NAMD-L: By Subject

NAMD

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NAMD-L: By Subject

By Subject

16073 messages sorted by: [ author ] [ date ] [ thread ] [ attachment ]
About this archive

Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Wed Feb 29 2012 - 01:22:45 CST

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

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

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

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

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

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

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

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

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

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

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

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

Eduard Schreiner (Tue Jul 06 2010 - 16:21:53 CDT)

Chris Chipot (Sat Apr 17 2010 - 19:34:24 CDT)

Chris Harrison (Tue Mar 16 2010 - 23:58:40 CDT)

Axel Kohlmeyer (Tue Mar 16 2010 - 06:59:05 CDT)

Joshua D. Moore (Thu Jan 29 2009 - 10:01:28 CST)

Axel Kohlmeyer (Tue Jan 20 2009 - 09:03:51 CST)

Axel Kohlmeyer (Tue Dec 23 2008 - 10:22:51 CST)

Peter Freddolino (Tue Oct 23 2007 - 18:20:52 CDT)

Peter Freddolino (Tue Oct 23 2007 - 18:18:22 CDT)

David Hardy (Tue Oct 23 2007 - 18:09:50 CDT)

Peter Freddolino (Tue Oct 23 2007 - 14:54:38 CDT)

Peter Freddolino (Wed Dec 20 2006 - 13:59:28 CST)

Peter Freddolino (Sat Dec 09 2006 - 12:40:48 CST)

Arturas Ziemys (Thu Sep 28 2006 - 08:10:19 CDT)

Giovanni Bellesia (Thu Feb 23 2006 - 12:45:28 CST)

Leandro Martínez (Thu Feb 23 2006 - 11:45:04 CST)

Sterling Paramore (Thu Feb 23 2006 - 11:34:36 CST)

Michael Grabe (Fri Oct 21 2005 - 12:15:15 CDT)

Leandro Martínez (Fri Apr 08 2005 - 13:50:34 CDT)

Michael Grabe (Fri Apr 08 2005 - 12:31:36 CDT)

Michel Espinoza-Fonseca (Fri Apr 08 2005 - 12:27:54 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)

