - bad global exclusion count
- Brian Bennion (Wed Jul 21 2004 - 17:29:51 CDT)
- Stern, Julie (Wed Jul 21 2004 - 16:20:34 CDT)
Minimisation error
- J. Rui Rodrigues (Fri Nov 28 2003 - 09:40:46 CST)
- Hua Wong (Fri Nov 28 2003 - 02:36:02 CST)
- Hua Wong (Fri Nov 28 2003 - 02:32:49 CST)
- Brian Bennion (Thu Nov 27 2003 - 21:49:25 CST)
- Hua Wong (Thu Nov 27 2003 - 08:47:29 CST)
minimization problem
- Ahmet Bakan (Thu Mar 18 2004 - 18:43:00 CST)
- Ahmet Bakan (Thu Mar 18 2004 - 18:31:09 CST)
- himanshu chandola (Fri Mar 19 2004 - 05:42:41 CST)
- Brian Bennion (Thu Mar 18 2004 - 18:00:23 CST)
- Olya Kravchenko (Thu Mar 18 2004 - 17:32:17 CST)
minimization problem - "Bad global exclusion count, possible error!"
- Brian Bennion (Fri Jan 30 2004 - 10:09:19 CST)
- Harindar Keer (Thu Jan 29 2004 - 18:21:19 CST)
- Frances Leung (Thu Jan 29 2004 - 21:20:54 CST)
- Brian Bennion (Thu Jan 29 2004 - 17:46:34 CST)
- Uday Chippada (Thu Jan 29 2004 - 17:05:54 CST)
- Brian Bennion (Thu Jan 29 2004 - 17:19:39 CST)
- Frances Leung (Thu Jan 29 2004 - 19:25:27 CST)
minimization problem - "Bad global exclusion count,possible error!"
- Brian Bennion (Fri Jan 30 2004 - 10:43:36 CST)
- Frances Leung (Fri Jan 30 2004 - 02:52:09 CST)
Minimization Question
- Jim Phillips (Thu Sep 18 2003 - 16:30:49 CDT)
- Saladino, Alex (Thu Sep 18 2003 - 15:25:08 CDT)
Minimization questions...
- Luis Rosales (Mon Sep 13 2004 - 19:53:16 CDT)
minimization scripts
- Tim Isgro (Mon Feb 09 2004 - 16:53:33 CST)
- Gerald Quon (Mon Feb 09 2004 - 12:09:29 CST)
Minimization with CHARMM
- Tim Isgro (Mon Feb 09 2004 - 17:04:13 CST)
- ted q (Sat Feb 07 2004 - 15:56:11 CST)
Minimizing and Equilibrating
- Shirley Hui (Thu Nov 18 2004 - 19:05:25 CST)
minimum imgae convention
- Vani Krishna (Mon Jun 28 2004 - 09:59:24 CDT)
missing atoms warnings for psfgen
- Jim Phillips (Thu Jan 22 2004 - 17:08:27 CST)
- Frances Leung (Mon Jan 19 2004 - 21:47:33 CST)
Missing coordinates and psfgen
- Eric R Johnson (Sat Feb 07 2004 - 14:56:55 CST)
MOE program and difference between MD and SA?
- Jim Phillips (Fri Nov 14 2003 - 15:20:00 CST)
- Brian Bennion (Fri Nov 14 2003 - 10:35:15 CST)
- yxiong_at_mail.ccnu.edu.cn (Fri Nov 14 2003 - 02:57:25 CST)
Molecular stress tensor
- Lei Guo (Sat Dec 20 2003 - 16:50:17 CST)
Momenta output format
- Jim Phillips (Tue Feb 03 2004 - 16:54:28 CST)
- Neema Salimi (Mon Feb 02 2004 - 13:59:45 CST)
More NAMD/gm2 problems
- Chris Samuel (Thu Apr 08 2004 - 00:55:40 CDT)
- Gengbin Zheng (Wed Mar 31 2004 - 02:17:57 CST)
- Chris Samuel (Wed Mar 31 2004 - 00:40:36 CST)
- David Chalmers (Tue Mar 30 2004 - 23:58:20 CST)
more than 99999 atoms in PDB files
- LEWYN LI (Mon Dec 13 2004 - 16:53:26 CST)
- Gilbert G.Feng (Mon Dec 13 2004 - 15:30:55 CST)
Move molecule
- Uday Chippada (Thu Nov 18 2004 - 14:07:50 CST)
- Edward Patrick Obrien (Thu Nov 18 2004 - 12:39:00 CST)
- Uday Chippada (Thu Nov 18 2004 - 10:18:36 CST)
mpi opteron myrinet
- Gengbin Zheng (Fri Dec 31 2004 - 00:08:20 CST)
- Damon Smith (Thu Dec 30 2004 - 23:51:01 CST)
- Gengbin Zheng (Thu Dec 30 2004 - 22:50:45 CST)
- Damon Smith (Thu Dec 30 2004 - 22:23:09 CST)
Myrinet and MPI
- ghg_at_xalt.am (Wed May 19 2004 - 09:20:20 CDT)
Myrinet and MPI question
- Gengbin Zheng (Thu Jul 22 2004 - 11:49:07 CDT)
- Brian Bennion (Thu Jul 22 2004 - 11:21:34 CDT)
- Hrant Gharabekyan (Thu Jul 22 2004 - 09:20:01 CDT)
NAMD "freezes" up
- Eric R Johnson (Tue May 11 2004 - 08:35:51 CDT)
- Eric R Johnson (Tue May 11 2004 - 04:20:58 CDT)
NAMD "freezes" up (further clarification)
- Eric R Johnson (Tue May 11 2004 - 12:34:32 CDT)
- Eric R Johnson (Tue May 11 2004 - 11:10:44 CDT)
- Brian Bennion (Tue May 11 2004 - 10:10:46 CDT)
- Eric R Johnson (Tue May 11 2004 - 08:49:33 CDT)
NAMD 2.5 Released
- Jim Phillips (Mon Sep 29 2003 - 14:02:48 CDT)
NAMD 2.5b2 Released
- Jim Phillips (Mon Sep 15 2003 - 19:51:49 CDT)
NAMD 2.5b3 Released
- Jim Phillips (Fri Sep 19 2003 - 18:02:58 CDT)
NAMD and Gromac OPLS parameters
- David Chalmers (Thu Feb 26 2004 - 21:46:12 CST)
namd and Tcl 8.3.5
- Sean Michael Whipkey (Wed Jul 07 2004 - 16:06:35 CDT)
- Brian Bennion (Wed Jul 07 2004 - 11:33:23 CDT)
- Sean Michael Whipkey (Wed Jul 07 2004 - 09:42:26 CDT)
NAMD and Vega?
- Alessandro Pedretti (Wed Feb 04 2004 - 06:33:52 CST)
- Josef Scheiber (Wed Feb 04 2004 - 05:04:01 CST)
NAMD at Data Star SDSC
- Shahid Qamar (Mon Nov 22 2004 - 15:19:11 CST)
NAMD C++ API
- Rad Balu (Sat May 29 2004 - 17:58:42 CDT)
NAMD for Opteron?
- Gengbin Zheng (Sun Jan 04 2004 - 18:32:21 CST)
- David Chalmers (Sun Jan 04 2004 - 17:55:15 CST)
NAMD interaction with VMD
- Adam Kubach (Tue Oct 19 2004 - 13:54:18 CDT)
NAMD linking problem
- Gengbin Zheng (Fri Jan 16 2004 - 15:46:09 CST)
- Valery Miftakhov (Tue Jan 13 2004 - 22:15:59 CST)
namd linux source or binary
- Cetin Baloglu (Wed Jul 07 2004 - 03:10:56 CDT)
NAMD minimisation
- Jan Saam (Thu Nov 27 2003 - 08:15:26 CST)
- Hua Wong (Thu Nov 27 2003 - 07:29:27 CST)
NAMD node freeze
- Eric R Johnson (Tue May 11 2004 - 08:43:42 CDT)
NAMD on HP with Itanium2 Processors
- Brian Bennion (Sun May 30 2004 - 01:27:19 CDT)
- Brian Bennion (Sat May 29 2004 - 17:48:32 CDT)
- Ioana Cozmuta (Fri May 28 2004 - 18:08:37 CDT)
NAMD on HP-IA64 Linux
- Gengbin Zheng (Sun May 30 2004 - 22:20:51 CDT)
- Ioana Cozmuta (Sun May 30 2004 - 20:58:00 CDT)
NAMD on itanium?
- freddie salsbury (Thu Mar 11 2004 - 18:04:10 CST)
namd on linux cluster
- Giovanni (Tue Feb 24 2004 - 13:45:44 CST)
NAMD on Linux cluster with Myrinet
- Chris Samuel (Mon Oct 18 2004 - 23:02:27 CDT)
- Gengbin Zheng (Mon Oct 18 2004 - 13:28:36 CDT)
- Alberto Santana (Mon Oct 18 2004 - 11:59:31 CDT)
- Gengbin Zheng (Thu Oct 14 2004 - 14:03:12 CDT)
- Alberto Santana (Thu Oct 14 2004 - 13:59:27 CDT)
- Brian Bennion (Thu Oct 14 2004 - 13:20:59 CDT)
- Alberto Santana (Thu Oct 14 2004 - 11:26:08 CDT)
- Gengbin Zheng (Tue Oct 12 2004 - 00:17:53 CDT)
- Florian Barth (Mon Oct 11 2004 - 19:49:48 CDT)
- Brian Bennion (Mon Oct 11 2004 - 15:53:14 CDT)
- Alberto Santana (Mon Oct 11 2004 - 14:19:31 CDT)
- Brian Bennion (Sat Oct 09 2004 - 21:59:57 CDT)
- Alberto Santana (Sat Oct 09 2004 - 20:42:55 CDT)
NAMD on OpenMosix.
- Nicholas M Glykos (Sat Feb 14 2004 - 10:40:44 CST)
NAMD on OSX built with XLC?