"-Wno-long-double" linking error
- Jim Phillips (Wed Dec 09 2009 - 18:05:25 CST)
- Axel Kohlmeyer (Wed Dec 09 2009 - 18:06:03 CST)
- David Tanner (Wed Dec 09 2009 - 14:24:14 CST)
"Adaptive" force direction in SMD?
- HAMON véronique (Tue Oct 03 2006 - 10:00:28 CDT)
"atoms moving too fast" error in bilayer simulation
- Himanshu Khandelia (Thu Feb 08 2007 - 15:04:12 CST)
- Peter Freddolino (Sun Feb 04 2007 - 08:15:38 CST)
- Himanshu Khandelia (Sun Feb 04 2007 - 06:11:03 CST)
- Peter Freddolino (Sat Feb 03 2007 - 08:38:58 CST)
- Himanshu Khandelia (Sat Feb 03 2007 - 01:21:35 CST)
- Peter Freddolino (Fri Feb 02 2007 - 09:29:44 CST)
- Himanshu Khandelia (Fri Feb 02 2007 - 07:31:53 CST)
"binaryoutput no" doesn't work
- Philipp Schoen1 (Wed Apr 11 2007 - 05:55:02 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)
"Constraint failure in RATTLE algorithm" when restart FEP
- Dong Luo (Mon Aug 01 2011 - 10:50:27 CDT)
- Dong Luo (Fri Jul 29 2011 - 14:36:44 CDT)
- Dong Luo (Thu Jul 28 2011 - 12:21:28 CDT)
"CWeb performance data sent to wrong processor..."
- Jon Halverson (Thu Jan 11 2007 - 15:47:57 CST)
"didn't find VdW parameter for atom type NH3" error
- Peter Freddolino (Tue Jun 29 2010 - 22:02:21 CDT)
- felmerino_at_uchile.cl (Tue Jun 29 2010 - 21:20:47 CDT)
- felmerino_at_uchile.cl (Tue Jun 29 2010 - 20:34:07 CDT)
- Peter Freddolino (Tue Jun 29 2010 - 13:17:44 CDT)
- Emily Chen (Tue Jun 29 2010 - 07:06:33 CDT)
"FATAL ERROR: Bad global improper count" revisited
- johan strumpfer (Tue Mar 22 2011 - 12:41:42 CDT)
- Markus K. Dahlgren (Tue Mar 22 2011 - 10:42:49 CDT)
"gradient tolerance" for minimization
- Jim Phillips (Thu Jul 22 2010 - 14:52:07 CDT)
- Parisa Akhski (Thu Jul 22 2010 - 11:29:19 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)
"GroupPressure no" resulting in negative pressure outputs
- Sebastian Stolzenberg (Thu Dec 02 2010 - 10:46:45 CST)
- Jérôme Hénin (Mon Nov 29 2010 - 10:26:16 CST)
- Sebastian Stolzenberg (Fri Nov 26 2010 - 13:03:56 CST)
- Jérôme Hénin (Thu Nov 25 2010 - 14:56:08 CST)
- Sebastian Stolzenberg (Thu Nov 25 2010 - 13:51:13 CST)
"Hands-On" Workshop on Computational Biophysics
- David Brandon (Fri Mar 11 2005 - 15:23:27 CST)
"Hands-On" Workshop on Computational Biophysics, July 6-10 and August 10-14, 2009
- TCBG Workshop (Thu Feb 05 2009 - 15:52:30 CST)
"Hands-On" Workshop on Computational Biophysics, March 21-25, 2011, Atlanta, GA, USA
- David Brandon (Tue Dec 21 2010 - 14:34:17 CST)
"Hands-On" Workshop on Computational Biophysics, November 1-5, 2010 & November 29-December 3, 2010 in Urbana, IL
- TCBG Workshops (Thu Aug 12 2010 - 17:04:39 CDT)
"make" Linux-amd64-g++ error
- Xiaoqing Wang (Mon May 16 2005 - 09:08:03 CDT)
- Xiaoqing Wang (Mon May 16 2005 - 07:45:38 CDT)
- Xiaoqing Wang (Sun May 15 2005 - 22:31:47 CDT)
"measure" command
- Jerome Henin (Wed Sep 27 2006 - 19:30:44 CDT)
- Dhiraj Srivastava (Wed Sep 27 2006 - 17:56:50 CDT)
"Not all atoms have unique coordinates"
- Marcos Sotomayor (Fri Jan 05 2007 - 13:39:17 CST)
- Neelanjana Sengupta (Fri Jan 05 2007 - 13:16:40 CST)
- Ana Celia Araujo Vila Verde (Fri Jan 05 2007 - 12:58:23 CST)
- Nitin Bhardwaj (Fri Jan 05 2007 - 12:31:18 CST)
"reinitvel" parameter in config file
- Dhiraj Srivastava (Thu Oct 12 2006 - 13:03:38 CDT)
- Lewyn Li (Thu Oct 12 2006 - 08:12:12 CDT)
- Ana Celia Araujo Vila Verde (Thu Oct 12 2006 - 07:50:30 CDT)
- Dhiraj Srivastava (Wed Oct 11 2006 - 18:34:21 CDT)
"RESTARTING CONJUGATE GRADIENT ALGORITHM"
- Peter Freddolino (Wed May 02 2007 - 20:15:32 CDT)
- Ugur Akgun (Wed May 02 2007 - 11:14:10 CDT)
"Segmentation violation" on running namd2.6b1
- Dong Luo (Mon Sep 19 2005 - 13:09:38 CDT)
- Dong Luo (Mon Sep 19 2005 - 10:36:30 CDT)
"Timeout waiting for node-program to connect" error, only sometimes
- Himanshu Khandelia (Wed May 09 2007 - 02:58:29 CDT)
"Unknown pragma ivdep and pragma vector" errors when compiling on BlueGene
- Joshua D. Moore (Fri Feb 02 2007 - 21:09:23 CST)
- Joshua D. Moore (Thu Feb 01 2007 - 23:29:59 CST)
"Warning" meaning
- Cosseddu, Salvatore (Mon Feb 27 2012 - 13:55:50 CST)
"within" command in NAMD?
- Sebastian Stolzenberg (Mon Jan 05 2009 - 14:20:51 CST)
"wrapAll on" with a complex
- Jerome Henin (Thu Oct 05 2006 - 22:08:18 CDT)
- Gianluca Interlandi (Tue Oct 03 2006 - 00:01:37 CDT)
# of processors
- Gengbin Zheng (Mon Apr 05 2004 - 00:41:44 CDT)
- Neema Salimi (Mon Mar 29 2004 - 13:02:30 CST)
#QNAN: Please help!
- Peter Freddolino (Thu Jul 20 2006 - 08:22:35 CDT)
- a-yermakova_at_northwestern.edu (Wed Jul 19 2006 - 14:09:40 CDT)
'cutting' colvars.traj file
- Bjoern Olausson (Tue May 03 2011 - 08:34:21 CDT)
- Branko (Tue May 03 2011 - 06:41:34 CDT)
- Branko (Tue May 03 2011 - 05:55:42 CDT)
- Bjoern Olausson (Tue May 03 2011 - 05:45:23 CDT)
- Bjoern Olausson (Wed Apr 27 2011 - 05:53:41 CDT)
- Branko (Sat Apr 23 2011 - 13:07:20 CDT)
- Wang Yi (Sat Apr 23 2011 - 12:54:15 CDT)
- Branko (Sat Apr 23 2011 - 12:28:58 CDT)
'dSmooth' no longer in the ABF procedure?
- Hugh Martin (Wed Dec 09 2009 - 10:44:45 CST)
- Jérôme Hénin (Wed Dec 09 2009 - 10:25:14 CST)
- Hugh Martin (Wed Dec 09 2009 - 09:08:30 CST)
'firsttimestep' treated as signed integer ?
- Nicholas M Glykos (Mon Aug 22 2011 - 12:01:26 CDT)
'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, February 11-15, 2012 in Urbana, Illinois
- David Brandon (Thu Nov 17 2011 - 13:46:56 CST)
'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 17-21, 2011, Bremen, Germany
- David Brandon (Fri Jul 29 2011 - 14:13:05 CDT)
(Infiniband-related?) NAMD 2.7b2 (ibverbs x86_64) runtime error during a MD run
- Pietro Amodeo (Tue Jan 19 2010 - 05:03:21 CST)
(is there) a dependence of dynamics on WRAPPING
- Giacomo Fiorin (Sat Aug 15 2009 - 08:59:46 CDT)
- satya work (Sat Aug 15 2009 - 01:33:26 CDT)
(NAMD2.7b1) loadtotalforces gives output even when there are no forces in system
- Aoife Fogarty (Tue Mar 15 2011 - 13:15:04 CDT)
- Hugh Heldenbrand (Mon Mar 07 2011 - 07:10:09 CST)
- Aoife Fogarty (Mon Mar 07 2011 - 03:43:14 CST)
(no subject)
- Madhulika Gupta (Tue Jan 24 2012 - 23:08:52 CST)
- Basak Isin (Mon Jan 23 2012 - 01:16:45 CST)
- ÐìÖÓºÓ (Mon Jan 02 2012 - 03:03:31 CST)
- Chandra Ramananjara (Tue Nov 22 2011 - 12:31:08 CST)
- Gabriel Jara (Tue Nov 22 2011 - 06:59:12 CST)
- Chandra Ramananjara (Tue Nov 22 2011 - 06:53:15 CST)
- Gurunath Katagi (Thu Nov 03 2011 - 03:01:19 CDT)
- Gurunath Katagi (Thu Nov 03 2011 - 03:00:22 CDT)
- Buddhadev Maiti (Fri Oct 28 2011 - 22:14:30 CDT)
- Axel Kohlmeyer (Tue Aug 23 2011 - 09:37:15 CDT)
- David Rogers (Mon Aug 22 2011 - 20:25:04 CDT)
- Andrea Holfelder (Thu Aug 18 2011 - 04:59:05 CDT)
- Anna James (Tue Aug 16 2011 - 08:38:14 CDT)
- Chandra Ramananjara (Sun May 15 2011 - 12:32:07 CDT)
- Chandra Ramananjara (Thu May 12 2011 - 19:58:21 CDT)
- Chandra Ramananjara (Sun May 08 2011 - 09:37:04 CDT)
- Chandra Ramananjara (Sat May 07 2011 - 14:00:37 CDT)
- Nicolas Sapay (Tue May 03 2011 - 11:51:42 CDT)
- David Rogers (Mon Apr 11 2011 - 22:26:09 CDT)
- Erik Nordgren (Mon Apr 11 2011 - 21:38:33 CDT)
- Buddhadev Maiti (Mon Apr 11 2011 - 14:27:13 CDT)
- Buddhadev Maiti (Fri Apr 08 2011 - 10:45:19 CDT)
- Alexandra Nemkevich (Thu Feb 03 2011 - 04:30:50 CST)
- Chen, Zhihong (chenz2) (Wed Jan 05 2011 - 18:43:15 CST)
- ipsita basu (Fri Oct 08 2010 - 06:00:41 CDT)
- fereshteh moradi (Wed Sep 22 2010 - 04:59:49 CDT)
- Zhang, Jiong (MU-Student) (Tue Sep 21 2010 - 20:01:38 CDT)
- Aakash C R (Sat Aug 28 2010 - 04:35:48 CDT)
- fereshteh moradi (Sun Aug 01 2010 - 23:25:34 CDT)
- Melanie Santos Marrero (Tue Jul 06 2010 - 15:35:18 CDT)
- Jun Zhang (Mon Jun 21 2010 - 08:13:01 CDT)
- Mert Gür (Mon May 17 2010 - 16:11:22 CDT)
- å¼ é‹† (Fri Apr 16 2010 - 22:04:17 CDT)
- #SHEPHERDSON IGNATIUS MARK# (Fri Apr 09 2010 - 20:24:37 CDT)
- Daniel Hornburg (Tue Mar 16 2010 - 07:17:02 CDT)
- Daniel Hornburg (Tue Mar 16 2010 - 06:19:40 CDT)
- Jim Parker (Thu Dec 03 2009 - 21:48:51 CST)
- Jim Parker (Thu Dec 03 2009 - 07:13:58 CST)
- l.mammucari_at_tin.it (Mon Nov 02 2009 - 15:47:14 CST)
- Luca M. (Mon Nov 02 2009 - 14:33:36 CST)
- Jim Phillips (Tue Sep 08 2009 - 17:21:54 CDT)
- Sujata Sovani (Tue Jul 28 2009 - 17:02:30 CDT)
- Wang,Ying (Wed May 06 2009 - 13:50:12 CDT)
- gurunath katagi (Fri Feb 20 2009 - 06:08:37 CST)
- gurunath katagi (Thu Feb 12 2009 - 03:13:47 CST)
- gurunath katagi (Wed Feb 11 2009 - 10:49:16 CST)
- OZGE ENGIN (Wed Jan 28 2009 - 03:29:03 CST)
- gurunath katagi (Tue Jan 20 2009 - 08:25:06 CST)
- karthik s (Tue Dec 23 2008 - 00:07:39 CST)
- CHINDEA Vlad (Thu Dec 11 2008 - 06:12:05 CST)
- Bertrand P. S. Russell (Sat Nov 01 2008 - 20:50:16 CDT)
- CHINDEA Vlad (Sun Oct 05 2008 - 15:27:31 CDT)
- Rudra Banerjee (Thu Oct 02 2008 - 23:01:25 CDT)
- Ariovaldo de Souza Junior (Fri Jun 20 2008 - 05:27:36 CDT)
- feng jack (Fri May 30 2008 - 16:04:44 CDT)
- me01136_at_cc.uoi.gr (Fri Mar 07 2008 - 12:29:57 CST)
- jfgaff_at_ncsu.edu (Sat Dec 22 2007 - 08:30:16 CST)
- cgji (Fri Nov 09 2007 - 02:43:27 CST)
- Demet Akten (Tue Nov 06 2007 - 03:26:52 CST)
- ramya narasimhan (Tue Oct 23 2007 - 00:45:16 CDT)
- mashaojienuaa (Fri Jun 29 2007 - 08:52:35 CDT)
- Raul Araya Secchi (Tue Jun 12 2007 - 16:10:48 CDT)
- Maxim Karachevtsev (Fri Feb 02 2007 - 02:00:12 CST)
- Marcelo Puiatti (Wed Dec 20 2006 - 12:30:55 CST)
- Nicolas SAPAY (Fri Dec 08 2006 - 16:40:54 CST)
- a-yermakova_at_northwestern.edu (Fri Jul 21 2006 - 15:04:47 CDT)
- Peter Freddolino (Wed Jul 12 2006 - 14:15:06 CDT)
- LEWYN LI (Wed Jul 12 2006 - 14:00:37 CDT)
- a-yermakova_at_northwestern.edu (Wed Jul 12 2006 - 11:46:35 CDT)
- Peter Freddolino (Mon Jul 10 2006 - 20:15:33 CDT)
- JC Gumbart (Mon Jul 10 2006 - 20:11:31 CDT)
- Richard Wood (Mon Jul 10 2006 - 19:58:12 CDT)
- Mark Abraham (Mon Jul 10 2006 - 18:52:23 CDT)
- a-yermakova_at_northwestern.edu (Mon Jul 10 2006 - 12:50:19 CDT)
- Michael Grabe (Mon Jun 12 2006 - 20:38:48 CDT)
- Michael Grabe (Tue Feb 28 2006 - 20:37:42 CST)
- Michael Grabe (Wed Feb 22 2006 - 19:47:43 CST)
- Xiuping Tao (Thu Feb 16 2006 - 15:49:52 CST)
- Michael Grabe (Thu Oct 27 2005 - 22:39:35 CDT)
- Shahid Qamar (Fri Oct 21 2005 - 11:20:08 CDT)
- Michael Grabe (Wed Oct 19 2005 - 19:09:19 CDT)
- Michael Grabe (Wed Oct 19 2005 - 14:53:14 CDT)
- Giovanni Bellesia (Thu Aug 11 2005 - 15:50:38 CDT)
- Wei Chen (Wed Apr 27 2005 - 11:04:07 CDT)
- valesrdp (Thu Apr 21 2005 - 03:54:58 CDT)
- Michael Grabe (Fri Apr 08 2005 - 12:04:37 CDT)
- 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)
(solved) charmrun: ssh_exchange_identification: Connection closed by remote host
- Leandro Martínez (Fri Sep 02 2011 - 14:44:24 CDT)
(Á¦¸ñ ¾øÀ½)
- Taeho Kim (Wed Feb 11 2009 - 22:29:19 CST)
(âÅÚ ÔÅÍÙ)
- I. Vyalov (Wed Sep 29 2010 - 04:46:48 CDT)
* CGtool force field *
- HAMID - (Wed Oct 26 2011 - 08:47:39 CDT)
- Axel Kohlmeyer (Sun Oct 23 2011 - 16:16:47 CDT)
- HAMID - (Sun Oct 23 2011 - 03:09:03 CDT)
- Chris Harrison (Sat Oct 22 2011 - 17:02:37 CDT)
- Axel Kohlmeyer (Sat Oct 22 2011 - 14:36:38 CDT)
- HAMID - (Sat Oct 22 2011 - 14:11:14 CDT)
- Axel Kohlmeyer (Sat Oct 22 2011 - 12:47:47 CDT)
- HAMID - (Sat Oct 22 2011 - 12:00:19 CDT)
*** topology file for AMP? ***
- Daniel Keedy (Tue Mar 06 2007 - 15:50:56 CST)
***** SPAM POSSIBLE ***** Warning: Not all atoms have unique coordinates.
- Jérôme Hénin (Thu Jul 08 2004 - 11:01:54 CDT)
*.dcd and *.dcd.BAK
- dora guzman (Sun Jul 29 2007 - 15:46:28 CDT)
- L. Michel Espinoza-Fonseca (Sun Jul 29 2007 - 13:39:50 CDT)
- Per Jr. Greisen (Sun Jul 29 2007 - 10:08:04 CDT)
+1 offset to VMD index file?
- Giacomo Fiorin (Tue Apr 28 2009 - 11:19:58 CDT)
- Jerome Henin (Tue Apr 28 2009 - 11:13:38 CDT)
- DimitryASuplatov (Tue Apr 28 2009 - 08:40:33 CDT)
, Build your vocab (word power)-Get emails daily Fr.ee
- Deepesh (Thu Jun 26 2008 - 00:02:52 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)
------------- Processor 0 Exiting: Called CmiAbort ------------
- jestin mandumpal (Thu Sep 13 2007 - 02:57:50 CDT)
.colvars.state file in ABF
- Jérôme Hénin (Wed Jan 05 2011 - 07:15:45 CST)
- Parisa Akhski (Tue Jan 04 2011 - 15:51:09 CST)
- Alex Liu (Mon Jan 03 2011 - 15:53:45 CST)
.COOR TO PDB FILE
- Ehsan Ban (Sat Aug 13 2011 - 02:47:27 CDT)
- JC Gumbart (Sat Aug 13 2011 - 01:29:04 CDT)
- Babban Mia (Sat Aug 13 2011 - 01:11:48 CDT)
.inter.bin files?
- Chao Mei (Thu Apr 02 2009 - 13:05:11 CDT)
- Joachim Hein (Thu Apr 02 2009 - 10:24:20 CDT)
.psf and .params files for IMD
- Harit Jani (Wed Dec 10 2003 - 19:08:54 CST)
.xsc file and .restart.xsc file
- lily jin (Tue Oct 09 2007 - 12:06:22 CDT)
0 coordinates for LES atoms in pdb file after solvation
- arijit_r_at_chem.iitkgp.ernet.in (Thu Jan 25 2007 - 22:11:04 CST)
- Dhiraj Srivastava (Thu Jan 25 2007 - 11:24:16 CST)
- arijit_r_at_chem.iitkgp.ernet.in (Thu Jan 25 2007 - 03:11:44 CST)
- Dhiraj Srivastava (Thu Jan 25 2007 - 01:45:32 CST)
1 D Periodic Boundary
- Xiongce Zhao (Tue Feb 15 2005 - 14:43:42 CST)
1-4 interactions scaling
- Peter Freddolino (Wed Oct 05 2005 - 22:15:36 CDT)
- Mauricio Carrillo Tripp (Mon Oct 03 2005 - 14:30:00 CDT)
1-4 pair generation
- David Hardy (Thu Sep 02 2010 - 13:30:57 CDT)
- Jianhui Tian (Thu Sep 02 2010 - 13:12:42 CDT)
128 core namd job fails to run
- Sangamesh B (Tue Aug 12 2008 - 10:14:03 CDT)
128+ proccessor jobs on 64bit Widows hang upon completion of the simulation.
- Ilya Chorny (Mon Jul 30 2007 - 16:36:02 CDT)
- Eric Bohm (Mon Jul 30 2007 - 10:26:01 CDT)
- Eric Bohm (Mon Jul 30 2007 - 11:13:09 CDT)
- Eric Bohm (Mon Jul 30 2007 - 08:09:28 CDT)
- Ilya Chorny (Mon Jul 30 2007 - 10:46:48 CDT)
- Ilya Chorny (Mon Jul 30 2007 - 10:22:59 CDT)
- Ilya Chorny (Mon Jul 30 2007 - 10:19:15 CDT)
- Ilya Chorny (Sun Jul 29 2007 - 22:54:57 CDT)
1QSU
- Tim Isgro (Thu Jan 15 2004 - 15:32:22 CST)
- Uday Chippada (Thu Jan 15 2004 - 13:45:03 CST)
1us simulation of 80k atom system -- how much gross structure movement is expected?
- Branko (Tue Jul 20 2010 - 07:58:01 CDT)
- Andrew Emerson (Tue Jul 20 2010 - 05:09:05 CDT)
- Peter Freddolino (Mon Jul 19 2010 - 20:52:48 CDT)
- Axel Kohlmeyer (Mon Jul 19 2010 - 21:03:22 CDT)
- Ian Stokes-Rees (Mon Jul 19 2010 - 20:06:05 CDT)
- Peter Freddolino (Mon Jul 19 2010 - 18:52:20 CDT)
- Francesco Oteri (Mon Jul 19 2010 - 13:39:54 CDT)
- Ian Stokes-Rees (Mon Jul 19 2010 - 12:18:55 CDT)
2 dimension PBC
- politr_at_huji.ac.il (Tue Jul 01 2008 - 07:15:29 CDT)
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)
2 molecule pair interactions
- Ben Chern (Wed Apr 16 2008 - 23:49:33 CDT)
- Peter Freddolino (Wed Apr 16 2008 - 17:11:52 CDT)
- Arturas Ziemys (Wed Apr 16 2008 - 16:26:27 CDT)
2 pdb files
- Peter Freddolino (Fri May 09 2008 - 07:15:00 CDT)
- Christine Horejs DI (Fri May 09 2008 - 06:58:01 CDT)
2 proteins
- L. Michel Espinoza-Fonseca (Tue Apr 17 2007 - 05:30:02 CDT)
- Christine Horejs (Tue Apr 17 2007 - 04:59:11 CDT)
2 Stray PME grid charges detected possible bug 2.7b2
- Jim Phillips (Wed Oct 13 2010 - 09:33:24 CDT)
- Branko (Sun Oct 10 2010 - 11:12:09 CDT)
2-D periodic boundary condition
- Rahul Bhownik (Fri Oct 12 2007 - 13:00:09 CDT)
2.6b1 source missing file
- Jim Phillips (Fri Aug 05 2005 - 10:42:38 CDT)
- Dow_Hurst (Tue Aug 02 2005 - 16:58:30 CDT)
2.7b metadynamics ::alpha module :: folding of a single helix in water
- Giacomo Fiorin (Mon Jul 27 2009 - 11:52:44 CDT)
- Ali Emileh (Wed Jul 22 2009 - 21:18:11 CDT)
- Giacomo Fiorin (Wed Jun 10 2009 - 08:57:38 CDT)
- Ali Emileh (Tue Jun 09 2009 - 18:02:12 CDT)
- Giacomo Fiorin (Tue Jun 09 2009 - 12:24:39 CDT)
- Ali Emileh (Tue Jun 09 2009 - 11:52:19 CDT)
- Giacomo Fiorin (Fri Jun 05 2009 - 10:53:48 CDT)
- Ali Emileh (Tue Jun 02 2009 - 18:39:25 CDT)
2.7b metadynamics ::hBond component :: folding of a single helix in water
- Giacomo Fiorin (Mon Jun 22 2009 - 15:18:52 CDT)
- Ali Emileh (Mon Jun 22 2009 - 14:23:57 CDT)
2.7b1 + CUDA + STMV
- Peter Freddolino (Tue Apr 21 2009 - 09:41:56 CDT)
- Charles Taylor (Tue Apr 21 2009 - 09:25:44 CDT)
2CPU+1GPU vs 1CPU+2GPU
- Ajasja LjubetiÄ (Mon Feb 13 2012 - 09:08:30 CST)
- Aron Broom (Mon Feb 13 2012 - 08:26:30 CST)
- Nicholas M Glykos (Mon Feb 13 2012 - 05:44:59 CST)
- Marcel UJI (IMAP) (Mon Feb 13 2012 - 05:21:18 CST)
2D Ewald summation
- Xiongce Zhao (Thu Aug 10 2006 - 10:08:46 CDT)
2D periodic boundary condn & PME
- Harindar Keer (Tue Jun 17 2008 - 14:12:28 CDT)
32 bit + 64 bit mixed architecture problem
- Axel Kohlmeyer (Thu Nov 12 2009 - 10:12:36 CST)
- Axel Kohlmeyer (Wed Nov 11 2009 - 12:08:02 CST)
- Yogesh Aher (Wed Nov 11 2009 - 10:17:27 CST)
32 vs. 64 bits
- Leandro Martinez (Fri May 14 2004 - 08:07:14 CDT)
4 sequential jobs work on laptops, but only first one works on supercomputer
- JT (Tue Apr 14 2009 - 01:24:25 CDT)
- JT (Mon Apr 13 2009 - 23:12:06 CDT)
- JT (Mon Apr 13 2009 - 21:59:23 CDT)
- JT (Mon Apr 13 2009 - 22:02:54 CDT)
- JT (Mon Apr 13 2009 - 18:00:49 CDT)
4 x Opteron 12-core or 4 x Xeon 8-core ?
- David McGiven (Thu Jan 20 2011 - 05:59:13 CST)
4th Annual Workshop on Charm++ and its Applications 2005
- Jim Phillips (Fri Aug 05 2005 - 17:40:30 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 bit NAMD on AIX and CatDCD
- Joshua D. Moore (Sat Jan 21 2006 - 13:22:11 CST)
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)
99999999.9999 as vander waals energy
- Uma Mageshwari (Sat Jul 11 2009 - 00:18:19 CDT)
<no subject>
- Grabe, Michael David (Mon Jul 16 2007 - 14:49:23 CDT)
- Brian Bennion (Thu Feb 26 2004 - 14:44:07 CST)
- klsale (Thu Feb 26 2004 - 13:02:36 CST)
=20=20How=20to=20compile=20NAMD?= 2.6 on core2 operons, x86_64-redhat-linux,which isqthe=20proper=20choice=20in=20Arch.?=
- xiaojing gong (Wed May 16 2007 - 01:42:59 CDT)
=20=20nodelist=20being=20ignore?= d during paralleling
- cong chen (Sun Apr 27 2008 - 21:50:34 CDT)
=20?= qHow=20to=20compile=20NAMD2.6=20on=20core2=20operons,=20x86=5F?= 64-redhat-linux,which is the proper choice in Arch .?=
- xiaojing gong (Fri May 18 2007 - 19:28:14 CDT)
=20?= qhow=20to=20constrain=20a=20dihedral=20angle=3F?=
- xiaojing gong (Wed Mar 29 2006 - 06:31:46 CST)
=20How=20to=20build=20charm++=20on=20c?= ore2 processor
- xiaojing gong (Thu Apr 12 2007 - 09:09:58 CDT)
> 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)
??: compilation of namd
- TAO WANG (Fri May 06 2011 - 00:56:41 CDT)
[***** SPAM *****] About APBS calculation
- Elsa Fernanda de Sousa Henriques (Fri Oct 30 2009 - 04:40:20 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: HD speed ??]
- Mark Abraham (Sun Apr 30 2006 - 12:28:04 CDT)
[Fwd: increasing RMSD after 2 ns minimization-equilibration]
- Mark Abraham (Wed Feb 08 2006 - 19:14:08 CST)
- dora guzman (Wed Feb 08 2006 - 17:05:51 CST)
[Fwd: SMD of titin domain]
- Mu Gao (Wed Feb 08 2006 - 19:23:29 CST)
- dora guzman (Wed Feb 08 2006 - 17:05:34 CST)
[Fwd: Specific Heat Calculation with VMD]
- Ayþe Özlem Sezerman (Fri May 26 2006 - 09:29:31 CDT)
[Fwd: total energy stuck between two levels]
- Amit Paliwal (Wed Jan 07 2004 - 05:10:03 CST)
[off topic] The mailing list's mailer ...
- Nicholas M Glykos (Wed Sep 09 2009 - 12:50:58 CDT)
[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)
[ppl] Compliling NAMD in RedHat
- Phil Miller (Tue Aug 02 2011 - 10:10:18 CDT)
[ppl] error compiling charm-6.2.2 for bluegenep-xlc
- Phil Miller (Wed Oct 27 2010 - 23:14:34 CDT)
- Hannes Loeffler (Thu Oct 28 2010 - 04:18:33 CDT)
[ppl] Help Regarding NAMD Application Testing
- Phil Miller (Mon Mar 21 2011 - 09:00:13 CDT)
[ppl] NAMD at linux on sparc
- Phil Miller (Sun Feb 06 2011 - 21:18:32 CST)
[ppl] Regarding Compiling in Redhat linux.
- Phil Miller (Wed Aug 03 2011 - 09:30:01 CDT)
_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)
_NAMD_crashes?= on winx64 during parallel run.
- Alexandre A. Vakhrouchev (Sun Jul 29 2007 - 00:42:38 CDT)
A "strange" observation during ColVar calculations
- Jérôme Hénin (Mon Mar 28 2011 - 09:51:21 CDT)
- Jérôme Hénin (Mon Mar 28 2011 - 08:33:42 CDT)
- Wang Yi (Mon Mar 28 2011 - 08:40:51 CDT)
- Wang Yi (Tue Mar 22 2011 - 12:54:29 CDT)
- Jérôme Hénin (Tue Mar 22 2011 - 11:30:56 CDT)
- Wang Yi (Mon Mar 21 2011 - 15:58:17 CDT)
- Giacomo Fiorin (Mon Mar 21 2011 - 15:46:27 CDT)
- Wang Yi (Mon Mar 21 2011 - 13:49:45 CDT)
a basic question
- Tamal Banerjee (Sun May 07 2006 - 12:04:31 CDT)
A basic question?
- Jerome Henin (Thu Sep 06 2007 - 09:04:16 CDT)
- Dr. Tamal Banerjee (Thu Sep 06 2007 - 05:33:09 CDT)
A beginner's question for using NAMD to do cell membrane simulation and molecular transportation
- Ramya Gamini (Sat Feb 21 2009 - 15:34:24 CST)
- Xu Dong (Sat Feb 21 2009 - 14:23:49 CST)
a bundle of coor files
- Massimiliano Porrini (Tue Jul 05 2011 - 10:34:16 CDT)
- Massimiliano Porrini (Sat Jul 02 2011 - 20:16:05 CDT)
- Rajan Vatassery (Sat Jul 02 2011 - 16:26:32 CDT)
- Massimiliano Porrini (Sat Jul 02 2011 - 13:21:56 CDT)
A confused question on amber param and in charmm form~
- Îº¿ (Fri Nov 26 2004 - 07:41:55 CST)
a cv-smd puzzle
- charlie (Thu Dec 16 2010 - 10:09:55 CST)
- Charlie (Thu Dec 16 2010 - 09:21:43 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 difficult problem to explain the SMD force difference
- Lewyn Li (Thu Feb 21 2008 - 06:59:26 CST)
- Shulin Zhuang (Wed Feb 20 2008 - 22:36:15 CST)
a display problem
- L. Michel Espinoza-Fonseca (Thu Mar 09 2006 - 10:53:08 CST)
- lily jin (Thu Mar 09 2006 - 10:22:57 CST)
a error during install charm-5.9
- snowyowls (Tue Jun 06 2006 - 08:13:49 CDT)
- snowyowls (Mon Jun 05 2006 - 18:45:14 CDT)
a gap in flowing water
- fereshteh moradi (Tue May 11 2010 - 06:45:31 CDT)
A namd2.8b1 bug ?
- Jim Phillips (Tue May 10 2011 - 21:02:49 CDT)
- charlie (Wed Apr 27 2011 - 02:23:56 CDT)
a name quesiton
- Leonardo G. Trabuco (Sat Apr 08 2006 - 14:34:11 CDT)
- Sterling Paramore (Sat Apr 08 2006 - 14:13:35 CDT)
- Leonardo G. Trabuco (Sat Apr 08 2006 - 13:15:56 CDT)
- lily jin (Fri Apr 07 2006 - 11:19:41 CDT)
A newer version of win32 libraries
- Ajasja LjubetiÄ (Tue May 10 2011 - 15:55:06 CDT)
- Jim Phillips (Tue May 10 2011 - 14:39:25 CDT)
- Ajasja LjubetiÄ (Mon May 09 2011 - 07:35:47 CDT)
a philosophical question...
- dstrahs_at_pace.edu (Mon Feb 19 2007 - 20:57:31 CST)
- Richard Wood (Mon Feb 19 2007 - 18:19:46 CST)
- Jerome Henin (Mon Feb 19 2007 - 18:09:49 CST)
- Richard Wood (Mon Feb 19 2007 - 17:16:52 CST)
- Richard Wood (Wed Jan 31 2007 - 18:01:46 CST)
- Alexander Vaughn (Tue Jan 30 2007 - 17:07:46 CST)
- Richard Wood (Tue Jan 30 2007 - 13:35:25 CST)
- L. Michel Espinoza-Fonseca (Tue Jan 30 2007 - 12:54:06 CST)
- Richard Wood (Tue Jan 30 2007 - 12:21:06 CST)
A possibel wrong coding in Parameters::read_charmm_parameter_file(char *)
- Marcos Sotomayor (Wed Apr 05 2006 - 11:01:27 CDT)
- Marcos Sotomayor (Wed Apr 05 2006 - 10:54:40 CDT)
- Qikai Li (Wed Apr 05 2006 - 10:25:56 CDT)
A problem of the forces-tutorial
- ÕÅÄþ (Thu Apr 08 2010 - 07:18:33 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 puzzling problem about adsorption energy in solution.
- Boyang Wang (Thu Jun 01 2006 - 17:39:26 CDT)
a question about equilibrium
- Joshua Adelman (Wed May 21 2008 - 21:07:35 CDT)
- taojinwuhan_at_sohu.com (Wed May 21 2008 - 20:32:14 CDT)
A question about MD simulation of peptide.
- Boyang Wang (Tue Sep 27 2005 - 12:24:59 CDT)
a question about modifying the NAMD input file
- Axel Kohlmeyer (Mon Oct 25 2010 - 12:56:36 CDT)
- ying yu (Mon Oct 25 2010 - 12:06:50 CDT)
a question about NAMD TI
- æž—æ˜Ÿé›¨ (Mon Jun 21 2010 - 04:17:57 CDT)
- æž—æ˜Ÿé›¨ (Sun Jun 20 2010 - 22:26:48 CDT)
A question about restaints force.
- Yang Gao (Fri Apr 25 2008 - 11:28:20 CDT)
- Victor Ovchinnikov (Fri Apr 25 2008 - 17:48:40 CDT)
- Gungor Ozer (Fri Apr 25 2008 - 16:17:13 CDT)
- Yang Gao (Fri Apr 25 2008 - 15:23:01 CDT)
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 question on Jarkynski equation
- Jun Zhang (Wed Jun 15 2011 - 00:25:17 CDT)
- Jun Zhang (Tue Jun 14 2011 - 23:03:53 CDT)
- johan strumpfer (Tue Jun 14 2011 - 09:51:22 CDT)
- Jérôme Hénin (Tue Jun 14 2011 - 09:09:13 CDT)
- Wang Yi (Tue Jun 14 2011 - 08:11:46 CDT)
- Jérôme Hénin (Tue Jun 14 2011 - 03:43:55 CDT)
- Jun Zhang (Mon Jun 13 2011 - 22:01:59 CDT)
A question on minimization
- Marcos Sotomayor (Fri Nov 04 2005 - 16:18:46 CST)
- santanu chatterjee (Fri Nov 04 2005 - 15:44:32 CST)
A question on psfgen
- JC Gumbart (Tue Oct 18 2005 - 02:09:05 CDT)
- santanu chatterjee (Tue Oct 18 2005 - 01:55:39 CDT)
A question on simulation with NPT ensemble
- santanu chatterjee (Fri Mar 03 2006 - 13:18:34 CST)
A question regarding generate pdb and psf file
- JC Gumbart (Tue Dec 06 2005 - 11:37:55 CST)
- Grace Shen (Tue Dec 06 2005 - 11:06:27 CST)
A script for performing calculations divided by quanta
- Nicholas M Glykos (Tue Aug 04 2009 - 08:15:17 CDT)
- Joshua Adelman (Mon Aug 03 2009 - 10:38:35 CDT)
- Mikhail Suyetin (Mon Aug 03 2009 - 10:30:28 CDT)
- Joshua Adelman (Mon Aug 03 2009 - 10:05:50 CDT)
- Mikhail Suyetin (Mon Aug 03 2009 - 08:26:28 CDT)
A serious problem of NAMD output.
- Wang, Boyang (Tue Jul 24 2007 - 20:43:50 CDT)
- Brian Bennion (Tue Jul 24 2007 - 18:43:05 CDT)
- Peter Freddolino (Tue Jul 24 2007 - 18:57:42 CDT)
- Peter Freddolino (Tue Jul 24 2007 - 17:44:32 CDT)
- Wang, Boyang (Tue Jul 24 2007 - 17:35:08 CDT)
A strange phenomenon in my dynamics system,any suggestion?
- ËïÍ¥¹ã (Fri Apr 07 2006 - 21:29:32 CDT)
A strange thing about psfgen~
- Îº¿ (Sat Nov 13 2004 - 06:21:35 CST)
a target molecule in a water box.
- Wei Chen (Mon Apr 25 2005 - 22:33:54 CDT)
- Wang, Boyang (Mon Apr 25 2005 - 21:12:02 CDT)
a timing question; 206,000atoms > 512cores not good
- Thomas C. Bishop (Mon Sep 28 2009 - 12:17:07 CDT)
A tool to set up alchemical FEP transformations
- Jérôme Hénin (Mon Mar 29 2004 - 10:27:12 CST)
a topology file in VMD
- Cesar Luis Avila (Wed Apr 25 2007 - 10:07:49 CDT)
- Cesar Luis Avila (Wed Apr 25 2007 - 08:58:01 CDT)
- SMAHANE CHALABI (Wed Apr 25 2007 - 02:57:42 CDT)
- SMAHANE CHALABI (Tue Apr 24 2007 - 10:28:07 CDT)
A way to check for non-unique coordinates?
- Axel Kohlmeyer (Fri Nov 21 2008 - 04:36:21 CST)
- Diego Alejandro Vargas (Thu Nov 20 2008 - 23:15:58 CST)
- Diego Alejandro Vargas (Thu Nov 20 2008 - 21:22:21 CST)
Abe versus Lincoln
- Gianluca Interlandi (Thu Apr 07 2011 - 16:55:51 CDT)
- johan strumpfer (Thu Apr 07 2011 - 16:23:16 CDT)
- Axel Kohlmeyer (Thu Apr 07 2011 - 16:18:09 CDT)
- Gianluca Interlandi (Thu Apr 07 2011 - 15:40:11 CDT)
- Axel Kohlmeyer (Thu Apr 07 2011 - 14:21:33 CDT)
- Gianluca Interlandi (Thu Apr 07 2011 - 13:57:41 CDT)
- Gianluca Interlandi (Thu Apr 07 2011 - 13:50:45 CDT)
- Axel Kohlmeyer (Thu Apr 07 2011 - 13:46:34 CDT)
- johan strumpfer (Thu Apr 07 2011 - 13:40:13 CDT)
- Gianluca Interlandi (Thu Apr 07 2011 - 13:22:37 CDT)
abf
- Jérôme Hénin (Tue Sep 06 2005 - 08:48:25 CDT)
- michael atkinson (Sun Sep 04 2005 - 22:21:29 CDT)
abf "force not a vector" error
- maria goranovic (Wed Jun 27 2007 - 01:42:51 CDT)
- Jerome Henin (Tue Jun 26 2007 - 13:49:49 CDT)
- maria goranovic (Tue Jun 26 2007 - 10:31:58 CDT)
ABF & distanceZ projection axis
- HAMID - (Thu Sep 22 2011 - 01:20:02 CDT)
- Giacomo Fiorin (Wed Sep 21 2011 - 19:22:36 CDT)
- HAMID - (Wed Sep 21 2011 - 16:15:45 CDT)
ABF & distanceZ projection axis more
- HAMID - (Thu Sep 22 2011 - 05:36:32 CDT)
- Jérôme Hénin (Thu Sep 22 2011 - 04:33:02 CDT)
- HAMID - (Thu Sep 22 2011 - 03:05:07 CDT)
ABF 'Xi' log output producing strange results
- Hugh Martin (Thu Aug 27 2009 - 23:41:18 CDT)
- Jerome Henin (Thu Aug 27 2009 - 16:39:35 CDT)
- Eric H. Lee (Thu Aug 27 2009 - 10:48:50 CDT)
- Hugh Martin (Thu Aug 27 2009 - 10:30:22 CDT)
ABF (fwd)
- Jerome Henin (Tue Nov 14 2006 - 18:52:10 CST)
- Matthew Davies (Tue Nov 14 2006 - 10:10:38 CST)
- Jerome Henin (Tue Nov 14 2006 - 08:49:03 CST)
- Matthew Davies (Tue Nov 14 2006 - 07:40:30 CST)
ABF (NAMD 2.7x) speed ?
- Ziemys, Arturas (Wed May 26 2010 - 07:24:54 CDT)
- Jérôme Hénin (Wed May 26 2010 - 04:52:22 CDT)
- Jérôme Hénin (Tue May 25 2010 - 10:47:32 CDT)
- Ziemys, Arturas (Tue May 25 2010 - 09:51:33 CDT)
ABF + LES
- Jerome Henin (Thu Oct 01 2009 - 12:19:48 CDT)
- Ziemys, Arturas (Thu Oct 01 2009 - 11:45:38 CDT)
ABF - changing the reaction coordinate
- Jerome Henin (Fri Jul 06 2007 - 10:54:02 CDT)
- Per Jr. Greisen (Fri Jul 06 2007 - 10:18:00 CDT)
ABF - PMF Calculation
- Jerome Henin (Fri Dec 14 2007 - 11:15:15 CST)
- Jason O'Young (Fri Dec 14 2007 - 10:00:48 CST)
ABF - restricting reaction coordinate
- Jerome Henin (Fri Dec 07 2007 - 15:04:21 CST)
- Subramanian Vaitheeswaran (Fri Dec 07 2007 - 14:49:55 CST)
- Jerome Henin (Fri Dec 07 2007 - 10:43:49 CST)
- Jerome Henin (Fri Dec 07 2007 - 10:01:47 CST)
- Subramanian Vaitheeswaran (Fri Dec 07 2007 - 09:38:36 CST)
- Subramanian Vaitheeswaran (Fri Dec 07 2007 - 08:55:48 CST)
ABF - sequence of MD runs
- Jérôme Hénin (Tue Jan 05 2010 - 11:26:22 CST)
- Krishnan, Marimuthu (Thu Dec 17 2009 - 21:55:59 CST)
ABF - stretching deca-alanine
- Jerome Henin (Mon Oct 22 2007 - 09:22:40 CDT)
- Jerome Henin (Mon Oct 22 2007 - 08:21:23 CDT)
- Per Jr. Greisen (Mon Oct 22 2007 - 06:34:25 CDT)
ABF - using gyration
- Jerome Henin (Thu Oct 30 2008 - 10:29:12 CDT)
- Subramanian Vaitheeswaran (Thu Oct 30 2008 - 09:59:29 CDT)
- Jerome Henin (Tue Oct 28 2008 - 15:11:43 CDT)
- Subramanian Vaitheeswaran (Tue Oct 28 2008 - 15:19:55 CDT)
- Jerome Henin (Tue Oct 28 2008 - 11:52:49 CDT)
- Subramanian Vaitheeswaran (Tue Oct 28 2008 - 10:18:08 CDT)
ABF - zCoord for more than one monomer
- Chris Chipot (Mon Nov 13 2006 - 07:47:30 CST)
- Ugur Akgun (Thu Nov 09 2006 - 10:19:47 CST)
abf - zeros as output
- Jerome Henin (Tue Oct 23 2007 - 13:32:14 CDT)
- Per Jr. Greisen (Tue Oct 23 2007 - 12:49:45 CDT)
ABF : dihedral-com.tcl
- Subramanian Vaitheeswaran (Wed Nov 21 2007 - 11:16:37 CST)
- Vlad Cojocaru (Wed Nov 21 2007 - 10:36:31 CST)
- Chris Chipot (Wed Nov 21 2007 - 10:36:37 CST)
- Subramanian Vaitheeswaran (Wed Nov 21 2007 - 09:59:37 CST)
abf and tcl scripting in NAMD
- Vlad Cojocaru (Wed Mar 26 2008 - 11:18:15 CDT)
ABF application
- Jerome Henin (Tue Nov 13 2007 - 11:37:27 CST)
- Vlad Cojocaru (Tue Nov 13 2007 - 11:52:53 CST)
- Vlad Cojocaru (Tue Nov 13 2007 - 09:39:43 CST)
- Vlad Cojocaru (Fri Nov 09 2007 - 03:23:57 CST)
- Jerome Henin (Thu Nov 08 2007 - 14:42:58 CST)
- Vlad Cojocaru (Thu Nov 08 2007 - 08:28:23 CST)
ABF atom selection
- Jérôme Hénin (Tue May 10 2011 - 09:59:08 CDT)
- Parisa Akhski (Tue May 10 2011 - 09:16:29 CDT)
- Jérôme Hénin (Sun May 08 2011 - 11:41:09 CDT)
- Parisa Akhski (Sat May 07 2011 - 18:14:24 CDT)
ABF atom selection question
- Parisa Akhski (Thu May 05 2011 - 21:50:00 CDT)
ABF backbone dihedral
- Sébastien Légaré (Tue Oct 28 2008 - 11:44:21 CDT)
ABF calculation - normalization of the PMF
- Jerome Henin (Wed Sep 30 2009 - 04:42:32 CDT)
- Giovanni Bellesia (Tue Sep 29 2009 - 10:40:01 CDT)
- Jerome Henin (Sun Sep 27 2009 - 16:36:23 CDT)
- Giovanni Bellesia (Sat Sep 19 2009 - 16:59:46 CDT)
ABF calculation using RMSD
- Giacomo Fiorin (Mon Apr 25 2011 - 22:26:54 CDT)
- Buddhadev Maiti (Mon Apr 25 2011 - 22:14:39 CDT)
- JC Gumbart (Wed Feb 16 2011 - 21:24:01 CST)
- Buddhadev Maiti (Wed Feb 16 2011 - 21:04:11 CST)
- Jérôme Hénin (Tue Feb 15 2011 - 04:46:25 CST)
- Buddhadev Maiti (Mon Feb 14 2011 - 19:08:32 CST)
ABF calculation with TclForces script in the configuration file
- Jerome Henin (Fri Jan 16 2009 - 11:20:27 CST)
- govardhan reddy (Fri Jan 16 2009 - 11:10:47 CST)
- govardhan reddy (Fri Jan 16 2009 - 09:18:40 CST)
ABF calculations
- Chris Chipot (Wed Nov 21 2007 - 18:37:32 CST)
- jia (Tue Nov 20 2007 - 09:14:42 CST)
- Chris Chipot (Mon Nov 19 2007 - 16:30:42 CST)
- Jerome Henin (Mon Nov 19 2007 - 15:56:17 CST)
- jia (Mon Nov 19 2007 - 14:33:51 CST)
ABF calculations: Jacobian term describing geometry entropy
- Jérôme Hénin (Mon Aug 23 2010 - 10:51:53 CDT)
- Giacomo Fiorin (Mon Aug 23 2010 - 11:00:43 CDT)
- chengh_at_ringo.chem.pitt.edu (Mon Aug 23 2010 - 08:13:37 CDT)
ABF colvar error-capped nanotube interaction
- Axel Kohlmeyer (Sun Mar 20 2011 - 12:13:43 CDT)
- sakthi kumaran (Sun Mar 20 2011 - 11:26:04 CDT)
- sakthi kumaran (Sun Mar 20 2011 - 01:55:30 CDT)
- Giacomo Fiorin (Sat Mar 19 2011 - 13:54:37 CDT)
- Axel Kohlmeyer (Sat Mar 19 2011 - 12:02:53 CDT)
- sakthi kumaran (Sat Mar 19 2011 - 11:12:57 CDT)
ABF Colvars Configuration File
- Giacomo Fiorin (Thu Aug 20 2009 - 10:59:35 CDT)
- Neelanjana Sengupta (Thu Aug 20 2009 - 09:21:41 CDT)
abf convergence problems
- Jorgen Simonsen (Thu Jan 22 2009 - 14:37:05 CST)
- Jerome Henin (Thu Jan 22 2009 - 14:17:26 CST)
- Jorgen Simonsen (Thu Jan 22 2009 - 12:56:40 CST)
- Jerome Henin (Thu Jan 22 2009 - 11:52:29 CST)
- Chris Chipot (Thu Jan 22 2009 - 11:54:08 CST)
- Jorgen Simonsen (Thu Jan 22 2009 - 11:16:36 CST)
ABF Displacement
- Jérôme Hénin (Mon Mar 29 2010 - 12:10:04 CDT)
- Patrick Yee (Sat Mar 27 2010 - 14:42:18 CDT)
ABF error calculation
- Jérôme Hénin (Sat Dec 12 2009 - 03:53:07 CST)
- Valeria M. (Fri Dec 11 2009 - 09:57:25 CST)
- BIN ZHANG (Fri Dec 11 2009 - 12:03:34 CST)
- Valeria M. (Fri Dec 11 2009 - 11:04:33 CST)
- Chris Chipot (Fri Feb 29 2008 - 16:26:00 CST)
- Jerome Henin (Fri Feb 29 2008 - 16:16:29 CST)
- Xu, Jiancong (Fri Feb 29 2008 - 14:47:48 CST)
ABF for conformational analysis
- Jérôme Hénin (Mon Nov 14 2005 - 03:34:21 CST)
- Uma Mahankali (Fri Nov 11 2005 - 16:54:11 CST)
Abf force output
- Jérôme Hénin (Wed Feb 09 2011 - 07:30:16 CST)
- stefhoor (Wed Feb 09 2011 - 04:12:50 CST)
- Jérôme Hénin (Wed Feb 09 2011 - 03:25:59 CST)
- stefhoor (Tue Feb 08 2011 - 20:58:39 CST)
ABF fullsamples
- Jerome Henin (Mon Dec 03 2007 - 18:13:40 CST)
- Chris Chipot (Mon Dec 03 2007 - 15:47:06 CST)
- Jason O'Young (Mon Dec 03 2007 - 13:18:40 CST)
ABF in various simulations
- Giacomo Fiorin (Mon May 17 2010 - 21:17:32 CDT)
- Robert Elder (Mon May 17 2010 - 18:43:41 CDT)
- stefhoor (Mon May 17 2010 - 15:18:57 CDT)
- Robert Elder (Mon May 17 2010 - 14:42:30 CDT)
- stefhoor (Mon May 17 2010 - 11:31:03 CDT)
- Jérôme Hénin (Mon May 17 2010 - 11:08:28 CDT)
- Patrick Yee (Mon May 17 2010 - 10:47:58 CDT)
- stefhoor (Mon May 17 2010 - 08:30:36 CDT)
ABF inFiles
- Subramanian Vaitheeswaran (Thu Jun 21 2007 - 12:29:02 CDT)
- Jerome Henin (Thu Jun 21 2007 - 11:57:35 CDT)
- Subramanian Vaitheeswaran (Thu Jun 21 2007 - 11:03:47 CDT)
ABF Method
- digenova (Thu Jul 03 2008 - 08:52:29 CDT)
- Eric H. Lee (Wed Jul 02 2008 - 10:45:15 CDT)
- Bonnie A Merchant (Wed Jul 02 2008 - 09:19:39 CDT)
ABF non-uniform sampling
- Branko (Sun May 02 2010 - 13:36:40 CDT)
- Giacomo Fiorin (Sat May 01 2010 - 14:37:22 CDT)
- Patrick Yee (Sat May 01 2010 - 11:14:52 CDT)
- Jérôme Hénin (Fri Apr 16 2010 - 04:48:17 CDT)
- Branko (Fri Apr 16 2010 - 05:04:37 CDT)
- Patrick Yee (Thu Apr 15 2010 - 22:19:45 CDT)
ABF on a single molecule
- Ugur Akgun (Mon Nov 06 2006 - 16:33:24 CST)
- Chris Chipot (Mon Nov 06 2006 - 15:19:17 CST)
- Ugur Akgun (Mon Nov 06 2006 - 14:19:04 CST)
- Chris Chipot (Sun Nov 05 2006 - 03:26:53 CST)
- Ugur Akgun (Thu Nov 02 2006 - 14:26:11 CST)
ABF on NAMD 2.7b3
- Chris Harrison (Tue Dec 21 2010 - 08:20:43 CST)
- JC Gumbart (Mon Dec 20 2010 - 18:11:08 CST)
- JC Gumbart (Mon Dec 20 2010 - 15:37:54 CST)
- Alex Liu (Mon Dec 20 2010 - 15:03:22 CST)
ABF or SMD
- jia (Fri Nov 16 2007 - 11:26:20 CST)
abf output
- Chris Chipot (Fri Apr 20 2007 - 17:08:47 CDT)
- Christine Horejs (Fri Apr 20 2007 - 07:19:12 CDT)
ABF Output File
- Jason Wyonn O'Young (Sun Dec 02 2007 - 12:47:26 CST)
- Chris Chipot (Sun Dec 02 2007 - 13:22:03 CST)
ABF parameters
- Jerome Henin (Mon Oct 01 2007 - 10:53:41 CDT)
- Subramanian Vaitheeswaran (Mon Oct 01 2007 - 08:45:12 CDT)
ABF problem with gyration radius/Cl and Br
- Jérôme Hénin (Wed Aug 11 2010 - 08:31:44 CDT)
- Branko (Wed Aug 11 2010 - 07:25:41 CDT)
ABF question
- Jérôme Hénin (Wed Sep 21 2011 - 07:01:50 CDT)
- Jérôme Hénin (Fri Dec 03 2010 - 10:45:24 CST)
- Parisa Akhski (Fri Dec 03 2010 - 09:16:07 CST)
- Parisa Akhski (Thu Jun 24 2010 - 16:03:15 CDT)
- Jérôme Hénin (Wed Jun 23 2010 - 05:17:56 CDT)
- Parisa Akhski (Tue Jun 22 2010 - 13:06:55 CDT)
- Parisa Akhski (Tue Jun 22 2010 - 11:43:06 CDT)
- Giacomo Fiorin (Tue May 25 2010 - 20:07:51 CDT)
- Patrick Yee (Tue May 25 2010 - 13:38:33 CDT)
- Jérôme Hénin (Tue May 25 2010 - 10:35:52 CDT)
- Ziemys, Arturas (Tue May 25 2010 - 08:51:39 CDT)
- Jérôme Hénin (Wed Jan 27 2010 - 04:18:13 CST)
- Austin B. Yongye (Tue Jan 26 2010 - 17:07:05 CST)
- Matthew Davies (Wed Feb 13 2008 - 11:00:44 CST)
- Jerome Henin (Mon Jan 14 2008 - 11:40:49 CST)
- Xu, Jiancong (Mon Jan 14 2008 - 11:19:27 CST)
- Xu, Jiancong (Mon Jan 14 2008 - 10:14:07 CST)
- Jerome Henin (Mon Jan 14 2008 - 11:02:35 CST)
- jia (Sun Jan 13 2008 - 12:55:37 CST)
- Jerome Henin (Wed Jan 09 2008 - 11:26:57 CST)
- Xu, Jiancong (Wed Jan 09 2008 - 10:04:19 CST)
- Chris Chipot (Wed Sep 19 2007 - 08:17:12 CDT)
- Matthew Davies (Wed Sep 19 2007 - 06:45:05 CDT)
ABF question (free energy partition)
- Chris Chipot (Sun Aug 09 2009 - 12:32:54 CDT)
- Lei Shi (Sun Aug 09 2009 - 11:36:10 CDT)
ABF question (sampling and colvars output file)
- Parisa Akhski (Mon Feb 07 2011 - 14:27:03 CST)
- Jérôme Hénin (Mon Feb 07 2011 - 11:16:28 CST)
- Jérôme Hénin (Mon Feb 07 2011 - 04:20:28 CST)
- Parisa Akhski (Sun Feb 06 2011 - 15:20:47 CST)
- Parisa Akhski (Tue Feb 01 2011 - 10:27:43 CST)
ABF questions
- Austin B. Yongye (Wed Jan 13 2010 - 11:45:51 CST)
- Jérôme Hénin (Wed Jan 13 2010 - 10:40:49 CST)
- Austin B. Yongye (Wed Jan 06 2010 - 09:56:28 CST)
- Branko (Wed Jan 06 2010 - 07:17:02 CST)
- Austin B. Yongye (Tue Jan 05 2010 - 16:19:57 CST)
- Austin B. Yongye (Tue Jan 05 2010 - 12:10:04 CST)
- Jérôme Hénin (Tue Jan 05 2010 - 11:44:58 CST)
- Austin B. Yongye (Tue Jan 05 2010 - 10:27:47 CST)
ABF questions (Concatenate output files/force constant)
- Jérôme Hénin (Thu Dec 09 2010 - 04:51:14 CST)
- Parisa Akhski (Wed Dec 08 2010 - 17:57:40 CST)
ABF reproducibility
- Jérôme Hénin (Mon Feb 14 2011 - 06:29:40 CST)
- Parisa Akhski (Sun Feb 13 2011 - 15:08:26 CST)
ABF Restart
- Jérôme Hénin (Fri Mar 18 2011 - 04:08:34 CDT)
- Buddhadev Maiti (Thu Mar 17 2011 - 21:46:37 CDT)
ABF restrain
- Chris Chipot (Thu Jul 05 2007 - 13:05:30 CDT)
- alex digenova bravo (Thu Jul 05 2007 - 11:48:12 CDT)
- Chris Chipot (Wed Jul 04 2007 - 17:17:41 CDT)
- alex digenova bravo (Wed Jul 04 2007 - 15:31:19 CDT)
ABF results interpretation
- HAMID - (Wed Sep 21 2011 - 10:22:38 CDT)
ABF simulation
- Jérôme Hénin (Sat Jan 07 2012 - 05:16:24 CST)
- Tugba Nogay (Fri Jan 06 2012 - 10:53:36 CST)
- Tyler Luchko (Thu Jun 29 2006 - 00:11:42 CDT)
- Lionel Perrin (Tue Jun 27 2006 - 03:47:16 CDT)
- Giovanni Bellesia (Mon Jun 26 2006 - 21:29:24 CDT)
- Tyler Luchko (Mon Jun 26 2006 - 19:45:02 CDT)
- Lionel Perrin (Wed Nov 02 2005 - 08:28:25 CST)
- Jérôme Hénin (Fri Oct 28 2005 - 04:05:52 CDT)
- Lionel Perrin (Wed Oct 26 2005 - 10:52:53 CDT)
- Lionel Perrin (Fri Oct 21 2005 - 04:03:02 CDT)
- Jérôme Hénin (Wed Oct 19 2005 - 04:11:17 CDT)
- Lionel Perrin (Thu Oct 06 2005 - 09:13:45 CDT)
- Jérôme Hénin (Wed Oct 05 2005 - 11:35:25 CDT)
- Chris Chipot (Wed Oct 05 2005 - 07:58:57 CDT)
- Lionel Perrin (Wed Oct 05 2005 - 06:41:44 CDT)
ABF Simulation Crash from TCL script
- Patrick Yee (Sun Apr 11 2010 - 14:07:52 CDT)
- Jérôme Hénin (Wed Mar 31 2010 - 04:55:00 CDT)
- Patrick Yee (Tue Mar 30 2010 - 17:10:49 CDT)
ABF simulation with extendedLagrangian on keeps crashing
- Jérôme Hénin (Thu May 12 2011 - 04:36:20 CDT)
- Ajasja LjubetiÄ (Thu May 12 2011 - 03:55:03 CDT)
- Jérôme Hénin (Thu May 05 2011 - 17:02:56 CDT)
- Giacomo Fiorin (Thu May 05 2011 - 16:22:09 CDT)
- Ajasja LjubetiÄ (Thu May 05 2011 - 15:50:34 CDT)
- Jérôme Hénin (Thu May 05 2011 - 10:23:23 CDT)
- Ajasja LjubetiÄ (Thu May 05 2011 - 03:38:16 CDT)
- Ajasja LjubetiÄ (Wed May 04 2011 - 06:31:58 CDT)
- Ajasja LjubetiÄ (Tue May 03 2011 - 11:02:12 CDT)
- Jérôme Hénin (Tue May 03 2011 - 10:23:17 CDT)
- Ajasja LjubetiÄ (Tue May 03 2011 - 08:11:26 CDT)
- Jérôme Hénin (Fri Apr 22 2011 - 15:38:07 CDT)
- Ajasja LjubetiÄ (Fri Apr 22 2011 - 09:27:24 CDT)
- Ajasja LjubetiÄ (Fri Apr 22 2011 - 03:34:29 CDT)
- Jérôme Hénin (Thu Apr 21 2011 - 09:43:21 CDT)
- Ajasja LjubetiÄ (Thu Apr 21 2011 - 06:30:47 CDT)
- Giacomo Fiorin (Wed Apr 20 2011 - 11:22:37 CDT)
- Ajasja Ljubetiè (Wed Apr 20 2011 - 09:22:21 CDT)
- Ajasja Ljubetiè (Tue Apr 19 2011 - 12:43:12 CDT)
- Ajasja LjubetiÄ (Tue Apr 19 2011 - 12:05:23 CDT)
- Giacomo Fiorin (Tue Apr 19 2011 - 11:41:55 CDT)
- Ajasja LjubetiÄ (Tue Apr 19 2011 - 11:05:09 CDT)
- Ajasja LjubetiÄ (Tue Apr 19 2011 - 10:55:57 CDT)
ABF simulations
- Branko (Tue Jun 23 2009 - 14:52:42 CDT)
- Ziemys, Arturas (Tue Jun 23 2009 - 13:04:24 CDT)
- Sumanth Jamadagni (Tue Jun 23 2009 - 11:32:43 CDT)
- Sébastien Légaré (Tue Jun 23 2009 - 11:01:22 CDT)
- Sumanth Jamadagni (Tue Jun 09 2009 - 21:08:10 CDT)
- Chris Chipot (Tue Jul 29 2008 - 09:55:41 CDT)
- Raul Araya (Mon Jul 28 2008 - 14:45:46 CDT)
ABF tutorial
- sudipta (Tue Jul 21 2009 - 05:40:58 CDT)
- sudipta (Tue Jul 21 2009 - 05:39:03 CDT)
- Chris Chipot (Mon Jul 20 2009 - 09:09:57 CDT)
- sudipta (Mon Jul 20 2009 - 08:57:54 CDT)
ABF tutorial; updated FEP tutorial
- Jerome Henin (Fri Mar 21 2008 - 18:53:58 CDT)
- Lei Shi (Thu Mar 20 2008 - 17:38:40 CDT)
- Jerome Henin (Thu Mar 20 2008 - 15:55:10 CDT)
ABF using distance-com but with negative xiMin
- Jerome Henin (Fri Jan 11 2008 - 17:19:32 CST)
- Philip Fowler (Fri Jan 11 2008 - 09:21:48 CST)
ABF with Alpha colvar can't be used on supercomputer?
- Yun Luo (Thu Sep 29 2011 - 14:25:57 CDT)
- Chris Harrison (Thu Sep 29 2011 - 10:11:32 CDT)
- Jérôme Hénin (Thu Sep 29 2011 - 09:56:46 CDT)
- JC Gumbart (Thu Sep 29 2011 - 08:05:19 CDT)
- Jérôme Hénin (Thu Sep 29 2011 - 05:04:42 CDT)
- JC Gumbart (Thu Sep 29 2011 - 01:05:53 CDT)
- Yun Luo (Wed Sep 28 2011 - 15:38:02 CDT)
abf with colvars example
- Branko (Thu Jun 04 2009 - 15:17:42 CDT)
- Roman Petrenko (Thu Jun 04 2009 - 14:35:53 CDT)
- Jerome Henin (Thu Jun 04 2009 - 13:44:06 CDT)
- David A. Horita (Thu Jun 04 2009 - 12:53:20 CDT)
ABF with different bin size
- Xu, Jiancong (Fri Feb 01 2008 - 11:11:58 CST)
ABF with z-coord
- Ugur Akgun (Fri Nov 24 2006 - 20:31:06 CST)
ABF-Zcoord:
- ÁõÓý (Wed Feb 04 2009 - 22:04:40 CST)
- Giacomo Fiorin (Wed Feb 04 2009 - 18:13:50 CST)
- ÁõÓý (Tue Feb 03 2009 - 07:29:23 CST)
ABF.TCl file ???
- Shahid Qamar (Tue Nov 01 2005 - 13:56:25 CST)
ABF: example works now; more questions.
- Jan Saam (Tue May 30 2006 - 08:57:15 CDT)
ABF: example works; more questions.
- Jan Saam (Wed May 31 2006 - 17:27:03 CDT)
- Jerome Henin (Tue May 30 2006 - 16:31:58 CDT)
- Jan Saam (Tue May 30 2006 - 12:38:05 CDT)
- Jan Saam (Tue May 30 2006 - 11:01:29 CDT)
ABF: moving system in Z direction
- Giacomo Fiorin (Tue Apr 20 2010 - 09:06:52 CDT)
- sefer baday (Tue Apr 20 2010 - 04:58:51 CDT)
- sefer baday (Mon Apr 19 2010 - 11:59:03 CDT)
- Giacomo Fiorin (Mon Apr 19 2010 - 12:16:08 CDT)
- Jérôme Hénin (Mon Apr 19 2010 - 11:20:35 CDT)
- sefer baday (Mon Apr 19 2010 - 08:49:09 CDT)
abf: multiple distance
- Jerome Henin (Fri Nov 30 2007 - 11:44:39 CST)
- Jerome Henin (Fri Nov 30 2007 - 11:34:09 CST)
- Vlad Cojocaru (Fri Nov 30 2007 - 10:05:43 CST)
- luca (Fri Nov 30 2007 - 09:50:58 CST)
- Jerome Henin (Fri Nov 30 2007 - 09:01:39 CST)
- Luca Bellucci (Thu Nov 29 2007 - 04:18:19 CST)
ABF: split reaction coordinate in widows
- Subramanian Vaitheeswaran (Tue Dec 18 2007 - 10:40:39 CST)
- Vlad Cojocaru (Tue Dec 18 2007 - 08:01:55 CST)
ABF:problems with calculating Free Energy Profile
- supram_at_nankai.edu.cn (Sun Nov 16 2008 - 20:55:39 CST)
ABF:restraint in free energy calculation in Zcoord-method
- ÁõÓý (Tue Feb 03 2009 - 22:15:42 CST)
ABF:reversibility and number of samples
- Jerome Henin (Fri May 23 2008 - 17:21:35 CDT)
- Subramanian Vaitheeswaran (Fri May 23 2008 - 16:55:53 CDT)
- Eric Cyr (Fri May 23 2008 - 15:11:29 CDT)
- Luca (Fri May 23 2008 - 14:26:03 CDT)
- Jerome Henin (Fri May 23 2008 - 12:15:11 CDT)
- Chris Chipot (Fri May 23 2008 - 10:43:59 CDT)
- Luca Bellucci (Fri May 23 2008 - 07:33:27 CDT)
abf_integrate
- Jérôme Hénin (Fri Aug 06 2010 - 05:20:59 CDT)
- Sabyashachi Mishra (Wed Aug 04 2010 - 04:50:08 CDT)
Abnormal EOF Error in Extra Bonds File
- Jim Phillips (Tue May 10 2011 - 20:15:18 CDT)
- Eli Fine (Tue Apr 26 2011 - 14:22:11 CDT)
Abnormal EOF found - buffer
- Rene Prieto (Sun Aug 10 2008 - 09:37:47 CDT)
- David Tanner (Fri Aug 08 2008 - 10:14:21 CDT)
- Rene Prieto (Thu Aug 07 2008 - 00:46:37 CDT)
Abnormal EOF found -buffer=*END*
- Patrick Yee (Mon Nov 02 2009 - 12:35:52 CST)
abnormal water surface after nvt and npt for POPC membrane
- Axel Kohlmeyer (Wed Oct 28 2009 - 10:55:16 CDT)
- pxq ÅÓÑ©ÇÛ (Tue Oct 27 2009 - 19:57:58 CDT)
About "alchDecouple" in FEP
- wenhao_at_uchicago.edu (Sun Oct 23 2011 - 07:47:26 CDT)
- Jérôme Hénin (Sat Oct 22 2011 - 11:51:27 CDT)
- wenhao_at_uchicago.edu (Sat Oct 22 2011 - 10:47:14 CDT)
About "equilibrate.conf' of FEP tutorial
- Jérôme Hénin (Sat Feb 20 2010 - 10:36:43 CST)
- Aurum Bai (Sat Feb 20 2010 - 07:15:58 CST)
About "get z" command in MD script language.
- Boyang Wang (Sat Jan 07 2006 - 20:57:08 CST)
About "mutate" command in psfgen package.
- Boyang Wang (Thu Feb 02 2006 - 22:56:17 CST)
- JC Gumbart (Thu Feb 02 2006 - 23:06:44 CST)
- JC Gumbart (Thu Feb 02 2006 - 18:47:10 CST)
- Boyang Wang (Thu Feb 02 2006 - 17:24:42 CST)
About "Parameterizing a Novel Residue" tutorial problem
- Aurum Bai (Wed Aug 12 2009 - 00:18:09 CDT)
About "Visualization and Analysis of CPMD data with VMD" tutorial
- Axel Kohlmeyer (Thu Dec 10 2009 - 00:11:45 CST)
- Aurum Bai (Wed Dec 09 2009 - 21:43:44 CST)
about 'loadforces' command...help!
- hl332_at_drexel.edu (Tue Jul 31 2007 - 15:00:17 CDT)
about *.psf
- Alessandro Pedretti (Fri May 27 2005 - 05:30:10 CDT)
- ËïæÃæÃ (Thu May 26 2005 - 23:59:07 CDT)
about abf
- Jerome Henin (Wed Sep 27 2006 - 15:31:02 CDT)
- Vani Krishna (Tue Sep 26 2006 - 22:41:06 CDT)
- ËïæÃæÃ (Tue Sep 26 2006 - 08:30:24 CDT)
About ADP
- Michel Espinoza-Fonseca (Tue Nov 01 2005 - 13:21:22 CST)
- Grace Shen (Tue Nov 01 2005 - 10:15:47 CST)
- Michel Espinoza-Fonseca (Tue Nov 01 2005 - 10:16:43 CST)
- Grace Shen (Tue Nov 01 2005 - 09:48:43 CST)
About Amber force fields
- Jan Saam (Sat Jan 19 2008 - 23:00:45 CST)
- Francesco Pietra (Sat Jan 19 2008 - 08:54:30 CST)
About APBS calculation
- «J ¦¼¯Â (Thu Oct 29 2009 - 09:22:48 CDT)
About calculating RMSD with rmsd.tcl
- Peter Freddolino (Wed Oct 05 2005 - 22:22:23 CDT)
- Boyang Wang (Fri Sep 30 2005 - 19:55:26 CDT)
about calculation of PMF from SMD trajectories
- Falgun Shah (Wed Mar 04 2009 - 11:58:52 CST)
about calculation of PMF from SMD trajectories (with pasted smd_config_file)
- Axel Kohlmeyer (Wed Mar 04 2009 - 12:52:47 CST)
- Falgun Shah (Wed Mar 04 2009 - 12:04:52 CST)
About charm++/namd on AMD64 cluster
- Gengbin Zheng (Mon Jan 03 2005 - 14:46:58 CST)
- q=F5=D0=A1=C7=E5?= (Mon Jan 03 2005 - 04:15:19 CST)
- Gengbin Zheng (Sun Jan 02 2005 - 02:50:56 CST)
- q=F5=D0=A1=C7=E5?= (Sun Jan 02 2005 - 02:01:32 CST)
About CHARMM charge
- L. Michel Espinoza-Fonseca (Mon Aug 28 2006 - 10:10:05 CDT)
- Jan Saam (Mon Aug 28 2006 - 05:46:22 CDT)
- Luca Bellucci (Mon Aug 28 2006 - 04:10:45 CDT)
about charmm force field
- oguz gurbulak (Fri Jun 10 2011 - 09:55:26 CDT)
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 Columb energy of 2 ions in Vacuum
- Jérôme Hénin (Fri Aug 26 2011 - 04:30:54 CDT)
- wenhao_at_uchicago.edu (Fri Aug 26 2011 - 02:30:48 CDT)
- JC Gumbart (Fri Aug 26 2011 - 01:37:05 CDT)
- wenhao_at_uchicago.edu (Thu Aug 25 2011 - 18:02:04 CDT)
- wenhao_at_uchicago.edu (Tue Aug 23 2011 - 22:32:08 CDT)
- wenhao_at_uchicago.edu (Tue Aug 23 2011 - 22:30:29 CDT)
- Edward Lyman (Tue Aug 23 2011 - 19:47:25 CDT)
- wenhao_at_uchicago.edu (Tue Aug 23 2011 - 17:28:04 CDT)
about compile namd2.7
- Axel Kohlmeyer (Sun Jul 19 2009 - 11:18:33 CDT)
- liupeng012 (Sun Jul 19 2009 - 05:58:05 CDT)
about conf file
- Jim Phillips (Thu May 26 2011 - 09:55:14 CDT)
- oguz gurbulak (Thu May 26 2011 - 09:11:29 CDT)
about counterions
- Peter Freddolino (Wed Dec 20 2006 - 10:07:29 CST)
- Mark Abraham (Tue Dec 19 2006 - 21:46:23 CST)
- taojinwuhan_at_sohu.com (Tue Dec 19 2006 - 21:18:19 CST)
About CUDA version of NAMD 2.7 B1
- Dow Hurst (Sat Mar 28 2009 - 14:20:30 CDT)
- Jim Phillips (Wed Mar 25 2009 - 08:34:29 CDT)
- wang (Wed Mar 25 2009 - 00:57:33 CDT)
About cutoff parameter for real space calculation in PME
- xiaojing gong (Sun May 27 2007 - 06:47:26 CDT)
about D amino acid
- Eduard Schreiner (Fri Jul 29 2011 - 04:27:39 CDT)
- AB (Fri Jul 29 2011 - 03:50:16 CDT)
about DCD file format document
- Ajasja LjubetiÄ (Mon Jul 12 2010 - 08:52:05 CDT)
- Nicholas M Glykos (Mon Jul 12 2010 - 08:15:50 CDT)
- Axel Kohlmeyer (Mon Jul 12 2010 - 07:29:02 CDT)
- Jun Zhang (Mon Jul 12 2010 - 06:43:02 CDT)
about delta-G in PMF calculation
- Hyonseok Hwang (Thu Apr 01 2004 - 22:36:27 CST)
about diahedra entry in top_all22_sugar.inp
- Leonardo Trabuco (Fri Oct 13 2006 - 15:14:58 CDT)
- bqluan (Fri Oct 13 2006 - 13:31:35 CDT)
About DPD
- «J ¦¼¯Â (Sun Aug 23 2009 - 09:52:59 CDT)
about ExcludeFromPressure
- mashaojie163 (Tue Oct 26 2004 - 21:59:50 CDT)
- mashaojie163 (Fri Oct 22 2004 - 03:52:15 CDT)
about extrabonds restrain
- JC Gumbart (Tue Aug 30 2011 - 08:41:35 CDT)
- Axel Kohlmeyer (Tue Aug 30 2011 - 08:06:04 CDT)
- Ling Wu (Mon Aug 29 2011 - 16:22:53 CDT)
About fastest CUDA cards
- Francesco Pietra (Fri Jul 29 2011 - 04:09:37 CDT)
about force fields
- oguz gurbulak (Tue Aug 19 2008 - 09:54:14 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 Hydrogen Bond correlation function
- Jun Zhang (Sat Nov 06 2010 - 23:24:02 CDT)
- Axel Kohlmeyer (Thu Nov 04 2010 - 08:59:45 CDT)
- Hannes Loeffler (Thu Nov 04 2010 - 08:42:59 CDT)
- Hannes Loeffler (Thu Nov 04 2010 - 08:11:16 CDT)
- Chris Harrison (Thu Nov 04 2010 - 06:49:40 CDT)
- Jun Zhang (Thu Nov 04 2010 - 00:55:28 CDT)
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 ions Representation in NAMD
- Gianluca Interlandi (Wed Sep 28 2005 - 07:33:39 CDT)
- yangbing00_at_mails.tsinghua.edu.cn (Wed Sep 28 2005 - 06:40:45 CDT)
About Langevin Damping Coefficient.
- Boyang Wang (Fri Feb 24 2006 - 17:57:24 CST)
About Langevin Dynamics.
- Boyang Wang (Thu Mar 02 2006 - 11:30:46 CST)
- Boyang Wang (Wed Mar 01 2006 - 12:18:30 CST)
about limitdist
- cong chen (Mon May 18 2009 - 06:11:48 CDT)
About loadcoors -- is there a loadvelocity?
- Boyang Wang (Fri May 19 2006 - 13:01:11 CDT)
about log file
- Bjoern Olausson (Thu Jun 09 2011 - 05:02:36 CDT)
- Molecular Dynamics (Thu Jun 09 2011 - 04:30:30 CDT)
About matdcd
- Mert Gür (Sun Apr 04 2010 - 04:20:50 CDT)
- Gong Xiaojing (Sat Apr 03 2010 - 21:23:39 CDT)
about MCTI output
- mashaojie163 (Mon Dec 27 2004 - 01:29:36 CST)
about md in npt
- Joshua Adelman (Wed Dec 28 2011 - 07:55:02 CST)
- Hasan haska (Wed Dec 28 2011 - 02:18:30 CST)
about membrane protein
- mashaojie163 (Mon Jun 14 2004 - 09:39:41 CDT)
about NAMD nonbonded routines
- (Tue Feb 23 2010 - 02:55:29 CST)
About NAN error
- cong chen (Fri Sep 18 2009 - 01:35:51 CDT)
about normal mode analisys
- Jojart Balazs (Fri Jun 29 2007 - 16:13:27 CDT)
- S³awek Or³owski (Fri Jun 29 2007 - 04:00:35 CDT)
About para file format
- cong chen (Sat Dec 01 2007 - 00:14:36 CST)
About PDB file with fixed atom flags.
- Michel Espinoza-Fonseca (Thu May 05 2005 - 14:29:01 CDT)
- Hidekazu WATANABE (Thu May 05 2005 - 12:36:21 CDT)
- Michel Espinoza-Fonseca (Wed May 04 2005 - 17:07:13 CDT)
- Hidekazu WATANABE (Wed May 04 2005 - 16:40:23 CDT)
About plumed installation problem in NAMD_2.6_AIX-POWER-MPI
- Axel Kohlmeyer (Tue Dec 28 2010 - 03:35:00 CST)
- Buddhadev Maiti (Mon Dec 27 2010 - 21:30:38 CST)
About pmf
- Sterling Paramore (Tue Jun 26 2007 - 16:58:01 CDT)
- JC Gumbart (Tue Jun 26 2007 - 15:24:01 CDT)
- Sting (Mon Jun 25 2007 - 21:38:26 CDT)
- JC Gumbart (Mon Jun 25 2007 - 14:30:51 CDT)
- Sting (Sat Jun 23 2007 - 21:23:24 CDT)
- Sting (Tue Jun 19 2007 - 22:38:39 CDT)
- bqluan (Tue Jun 19 2007 - 10:35:02 CDT)
- JC Gumbart (Tue Jun 19 2007 - 00:02:42 CDT)
- Sting (Mon Jun 18 2007 - 23:00:38 CDT)
- Sting (Thu Jun 14 2007 - 21:49:03 CDT)
- mashaojie163 (Sun Jun 20 2004 - 21:10:00 CDT)
about PMF and MCTI
- Luca Bellucci (Fri May 11 2007 - 09:02:33 CDT)
About Potential Addition in NAMD
- yangbing00_at_mails.tsinghua.edu.cn (Wed Sep 28 2005 - 06:45:18 CDT)
About pressureProfile command for non-equilibrium system.
- Boyang Wang (Wed Jul 26 2006 - 19:50:20 CDT)
about protein phosphorylation
- Zhang, Jiong (MU-Student) (Wed Sep 22 2010 - 11:59:36 CDT)
about protonation of HIS in membrane protein
- Michel Espinoza-Fonseca (Wed Apr 13 2005 - 19:47:52 CDT)
- Aaron Oakley (Wed Apr 13 2005 - 19:10:18 CDT)
- Baoqiang Cao (Wed Apr 13 2005 - 09:21:08 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 psfgen
- Ramya Gamini (Sat Jul 04 2009 - 14:43:53 CDT)
- Ramya Gamini (Sat Jul 04 2009 - 14:33:32 CDT)
- emilia.l.wu (Sat Jul 04 2009 - 10:53:18 CDT)
- Ramya Gamini (Sat Jul 04 2009 - 09:40:46 CDT)
- emilia.l.wu (Sat Jul 04 2009 - 08:59:44 CDT)
About QM-MM
- Christopher Harrison (Thu Aug 30 2007 - 08:30:05 CDT)
- Francesco Pietra (Thu Aug 30 2007 - 00:50:35 CDT)
- Dow_Hurst (Thu Aug 30 2007 - 00:02:52 CDT)
- Dhiraj Srivastava (Wed Aug 29 2007 - 12:05:26 CDT)
- Dhiraj Srivastava (Wed Aug 29 2007 - 11:45:39 CDT)
- Ilya Chorny (Wed Aug 29 2007 - 12:26:19 CDT)
- Francesco Pietra (Wed Aug 29 2007 - 11:54:12 CDT)
- Francesco Pietra (Wed Aug 29 2007 - 11:34:45 CDT)
- Francesco Pietra (Wed Aug 29 2007 - 11:59:28 CDT)
- Dhiraj Srivastava (Wed Aug 29 2007 - 11:31:00 CDT)
- Francesco Pietra (Wed Aug 29 2007 - 01:38:17 CDT)
- Eduardo Tejera (Tue Aug 28 2007 - 18:26:48 CDT)
- Francesco Pietra (Tue Aug 28 2007 - 15:19:05 CDT)
- Francesco Pietra (Tue Aug 28 2007 - 14:46:49 CDT)
- Christopher Harrison (Tue Aug 28 2007 - 12:42:51 CDT)
- Ilya Chorny (Tue Aug 28 2007 - 10:21:24 CDT)
- Francesco Pietra (Tue Aug 28 2007 - 08:18:18 CDT)
about recentering of namd trajectory
- zhangliqun (Tue Aug 17 2010 - 10:50:54 CDT)
About ref frame for rmsd vs time
- Francesco Pietra (Wed Jan 30 2008 - 00:52:48 CST)
about restart
- namd_chcwaaa_at_yahoo.com.cn (Thu Oct 08 2009 - 06:46:07 CDT)
- Michel Espinoza-Fonseca (Thu May 05 2005 - 21:50:29 CDT)
- Boyang Wang (Thu May 05 2005 - 18:50:52 CDT)
About restart.vel.old file.
- Boyang Wang (Fri Apr 07 2006 - 22:15:58 CDT)
about rigid bonds
- Axel Kohlmeyer (Wed Apr 13 2011 - 10:38:19 CDT)
- Jim Phillips (Wed Apr 13 2011 - 10:32:07 CDT)
- oguz gurbulak (Wed Apr 13 2011 - 03:39:34 CDT)
- Brian Bennion (Tue Jan 18 2005 - 10:29:19 CST)
- mashaojie163 (Mon Jan 17 2005 - 07:24:39 CST)
About RMSD
- cong chen (Tue Nov 20 2007 - 03:29:32 CST)
About RMSD based PMF's
- Jérôme Hénin (Fri May 14 2010 - 06:05:28 CDT)
- Felipe Merino (Thu May 13 2010 - 23:03:44 CDT)
About RMSD calculation.
- Boyang Wang (Fri Oct 28 2005 - 16:56:09 CDT)
- Peter Freddolino (Fri Oct 28 2005 - 16:20:48 CDT)
- Boyang Wang (Fri Oct 28 2005 - 15:55:41 CDT)
- LEWYN LI (Fri Oct 28 2005 - 15:30:20 CDT)
- Boyang Wang (Fri Oct 28 2005 - 10:49:14 CDT)
about signal 11 received,exiting
- mashaojie163 (Fri Nov 09 2007 - 10:11:15 CST)
About SMD
- Roman Petrenko (Thu Aug 13 2009 - 10:33:34 CDT)
- Yang MIngjun (Tue Aug 11 2009 - 22:11:51 CDT)
- Sting (Sat Jun 16 2007 - 04:14:57 CDT)
- Sting (Fri Jun 15 2007 - 04:46:54 CDT)
about symmetry operations
- mashaojie163 (Wed Jul 07 2004 - 10:23:45 CDT)
about TCL boundary forces
- Giovanni Bellesia (Mon May 22 2006 - 14:31:14 CDT)
- gbellesia_at_chem.ucsb.edu (Sat Apr 29 2006 - 17:16:54 CDT)
about temperature reassign?
- yxiong_at_mail.ccnu.edu.cn (Sat Dec 06 2003 - 03:42:30 CST)
About the command "loadtotalforces"
- Marc Q. Ma (Fri Aug 26 2005 - 09:25:58 CDT)
- Jim Phillips (Thu Aug 25 2005 - 18:14:34 CDT)
- LEWYN LI (Mon Aug 22 2005 - 21:25:44 CDT)
About the command "set z [lindex $coorList($i) 2]".
- Boyang Wang (Sun Apr 16 2006 - 19:45:30 CDT)
- Marcos Sotomayor (Sun Apr 16 2006 - 18:33:04 CDT)
- Boyang Wang (Sat Apr 15 2006 - 19:47:04 CDT)
About the err of "Constraint failure"
- Aurum Bai (Sun Feb 21 2010 - 03:13:25 CST)
About the err of "distanceZ"!
- Jian Liu (Mon Feb 22 2010 - 07:57:37 CST)
- Aurum Bai (Mon Feb 22 2010 - 03:28:31 CST)
About the error of "Tcl interface"
- wang (Thu Jul 06 2006 - 00:26:31 CDT)
- wang (Wed Jul 05 2006 - 21:05:27 CDT)
about the memery lock in openMPI on infiniband
- Jim Phillips (Tue Mar 24 2009 - 22:44:29 CDT)
- ÁõÅô (Mon Mar 09 2009 - 04:27:11 CDT)
- ÁõÅô (Sun Mar 08 2009 - 03:55:40 CDT)
About the module of "External Electric Field "
- Michael Grabe (Tue Jul 18 2006 - 20:50:29 CDT)
- wang (Tue Jul 18 2006 - 19:50:43 CDT)
- Peter Freddolino (Wed Jul 12 2006 - 02:02:03 CDT)
- wang (Wed Jul 12 2006 - 01:47:29 CDT)
about the MSE residue
- Peter Freddolino (Mon Mar 27 2006 - 08:42:39 CST)
- Shulin Zhuang (Sun Mar 26 2006 - 23:42:16 CST)
About the namd tutorial err
- Aurum Bai (Tue Aug 18 2009 - 23:55:01 CDT)
About the Nucleic Acid parameter and protein parameters
- Aurum Bai (Sun Dec 06 2009 - 05:59:36 CST)
About the potantial of IONS
- Mauricio Carrillo Tripp (Fri Oct 07 2005 - 10:29:17 CDT)
- yangbing00_at_mails.tsinghua.edu.cn (Thu Oct 06 2005 - 22:16:17 CDT)
About the potential of NAMD
- Brian Bennion (Fri Oct 07 2005 - 10:35:42 CDT)
- yangbing00_at_mails.tsinghua.edu.cn (Thu Oct 06 2005 - 22:53:46 CDT)
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 the solvate package
- ehenriques_at_qui.uc.pt (Fri Aug 20 2010 - 03:47:28 CDT)
- c00jsw00 (Thu Aug 19 2010 - 22:25:31 CDT)
About the Source code.
- Boyang Wang (Mon Dec 26 2005 - 21:40:56 CST)
About the unit of "efield"
- a-yermakova_at_northwestern.edu (Wed Jul 19 2006 - 13:24:39 CDT)
- wang (Tue Jul 18 2006 - 00:28:03 CDT)
about this bug alert
- jz7_at_duke.edu (Thu Jun 03 2004 - 09:46:54 CDT)
About timestep again.
- Boyang Wang (Mon May 08 2006 - 17:38:07 CDT)
About timestep again. -- Fastest motion O-H streching period 10 fs.