- Matt Harrington (Fri Oct 08 2004 - 13:48:21 CDT)
NAMD on p690 IBM cluster
- Vlad Cojocaru (Tue Jan 27 2004 - 03:56:35 CST)
namd on PPC, linux
- Nathalie Reuter (Wed Jun 23 2004 - 04:40:05 CDT)
NAMD on the TeraGrid
- Gengbin Zheng (Thu Jul 15 2004 - 10:53:20 CDT)
- p.w.fowler_at_qmul.ac.uk (Thu Jul 15 2004 - 05:12:47 CDT)
NAMD on Xeon EM64T
- Chris Samuel (Thu Dec 02 2004 - 22:18:39 CST)
- Alberto Santana (Wed Dec 01 2004 - 06:42:05 CST)
NAMD parser
- Xiaobing Tian (Fri Apr 30 2004 - 14:56:18 CDT)
- Mike McCallum (Thu Apr 29 2004 - 17:03:02 CDT)
- Xiaobing Tian (Thu Apr 29 2004 - 16:25:14 CDT)
- Xiaobing Tian (Thu Apr 29 2004 - 11:16:35 CDT)
NAMD prog. guide
- Giovanni Bellesia (Sat Sep 18 2004 - 19:53:46 CDT)
NAMD programming guide
- Harindar Keer (Thu Sep 16 2004 - 19:55:52 CDT)
Namd RedHat9 compilation problem
- Gengbin Zheng (Tue Jun 15 2004 - 11:39:49 CDT)
- ghg_at_xalt.am (Tue Jun 15 2004 - 05:56:36 CDT)
NAMD Source
- Robert Brunner (Fri Nov 19 2004 - 10:54:16 CST)
- Hassan K. Al-Ali Merheby (Fri Nov 19 2004 - 02:06:44 CST)
NAMD support for Myranet GM2 drivers
- Gengbin Zheng (Fri Mar 19 2004 - 01:30:49 CST)
- David Chalmers (Thu Mar 18 2004 - 22:29:52 CST)
NAMD with Amber
- Amit Paliwal (Fri May 14 2004 - 12:42:10 CDT)
NAMD with HPUX/IA64.
- Hansang Bae (Tue Jun 29 2004 - 13:31:20 CDT)
Namd with intel compilers.
- Gengbin Zheng (Wed Mar 17 2004 - 10:52:27 CST)
- Hansang Bae (Tue Mar 16 2004 - 14:51:47 CST)
namd-L: tcl script for calculate RMS of MD calculation
- yxiong_at_mail.ccnu.edu.cn (Thu Apr 15 2004 - 03:01:28 CDT)
NAMD-MPI compilation on P4 cluster
- Amit Paliwal (Sat Sep 04 2004 - 18:37:55 CDT)
namd/charmm steroid parameterization
- Brian Bennion (Fri Oct 24 2003 - 11:08:07 CDT)
NAMD2.5 and the TeraGrid
- p.w.fowler_at_qmul.ac.uk (Wed Jul 07 2004 - 06:02:40 CDT)
namd2.5 on myrinet cluster
- Florian Barth (Sun Apr 04 2004 - 18:34:40 CDT)
- Gengbin Zheng (Sat Apr 03 2004 - 20:40:12 CST)
- Florian Barth (Sat Apr 03 2004 - 17:59:39 CST)
NAMD2.5b2 and amber force field
- Jim Phillips (Mon Sep 29 2003 - 12:34:55 CDT)
- james tomomi macdonald (Mon Sep 29 2003 - 12:02:09 CDT)
NAMD: force field for hybrid systems (fwd)
- Ioana Cozmuta (Sun Oct 12 2003 - 12:59:01 CDT)
NAMD: Force Fields
- Olya Kravchenko (Fri Apr 23 2004 - 11:32:52 CDT)
- Galina Petrova (Fri Apr 23 2004 - 09:00:57 CDT)
NamdCompile Problem
- Brian Bennion (Thu Dec 16 2004 - 14:39:33 CST)
- Gengbin Zheng (Thu Dec 16 2004 - 13:19:57 CST)
- HUSSER Jacky 113956 (Thu Dec 16 2004 - 05:17:41 CST)
namdplot
- LEWYN LI (Thu Dec 09 2004 - 11:17:33 CST)
- vivek sharma (Thu Dec 09 2004 - 10:38:14 CST)
- Blake Charlebois (Thu Dec 09 2004 - 07:15:41 CST)
- nordgren_at_sas.upenn.edu (Thu Dec 09 2004 - 05:59:11 CST)
- vivek sharma (Thu Dec 09 2004 - 02:13:26 CST)
NAN GRADIENT TOLERANCE - & - RESTARTING CONJUGATE GRADIENT ALGORITHM
- Peter Spijker (Thu May 20 2004 - 12:47:57 CDT)
- Peter Spijker (Wed May 19 2004 - 18:30:57 CDT)
Need of an ASCII-PHI converter, any help is appreciated to use wat2ions from Delphi output
- Eric Hajjar (Fri Jul 30 2004 - 02:45:05 CDT)
Need to add Hydrogens to over 300 distinct PDB's
- Edward Patrick Obrien (Wed Aug 11 2004 - 13:05:33 CDT)
- Edward Patrick Obrien (Tue Aug 10 2004 - 10:20:47 CDT)
- Kamp, Marc vander (Tue Aug 10 2004 - 09:46:15 CDT)
- Edward Patrick Obrien (Mon Aug 09 2004 - 13:03:40 CDT)
New cluster configuration?
- nalianarmen (Fri May 07 2004 - 17:19:11 CDT)
Node 0 could not initialize network!
- Alberto Santana (Sun Jul 04 2004 - 13:25:32 CDT)
- Alberto Santana (Sat Jul 03 2004 - 18:16:01 CDT)
Node list
- Shahid Qamar (Wed Aug 18 2004 - 19:25:41 CDT)
nodelist ignored?
- Jim Phillips (Mon Sep 29 2003 - 14:27:45 CDT)
- Gengbin Zheng (Mon Sep 29 2003 - 14:23:42 CDT)
- Nathalie Reuter (Mon Sep 29 2003 - 12:26:51 CDT)
Not all atoms have unique coordinates - revisited
- Brian Bennion (Mon Oct 04 2004 - 10:22:04 CDT)
- Alberto Santana (Sat Oct 02 2004 - 08:32:59 CDT)
- Brian Bennion (Sat Oct 02 2004 - 00:37:12 CDT)
- Alberto Santana (Fri Oct 01 2004 - 18:52:27 CDT)
NPT calculations in NAMD
- Leandro Martinez (Tue Jun 01 2004 - 07:17:58 CDT)
- Peter Jones (Mon May 31 2004 - 22:04:51 CDT)
- Hui-Hsu (Gavin) Tsai [contr] (Mon May 31 2004 - 11:06:04 CDT)
NPT ensemble restart, put in new basis vectors?
- Edward Patrick Obrien (Sun Apr 25 2004 - 13:19:21 CDT)
numerical inaccuracy upon restart
- tepper_at_amolf.nl (Mon Sep 06 2004 - 06:30:22 CDT)
- Jim Phillips (Fri Sep 03 2004 - 17:21:25 CDT)
- Harald Tepper (Tue Aug 31 2004 - 05:21:21 CDT)
- nordgren_at_sas.upenn.edu (Wed Aug 25 2004 - 22:40:31 CDT)
- Blake Charlebois (Wed Aug 25 2004 - 09:24:08 CDT)
- Harald Tepper (Wed May 19 2004 - 08:45:07 CDT)
octahedral period BCs
- Mark Abraham (Wed Jul 07 2004 - 22:43:57 CDT)
- Mark Abraham (Wed Jul 07 2004 - 22:35:44 CDT)
- Peter Jones (Wed Jul 07 2004 - 21:34:52 CDT)
- Peter Jones (Fri Mar 12 2004 - 08:01:13 CST)
opinions on queueing system choices?
- Matt Harrington (Wed Apr 21 2004 - 16:04:31 CDT)
Order of improper dihedrals
- Ben Roberts (Tue Jul 06 2004 - 00:21:01 CDT)
output files always go to same node
- Alberto Santana (Mon Sep 20 2004 - 18:31:03 CDT)
Output files creation problem in MPI.
- Hrant Gharabekyan (Mon Jul 19 2004 - 07:59:38 CDT)
- Hrant Gharabekyan (Mon Jul 19 2004 - 02:35:11 CDT)
Output only protein .dcd
- Meric Ayse Ovacik (Wed Sep 15 2004 - 02:23:03 CDT)
- Nur Aida Abdul Rahim (Tue Sep 14 2004 - 13:41:38 CDT)
output to multiple files
- Leandro Martinez (Tue Oct 26 2004 - 13:09:26 CDT)
- Brian Bennion (Fri Oct 22 2004 - 14:37:37 CDT)
- Leandro Martinez (Thu Oct 21 2004 - 12:06:52 CDT)
output warning in using namd2 "Warning: Not all atoms have unique coordinates."