- Peter Freddolino (Mon May 08 2006 - 16:09:25 CDT)
- Boyang Wang (Mon May 08 2006 - 11:14:37 CDT)
about topology generation
- JC Gumbart (Tue Dec 05 2006 - 13:07:43 CST)
- Dhiraj Srivastava (Tue Dec 05 2006 - 01:34:08 CST)
- Sting (Tue Dec 05 2006 - 01:03:56 CST)
- Sting (Mon Dec 04 2006 - 22:18:26 CST)
About viscosity calculation
- Armen H. Poghosyan (Sun Feb 21 2010 - 18:22:12 CST)
abrupt deviation in rmsd values
- Monika Sharma (Fri May 04 2007 - 12:41:24 CDT)
- Peter Freddolino (Thu May 03 2007 - 19:25:27 CDT)
- Giovanni Bellesia (Thu May 03 2007 - 11:34:22 CDT)
- Monika Sharma (Thu May 03 2007 - 10:43:29 CDT)
- Peter Freddolino (Wed May 02 2007 - 20:28:57 CDT)
- Monika Sharma (Wed May 02 2007 - 10:35:38 CDT)
ABSOLUTE IMPRECISION and RELATIVE IMPRECISION IN TABLE FORCE
- Joshua D. Moore (Fri Dec 23 2005 - 03:01:17 CST)
Accelerated MD documentation?
- Chris Harrison (Sat Mar 19 2011 - 00:15:15 CDT)
- Bjoern Olausson (Tue Mar 15 2011 - 10:47:21 CDT)
- Francesco Pietra (Tue Mar 15 2011 - 10:20:18 CDT)
- Chris Harrison (Tue Mar 15 2011 - 09:28:35 CDT)
- Chris Harrison (Tue Mar 15 2011 - 09:22:55 CDT)
- Bjoern Olausson (Tue Mar 15 2011 - 08:59:48 CDT)
- patrick wintrode (Tue Mar 15 2011 - 08:05:19 CDT)
Accelerated MD with membrane embedded proteins.
- Raul Araya (Mon Mar 28 2011 - 13:45:36 CDT)
Accelerated MD: question about dual boost mode
- Bjoern Olausson (Tue May 10 2011 - 10:17:59 CDT)
- Bjoern Olausson (Tue May 10 2011 - 07:32:13 CDT)
- Jeff Wereszczynski (Thu Mar 31 2011 - 17:07:07 CDT)
- patrick wintrode (Thu Mar 31 2011 - 15:01:49 CDT)
Accelerated MD?
- Chris Harrison (Thu Sep 23 2010 - 11:17:07 CDT)
- patrick wintrode (Thu Sep 23 2010 - 09:44:41 CDT)
Accelerated Molecular Dynamics
- Vijay Vammi (Wed Nov 02 2011 - 20:42:07 CDT)
- Vijay Vammi (Tue Oct 25 2011 - 23:45:32 CDT)
- Vijay Vammi (Tue Oct 25 2011 - 21:04:49 CDT)
- Yi Wang (Tue Oct 25 2011 - 18:03:33 CDT)
- Vijay Vammi (Tue Oct 25 2011 - 16:11:54 CDT)
Accelerating groups of atoms
- Cesar Luis Avila (Tue Sep 05 2006 - 15:18:59 CDT)
Acceptable pressure values
- Peter Freddolino (Tue May 27 2008 - 14:33:00 CDT)
- Fabio Zegarra (Mon May 26 2008 - 19:32:21 CDT)
- Peter Freddolino (Sat May 24 2008 - 09:27:24 CDT)
- Fabio Zegarra (Fri May 23 2008 - 17:24:22 CDT)
Acceptance ratio of REMD simulation
- jaya c.jose (Tue Sep 07 2010 - 05:47:04 CDT)
Accepted temperature and pressure oscillation
- cong chen (Wed Oct 31 2007 - 03:14:55 CDT)
Access to CVS
- Roman Petrenko (Tue Dec 16 2008 - 20:14:00 CST)
- Christopher Share (Tue Dec 16 2008 - 19:08:53 CST)
Accessing atoms and velocities during NVE run
- Axel Kohlmeyer (Fri Feb 06 2009 - 15:42:20 CST)
- Nd S (Fri Feb 06 2009 - 15:14:59 CST)
- Chris Harrison (Fri Feb 06 2009 - 15:00:36 CST)
- Nd S (Fri Feb 06 2009 - 13:33:53 CST)
- Brian Bennion (Fri Feb 06 2009 - 13:08:24 CST)
- Chris Harrison (Fri Feb 06 2009 - 12:06:58 CST)
- Nd S (Fri Feb 06 2009 - 10:57:02 CST)
Accessing beta / occupancy values from NAMD tcl
- Jérôme Hénin (Mon Jun 27 2005 - 11:52:05 CDT)
- wmsmith (Mon Jun 27 2005 - 10:24:47 CDT)
Accessing Colvars Within NAMD TCL
- Jérôme Hénin (Thu Jun 30 2011 - 12:05:01 CDT)
- David Rogers (Thu Jun 30 2011 - 10:28:33 CDT)
accuracy of measurement
- Gianluca Interlandi (Mon Feb 21 2011 - 22:11:43 CST)
- Pletezhov Alexandr (Mon Feb 21 2011 - 17:14:16 CST)
ACE patch
- paul.dalhaimer_at_yale.edu (Wed Apr 12 2006 - 10:56:46 CDT)
Acetaldehyde Dihedral Parameters
- Peter Freddolino (Wed Jun 06 2007 - 14:28:20 CDT)
- L. Michel Espinoza-Fonseca (Wed Jun 06 2007 - 12:21:38 CDT)
- Peter Freddolino (Wed Jun 06 2007 - 11:51:57 CDT)
- Peter Freddolino (Wed Jun 06 2007 - 11:19:42 CDT)
- L. Michel Espinoza-Fonseca (Wed Jun 06 2007 - 11:05:20 CDT)
- Kevser Göçmen Topal (Wed Jun 06 2007 - 10:33:14 CDT)
Acetyl group patch for lysine residue
- ehenriques_at_qui.uc.pt (Mon May 17 2010 - 03:56:01 CDT)
- Prija Ponnan (Sat May 15 2010 - 08:19:51 CDT)
AcetylProlineAmide topology
- Neelanjana Sengupta (Wed Jan 17 2007 - 12:35:45 CST)
acridine orange
- Rudra Banerjee (Thu Mar 19 2009 - 23:54:50 CDT)
across the nodes, namd jobs don't get enough CPU!
- M. Madhu (Fri Jul 07 2006 - 11:00:59 CDT)
Add bonds and topology file problem
- Edroaldo Lummertz da Rocha (Sun May 01 2011 - 16:57:16 CDT)
- Axel Kohlmeyer (Sun May 01 2011 - 15:52:30 CDT)
- Edroaldo Lummertz da Rocha (Sun May 01 2011 - 15:20:01 CDT)
add calcium chloride
- Thomas C. Bishop (Wed Apr 16 2008 - 10:12:24 CDT)
- Christine Horejs DI (Wed Apr 16 2008 - 08:22:28 CDT)
- Christine Horejs DI (Wed Apr 16 2008 - 07:30:41 CDT)
- Peter Freddolino (Mon Apr 07 2008 - 08:09:58 CDT)
- Christine Horejs DI (Mon Apr 07 2008 - 03:21:59 CDT)
Add ions
- Christopher Gillespie (Wed Nov 05 2008 - 07:06:51 CST)
- ydhuang2727 (Wed Nov 05 2008 - 02:16:33 CST)
- Blake Charlebois (Mon Aug 08 2005 - 09:34:41 CDT)
- Mahalakshmi Sahasranaman (Mon Aug 08 2005 - 07:41:33 CDT)
add Mg2+
- Lixia Jin Day (Thu Dec 13 2007 - 11:30:26 CST)
add water on the top of the protein border
- Xiaoqing Wang (Wed Apr 06 2005 - 09:11:47 CDT)
added more bases to DNA using psfgen
- Stern, Julie (Thu Jul 21 2005 - 21:50:55 CDT)
addforce
- Arturas Ziemys (Wed Dec 13 2006 - 14:16:43 CST)
- Pijush Ghosh (Tue Jun 14 2005 - 14:23:05 CDT)
- LEWYN LI (Tue Jun 14 2005 - 14:07:10 CDT)
- Leandro Martínez (Tue Jun 14 2005 - 10:02:28 CDT)
- Leandro Martínez (Tue Apr 19 2005 - 11:37:55 CDT)
- Jérôme Hénin (Tue Apr 19 2005 - 11:21:21 CDT)
- Marc Q. Ma (Tue Apr 19 2005 - 11:17:20 CDT)
- Leandro Martínez (Tue Apr 19 2005 - 09:38:50 CDT)
addforce on the com of a group of atoms and loadforces command
- Vlad Cojocaru (Tue Dec 23 2008 - 07:57:29 CST)
Adding a new bond to CHARMM
- DimitryASuplatov (Sat Apr 25 2009 - 08:56:05 CDT)
- DimitryASuplatov (Sat Apr 25 2009 - 08:23:19 CDT)
Adding amino acids to an existing pdb structure
- LEWYN LI (Sun Dec 04 2005 - 21:30:49 CST)
adding constraints
- doty alexiou (Thu Nov 26 2009 - 15:40:09 CST)
Adding extra bond
- Francesco Oteri (Fri Dec 17 2010 - 05:52:46 CST)
- Axel Kohlmeyer (Fri Dec 17 2010 - 04:20:11 CST)
- Erik Nordgren (Thu Dec 16 2010 - 13:00:34 CST)
- Francesco Oteri (Sun Dec 12 2010 - 04:22:05 CST)
adding extra ions to neutralize charge on protein
- Anahita Tafvizi (Thu Oct 19 2006 - 12:30:02 CDT)
- Dhiraj Srivastava (Thu Oct 19 2006 - 11:42:48 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)
Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints )
- wmsmith (Wed Jun 29 2005 - 13:43:44 CDT)
- JC Gumbart (Wed Jun 29 2005 - 11:18:23 CDT)
- Sascha Tayefeh (Wed Jun 29 2005 - 09:56:54 CDT)
- JC Gumbart (Wed Jun 29 2005 - 09:40:41 CDT)
- Sascha Tayefeh (Wed Jun 29 2005 - 09:31:23 CDT)
Adding special VdW parameters
- Axel Kohlmeyer (Sat Dec 25 2010 - 11:22:38 CST)
- Luca Bellucci (Sat Dec 25 2010 - 10:04:55 CST)
adding specific forces between atoms
- Michael Zimmermann (Mon Sep 21 2009 - 15:44:48 CDT)
ADENOSINE-5-DIPHOSPHORIBOSE topology
- Eduard Schreiner (Tue Oct 05 2010 - 22:11:50 CDT)
- Raul Araya (Tue Oct 05 2010 - 20:56:42 CDT)
adjusted background load
- Roman Petrenko (Sat Sep 20 2008 - 10:13:08 CDT)
Adjusting Density of waterbox used by solvate
- Wolbach, Jeffrey P $WOLBACH$ (Mon Jun 13 2005 - 11:36:11 CDT)
- Leonardo Sepulveda Durán (Sun Jun 12 2005 - 21:51:51 CDT)
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)
Advice on buying GPUs
- Axel Kohlmeyer (Mon Jun 06 2011 - 06:50:16 CDT)
- Ajasja LjubetiÄ (Mon Jun 06 2011 - 06:39:31 CDT)
- Ajasja Ljubetiè (Thu Jun 02 2011 - 09:46:55 CDT)
- Axel Kohlmeyer (Thu Jun 02 2011 - 09:06:08 CDT)
- Ajasja Ljubetiè (Thu Jun 02 2011 - 08:27:47 CDT)
- Axel Kohlmeyer (Thu Jun 02 2011 - 06:17:14 CDT)
- Ajasja LjubetiÄ (Thu Jun 02 2011 - 03:13:10 CDT)
- Ajasja LjubetiÄ (Wed Jun 01 2011 - 09:43:24 CDT)
advice on van Hove
- Arturas Ziemys (Thu Jan 15 2009 - 12:08:40 CST)
Advisable limit on the number of quadrants a 2D ABF simulation can be split.
- Jérôme Hénin (Mon Mar 28 2011 - 09:42:33 CDT)
- Ajasja LjubetiÄ (Mon Mar 28 2011 - 09:06:40 CDT)
- Jérôme Hénin (Fri Mar 25 2011 - 06:25:30 CDT)
- Ajasja LjubetiÄ (Fri Mar 25 2011 - 04:52:09 CDT)
affecting the atom velocities
- Luca Muccioli (Fri Jun 15 2007 - 04:02:01 CDT)
- Philipp Schoen1 (Fri Jun 15 2007 - 02:20:55 CDT)
alanine dipeptide: no dihdral energy terms?
- Peter Freddolino (Fri Mar 27 2009 - 14:42:54 CDT)
- Sebastian Stolzenberg (Thu Mar 26 2009 - 19:21:04 CDT)
- Peter Freddolino (Mon Mar 23 2009 - 22:45:01 CDT)
- Sebastian Stolzenberg (Mon Mar 23 2009 - 22:33:03 CDT)
alchDecouple
- Jérôme Hénin (Mon Jul 25 2011 - 15:19:14 CDT)
- Jérôme Hénin (Sat Jul 23 2011 - 02:44:36 CDT)
- esmael (Fri Jul 22 2011 - 19:10:59 CDT)
Alchemical calculations in CUDA version of NAMD?
- Chris Harrison (Wed Mar 17 2010 - 02:37:21 CDT)
- Lela Vukovic (Wed Mar 17 2010 - 01:28:50 CDT)
- Lela Vukovic (Wed Mar 03 2010 - 12:01:03 CST)
- Lela Vukovic (Wed Mar 03 2010 - 11:33:36 CST)
alchemical fep amber topology
- Chris Harrison (Sat Mar 14 2009 - 08:47:49 CDT)
- Chris Harrison (Sat Mar 14 2009 - 08:33:48 CDT)
- Floris Buelens (Sat Mar 14 2009 - 05:53:37 CDT)
- Floris Buelens (Sat Mar 14 2009 - 06:16:37 CDT)
- George Madalin Giambasu (Fri Mar 13 2009 - 15:38:29 CDT)
- Jerome Henin (Fri Mar 13 2009 - 15:43:47 CDT)
- Jerome Henin (Fri Mar 13 2009 - 15:26:34 CDT)
- Jerome Henin (Fri Mar 13 2009 - 15:24:43 CDT)
- George Madalin Giambasu (Fri Mar 13 2009 - 13:55:22 CDT)
Alchemical FEP calculations in NAMD
- Satyavani Vemparala (Fri Feb 20 2004 - 22:09:43 CST)
Alchemical FEP NAMD tutorial - problems with reproducing the results
- Chris Chipot (Thu Feb 21 2008 - 03:19:42 CST)
- Jawahar Neelankatan (Wed Feb 20 2008 - 14:48:54 CST)
- Chris Chipot (Tue Feb 19 2008 - 07:14:13 CST)
- Jawahar Neelankatan (Mon Feb 18 2008 - 21:25:54 CST)
alchemical FEP question
- seleg25_at_rsvs.ulaval.ca (Sun Dec 21 2008 - 12:14:41 CST)
- SÃ©bastien LÃ©garÃ© (Sun Dec 21 2008 - 20:03:07 CST)
- Chris Chipot (Sun Dec 21 2008 - 13:27:57 CST)
- Christophe.Chipot_at_edam.uhp-nancy.fr (Sat Dec 20 2008 - 05:23:16 CST)
- Nandhini Sokkalingam (Fri Dec 19 2008 - 21:44:52 CST)
Alchemical FEP tutorial files
- Christian Jorgensen (Thu Oct 07 2010 - 09:35:31 CDT)
- Chris Harrison (Thu Oct 07 2010 - 07:23:24 CDT)
- JC Gumbart (Thu Oct 07 2010 - 07:36:13 CDT)
- Christian Jorgensen (Thu Oct 07 2010 - 06:55:09 CDT)
Alchemical Free Energy Perturbation
- Jérôme Hénin (Thu Mar 02 2006 - 07:39:16 CST)
- jsachs_at_mail.csb.yale.edu (Wed Mar 01 2006 - 15:31:07 CST)
- Jérôme Hénin (Tue Feb 28 2006 - 12:50:00 CST)
- Michael Grabe (Tue Feb 28 2006 - 12:09:50 CST)
- jsachs_at_mail.csb.yale.edu (Tue Feb 28 2006 - 10:00:13 CST)
- Jérôme Hénin (Tue Feb 28 2006 - 09:03:55 CST)
- Jawahar Neelankatan (Sat Feb 25 2006 - 00:40:02 CST)
- Jawahar Neelankatan (Sat Feb 25 2006 - 01:36:29 CST)
- by way of Jérôme Hénin (Mon Jan 05 2004 - 09:10:52 CST)
- AMIT PALIWAL (Mon Jan 05 2004 - 00:37:05 CST)
Alchemical Free Energy Perturbation Simulation
- yi wang (Wed Aug 02 2006 - 12:10:51 CDT)
- Jawahar Neelankatan (Fri Jul 28 2006 - 11:18:20 CDT)
Alchemical free-energy methods and electroneutrality
- JC Gumbart (Sat Jan 28 2012 - 15:47:54 CST)
- Rajan Vatassery (Sat Jan 28 2012 - 15:31:18 CST)
- Thomas Albers (Sat Jan 28 2012 - 13:35:27 CST)
alchemical transformation
- Jerome Henin (Thu Aug 17 2006 - 14:44:27 CDT)
- Michael A. Wilson (Thu Aug 17 2006 - 12:04:55 CDT)
alchemify FEP
- Wei Chen (Fri Feb 18 2005 - 12:54:44 CST)
- Michael Grabe (Fri Feb 18 2005 - 01:26:17 CST)
- Jérôme Hénin (Thu Feb 17 2005 - 15:04:18 CST)
- Wei Chen (Thu Feb 17 2005 - 13:14:20 CST)
alchemify with CMAP?
- Jerome Henin (Mon Apr 20 2009 - 11:42:05 CDT)
- Jerome Henin (Fri Apr 17 2009 - 14:44:11 CDT)
- Sébastien Légaré (Fri Apr 17 2009 - 11:01:08 CDT)
- Jerome Henin (Thu Apr 16 2009 - 19:21:51 CDT)
- Chris Chipot (Thu Apr 16 2009 - 19:21:19 CDT)
- Sebastian Stolzenberg (Thu Apr 16 2009 - 19:11:53 CDT)
alchemy FEP query
- Madhurima Jana (Fri Jul 16 2010 - 01:05:44 CDT)
AlF4
- Laurent Chaloin (Thu Sep 17 2009 - 04:54:14 CDT)
aligning ligands
- Narender Singh Maan (Fri Feb 23 2007 - 12:39:45 CST)
Aligning structures
- Dong Luo (Fri Mar 10 2006 - 11:11:03 CST)
- Luis Gracia (Fri Mar 10 2006 - 08:45:18 CST)
- EPF $Esben Peter Friis$ (Fri Mar 10 2006 - 01:34:40 CST)
- Peter Freddolino (Thu Mar 09 2006 - 21:37:05 CST)
- Richard Wood (Thu Mar 09 2006 - 21:20:45 CST)
Aligning the distance between two centroids with an axis
- Mert Gür (Sat Jan 31 2009 - 02:13:38 CST)
- Chris Harrison (Fri Jan 30 2009 - 21:31:43 CST)
- Grace Brannigan (Fri Jan 30 2009 - 10:01:55 CST)
- Nicholas M Glykos (Fri Jan 30 2009 - 05:08:19 CST)
- Mert Gür (Fri Jan 30 2009 - 04:02:55 CST)
aligning two molecules by principal axes of inertia using measure.c
- Ajasja LjubetiÄ (Mon Jun 20 2011 - 09:40:20 CDT)
- Ada Sedova (Mon Jun 20 2011 - 08:18:41 CDT)
Alignment of velocity dcd file
- Axel Kohlmeyer (Sat Aug 22 2009 - 15:49:19 CDT)
- Mert Gür (Sat Aug 22 2009 - 15:03:10 CDT)
alkane-silicon_dioxide simulation
- Eduardo Cruz-Chu (Thu Jul 10 2008 - 15:46:25 CDT)
- Raul Araya Secchi (Thu Jul 10 2008 - 15:18:06 CDT)
all atom simulations with explicit water molecules and langevin thermostat
- Margaret S. Cheung (Fri Oct 05 2007 - 09:54:20 CDT)
- Jojart Balazs (Fri Oct 05 2007 - 05:41:14 CDT)
- Margaret S. Cheung (Thu Oct 04 2007 - 16:28:14 CDT)
all atom simulations with explicit water molecules and langevinthermostat
- wzhuang (Thu Oct 04 2007 - 20:16:04 CDT)
All or Nothing at All??
- Angelo R. Rossi (Sat Oct 29 2005 - 11:41:32 CDT)
Allowed CMAP dimensions
- yandong Huang (Tue Dec 28 2010 - 03:39:33 CST)
- Ajasja LjubetiÄ (Fri Nov 26 2010 - 10:23:23 CST)
- Ajasja LjubetiÄ (Tue Nov 23 2010 - 11:07:33 CST)
Allowed CMAP dimensions in NAMD
- A D (Thu Mar 18 2010 - 20:11:24 CDT)
alpha character error in the psf file
- Peter Freddolino (Wed Jan 28 2009 - 07:18:52 CST)
- OZGE ENGIN (Wed Jan 28 2009 - 07:22:51 CST)
- OZGE ENGIN (Wed Jan 28 2009 - 03:30:26 CST)
Alpha P.M.F. with NAMD 2.8
- Prathit Chatterjee (Fri Jun 03 2011 - 07:55:52 CDT)
- Giacomo Fiorin (Fri Jun 03 2011 - 07:16:05 CDT)
- Ajasja LjubetiÄ (Fri Jun 03 2011 - 07:05:47 CDT)
- Prathit Chatterjee (Fri Jun 03 2011 - 06:21:46 CDT)
alpha pmf
- Jérôme Hénin (Tue May 10 2011 - 03:37:24 CDT)
- Giacomo Fiorin (Mon May 09 2011 - 16:05:19 CDT)
- Prathit Chatterjee (Sat May 07 2011 - 00:33:28 CDT)
- Jérôme Hénin (Fri May 06 2011 - 07:58:37 CDT)
- Prathit Chatterjee (Fri May 06 2011 - 05:54:55 CDT)
- Giacomo Fiorin (Thu May 05 2011 - 09:31:51 CDT)
- Prathit Chatterjee (Thu May 05 2011 - 01:21:02 CDT)
- Jérôme Hénin (Wed May 04 2011 - 04:17:16 CDT)
- Ajasja LjubetiÄ (Wed May 04 2011 - 03:04:14 CDT)
- felmerino_at_uchile.cl (Wed May 04 2011 - 02:37:06 CDT)
- Prathit Chatterjee (Wed May 04 2011 - 00:55:40 CDT)
altering residues in .pdb files
- Grace Brannigan (Mon Mar 29 2010 - 15:20:39 CDT)
- muniyamuthu.raviprasad_at_ndsu.edu (Mon Mar 29 2010 - 11:20:08 CDT)
- Peter Jones (Fri Mar 26 2010 - 20:29:00 CDT)
- Thomas Kahn (Fri Mar 26 2010 - 18:34:53 CDT)
Altix Performance Tuning
- Alessandro Cembran (Wed Sep 20 2006 - 11:03:53 CDT)
- Jim Phillips (Wed Sep 20 2006 - 00:07:00 CDT)
- Mark Abraham (Mon Sep 18 2006 - 13:42:53 CDT)
- Alessandro Cembran (Mon Sep 18 2006 - 13:18:52 CDT)
Altix performances
- Alessandro Cembran (Tue Jun 13 2006 - 17:40:59 CDT)
Am I using the right version for accelerated MD?
- Chris Harrison (Tue Mar 22 2011 - 16:11:35 CDT)
- patrick wintrode (Tue Mar 22 2011 - 15:34:29 CDT)
Amber and SHAKE algorimth
- Marcela P.Aliste (Thu Feb 24 2005 - 16:14:26 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 ff system has too high velocities in NAMD
- Marc Q. Ma (Wed Apr 13 2005 - 08:59:31 CDT)
- Lina Nilsson (Wed Apr 13 2005 - 03:16:45 CDT)
Amber ff99sb force-field in namd
- Benjamin Bouvier (Wed Mar 18 2009 - 18:19:23 CDT)
- Joshua Adelman (Wed Mar 18 2009 - 17:25:13 CDT)
AMBER ff99SB on NAMD
- Luis Cunha (Sun Nov 02 2008 - 09:21:17 CST)
- Luca (Sun Nov 02 2008 - 02:26:52 CST)
- Luis Cunha (Sat Nov 01 2008 - 19:43:30 CDT)
AMBER force field in NAMD
- Wei Chen (Fri Sep 10 2010 - 12:48:15 CDT)
- Patargias, George (Fri Sep 10 2010 - 09:48:01 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 Parameter in NAMD
- snoze pa (Wed Feb 08 2006 - 18:42:00 CST)
AMBER parameters and SMD
- Valodymyr Nechyporuk-Zloy (Mon Jul 26 2004 - 04:42:55 CDT)
amber parameters for congo red
- Shaheen Ahmed (Thu Jun 19 2008 - 02:19:08 CDT)
- L. Michel Espinoza-Fonseca (Thu Jun 19 2008 - 04:07:31 CDT)
- L. Michel Espinoza-Fonseca (Wed Jun 18 2008 - 16:07:30 CDT)
- Shaheen Ahmed (Wed Jun 18 2008 - 15:29:22 CDT)
Amber PARM Input File Example?
- Vlad Cojocaru (Fri Apr 27 2007 - 10:19:56 CDT)
- Huy N. Ha (Fri Apr 27 2007 - 07:39:57 CDT)
- wang (Fri Apr 27 2007 - 02:43:38 CDT)
- Mark Abraham (Fri Apr 27 2007 - 00:58:33 CDT)
- Huy N. Ha (Fri Apr 27 2007 - 00:51:37 CDT)
Amber topology in CUDA NAMD - can it be done?
- Jim Phillips (Tue Oct 19 2010 - 11:43:10 CDT)
- Axel Kohlmeyer (Tue Oct 19 2010 - 08:32:45 CDT)
- Axel Kohlmeyer (Tue Oct 19 2010 - 08:42:15 CDT)
- Benjamin Bouvier (Tue Oct 19 2010 - 07:27:48 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)
AMD Multicore + CUDA Benchmarks, are them ok ?
- Axel Kohlmeyer (Thu May 05 2011 - 08:57:18 CDT)
- Axel Kohlmeyer (Thu May 05 2011 - 08:47:56 CDT)
- Nicholas M Glykos (Thu May 05 2011 - 04:31:52 CDT)
- David McGiven (Thu May 05 2011 - 04:08:30 CDT)
AMD-PhenomII-1075_GTX470 NAMD-CUDA performance
- Axel Kohlmeyer (Mon Jun 06 2011 - 06:57:35 CDT)
- Axel Kohlmeyer (Mon Jun 06 2011 - 06:29:38 CDT)
- Axel Kohlmeyer (Mon Jun 06 2011 - 05:50:24 CDT)
- Francesco Pietra (Mon Jun 06 2011 - 02:54:52 CDT)
AMD64 or PIV Prescott ...
- Slawomir Orlowski (Tue Jan 11 2005 - 05:52:48 CST)
amidated C-terminus (NH2) with OPLS force field
- Giovanni Bellesia (Mon Apr 17 2006 - 17:34:57 CDT)
Ammasso interconnect performance, LDB question
- Dow Hurst (Mon Sep 05 2005 - 23:21:12 CDT)
ammonia to methane
- Dale l. Schruben (Wed Apr 07 2010 - 11:37:10 CDT)
ammonia to methane/ c/o Jerome Henin
- Dale l. Schruben (Mon Apr 26 2010 - 21:18:01 CDT)
- ehenriques_at_qui.uc.pt (Mon Apr 26 2010 - 08:38:41 CDT)
- Jérôme Hénin (Fri Apr 23 2010 - 10:57:05 CDT)
- Dale l. Schruben (Fri Apr 23 2010 - 10:19:19 CDT)
ammonia to methane/DISREGARD this post-changes to files below make methane work now
- Dale l. Schruben (Wed Apr 07 2010 - 22:36:49 CDT)
an aptamer and a lot of stupid problems
- Xxxxxxxx Xxxxxxx (Mon Feb 11 2008 - 23:09:38 CST)
an important question for equilibration script
- Jernej Zidar (Thu Sep 29 2011 - 18:42:58 CDT)
- matziast_at_med.uth.gr (Thu Sep 29 2011 - 15:44:58 CDT)
An outlier appear on the curve of RMSD
- JC Gumbart (Sun Jul 26 2009 - 21:14:22 CDT)
- wayj86 wayj86 (Sun Jul 26 2009 - 20:42:13 CDT)
- wayj86 wayj86 (Thu Jul 23 2009 - 22:37:04 CDT)
analysis of dcd
- Gianluca Interlandi (Mon Feb 01 2010 - 01:13:45 CST)
- Roman Petrenko (Sun Jan 31 2010 - 23:25:36 CST)
- ipsita basu (Sun Jan 31 2010 - 22:58:41 CST)
Analysis of FEP output file
- Chris Chipot (Thu Feb 16 2012 - 07:35:12 CST)
- Chris Harrison (Wed Feb 15 2012 - 15:29:59 CST)
- sudipta (Tue Jan 31 2012 - 11:41:33 CST)
Analysis of NAMD output with CHARMM
- \ (Mon Feb 14 2005 - 12:15:58 CST)
- Nathalie Reuter (Mon Feb 14 2005 - 09:51:07 CST)
- Nathalie Reuter (Mon Feb 14 2005 - 07:21:56 CST)
- Leyla Celik (Mon Feb 14 2005 - 09:44:53 CST)
- Gianluca Interlandi (Mon Feb 14 2005 - 08:07:49 CST)
- Leyla Celik (Mon Feb 14 2005 - 07:48:28 CST)
- Leyla Celik (Mon Feb 14 2005 - 02:47:42 CST)
Analysis of Results of only Lipid Bilayer Simulations
- jani vinod (Wed May 19 2010 - 06:36:09 CDT)
- Saumya (Wed May 19 2010 - 05:22:06 CDT)
analysis question
- Bjoern Olausson (Tue Jul 19 2011 - 05:43:34 CDT)
- Namd Namd (Tue Jul 19 2011 - 04:32:06 CDT)
Andres Morales sent you a little gift
- Andres Morales (Sun Apr 11 2010 - 20:33:49 CDT)
Angle 2, Where is the problem [IMPORTANT]
- linefinc (Tue Jun 20 2006 - 11:02:28 CDT)
- Giovanni Bellesia (Tue Jun 20 2006 - 01:15:37 CDT)
- JC Gumbart (Tue Jun 20 2006 - 01:00:09 CDT)
- linefinc (Mon Jun 19 2006 - 11:50:41 CDT)
Angle CO2 Problem
- Brian Bennion (Fri Jun 16 2006 - 10:28:49 CDT)
- Brian Bennion (Fri Jun 16 2006 - 10:08:04 CDT)
- linefinc (Fri Jun 16 2006 - 06:08:23 CDT)
angle deformation
- Leonardo Trabuco (Fri Dec 19 2008 - 19:45:44 CST)
- Peter Freddolino (Fri Dec 19 2008 - 19:11:38 CST)
- CHINDEA Vlad (Fri Dec 19 2008 - 18:02:06 CST)
- JC Gumbart (Thu Dec 18 2008 - 23:04:17 CST)
- CHINDEA Vlad (Wed Dec 17 2008 - 17:00:49 CST)
angle in colvars
- Jerome Henin (Mon Nov 09 2009 - 09:09:17 CST)
- Felipe Merino (Mon Nov 09 2009 - 06:19:03 CST)
- Dimitar V Pachov (Sun Nov 08 2009 - 22:17:20 CST)
- Felipe Merino (Sun Nov 08 2009 - 21:52:10 CST)
Angle in parameter file
- Ajasja LjubetiÄ (Thu Oct 21 2010 - 07:13:17 CDT)
- Christian Jorgensen (Thu Oct 21 2010 - 06:08:03 CDT)
ANGLE PARAMETERS (It works now)
- Shirley Li (Thu Dec 22 2005 - 16:54:06 CST)
angles
- Giacomo Fiorin (Thu Mar 31 2011 - 18:05:28 CDT)
- flavio seixas (Thu Mar 31 2011 - 15:57:33 CDT)
Angles and dihedral generation
- Cesar Luis Avila (Fri Sep 01 2006 - 20:02:36 CDT)
ANN: MDAnalysis 0.3 python library
- nmichaud_at_jhu.edu (Mon Nov 12 2007 - 16:01:11 CST)
ANN: MDAnalysis python library
- nmichaud_at_jhu.edu (Tue Nov 13 2007 - 16:42:06 CST)
Announcement: QM/MM Workshop
- Jerome Henin (Thu Apr 19 2007 - 13:13:36 CDT)
Announcement: TCBG workshop at Pittsburgh Supercomputing Center May 10-14, 2010
- TCBG Workshops (Tue Jan 26 2010 - 13:41:36 CST)
anomalous behaviour of ASPP and GLUP during MD run
- Andreini Matteo (Thu Feb 25 2010 - 10:57:23 CST)
- Michel Espinoza-Fonseca (Thu Feb 25 2010 - 10:51:36 CST)
- La Fosca (Thu Feb 25 2010 - 09:04:29 CST)
- Andreini Matteo (Thu Feb 25 2010 - 08:24:45 CST)
- Andreini Matteo (Thu Feb 25 2010 - 02:31:45 CST)
Another PSF question...
- Richard Wood (Tue Feb 15 2011 - 16:13:13 CST)
Another question about MD simulation of a domain.
- \ (Tue Sep 27 2005 - 14:15:59 CDT)
- Boyang Wang (Tue Sep 27 2005 - 12:30:43 CDT)
Another question on Diffusion
- Vinit Rege (Wed Nov 08 2006 - 19:02:30 CST)
- Peter Freddolino (Wed Nov 08 2006 - 17:14:08 CST)
- Peter Freddolino (Wed Nov 08 2006 - 17:12:23 CST)
- Neelanjana Sengupta (Wed Nov 08 2006 - 15:58:09 CST)
- Vinit Rege (Wed Nov 08 2006 - 13:15:49 CST)
Another strange error: MStream checksums do not agree
- Axel Kohlmeyer (Thu Jul 09 2009 - 06:40:19 CDT)
- Vlad Cojocaru (Thu Jul 09 2009 - 03:05:13 CDT)
any experiences with executing parallel NAMD in a NAMD simulation
- Yinglong Miao (Tue Feb 10 2009 - 10:13:56 CST)
- Peter Freddolino (Tue Feb 10 2009 - 12:45:34 CST)
- Peter Freddolino (Tue Feb 10 2009 - 09:26:02 CST)
- Yinglong Miao (Mon Feb 09 2009 - 22:26:37 CST)
- Peter Freddolino (Mon Feb 09 2009 - 22:13:43 CST)
- Yinglong Miao (Mon Feb 09 2009 - 19:56:44 CST)
- Peter Freddolino (Mon Feb 09 2009 - 16:26:39 CST)
- Yinglong Miao (Mon Feb 09 2009 - 15:59:07 CST)
Any flag values returned when executing "minimize" and "run"?
- Yinglong Miao (Tue Nov 20 2007 - 12:46:10 CST)
- Victor Ovchinnikov (Tue Nov 20 2007 - 11:35:51 CST)
- Peter Freddolino (Tue Nov 20 2007 - 11:20:39 CST)
- Yinglong Miao (Tue Nov 20 2007 - 10:10:52 CST)
- Peter Freddolino (Tue Nov 20 2007 - 09:19:33 CST)
- Yinglong Miao (Mon Nov 19 2007 - 10:52:44 CST)
any script to build membrane+protein+solvent?
- Leandro Martínez (Sat Apr 09 2005 - 07:20:07 CDT)
- Xiaoqing Wang (Fri Apr 08 2005 - 21:23:48 CDT)
- Baoqiang Cao (Fri Apr 08 2005 - 10:02:36 CDT)
any SD minimization in NAMD?
- L. Michel Espinoza-Fonseca (Fri Jul 14 2006 - 11:36:09 CDT)
- Ching Wong (Thu Jul 13 2006 - 14:59:57 CDT)
Anyone have catdcd-4.0 for BlueGene?
- Joshua D. Moore (Mon Jan 08 2007 - 15:34:09 CST)
Anyone having problems under Solaris 7?
- Charles Danko (Mon Oct 11 2004 - 11:05:33 CDT)
apoa1 bencmark for 2.7 MPI compiled
- Branko (Fri Feb 05 2010 - 16:02:29 CST)
- Branko (Fri Feb 05 2010 - 13:00:21 CST)
ApoB structure
- Alexandre A. Vakhrouchev (Thu Jun 12 2008 - 01:12:02 CDT)
apologize for the typo
- Bennion, Brian (Fri Feb 12 2010 - 13:13:30 CST)
Appending dcd when restarting a simulation
- Eric H. Lee (Thu Jul 24 2008 - 08:58:21 CDT)
- Axel Kohlmeyer (Thu Jul 24 2008 - 08:52:56 CDT)
- pellegrini (Thu Jul 24 2008 - 03:17:02 CDT)
Appending to the existing dcd file after restart
- Andrei Istomin (Wed Jan 30 2008 - 02:06:55 CST)
apply force along an internally defined direction
- Chris Chipot (Mon Oct 29 2007 - 13:22:52 CDT)
- Vlad Cojocaru (Mon Oct 29 2007 - 12:59:00 CDT)
- Jerome Henin (Mon Oct 29 2007 - 11:20:29 CDT)
- Vlad Cojocaru (Mon Oct 29 2007 - 07:24:02 CDT)
apply periodic boundary condition in one direction
- ali alizadeh (Thu May 31 2007 - 07:53:37 CDT)
Applying a positional restraint with colvars module
- Giacomo Fiorin (Mon Aug 16 2010 - 16:26:23 CDT)
- bkziervogel_at_uchicago.edu (Mon Aug 16 2010 - 12:06:24 CDT)
Applying conformational constraints during simulation
- poker_at_physics.usyd.edu.au (Tue Oct 23 2007 - 08:51:25 CDT)
- Victor Ovchinnikov (Mon Oct 22 2007 - 23:21:09 CDT)
- poker_at_physics.usyd.edu.au (Mon Oct 22 2007 - 22:08:46 CDT)
applying experimental constraints to a MD simulation
- Jerome Henin (Fri Mar 16 2007 - 11:57:25 CDT)
- L. Michel Espinoza-Fonseca (Fri Mar 16 2007 - 11:31:41 CDT)
- Luca Muccioli (Mon Mar 12 2007 - 02:45:29 CDT)
- L. Michel Espinoza-Fonseca (Sun Mar 11 2007 - 18:55:26 CDT)
- Mark Abraham (Sun Mar 11 2007 - 18:36:01 CDT)
- L. Michel Espinoza-Fonseca (Sun Mar 11 2007 - 18:14:16 CDT)
Applying SMD to a domain of protein
- harish vashisth (Fri Feb 01 2008 - 11:13:58 CST)
- Monika (Fri Feb 01 2008 - 00:49:37 CST)
applying stress to study elasticity
- Axel Kohlmeyer (Fri Oct 24 2008 - 13:35:20 CDT)
- Lam Nguyen (Fri Oct 24 2008 - 12:56:49 CDT)
- Jen Hsin (Fri Oct 24 2008 - 11:20:05 CDT)
- Lam Nguyen (Fri Oct 24 2008 - 11:06:35 CDT)
Applying weak harmonic force between two proteins
- Floris Buelens (Thu May 22 2008 - 09:06:57 CDT)
- Joshua Adelman (Wed May 21 2008 - 11:42:15 CDT)
- greddy1_at_umd.edu (Wed May 21 2008 - 11:12:18 CDT)
Approach energy with SMD
- Austin B. Yongye (Mon Nov 03 2008 - 11:01:26 CST)
Approach energy with SMD (2)
- Austin B. Yongye (Fri Nov 14 2008 - 13:31:36 CST)
Appropriate dcdfreq
- poker_at_physics.usyd.edu.au (Fri Jun 04 2010 - 01:22:07 CDT)
- Philip Peartree (Thu Jun 03 2010 - 15:33:53 CDT)
April promo on watches
- Priscilla Dahl (Tue Jun 10 2008 - 16:41:36 CDT)
aquaporin question
- Samuel Flores (Thu Jun 16 2005 - 15:39:11 CDT)
are tclForces included in minimization?
- Michael Zimmermann (Fri May 28 2010 - 00:41:26 CDT)
area of a hydrophobic patch
- Aaron Oakley (Thu Feb 03 2005 - 16:35:56 CST)
- Narender Singh Maan (Wed Feb 02 2005 - 23:23:24 CST)
Area per lipid error
- Andres Morales N (Mon Oct 17 2011 - 21:12:33 CDT)
area per lipid for a protein embedded membrane system
- M. Madhu (Sun Mar 12 2006 - 09:44:59 CST)
- Nicolas Sapay (Sat Mar 11 2006 - 04:42:32 CST)
- M. Madhu (Fri Mar 10 2006 - 12:25:51 CST)
- nsapay_at_ibcp.fr (Fri Mar 10 2006 - 12:08:54 CST)
- M. Madhu (Fri Mar 10 2006 - 11:08:41 CST)
Area per lipid.
- Ming (Mon Nov 05 2007 - 01:02:53 CST)
Argon solvent
- Jérôme Hénin (Tue Feb 17 2004 - 12:03:16 CST)
- Gianni De Fabritiis (Tue Feb 17 2004 - 09:55:02 CST)
aromatic-aromatic interaction
- L. Michel Espinoza-Fonseca (Fri May 30 2008 - 06:57:51 CDT)
- ramya narasimhan (Thu May 29 2008 - 00:20:43 CDT)
Asking for some sample PDB and PSF files of carbon nanotube
- Axel Kohlmeyer (Wed Dec 15 2010 - 10:52:08 CST)
- JC Gumbart (Wed Dec 15 2010 - 10:52:32 CST)
- Leandro Martínez (Wed Dec 15 2010 - 04:55:59 CST)
- ºÎØ¹»Ô (Wed Dec 15 2010 - 04:19:22 CST)
Aslos
- End'tasa (Fri Aug 28 2009 - 11:55:17 CDT)
asphaltene parameters
- jose correa (Mon Sep 29 2008 - 18:55:27 CDT)
- L. Michel Espinoza-Fonseca (Mon Sep 29 2008 - 09:36:02 CDT)
- jose correa (Mon Sep 29 2008 - 08:55:30 CDT)
Assertion failed in file @ KRAKEN
- Axel Kohlmeyer (Wed Nov 09 2011 - 11:00:04 CST)
- PAUL NEWMAN (Wed Nov 09 2011 - 10:07:07 CST)
Assign the ligand force field parameters
- Grace Shen (Mon Oct 24 2005 - 16:32:13 CDT)
assigning atom type for parameterization
- Jan Saam (Fri Sep 08 2006 - 20:21:32 CDT)
- Dhiraj Srivastava (Fri Sep 08 2006 - 15:23:02 CDT)
Assigning partial charges in topology file
- Christian Jorgensen (Thu Oct 14 2010 - 13:57:30 CDT)
asymmetric water found!
- Peter Freddolino (Wed Jan 28 2009 - 10:00:03 CST)
- OZGE ENGIN (Wed Jan 28 2009 - 07:26:07 CST)
Asymmetric water molecule found
- Peter Freddolino (Tue May 12 2009 - 06:45:32 CDT)
- Jorgen Simonsen (Tue May 12 2009 - 05:00:45 CDT)
Asymmetric water molecule found???
- Elsa F. Sousa Henriques (Wed May 03 2006 - 02:59:26 CDT)
atom charges for protonated carboxyl termini
- Peter Jones (Mon Feb 22 2010 - 18:46:25 CST)
- Zumot, Elia Nabil (Mon Feb 22 2010 - 14:48:59 CST)
Atom constraint in certain direction
- Priyan Amaras (Thu Nov 05 2009 - 11:15:31 CST)
Atom distance & ptraj
- Peter Freddolino (Thu Jan 05 2006 - 13:59:48 CST)
- bo baker (Thu Jan 05 2006 - 11:47:46 CST)
atom distances
- bo baker (Wed Jan 04 2006 - 18:09:31 CST)
- Pijush Ghosh (Wed Jan 04 2006 - 15:14:53 CST)
- nmichaud_at_jhu.edu (Wed Jan 04 2006 - 16:49:08 CST)
- bo baker (Wed Jan 04 2006 - 15:22:59 CST)
- bo baker (Wed Jan 04 2006 - 14:17:29 CST)
Atom movement within a range of Z value
- Jérôme Hénin (Wed May 12 2010 - 02:31:51 CDT)
- Eduardo Cruz-Chu (Tue May 11 2010 - 15:45:59 CDT)
- Axel Kohlmeyer (Tue May 11 2010 - 15:27:44 CDT)
- muniyamuthu.raviprasad_at_ndsu.edu (Tue May 11 2010 - 14:47:15 CDT)
atom name based paremeters
- Jim Phillips (Tue Sep 05 2006 - 23:40:58 CDT)
- E. Prabhu Raman (Tue Sep 05 2006 - 14:31:30 CDT)
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 Positions during simulation
- Francisco Castro (Wed Dec 14 2005 - 16:27:12 CST)
atom restraints
- jsachs_at_mail.csb.yale.edu (Wed Jan 18 2006 - 15:02:26 CST)
atom select within hbond analysis
- sajad falsafi (Tue Jun 07 2011 - 09:21:09 CDT)
- Branko (Tue Jun 07 2011 - 07:40:09 CDT)
atom specification in smd/tclforces for amber topology/parameter based systems
- Jerry Ebalunode (Mon Mar 07 2005 - 14:50:20 CST)
atom type
- Chris Harrison (Fri Nov 19 2010 - 09:39:56 CST)
- Chris Harrison (Fri Nov 19 2010 - 06:41:57 CST)
- matziast_at_med.uth.gr (Fri Nov 19 2010 - 06:21:47 CST)
- matziast_at_med.uth.gr (Fri Nov 19 2010 - 05:03:28 CST)
Atom type explaination for NAMD
- myang (Wed May 26 2004 - 18:04:05 CDT)
Atom type for protonated pyridine N
- Branko (Fri Mar 26 2010 - 02:24:16 CDT)
- Branko (Fri Mar 26 2010 - 02:31:59 CDT)
atom type HZ4 not found
- Peter Freddolino (Sat Aug 05 2006 - 16:31:20 CDT)
- L. Michel Espinoza-Fonseca (Sat Aug 05 2006 - 16:10:33 CDT)
- Dhiraj Srivastava (Sat Aug 05 2006 - 13:27:12 CDT)
Atom velocities too high.
- Joshua Adelman (Sun Oct 19 2008 - 11:48:34 CDT)
- Diego Alejandro Vargas (Sun Oct 19 2008 - 09:59:10 CDT)
Atomic partial charge
- Luca Bellucci (Mon Oct 09 2006 - 05:35:36 CDT)
atomic structure of some surfaces
- Roman Petrenko (Fri Sep 18 2009 - 15:31:18 CDT)
- Eduardo Cruz-Chu (Sat Sep 12 2009 - 15:31:12 CDT)
- Roman Petrenko (Thu Sep 10 2009 - 19:57:14 CDT)
atomlist command in matdcd
- Dhiraj Srivastava (Sun Nov 12 2006 - 02:20:25 CST)
Atoms mooving too fast ... still the problem
- Peter Freddolino (Tue Apr 03 2007 - 20:12:05 CDT)
- Andrea Diaz (Tue Apr 03 2007 - 19:51:39 CDT)
atoms moving fast
- Victor Ovchinnikov (Sat Sep 08 2007 - 10:22:53 CDT)
- Xiang Mao (Sat Sep 08 2007 - 08:31:30 CDT)
Atoms moving too fast
- Brian Bennion (Tue Dec 06 2005 - 15:28:50 CST)
- LEWYN LI (Tue Dec 06 2005 - 13:55:24 CST)
- Marcos Sotomayor (Tue Dec 06 2005 - 13:43:54 CST)
- Eric Perim (Tue Dec 06 2005 - 13:05:10 CST)
- 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)
Atoms moving too fast error
- Dhiraj Srivastava (Fri Oct 27 2006 - 18:01:00 CDT)
- Vishal Kopardé (Fri Oct 27 2006 - 17:12:23 CDT)
Atoms moving too fast OR constraint failure in RATTLE algorithm
- Diego Alejandro Vargas (Wed Nov 12 2008 - 19:00:37 CST)
- Diego Alejandro Vargas (Sat Nov 08 2008 - 17:31:30 CST)
- Diego Alejandro Vargas (Wed Nov 05 2008 - 23:17:56 CST)
- Joshua Adelman (Tue Nov 04 2008 - 12:58:44 CST)
- Diego Alejandro Vargas (Tue Nov 04 2008 - 12:34:00 CST)
ATP and Stream files
- Luis Agullo (LAB) (Fri Oct 16 2009 - 03:39:30 CDT)
- L. Michel Espinoza-Fonseca (Fri Oct 16 2009 - 00:42:52 CDT)
- Dimitar V Pachov (Thu Oct 15 2009 - 08:55:02 CDT)
- Luis Agullo (LAB) (Thu Oct 15 2009 - 07:49:58 CDT)
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)
ATP in the Topology file
- Pedro Borkowski (Fri Jul 29 2005 - 11:31:27 CDT)
ATP molecule
- Per Jr. Greisen (Thu Jul 19 2007 - 13:23:24 CDT)
- snoze pa (Thu Jul 19 2007 - 12:40:35 CDT)
- L. Michel Espinoza-Fonseca (Thu Jul 19 2007 - 10:42:06 CDT)
- snoze pa (Thu Jul 19 2007 - 10:22:43 CDT)
ATP nucleotides using NAMD
- greisen_at_binf.ku.dk (Fri Oct 14 2005 - 04:56:45 CDT)
ATP PDB file
- Per Jr. Greisen (Fri Oct 14 2005 - 07:25:40 CDT)
ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing
- Axel Kohlmeyer (Tue Jan 10 2012 - 14:21:26 CST)
- Bennion, Brian (Tue Jan 10 2012 - 14:18:06 CST)
- Gurunath Katagi (Tue Jan 10 2012 - 14:03:03 CST)
attractive harmonic potential between 2 molecules
- Adam Fraser (Mon Aug 06 2007 - 10:25:29 CDT)
autocorrelation analysis in timeseries
- Aaron Oakley (Mon Jan 31 2005 - 16:21:56 CST)
autocorrelation function !
- Subhasish Chatterjee (Fri Mar 03 2006 - 20:17:56 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)
AutoIMD
- Richard Wood (Fri Jan 06 2006 - 12:36:03 CST)
autoimd on windows
- Anna Modzelewska (Mon Jun 20 2005 - 06:40:29 CDT)
autoionize & namd2
- Michel Espinoza-Fonseca (Thu Sep 22 2005 - 02:51:08 CDT)
- Michel Espinoza-Fonseca (Wed Sep 21 2005 - 09:57:17 CDT)
- paul.dalhaimer_at_yale.edu (Wed Sep 21 2005 - 09:47:37 CDT)
- Michel Espinoza-Fonseca (Wed Sep 21 2005 - 09:32:45 CDT)
- Michel Espinoza-Fonseca (Wed Sep 21 2005 - 02:24:09 CDT)
- bo baker (Tue Sep 20 2005 - 18:07:34 CDT)
autoionize and psfgen, which one first?
- JC Gumbart (Thu Oct 06 2005 - 16:11:43 CDT)
- Shirley Li (Thu Oct 06 2005 - 16:01:42 CDT)
Autoionize error: spontaneously quits
- dora guzman (Fri Jun 23 2006 - 12:18:02 CDT)
- dora guzman (Wed Jun 21 2006 - 18:38:51 CDT)
Autoionize plugin problem
- Gaurav Sharma (Tue Dec 14 2004 - 12:52:03 CST)
autoionize plugin..
- hl332_at_drexel.edu (Mon Jul 10 2006 - 11:32:18 CDT)
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)
Autoionize: net charge NOT equal to zero
- Shirley Li (Wed Oct 19 2005 - 11:44:34 CDT)
Automatic GPU selection in NAMD ?
- David McGiven (Thu May 19 2011 - 04:42:39 CDT)
- Jim Phillips (Wed May 18 2011 - 13:22:57 CDT)
- David McGiven (Tue May 17 2011 - 09:35:57 CDT)
- Axel Kohlmeyer (Tue May 17 2011 - 07:19:44 CDT)
- Jesper Sørensen (Tue May 17 2011 - 06:17:43 CDT)
- David McGiven (Tue May 17 2011 - 06:02:29 CDT)
- Jesper Sørensen (Tue May 17 2011 - 05:41:03 CDT)
- David McGiven (Tue May 17 2011 - 05:34:21 CDT)
- Jesper Sørensen (Tue May 17 2011 - 05:05:27 CDT)
- David McGiven (Tue May 17 2011 - 04:58:56 CDT)
Automatic namd 2.7b1 installation
- DimitryASuplatov (Mon Nov 09 2009 - 11:36:22 CST)
Automatic PSF Builder Problem
- ehenriques_at_qui.uc.pt (Sat Mar 12 2011 - 10:49:05 CST)
- Marc Charendoff (Fri Mar 11 2011 - 10:43:15 CST)
Autopsf
- L. Michel Espinoza-Fonseca (Fri Jul 21 2006 - 16:49:34 CDT)
- Peter Freddolino (Fri Jul 21 2006 - 16:10:39 CDT)
- a-yermakova_at_northwestern.edu (Fri Jul 21 2006 - 16:00:41 CDT)
autopsf and hydrogen-sites
- Peter Freddolino (Wed Oct 01 2008 - 07:59:00 CDT)
- Christine Horejs DI (Wed Oct 01 2008 - 04:09:44 CDT)
Autopsf error with a modified top file
- CHINDEA Vlad (Sat Feb 21 2009 - 06:04:19 CST)
- Peter Freddolino (Fri Feb 20 2009 - 23:19:22 CST)
- CHINDEA Vlad (Fri Feb 20 2009 - 19:28:28 CST)
- Peter Freddolino (Thu Feb 19 2009 - 19:52:52 CST)
- CHINDEA Vlad (Thu Feb 19 2009 - 18:15:45 CST)
- Peter Freddolino (Wed Feb 18 2009 - 15:24:59 CST)
- CHINDEA Vlad (Wed Feb 18 2009 - 15:17:52 CST)
Average energy in NAMD
- JC Gumbart (Sun Jun 01 2008 - 21:02:40 CDT)
- Axel Kohlmeyer (Sun Jun 01 2008 - 16:51:15 CDT)
- Axel Kohlmeyer (Sun Jun 01 2008 - 19:22:51 CDT)
- JC Gumbart (Sun Jun 01 2008 - 18:06:29 CDT)
- feng jack (Sun Jun 01 2008 - 16:31:16 CDT)
Average Velocity and How to choose Right Alias
- abhijit ramachandran (Thu Aug 07 2008 - 16:13:06 CDT)
Avoiding alpha-helix distortions
- Chris Harrison (Sun Jul 06 2008 - 07:52:41 CDT)
- Eric H. Lee (Sat Jul 05 2008 - 12:22:24 CDT)
- Praveen Agrawal (Sat Jul 05 2008 - 00:38:45 CDT)
- Eric H. Lee (Wed Jul 02 2008 - 10:41:01 CDT)
- Peter Freddolino (Wed Jul 02 2008 - 07:59:15 CDT)
- Valeria Losasso (Wed Jul 02 2008 - 03:38:20 CDT)
Avoiding Rotation and translation of protein
- Marc Q. Ma (Fri Jun 10 2005 - 11:35:04 CDT)
- Marc Q. Ma (Wed Jun 08 2005 - 16:58:02 CDT)
- Shirley Hui (Wed Jun 08 2005 - 12:45:04 CDT)
- Blake Charlebois (Wed Jun 08 2005 - 12:39:06 CDT)
- Leonardo Sepulveda Durán (Wed Jun 08 2005 - 10:58:33 CDT)
Avoiding self-interaction with PME.
- Niels Christensen (Sun Nov 25 2007 - 09:59:57 CST)
AW:
- Norman Geist (Wed Nov 23 2011 - 00:01:50 CST)
AW: .COOR TO PDB FILE
- Norman Geist (Mon Aug 15 2011 - 00:34:58 CDT)
AW: 2CPU+1GPU vs 1CPU+2GPU
- Marcel UJI (IMAP) (Tue Feb 14 2012 - 05:07:26 CST)
- Axel Kohlmeyer (Tue Feb 14 2012 - 08:24:53 CST)
- Axel Kohlmeyer (Tue Feb 14 2012 - 08:19:59 CST)
- Nicholas M Glykos (Tue Feb 14 2012 - 04:04:20 CST)
- Marcel UJI (IMAP) (Tue Feb 14 2012 - 03:26:50 CST)
- Norman Geist (Tue Feb 14 2012 - 01:18:44 CST)
AW: about extrabonds restrain
- Ling Wu (Tue Aug 30 2011 - 07:58:25 CDT)
- Norman Geist (Tue Aug 30 2011 - 01:18:37 CDT)
AW: aligning two molecules by principal axes of inertia using measure.c
- Norman Geist (Mon Jun 20 2011 - 09:30:02 CDT)
AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance
- Norman Geist (Mon Jun 06 2011 - 06:49:06 CDT)
- Norman Geist (Mon Jun 06 2011 - 07:22:45 CDT)
- Norman Geist (Mon Jun 06 2011 - 06:11:18 CDT)
- Norman Geist (Mon Jun 06 2011 - 04:51:31 CDT)
AW: Automatic GPU selection in NAMD ?
- Norman Geist (Wed May 18 2011 - 00:24:45 CDT)
AW: AW:
- Norman Geist (Wed Nov 23 2011 - 01:25:12 CST)
- Norman Geist (Wed Nov 23 2011 - 00:59:15 CST)
- Norman Geist (Wed Nov 23 2011 - 01:00:42 CST)
AW: AW: 2CPU+1GPU vs 1CPU+2GPU
- Nicholas M Glykos (Wed Feb 15 2012 - 03:22:43 CST)
- Norman Geist (Wed Feb 15 2012 - 01:45:32 CST)
- Norman Geist (Tue Feb 14 2012 - 06:14:22 CST)
AW: AW: about extrabonds restrain
- Norman Geist (Wed Aug 31 2011 - 00:05:47 CDT)
AW: AW: Automatic GPU selection in NAMD ?
- Norman Geist (Thu May 19 2011 - 01:41:37 CDT)
AW: AW: AW: 2CPU+1GPU vs 1CPU+2GPU
- Nicholas M Glykos (Wed Feb 15 2012 - 03:55:01 CST)
- Norman Geist (Wed Feb 15 2012 - 03:46:09 CST)
AW: AW: AW: AW: namd-ibverbs fails to start
- Norman Geist (Thu Nov 24 2011 - 00:15:52 CST)
AW: AW: AW: NAMD crashes with OpenMPI/OpenMX
- Jim Phillips (Wed Jun 15 2011 - 11:17:47 CDT)
- Norman Geist (Wed Jun 15 2011 - 10:37:47 CDT)
AW: AW: AW: namd-ibverbs fails to start
- Norman Geist (Wed Nov 23 2011 - 00:09:41 CST)
AW: AW: AW: question about wrap atoms to its original coordinates
- Norman Geist (Mon May 23 2011 - 01:03:53 CDT)
AW: AW: Consistent temperature increase in CUDA runs
- Norman Geist (Wed Feb 29 2012 - 00:17:26 CST)
AW: AW: Energy minimization of membrane
- Norman Geist (Mon Feb 06 2012 - 01:01:41 CST)
- Norman Geist (Fri Feb 03 2012 - 06:02:39 CST)
- Norman Geist (Fri Feb 03 2012 - 05:54:19 CST)
AW: AW: NAMD crashes with OpenMPI/OpenMX
- Jim Phillips (Wed Jun 15 2011 - 11:25:34 CDT)
- Thomas Albers (Wed Jun 15 2011 - 10:01:00 CDT)
- Norman Geist (Wed Jun 15 2011 - 09:37:40 CDT)
- Norman Geist (Wed Jun 15 2011 - 01:01:25 CDT)
AW: AW: namd-ibverbs fails to start
- Norman Geist (Wed Nov 23 2011 - 00:16:28 CST)
- Norman Geist (Tue Nov 22 2011 - 00:47:00 CST)
- Norman Geist (Tue Nov 22 2011 - 00:49:46 CST)
AW: AW: question about wrap atoms to its original coordinates
- Norman Geist (Fri May 20 2011 - 00:04:48 CDT)
AW: AW: Running NAMD parallel on two machines with 3 CUDAs
- Norman Geist (Fri May 06 2011 - 01:36:20 CDT)
AW: AW: save the last frame as a pdb file using dcd file
- Norman Geist (Thu Sep 22 2011 - 04:33:07 CDT)
AW: Batch Mode MD simulation Script for NAMD
- Norman Geist (Mon Aug 15 2011 - 00:29:43 CDT)
- Norman Geist (Mon Aug 15 2011 - 00:34:15 CDT)
- Norman Geist (Fri Aug 12 2011 - 07:02:29 CDT)
- Norman Geist (Fri Aug 12 2011 - 00:47:19 CDT)
AW: cell size
- Norman Geist (Thu Dec 15 2011 - 00:16:59 CST)
AW: compilation of namd
- Norman Geist (Fri May 06 2011 - 01:16:56 CDT)
- Norman Geist (Fri May 06 2011 - 00:46:01 CDT)
AW: Consistent temperature increase in CUDA runs
- Vlad Cojocaru (Tue Feb 28 2012 - 03:24:30 CST)
- Nicholas M Glykos (Tue Feb 28 2012 - 08:40:29 CST)
- Axel Kohlmeyer (Tue Feb 28 2012 - 06:14:18 CST)
- JC Gumbart (Tue Feb 28 2012 - 02:57:30 CST)
- Norman Geist (Tue Feb 28 2012 - 00:19:29 CST)
- Norman Geist (Mon Feb 27 2012 - 00:28:03 CST)
AW: Constraint failure during equalibration
- Norman Geist (Wed Sep 14 2011 - 00:31:59 CDT)
AW: Corrupt dcd files
- Marc Baaden (Sun May 15 2011 - 06:28:38 CDT)
- Marc Baaden (Sat May 14 2011 - 16:23:30 CDT)
- Jim Phillips (Thu May 12 2011 - 17:20:36 CDT)
- Norman Geist (Thu May 12 2011 - 01:53:23 CDT)
- Norman Geist (Thu May 12 2011 - 01:51:56 CDT)
- Norman Geist (Thu May 12 2011 - 01:46:51 CDT)
AW: crossing the border by protein/ion complex
- Norman Geist (Wed Feb 08 2012 - 00:54:30 CST)
AW: CUDA on GPU Cluster
- Norman Geist (Mon Aug 22 2011 - 00:47:16 CDT)
AW: CUDA simulation memory usage
- Norman Geist (Wed May 18 2011 - 07:10:58 CDT)
AW: deca-Ala simulations with different cutoff produce different results
- Norman Geist (Mon May 16 2011 - 04:20:58 CDT)
AW: Energy minimization of membrane
- Chris Harrison (Thu Feb 09 2012 - 01:28:36 CST)
- Chris Harrison (Thu Feb 09 2012 - 01:25:56 CST)
- R. Charbel Maroun (Fri Feb 03 2012 - 08:53:37 CST)
- Ajasja LjubetiÄ (Fri Feb 03 2012 - 05:25:01 CST)
- kanchi subbarao rao (Fri Feb 03 2012 - 05:20:29 CST)
- R. Charbel Maroun (Fri Feb 03 2012 - 04:58:17 CST)
- Norman Geist (Fri Feb 03 2012 - 01:14:50 CST)
AW: Error with "namd"
- Norman Geist (Wed Oct 26 2011 - 02:05:17 CDT)
AW: ffTK in the just released VMD 1.9.1
- Norman Geist (Mon Feb 06 2012 - 01:04:05 CST)
AW: free energy of binding
- Norman Geist (Thu Jul 07 2011 - 05:35:07 CDT)
AW: glycosaminoglycan with GLYCAM06 in amber format
- Massimiliano Porrini (Thu Dec 22 2011 - 11:12:10 CST)
- felmerino_at_uchile.cl (Wed Dec 21 2011 - 12:44:08 CST)
- Norman Geist (Wed Dec 21 2011 - 00:51:03 CST)
- Norman Geist (Wed Dec 21 2011 - 00:54:50 CST)
- Norman Geist (Tue Dec 20 2011 - 06:45:32 CST)
- Norman Geist (Mon Dec 19 2011 - 07:35:58 CST)
- Norman Geist (Mon Dec 19 2011 - 00:45:19 CST)
AW: IB fabrics
- Norman Geist (Mon Jan 09 2012 - 00:49:02 CST)
AW: Ib version and nodelist
- Norman Geist (Mon Aug 22 2011 - 00:50:56 CDT)
AW: Infiniband and commodity hardware
- Norman Geist (Mon Sep 19 2011 - 01:03:41 CDT)
AW: Installing NAMD on a 64-bit linux (NVIDIA CUDA)
- Norman Geist (Tue Jan 31 2012 - 00:53:47 CST)
AW: installing namd on ibm cluster (powerpc)
- Norman Geist (Mon Dec 05 2011 - 03:30:48 CST)
- Norman Geist (Mon Dec 05 2011 - 00:29:43 CST)
AW: Keep PBC box size in Z-direction constant?
- Norman Geist (Wed Feb 22 2012 - 00:24:02 CST)
- Norman Geist (Tue Feb 21 2012 - 00:27:45 CST)
AW: Letzte Hilfe
- Bjoern Olausson (Tue Aug 16 2011 - 06:17:36 CDT)
- Norman Geist (Mon Aug 15 2011 - 07:16:39 CDT)
AW: max number of CPU PEs per GPU?
- Norman Geist (Fri Jun 10 2011 - 06:25:45 CDT)
- Norman Geist (Fri Jun 10 2011 - 02:56:30 CDT)
AW: Minimization doesn't stop when converged
- Norman Geist (Fri Oct 07 2011 - 04:54:47 CDT)
AW: Minimization is taking a lot of computing time.
- Norman Geist (Wed Aug 10 2011 - 01:21:10 CDT)
- Norman Geist (Wed Aug 10 2011 - 00:44:55 CDT)
- Norman Geist (Fri Aug 05 2011 - 05:54:49 CDT)
AW: Multinode NAMD CUDA GPU Selection
- Axel Kohlmeyer (Fri Aug 19 2011 - 06:33:28 CDT)
- Norman Geist (Fri Aug 19 2011 - 00:53:31 CDT)
- Norman Geist (Fri Aug 19 2011 - 00:22:56 CDT)
AW: Multiple Runs in a Single Conf File
- Norman Geist (Thu Jun 09 2011 - 00:40:18 CDT)
- Norman Geist (Wed Jun 08 2011 - 03:27:54 CDT)
AW: NAMD crashes with OpenMPI/OpenMX
- Norman Geist (Mon Jun 20 2011 - 00:36:54 CDT)
- Thomas Albers (Wed Jun 15 2011 - 09:10:28 CDT)
AW: Namd-I: namd compiling problem
- Norman Geist (Thu Aug 04 2011 - 00:33:59 CDT)
- Norman Geist (Wed Aug 03 2011 - 00:23:52 CDT)
AW: namd-ibverbs fails to start
- Axel Kohlmeyer (Tue Nov 22 2011 - 08:02:12 CST)
AW: NAMDenergy plugin_van der Waal interactions
- Norman Geist (Wed Feb 22 2012 - 00:20:15 CST)
- Norman Geist (Tue Feb 21 2012 - 00:16:40 CST)
AW: nvidia cuda driver version
- Norman Geist (Mon Aug 08 2011 - 00:04:40 CDT)
AW: patch becoming too small
- Norman Geist (Tue Aug 09 2011 - 02:41:19 CDT)
AW: Peptide planarity Dihedral angle restraints
- Norman Geist (Fri Dec 09 2011 - 00:18:47 CST)
AW: Problem running NAMD 2.8 with ibverbs
- Norman Geist (Thu Jan 12 2012 - 07:34:31 CST)
- Norman Geist (Mon Jan 09 2012 - 00:32:06 CST)
AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..."
- Norman Geist (Thu Jun 09 2011 - 00:44:01 CDT)
- Norman Geist (Thu Jun 09 2011 - 00:36:44 CDT)
- Norman Geist (Thu Jun 09 2011 - 00:26:13 CDT)
AW: Problem with parameter file in Pair Interaction Calculation
- M Mahjour (Tue Jan 10 2012 - 10:48:33 CST)
- Kovacs, Sandor (Tue Jan 10 2012 - 01:14:04 CST)
- Norman Geist (Tue Jan 10 2012 - 00:41:23 CST)
AW: question about wrap atoms to its original coordinates
- jnsong (Thu May 19 2011 - 21:31:54 CDT)
- Norman Geist (Wed May 18 2011 - 00:34:33 CDT)
AW: Reading files for multiple threaded simulations
- Norman Geist (Fri Nov 04 2011 - 02:28:50 CDT)
- Norman Geist (Thu Nov 03 2011 - 02:26:05 CDT)
- Norman Geist (Wed Nov 02 2011 - 01:45:32 CDT)
AW: Running NAMD parallel on two machines with 3 CUDAs
- Norman Geist (Fri May 06 2011 - 00:41:11 CDT)
- Norman Geist (Fri May 06 2011 - 00:36:27 CDT)
AW: save the last frame as a pdb file using dcd file
- Norman Geist (Thu Sep 22 2011 - 03:15:43 CDT)
AW: scaling
- Norman Geist (Mon Jan 02 2012 - 00:44:13 CST)
AW: script for equilibration
- Norman Geist (Tue Oct 04 2011 - 00:18:04 CDT)
AW: Sticking TIP4P water molecules AMBER
- Norman Geist (Tue Dec 20 2011 - 00:33:08 CST)
AW: stochastical boundary conditions in NAMD
- Norman Geist (Wed Dec 07 2011 - 00:38:58 CST)
AW: temperature-TS with NAMDplot
- Norman Geist (Fri Jul 08 2011 - 06:02:14 CDT)
AW: update: segmentation faults with AMBER topology and RAMD tcl scripts
- Vlad Cojocaru (Thu Feb 25 2010 - 03:02:25 CST)
- Francesco Pietra (Wed Feb 24 2010 - 15:57:17 CST)
- Balazs Jojart (Wed Feb 24 2010 - 01:52:26 CST)
- Vlad Cojocaru (Wed Feb 24 2010 - 05:52:49 CST)
- yudaqi (Wed Feb 24 2010 - 06:37:25 CST)
- Balazs Jojart (Wed Feb 24 2010 - 05:41:28 CST)
- Vlad Cojocaru (Wed Feb 24 2010 - 02:43:15 CST)
AW: water equilibration
- Narasimhan LOGANATHAN (Fri Aug 05 2011 - 07:53:22 CDT)
- Norman Geist (Fri Aug 05 2011 - 05:56:04 CDT)
AW: water is forming bonds between oxigens
- Norman Geist (Wed Jun 15 2011 - 01:05:35 CDT)
AW: water molecules
- Norman Geist (Tue Jan 03 2012 - 00:34:15 CST)
AW: what restraint can I use to prevent membrane diffusion on the Z-axis?
- Norman Geist (Tue Feb 28 2012 - 00:42:24 CST)
AW: Win64-MPI
- Norman Geist (Tue Jul 12 2011 - 08:20:11 CDT)
Backbone dihedral ABF
- Sébastien Légaré (Tue Oct 28 2008 - 11:50:02 CDT)
backbone restraints
- Jérôme Hénin (Wed May 26 2010 - 14:47:13 CDT)
- Michael Zimmermann (Wed May 26 2010 - 10:46:09 CDT)
Background load problem
- Peter Freddolino (Fri Feb 27 2009 - 15:10:29 CST)
- Anirban (Fri Feb 27 2009 - 03:38:16 CST)
- Peter Freddolino (Thu Feb 26 2009 - 11:45:00 CST)
- Axel Kohlmeyer (Thu Feb 26 2009 - 10:13:06 CST)
- Nicholas M Glykos (Thu Feb 26 2009 - 09:29:58 CST)
- Anirban (Thu Feb 26 2009 - 08:15:04 CST)
- Peter Freddolino (Thu Feb 26 2009 - 07:50:36 CST)
- Anirban Ghosh (Thu Feb 26 2009 - 03:34:53 CST)
Bactenecine
- Branko (Wed Mar 16 2011 - 16:35:57 CDT)
- johan strumpfer (Wed Mar 16 2011 - 15:54:46 CDT)
- Andres Morales N (Wed Mar 16 2011 - 14:22:09 CDT)
- Andres Morales N (Mon Mar 14 2011 - 23:11:05 CDT)
Bad atom ID in extra bond file
- Jim Phillips (Fri Sep 17 2010 - 14:22:59 CDT)
- Kwee Hong (Sat Sep 04 2010 - 05:08:03 CDT)
- Leonardo Trabuco (Sat Sep 04 2010 - 04:41:00 CDT)
- Kwee Hong (Sat Sep 04 2010 - 03:10:25 CDT)
bad exclusion count
- Francesco Iori (Fri Nov 17 2006 - 15:19:37 CST)
bad exclusion error - searching remedies
- Arturas Ziemys (Mon Aug 18 2008 - 18:12:48 CDT)
Bad global dihedral count.
- Wang, Boyang (Fri Jan 18 2008 - 14:44:11 CST)
Bad global exclusion count
- Yogesh Aher (Wed Jul 15 2009 - 09:49:33 CDT)
- Chris Harrison (Mon Jul 13 2009 - 09:54:50 CDT)
- Yogesh Aher (Mon Jul 13 2009 - 05:57:18 CDT)
- Harindar Keer (Fri Jan 16 2004 - 14:06:28 CST)
bad global exclusion count error
- Jim Pfaendtner (Thu Aug 02 2007 - 15:56:18 CDT)
Bad Global Exclusion Count Errors in (Relatively) Simple System
- Axel Kohlmeyer (Tue Nov 16 2010 - 21:27:25 CST)
- Jason Richard Mick (Tue Nov 16 2010 - 18:32:49 CST)
bad global exclusion count in LES
- Dhiraj Srivastava (Fri Aug 18 2006 - 02:11:11 CDT)
Bad global exclusion count.
- Pijush Ghosh (Tue May 10 2005 - 14:12:06 CDT)
- Boyang Wang (Tue May 10 2005 - 11:56:32 CDT)
Balancer and singularities ...
- Nicholas M Glykos (Thu Jun 10 2010 - 10:52:05 CDT)
balck box: what is the coupling constant when using langenvinFile?
- JC Gumbart (Fri Jul 13 2007 - 19:35:07 CDT)
- Philipp Schön (Fri Jul 13 2007 - 06:53:38 CDT)
barostats in NAMD
- Peter Freddolino (Tue Jun 26 2007 - 09:38:17 CDT)
- Audrey Salazar (Mon Jun 25 2007 - 18:41:55 CDT)
base stacking analysis of the trajectory of a nucleic acids simulation
- Chris Harrison (Sun Jan 04 2009 - 12:12:07 CST)
- Tianjiao Wang (Tue Dec 30 2008 - 15:54:31 CST)
bash: namd2: command not found
- Joshua Adelman (Tue Dec 02 2008 - 00:40:37 CST)
- Sukesh Chandra Gain (Tue Dec 02 2008 - 00:31:42 CST)
basic pdb file run with namd and vmd
- J T (Wed May 23 2007 - 21:49:02 CDT)
- Kayode Karunwi (Wed May 23 2007 - 16:05:01 CDT)
basic question about drawing methods
- Ramya Gamini (Thu Aug 28 2008 - 11:55:16 CDT)
- Subhashis Biswas (Thu Aug 28 2008 - 10:25:16 CDT)
Basic question about steered moledular dynamic(SMD) simulation
- JC Gumbart (Wed May 31 2006 - 09:19:11 CDT)
- q=90=B4=E6=B4=AA=E6=98=8E?= (Wed May 31 2006 - 01:45:20 CDT)
- JC Gumbart (Tue May 30 2006 - 11:47:58 CDT)
- q=E2=BA=E9=C3=F7?= (Wed May 31 2006 - 03:48:41 CDT)
- q=E2=BA=E9=C3=F7?= (Wed May 31 2006 - 00:05:38 CDT)
- JC Gumbart (Mon May 29 2006 - 12:01:21 CDT)
- q=E2=BA=E9=C3=F7?= (Tue May 30 2006 - 11:22:42 CDT)
- JC Gumbart (Mon May 29 2006 - 09:51:02 CDT)
- q=90=B4=E6=B4=AA=E6=98=8E?= (Mon May 29 2006 - 03:54:12 CDT)
- JC Gumbart (Mon May 29 2006 - 00:36:34 CDT)
- q=E2=BA=E9=C3=F7?= (Mon May 29 2006 - 00:49:42 CDT)
Basic question.
- Peter Freddolino (Sat May 27 2006 - 15:20:56 CDT)
- Taeho Kim (Fri May 26 2006 - 22:03:20 CDT)
- Peter Freddolino (Fri May 26 2006 - 21:41:43 CDT)
- Taeho Kim (Fri May 26 2006 - 20:24:54 CDT)
- 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)
basic: combining two pdb files?
- Luis Rosales (Fri Jun 24 2005 - 03:25:46 CDT)
- Wei Chen (Thu Jun 23 2005 - 21:03:30 CDT)
- Meunier, Vincent (Thu Jun 23 2005 - 20:16:45 CDT)
Batch Mode MD simulation Script for NAMD
- JC Gumbart (Sat Aug 13 2011 - 08:45:56 CDT)
- Babban Mia (Sat Aug 13 2011 - 07:36:56 CDT)
- Ismail, Mohd F. (Fri Aug 12 2011 - 14:40:31 CDT)
- Babban Mia (Fri Aug 12 2011 - 13:55:03 CDT)
- Ismail, Mohd F. (Fri Aug 12 2011 - 13:07:59 CDT)
- Babban Mia (Fri Aug 12 2011 - 12:59:45 CDT)
- Babban Mia (Fri Aug 12 2011 - 12:06:28 CDT)
- Jernej Zidar (Fri Aug 12 2011 - 08:03:21 CDT)
- Axel Kohlmeyer (Fri Aug 12 2011 - 07:53:13 CDT)
- Jeffrey Potoff (Fri Aug 12 2011 - 06:45:12 CDT)
- Babban Mia (Fri Aug 12 2011 - 05:46:32 CDT)
- Babban Mia (Thu Aug 11 2011 - 18:56:19 CDT)
Benchmark calculation
- rebeca_at_mmb.pcb.ub.es (Thu Aug 14 2008 - 12:36:55 CDT)
Benchmark for NAMD2.7 (curent version)
- Branko (Wed Jan 05 2011 - 14:19:19 CST)
benchmarking mistake?
- Ioana Cozmuta (Sun May 30 2004 - 20:12:52 CDT)
benchmarking of NAMD: sustained performance (TF)
- Axel Kohlmeyer (Thu May 29 2008 - 09:05:40 CDT)
- Philip Peartree (Thu May 29 2008 - 04:35:50 CDT)
- satya work (Wed May 28 2008 - 22:47:30 CDT)
benchmarking on Cray XT4
- Philip Peartree (Tue Mar 16 2010 - 07:59:49 CDT)
- Axel Kohlmeyer (Tue Mar 16 2010 - 10:35:56 CDT)
- Hannes Loeffler (Tue Mar 16 2010 - 09:32:38 CDT)
- Axel Kohlmeyer (Tue Mar 16 2010 - 06:49:58 CDT)
- Hannes Loeffler (Tue Mar 16 2010 - 05:50:17 CDT)
Benzamidine parameters
- Caio Julio Martins Veloso (Sat Mar 25 2006 - 12:54:52 CST)
benzene in NAMD
- Boyang Wang (Sat May 14 2005 - 15:33:13 CDT)
Benzene PSF
- Jerome Henin (Thu Apr 30 2009 - 11:22:01 CDT)
- Matt Krems (Wed Apr 29 2009 - 19:04:27 CDT)
- Chris Harrison (Wed Apr 29 2009 - 19:29:25 CDT)
Berendsen or Langevin Temp control?
- Edward Patrick Obrien (Wed Nov 10 2004 - 15:54:07 CST)
Berendsen pressure control problem
- Jason Lee (Thu Jan 26 2006 - 14:15:29 CST)
berendsen thermostat
- Jérôme Hénin (Mon Nov 15 2010 - 09:24:13 CST)
- Axel Kohlmeyer (Mon Nov 15 2010 - 08:56:01 CST)
- divya nayar (Mon Nov 15 2010 - 08:15:37 CST)
Berendsen, explicit water
- Sandra Rennebaum, Biochemisches Inst. (Tue Aug 18 2009 - 04:54:07 CDT)
Berendsen- two baths
- Sandra Rennebaum, Biochemisches Inst. (Tue Aug 11 2009 - 01:55:10 CDT)
Besides PSFGEN, (Thank you)
- Shirley Li (Fri Dec 23 2005 - 17:42:54 CST)
Besides PSFGEN, are there any other good ways of generating .psf file
- Joshua D. Moore (Thu Dec 22 2005 - 21:01:31 CST)
- Shirley Li (Thu Dec 22 2005 - 19:01:36 CST)
best choice of linux cluster to run NAMD
- Nikolai Skrynnikov (Thu Jul 01 2004 - 03:02:10 CDT)
Best NAMD version for Rocks 4.3 IBM xseries 3665
- andrea carotti (Tue Sep 04 2007 - 06:06:32 CDT)
Best tool to use to generate a custom (patched) polypeptide PDB?
- Jason Richard Mick (Thu May 06 2010 - 17:23:54 CDT)
beta column
- Nicholas Musolino (Fri Sep 10 2010 - 07:48:46 CDT)
- ehenriques_at_qui.uc.pt (Fri Sep 10 2010 - 04:25:10 CDT)
- Swarna M Patra (Fri Sep 10 2010 - 00:57:04 CDT)
beta-peptides ...
- Nicholas M Glykos (Mon Oct 31 2005 - 06:34:20 CST)
bicarbonate parameters
- Brian R Novak (Wed Jul 08 2009 - 13:31:28 CDT)
big systems using namd on 700 cpus
- Brian Bennion (Mon Dec 29 2003 - 13:47:04 CST)
BigDCD
- Per Jr. Greisen (Thu Aug 02 2007 - 03:40:13 CDT)
- Ioana Cozmuta (Wed Nov 05 2003 - 17:00:40 CST)
bigdcd file help
- Nicholas M Glykos (Tue Jul 05 2011 - 13:35:43 CDT)
- snoze pa (Tue Jul 05 2011 - 13:19:06 CDT)
- snoze pa (Tue Jul 05 2011 - 09:56:15 CDT)
- sajad falsafi (Mon Jul 04 2011 - 08:52:36 CDT)
- Cosseddu, Salvatore (Mon Jul 04 2011 - 04:11:55 CDT)
- snoze pa (Mon Jul 04 2011 - 01:29:23 CDT)
bilayer thickness in simulation of POPC membranes
- Ilya Chorny (Mon Aug 13 2007 - 10:00:10 CDT)
- maria goranovic (Mon Aug 13 2007 - 09:16:09 CDT)
- maria goranovic (Mon Aug 13 2007 - 07:55:48 CDT)
- Vlad Cojocaru (Fri Aug 10 2007 - 10:56:41 CDT)
Bin Coordinate file to pdb
- Chris Harrison (Thu Jul 08 2010 - 18:26:51 CDT)
- Philip Peartree (Thu Jul 08 2010 - 15:50:34 CDT)
Binary conversions
- Jim Phillips (Wed Dec 03 2003 - 15:08:17 CST)
- Hua Wong (Tue Dec 02 2003 - 02:11:10 CST)
Binary for MacOSX-i686
- Peter Freddolino (Wed Jun 28 2006 - 14:08:03 CDT)
- Mikolai Fajer (Wed Jun 28 2006 - 13:53:00 CDT)
binary install question
- winsvern_at_isu.edu (Tue Apr 15 2008 - 15:23:29 CDT)
binary restraint reference coordinates?
- Cameron Mura (Thu Mar 31 2005 - 20:31:42 CST)
binary trajectories
- Axel Kohlmeyer (Fri Jan 09 2009 - 08:29:27 CST)
- karthik s (Fri Jan 09 2009 - 04:53:54 CST)
binary troubles
- Brian Bennion (Fri Dec 05 2003 - 13:40:35 CST)
- Michael Grabe (Fri Dec 05 2003 - 13:14:54 CST)
binary.coor to ascII.coor
- Richard Law (Thu Apr 27 2006 - 12:51:03 CDT)
- LEWYN LI (Thu Apr 27 2006 - 12:49:45 CDT)
- paul.dalhaimer_at_yale.edu (Thu Apr 27 2006 - 12:14:52 CDT)
binaryoutput option doesn't work for dcd file
- Jerome Henin (Sat Aug 18 2007 - 10:40:35 CDT)
- Devendra (Sat Aug 18 2007 - 09:26:28 CDT)
binaryrestart/binaryoutput problem
- Francesco Pietra (Tue Mar 01 2011 - 02:54:26 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 Energies for a Peptide-RNA System
- rossi_at_york.cuny.edu (Sat Sep 17 2005 - 14:37:11 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
- Shirley Hui (Thu Feb 01 2007 - 15:40:27 CST)
- bora erdemli (Mon Dec 20 2004 - 08:39:06 CST)
binding free energy , binding constant
- Wei Chen (Fri Jun 17 2005 - 15:46:35 CDT)
- Chris Chipot (Fri Jun 17 2005 - 11:07:11 CDT)
- sabri bora erdemli (Fri Jun 17 2005 - 08:11:33 CDT)
Binding free energy by LIE
- Narender Singh Maan (Fri Sep 28 2007 - 14:21:21 CDT)
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)
Bio-Image summer school in Paris this year
- Marc Baaden (Wed Mar 16 2005 - 05:42:59 CST)
Bioinformatics Symposium at C-DAC, Pune
- Anirban Ghosh (Fri Sep 03 2010 - 00:41:23 CDT)
biotin charmm topology/parameters
- Barry Isralewitz (Tue Aug 28 2007 - 10:00:21 CDT)
- Matthew Wilce (Mon Aug 27 2007 - 18:41:46 CDT)
- Matthew Wilce (Mon Aug 27 2007 - 01:48:13 CDT)
biotin parameters and topology
- Brian R Novak (Tue Apr 28 2009 - 15:43:15 CDT)
- Peter Freddolino (Tue Apr 28 2009 - 15:13:08 CDT)
- Brian R Novak (Tue Apr 28 2009 - 12:37:53 CDT)
Biotin-X charmm topology
- Taekyung Kwon (Sat Nov 29 2008 - 17:13:47 CST)
Bizarre atom behavior
- Chang, Christopher (Thu Apr 06 2006 - 16:40:04 CDT)