- Jerry Ebalunode (Wed Sep 17 2003 - 06:21:53 CDT)
- Jim Phillips (Tue Sep 16 2003 - 21:19:03 CDT)
- Jerry Ebalunode (Tue Sep 16 2003 - 13:44:49 CDT)
output warning in using namd2 "Warning: Not all atoms have unique coordinates." more errors
- Jim Phillips (Wed Sep 17 2003 - 13:07:47 CDT)
- Jerry Ebalunode (Wed Sep 17 2003 - 07:54:46 CDT)
pair Interaction and electric field
- Jim Phillips (Mon Oct 27 2003 - 13:22:52 CST)
- Ioana Cozmuta (Sun Oct 19 2003 - 14:09:22 CDT)
pair Interaction Calculation
- Ioana Cozmuta (Thu Oct 16 2003 - 17:50:47 CDT)
- Ioana Cozmuta (Thu Oct 16 2003 - 17:36:18 CDT)
pair interaction calculations
- Xin Chen (Thu Jul 29 2004 - 17:18:36 CDT)
Pair interaction calculations in precompiled NAMD
- Liu, Zhanwu (Mon Feb 02 2004 - 05:34:03 CST)
Pair interaction energies: TCL error
- Vani Krishna (Fri Sep 24 2004 - 21:06:30 CDT)
Pair interaction energy
- Brian Bennion (Fri Jan 30 2004 - 12:38:35 CST)
- Ioana Cozmuta (Fri Jan 30 2004 - 12:28:05 CST)
- Brian Bennion (Fri Jan 30 2004 - 12:08:38 CST)
- Ioana Cozmuta (Fri Jan 30 2004 - 11:57:16 CST)
- Sundaramoorthy, Munirathinam (Fri Jan 30 2004 - 10:46:22 CST)
pair interaction forces
- Kamp, Marc vander (Mon Jul 26 2004 - 03:24:20 CDT)
Pair interaction output.
- Gadi Oron (Thu Feb 12 2004 - 06:21:23 CST)
Pair interaction, PBC included?
- Edward Patrick Obrien (Sat Nov 20 2004 - 14:22:39 CST)
pair-interaction energy
- Vani Krishna (Sun Oct 17 2004 - 17:37:18 CDT)
palindromic error reading in a restart file.
- Brian Bennion (Thu Feb 26 2004 - 12:04:49 CST)
Paper on Classical treatment for calculating pKas
- Volodymyr Nechiporuk-Zloy (Mon Mar 15 2004 - 03:31:21 CST)
- Brian Bennion (Fri Mar 12 2004 - 13:40:33 CST)
Parallelization of a code from TCB Summer School 2003
- Alex V. (Mon Apr 19 2004 - 02:49:05 CDT)
- Yang Yang (Fri Apr 16 2004 - 21:54:46 CDT)
Parameter File Problem
- Brian Bennion (Mon May 10 2004 - 23:59:53 CDT)
- beckloni_at_umdnj.edu (Mon May 10 2004 - 19:47:24 CDT)
parameter for phosphonate
- yxiong_at_mail.ccnu.edu.cn (Wed Nov 26 2003 - 07:23:45 CST)
- yxiong_at_mail.ccnu.edu.cn (Wed Nov 26 2003 - 00:14:37 CST)
Parameter-Topology-Repository
- Jan Saam (Wed Nov 19 2003 - 11:56:41 CST)
Parameter/topology repository
- Jim Phillips (Fri Nov 07 2003 - 11:05:11 CST)
- Brian Bennion (Fri Nov 07 2003 - 10:12:22 CST)
- Jan Saam (Fri Nov 07 2003 - 06:05:13 CST)
Parameters and topologies for aa at different protonation states
- Brian Bennion (Fri Jan 23 2004 - 11:14:18 CST)
- Bartosz Dobrzelecki (Fri Jan 23 2004 - 06:45:26 CST)
Parameters for iodine atoms
- Leandro Martinez (Thu Aug 05 2004 - 12:55:28 CDT)
PBCwrap: wrapping DCD files
- Vani Krishna (Mon Jun 28 2004 - 22:03:45 CDT)
PC-DL Deluxe, Dual Xeon
- Armen Nalian (Wed Aug 04 2004 - 17:32:54 CDT)
peptid bond omega, problems with settings?
- Hua Wong (Fri Apr 16 2004 - 09:25:22 CDT)
- Brian Bennion (Thu Apr 15 2004 - 11:25:56 CDT)
- Hua Wong (Thu Apr 15 2004 - 02:27:38 CDT)
periodic boundary conditions with lipids
- Jee Eun Rim (Wed Dec 17 2003 - 12:29:45 CST)
periodic boxes
- Jim Phillips (Fri Nov 07 2003 - 10:47:13 CST)
- Michael Grabe (Mon Nov 03 2003 - 23:13:50 CST)
Periodic cel too small
- Alemayehu Gorfe Abebe (Tue Jan 13 2004 - 08:33:39 CST)
periodic cell has become too small
- li (Thu Apr 08 2004 - 02:32:31 CDT)
Periodic cell has become too small for original patch grid?
- yxiong_at_mail.ccnu.edu.cn (Wed Dec 24 2003 - 03:44:58 CST)
Periodic cell size
- Blake Charlebois (Wed Dec 08 2004 - 23:54:04 CST)
- Brian Bennion (Wed Dec 08 2004 - 11:43:02 CST)
- Edward Patrick Obrien (Wed Dec 08 2004 - 10:54:37 CST)
- Suxing Hu (Wed Dec 08 2004 - 10:06:24 CST)
Periodic cell too small
- Brian Bennion (Tue May 25 2004 - 17:39:45 CDT)
- Ekta Khurana (Tue May 25 2004 - 16:22:00 CDT)
- Alemayehu Gorfe Abebe (Tue Jan 13 2004 - 16:42:59 CST)
phase equilibria using NAMD
- Brian Bennion (Thu Jul 22 2004 - 10:53:00 CDT)
- nasrat kamal (Wed Jul 21 2004 - 07:33:45 CDT)
PME ERROR
- Brian Bennion (Wed Dec 01 2004 - 12:02:55 CST)
- Eunice Ramirez Melendez (Wed Dec 01 2004 - 01:52:13 CST)
PME grid sizes
- Satyavani Vemparala (Thu Feb 26 2004 - 17:05:01 CST)
PME off
- Kamp, Marc vander (Tue Jul 06 2004 - 01:50:24 CDT)
- Michael Grabe (Mon Jul 05 2004 - 17:21:47 CDT)
PMEGridSize
- Jim Phillips (Mon Oct 13 2003 - 13:34:44 CDT)
- Peter Jones (Fri Oct 10 2003 - 02:08:19 CDT)
PMEgrindsize for hexagon
- ego_wayne-namd_at_yahoo.com.cn (Sat Oct 23 2004 - 07:47:38 CDT)
pmf error
- mashaojie163 (Mon Jun 21 2004 - 10:17:20 CDT)
Polymer Simulations
- AHMET BAKAN (Mon Dec 15 2003 - 16:49:22 CST)
Position of the Virtual atom
- Shahid Qamar (Wed Jul 28 2004 - 16:46:29 CDT)
Potential Terms
- Jim Phillips (Wed Jan 07 2004 - 09:45:11 CST)
- AHMET BAKAN (Mon Jan 05 2004 - 12:20:02 CST)
pressure profile
- Mauricio Carrillo Tripp (Mon Jun 07 2004 - 17:00:51 CDT)
previous question about multiplicity
- Brian Bennion (Wed Jan 28 2004 - 15:32:35 CST)
- Jim Phillips (Wed Jan 28 2004 - 14:27:50 CST)
- Jim Phillips (Wed Jan 28 2004 - 14:12:45 CST)
- Brian Bennion (Wed Jan 28 2004 - 14:18:20 CST)
- Brian Bennion (Tue Jan 27 2004 - 19:06:02 CST)
Problem using Gromacs topology file
- Josef Scheiber (Fri May 14 2004 - 03:59:24 CDT)
problem with flipbinpdb
- yxiong_at_mail.ccnu.edu.cn (Sat Dec 06 2003 - 02:33:01 CST)
Problem with PSFGEN?
- Shirley Hui (Thu Sep 09 2004 - 21:51:53 CDT)
problem with running namd on Linux cluster
- Gengbin Zheng (Tue Jan 20 2004 - 11:18:20 CST)
- zhilei chen (Mon Jan 19 2004 - 11:51:11 CST)
Problem with Tcl & psfgen
- Jim Phillips (Tue Feb 17 2004 - 17:33:20 CST)
- scott.brown_at_abbott.com (Tue Feb 17 2004 - 13:36:56 CST)
problem:psfgen- not unique coordinates
- Tim Isgro (Mon Feb 09 2004 - 20:05:30 CST)
- Satyavani Vemparala (Mon Feb 09 2004 - 15:14:02 CST)
problems compiling charm++ for clustermatic 4
- Mike Grommet (Tue Dec 16 2003 - 08:47:52 CST)
- Zheng Gengbin (Tue Dec 16 2003 - 02:21:36 CST)
Problems compiling Charm++ for Myrinet
- Gengbin Zheng (Tue Mar 30 2004 - 12:40:05 CST)
- David Chalmers (Mon Mar 29 2004 - 18:53:46 CST)
problems on Fedora Core 3
- lc_at_chem.au.dk (Fri Dec 31 2004 - 13:10:04 CST)
- Gengbin Zheng (Thu Dec 30 2004 - 15:23:30 CST)
- John Saeger (Thu Dec 30 2004 - 13:20:16 CST)
- Ruxandra Dima (Tue Dec 28 2004 - 22:48:43 CST)
problems with namdplot fixed by using new plotting program
- Cheri M Turman (Tue Apr 27 2004 - 16:34:42 CDT)
problems with psfgen
- yxiong_at_mail.ccnu.edu.cn (Thu Nov 27 2003 - 06:57:35 CST)
- Hua Wong (Thu Nov 27 2003 - 04:39:25 CST)
Problems witn parameter files!