- Peter Freddolino (Thu Apr 06 2006 - 00:39:41 CDT)
- Chang, Christopher (Wed Apr 05 2006 - 11:35:54 CDT)
blank between nanotube and the bulk water
- fereshteh moradi (Fri May 07 2010 - 23:29:22 CDT)
Blue Waters
- Andy Somogyi (Tue Aug 09 2011 - 10:18:49 CDT)
Boiling temperature of water.
- Mark Abraham (Thu Jun 22 2006 - 21:48:16 CDT)
- Boyang Wang (Thu Jun 22 2006 - 21:38:54 CDT)
- Boyang Wang (Thu Jun 22 2006 - 19:20:09 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)
Bond energy become Zero!!!
- Peter Freddolino (Thu Jun 05 2008 - 08:25:55 CDT)
- Ming (Thu Jun 05 2008 - 04:17:01 CDT)
bond length in terminal patches
- Peter Freddolino (Sat Nov 22 2008 - 20:33:38 CST)
- CHINDEA Vlad (Sat Nov 22 2008 - 16:29:55 CST)
bond lengths angles in namd
- Ajasja LjubetiÄ (Thu Jan 27 2011 - 07:14:26 CST)
- Jérôme Hénin (Thu Jan 27 2011 - 06:55:28 CST)
- oguz gurbulak (Thu Jan 27 2011 - 06:35:34 CST)
- oguz gurbulak (Thu Jan 27 2011 - 05:43:09 CST)
bonded FAD topology file
- Demet Akten (Tue Feb 16 2010 - 07:23:13 CST)
bonding in periodic boundary conditions
- d b (Tue Aug 11 2009 - 15:05:08 CDT)
bonding to image
- Glenn Johnson (Mon Apr 11 2005 - 16:02:28 CDT)
- Glenn Johnson (Mon Apr 11 2005 - 13:56:33 CDT)
Bonds are too long after simulation
- Anthony Rey (Wed Sep 07 2011 - 22:48:37 CDT)
- Axel Kohlmeyer (Wed Sep 07 2011 - 13:18:26 CDT)
- flavio seixas (Wed Sep 07 2011 - 13:10:13 CDT)
- Markus K. Dahlgren (Wed Sep 07 2011 - 12:54:16 CDT)
- Anthony Rey (Wed Sep 07 2011 - 10:32:11 CDT)
BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars)
- Francesco Pietra (Fri Mar 11 2011 - 11:46:30 CST)
- snoze pa (Tue May 06 2008 - 10:20:47 CDT)
- snoze pa (Mon May 05 2008 - 16:49:43 CDT)
Boundary potential of colvar alpha not working?
- Jérôme Hénin (Thu Oct 13 2011 - 10:23:41 CDT)
- Yun Luo (Thu Oct 13 2011 - 08:21:15 CDT)
- Yun Luo (Thu Oct 13 2011 - 09:03:46 CDT)
- Jérôme Hénin (Thu Oct 13 2011 - 08:54:35 CDT)
- Jérôme Hénin (Thu Oct 13 2011 - 07:14:53 CDT)
- Yun Luo (Wed Oct 12 2011 - 09:34:27 CDT)
Box Dimension
- Valodymyr Nechyporuk-Zloy (Tue Jun 29 2004 - 09:00:53 CDT)
Box size
- Mark Abraham (Mon Jul 03 2006 - 23:37:27 CDT)
- santanu chatterjee (Mon Jul 03 2006 - 16:33:33 CDT)
- Gan, Yong $UMC-Student$ (Tue Oct 25 2005 - 11:50:06 CDT)
box size changes under anisotropic pressure coupling
- Philip Blood (Fri Apr 08 2005 - 14:28:11 CDT)
- Jerome Henin (Fri Apr 08 2005 - 13:44:19 CDT)
- Philip Blood (Fri Apr 08 2005 - 11:14:40 CDT)
bracket in the log file
- Lei Zhang (Tue Mar 17 2009 - 16:29:07 CDT)
Bringing UMA-type mainboards to TESLA
- Biff Forbush (Wed Feb 10 2010 - 12:34:57 CST)
- Axel Kohlmeyer (Tue Feb 09 2010 - 18:03:38 CST)
- Francesco Pietra (Tue Feb 09 2010 - 15:59:16 CST)
Bringing Up To Temp
- Tim Cm (Sun Aug 15 2004 - 16:48:42 CDT)
Bromine
- Matthew Wilce (Wed Jul 20 2005 - 01:43:43 CDT)
Buffering problems while attempting to read log file
- Zach Hensel (Fri Feb 10 2006 - 14:20:11 CST)
- Zach Hensel (Fri Feb 10 2006 - 11:08:29 CST)
Bug advisory: ABF integration tool
- Jerome Henin (Wed Aug 12 2009 - 17:49:24 CDT)
Bug advisory: RMSD and ABF
- Jerome Henin (Mon Jun 08 2009 - 17:55:10 CDT)
Bug alert!!!
- Brian Bennion (Tue Jan 04 2005 - 10:46:40 CST)
- bora erdemli (Tue Jan 04 2005 - 01:13:37 CST)
- 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!
- Xiaoqing Wang (Mon Jan 24 2005 - 01:26:21 CST)
- 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 NAMD CVS starting March 7, now fixed
- Jim Phillips (Tue Apr 08 2008 - 14:22:55 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 in pressure calculation with E field?
- Peter Freddolino (Sat Dec 09 2006 - 14:19:01 CST)
bug or custom?
- BIN ZHANG (Thu Jul 09 2009 - 13:53:52 CDT)
- BIN ZHANG (Thu Jul 09 2009 - 13:00:44 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)
bugfixes in the colvars module (ABF, metadynamics etc.)
- Giacomo Fiorin (Wed Jun 24 2009 - 16:00:27 CDT)
Build .pdb and .psf after coarse graining results in errors
- Edroaldo Lummertz da Rocha (Thu May 19 2011 - 13:37:15 CDT)
build a layer
- Eduardo (Wed Aug 25 2010 - 12:29:27 CDT)
- hamid mosaddeghi (Wed Aug 25 2010 - 07:58:46 CDT)
build a wall
- sara (Wed Aug 25 2010 - 11:01:39 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 charm++ and namd
- Peter Freddolino (Thu Jul 31 2008 - 08:39:07 CDT)
- Vlad Cojocaru (Thu Jul 31 2008 - 07:57:36 CDT)
- Peter Freddolino (Thu Jul 31 2008 - 07:38:31 CDT)
- Vlad Cojocaru (Thu Jul 31 2008 - 06:46:31 CDT)
- Vlad Cojocaru (Thu Jul 31 2008 - 05:06:44 CDT)
build missing residues in pdb
- Schreiner Eduard (Mon Nov 24 2008 - 00:09:18 CST)
- Anuradha Mittal (Sun Nov 23 2008 - 18:48:47 CST)
build NAMD
- bioinfo Gu (Mon Sep 08 2003 - 09:54:12 CDT)
build nanoparticle
- Nicholas Musolino (Wed Oct 27 2010 - 13:25:57 CDT)
- sara (Wed Oct 27 2010 - 11:10:58 CDT)
build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version
- Gengbin Zheng (Tue Mar 14 2006 - 00:02:33 CST)
- Brian Bennion (Mon Mar 13 2006 - 14:18:15 CST)
- Sabuj Pattanayek (Mon Mar 13 2006 - 14:09:45 CST)
- Sabuj Pattanayek (Mon Mar 13 2006 - 12:31:56 CST)
build smp version of namd with intel 10.1
- Vlad Cojocaru (Fri Aug 08 2008 - 05:18:42 CDT)
- Gengbin Zheng (Thu Aug 07 2008 - 10:49:00 CDT)
- Axel Kohlmeyer (Thu Aug 07 2008 - 12:08:34 CDT)
- Vlad Cojocaru (Thu Aug 07 2008 - 10:44:02 CDT)
Building 64-bit NAMD
- Warner Yuen (Mon Aug 27 2007 - 10:23:58 CDT)
building a MARTINI bilayer
- Peter Freddolino (Wed Apr 21 2010 - 13:16:00 CDT)
- Edward Lyman (Wed Apr 21 2010 - 12:41:35 CDT)
Building a pdb file
- Peter Freddolino (Tue Jul 03 2007 - 16:43:14 CDT)
- Audrey Salazar (Tue Jul 03 2007 - 16:14:41 CDT)
BUILDING BPTI
- Jim Phillips (Thu Mar 26 2009 - 16:22:58 CDT)
- jose correa (Thu Mar 26 2009 - 14:53:43 CDT)
Building Charm .. mpi-linux-amd64-ifort/tmp/traceCore.h .. and .. mpi-linux-amd64-ifort/tmp/MsgPacker.h
- Graham Jenkins (Sat Oct 27 2007 - 15:56:34 CDT)
building charm++ on macosX
- yu275197_at_yorku.ca (Sat Feb 07 2004 - 16:51:15 CST)
Building cluster
- Jimmy Tang (Sun Mar 19 2006 - 05:01:17 CST)
- Cesar Luis Avila (Sat Mar 18 2006 - 12:54:38 CST)
Building for SunGrid
- Jonathan D. Proulx (Tue Aug 15 2006 - 09:05:38 CDT)
Building molecule from topology file
- Peter Freddolino (Sat Aug 26 2006 - 10:44:23 CDT)
- Lechuga, Javier (Sat Aug 26 2006 - 06:57:40 CDT)
Building NAMD 2.6b1 on IBM Power5
- Joachim Hein (Tue Dec 06 2005 - 03:49:53 CST)
Building NAMD 64-bit Mac OSX with GCC
- Warner Yuen (Sun Aug 05 2007 - 15:17:02 CDT)
Building NAMD for Opteron Cluster with ICC
- Peter Freddolino (Sat Mar 07 2009 - 21:56:29 CST)
- Chris Share (Sat Mar 07 2009 - 21:02:39 CST)
- Peter Freddolino (Fri Mar 06 2009 - 23:18:12 CST)
- Chris Share (Fri Mar 06 2009 - 21:53:02 CST)
Building Namd on a linux cluster.
- Axel Kohlmeyer (Fri May 30 2008 - 19:25:00 CDT)
- Khaled Barakat (Fri May 30 2008 - 19:30:23 CDT)
- Axel Kohlmeyer (Fri May 30 2008 - 14:41:27 CDT)
- Khaled Barakat (Fri May 30 2008 - 14:32:09 CDT)
- Axel Kohlmeyer (Fri May 30 2008 - 07:38:12 CDT)
- Alexandre A. Vakhrouchev (Fri May 30 2008 - 00:38:25 CDT)
- Khaled Barakat (Thu May 29 2008 - 21:39:53 CDT)
building namd on CRAY-XT3
- Axel Kohlmeyer (Wed Nov 05 2008 - 02:10:32 CST)
- BIN ZHANG (Wed Nov 05 2008 - 01:19:37 CST)
- Axel Kohlmeyer (Wed Nov 05 2008 - 00:49:51 CST)
- BIN ZHANG (Wed Nov 05 2008 - 00:16:34 CST)
- BIN ZHANG (Tue Nov 04 2008 - 13:38:35 CST)
Building NAMD on SGI Altix
- Rogan Carr (Mon Apr 14 2008 - 15:04:27 CDT)
Building NAMD with Myrinet MX
- Warner Yuen (Wed Aug 15 2007 - 15:59:24 CDT)
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)
Building NAMD/CHARM++ Mac OS X Intel
- Warner Yuen (Mon Aug 06 2007 - 10:52:19 CDT)
Building PDB files for DNA.
- Andrew D. Fant (Fri Dec 15 2006 - 12:08:23 CST)
- Nicholas M Glykos (Fri Dec 15 2006 - 11:42:03 CST)
- Wang, Boyang (Fri Dec 15 2006 - 10:29:55 CST)
Building PSF file for protein with ions
- ehenriques_at_qui.uc.pt (Wed Sep 01 2010 - 09:02:17 CDT)
- anas . (Wed Sep 01 2010 - 05:22:50 CDT)
bulid psf for structure already with hydrogens
- JC Gumbart (Sun Jul 23 2006 - 19:47:03 CDT)
- Ching Wong (Wed Jul 19 2006 - 14:02:32 CDT)
bulk density in RDF.tcl
- griadi_at_utalca.cl (Wed Mar 29 2006 - 16:55:07 CST)
- ARTURAS ZIEMYS (Wed Mar 29 2006 - 10:28:44 CST)
Bun in charmd?
- Gengbin Zheng (Sun Dec 21 2003 - 14:11:56 CST)
- Gadi Oron (Sun Dec 21 2003 - 08:53:49 CST)
bunch of water molecules
- sathish kumar gurupatham (Fri Aug 10 2007 - 13:30:45 CDT)
- Jerome Henin (Thu Aug 09 2007 - 15:03:12 CDT)
- sathish kumar gurupatham (Thu Aug 09 2007 - 13:39:51 CDT)
C NH1 C minimization error
- Sourmaidou, Damiani (Thu Jan 17 2008 - 06:43:18 CST)
c-shell into NAMD configuration file
- nordgren_at_sas.upenn.edu (Wed Jun 15 2005 - 09:23:20 CDT)
- Ioana Cozmuta (Mon Jun 13 2005 - 02:02:48 CDT)
C1 splitting documentation
- Floris Buelens (Fri Oct 05 2007 - 08:10:21 CDT)
C:CA bond getting stretched
- Dhiraj Srivastava (Mon Jan 15 2007 - 01:45:37 CST)
CA CL CA angle?
- Richard Wood (Wed Nov 02 2005 - 10:31:05 CST)
- Brian Bennion (Tue Nov 01 2005 - 12:57:43 CST)
- Richard Wood (Tue Nov 01 2005 - 11:11:44 CST)
Ca trace only
- Sergio Anis (Wed Jul 20 2005 - 06:52:05 CDT)
- Shirley Hui (Tue Jul 19 2005 - 18:37:11 CDT)
Ca++ topology&param files
- mustapha.hamdi_at_ensi-bourges.fr (Fri Sep 30 2005 - 04:11:31 CDT)
Calcium ion binding protein
- JC Gumbart (Wed Oct 22 2008 - 09:40:47 CDT)
- vsweta_at_iastate.edu (Tue Oct 21 2008 - 16:27:31 CDT)
Calcium ion-Protein Binding
- MIke S (Mon Sep 22 2008 - 13:33:39 CDT)
- JC Gumbart (Mon Sep 22 2008 - 13:42:28 CDT)
- MIke S (Mon Sep 22 2008 - 12:54:20 CDT)
- JC Gumbart (Thu Sep 18 2008 - 14:22:41 CDT)
- MIke S (Thu Sep 18 2008 - 14:13:34 CDT)
Calcium ions and psfgen
- MIke S (Wed Sep 17 2008 - 18:18:47 CDT)
- V.Ovchinnikov (Wed Sep 17 2008 - 18:12:18 CDT)
- MIke S (Wed Sep 17 2008 - 16:53:16 CDT)
calculate energy with water excluded
- li (Mon May 17 2004 - 01:04:39 CDT)
calculate enthalpy of binding
- Peter Freddolino (Tue Sep 27 2005 - 17:27:44 CDT)
- Georgios Papadopoulos (Tue Sep 27 2005 - 11:33:33 CDT)
calculate interaction energies for a system with amber forcefield
- Peter Freddolino (Sun Sep 02 2007 - 17:18:22 CDT)
- Rima Chaudhuri (Sat Sep 01 2007 - 19:15:36 CDT)
Calculate Potential Energy
- Shirley Hui (Sat May 15 2004 - 17:20:03 CDT)
calculate potential energy from DCD file
- casoni\_at_libero\.it (Tue Sep 05 2006 - 07:21:57 CDT)
calculate side-chain dihedral/torsion angles
- Ajasja LjubetiÄ (Mon Apr 12 2010 - 02:40:47 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 displacement in a system with periodic boundary
- Fred (Rui FENG) (Tue May 12 2009 - 02:52:49 CDT)
- BIN ZHANG (Tue May 12 2009 - 02:25:48 CDT)
- Fred (Rui FENG) (Tue May 12 2009 - 01:37:58 CDT)
- Eric H. Lee (Tue May 12 2009 - 01:15:56 CDT)
- Fred (Rui FENG) (Tue May 12 2009 - 01:07:22 CDT)
- Eric H. Lee (Mon May 11 2009 - 23:49:25 CDT)
- Joshua Adelman (Mon May 11 2009 - 23:44:23 CDT)
- Fred (Rui FENG) (Mon May 11 2009 - 23:26:21 CDT)
calculating energy for large log files
- Axel Kohlmeyer (Thu May 21 2009 - 09:30:51 CDT)
- gurunath katagi (Thu May 21 2009 - 02:30:40 CDT)
calculating energy term from extrabonds
- Segun Jung (Mon Feb 07 2011 - 23:50:43 CST)
- Segun Jung (Mon Feb 07 2011 - 20:08:33 CST)
Calculating forces
- Gaurav Sharma (Thu Sep 01 2005 - 12:32:59 CDT)
calculating forces from dcd trajectory
- BIN ZHANG (Thu May 21 2009 - 12:40:15 CDT)
- Peter Freddolino (Thu May 21 2009 - 06:55:47 CDT)
- Peter Freddolino (Thu May 21 2009 - 06:54:08 CDT)
- BIN ZHANG (Wed May 20 2009 - 12:18:20 CDT)
- Peter Freddolino (Wed May 20 2009 - 06:51:11 CDT)
- BIN ZHANG (Wed May 20 2009 - 02:18:26 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 interaction energy in NAMD
- BIN ZHANG (Sun Mar 28 2010 - 13:50:38 CDT)
- DimitryASuplatov (Sun Mar 28 2010 - 04:28:52 CDT)
Calculating macroscopic properties
- Mark Abraham (Thu May 03 2007 - 00:42:26 CDT)
- poker_at_physics.usyd.edu.au (Wed May 02 2007 - 22:00:28 CDT)
- Marcos Sotomayor (Tue May 01 2007 - 11:49:44 CDT)
- JC Gumbart (Tue May 01 2007 - 01:13:35 CDT)
- Mark Abraham (Mon Apr 30 2007 - 21:51:49 CDT)
- poker_at_physics.usyd.edu.au (Mon Apr 30 2007 - 21:38:37 CDT)
Calculating or Outputing Forces
- Joshua D. Moore (Thu Jun 29 2006 - 12:55:38 CDT)
- Joshua D. Moore (Wed Jun 28 2006 - 14:18:56 CDT)
- Joshua D. Moore (Mon Jun 26 2006 - 21:00:44 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)
Calculating PMF from a constant velocity SMD simulation!
- Gungor Ozer (Sat Apr 05 2008 - 19:10:06 CDT)
calculation (continue)
- edu (Wed Jun 21 2006 - 16:03:40 CDT)
Calculation of CHARMM Parameters from GAMESS Output.
- JC Gumbart (Mon Feb 05 2007 - 10:15:40 CST)
- Klon, Anthony (Mon Feb 05 2007 - 09:27:09 CST)
Calculation of distance traveled by an atom
- Aron Broom (Tue Dec 06 2011 - 02:43:34 CST)
- M.Raviprasad (Mon Dec 05 2011 - 23:11:19 CST)
- M.Raviprasad (Mon Dec 05 2011 - 23:19:54 CST)
- Axel Kohlmeyer (Mon Dec 05 2011 - 23:22:53 CST)
- Aron Broom (Mon Dec 05 2011 - 17:38:33 CST)
- Axel Kohlmeyer (Mon Dec 05 2011 - 17:36:58 CST)
- M.Raviprasad (Mon Dec 05 2011 - 14:54:27 CST)
Calculation of IR spectra using VMD IRspec Plug-in
- Axel Kohlmeyer (Sun Feb 20 2011 - 12:40:41 CST)
- Branko (Sat Feb 19 2011 - 11:54:48 CST)
- Mikhail Suyetin (Thu Feb 17 2011 - 01:22:00 CST)
calculation of non-bonded interactions
- Jindal Shah (Mon Oct 23 2006 - 09:55:59 CDT)
calculation of periodic box
- Roman Petrenko (Tue Nov 17 2009 - 22:51:27 CST)
- Michael Thomas (Tue Nov 17 2009 - 22:56:55 CST)
- Michael Thomas (Tue Nov 17 2009 - 22:16:05 CST)
- Joshua Adelman (Tue Nov 17 2009 - 22:29:13 CST)
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)
calculation van der Waals force field parameters
- Mikhail Suyetin (Wed Feb 17 2010 - 13:27:50 CST)
Can AMBER topology be used in NAMD-CUDA?
- Lela Vukovic (Fri Apr 09 2010 - 14:54:08 CDT)
Can any one help me with this parallel issue
- Morad Alawneh (Tue Jan 31 2006 - 09:42:58 CST)
- Sterling Paramore (Mon Jan 30 2006 - 14:42:42 CST)
- Morad Alawneh (Mon Jan 30 2006 - 14:35:09 CST)
- Sterling Paramore (Mon Jan 30 2006 - 10:02:17 CST)
- Morad Alawneh (Sun Jan 29 2006 - 18:17:06 CST)
Can DCD trajectory files contain only protein but water surround
- Axel Kohlmeyer (Thu Jan 13 2011 - 19:57:05 CST)
- yandongÂ Huang (Thu Jan 13 2011 - 08:44:10 CST)
Can extending MIN solve the problem of "Constraint failure in RATTLE algorithm"
- dimka (Sat Dec 24 2005 - 19:51:31 CST)
- Shirley Li (Sat Dec 24 2005 - 12:58:55 CST)
can I change coordinate before restart?
- Joshua Adelman (Wed Apr 22 2009 - 15:11:55 CDT)
- Joshua Adelman (Tue Apr 21 2009 - 20:50:47 CDT)
- Mark M Huntress (Tue Apr 21 2009 - 16:03:55 CDT)
Can I do protein-ligand docking using NAMD?
- JC Gumbart (Wed Feb 16 2011 - 01:08:36 CST)
- Bo Liu (Wed Feb 16 2011 - 00:30:54 CST)
- Àî¼Ñ¼ü (Tue Feb 15 2011 - 23:32:03 CST)
Can I do ¡°accelerated molecular dynamics¡±in NAMD?
- L. Michel Espinoza-Fonseca (Wed Jul 25 2007 - 15:43:27 CDT)
- Qiang Zhong (Wed Jul 25 2007 - 08:22:49 CDT)
Can I get the pressure value in a cube?
- Peter Freddolino (Mon Feb 23 2009 - 03:29:58 CST)
- Fred (Rui FENG) (Mon Feb 23 2009 - 00:57:29 CST)
- Peter Freddolino (Fri Feb 20 2009 - 10:09:52 CST)
- Fred (Rui FENG) (Thu Feb 19 2009 - 23:49:26 CST)
- Peter Freddolino (Thu Feb 19 2009 - 22:26:27 CST)
- Fred (Rui FENG) (Thu Feb 19 2009 - 22:12:35 CST)
Can I miminimize some atoms in system
- Shahid Qamar (Tue Oct 25 2005 - 16:40:06 CDT)
can i restrain the center of molecule in aqueous solution?
- li (Tue Apr 20 2004 - 03:43:12 CDT)
Can I set a range to limit the ABF
- Giacomo Fiorin (Wed Apr 20 2011 - 11:25:44 CDT)
- Shen, Han (Wed Apr 20 2011 - 10:24:46 CDT)
can i somehow use reassigntemp for selected atoms only?
- Philipp Schön (Tue Jul 10 2007 - 11:06:51 CDT)
Can I use "vecnorm" in the tclforce scripts?
- Alexander A. Vakhrushev (Thu Sep 18 2008 - 09:29:43 CDT)
- Ming (Thu Sep 18 2008 - 08:58:19 CDT)
Can I use another solvent rather than TI3P model in namd for MD simulations ?
- Axel Kohlmeyer (Mon Jun 29 2009 - 08:32:30 CDT)
- Joshua Adelman (Sun Jun 28 2009 - 20:14:02 CDT)
- Wang Yf (Sat Jun 27 2009 - 22:30:04 CDT)
Can I use FEP in NAMD for reaction of ATP with Kinase?
- Qiang Zhong (Fri Jul 20 2007 - 06:46:38 CDT)
Can I use namd for carbon nanotubes?
- Rob (Tue Mar 28 2006 - 22:16:44 CST)
Can NAMD be used as for general Newtonian mechanics simulations?
- Vincent Kraeutler (Sat Jul 28 2007 - 07:11:27 CDT)
- Arneh Babakhani (Fri Jul 27 2007 - 15:21:20 CDT)
Can NAMD control pressure gradually increase?
- weikai (Fri Oct 21 2005 - 02:30:41 CDT)
Can NAMD deal with solid-state system?
- weikai (Wed Aug 31 2005 - 21:57:21 CDT)
Can NAMD perform random expulsion molecular dynamics(REMD)?
- Sting (Sat Jun 30 2007 - 09:03:02 CDT)
Can NAMD perform random expulsion moleculardynamics(REMD)?
- Sting (Sat Jun 30 2007 - 21:12:50 CDT)
Can paratools really parametrize a structure? Is it really finished?
- JC Gumbart (Mon Feb 28 2011 - 13:31:16 CST)
- Ranyere Deyler (Mon Feb 28 2011 - 13:28:30 CST)
- JC Gumbart (Mon Feb 28 2011 - 11:23:54 CST)
- Ranyere Deyler (Mon Feb 28 2011 - 10:56:35 CST)
can RHDO crystal shape works in NAMD
- pxq_at_dicp.ac.cn (Fri Jul 01 2011 - 01:33:14 CDT)
can someone comment?
- hl332_at_drexel.edu (Sat Apr 07 2007 - 17:36:12 CDT)
- Cesar Avila (Sat Apr 07 2007 - 11:57:49 CDT)
- hl332_at_drexel.edu (Fri Apr 06 2007 - 22:17:32 CDT)
Can someone PLEASE explain the "firsttimestep" parameter ?
- surendra negi (Wed Mar 22 2006 - 18:19:39 CST)
- Himanshu Khandelia (Wed Mar 22 2006 - 16:45:17 CST)
- Brian Bennion (Wed Mar 22 2006 - 16:43:18 CST)
- snoze pa (Wed Mar 22 2006 - 16:24:49 CST)
- Marcos Sotomayor (Wed Mar 22 2006 - 15:53:16 CST)
- Sterling Paramore (Wed Mar 22 2006 - 15:40:02 CST)
- Himanshu Khandelia (Wed Mar 22 2006 - 14:49:03 CST)
can the harmonic constraint parameters be changed between run or minimize?
- Chongbo Sun (Sun Nov 23 2008 - 14:03:39 CST)
Can this be modelled in NAMD
- S.K. Ghosh (Fri Aug 01 2008 - 11:38:38 CDT)
can TMD alignment prior to force calculation be turned off?
- Jérôme Hénin (Sun Jan 08 2012 - 17:18:28 CST)
- Michael Zimmermann (Sun Jan 08 2012 - 17:03:41 CST)
- Axel Kohlmeyer (Sun Jan 08 2012 - 15:19:55 CST)
- Michael Zimmermann (Sun Jan 08 2012 - 15:04:15 CST)
Can we 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)
can we run EM of 2 or more proteins simultaneously
- Kalyan chaitanya (Tue Jan 22 2008 - 08:47:16 CST)
can we run FEP calculation in water sphere?
- wenhao_at_uchicago.edu (Fri Sep 09 2011 - 03:21:01 CDT)
Can you imagine?
- Steven Juarez (Sat Jun 09 2007 - 15:44:10 CDT)
Can you satisfy your girlfriend?
- Deborah Stanton (Mon Jun 11 2007 - 17:18:55 CDT)
- Todd Prince (Mon Jun 11 2007 - 05:04:59 CDT)
- Zoe Baker (Sat Jun 09 2007 - 17:16:07 CDT)
Can't find a good drug store?
- Derek Finley (Sat Jun 09 2007 - 13:20:14 CDT)
CAN'T FIND BOND PARAMETERS FOR BOND (error)
- Jérôme Hénin (Thu Mar 10 2005 - 07:59:14 CST)
- sabri bora erdemli (Thu Mar 10 2005 - 05:36:33 CST)
- Jérôme Hénin (Thu Mar 10 2005 - 05:16:35 CST)
- sabri bora erdemli (Thu Mar 10 2005 - 03:23:02 CST)
CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES
- Francesco Pietra (Sun Feb 14 2010 - 10:26:01 CST)
CAN'T FIND BOND PARAMETERS FOR BOND FE - S
- surendra negi (Fri Sep 02 2005 - 15:36:43 CDT)
Can't find C-PDB bond parameters
- JC Gumbart (Mon Feb 15 2010 - 12:06:41 CST)
- Francesco Pietra (Mon Feb 15 2010 - 11:44:52 CST)
- JC Gumbart (Mon Feb 15 2010 - 08:15:53 CST)
- Francesco Pietra (Mon Feb 15 2010 - 03:46:29 CST)
CAN'T FIND DIHEDRAL PARAMETERS FOR CN8B CN7 ON5 HN5
- Sujata Sovani (Fri Sep 04 2009 - 15:35:56 CDT)
can't load forces in tclforces
- James Servantie (Thu Sep 17 2009 - 05:54:21 CDT)
Can't stand sex all night long?
- Tara England (Sat Jun 09 2007 - 19:28:38 CDT)
cannot find -lsrfftw... collect2: ld returned 1 exit status
- Axel Kohlmeyer (Sun Jul 13 2008 - 15:54:54 CDT)
- Anupam Nath Jha (Sun Jul 13 2008 - 12:59:09 CDT)
Cannot find bond parameters
- Axel Kohlmeyer (Tue Jun 28 2011 - 11:09:12 CDT)
- Gayatri Rathod (Tue Jun 28 2011 - 11:03:45 CDT)
Cannot open file 'pair.pdb'
- Sandeep Agrawal (Mon May 15 2006 - 07:32:42 CDT)
Cannot specify both an initial temperature and a velocity file
- Marcos Sotomayor (Thu May 04 2006 - 10:02:27 CDT)
- Marc Q. Ma (Thu May 04 2006 - 08:45:53 CDT)
- Osman Yogurtcu (Thu May 04 2006 - 06:44:03 CDT)
Cannot spot error in namd config file
- Claw Isthelaw (Thu Jun 26 2008 - 10:41:53 CDT)
Can´t use charmm to perform dcd analysis
- Himanshu Khandelia (Mon May 21 2007 - 01:17:58 CDT)
- Victor Capistrán (Sun May 20 2007 - 22:56:18 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)
capping of end residues
- sudipta sinha (Mon Jun 09 2008 - 23:55:56 CDT)
capping using Amber FF
- Hui-Hsu Tsai (Tue Mar 01 2005 - 12:32:24 CST)
caps
- AYTUG TUNCEL (Mon Jul 10 2006 - 12:53:23 CDT)
carbohydrates: CHARMM versus AMBER
- Matthew Tessier (Thu Oct 30 2008 - 09:43:27 CDT)
- Dong Xu (Wed Oct 29 2008 - 18:47:49 CDT)
- Matthew Tessier (Wed Jul 02 2008 - 08:02:24 CDT)
- L. Michel Espinoza-Fonseca (Fri Jun 27 2008 - 17:44:41 CDT)
- Gianluca Interlandi (Fri Jun 27 2008 - 17:16:26 CDT)
- Gianluca Interlandi (Fri Jun 27 2008 - 14:16:08 CDT)
carma v.0.9
- Nicholas M Glykos (Mon Sep 22 2008 - 05:52:23 CDT)
Carma v.1.0 released.
- Nicholas M Glykos (Wed Oct 06 2010 - 06:14:15 CDT)
Carma v.1.1 released.
- Nicholas M Glykos (Thu Oct 27 2011 - 12:54:24 CDT)
Cartesian vs dihedral angle space PCA
- Nicholas M Glykos (Tue Jul 13 2010 - 04:35:22 CDT)
- patrick wintrode (Mon Jul 12 2010 - 10:12:29 CDT)
Catdcd
- Naveen Michaud-Agrawal (Wed Jan 26 2005 - 08:44:45 CST)
catDCD 32 bit Vs. 64 bit Version
- Philip Peartree (Thu Feb 07 2008 - 09:28:15 CST)
- Philip Peartree (Sat Feb 02 2008 - 10:21:44 CST)
- juneja_at_speakeasy.net (Fri Feb 01 2008 - 10:59:52 CST)
- Peter Freddolino (Fri Feb 01 2008 - 09:56:19 CST)
- juneja_at_speakeasy.net (Fri Feb 01 2008 - 04:00:51 CST)
- Peter Freddolino (Thu Jan 31 2008 - 13:26:09 CST)
- juneja_at_speakeasy.net (Thu Jan 31 2008 - 11:51:28 CST)
- Monika Sharma (Thu Jan 31 2008 - 08:09:46 CST)
- Alok Juneja (Thu Jan 31 2008 - 03:51:40 CST)
catdcd and dcdunitcell
- John Stone (Mon Jul 25 2005 - 13:50:03 CDT)
- Joshua D. Moore (Mon Jul 25 2005 - 14:16:16 CDT)
- Joshua D. Moore (Fri Jul 22 2005 - 16:04:00 CDT)
- Ben Roberts (Tue Jun 28 2005 - 18:27:07 CDT)
- Philip Fowler (Tue Jun 28 2005 - 11:07:38 CDT)
- Jérôme Hénin (Tue Jun 28 2005 - 10:54:09 CDT)
- Philip Fowler (Tue Jun 28 2005 - 09:27:06 CDT)
- Jérôme Hénin (Tue Jun 28 2005 - 09:14:32 CDT)
- Philip Fowler (Tue Jun 28 2005 - 07:18:15 CDT)
- Philip Fowler (Tue Jun 28 2005 - 07:15:36 CDT)
- Ben Roberts (Mon Jun 27 2005 - 07:47:39 CDT)
- Philip Fowler (Mon Jun 27 2005 - 05:07:01 CDT)
CatDCD installation
- bkziervogel_at_uchicago.edu (Mon Aug 30 2010 - 11:24:04 CDT)
catdcd-generated files and CHARMM
- Mauricio Carrillo Tripp (Thu Jul 21 2005 - 16:10:11 CDT)
- Mauricio Carrillo Tripp (Thu Jul 21 2005 - 14:05:10 CDT)
- Chang, Christopher (Thu Jul 21 2005 - 11:55:25 CDT)
Cationic Dummy Atom models
- Hok-Hei Tam (Sun Mar 21 2010 - 16:31:39 CDT)
CCL:where to find the force field parameters for F and P atom?
- Joey Harriman (Fri Dec 12 2003 - 09:22:15 CST)
CCS ERROR during simulation
- Jason Lee (Mon Jul 25 2005 - 08:52:16 CDT)
cell basis vector restart
- Jeffrey J. Potoff (Tue Mar 02 2010 - 13:09:37 CST)
- Mark M Huntress (Tue Mar 02 2010 - 12:09:07 CST)
- Mark M Huntress (Tue Mar 02 2010 - 09:51:21 CST)
- Mark M Huntress (Mon Mar 01 2010 - 16:47:47 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)
Cell Data in DCD files - CHARMM compatibility
- Joshua D. Moore (Fri Aug 07 2009 - 22:26:07 CDT)
- Dimitar V Pachov (Fri Aug 07 2009 - 19:50:30 CDT)
Cell membranes with lipids different from POPC and POPE
- Lechuga, Javier (Mon Jul 31 2006 - 18:03:59 CDT)
cell on namd 2.7b1
- Axel Kohlmeyer (Wed Apr 29 2009 - 08:34:08 CDT)
- alessandro.venturelli_at_univr.it (Wed Apr 29 2009 - 08:10:01 CDT)
cell size
- Hasan haska (Wed Dec 14 2011 - 06:41:10 CST)
- Aron Broom (Tue Dec 13 2011 - 10:03:58 CST)
- Axel Kohlmeyer (Tue Dec 13 2011 - 10:00:43 CST)
- Hasan haska (Tue Dec 13 2011 - 09:47:50 CST)
- Axel Kohlmeyer (Tue Dec 13 2011 - 08:21:18 CST)
- Hasan haska (Tue Dec 13 2011 - 08:10:49 CST)
CellBasisVector
- jfgaff_at_ncsu.edu (Mon Jun 25 2007 - 19:53:47 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)
cellBasisVectors and xsc files
- Wei Chen (Wed Jul 20 2005 - 10:47:21 CDT)
- JC Gumbart (Tue Jul 19 2005 - 21:03:07 CDT)
- Stern, Julie (Tue Jul 19 2005 - 20:53:01 CDT)
cellBasisvectors/.xsc fixing/colvars while running amber ff
- Giacomo Fiorin (Fri Oct 21 2011 - 17:06:43 CDT)
- Francesco Pietra (Fri Oct 21 2011 - 13:13:57 CDT)
cellOrigin
- Marc Q. Ma (Tue Feb 22 2005 - 14:06:04 CST)
center of mass for SMD
- JC Gumbart (Wed Feb 11 2009 - 22:44:01 CST)
- Falgun Shah (Tue Feb 10 2009 - 17:52:06 CST)
Center of Mass Harmonic Potentials
- Jérôme Hénin (Tue Jan 19 2010 - 01:56:34 CST)
- Axel Kohlmeyer (Mon Jan 18 2010 - 19:33:18 CST)
- Keith Battle (Mon Jan 18 2010 - 18:59:25 CST)
center of mass motion: problems
- Leandro Martínez (Thu Dec 08 2005 - 17:49:23 CST)
- Vani Krishna (Thu Dec 08 2005 - 16:27:06 CST)
center of mass of dummyAtom in colvar
- Giacomo Fiorin (Wed Oct 28 2009 - 13:04:41 CDT)
- Giacomo Fiorin (Wed Oct 14 2009 - 19:19:31 CDT)
- Giacomo Fiorin (Wed Oct 14 2009 - 18:57:43 CDT)
- BIN ZHANG (Wed Oct 14 2009 - 19:06:01 CDT)
- BIN ZHANG (Wed Oct 14 2009 - 16:57:13 CDT)
center-of-mass tcl and coordinate wrapping
- Ilja Khavrutskii (Sun Feb 24 2008 - 15:45:15 CST)
centre of mass fixed
- Moumita Maiti (Sun Jul 08 2007 - 11:29:50 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)
CFP: 3rd Annual CMM Workshop on QM/MM Simulations
- CMM QM/MM Workshop (Mon May 19 2008 - 13:43:55 CDT)
CG bead definition
- BIN ZHANG (Thu Oct 22 2009 - 18:05:32 CDT)
- BIN ZHANG (Tue Oct 20 2009 - 15:12:04 CDT)
CG equilibration recurring crashes
- Axel Kohlmeyer (Sun Dec 27 2009 - 12:44:08 CST)
- Axel Kohlmeyer (Sun Dec 27 2009 - 09:47:46 CST)
- Francesco Pietra (Sun Dec 27 2009 - 08:47:12 CST)
CG modeling using NAMD
- Peter Freddolino (Sat Nov 22 2008 - 20:49:22 CST)
- BIN ZHANG (Sat Nov 22 2008 - 18:54:05 CST)
CG Name Prefix Problem
- Anton Arkhipov (Fri Oct 24 2008 - 10:30:05 CDT)
- Anirban Ghosh (Fri Oct 24 2008 - 00:24:58 CDT)
CG parameterization problem
- Stefan Franzen (Tue Apr 26 2011 - 05:07:32 CDT)
CG parameters from dcd file for protein CG modelling
- Nicolás Pérez (Sun Feb 27 2011 - 13:32:18 CST)
cg protein folding
- Axel Kohlmeyer (Wed Mar 18 2009 - 13:57:31 CDT)
- Hannes Loeffler (Wed Mar 18 2009 - 11:42:46 CDT)
- doty alexiou (Wed Mar 18 2009 - 09:51:17 CDT)
CG-MD high electrostatic energy values
- sibel.cakan (Fri Jun 24 2011 - 03:40:32 CDT)
CG_MD temperature
- Sibel Cakan (Fri Jan 28 2011 - 07:52:15 CST)
CGMD ? Hydrophobic scale
- Peter Freddolino (Fri May 01 2009 - 22:18:00 CDT)
- BIN ZHANG (Fri May 01 2009 - 17:00:12 CDT)
CGMD parameters
- Peter Freddolino (Wed Dec 24 2008 - 07:27:25 CST)
- BIN ZHANG (Tue Dec 23 2008 - 20:06:32 CST)
CGMD problem
- Anton Arkhipov (Sat Dec 06 2008 - 16:31:18 CST)
- BIN ZHANG (Sat Dec 06 2008 - 16:19:32 CST)
- Anton Arkhipov (Sat Dec 06 2008 - 15:45:15 CST)
- BIN ZHANG (Sat Dec 06 2008 - 14:30:39 CST)
- Anton Arkhipov (Wed Dec 03 2008 - 11:39:32 CST)
- Peter Freddolino (Tue Dec 02 2008 - 22:39:52 CST)
- BIN ZHANG (Tue Dec 02 2008 - 11:10:34 CST)
cgmd stability
- Peter Freddolino (Thu Feb 26 2009 - 02:13:16 CST)
- wang (Wed Feb 25 2009 - 21:43:41 CST)
- Peter Freddolino (Tue Feb 24 2009 - 04:22:31 CST)
- wang (Mon Feb 23 2009 - 23:49:47 CST)
- Peter Freddolino (Mon Feb 23 2009 - 22:05:03 CST)
- BIN ZHANG (Thu Feb 19 2009 - 11:25:41 CST)
- Peter Freddolino (Thu Feb 19 2009 - 06:46:40 CST)
- Peter Freddolino (Thu Feb 19 2009 - 07:16:46 CST)
- wang (Thu Feb 19 2009 - 03:15:56 CST)
- BIN ZHANG (Thu Feb 19 2009 - 00:31:35 CST)
- Peter Freddolino (Wed Feb 18 2009 - 23:41:27 CST)
- BIN ZHANG (Wed Feb 18 2009 - 20:20:52 CST)
- Peter Freddolino (Wed Feb 18 2009 - 20:05:57 CST)
- BIN ZHANG (Wed Feb 18 2009 - 17:13:14 CST)
CGMD timestep
- Jerome Henin (Mon Dec 08 2008 - 16:00:03 CST)
- Axel Kohlmeyer (Mon Dec 08 2008 - 12:11:54 CST)
- BIN ZHANG (Mon Dec 08 2008 - 11:51:46 CST)
- BIN ZHANG (Mon Dec 08 2008 - 11:29:05 CST)
- Axel Kohlmeyer (Mon Dec 08 2008 - 11:37:37 CST)
- Axel Kohlmeyer (Mon Dec 08 2008 - 03:26:43 CST)
- BIN ZHANG (Sun Dec 07 2008 - 14:44:23 CST)
chage free energy
- Peter Freddolino (Fri Jun 16 2006 - 13:11:52 CDT)
- edu (Fri Jun 16 2006 - 13:58:08 CDT)
Cham++ errors
- Kramer Campen (Tue Aug 08 2006 - 15:01:07 CDT)
Chamrun/NAMD processes and PBS cluster
- Nicolas Sapay (Mon Dec 05 2005 - 07:55:15 CST)
change center of spherical BC during sim
- paco ty (Mon Nov 12 2007 - 14:33:34 CST)
change force field in NAMD
- Erik Santiso (Fri Oct 22 2010 - 11:05:50 CDT)
- Erik Santiso (Fri Oct 15 2010 - 15:30:04 CDT)
- Axel Kohlmeyer (Fri Oct 15 2010 - 10:58:33 CDT)
- Chen, Zhihong (chenz2) (Fri Oct 15 2010 - 09:50:14 CDT)
- Chen, Zhihong (chenz2) (Fri Oct 15 2010 - 09:51:04 CDT)
- Chen, Zhihong (chenz2) (Thu Oct 07 2010 - 09:49:45 CDT)
- Jérôme Hénin (Tue Oct 05 2010 - 03:38:27 CDT)
- Chen, Zhihong (chenz2) (Mon Oct 04 2010 - 14:11:11 CDT)
- Chen, Zhihong (chenz2) (Fri Sep 24 2010 - 14:36:09 CDT)
change in box geometry for simulation of pure water
- Axel Kohlmeyer (Thu Aug 28 2008 - 14:06:47 CDT)
- Chris Harrison (Wed Aug 27 2008 - 21:23:22 CDT)
- maria goranovic (Thu Aug 28 2008 - 02:11:31 CDT)
- Peter Freddolino (Wed Aug 27 2008 - 22:58:07 CDT)
- maria goranovic (Wed Aug 27 2008 - 07:48:12 CDT)
change in Disulphide Patches
- Navratna Vajpai (Mon May 08 2006 - 03:05:28 CDT)
change segID using segment command in psfgen
- Low Soo Mei (Thu Mar 06 2008 - 19:33:33 CST)
- JC Gumbart (Thu Mar 06 2008 - 08:28:12 CST)
- Low Soo Mei (Thu Mar 06 2008 - 03:01:18 CST)
change solvent
- ehenriques_at_qui.uc.pt (Thu Aug 19 2010 - 05:32:51 CDT)
- Branko (Wed Aug 18 2010 - 10:54:18 CDT)
- Nicholas Musolino (Wed Aug 18 2010 - 12:00:57 CDT)
- Leandro Martínez (Wed Aug 18 2010 - 11:36:59 CDT)
- sara (Wed Aug 18 2010 - 10:26:20 CDT)
Changes to dihedral angles
- Neelanjana Sengupta (Wed Aug 09 2006 - 17:14:36 CDT)
changing dcd output file DURING run?
- Sebastian Stolzenberg (Thu May 29 2008 - 12:49:36 CDT)
changing default directory in VMD?
- Samuel Flores (Thu Jun 16 2005 - 14:20:31 CDT)
- Shirley Hui (Wed Jun 15 2005 - 15:34:51 CDT)
- Blake Charlebois (Wed Jun 15 2005 - 15:21:43 CDT)
- Samuel Flores (Wed Jun 15 2005 - 14:09:25 CDT)
changing file
- Wei Chen (Wed Jul 20 2005 - 10:43:24 CDT)
- Giovanni Bellesia (Wed Jul 20 2005 - 04:57:29 CDT)
- Jérôme Hénin (Wed Jul 20 2005 - 05:07:19 CDT)
- Deborah Jameson (Wed Jul 20 2005 - 03:18:12 CDT)
Changing functions without recompiling
- Cole Gleason (Tue Oct 19 2010 - 13:53:17 CDT)
- Jim Phillips (Tue Oct 19 2010 - 11:56:40 CDT)
- Axel Kohlmeyer (Mon Oct 18 2010 - 22:12:10 CDT)
- Cole Gleason (Mon Oct 18 2010 - 21:24:01 CDT)
- Cole Gleason (Mon Oct 18 2010 - 21:27:27 CDT)
- Joshua Adelman (Mon Oct 18 2010 - 20:42:42 CDT)
- Nicholas Musolino (Mon Oct 18 2010 - 20:20:58 CDT)
- Axel Kohlmeyer (Mon Oct 18 2010 - 17:39:28 CDT)
- Cole Gleason (Mon Oct 18 2010 - 16:53:32 CDT)
Changing loop to helix: restraining about 20 dihedral angles
- maria goranovic (Mon Jun 25 2007 - 07:06:28 CDT)
- Jerome Henin (Sun Jun 24 2007 - 11:37:53 CDT)
- maria goranovic (Sun Jun 24 2007 - 07:06:32 CDT)
- Subramanian Vaitheeswaran (Thu Jun 21 2007 - 11:29:40 CDT)
- Peter Freddolino (Thu Jun 21 2007 - 09:06:00 CDT)
- maria goranovic (Thu Jun 21 2007 - 01:33:30 CDT)
- maria goranovic (Tue Jun 19 2007 - 10:59:16 CDT)
changing parameter files during simulation run
- sukesh shenoy (Fri Oct 27 2006 - 10:18:55 CDT)
changing position of atoms during NAMD simulation
- michael_at_perfect-kreim.de (Mon Jan 14 2008 - 07:11:52 CST)
changing protonation states for a pdb with more than a single polypeptide
- Elia Zomot (Tue May 12 2009 - 18:47:41 CDT)
Changing SMD parameters
- Gadi Oron (Mon Feb 09 2004 - 07:32:11 CST)
changing solventDielectric in GBIS
- Andres Colubri (Mon Jun 13 2011 - 08:17:36 CDT)
- Ajasja LjubetiÄ (Mon Jun 13 2011 - 07:50:42 CDT)
- Andres Colubri (Mon Jun 13 2011 - 07:36:41 CDT)
Changing the atomtype of a particle on the fly
- Axel Kohlmeyer (Mon Oct 05 2009 - 02:14:41 CDT)
- daniel aguayo (Sun Oct 04 2009 - 18:59:00 CDT)
- Axel Kohlmeyer (Fri Oct 02 2009 - 14:57:43 CDT)
- BIN ZHANG (Fri Oct 02 2009 - 13:50:21 CDT)
- Axel Kohlmeyer (Fri Oct 02 2009 - 13:30:57 CDT)
- Axel Kohlmeyer (Fri Oct 02 2009 - 13:09:12 CDT)
- BIN ZHANG (Fri Oct 02 2009 - 01:15:07 CDT)
Changing the Potential Energy Function
- Axel Kohlmeyer (Thu Feb 04 2010 - 22:50:30 CST)
- Hok-Hei Tam (Thu Feb 04 2010 - 22:08:41 CST)
Changing the protonation states of residues
- hl332_at_drexel.edu (Tue Mar 06 2007 - 18:31:08 CST)
- Gaurav Sharma (Tue Mar 06 2007 - 18:08:04 CST)
- Nabajyoti Goswami (Mon Mar 05 2007 - 03:27:07 CST)
Changing the Secondary Structure of a Protein
- Giacomo Fiorin (Sun Dec 28 2008 - 16:33:28 CST)
- Peter Freddolino (Sun Dec 28 2008 - 08:48:38 CST)
- JC Gumbart (Sun Dec 28 2008 - 08:55:03 CST)
- MIke S (Sun Dec 28 2008 - 01:18:23 CST)
changing velocity during simulation
- JC Gumbart (Wed Oct 11 2006 - 15:05:44 CDT)
- olga hrydziuszko (Wed Oct 11 2006 - 09:05:28 CDT)
- olga hrydziuszko (Wed Oct 11 2006 - 08:10:17 CDT)
changuing dihedral angle slowly
- Leonardo Sepulveda Durán (Fri Jun 24 2005 - 17:35:20 CDT)
changuing dihedral angle slowly (complete message)
- Leonardo Sepulveda Durán (Fri Jun 24 2005 - 17:47:02 CDT)
Channel flow equilibration
- Jim Phillips (Wed Jun 15 2011 - 17:02:10 CDT)
- Mao Mao (Wed Jun 15 2011 - 11:46:26 CDT)
Characteristic time of atomic vibrations and collisions?
- Yinglong Miao (Tue Jan 15 2008 - 10:06:29 CST)
- Victor Ovchinnikov (Mon Jan 14 2008 - 17:33:42 CST)
- Yinglong Miao (Mon Jan 14 2008 - 16:16:11 CST)
charamrun / Rocks distribution problem
- Mounir Tarek (Mon Oct 25 2004 - 10:20:28 CDT)
charge calculation
- Kwee Hong (Sat Aug 28 2010 - 09:09:12 CDT)
charge on protein
- Dhiraj Srivastava (Thu Oct 19 2006 - 13:50:59 CDT)
- Leonardo Trabuco (Wed Oct 18 2006 - 22:17:56 CDT)
- Mark Abraham (Wed Oct 18 2006 - 22:16:02 CDT)
- Dhiraj Srivastava (Wed Oct 18 2006 - 21:57:28 CDT)
Charged Atoms in External Magnetic Field
- Westley A Sherman (Thu Nov 16 2006 - 18:50:12 CST)
Charges in NAMD topology file
- Richard Wood (Fri Apr 20 2007 - 09:53:08 CDT)
- Jawahar Neelankatan (Fri Apr 20 2007 - 07:10:59 CDT)
- JC Gumbart (Thu Apr 19 2007 - 18:21:34 CDT)
- Jawahar Neelankatan (Thu Apr 19 2007 - 16:51:08 CDT)
charges in psf and in namd (or vmd)
- fett_at_vtr.net (Wed Jun 02 2010 - 11:12:07 CDT)
charges in topology
- regafan_at_usc.es (Wed Nov 15 2006 - 11:34:32 CST)
Charm compile: "xlC: command not found"
- Peter Freddolino (Mon Jul 02 2007 - 10:32:56 CDT)
- Jianhui Tian (Mon Jul 02 2007 - 09:55:36 CDT)
charm installation problem
- Govardhan Reddy (Sun May 27 2007 - 16:43:43 CDT)
CHARM parameter file needed for simple organic molecules like Methanol, Formamide, Chloroform, TCE, Toluene
- MD. ZILLUR RAHMAN (Sun Mar 21 2010 - 22:07:46 CDT)
charm++ 5.9 build fails, NAMD 2.6b1 make fails
- Dow_Hurst (Tue Aug 02 2005 - 17:16:55 CDT)
charm++ 5.9 megatest failure too
- Dow Hurst (Wed Aug 03 2005 - 22:11:54 CDT)
- Eric Bohm (Tue Aug 02 2005 - 17:49:31 CDT)
- Dow Hurst (Wed Aug 03 2005 - 07:37:49 CDT)
- Gengbin Zheng (Tue Aug 02 2005 - 18:21:51 CDT)
- Dow_Hurst (Tue Aug 02 2005 - 17:25:38 CDT)
charm++ build problem
- Yogesh (Thu May 14 2009 - 08:24:42 CDT)
Charm++ compilation
- sudipta sinha (Tue May 27 2008 - 01:51:12 CDT)
- Philip Peartree (Wed Aug 22 2007 - 10:32:50 CDT)
- Dow_Hurst (Wed Aug 22 2007 - 09:58:56 CDT)
- Philip Peartree (Wed Aug 22 2007 - 08:35:00 CDT)
charm++ compile problem on x86_64
- Steven A. DuChene (Fri Jan 14 2005 - 17:09:42 CST)
- Gengbin Zheng (Fri Jan 14 2005 - 15:32:10 CST)
- Steven A. DuChene (Fri Jan 14 2005 - 15:24:02 CST)
Charm++ Fatal error ! Periodic cell has become too small for original patch grid!
- Peter Freddolino (Fri Nov 07 2008 - 14:38:47 CST)
- Roman Petrenko (Fri Nov 07 2008 - 13:57:33 CST)
- Peter Freddolino (Fri Nov 07 2008 - 12:45:34 CST)
- Dave Rogers (Fri Nov 07 2008 - 12:23:52 CST)
- Joshua Adelman (Fri Nov 07 2008 - 11:31:59 CST)
- CHINDEA Vlad (Thu Nov 06 2008 - 17:40:35 CST)
charm++ how to handle SMP/Multicore
- Bjoern Olausson (Thu Aug 20 2009 - 11:41:16 CDT)
- Bjoern Olausson (Sun Aug 09 2009 - 17:01:48 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++ over MPI
- Gengbin Zheng (Fri Feb 17 2006 - 10:30:18 CST)
- Bogdan Costescu (Fri Feb 17 2006 - 06:27:52 CST)
- Gengbin Zheng (Thu Feb 16 2006 - 15:40:18 CST)
- Bogdan Costescu (Thu Feb 16 2006 - 08:48:43 CST)
- Gengbin Zheng (Wed Feb 15 2006 - 11:00:53 CST)
- Bogdan Costescu (Tue Feb 14 2006 - 11:07:19 CST)
Charm++ Problem
- Brian Bennion (Thu Feb 26 2004 - 12:09:18 CST)
- Ben Brooks (Thu Feb 26 2004 - 11:32:28 CST)
Charm++ problem on EM64T/Myrinet cluster
- Gengbin Zheng (Fri Apr 01 2005 - 01:23:51 CST)
- Chona S. Guiang (Thu Mar 31 2005 - 16:08:38 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)
CHARM/NAMD network problems on amd64 Clustermatic
- Rene Salmon (Wed May 25 2005 - 12:12:05 CDT)
- Gengbin Zheng (Wed May 11 2005 - 22:21:36 CDT)
- Rene Salmon (Wed May 11 2005 - 13:07:25 CDT)
charm27 forcefield_topology
- Peter Freddolino (Wed Feb 25 2009 - 15:09:23 CST)
- Falgun Shah (Wed Feb 25 2009 - 11:02:02 CST)
CHARMM
- Eunice Ramirez Melendez (Mon Sep 06 2004 - 21:30:50 CDT)
Charmm 1,4 Interactions - Scaling Question
- Paul R Brenner (Fri Jun 17 2005 - 09:08:54 CDT)
- Jan Saam (Thu Jun 16 2005 - 18:20:22 CDT)
- Paul R Brenner (Thu Jun 16 2005 - 12:00:05 CDT)
charmm 19 parameters
- Hasan haska (Fri Mar 25 2011 - 09:49:24 CDT)
- Hasan haska (Fri Mar 25 2011 - 09:38:41 CDT)
Charmm 22 vs Charmm 27
- Joshua D. Moore (Sat Oct 06 2007 - 11:55:47 CDT)
- Richard Wood (Sat Oct 06 2007 - 11:24:47 CDT)
- Ilya Chorny (Sat Oct 06 2007 - 10:30:25 CDT)
- Richard Wood (Fri Oct 05 2007 - 17:10:54 CDT)
- Thomas Gaillard (Fri Oct 05 2007 - 16:07:47 CDT)
- Ilya Chorny (Fri Oct 05 2007 - 15:02:51 CDT)
- Ilya Chorny (Fri Oct 05 2007 - 14:13:33 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 carbohydrate force field
- JC Gumbart (Tue Aug 31 2010 - 13:55:44 CDT)
- Chris Harrison (Tue Aug 31 2010 - 13:30:03 CDT)
- Jianhui Tian (Tue Aug 31 2010 - 13:09:58 CDT)
charmm charge style
- Jan Saam (Wed Jan 02 2008 - 15:48:27 CST)
- carlos alberto gueto tettay (Thu Dec 27 2007 - 12:55:00 CST)
CHARMM compatible Methotrexate params
- Aaron Oakley (Thu Nov 24 2005 - 22:17:18 CST)
CHARMM FF parameters for O2 Gas
- m.raviprasad_at_ndsu.edu (Fri Aug 06 2010 - 14:39:11 CDT)
charmm force field
- Swarna M Patra (Thu Feb 03 2011 - 21:55:22 CST)
CHARMM forcefield is free?
- wavedalla\_at_libero\.it (Thu Jul 19 2007 - 01:12:35 CDT)
Charmm format topology and parameter files for FAD
- Richard Wood (Mon Sep 17 2007 - 17:30:59 CDT)
- mon_sharma_at_research.iiit.ac.in (Mon Sep 17 2007 - 14:17:26 CDT)
CHARMM General Force Field (CGENFF)
- Gianluca Interlandi (Wed Feb 16 2011 - 18:56:33 CST)
Charmm is not free so how to learn it
- jfgaff_at_ncsu.edu (Sun Jun 15 2008 - 18:51:19 CDT)
- Philip Peartree (Sun Jun 15 2008 - 09:38:02 CDT)
- abhijit ramachandran (Fri Jun 13 2008 - 15:01:50 CDT)
CHARMM Lorentz-berthelot mixing rules
- Jim Phillips (Mon Oct 18 2010 - 11:38:12 CDT)
- divya nayar (Mon Oct 18 2010 - 05:21:52 CDT)
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 parameter and topology files
- Jerome Henin (Tue May 27 2008 - 11:20:30 CDT)
- me00109_at_cc.uoi.gr (Tue May 27 2008 - 10:17:52 CDT)
Charmm parameter for H2 gas
- Mikhail Suyetin (Wed Jun 29 2011 - 05:00:05 CDT)
- Zhao Lina (Wed Jun 29 2011 - 04:41:15 CDT)
Charmm parameters for
- Joakim Swedberg (Wed Apr 28 2010 - 21:47:03 CDT)
CHARMM parameters for H2S
- Jeffrey J. Potoff (Sat Jul 19 2008 - 22:34:21 CDT)
- Raul Araya (Fri Jul 18 2008 - 17:51:50 CDT)
CHARMM parameters for Mn 2+ ion
- Lisa Brown (Fri Mar 25 2011 - 10:43:45 CDT)
charmm parameters for PEG
- li jianguo (Sat Jun 04 2005 - 23:42:26 CDT)
charmm paramter
- Boyang Wang (Thu May 05 2005 - 22:23:56 CDT)
- akash.khandelwal_at_ndsu.edu (Thu May 05 2005 - 20:57:34 CDT)
CHARMM partial charges and paratool
- Jose R. Sabino (Fri Aug 03 2007 - 16:48:55 CDT)
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 str file
- Peter Freddolino (Thu Jul 19 2007 - 15:58:10 CDT)
- snoze pa (Thu Jul 19 2007 - 15:04:22 CDT)
CHARMM to NAMD
- Dimitar V Pachov (Thu Sep 03 2009 - 10:54:17 CDT)
- Yang MIngjun (Thu Sep 03 2009 - 01:37:21 CDT)
- Yang MIngjun (Tue Sep 01 2009 - 09:03:13 CDT)
Charmm to Namd!!
- Himanshu Khandelia (Wed Sep 19 2007 - 10:39:23 CDT)
- Philip Peartree (Wed Sep 19 2007 - 07:51:59 CDT)
- priyanka srivastava (Wed Sep 19 2007 - 05:49:22 CDT)
CHARMM top and par files for PO4
- Alexe Bojovschi (Mon Aug 14 2006 - 03:53:20 CDT)
charmm toppology : internal coordinates
- Arturas Ziemys (Tue Aug 22 2006 - 16:39:00 CDT)
Charmm++5.9 build on Mac OS X by IB xlc compiler
- Gengbin Zheng (Sun Sep 04 2005 - 11:08:03 CDT)
- Jason Lee (Fri Sep 02 2005 - 10:55:13 CDT)
- Gengbin Zheng (Fri Sep 02 2005 - 00:34:03 CDT)
- Jason Lee (Thu Sep 01 2005 - 16:46:24 CDT)
- Gengbin Zheng (Wed Aug 31 2005 - 14:18:07 CDT)
- Gengbin Zheng (Wed Aug 31 2005 - 12:32:56 CDT)
- Jason Lee (Tue Aug 30 2005 - 18:04:43 CDT)
- Gengbin Zheng (Tue Aug 09 2005 - 11:59:15 CDT)
- Jason Lee (Mon Aug 08 2005 - 14:58:21 CDT)
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 fatal error
- arijit_r_at_chem.iitkgp.ernet.in (Mon Dec 19 2005 - 22:24:36 CST)
- Michel Espinoza-Fonseca (Mon Dec 19 2005 - 15:30:41 CST)
- Arturas Ziemys (Mon Dec 19 2005 - 14:06:00 CST)
Charmm27 Xplor format
- Peter Jones (Tue Nov 30 2004 - 03:56:22 CST)
charmrun + NAMD on dual quad-core intel procs
- Ravinder Abrol (Mon Mar 26 2007 - 15:39:09 CDT)
Charmrun and ssh problem
- Andrea Cristiani (Tue Sep 18 2007 - 04:50:23 CDT)
charmrun constantly hanging
- Axel Kohlmeyer (Sat Nov 26 2011 - 10:06:22 CST)
- jani vinod (Sat Nov 26 2011 - 01:06:22 CST)
- Axel Kohlmeyer (Fri Nov 25 2011 - 08:27:08 CST)
- jani vinod (Fri Nov 25 2011 - 00:59:35 CST)
Charmrun issues and namd on Win 64
- Gengbin Zheng (Wed Jul 11 2007 - 01:34:26 CDT)
- Ilya Chorny (Sat Jul 07 2007 - 16:21:33 CDT)
- Ilya Chorny (Fri Jul 06 2007 - 18:53:23 CDT)
- Gengbin Zheng (Fri Jul 06 2007 - 16:17:28 CDT)
- Ilya Chorny (Fri Jul 06 2007 - 14:51:50 CDT)
charmrun not found
- Alexandre A. Vakhrouchev (Tue Jun 24 2008 - 22:50:45 CDT)
- Diego Alejandro Vargas (Tue Jun 24 2008 - 21:59:24 CDT)
charmrun simulations over macpros
- pedro.borkowski_at_utoronto.ca (Wed Jun 20 2007 - 20:44:42 CDT)
- Cesar Luis Avila (Wed Jun 20 2007 - 13:30:10 CDT)
- pedro.borkowski_at_utoronto.ca (Fri Jun 15 2007 - 13:07:02 CDT)
charmrun socket error
- Chris Harrison (Sat Oct 11 2008 - 17:02:49 CDT)
- David A. Horita (Thu Oct 09 2008 - 13:49:21 CDT)
CHARMRUN vs MPI
- Jason O'Young (Fri Aug 10 2007 - 13:14:22 CDT)
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)
Charmrun/INTEL MAC/2.7
- Marius Micluta (Fri Jun 05 2009 - 04:36:57 CDT)
- Grabe, Michael David (Thu Jun 04 2009 - 09:21:21 CDT)
Charmrun: error on request socket--
- Kwee Hong (Thu Oct 28 2010 - 22:05:27 CDT)
- Jim Phillips (Thu Oct 28 2010 - 14:14:28 CDT)
- Kwee Hong (Wed Oct 27 2010 - 21:01:33 CDT)
- Kwee Hong (Wed Oct 27 2010 - 12:08:11 CDT)
charmrun: execve failed to start; intel dual core Redhat
- Richard Baxter (Sat Nov 03 2007 - 23:24:50 CDT)
- Richard Baxter (Thu Nov 01 2007 - 16:42:55 CDT)
- Richard Baxter (Fri Nov 02 2007 - 10:42:30 CDT)
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- Kalyan Pulipaka (Sat Oct 02 2010 - 21:57:26 CDT)
checking for correct construction of dihedrals, etc.
- Ralph Jimenez (Mon Dec 19 2005 - 16:51:52 CST)
checkpoint / revert
- Arturas Ziemys (Thu Jun 14 2007 - 13:09:24 CDT)
Checkpoint on IRIX of namd 2.5 job not MPI enabled
- Dow_Hurst (Thu Apr 07 2005 - 09:40:55 CDT)
checkpoint software for NAMD?
- Gianluca Interlandi (Thu Sep 21 2006 - 16:55:46 CDT)
- Dan Strahs (Thu Sep 21 2006 - 15:37:47 CDT)
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- homerbruce571 homerbruce571 (Sat Jun 28 2008 - 09:32:28 CDT)
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)
Cholesterol structure
- Alexandre A. Vakhrouchev (Thu Jan 31 2008 - 08:06:03 CST)
- Alexandre A. Vakhrouchev (Thu Jan 31 2008 - 02:02:46 CST)
- Per Jr. Greisen (Thu Jan 31 2008 - 01:29:52 CST)
- Alexandre A. Vakhrouchev (Thu Jan 31 2008 - 01:38:03 CST)
- Alexandre A. Vakhrouchev (Thu Jan 31 2008 - 00:50:13 CST)
- Richard Wood (Tue Jan 29 2008 - 09:19:07 CST)
- Alexandre A. Vakhrouchev (Tue Jan 29 2008 - 04:48:07 CST)
cholestrerol
- Ajasja LjubetiÄ (Mon Aug 30 2010 - 06:15:38 CDT)
- Swarna M Patra (Mon Aug 30 2010 - 04:29:38 CDT)
cis/trans prolyl
- sfrickenhaus (Sat Aug 11 2007 - 03:40:55 CDT)
claen water
- Nicholas M Glykos (Mon Aug 30 2010 - 08:26:44 CDT)
- Axel Kohlmeyer (Mon Aug 30 2010 - 07:53:17 CDT)
- Nicholas M Glykos (Mon Aug 30 2010 - 04:22:31 CDT)
- Swarna M Patra (Sun Aug 29 2010 - 22:28:22 CDT)
clarification needed for wrapAll and wrapWater
- Yinglong Miao (Thu Mar 06 2008 - 08:13:40 CST)
Clarification regarding some finer details in ABF simulations
- Jerome Henin (Tue Aug 18 2009 - 16:01:56 CDT)
- Hugh Martin (Tue Aug 18 2009 - 10:01:08 CDT)
- Jerome Henin (Sat Aug 15 2009 - 15:55:35 CDT)
- Hugh Martin (Mon Aug 10 2009 - 12:33:47 CDT)
Class I vs Class II force fields
- Aaron Oakley (Tue Jul 26 2005 - 00:42:01 CDT)
Classic timepieces replicas
- Axel Kohlmeyer (Tue Jun 10 2008 - 04:37:57 CDT)
- Alexandre A. Vakhrouchev (Tue Jun 10 2008 - 04:41:40 CDT)
- Cole Cox (Mon Jun 09 2008 - 19:10:25 CDT)
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)
cluster / scratch space
- ziemys_at_ecr6.ohio-state.edu (Thu May 11 2006 - 09:28:06 CDT)
Cluster on commodity hardware
- Thomas Albers (Mon Oct 31 2011 - 12:37:30 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 conformations
- Himanshu Khandelia (Mon Nov 20 2006 - 15:05:09 CST)
- L. Michel Espinoza-Fonseca (Mon Nov 20 2006 - 14:49:16 CST)
- Dave Venky (Mon Nov 20 2006 - 12:42:58 CST)
clustering macs
- yu275197_at_yorku.ca (Tue Feb 10 2004 - 16:04:58 CST)
Clustering of conformation
- Jerry Ebalunode (Tue Apr 18 2006 - 11:12:22 CDT)
- L. Michel Espinoza-Fonseca (Tue Apr 18 2006 - 05:08:07 CDT)
- Leo.Ghemtio_at_sanofi-aventis.com (Tue Apr 18 2006 - 04:25:02 CDT)
clustering of trajectory
- Jun Zhang (Tue Jul 05 2011 - 20:18:16 CDT)
- Nicholas M Glykos (Tue Jul 05 2011 - 09:57:50 CDT)
- Bala subramanian (Tue Jul 05 2011 - 09:46:24 CDT)
clustermatic 4
- Peter Jones (Wed May 30 2007 - 21:18:26 CDT)
clustermatic 4 and 5 Namd/charm
- John Saeger (Sun Jan 02 2005 - 14:18:31 CST)
- Gengbin Zheng (Sat Jan 01 2005 - 15:15:45 CST)
- Rene Salmon (Sat Jan 01 2005 - 14:56:56 CST)
- 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 and NFS mount
- Gianluca Interlandi (Sun May 07 2006 - 15:49:40 CDT)
clustermatic nodelist file
- Rene Salmon (Fri Mar 04 2005 - 14:53:47 CST)
- Gengbin Zheng (Wed Mar 02 2005 - 21:29:40 CST)
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
- L. Michel Espinoza-Fonseca (Wed May 10 2006 - 14:52:43 CDT)
- Per Jr. Greisen (Wed May 10 2006 - 12:04:07 CDT)
- Per Jr. Greisen (Tue May 09 2006 - 06:16:45 CDT)
CMAP and NAMD
- Leonardo G. Trabuco (Mon Jun 05 2006 - 20:34:06 CDT)
- L. Michel Espinoza-Fonseca (Mon Jun 05 2006 - 19:16:21 CDT)
CMAP dimension limited to 24 dimensions
- Grace Brannigan (Fri Mar 19 2010 - 14:29:13 CDT)
- alpertunga daðcan (Thu Mar 18 2010 - 21:42:03 CDT)
CMAP dimensions in NAMD
- A D (Thu Mar 18 2010 - 19:07:43 CDT)
CMAP in CHARMM force field
- Jorge Pikunic (Fri Oct 08 2004 - 12:27:47 CDT)
CMAP in NAMD output
- Jérôme Hénin (Mon Jan 04 2010 - 17:07:38 CST)
- Yang MIngjun (Mon Jan 04 2010 - 01:50:47 CST)
CMAP in NAMD simulation
- Leonardo Trabuco (Sat Oct 14 2006 - 17:34:51 CDT)
- Neelanjana Sengupta (Sat Oct 14 2006 - 17:26:23 CDT)
CMAP in NAMD?
- Leonardo G. Trabuco (Wed Apr 05 2006 - 21:56:40 CDT)
- mpavlova_at_purdue.edu (Wed Apr 05 2006 - 16:34:58 CDT)
CMAP in VMD error
- JC Gumbart (Thu Oct 13 2005 - 16:16:04 CDT)
- greisen_at_binf.ku.dk (Thu Oct 13 2005 - 15:58:33 CDT)
CMAP problem
- Morad Alawneh (Tue Jan 03 2006 - 13:45:41 CST)
CMAP w/ D-amino acid
- Ziemys, Arturas (Fri Oct 02 2009 - 10:51:24 CDT)
CmiAbort+0x5f
- Demet Akten (Fri Apr 02 2010 - 05:25:54 CDT)
CNT modeling
- Jonathan Lee (Thu Jun 14 2007 - 14:44:32 CDT)
- Jonathan Lee (Wed Jun 13 2007 - 13:02:58 CDT)
- Cesar Luis Avila (Tue Jun 12 2007 - 16:05:21 CDT)
- Jonathan Lee (Tue Jun 12 2007 - 15:29:49 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)
Coarse grained model force fields
- Anton Arkhipov (Thu Sep 04 2008 - 14:17:52 CDT)
- Myunggi Yi (Thu Sep 04 2008 - 14:01:49 CDT)
Coarse grained psf file and parameter
- luca (Fri Jan 04 2008 - 08:37:21 CST)
coarse grained simulation
- Demet Akten (Fri Mar 28 2008 - 09:11:19 CDT)
COARSE GRAINED WATER MODEL
- Valeria Marquez (Tue Oct 20 2009 - 10:16:04 CDT)
- L. Michel Espinoza-Fonseca (Tue Oct 20 2009 - 09:36:00 CDT)
- Valeria Marquez (Tue Oct 20 2009 - 08:52:10 CDT)
coarse graining
- Anton Arkhipov (Sat Aug 07 2010 - 20:41:23 CDT)
- ipsita basu (Tue Aug 03 2010 - 04:43:20 CDT)
Coarse Graining problem resolved
- Stefan Franzen (Tue Apr 26 2011 - 05:32:21 CDT)
Coarse Graining setup question
- Stefan Franzen (Tue Apr 26 2011 - 05:13:23 CDT)
coarse-grained MD
- Demet Akten (Fri Feb 11 2011 - 03:34:56 CST)
coarse-grained model building
- Anton Arkhipov (Tue Apr 06 2010 - 10:31:57 CDT)
- Edward Lyman (Mon Apr 05 2010 - 13:12:50 CDT)
Coarse-grained Modeling/User defined FF
- Peter Freddolino (Thu Mar 29 2007 - 13:23:17 CDT)
- Joshua Adelman (Thu Mar 29 2007 - 13:13:17 CDT)
Coarse-Graining MD don't work perfect as expected
- Boyang Wang (Fri Dec 30 2011 - 03:57:44 CST)
- ÐìÖÓºÓ (Thu Dec 29 2011 - 00:50:31 CST)
Coarse_Graining tempetrature
- Sibel Cakan (Fri Jan 28 2011 - 09:12:43 CST)
- Sibel Cakan (Fri Jan 28 2011 - 08:31:02 CST)
Code question: Partitioning the patch contents into water and non-water
- Floris Buelens (Mon Sep 10 2007 - 11:00:13 CDT)
- Floris Buelens (Sat Aug 18 2007 - 05:20:32 CDT)
- Jim Phillips (Fri Aug 17 2007 - 11:10:55 CDT)
- David Hardy (Fri Aug 17 2007 - 10:24:18 CDT)
- Vincent Kraeutler (Fri Aug 17 2007 - 04:01:24 CDT)
collective variable calculation from dcd file
- Jérôme Hénin (Thu Dec 22 2011 - 05:20:15 CST)
- Branko (Wed Dec 21 2011 - 15:38:39 CST)
- Giovanni Bellesia (Wed Dec 21 2011 - 15:20:27 CST)
- Branko (Wed Dec 21 2011 - 15:15:06 CST)
- Giovanni Bellesia (Wed Dec 21 2011 - 14:44:47 CST)
collective variable space PMF, including biasing potential terms?
- Chris Chipot (Wed May 13 2009 - 18:16:54 CDT)
- Axel Kohlmeyer (Wed May 13 2009 - 17:52:30 CDT)
- Roman Petrenko (Wed May 13 2009 - 17:45:29 CDT)
- Chris Chipot (Wed May 13 2009 - 17:37:04 CDT)
- Roman Petrenko (Wed May 13 2009 - 17:00:49 CDT)
- Giacomo Fiorin (Wed May 13 2009 - 16:38:56 CDT)
- Jerome Henin (Wed May 13 2009 - 16:23:49 CDT)
- Sebastian Stolzenberg (Wed May 13 2009 - 14:48:05 CDT)
collective variables
- Giacomo Fiorin (Wed Jun 17 2009 - 15:43:21 CDT)
- Cesar Millan (Wed Jun 17 2009 - 15:29:02 CDT)
- Giacomo Fiorin (Wed Jun 17 2009 - 13:26:44 CDT)
- Jarrod Nickel (Wed Jun 17 2009 - 11:07:26 CDT)
collision correction of Locally Enhanced Sampling
- Dhiraj Srivastava (Sun Jul 30 2006 - 15:14:52 CDT)
coloring method in VMD
- Axel Kohlmeyer (Thu Oct 20 2011 - 18:21:30 CDT)
- lam nguyen (Thu Oct 20 2011 - 18:19:14 CDT)
colvar and tclForces with CUDA
- Jiyong Park (Sun Sep 25 2011 - 02:02:29 CDT)
colvar atom syntax
- Jérôme Hénin (Wed Jun 16 2010 - 11:42:09 CDT)
- Giacomo Fiorin (Wed Jun 16 2010 - 11:20:33 CDT)
- Michael Zimmermann (Wed Jun 16 2010 - 10:24:50 CDT)
- Jérôme Hénin (Wed Jun 16 2010 - 07:24:51 CDT)
- Michael Zimmermann (Tue Jun 15 2010 - 15:59:09 CDT)
- Giacomo Fiorin (Thu Jun 10 2010 - 17:20:18 CDT)
- Michael Zimmermann (Thu Jun 10 2010 - 15:40:53 CDT)
- Michael Zimmermann (Thu Jun 10 2010 - 15:15:41 CDT)
- Giacomo Fiorin (Tue Jun 08 2010 - 15:01:41 CDT)
- Michael Zimmermann (Tue Jun 08 2010 - 13:11:29 CDT)
colvar error
- Jérôme Hénin (Fri Mar 26 2010 - 06:34:11 CDT)
- Ferenc Ötvös, PhD (Fri Mar 26 2010 - 04:45:27 CDT)
colvar for PMF calculation
- Jérôme Hénin (Wed Apr 21 2010 - 05:13:48 CDT)
- Navendu bhatnagar (Tue Apr 20 2010 - 18:02:28 CDT)
colvar module question
- BIN ZHANG (Tue Jan 26 2010 - 23:54:19 CST)
- Giacomo Fiorin (Tue Jan 26 2010 - 08:18:15 CST)
- BIN ZHANG (Tue Jan 26 2010 - 01:32:50 CST)
- BIN ZHANG (Mon Jan 25 2010 - 15:09:24 CST)
Colvar on 2.7b2 win vs Linux MPI instalation
- Axel Kohlmeyer (Tue Feb 09 2010 - 16:01:44 CST)
- Branko (Tue Feb 09 2010 - 15:15:46 CST)
- Jerome Henin (Fri Jan 22 2010 - 15:19:33 CST)
- Branko (Sat Jan 23 2010 - 05:32:48 CST)
- Branko (Fri Jan 22 2010 - 14:28:30 CST)
colvar restrain of water in lipid system
- Jérôme Hénin (Mon Aug 29 2011 - 11:17:47 CDT)
- Giacomo Fiorin (Mon Aug 29 2011 - 11:06:44 CDT)
- Ling Wu (Mon Aug 29 2011 - 09:55:45 CDT)
- Giacomo Fiorin (Mon Aug 29 2011 - 09:36:39 CDT)
- Ling Wu (Mon Aug 29 2011 - 09:13:58 CDT)
- Ling Wu (Fri Aug 26 2011 - 14:44:21 CDT)
colvar: atom group defn. fails
- Jérôme Hénin (Fri Apr 16 2010 - 07:17:38 CDT)
- y_ja_at_163.com (Fri Apr 16 2010 - 05:35:46 CDT)
- Neelanjana Sengupta (Fri Apr 16 2010 - 05:29:29 CDT)
colvar: coordnum output
- Neelanjana Sengupta (Thu May 06 2010 - 05:17:19 CDT)
- Jérôme Hénin (Sat May 01 2010 - 03:28:02 CDT)
- Giacomo Fiorin (Fri Apr 30 2010 - 09:25:14 CDT)
- Jérôme Hénin (Fri Apr 30 2010 - 07:44:20 CDT)
- Neelanjana Sengupta (Fri Apr 30 2010 - 07:32:55 CDT)
- Jérôme Hénin (Fri Apr 30 2010 - 07:16:44 CDT)
- Neelanjana Sengupta (Fri Apr 30 2010 - 05:34:29 CDT)
Colvars "tilt" component force constant units for WHAM
- Robert Elder (Fri Jul 22 2011 - 11:06:16 CDT)
- Robert Elder (Tue Jul 12 2011 - 16:36:55 CDT)
- Giacomo Fiorin (Tue Jul 12 2011 - 23:19:31 CDT)
- Robert Elder (Tue Jul 12 2011 - 16:48:48 CDT)
Colvars and COM restraints for protein+membrane; plus a minor bug
- Jérôme Hénin (Fri Sep 24 2010 - 04:59:59 CDT)
- Marc Baaden (Fri Sep 24 2010 - 03:44:41 CDT)
- Jérôme Hénin (Thu Sep 23 2010 - 14:37:52 CDT)
- Marc Baaden (Thu Sep 23 2010 - 09:24:59 CDT)
Colvars Configuration File
- Giacomo Fiorin (Wed Aug 19 2009 - 17:16:24 CDT)
- Neelanjana Sengupta (Wed Aug 19 2009 - 05:03:34 CDT)
- Giacomo Fiorin (Mon Aug 17 2009 - 08:46:45 CDT)
- Neelanjana Sengupta (Sun Aug 16 2009 - 23:52:30 CDT)
- Neelanjana Sengupta (Sat Aug 15 2009 - 10:12:55 CDT)
- Giacomo Fiorin (Sat Aug 15 2009 - 08:56:38 CDT)
- Neelanjana Sengupta (Sat Aug 15 2009 - 02:16:19 CDT)
colvars don't run with minimization ...
- Leonardo Herrera (Tue Jun 15 2010 - 11:45:02 CDT)
- Giacomo Fiorin (Mon Jun 14 2010 - 23:06:03 CDT)
- Leonardo Herrera (Mon Jun 14 2010 - 19:44:21 CDT)
colvars error running ABF
- Axel Kohlmeyer (Tue Apr 13 2010 - 22:03:23 CDT)
- Patrick Yee (Tue Apr 13 2010 - 20:47:21 CDT)
colvars fixes
- Giacomo Fiorin (Tue Mar 09 2010 - 19:36:08 CST)
Colvars in NAMD 2.7b4
- Jérôme Hénin (Tue Sep 21 2010 - 07:06:29 CDT)
colvars orientation problem appears in 2.8 only?
- Jérôme Hénin (Fri Apr 29 2011 - 06:16:55 CDT)
- JC Gumbart (Thu Apr 28 2011 - 18:41:17 CDT)
colvars PMF history problem
- Ajasja LjubetiÄ (Wed Mar 09 2011 - 03:40:18 CST)
- Jérôme Hénin (Tue Mar 08 2011 - 22:55:42 CST)
- Axel Kohlmeyer (Mon Mar 07 2011 - 17:56:05 CST)
- Nikolaos Glykos (Mon Mar 07 2011 - 16:54:35 CST)
- Ajasja LjubetiÄ (Mon Mar 07 2011 - 15:01:08 CST)
- Ajasja LjubetiÄ (Mon Mar 07 2011 - 14:50:06 CST)
- Nicholas M Glykos (Mon Mar 07 2011 - 11:14:40 CST)
- Axel Kohlmeyer (Mon Mar 07 2011 - 10:03:24 CST)
- Ajasja Ljubetiè (Mon Mar 07 2011 - 09:43:02 CST)
- Axel Kohlmeyer (Mon Mar 07 2011 - 09:27:19 CST)
- Ajasja LjubetiÄ (Mon Mar 07 2011 - 08:43:08 CST)
colvars, discontinuous rotation
- JC Gumbart (Wed Jul 27 2011 - 23:27:23 CDT)
- Giacomo Fiorin (Wed Jul 27 2011 - 21:20:41 CDT)
- JC Gumbart (Wed Jul 27 2011 - 20:41:30 CDT)
colvars-history file
- Jérôme Hénin (Wed Dec 29 2010 - 02:24:17 CST)
- Alex Liu (Sat Dec 25 2010 - 18:39:21 CST)
colvars: Error: in parsing "centers"
- Giacomo Fiorin (Thu Jun 10 2010 - 21:10:55 CDT)
- Leonardo Herrera (Thu Jun 10 2010 - 19:25:16 CDT)
colvars: Error: undefined output or restart file.
- Bonnie Merchant (Mon Jun 29 2009 - 11:00:07 CDT)
- Giacomo Fiorin (Fri Jun 26 2009 - 15:03:27 CDT)
- Jerome Henin (Fri Jun 26 2009 - 14:26:47 CDT)
- Bonnie Merchant (Fri Jun 26 2009 - 13:41:42 CDT)
colvars: free energy change with rmsd
- Jérôme Hénin (Tue May 04 2010 - 10:41:19 CDT)
- Jérôme Hénin (Tue May 04 2010 - 10:37:47 CDT)
- Jérôme Hénin (Wed Apr 14 2010 - 04:39:57 CDT)
- Kyle Hong (Wed Apr 14 2010 - 04:05:03 CDT)
- Neelanjana Sengupta (Wed Apr 14 2010 - 00:54:08 CDT)
Colvars: Using "Alpha" Component
- Giacomo Fiorin (Fri Sep 24 2010 - 16:35:44 CDT)
- Alexander Predeus (Fri Sep 24 2010 - 16:56:21 CDT)
- Giacomo Fiorin (Fri Sep 24 2010 - 17:01:27 CDT)
- Alexander Predeus (Fri Sep 24 2010 - 16:10:46 CDT)
- Giacomo Fiorin (Fri Sep 24 2010 - 15:48:59 CDT)
- Alexander Predeus (Fri Sep 24 2010 - 13:25:31 CDT)
- Jérôme Hénin (Fri Sep 24 2010 - 03:27:40 CDT)
- Alexander Predeus (Thu Sep 23 2010 - 19:26:31 CDT)
colvarsInput filename problem
- Jérôme Hénin (Thu Jan 07 2010 - 04:28:09 CST)
- BIN ZHANG (Wed Jan 06 2010 - 19:51:43 CST)
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 restraint in NAMD
- JC Gumbart (Wed Aug 22 2007 - 11:49:13 CDT)