- Galina Petrova (Mon May 10 2004 - 08:54:25 CDT)
Processor load
- Alex V. (Sun Mar 28 2004 - 09:11:01 CST)
processors information
- Ioana Cozmuta (Wed Dec 10 2003 - 21:28:23 CST)
Protonated aspartic acid
- apw397_at_soton.ac.uk (Wed Mar 24 2004 - 06:10:11 CST)
Protonated GLU/ASP in PSF generation
- Vani Krishna (Sun Aug 29 2004 - 16:23:00 CDT)
psf file for zeolite-water system
- Fangqiang Zhu (Mon Feb 23 2004 - 14:16:26 CST)
- $B:,>k(J $B6Q(J (Mon Feb 23 2004 - 02:22:31 CST)
- Ozgur YAZAYDIN (Sun Feb 22 2004 - 21:21:03 CST)
PSF file generation
- beckloni_at_umdnj.edu (Mon May 10 2004 - 10:48:22 CDT)
- Brian Bennion (Mon May 10 2004 - 10:39:42 CDT)
- beckloni_at_umdnj.edu (Sun May 09 2004 - 10:00:59 CDT)
PSF generation
- Josef Scheiber (Mon Dec 08 2003 - 02:50:37 CST)
- yxiong_at_mail.ccnu.edu.cn (Sun Dec 07 2003 - 19:12:58 CST)
- AHMET BAKAN (Sun Dec 07 2003 - 10:08:47 CST)
psf question
- Brian Bennion (Tue Mar 16 2004 - 11:02:21 CST)
- Hua Wong (Tue Mar 16 2004 - 03:12:38 CST)
psfgen
- Brian Bennion (Mon Nov 29 2004 - 17:01:33 CST)
- Hemant Kushwaha (Mon Nov 29 2004 - 01:16:44 CST)
- Brian Bennion (Wed Jul 21 2004 - 18:23:41 CDT)
- klsale (Wed Jul 21 2004 - 14:57:56 CDT)
- Ken Sale (Wed Jul 21 2004 - 15:14:43 CDT)
psfgen : wrong guess for leucine hydrogen
- li (Wed Jun 16 2004 - 01:58:18 CDT)
- Jérôme Hénin (Tue Jun 15 2004 - 10:33:47 CDT)
psfgen issue
- Rad Balu (Sun Jun 06 2004 - 22:03:07 CDT)
- Edward Patrick Obrien (Mon Jun 07 2004 - 09:23:23 CDT)
- Rad Balu (Sat Jun 05 2004 - 12:49:34 CDT)
psfgen non-bonded atom pairs
- Shirley Hui (Sat May 22 2004 - 12:35:52 CDT)
- Shirley Hui (Sat May 22 2004 - 01:08:57 CDT)
psfgen problem
- Brian Bennion (Wed Jun 09 2004 - 15:59:33 CDT)
- Kamp, Marc vander (Wed Jun 09 2004 - 04:22:00 CDT)
- Brian Bennion (Tue Jun 08 2004 - 12:01:58 CDT)
- Kamp, Marc vander (Tue Jun 08 2004 - 04:53:39 CDT)
PSFGEN problems in nanotube tutorial
- David L. Azevedo (Fri Oct 01 2004 - 01:36:36 CDT)
psfgen question
- li (Fri Mar 26 2004 - 01:06:21 CST)
- Brian Bennion (Fri Jan 30 2004 - 10:13:35 CST)
- MinSoo Kim (Fri Jan 30 2004 - 04:00:35 CST)
psfgen questions welcome on NAMD-L
- Jim Phillips (Fri Nov 14 2003 - 14:52:22 CST)
psfgen: failed on segment
- Olya Kravchenko (Fri May 14 2004 - 19:46:26 CDT)
psfgen: pdb and nucleic acid
- Brian Bennion (Wed Dec 03 2003 - 14:30:29 CST)
- David E. Konerding (Wed Dec 03 2003 - 13:52:52 CST)
Pt LJ Parameters
- Ahmet Bakan (Wed Jul 21 2004 - 11:56:52 CDT)
pulling plus restraint
- li (Thu Sep 16 2004 - 03:56:47 CDT)
query on memory usuage
- g srinivasa murthy (Sat Feb 21 2004 - 22:58:26 CST)
question about autogen in topology file
- jz7_at_duke.edu (Thu Jun 10 2004 - 13:41:00 CDT)
Question about AUTOGENERATE
- Jim Phillips (Wed Nov 05 2003 - 12:38:32 CST)
- Brian Bennion (Tue Nov 04 2003 - 10:24:58 CST)
- Zhilei Chen (Tue Nov 04 2003 - 09:48:01 CST)
- Jim Phillips (Mon Nov 03 2003 - 21:43:56 CST)
- Zhilei Chen (Mon Nov 03 2003 - 20:50:09 CST)
Question about external forces
- Yang Yang (Tue Apr 27 2004 - 01:55:13 CDT)
Question about Gradient Tolerance during minimization
- Wolbach, Jeffrey P $WOLBACH$ (Wed Sep 08 2004 - 13:00:15 CDT)
question about running equilibration in NAMD
- Brian Bennion (Tue Jun 08 2004 - 15:50:28 CDT)
- jz7_at_duke.edu (Tue Jun 08 2004 - 14:25:41 CDT)
question about using Amber force field in namd
- Kamp, Marc vander (Thu Jun 03 2004 - 01:19:12 CDT)
- Brian Bennion (Wed Jun 02 2004 - 16:31:48 CDT)
- Brian Bennion (Wed Jun 02 2004 - 16:21:21 CDT)
- jz7_at_duke.edu (Wed Jun 02 2004 - 16:13:14 CDT)
- Brian Bennion (Wed Jun 02 2004 - 16:07:28 CDT)
- jz7_at_duke.edu (Wed Jun 02 2004 - 09:35:54 CDT)
question on a chared system MD simulation
- Hyonseok Hwang (Sun Jun 06 2004 - 18:05:35 CDT)
question on autocorrelation function and temperature controlling
- Hyonseok Hwang (Fri Apr 30 2004 - 17:09:44 CDT)
question on Berendsen's temperature coupling method
- Vlad Cojocaru (Fri Jan 23 2004 - 02:54:03 CST)
- Jim Phillips (Thu Jan 22 2004 - 17:19:22 CST)
- Hyonseok Hwang (Tue Jan 20 2004 - 13:13:59 CST)
Question on finding suitable force field for MD simulations
- Fung Wai Keung (Fri Mar 12 2004 - 21:00:06 CST)
question on force autocorrelation function
- Hyonseok Hwang (Wed Oct 13 2004 - 11:20:47 CDT)
Question on harmonic constraints
- Edward Patrick Obrien (Thu Oct 14 2004 - 19:39:00 CDT)
question on Lithium force field
- Hyonseok Hwang (Wed Jun 16 2004 - 16:20:12 CDT)
question on pair interaction energy and force
- Hyonseok Hwang (Tue Sep 21 2004 - 23:39:41 CDT)
question on PMF output
- Hyonseok Hwang (Mon Mar 08 2004 - 12:08:13 CST)
question on potential energy for individual atoms
- Jim Phillips (Mon Jan 26 2004 - 17:52:55 CST)
- Hyonseok Hwang (Fri Jan 23 2004 - 19:59:53 CST)
question on self-diffusion constant of TIP3P water
- Brian Bennion (Wed May 05 2004 - 18:18:19 CDT)
- Brian Bennion (Wed May 05 2004 - 17:37:46 CDT)
- Hyonseok Hwang (Wed May 05 2004 - 16:54:45 CDT)
question on the coordinates of hydrogen atoms
- Hyonseok Hwang (Fri Jan 02 2004 - 17:45:50 CST)
question on the parallel job on NCSA Xeon cluster
- Gengbin Zheng (Tue Aug 17 2004 - 23:01:02 CDT)
- Hyonseok Hwang (Tue Aug 17 2004 - 22:51:13 CDT)
question on the wrapping algorithm in NAMD
- Hyonseok Hwang (Thu May 27 2004 - 18:18:26 CDT)
question on veldcd
- Hyonseok Hwang (Mon Jun 14 2004 - 10:19:59 CDT)
- Hyonseok Hwang (Fri Jun 11 2004 - 12:35:42 CDT)
Question:about equilibration~
- Îº¿ (Thu Nov 25 2004 - 22:05:59 CST)
Question:about harmonic restraint decrease!
- Jérôme Hénin (Fri Nov 26 2004 - 03:22:51 CST)
- Îº¿ (Wed Nov 24 2004 - 22:13:49 CST)
Questions
- Edward Patrick Obrien (Mon Jul 19 2004 - 17:02:29 CDT)
- Manali Mehendale (Mon Jul 19 2004 - 14:08:10 CDT)
questions about "psfgen".
- Lv Shouqin (Sat Jun 12 2004 - 00:12:14 CDT)
questions about set cellBasisVector and a ligand ...
- Edward Patrick Obrien (Thu Apr 29 2004 - 12:59:15 CDT)
- Xiaobing Tian (Thu Apr 29 2004 - 10:06:53 CDT)
Questions on periodic boundary condition
- LEWYN LI (Thu Sep 02 2004 - 11:00:47 CDT)
- Edward Patrick Obrien (Thu Sep 02 2004 - 10:51:56 CDT)
- LEWYN LI (Thu Sep 02 2004 - 00:38:24 CDT)
radial distribution function
- Liu, Zhanwu (Fri Aug 13 2004 - 08:40:51 CDT)
- bora erdemli (Fri Aug 13 2004 - 08:16:51 CDT)
RATTLE Alg
- junxie_at_uwm.edu (Fri Jan 09 2004 - 16:41:51 CST)
reading in large water boxes (PDB format)?
- Juan Alfredo Freites (Sun Dec 07 2003 - 19:32:09 CST)
- David E. Konerding (Sun Dec 07 2003 - 12:26:32 CST)
recentering protein in the waterbox
- Gianluca Interlandi (Fri Jun 18 2004 - 18:16:35 CDT)
- Jerry Ebalunode (Fri Jun 18 2004 - 07:04:58 CDT)
recommendation for 32 CPU cluster: Opteron or ?
- Matt Harrington (Tue Aug 24 2004 - 17:52:03 CDT)
Regarding SMD atom and forces
- Uday Chippada (Tue Feb 17 2004 - 12:37:37 CST)
- Uday Chippada (Wed Feb 11 2004 - 16:00:11 CST)
render format
- Brian Bennion (Mon Aug 02 2004 - 14:44:08 CDT)
- John Stone (Mon Aug 02 2004 - 13:14:50 CDT)
- Marcela Madrid (Mon Aug 02 2004 - 13:15:17 CDT)
replica exchange
- Justin Gullingsrud (Mon Aug 30 2004 - 16:09:42 CDT)
replica-ex NAMD?
- Sichun Yang (Wed May 19 2004 - 12:28:20 CDT)
repulsive/hard sphere simulation
- Jim Phillips (Fri Nov 07 2003 - 10:42:57 CST)
- AMIT PALIWAL (Wed Nov 05 2003 - 15:53:17 CST)
- AMIT PALIWAL (Wed Nov 05 2003 - 15:50:53 CST)
- Brian Bennion (Wed Nov 05 2003 - 15:22:16 CST)
- AMIT PALIWAL (Wed Nov 05 2003 - 15:07:21 CST)
Reset
- Saladino, Alex (Tue Jul 13 2004 - 10:28:49 CDT)
Reset reference position
- Saladino, Alex (Wed Jul 14 2004 - 13:46:38 CDT)
Residence time
- Uday Chippada (Tue Dec 28 2004 - 10:58:41 CST)
- Ioana Cozmuta (Tue Mar 23 2004 - 21:51:10 CST)
resolved: BUG ALERT: Mother atom with hydrogenGroupSize of 0!
- Vani Krishna (Fri Dec 17 2004 - 18:47:21 CST)
restart files
- himanshu chandola (Sun Apr 04 2004 - 19:51:34 CDT)
restart files after minimization?
- Peter Bazeley (Thu Dec 23 2004 - 18:52:53 CST)
restart simulation
- Tim Isgro (Tue May 11 2004 - 00:31:18 CDT)
- J. Rui Rodrigues (Mon May 10 2004 - 17:10:25 CDT)
- Marcela P.Aliste (Mon May 10 2004 - 16:01:28 CDT)
Restart using amber force field
- Sichun Yang (Fri Feb 27 2004 - 16:13:25 CST)
- Fangqiang Zhu (Fri Feb 27 2004 - 15:00:29 CST)
- Sichun Yang (Fri Feb 27 2004 - 11:30:47 CST)
Restarting problem with Langevin dynamics
- Xin Chen (Wed Apr 07 2004 - 13:45:39 CDT)
- Brian Bennion (Wed Apr 07 2004 - 13:50:00 CDT)
- Brian Bennion (Wed Apr 07 2004 - 09:59:45 CDT)
- Xin Chen (Wed Apr 07 2004 - 01:01:55 CDT)
- Xin Chen (Tue Apr 06 2004 - 00:05:19 CDT)
- Xin Chen (Wed Mar 31 2004 - 15:11:58 CST)
restarting suspended namd jobs
- Jim Phillips (Thu Nov 13 2003 - 15:55:45 CST)
- J. Rui Rodrigues (Mon Nov 10 2003 - 13:56:54 CST)
restraints
- Michael Grabe (Wed Feb 25 2004 - 15:47:31 CST)
- Jim Phillips (Tue Dec 16 2003 - 22:19:08 CST)
- Michael Grabe (Mon Dec 15 2003 - 20:04:29 CST)
retinal parameters
- Brian Bennion (Thu Feb 12 2004 - 10:11:48 CST)
- Anna Modzelewska (Thu Feb 12 2004 - 05:28:40 CST)
rmsd and simulation
- Charles McCallum (Fri Nov 05 2004 - 11:23:58 CST)
- bora erdemli (Fri Nov 05 2004 - 03:24:59 CST)
rmsd calculation
- Charles Danko (Tue Nov 23 2004 - 09:50:49 CST)
- Francesco Iori (Tue Nov 23 2004 - 06:56:32 CST)
rmsd problem
- bora erdemli (Thu Aug 26 2004 - 14:10:05 CDT)
rmsd problem,script and version
- bora erdemli (Fri Sep 03 2004 - 00:23:42 CDT)
rot constraints
- himanshu chandola (Tue Nov 18 2003 - 20:42:17 CST)
rotating constraints
- Jim Phillips (Mon Feb 02 2004 - 13:27:10 CST)
- himanshu chandola (Fri Jan 30 2004 - 01:28:51 CST)
- himanshu chandola (Tue Nov 18 2003 - 20:17:14 CST)
rotating constraints constant
- himanshu chandola (Wed Mar 03 2004 - 05:57:11 CST)
- himanshu chandola (Wed Mar 03 2004 - 02:12:34 CST)
rotation constraints
- Jim Phillips (Thu Nov 13 2003 - 15:18:49 CST)
- Jim Phillips (Thu Nov 13 2003 - 15:20:49 CST)
- himanshu chandola (Tue Nov 11 2003 - 17:59:45 CST)
- himanshu chandola (Fri Nov 07 2003 - 23:49:26 CST)
rotational energy, Tcl and environment variable(s) in Linux 2.5
- Shantenu Jha (Thu Dec 04 2003 - 15:59:10 CST)
- Fangqiang Zhu (Tue Dec 02 2003 - 00:38:01 CST)
- Shantenu Jha (Sun Nov 30 2003 - 18:47:07 CST)
rotational energy, Tcl and environment variable(s) inLinux 2.5
- Fangqiang Zhu (Thu Dec 04 2003 - 18:05:24 CST)
rsh on nodes
- nalianarmen (Mon May 03 2004 - 23:30:38 CDT)
Running AIX version of NAMD on IBM cluster
- Jim Phillips (Mon Feb 23 2004 - 10:50:50 CST)
- Brian Bennion (Thu Feb 19 2004 - 14:06:20 CST)
- Gengbin Zheng (Wed Feb 18 2004 - 21:37:55 CST)
- Hansang Bae (Tue Feb 17 2004 - 17:13:47 CST)
- aida_at_mit.edu (Wed Feb 04 2004 - 14:54:21 CST)
running multiple minimizations
- Stern, Julie (Fri Mar 19 2004 - 09:20:34 CST)
Running namd on Rice Teracluster
- Chris Samuel (Tue Apr 13 2004 - 20:47:46 CDT)
- Chris Samuel (Tue Apr 13 2004 - 20:43:18 CDT)
- Gengbin Zheng (Mon Apr 12 2004 - 13:28:10 CDT)
- Amarda Shehu (Sun Apr 11 2004 - 19:15:41 CDT)
running namd on solaris 5.6
- Jim Phillips (Thu Oct 30 2003 - 13:41:19 CST)
- himanshu chandola (Thu Oct 30 2003 - 22:50:16 CST)
Running on Alpha cluster
- Gengbin Zheng (Fri Mar 26 2004 - 11:43:38 CST)
- Alex V. (Fri Mar 26 2004 - 03:31:22 CST)
- Gengbin Zheng (Mon Mar 15 2004 - 10:07:24 CST)
- Alex V. (Fri Mar 12 2004 - 22:27:26 CST)
- Alex V. (Wed Mar 10 2004 - 03:40:12 CST)
running vmd in batch mode
- Ioana Cozmuta (Thu Nov 06 2003 - 15:46:19 CST)
Sample Configuratiion files
- Cheri M Turman (Wed Nov 03 2004 - 19:47:25 CST)
- Charles Danko (Wed Nov 03 2004 - 15:50:49 CST)
- Leandro Martinez (Wed Nov 03 2004 - 15:40:38 CST)
- Raymond C. Fort Jr. (Wed Nov 03 2004 - 14:59:44 CST)
Sampling trajectories
- Harindar Keer (Fri Jun 04 2004 - 17:03:02 CDT)
saving forces using loadforces
- Ragan Robertson (Sat Dec 11 2004 - 15:39:42 CST)
SC2003 and NAMD support
- Jim Phillips (Fri Nov 14 2003 - 16:41:25 CST)
Scale on Force vs Time plot?
- Shahid Qamar (Thu Jul 22 2004 - 15:06:53 CDT)
Scyld cluster
- Jim Phillips (Wed Oct 22 2003 - 16:59:38 CDT)
- Amit Paliwal (Wed Oct 22 2003 - 12:26:55 CDT)
- Jim Phillips (Wed Oct 22 2003 - 16:09:42 CDT)
- Amit Paliwal (Wed Oct 22 2003 - 07:52:06 CDT)
seed value in SMD
- Jim Phillips (Mon Jan 26 2004 - 17:46:59 CST)
- Ioana Cozmuta (Thu Jan 22 2004 - 20:54:15 CST)
seg fault
- Brian Bennion (Tue Sep 16 2003 - 16:22:44 CDT)
seg fault and namdplot problem
- Jim Phillips (Tue Sep 23 2003 - 21:44:24 CDT)
- Cheri M Turman (Mon Sep 22 2003 - 18:58:30 CDT)
- Jim Phillips (Mon Sep 22 2003 - 18:20:20 CDT)
- Cheri M Turman (Mon Sep 22 2003 - 16:22:46 CDT)
Segmantation fault writing dcd files.
- Ivan Vinogradov (Fri Mar 12 2004 - 09:07:26 CST)
segmantation violation
- li (Tue Feb 12 2008 - 09:13:36 CST)
segmentation fault
- Jim Phillips (Tue Sep 16 2003 - 15:27:10 CDT)
- Cheri M Turman (Tue Sep 16 2003 - 14:12:43 CDT)
Segmentation fault.
- Alex V. (Wed Mar 10 2004 - 09:04:33 CST)
- ivan.vinogradov_at_utoronto.ca (Thu Mar 11 2004 - 16:21:24 CST)
Segmentation violation
- Gengbin Zheng (Tue Jul 20 2004 - 14:18:06 CDT)
- Brian Bennion (Tue Jul 20 2004 - 12:30:06 CDT)
- Eunice Ramirez Melendez (Mon Jul 19 2004 - 22:26:22 CDT)
selectConstrZ
- Ekta Khurana (Mon Mar 08 2004 - 12:01:09 CST)
setting constraints to off in execution script
- Kamp, Marc vander (Mon Jun 21 2004 - 04:20:26 CDT)
SHAKE algorithm and MD at constant T and P?
- yxiong_at_mail.ccnu.edu.cn (Thu Dec 04 2003 - 19:54:15 CST)
Simulated Annealing Config
- Jérôme Hénin (Tue Jun 15 2004 - 12:20:45 CDT)
- Ahmet Bakan (Tue Jun 15 2004 - 08:24:59 CDT)
simulated annealing script
- Jim Phillips (Thu Sep 25 2003 - 18:47:22 CDT)
- Cheri M Turman (Thu Sep 25 2003 - 13:15:10 CDT)
Simulating DNA in vacuum
- C. Ecker (Fri Nov 14 2003 - 08:47:54 CST)
Simulating RNA+PROTEIN complexes
- Jim Phillips (Fri Dec 19 2003 - 16:26:31 CST)
- Bartosz Dobrzelecki (Fri Dec 19 2003 - 14:30:23 CST)
Simulation with ammonia
- AHMET BAKAN (Fri Jun 04 2004 - 17:23:39 CDT)
- AHMET BAKAN (Fri Jun 04 2004 - 15:01:04 CDT)
- Leandro Martinez (Fri Jun 04 2004 - 13:13:45 CDT)
- Marek Dynowski (Fri Jun 04 2004 - 10:53:27 CDT)
simulations ceased without any hint
- Brian Bennion (Fri Apr 16 2004 - 00:09:26 CDT)
- li (Thu Apr 15 2004 - 22:23:13 CDT)
Single point energy calculation
- Rad Balu (Mon May 31 2004 - 04:13:16 CDT)
- Ben Roberts (Sun May 30 2004 - 21:05:00 CDT)
Small Organic Compounds with NAMD
- AHMET BAKAN (Sat Oct 18 2003 - 18:40:37 CDT)
SMD -apply the force via Tcl script
- Taeho Kim (Tue Nov 04 2003 - 11:27:52 CST)
SMD and minimizations
- mdcooper (Tue Oct 26 2004 - 14:31:38 CDT)
SMD atoms not read properly!
- Vani Krishna (Tue Aug 10 2004 - 07:49:42 CDT)
SMD force
- Ioana Cozmuta (Sat Jan 03 2004 - 22:01:45 CST)
SMD force (fwd)
- Ioana Cozmuta (Tue Jan 06 2004 - 18:25:20 CST)
- Fangqiang Zhu (Tue Jan 06 2004 - 17:14:56 CST)
- Ioana Cozmuta (Mon Jan 05 2004 - 13:36:16 CST)
SMD on a group of atoms: Confusion
- Blake Charlebois (Fri Sep 03 2004 - 05:41:24 CDT)
- Vani Krishna (Wed Sep 01 2004 - 10:47:41 CDT)
SMD with different pH
- Brian Bennion (Wed Mar 10 2004 - 10:47:37 CST)
- Volodymyr Nechiporuk-Zloy (Wed Mar 10 2004 - 06:37:39 CST)
- Brian Bennion (Fri Mar 05 2004 - 10:16:09 CST)
- Volodymyr Nechiporuk-Zloy (Fri Mar 05 2004 - 07:52:55 CST)
SMD-velocity unit
- Ioana Cozmuta (Sat Jan 10 2004 - 18:24:18 CST)
SMD: constant velocity or force pulling?
- Ioana Cozmuta (Thu Oct 30 2003 - 21:02:54 CST)
SMD: Group of atoms COM fixed?
- Vani Krishna (Thu Sep 02 2004 - 20:58:44 CDT)
SMD: many atom pulling
- Harindar Keer (Thu Mar 04 2004 - 21:29:12 CST)
Solute KE
- Shantenu Jha (Thu Dec 04 2003 - 17:08:23 CST)
- Shantenu Jha (Thu Dec 04 2003 - 16:36:31 CST)
solvate
- Brian Bennion (Mon Nov 03 2003 - 11:27:56 CST)
- himanshu chandola (Sun Nov 02 2003 - 17:41:24 CST)
Solvate Package
- Satyavani Vemparala (Wed Mar 10 2004 - 18:22:54 CST)
solvent bands and periodic boundary conditions
- Stern, Julie (Wed May 19 2004 - 10:45:09 CDT)
Solvent mixture
- Ahmet Bakan (Fri Nov 05 2004 - 17:02:06 CST)
- Brian Bennion (Fri Nov 05 2004 - 16:53:11 CST)
- Edward Patrick Obrien (Fri Nov 05 2004 - 16:43:21 CST)
- Brian Bennion (Fri Nov 05 2004 - 15:40:47 CST)
- Josef Scheiber (Thu Nov 04 2004 - 02:29:17 CST)
some cluster questions
- Leandro Martinez (Wed Feb 18 2004 - 07:51:13 CST)
Some parameters
- AHMET BAKAN (Tue Dec 09 2003 - 06:06:50 CST)
Some question about Constraint~
- Îº¿ (Sun Nov 14 2004 - 21:02:34 CST)
something about the TIP3P water model
- Fangqiang Zhu (Thu Nov 27 2003 - 23:11:33 CST)
- PQCHEN (Wed Nov 26 2003 - 20:05:59 CST)
sorted out problem
- himanshu chandola (Fri Nov 14 2003 - 14:24:45 CST)
Source code for NAMD
- Satyavani Vemparala (Tue Feb 10 2004 - 10:30:13 CST)
Source file in the tutorial
- Xin Chen (Thu Apr 22 2004 - 16:58:46 CDT)
spherical boundary condition
- griadi_at_utalca.cl (Mon Nov 29 2004 - 02:29:51 CST)
- Giovanni Bellesia (Tue Nov 23 2004 - 07:35:17 CST)
Spherical Boundary Conditions
- Edward Patrick Obrien (Tue Oct 05 2004 - 16:14:12 CDT)
Spring Constant
- Uday Chippada (Mon Mar 29 2004 - 17:48:56 CST)
start fep calculation
- mashaojie163 (Fri Jun 11 2004 - 21:13:45 CDT)
statistical test
- Aaron Oakley (Wed Dec 15 2004 - 23:17:57 CST)
still problems with namdplot
- Gadi Oron (Sun Apr 18 2004 - 01:51:42 CDT)
- Cheri M Turman (Thu Apr 15 2004 - 14:13:57 CDT)
Stray PME grid charges
- Vani Krishna (Tue Sep 07 2004 - 21:16:35 CDT)
- Harindar Keer (Tue Sep 07 2004 - 13:42:39 CDT)
submitting a job in a queue
- Alex V. (Fri Jun 04 2004 - 13:46:18 CDT)
- Gengbin Zheng (Thu Jun 03 2004 - 11:33:25 CDT)
- Giovanni (Wed Jun 02 2004 - 10:55:37 CDT)
surface pressure/tension
- Erik Nordgren (Thu Sep 09 2004 - 13:56:27 CDT)
- nordgren_at_sas.upenn.edu (Sun Aug 22 2004 - 02:37:11 CDT)
Surface tension
- Adrian Wiley (Wed Mar 17 2004 - 10:43:37 CST)
Suse 9.0 or Fedora Core 1.0
- Alex V. (Fri Jul 02 2004 - 07:27:08 CDT)
- nalianarmen (Thu Jul 01 2004 - 23:37:18 CDT)
switch for equilibrisation
- Jim Phillips (Tue Oct 28 2003 - 18:11:33 CST)
- himanshu chandola (Wed Oct 22 2003 - 17:24:29 CDT)
switching SMD in execution script?
- barner_at_physik.hu-berlin.de (Tue Sep 21 2004 - 09:43:17 CDT)
Symmetry operations
- \ (Thu Sep 02 2004 - 21:44:39 CDT)
- Aaron Oakley (Tue Aug 24 2004 - 18:34:47 CDT)
- \ (Tue Aug 24 2004 - 13:58:19 CDT)
- Juan Carlos Mobarec (Mon Aug 23 2004 - 19:21:22 CDT)
- Brian Bennion (Mon Aug 23 2004 - 17:55:24 CDT)
- \ (Mon Aug 23 2004 - 16:42:22 CDT)
System minimization: fail after 199 steps
- Charles Danko (Fri Dec 10 2004 - 13:32:28 CST)
- Charles Danko (Thu Dec 09 2004 - 16:01:26 CST)
- Brian Bennion (Thu Dec 09 2004 - 12:19:20 CST)
- Charles Danko (Thu Dec 09 2004 - 11:20:26 CST)
- Brian Bennion (Tue Nov 23 2004 - 12:46:15 CST)
- Charles Danko (Mon Nov 15 2004 - 11:10:40 CST)
- Brian Bennion (Thu Nov 11 2004 - 10:18:49 CST)
- Charles Danko (Thu Nov 11 2004 - 10:07:00 CST)
- Brian Bennion (Tue Nov 09 2004 - 15:40:39 CST)
- Charles Danko (Tue Nov 09 2004 - 12:24:00 CST)
- Brian Bennion (Wed Nov 03 2004 - 13:05:56 CST)
- Charles Danko (Wed Nov 03 2004 - 11:53:06 CST)
- \ (Tue Nov 02 2004 - 13:22:50 CST)
- Brian Bennion (Tue Nov 02 2004 - 13:09:32 CST)
- Charles Danko (Tue Nov 02 2004 - 11:20:21 CST)
- Brian Bennion (Mon Nov 01 2004 - 17:56:32 CST)
- Charles Danko (Mon Nov 01 2004 - 16:30:12 CST)
Systems of > 100,000 atoms, *.psf files & *.crd files
- Brian Bennion (Wed May 12 2004 - 10:19:29 CDT)
- Crozier, Paul S (Tue May 11 2004 - 18:02:51 CDT)
TCBG "Hands-On" Workshop on Computational Biophysics in Boston, Dec. 5-9
- David P. Brandon (Tue Nov 02 2004 - 10:16:21 CST)
Tcl dihedral restraints in CG minimisation
- Jérôme Hénin (Tue Nov 02 2004 - 18:24:07 CST)
- Ben Roberts (Tue Nov 02 2004 - 17:01:28 CST)
tcl interface
- Jérôme Hénin (Thu Nov 13 2003 - 05:16:20 CST)
- C. Ecker (Thu Nov 13 2003 - 05:07:04 CST)
Tcl load
- Saladino, Alex (Thu Jul 15 2004 - 14:52:25 CDT)
Tcl loops in configuration files
- Streiff, John H. (Tue Sep 14 2004 - 10:26:12 CDT)
TCL question
- Gadi Oron (Sun Mar 14 2004 - 08:13:55 CST)
- Jim Phillips (Thu Jan 22 2004 - 16:52:35 CST)
- Ioana Cozmuta (Mon Jan 19 2004 - 16:41:52 CST)
tcl script for calculate RMS of MD calculation ?
- ying xiong (Sat May 01 2004 - 21:06:04 CDT)
tcl scripting interface in namd 2.5 for IBM-SP
- Jorge Pikunic (Mon Jun 28 2004 - 16:23:14 CDT)
TCL: can't use floating-point value as operand of "-"
- li (Mon Sep 27 2004 - 21:57:12 CDT)
- li (Mon Sep 27 2004 - 03:16:52 CDT)
TCL: getting forces
- Fangqiang Zhu (Fri Mar 05 2004 - 14:04:31 CST)
- Bartosz Dobrzelecki (Fri Mar 05 2004 - 04:58:31 CST)
Tcl: loadtotalforces
- Jérôme Hénin (Mon Mar 29 2004 - 07:33:29 CST)
- g srinivasa murthy (Mon Mar 29 2004 - 05:11:49 CST)
temp coupling coefficients
- Jérôme Hénin (Tue Mar 02 2004 - 15:39:24 CST)
- Hyonseok Hwang (Tue Mar 02 2004 - 13:18:22 CST)
- Jérôme Hénin (Tue Mar 02 2004 - 03:58:28 CST)
- Peter Jones (Tue Mar 02 2004 - 01:03:53 CST)
Temp in SMD
- Fangqiang Zhu (Sat Nov 29 2003 - 00:34:30 CST)
- taeho.kim_at_utoronto.ca (Fri Nov 28 2003 - 17:53:27 CST)
Temperature
- Edward Patrick Obrien (Mon Aug 30 2004 - 13:12:17 CDT)
- Raymond C. Fort Jr. (Mon Aug 30 2004 - 12:47:07 CDT)
Temperature control methods in NAMD
- Satyavani Vemparala (Sat Feb 14 2004 - 07:32:22 CST)
- Satyavani Vemparala (Wed Feb 11 2004 - 18:07:13 CST)
temperature control question
- Hyonseok Hwang (Sun Feb 08 2004 - 22:31:39 CST)
Temperature control?
- Gianluca Interlandi (Wed Apr 21 2004 - 10:32:14 CDT)
temperature coupling in NAMD
- Satyavani Vemparala (Tue Feb 24 2004 - 15:09:57 CST)
temperature question in logfile
- Brian Bennion (Tue Apr 20 2004 - 18:21:12 CDT)
- Cheri M Turman (Tue Apr 20 2004 - 17:13:28 CDT)
Temperature reassignment problem
- Kamp, Marc vander (Wed Jun 23 2004 - 05:13:34 CDT)
- Kamp, Marc vander (Mon Jun 21 2004 - 04:19:03 CDT)
temperature rescaling and canonical ensemble
- Blake Charlebois (Fri Oct 01 2004 - 01:15:05 CDT)
- Jan Lipfert (Thu Sep 30 2004 - 23:27:28 CDT)
tert-butylthiol CHARMM params
- Cosmin ROMAN (Mon Oct 27 2003 - 05:46:47 CST)
test and a short question!
- Fangqiang Zhu (Mon Jan 19 2004 - 15:15:15 CST)
- Vlad Cojocaru (Mon Jan 19 2004 - 08:18:50 CST)
Thank you
- Brian Bennion (Mon Sep 15 2003 - 23:43:52 CDT)
thankyou
- MinSoo Kim (Fri Jan 30 2004 - 12:54:32 CST)
the Atom velocity is beyond the limit?
- Fangqiang Zhu (Fri Nov 28 2003 - 23:44:19 CST)
- yxiong_at_mail.ccnu.edu.cn (Fri Nov 28 2003 - 03:33:03 CST)
the problem on segment a ligand in NAMD ?
- yxiong_at_mail.ccnu.edu.cn (Fri Nov 28 2003 - 02:02:24 CST)
- Fangqiang Zhu (Fri Nov 28 2003 - 00:41:19 CST)
- Brian Bennion (Fri Nov 28 2003 - 00:30:13 CST)
- yxiong_at_mail.ccnu.edu.cn (Thu Nov 27 2003 - 21:53:42 CST)
Thermostat problems
- Sarah Williams (Tue Jul 20 2004 - 04:13:19 CDT)
three-site carbon monoxide model
- Brian Bennion (Thu May 27 2004 - 17:12:22 CDT)
- ELENA JEAN LEVIN (Thu May 27 2004 - 16:40:11 CDT)
timeout on running namd
- Gengbin Zheng (Tue Mar 30 2004 - 13:23:15 CST)
- Amarda Shehu (Tue Mar 30 2004 - 12:09:02 CST)
Timestep in restart output
- Tim Isgro (Thu Feb 26 2004 - 21:01:21 CST)
- Brian Bennion (Thu Feb 26 2004 - 15:29:38 CST)
- Sichun Yang (Thu Feb 26 2004 - 12:38:08 CST)
TIP3P model
- Amit Paliwal (Wed Dec 17 2003 - 13:10:45 CST)
TIP5P
- Brian Bennion (Fri Feb 27 2004 - 13:39:04 CST)
- Aaron Oakley (Thu Feb 26 2004 - 18:40:22 CST)
To PME , Do the simulation need a neutral charged system?
- Jérôme Hénin (Tue Sep 21 2004 - 05:16:26 CDT)
- mashaojie163 (Tue Sep 21 2004 - 04:54:57 CDT)
too much rattle
- Amarda Shehu (Fri Feb 13 2004 - 12:24:12 CST)
- Brian Bennion (Fri Feb 13 2004 - 12:51:50 CST)
- Brian Bennion (Thu Feb 12 2004 - 16:50:30 CST)
- Amarda Shehu (Thu Feb 12 2004 - 16:16:40 CST)
top files for ligands
- Oliver Hucke (Wed Oct 08 2003 - 13:02:42 CDT)
Topology and parameters files for FAD cofator
- PQCHEN (Fri Nov 28 2003 - 04:04:55 CST)
topology file for compound
- Yanlong Xu (Mon Jul 26 2004 - 12:15:28 CDT)
Topology file for model compounds
- AHMET BAKAN (Tue Oct 14 2003 - 10:24:40 CDT)
torsion angle
- bora erdemli (Mon Sep 06 2004 - 06:18:22 CDT)
Torsion potential barrier (low?) in NAMD
- Vani Krishna (Wed Jul 28 2004 - 10:57:56 CDT)
Torsional barrier(adding parameters)
- Vani Krishna (Mon Aug 02 2004 - 10:11:48 CDT)
total energy stuck between two levels
- Jim Phillips (Wed Jan 07 2004 - 09:22:27 CST)
- Jérôme Hénin (Wed Jan 07 2004 - 02:42:33 CST)
- AMIT PALIWAL (Tue Jan 06 2004 - 22:20:10 CST)
truncated octahedron boundary conditions
- Mike Bradley (Wed Jul 21 2004 - 16:26:09 CDT)
Truncation errors.
- hansang bae (Mon Dec 29 2003 - 09:19:53 CST)
turning off fixed atoms in the middle of simulation
- Jim Phillips (Wed Dec 15 2004 - 11:15:47 CST)
- Vani Krishna (Wed Dec 15 2004 - 10:42:17 CST)
type of the water molecule
- Brian Bennion (Fri Jul 23 2004 - 11:55:57 CDT)
- bora erdemli (Fri Jul 23 2004 - 10:31:49 CDT)
undefined loops
- Brian Bennion (Thu Mar 18 2004 - 12:16:58 CST)
- Stern, Julie (Thu Mar 18 2004 - 11:47:39 CST)
uninitialized coordinates
- Brian Bennion (Mon Nov 10 2003 - 10:40:31 CST)
- himanshu chandola (Sun Nov 09 2003 - 02:22:35 CST)
Unit cell coordinates and radial distribution functions
- Ben Roberts (Mon Jul 19 2004 - 21:12:38 CDT)
Unit of force using Haptic in IMD
- Harit Jani (Fri May 14 2004 - 01:33:10 CDT)
Unwrap molecules
- Ekta Khurana (Sun Mar 21 2004 - 21:55:06 CST)
updating coordinates using IMD
- Fangqiang Zhu (Mon Dec 01 2003 - 11:47:08 CST)
- David E. Konerding (Wed Nov 26 2003 - 14:09:10 CST)
Urea and GdHCl parameters
- Ahmet Bakan (Mon Mar 15 2004 - 13:15:18 CST)
- Ruxandra Dima (Mon Mar 15 2004 - 12:01:51 CST)
urestraint
- Michael Grabe (Thu May 13 2004 - 16:24:35 CDT)
Urey-Bradley term
- Fangqiang Zhu (Wed Nov 19 2003 - 17:39:23 CST)
- Cosmin ROMAN (Wed Nov 19 2003 - 04:05:27 CST)
- Fangqiang Zhu (Tue Nov 18 2003 - 18:24:46 CST)
- Cosmin ROMAN (Tue Nov 18 2003 - 08:34:18 CST)
Urey-Bradley term?
- Gianluca Interlandi (Tue Jun 08 2004 - 12:29:34 CDT)
user-supplied conformational restraints
- Hyonseok Hwang (Thu Feb 05 2004 - 15:41:49 CST)
- Simon Sharpe (Thu Feb 05 2004 - 14:13:31 CST)
Using checkpoints in simulation
- himanshu chandola (Fri Apr 09 2004 - 19:41:18 CDT)
- Alex V. (Fri Apr 09 2004 - 05:08:35 CDT)
using restart files
- himanshu chandola (Fri Apr 09 2004 - 02:36:55 CDT)
- Ioana Cozmuta (Thu Apr 08 2004 - 14:59:26 CDT)
- Brian Bennion (Thu Apr 08 2004 - 10:00:01 CDT)
- himanshu chandola (Thu Apr 08 2004 - 18:00:14 CDT)
Vaccum simulation
- nordgren_at_sas.upenn.edu (Wed Dec 08 2004 - 15:57:10 CST)
- Narender Singh (Wed Dec 08 2004 - 10:57:48 CST)
Variation of results in iterations
- Blake Charlebois (Tue Dec 07 2004 - 20:12:18 CST)
- Edward Patrick Obrien (Mon Dec 06 2004 - 22:13:26 CST)
- Pijush Ghosh (Mon Dec 06 2004 - 22:00:21 CST)
- Robert Brunner (Mon Dec 06 2004 - 21:15:00 CST)
- Edward Patrick Obrien (Mon Dec 06 2004 - 19:37:43 CST)
- Jérôme Hénin (Mon Dec 06 2004 - 19:01:32 CST)
- Edward Patrick Obrien (Mon Dec 06 2004 - 17:44:43 CST)
- Pijush Ghosh (Mon Dec 06 2004 - 17:25:43 CST)
VMD problems
- Cesar Delgado (Mon Dec 01 2003 - 13:05:39 CST)
- Hua Wong (Mon Dec 01 2003 - 07:46:44 CST)
vmd-l: Autoionize plugin problem
- John Stone (Thu Dec 16 2004 - 11:30:21 CST)
vmd-l: bigdcd
- Ioana Cozmuta (Wed Nov 05 2003 - 18:29:25 CST)
- Brian Bennion (Wed Nov 05 2003 - 17:52:38 CST)
vmd-l: convert DCD files to GROMACS .XTC format
- John Stone (Tue Aug 31 2004 - 15:11:09 CDT)
vmd-l: how can I get hole program
- mashaojie163 (Sun Oct 10 2004 - 09:23:13 CDT)
vmd-l: incompatibility between VMD & NAMD for reading Amber crd files
- Kamp, Marc vander (Tue Jun 22 2004 - 04:20:16 CDT)
- John Stone (Mon Jun 21 2004 - 14:53:13 CDT)
- Kamp, Marc vander (Mon Jun 21 2004 - 14:39:05 CDT)
- John Stone (Mon Jun 21 2004 - 09:58:31 CDT)
vmd-l: POV-Ray
- Oscar Moran (Wed Nov 12 2003 - 03:49:31 CST)
vmd-l: Protonated GLU/ASP in PSF generation
- Justin Gullingsrud (Sun Aug 29 2004 - 21:01:52 CDT)
vmd-l: psfgen and xplor topology
- Charles McCallum (Tue Oct 26 2004 - 11:36:37 CDT)
vmd-l: PSFGEN problem
- Brian Bennion (Mon Oct 11 2004 - 11:19:56 CDT)
vmd-l: rmsd problem
- John Stone (Tue Aug 31 2004 - 15:11:47 CDT)
vmd-l: running vmd in batch mode
- John Stone (Thu Nov 06 2003 - 19:26:27 CST)
- Ioana Cozmuta (Thu Nov 06 2003 - 19:19:30 CST)
warning messages in psfgen
- tsaih_at_ncifcrf.gov (Wed Mar 24 2004 - 14:35:43 CST)
Warning: 1 margin violations
- li (Sun Feb 10 2008 - 15:12:43 CST)
Warning: 8 margin violations
- li (Sat Jan 05 2008 - 10:05:25 CST)
Warning: Not all atoms have unique coordinates.
- Shirley Hui (Thu Jul 08 2004 - 18:15:29 CDT)
- Shirley Hui (Thu Jul 08 2004 - 17:45:47 CDT)
- Brian Bennion (Thu Jul 08 2004 - 11:06:08 CDT)
- Shirley Hui (Thu Jul 08 2004 - 09:25:13 CDT)
warnings during NAMD simulations.
- li (Sat Feb 23 2008 - 08:43:42 CST)
- Lv Shouqin (Fri Feb 20 2004 - 06:25:12 CST)
water box
- Amit Paliwal (Tue Mar 30 2004 - 08:45:01 CST)
- Brian Bennion (Tue Mar 30 2004 - 12:36:30 CST)
- Amit Paliwal (Tue Mar 30 2004 - 06:03:30 CST)
water box is too small
- li (Mon Feb 11 2008 - 08:37:46 CST)
Weird dihedral error
- Brian Bennion (Mon Apr 19 2004 - 12:22:35 CDT)
- Brian Bennion (Tue Jan 27 2004 - 13:16:51 CST)
weird energies during minimization
- Brian Bennion (Fri Dec 19 2003 - 16:25:19 CST)
- Jim Phillips (Fri Dec 19 2003 - 16:23:36 CST)
- Brian Bennion (Fri Dec 19 2003 - 13:04:56 CST)
What binaries should I take?
- Gianluca Interlandi (Fri Jun 18 2004 - 08:38:39 CDT)
- Edward Patrick Obrien (Fri Jun 18 2004 - 08:18:38 CDT)
- Valodymyr Nechyporuk-Zloy (Fri Jun 18 2004 - 03:49:14 CDT)
What the result difference between AMD and Intel CPUS?
- Blake Charlebois (Mon Dec 20 2004 - 09:43:57 CST)
- Îº¿ (Mon Dec 20 2004 - 08:30:14 CST)
What, if no temperatue control specified?
- Jérôme Hénin (Fri Apr 23 2004 - 14:19:48 CDT)
- Brian Bennion (Fri Apr 23 2004 - 10:57:09 CDT)
- Gianluca Interlandi (Fri Apr 23 2004 - 03:59:45 CDT)
- Brian Bennion (Thu Apr 22 2004 - 12:02:41 CDT)
- Juan Alfredo Freites (Thu Apr 22 2004 - 11:54:16 CDT)
- Brian Bennion (Thu Apr 22 2004 - 10:20:05 CDT)
- Mike McCallum (Thu Apr 22 2004 - 09:43:13 CDT)
- Gianluca Interlandi (Thu Apr 22 2004 - 05:56:39 CDT)
Where to download the inorganic pdb file
- myang (Wed May 19 2004 - 14:02:49 CDT)
- Brian Bennion (Wed May 19 2004 - 10:20:11 CDT)
- myang (Wed May 19 2004 - 00:49:05 CDT)
where to find the force field parameters for F and P atom?
- yxiong_at_mail.ccnu.edu.cn (Tue Dec 09 2003 - 20:04:01 CST)
Which version MPICH-VMI does namd-ia64-vmi run on? intel compiled version or gcc complied version?
- Gengbin Zheng (Thu Dec 11 2003 - 16:08:08 CST)
- Jerry Ebalunode (Thu Dec 11 2003 - 03:11:03 CST)
Why "fixedAtomsForces on" for constant pressure?
- Jim Phillips (Wed Dec 03 2003 - 16:24:45 CST)
- Fangqiang Zhu (Tue Dec 02 2003 - 00:04:16 CST)
- Jan Saam (Tue Nov 25 2003 - 18:30:09 CST)
Why Vmd didn't show the Pt-Cl bond
- Edward Patrick Obrien (Wed May 19 2004 - 20:10:40 CDT)
- myang (Wed May 19 2004 - 18:46:31 CDT)
Working on cluster to do umbrella sampling
- Michael Grabe (Mon Nov 22 2004 - 13:47:14 CST)
- Enrico Piccinini (Fri Nov 19 2004 - 04:39:13 CST)
wrapping DCD files
- Vani Krishna (Mon Jun 28 2004 - 14:25:24 CDT)
Writing pdb file.. easier way?
- griadi_at_utalca.cl (Tue Nov 23 2004 - 12:44:03 CST)
- Jérôme Hénin (Thu Nov 18 2004 - 17:28:36 CST)
- Uday Chippada (Thu Nov 18 2004 - 17:19:14 CST)
- Neema Salimi (Thu Nov 18 2004 - 16:54:58 CST)
- LEWYN LI (Thu Nov 18 2004 - 16:29:36 CST)
- Uday Chippada (Thu Nov 18 2004 - 15:58:20 CST)
xplor to charmm
- EPF $Esben Peter Friis$ (Mon Nov 01 2004 - 15:21:08 CST)
xsc file reading and segmentation fault
- li (Sat Nov 06 2004 - 20:16:28 CST)
xsc information in the dcd file?
- Gianluca Interlandi (Thu Dec 16 2004 - 11:25:50 CST)
- Jérôme Hénin (Wed Dec 15 2004 - 12:22:39 CST)
- Gianluca Interlandi (Wed Dec 15 2004 - 10:57:26 CST)
Xserve G5
- Streiff, John H. (Fri Aug 27 2004 - 15:37:48 CDT)
xst format
- Fangqiang Zhu (Thu Nov 27 2003 - 23:27:34 CST)
- Zoe Cournia (Thu Nov 27 2003 - 04:17:44 CST)
your mail
- Brian Bennion (Sun Feb 22 2004 - 00:44:16 CST)
zinc parameter?
- Fangqiang Zhu (Mon Nov 17 2003 - 18:24:08 CST)
- yxiong_at_mail.ccnu.edu.cn (Sun Nov 16 2003 - 02:09:54 CST)

Last message date: Fri Dec 31 2004 - 13:16:29 CST
Archived on: Wed Feb 29 2012 - 15:38:07 CST

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