- Victor Ovchinnikov (Wed Aug 22 2007 - 10:55:56 CDT)
COM velocity
- Amit Paliwal (Thu Apr 15 2004 - 04:50:29 CDT)
Combine pdb and psf files
- Luis Rosales (Fri Apr 29 2005 - 18:26:06 CDT)
- Gan, Yong $UMC-Student$ (Fri Apr 29 2005 - 16:04:23 CDT)
combine pdb files
- JC Gumbart (Sun Jun 03 2007 - 10:33:02 CDT)
- Jeffrey J. Potoff (Sun Jun 03 2007 - 10:11:49 CDT)
- Alexandre A. Vakhrouchev (Sun Jun 03 2007 - 08:39:30 CDT)
- Richard Casey (Sun Jun 03 2007 - 07:24:35 CDT)
combine PMF/dual FEP -> correct free energies?
- Jerome Henin (Fri Dec 12 2008 - 11:10:14 CST)
- Sebastian Stolzenberg (Thu Dec 11 2008 - 19:09:28 CST)
combine.tcl
- JC Gumbart (Tue Nov 21 2006 - 22:44:51 CST)
- Peter Freddolino (Tue Nov 21 2006 - 15:12:55 CST)
- Annalisa Marsico (Tue Nov 21 2006 - 12:40:00 CST)
combined QM/MM calculation with NAMD
- Jerome Henin (Thu Sep 14 2006 - 11:49:41 CDT)
- Dhiraj Srivastava (Thu Sep 14 2006 - 10:35:28 CDT)
combining 2 dcd files into one
- Anirban Ghosh (Fri Oct 31 2008 - 13:43:14 CDT)
- Christopher Gillespie (Thu Oct 30 2008 - 16:26:34 CDT)
- Rabab Toubar (Thu Oct 30 2008 - 15:20:34 CDT)
combining abf reaction path
- Chris Chipot (Sat Jan 31 2009 - 13:03:29 CST)
- Arturas Ziemys (Sat Jan 31 2009 - 12:20:55 CST)
combining metadynamics simulations
- Giacomo Fiorin (Fri Aug 26 2011 - 09:18:01 CDT)
- Giovanni Bellesia (Fri Aug 26 2011 - 08:40:29 CDT)
combining segments
- Robert Brunner (Mon Aug 10 2009 - 11:32:26 CDT)
- d b (Mon Aug 10 2009 - 09:06:51 CDT)
combining thermodynamic integration with replica exchange in NAMD
- Hugh Heldenbrand (Mon Jul 25 2011 - 10:05:50 CDT)
command line arguments in NAMD ?
- Himanshu Khandelia (Tue Mar 14 2006 - 17:49:31 CST)
command to run MPI and ABF
- Shahid Qamar (Thu Oct 06 2005 - 18:10:39 CDT)
Comments on 'restart' simulation
- Pijush Ghosh (Thu Oct 12 2006 - 16:33:10 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)
Comparision of GPU and multi-CPUs version of NAMD
- Jianing Song (Sun Oct 10 2010 - 09:51:54 CDT)
compilation error "could not set locale" with intel 11.0
- Vlad Cojocaru (Fri Jul 31 2009 - 03:35:12 CDT)
- Vlad Cojocaru (Fri Jul 31 2009 - 03:03:53 CDT)
compilation of charm++
- L. Michel Espinoza-Fonseca (Fri Jan 26 2007 - 06:53:47 CST)
Compilation of Charm++ on Linux opteron cluster with MPICH-GM installed
- Gengbin Zheng (Wed May 25 2005 - 23:05:47 CDT)
Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers
- Philip Peartree (Sat Dec 15 2007 - 22:04:08 CST)
- Dow_Hurst (Sat Dec 15 2007 - 21:49:11 CST)
- Philip Peartree (Fri Dec 14 2007 - 16:01:56 CST)
- Philip Peartree (Fri Dec 14 2007 - 12:52:44 CST)
- Philip Peartree (Fri Dec 14 2007 - 07:29:01 CST)
- Philip Peartree (Wed Dec 12 2007 - 17:47:59 CST)
- Philip Peartree (Wed Dec 12 2007 - 16:54:09 CST)
- Philip Peartree (Wed Dec 12 2007 - 15:22:14 CST)
- Philip Peartree (Wed Dec 12 2007 - 09:20:23 CST)
Compilation of Charm++ then NAMD 2.6 on Opteron with Portlandcompilers
- Philip Peartree (Wed Dec 12 2007 - 15:35:10 CST)
compilation of namd
- johan strumpfer (Fri May 06 2011 - 09:09:35 CDT)
- TAO WANG (Thu May 05 2011 - 21:08:37 CDT)
Compilation of NAMD on 64-bit NUMA
- Jim Phillips (Mon Aug 22 2005 - 17:47:52 CDT)
- Imran Khan (Wed Aug 17 2005 - 04:58:23 CDT)
Compilation of NAMD on 64-bit NUMA with icc
- Brian Bennion (Tue Oct 18 2005 - 10:47:16 CDT)
- ashwin joshi (Tue Oct 18 2005 - 02:46:18 CDT)
Compilation of NAMD on opteron cluster with myrinet
- junwang (Mon May 23 2005 - 19:44:41 CDT)
compilation of the CVS code
- Vlad Cojocaru (Mon Aug 04 2008 - 10:02:03 CDT)
- Peter Freddolino (Mon Aug 04 2008 - 09:22:00 CDT)
- Peter Freddolino (Mon Aug 04 2008 - 07:36:20 CDT)
- Vlad Cojocaru (Mon Aug 04 2008 - 01:53:41 CDT)
- Vlad Cojocaru (Mon Aug 04 2008 - 01:46:11 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 IBM-Power (Linux)
- Monika Sharma (Tue Jul 03 2007 - 13:00:18 CDT)
- Monika Sharma (Mon Jul 02 2007 - 06:10:20 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)
Compilation problems on intel woodcrest
- Brian Bennion (Thu Sep 07 2006 - 12:59:52 CDT)
- Jacob Poehlsgaard (Thu Sep 07 2006 - 06:51:41 CDT)
compilaton error
- Leonardo Trabuco (Fri May 02 2008 - 01:25:35 CDT)
- Swarna Patra (Fri May 02 2008 - 01:06:48 CDT)
- Leonardo Trabuco (Thu May 01 2008 - 23:47:06 CDT)
- Swarna Patra (Thu May 01 2008 - 20:04:47 CDT)
- Leonardo Trabuco (Thu May 01 2008 - 11:32:22 CDT)
- Swarna Patra (Wed Apr 30 2008 - 23:32:45 CDT)
compile "mpi" charm++ on amd64
- Gengbin Zheng (Tue May 10 2005 - 01:31:51 CDT)
- Xiaoqing Wang (Mon May 09 2005 - 22:09:32 CDT)
Compile charm++ with icc
- Shaowen Hu (Sat Nov 18 2006 - 15:42:36 CST)
compile error on amd64 in src/ComputeTclBC.C
- Sabuj Pattanayek (Wed Mar 15 2006 - 15:55:03 CST)
- Sabuj Pattanayek (Wed Mar 15 2006 - 15:54:02 CST)
- Gengbin Zheng (Wed Mar 15 2006 - 14:38:19 CST)
- Sabuj Pattanayek (Wed Mar 15 2006 - 14:27:53 CST)
compile NAMD 2.7b1 on Intel Xeon(R) infiniband cluster
- Axel Kohlmeyer (Sat Apr 25 2009 - 09:01:24 CDT)
- DimitryASuplatov (Sat Apr 25 2009 - 03:51:27 CDT)
- æµ·æ¸… æ¢ (Sat Apr 25 2009 - 01:44:24 CDT)
Compile NAMD on Bluegene
- Christopher Gillespie (Mon Sep 22 2008 - 16:54:48 CDT)
- Yang Gao (Mon Sep 22 2008 - 10:37:58 CDT)
- Dong Luo (Fri Jun 16 2006 - 13:56:46 CDT)
- Dong Luo (Thu Jun 15 2006 - 14:16:30 CDT)
- Gengbin Zheng (Thu Jun 15 2006 - 12:16:40 CDT)
- Gengbin Zheng (Thu Jun 15 2006 - 12:04:49 CDT)
- Dong Luo (Thu Jun 15 2006 - 11:35:18 CDT)
- Dong Luo (Thu Jun 15 2006 - 09:48:32 CDT)
- Gengbin Zheng (Thu Jun 15 2006 - 01:11:34 CDT)
- Mgr. Lubos Vrbka (Thu Jun 15 2006 - 01:01:25 CDT)
- Dong Luo (Wed Jun 14 2006 - 16:17:13 CDT)
compile NAMD on Intel-64
- Peter Freddolino (Mon Jul 02 2007 - 10:57:55 CDT)
- Ilya Chorny (Mon Jul 02 2007 - 10:41:17 CDT)
- Wei Liu (Mon Jul 02 2007 - 09:38:31 CDT)
Compile NAMD on MIPS cpu(Loongson 2F)
- Guo Zhi (Fri Sep 05 2008 - 23:23:38 CDT)
compile NAMD with TCP and SMP
- sudipta (Wed Jun 10 2009 - 00:19:18 CDT)
compile NAMD/CHARM on infiniband cluster
- Rene Salmon (Fri Feb 24 2006 - 16:20:16 CST)
compile namd2.7b1 on infiniband
- Axel Kohlmeyer (Tue Jun 02 2009 - 22:17:01 CDT)
- liupeng012 (Tue Jun 02 2009 - 21:43:16 CDT)
Compile Problem
- xiaojing gong (Thu Apr 23 2009 - 07:42:51 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)
Compiled NAMD on SGI Altix
- Sterling Paramore (Tue Jan 17 2006 - 11:44:33 CST)
- Margaret Kahn (Mon Jan 16 2006 - 19:13:45 CST)
- Sterling Paramore (Mon Jan 16 2006 - 18:51:18 CST)
Compiled Windows HPC version.
- Chewning, Joseph (Tue Oct 04 2011 - 07:04:31 CDT)
compiler flags.
- gengbin (Wed Jul 14 2004 - 23:58:54 CDT)
- Brian Bennion (Wed Jul 14 2004 - 23:41:22 CDT)
Compiling
- Gengbin Zheng (Sun Jan 09 2005 - 11:00:43 CST)
- Ruxandra Dima (Thu Jan 06 2005 - 20:13:50 CST)
- Damon Smith (Thu Jan 06 2005 - 19:02:04 CST)
Compiling 8Core macs
- Robert Brunner (Wed Nov 26 2008 - 15:21:58 CST)
- Christopher Hartshorn (Tue Nov 25 2008 - 15:28:51 CST)
- Christopher Hartshorn (Mon Nov 24 2008 - 17:03:40 CST)
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 charm++ failed on window with Cygwin
- accomp lin (Sun Dec 28 2008 - 01:23:13 CST)
compiling charm++ with g++ 4.1
- Leandro Martínez (Mon Nov 20 2006 - 14:27:43 CST)
- Leandro Martínez (Mon Nov 20 2006 - 10:26:22 CST)
Compiling charm++-5.9: Problems with g++
- Gianluca Interlandi (Sat Aug 20 2005 - 05:36:26 CDT)
compiling error of NAMD2.7b1
- Joachim Hein (Tue Apr 21 2009 - 04:18:14 CDT)
- Peter Freddolino (Mon Apr 20 2009 - 14:49:07 CDT)
- Peter Freddolino (Mon Apr 20 2009 - 14:47:09 CDT)
- BIN ZHANG (Mon Apr 20 2009 - 13:41:01 CDT)
- Joachim Hein (Mon Apr 20 2009 - 12:53:59 CDT)
- Joachim Hein (Mon Apr 20 2009 - 13:22:11 CDT)
- Peter Freddolino (Mon Apr 20 2009 - 13:12:01 CDT)
- BIN ZHANG (Mon Apr 20 2009 - 12:30:17 CDT)
- Joachim Hein (Mon Apr 20 2009 - 06:05:38 CDT)
- zhngbn_at_gmail.com (Sun Apr 19 2009 - 03:02:44 CDT)
compiling latest CVS on altix
- L. Michel Espinoza-Fonseca (Sat Dec 13 2008 - 10:10:24 CST)
compiling linux scyld mpi 64bit
- Eric Franz (Tue Jun 29 2004 - 10:40:31 CDT)
compiling namd
- Michal Walczak (Sat Oct 28 2006 - 09:43:11 CDT)
- 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 2.6 from Source: no charm-5.9.tar
- Audrey Salazar (Tue Aug 28 2007 - 14:27:50 CDT)
- Audrey Salazar (Tue Aug 28 2007 - 13:42:14 CDT)
- Thomas Gaillard (Tue Aug 28 2007 - 14:23:40 CDT)
Compiling NAMD 2.7 with the PLUMED patch
- Davide Branduardi (Thu Jan 06 2011 - 17:42:56 CST)
- Gianluca Interlandi (Thu Jan 06 2011 - 17:41:23 CST)
- Gianluca Interlandi (Thu Jan 06 2011 - 16:55:03 CST)
compiling NAMD failed on windows with Cygwin
- accomp lin (Tue Jan 13 2009 - 22:31:12 CST)
- Axel Kohlmeyer (Sun Jan 11 2009 - 14:11:04 CST)
- accomp lin (Sun Jan 11 2009 - 02:02:54 CST)
- Axel Kohlmeyer (Sat Jan 10 2009 - 09:20:44 CST)
- accomp lin (Fri Jan 09 2009 - 22:06:37 CST)
- Axel Kohlmeyer (Mon Dec 29 2008 - 09:36:45 CST)
- accomp lin (Sun Dec 28 2008 - 22:32:51 CST)
Compiling NAMD for CUDA
- Thomas Albers (Sat Jun 11 2011 - 21:53:56 CDT)
- Axel Kohlmeyer (Sat Jun 11 2011 - 16:43:28 CDT)
- Thomas Albers (Sat Jun 11 2011 - 16:23:01 CDT)
Compiling NAMD from SRC: Tungsten@NCSA
- Vani Krishna (Fri Sep 10 2004 - 19:54:55 CDT)
compiling namd gpu
- Jun Zhang (Wed Dec 22 2010 - 18:17:01 CST)
- Jacopo Sgrignani (Tue Dec 21 2010 - 03:13:57 CST)
compiling namd intel 9.1
- Alberto Santana (Wed May 16 2007 - 06:06:35 CDT)
compiling NAMD on a redhat-pentium-dell workstation
- paul.dalhaimer_at_yale.edu (Tue May 03 2005 - 11:54:56 CDT)
compiling namd on amd opteron arch : TCL problems (fwd)
- Jerry Ebalunode (Fri Apr 23 2004 - 17:07:40 CDT)
compiling Namd on amd64
- olivier Walker (Fri Mar 11 2005 - 02:42:30 CST)
- olivier Walker (Thu Mar 10 2005 - 11:55:03 CST)
- Brian Bennion (Thu Mar 10 2005 - 10:20:46 CST)
- olivier Walker (Thu Mar 10 2005 - 04:08:08 CST)
- Wenyu Zhong (Thu Apr 15 2004 - 06:35:08 CDT)
- Wenyu Zhong (Thu Apr 15 2004 - 01:42:17 CDT)
Compiling NAMD on AMD64 dual core
- Cesar Luis Avila (Mon Jul 10 2006 - 10:57:59 CDT)
- Cesar Luis Avila (Tue Jul 04 2006 - 10:46:58 CDT)
compiling NAMD on an elan-linux-ia64 arch
- Peter Freddolino (Fri Apr 13 2007 - 21:33:32 CDT)
- Vlad Cojocaru (Fri Apr 13 2007 - 03:50:20 CDT)
- Peter Freddolino (Thu Apr 12 2007 - 16:01:44 CDT)
- Vlad Cojocaru (Thu Apr 12 2007 - 04:51:41 CDT)
Compiling NAMD on Cray XE6
- Jeff Wereszczynski (Mon Feb 28 2011 - 11:38:48 CST)
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 ibm-power + red hat linux
- Caio Julio Martins Veloso (Tue May 22 2007 - 20:23:36 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 MAC with Cuda
- Stan Skafidas (Wed Aug 10 2011 - 07:16:49 CDT)
compiling NAMD on OSC P4 cluster
- Amit Paliwal (Fri Sep 03 2004 - 12:11:51 CDT)
Compiling NAMD on PPC G4 w/Apple's Leopard
- Joshua Adelman (Sun Dec 23 2007 - 10:31:57 CST)
Compiling NAMD on Ranger
- shayan_at_msu.edu (Wed Apr 08 2009 - 12:51:26 CDT)
- shayan_at_msu.edu (Wed Apr 08 2009 - 10:09:11 CDT)
- Peter Freddolino (Wed Apr 08 2009 - 10:16:36 CDT)
- Axel Kohlmeyer (Wed Apr 08 2009 - 08:15:51 CDT)
- shayan_at_msu.edu (Wed Apr 08 2009 - 07:33:26 CDT)
compiling namd on SGI Altix
- Blake Mertz (Tue Dec 23 2008 - 11:09:10 CST)
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 NAMD under SGE and OpenMPI
- Gabriel Jara (Thu May 13 2010 - 11:34:49 CDT)
compiling NAMD w. infiniband
- Irene Newhouse (Fri Jun 04 2010 - 16:21:37 CDT)
Compiling NAMD with mpicc myrinet
- Jerry Ebalunode (Thu Mar 10 2005 - 15:45:54 CST)
- Brian Bennion (Thu Mar 10 2005 - 14:08:44 CST)
- Edward Patrick Obrien (Thu Mar 10 2005 - 12:19:50 CST)
compiling namd2
- Sabuj Pattanayek (Mon Nov 05 2007 - 13:09:01 CST)
- Tom Joseph (Mon Nov 05 2007 - 13:18:25 CST)
- hazards_at_musc.edu (Mon Nov 05 2007 - 10:18:22 CST)
compiling namd: cannot find -lmodulecommlib
- Corenflos, Steven Charles (Wed Apr 23 2008 - 14:42:18 CDT)
compiling NAMD: plugins
- Kyle Gustafson (Mon Jul 25 2005 - 19:53:01 CDT)
Compiling on G5 using xlC
- klsale (Thu Feb 26 2004 - 15:38:47 CST)
- Gengbin Zheng (Thu Feb 26 2004 - 15:40:59 CST)
Compiling on Linux-PPC970-Myrinet-MPI-xlC
- Chris Samuel (Wed Mar 30 2005 - 00:05:44 CST)
- Chris Samuel (Sun Mar 20 2005 - 20:04:50 CST)
- Chris Samuel (Thu Mar 17 2005 - 23:23:24 CST)
- Chris Samuel (Wed Mar 16 2005 - 04:37:07 CST)
- Gengbin Zheng (Wed Mar 16 2005 - 00:24:54 CST)
- Chris Samuel (Wed Mar 16 2005 - 00:06:21 CST)
- Brian Bennion (Thu Mar 10 2005 - 18:22:43 CST)
- Jordi Camps (Thu Mar 10 2005 - 18:08:02 CST)
- Brian Bennion (Thu Mar 10 2005 - 15:59:33 CST)
- Gengbin Zheng (Thu Mar 10 2005 - 15:54:56 CST)
- Brian Bennion (Thu Mar 10 2005 - 14:11:29 CST)
- Jordi Camps (Thu Mar 10 2005 - 12:57:47 CST)
Compiling Questions
- Ulf Markwardt (Thu Feb 08 2007 - 07:01:40 CST)
- Joshua D. Moore (Wed Feb 07 2007 - 23:55:39 CST)
Compiling the NAMD on HPUX-ia64 system Error!
- Gengbin Zheng (Sat Jan 15 2005 - 11:03:51 CST)
- Îº¿ (Sat Jan 15 2005 - 08:35:00 CST)
Complementary programs for NAMD
- Glenn Johnson (Mon Feb 14 2005 - 13:32:24 CST)
Complete Beginner
- Philip Peartree (Mon Aug 20 2007 - 07:38:30 CDT)
Complie NAMD on Suse Linux
- Gengbin Zheng (Wed Feb 09 2005 - 17:53:10 CST)
- Jason Lee (Wed Feb 09 2005 - 16:51:28 CST)
- Gengbin Zheng (Mon Feb 07 2005 - 13:02:32 CST)
- Brian Bennion (Mon Feb 07 2005 - 11:56:01 CST)
- Jason Lee (Mon Feb 07 2005 - 09:32:02 CST)
- cunning cunning (Thu Feb 03 2005 - 08:18:46 CST)
Compliling NAMD in RedHat9
- Gengbin Zheng (Wed May 11 2005 - 22:09:15 CDT)
- Karina Martinez (Wed May 11 2005 - 21:59:28 CDT)
Component distanceZ-ABF
- Jérôme Hénin (Tue Sep 06 2011 - 04:27:44 CDT)
- Parisa Akhski (Mon Sep 05 2011 - 13:07:26 CDT)
- Jérôme Hénin (Mon Sep 05 2011 - 10:56:06 CDT)
- Parisa Akhski (Mon Sep 05 2011 - 09:42:17 CDT)
- Jérôme Hénin (Fri Sep 02 2011 - 16:19:53 CDT)
- Parisa Akhski (Fri Sep 02 2011 - 11:21:56 CDT)
compute nonbonding interactions on bonded atoms
- Lorant Janosi (Fri Dec 29 2006 - 23:10:12 CST)
computer network
- snoze pa (Mon Feb 13 2006 - 11:26:51 CST)
Computing cost of frozen atoms
- Jacob Poehlsgaard (Wed Apr 19 2006 - 04:03:53 CDT)
- Jacob Pøhlsgaard (Wed Apr 19 2006 - 03:33:28 CDT)
- Marc Q. Ma (Tue Apr 18 2006 - 12:50:59 CDT)
- Sterling Paramore (Tue Apr 18 2006 - 11:09:05 CDT)
- Jacob Pøhlsgaard (Tue Apr 18 2006 - 04:39:20 CDT)
Computing interaction energies in namd
- Jérôme Hénin (Wed Feb 23 2011 - 03:42:14 CST)
- Axel Kohlmeyer (Tue Feb 22 2011 - 19:07:11 CST)
- Samy Hamdouche (Tue Feb 22 2011 - 18:21:46 CST)
- JC Gumbart (Tue Feb 22 2011 - 14:48:51 CST)
- Samy Hamdouche (Tue Feb 22 2011 - 14:40:31 CST)
Computing Potential of Mean Force --SMD-cv
- gamini_at_ncbs.res.in (Thu Jul 13 2006 - 07:58:37 CDT)
- Peter Freddolino (Wed Jul 12 2006 - 02:25:53 CDT)
- gamini_at_ncbs.res.in (Tue Jul 11 2006 - 15:36:45 CDT)
computing resource
- Wei Chen (Mon Mar 14 2005 - 23:08:48 CST)
Computing several pair interactions
- Samy Hamdouche (Tue Feb 15 2011 - 18:11:25 CST)
concatenate pmf files in colvars
- Parisa Akhski (Sat Jan 01 2011 - 12:23:06 CST)
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)
concatenating two or more dcd files
- Marc Q. Ma (Mon Apr 18 2005 - 12:13:51 CDT)
- Jorge Pikunic (Mon Apr 18 2005 - 10:44:07 CDT)
Condition for stopping MD sim. with NAMD
- Nicolas Floquet (Tue May 17 2005 - 02:56:45 CDT)
conditional statements in conf files
- Glenn Johnson (Mon Feb 14 2005 - 15:49:46 CST)
- Glenn Johnson (Mon Feb 14 2005 - 14:59:02 CST)
conf file for coarse grained simulation
- Peter Freddolino (Mon Dec 14 2009 - 19:15:57 CST)
- Francesco Pietra (Sun Dec 13 2009 - 15:08:59 CST)
conf file script ( help needed )
- flavio seixas (Mon Jun 06 2011 - 07:02:41 CDT)
- flavio seixas (Sat Jun 04 2011 - 07:53:08 CDT)
- Axel Kohlmeyer (Fri Jun 03 2011 - 08:45:27 CDT)
- Molecular Dynamics (Fri Jun 03 2011 - 08:37:57 CDT)
config files
- Gengbin Zheng (Tue Jun 07 2005 - 14:23:31 CDT)
- Mark A. Hallman (Tue Jun 07 2005 - 12:17:35 CDT)
config files no longer working after software 'upgrades'
- Peter Freddolino (Tue Sep 16 2008 - 19:39:07 CDT)
- Irene Newhouse (Tue Sep 16 2008 - 18:18:43 CDT)
configuration file
- Demet Akten (Wed Sep 22 2010 - 02:51:48 CDT)
- Jeffrey J. Potoff (Tue Mar 06 2007 - 08:22:18 CST)
- Rita Cassia (Tue Mar 06 2007 - 07:54:51 CST)
configuration files
- Michael Grabe (Wed Nov 19 2003 - 16:38:24 CST)
Configurational temperature - coordinates
- Alexe Bojovschi (Wed Jan 18 2006 - 21:11:32 CST)
Configurations-Statistical Mechanics
- Mert Gür (Sat Apr 26 2008 - 13:00:08 CDT)
Confira meu perfil no Facebook
- Ariovaldo De Souza Junior (Sat Jan 03 2009 - 12:31:41 CST)
conformational alignment
- Giovanni Bellesia (Wed Mar 30 2005 - 16:40:36 CST)
- Wen Li (Wed Mar 30 2005 - 15:21:26 CST)
Conjugate gradient reference
- Athanassios Stavrakoudis (Fri Oct 15 2010 - 11:24:58 CDT)
- Philip Peartree (Fri Oct 15 2010 - 10:33:16 CDT)
Consecutive Simulations
- Lewyn Li (Thu Feb 25 2010 - 10:08:47 CST)
- Keith Battle (Thu Feb 25 2010 - 09:25:33 CST)
Consistent temperature increase in CUDA runs
- Aron Broom (Mon Feb 27 2012 - 08:31:46 CST)
- Aron Broom (Fri Feb 24 2012 - 19:53:08 CST)
- Aron Broom (Fri Feb 24 2012 - 14:49:28 CST)
- Norman Geist (Fri Feb 24 2012 - 00:51:38 CST)
conskfile
- Axel Kohlmeyer (Sat Aug 30 2008 - 13:33:07 CDT)
- Shultz, Jack (Sat Aug 30 2008 - 12:46:29 CDT)
const vel SMD
- Narender Singh Maan (Fri Feb 16 2007 - 14:03:40 CST)
constant angle NPT simulation
- Joseph E. Curtis, Ph. D. (Thu Nov 04 2004 - 12:16:21 CST)
Constant electric field to selected atoms.
- hamdi (Wed Jun 07 2006 - 09:08:32 CDT)
Constant Energy Simulations
- Peter Freddolino (Fri Jun 30 2006 - 10:37:16 CDT)
- Eric Perim (Fri Jun 30 2006 - 08:42:48 CDT)
Constant pressure
- Kwee Hong (Thu Nov 25 2010 - 13:16:52 CST)
- Sebastian Stolzenberg (Thu Nov 25 2010 - 13:04:51 CST)
- Kwee Hong (Thu Nov 25 2010 - 10:29:29 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 pressure simulation: can I get the changed volume?
- Fred (Rui FENG) (Thu Feb 19 2009 - 04:25:26 CST)
- Fred (Rui FENG) (Thu Feb 19 2009 - 04:26:50 CST)
- Fred (Rui FENG) (Thu Feb 19 2009 - 01:52:55 CST)
constant velocity SMD
- JC Gumbart (Fri Jan 26 2007 - 12:48:52 CST)
- Narender Singh Maan (Fri Jan 26 2007 - 12:49:07 CST)
- Cesar Luis Avila (Fri Jan 26 2007 - 12:34:36 CST)
- Narender Singh Maan (Fri Jan 26 2007 - 12:33:18 CST)
- JC Gumbart (Fri Jan 26 2007 - 11:59:46 CST)
- Narender Singh Maan (Fri Jan 26 2007 - 11:44:41 CST)
- Narender Singh Maan (Fri Jan 26 2007 - 11:11:39 CST)
constant velocity smd with distance restraints
- Gilbert G.Feng (Fri Dec 03 2004 - 14:22:50 CST)
Constant z axis
- Nd S (Mon Oct 13 2008 - 12:27:23 CDT)
- Chris Harrison (Sat Oct 11 2008 - 17:13:54 CDT)
- Chris Harrison (Sat Oct 11 2008 - 22:59:31 CDT)
- Navdeep (Sat Oct 11 2008 - 22:25:56 CDT)
- Nd S (Wed Oct 08 2008 - 19:59:43 CDT)
Constrain centers of mass for selected atoms
- poker_at_physics.usyd.edu.au (Thu Feb 07 2008 - 18:36:00 CST)
- michael_at_perfect-kreim.de (Thu Feb 07 2008 - 04:12:39 CST)
Constrain EVERY bond length and bond angle
- Neelanjana Sengupta (Tue Jan 16 2007 - 13:18:59 CST)
Constrain only in Z direction
- xiaojing gong (Sun Apr 09 2006 - 22:32:02 CDT)
constrain or fix the system only in Z direction
- JC Gumbart (Thu Jul 21 2005 - 09:34:22 CDT)
- xiaojing gong (Thu Jul 21 2005 - 07:01:33 CDT)
Constrain=?ISO-8859-1?Q? centers of mass for ?= selected atoms
- michael_at_perfect-kreim.de (Thu Feb 07 2008 - 07:03:17 CST)
constrained simulation
- JC Gumbart (Fri Oct 27 2006 - 11:15:04 CDT)
- Dhiraj Srivastava (Fri Oct 27 2006 - 03:32:15 CDT)
Constraining a molecule and measuring the corresponding constraint force
- JC Gumbart (Sat Sep 30 2006 - 09:20:47 CDT)
- Doug Moby (Sat Sep 30 2006 - 08:36:31 CDT)
Constraining angles ??
- Jim Phillips (Fri Sep 08 2006 - 17:42:19 CDT)
- tamal_at_iitk.ac.in (Fri Sep 08 2006 - 13:36:31 CDT)
Constraining center of mass of monomers
- S.K. Ghosh (Wed Jul 16 2008 - 17:45:57 CDT)
constraining center of mass-constrained MD
- Vani Krishna (Thu Feb 17 2005 - 02:51:12 CST)
constraining distance
- Anahita Tafvizi (Wed Oct 04 2006 - 13:16:29 CDT)
constraining movement of atoms
- himanshu chandola (Thu Oct 16 2003 - 02:49:01 CDT)
constraining water so that it does not get inside bilayer
- Himanshu Khandelia (Mon Mar 06 2006 - 14:06:35 CST)
constraint constant in equilibration
- xiaojing gong (Sat Jul 30 2005 - 00:19:26 CDT)
constraint energy contributions
- Michael Thomas (Tue Oct 06 2009 - 06:33:25 CDT)
Constraint failure
- Michel Espinoza-Fonseca (Mon Sep 26 2005 - 13:54:52 CDT)
- Po Hu (Sat Sep 24 2005 - 13:42:42 CDT)
- Xiaoqing Wang (Tue Jan 11 2005 - 21:07:08 CST)
Constraint failure & velocity problem
- bo liu (Thu Sep 04 2008 - 00:26:14 CDT)
- Shultz, Jack (Wed Sep 03 2008 - 20:13:24 CDT)
- bo liu (Wed Sep 03 2008 - 00:08:15 CDT)
- Peter Freddolino (Tue Sep 02 2008 - 14:00:41 CDT)
- Shultz, Jack (Tue Sep 02 2008 - 13:40:09 CDT)
Constraint failure during equalibration
- Jiao, Dian NMN (-EXP) (Tue Sep 13 2011 - 12:45:50 CDT)
- Jiao, Dian NMN (-EXP) (Tue Sep 13 2011 - 12:55:22 CDT)
Constraint failure 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)
Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step?
- Bjoern Olausson (Thu Sep 10 2009 - 05:38:18 CDT)
- Bjoern Olausson (Thu Sep 10 2009 - 05:26:00 CDT)
- Nicholas M Glykos (Wed Sep 09 2009 - 10:46:51 CDT)
- Elia Zumot (Wed Sep 09 2009 - 10:40:29 CDT)
- Axel Kohlmeyer (Wed Sep 09 2009 - 09:51:42 CDT)
- Bjoern Olausson (Tue Sep 08 2009 - 03:12:04 CDT)
- Bjoern Olausson (Tue Sep 08 2009 - 03:13:02 CDT)
Constraint failure in RATTLE algorithm for atom 268
- Ajasja LjubetiÄ (Fri Oct 29 2010 - 05:46:16 CDT)
- surendra jain (Fri Oct 29 2010 - 04:54:38 CDT)
constraint failure in RATTLE algorithm for atom 3205
- ydhuang2727 (Fri Nov 14 2008 - 19:42:20 CST)
- Schreiner Eduard (Fri Nov 14 2008 - 20:13:30 CST)
Constraint Failure in SMD simulation
- felmerino_at_uchile.cl (Tue Jul 13 2010 - 23:18:47 CDT)
- Ramin Omidvar (Tue Jul 13 2010 - 08:04:20 CDT)
- felmerino_at_uchile.cl (Wed May 19 2010 - 14:48:31 CDT)
- Ramin Omidvar (Wed May 19 2010 - 11:51:20 CDT)
constraint failure problem.
- ydhuang2727 (Wed Nov 26 2008 - 20:54:30 CST)
Constraint failure; simulation has become unstable
- Axel Kohlmeyer (Mon Jan 10 2011 - 08:49:07 CST)
- Joshua Adelman (Sat Jan 08 2011 - 09:49:18 CST)
- Wendy González (Sat Jan 08 2011 - 08:29:37 CST)
- Athanassios Stavrakoudis (Sat Jan 08 2011 - 08:05:15 CST)
- Wendy González (Sat Jan 08 2011 - 07:53:11 CST)
- Joshua Adelman (Fri Jan 07 2011 - 18:18:05 CST)
- Wendy González (Fri Jan 07 2011 - 14:42:46 CST)
- Wendy González (Fri Jan 07 2011 - 15:18:20 CST)
- Wendy González (Fri Jan 07 2011 - 15:25:23 CST)
- Athanassios Stavrakoudis (Fri Jan 07 2011 - 15:04:08 CST)
Constraint failures and TI electrostatic calcs
- Courtney Taylor (Mon Dec 06 2010 - 14:18:40 CST)
- Courtney Taylor (Mon Dec 06 2010 - 13:26:52 CST)
constraints
- Roman Petrenko (Thu Dec 03 2009 - 16:02:52 CST)
- doty alexiou (Thu Dec 03 2009 - 15:06:49 CST)
- dota (Wed Apr 08 2009 - 04:23:40 CDT)
Constraints in NAMD
- Joshua Adelman (Wed Apr 22 2009 - 10:37:39 CDT)
- Jerome Henin (Wed Apr 22 2009 - 10:30:44 CDT)
- DimitryASuplatov (Wed Apr 22 2009 - 09:50:37 CDT)
Constraints on the plane and on the atom positions (in the same simulation)
- Jim Phillips (Fri Aug 06 2010 - 09:40:30 CDT)
- Ajasja LjubetiÄ (Fri Aug 06 2010 - 03:15:16 CDT)
constraints on zinc ions
- Richard Wood (Mon May 28 2007 - 11:04:17 CDT)
- Peter Freddolino (Mon May 28 2007 - 08:58:19 CDT)
- Wei Liu (Mon May 28 2007 - 07:42:17 CDT)
Constraints protocol
- Peter Freddolino (Mon Oct 13 2008 - 13:34:58 CDT)
- Kamilla Kopec (Mon Oct 13 2008 - 09:41:30 CDT)
constraintScaling - FOR LOOP
- Peter Freddolino (Fri May 30 2008 - 08:30:07 CDT)
- Semorale (Wed May 28 2008 - 20:29:23 CDT)
constraintScaling parameter
- Peter Jones (Sun Mar 14 2004 - 10:33:40 CST)
constraintScaling to gradually release harmonic restraints during minimization
- Scott Boyken (Tue Jul 20 2010 - 15:22:08 CDT)
construct a protein surrounded by membrane
- mashaojie (Fri Mar 19 2004 - 08:41:20 CST)
- mashaojie (Fri Mar 19 2004 - 01:52:37 CST)
Constructing a small molecule
- Peter Freddolino (Mon Aug 06 2007 - 08:14:32 CDT)
- Yu Liu (Sun Aug 05 2007 - 20:41:58 CDT)
constructing a topology entry for hexadecane
- Victor Ovchinnikov (Fri Jun 29 2007 - 10:37:19 CDT)
- Adam Fraser (Fri Jun 29 2007 - 08:31:57 CDT)
- Adam Fraser (Thu Jun 28 2007 - 18:25:27 CDT)
Continue a run ?
- Georgios Papadopoulos (Mon Mar 13 2006 - 11:27:52 CST)
Continuing simulation after constraint failure error?
- Sadhu, Shubho (NIH/NCI) [F] (Thu Aug 06 2009 - 14:23:06 CDT)
- Giacomo Fiorin (Thu Aug 06 2009 - 13:17:48 CDT)
- Sujata Sovani (Thu Aug 06 2009 - 11:59:28 CDT)
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)
COntraints for lipid bilayer simulation
- priti arora (Tue Apr 24 2007 - 05:56:12 CDT)
Control DCD file
- TAEJIN KIM (Mon Jun 07 2010 - 17:09:20 CDT)
control distance between solvent and solute
- Jim Phillips (Wed Jul 20 2011 - 11:57:16 CDT)
- Kang Hee Cho (Fri Jul 15 2011 - 20:07:56 CDT)
Controlling fans on a GTX 560 ti
- Ajasja LjubetiÄ (Tue Jan 17 2012 - 09:10:51 CST)
- Axel Kohlmeyer (Tue Jan 17 2012 - 08:35:42 CST)
- Ajasja LjubetiÄ (Tue Jan 17 2012 - 08:25:29 CST)
- Axel Kohlmeyer (Mon Jan 16 2012 - 19:29:26 CST)
- Axel Kohlmeyer (Fri Jul 22 2011 - 09:19:59 CDT)
- Ajasja LjubetiÄ (Fri Jul 22 2011 - 09:12:29 CDT)
- Axel Kohlmeyer (Fri Jul 22 2011 - 08:56:17 CDT)
- Ajasja LjubetiÄ (Fri Jul 22 2011 - 05:24:26 CDT)
Controlling the area per lipid
- Richard Swenson (Thu Nov 01 2007 - 11:53:28 CDT)
- Ilya Chorny (Thu Nov 01 2007 - 10:32:50 CDT)
- Himanshu Khandelia (Thu Nov 01 2007 - 06:20:10 CDT)
- Ilya Chorny (Thu Nov 01 2007 - 01:45:31 CDT)
- JC Gumbart (Thu Nov 01 2007 - 00:56:27 CDT)
- Ilya Chorny (Wed Oct 31 2007 - 20:23:44 CDT)
convergence and stability of simulation
- Jorgen Simonsen (Mon Aug 15 2011 - 14:08:29 CDT)
convergence monitoring...
- Raul Araya Secchi (Tue Jun 05 2007 - 14:52:57 CDT)
convergence of ABF
- Jorgen Simonsen (Sun Jan 17 2010 - 20:42:30 CST)
- Eric H. Lee (Thu Sep 18 2008 - 05:19:49 CDT)
- Jorgen Simonsen (Fri Sep 12 2008 - 10:03:17 CDT)
- Jorgen Simonsen (Mon Sep 08 2008 - 09:16:20 CDT)
Convergence of ABF calculation: n_samples
- Jerome Henin (Wed Dec 05 2007 - 10:14:37 CST)
- Chris Chipot (Wed Dec 05 2007 - 09:53:39 CST)
- Subramanian Vaitheeswaran (Wed Dec 05 2007 - 08:39:47 CST)
Conversion for forces
- Michael Grabe (Tue Jun 20 2006 - 15:42:50 CDT)
- JC Gumbart (Tue Jun 20 2006 - 14:28:10 CDT)
- Gianluca Interlandi (Tue Jun 20 2006 - 14:05:28 CDT)
Conversion of .dcd into .xtc format
- Alessandro Pedretti (Wed May 16 2007 - 09:33:13 CDT)
- L. Michel Espinoza-Fonseca (Wed May 16 2007 - 07:22:26 CDT)
- priti arora (Wed May 16 2007 - 07:03:11 CDT)
convert .dcd into .trr
- L. Michel Espinoza-Fonseca (Tue May 02 2006 - 13:07:47 CDT)
- Shirley Li (Tue May 02 2006 - 12:37:53 CDT)
convert DCD files to GROMACS .XTC format
- Vani Krishna (Sat Aug 28 2004 - 17:43:11 CDT)
convert namd structure/coordinate files to gromacs topology file
- Glenn Johnson (Fri Mar 18 2005 - 14:00:54 CST)
convert pdb format to normal pdb format
- flavio seixas (Wed Aug 24 2011 - 18:05:18 CDT)
- hamze rahimi (Wed Aug 24 2011 - 04:48:09 CDT)
convert_from_namd_to_amber
- Wei Chen (Tue Jun 28 2005 - 22:02:18 CDT)
Converting a PSF file from one forcefield top another
- Christopher Harrison (Sat Oct 13 2007 - 14:55:34 CDT)
- Ilya Chorny (Sat Oct 13 2007 - 15:01:42 CDT)
- Christopher Harrison (Sat Oct 13 2007 - 14:43:35 CDT)
- Ilya Chorny (Sat Oct 13 2007 - 13:14:30 CDT)
converting AMBER trajectory file to CHARMM trajectory file
- Giacomo Fiorin (Tue Nov 11 2008 - 08:43:54 CST)
- sunita gupta (Tue Nov 11 2008 - 04:37:27 CST)
Converting DCD file to XTC format
- Alessandro Pedretti (Wed Jan 16 2008 - 02:11:20 CST)
- Jianping Lin (Tue Jan 15 2008 - 17:09:39 CST)
Converting Gromacs OPLS parameters to Charmm format
- Joshua D. Moore (Tue May 17 2005 - 17:35:18 CDT)
- 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 *BACK* to CHARMM
- Philip Peartree (Fri Feb 15 2008 - 03:17:12 CST)
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)
COOH patch?
- MIke S (Wed Sep 17 2008 - 11:39:25 CDT)
- MIke S (Mon Sep 01 2008 - 18:46:36 CDT)
- Thomas Gaillard (Sat Aug 30 2008 - 19:08:41 CDT)
- MIke S (Sat Aug 30 2008 - 17:24:20 CDT)
coord file output minus solvation box
- Joshua Adelman (Thu Jul 31 2008 - 12:05:08 CDT)
- brosbam_at_berkeley.edu (Wed Jul 30 2008 - 18:21:18 CDT)
coordinate not the same between the input and frame 0
- Kwee Hong (Tue Oct 26 2010 - 05:06:22 CDT)
- Nicholas M Glykos (Tue Oct 26 2010 - 05:10:29 CDT)
- Kwee Hong (Tue Oct 26 2010 - 03:27:25 CDT)
Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line
- Hugh Martin (Fri Mar 06 2009 - 23:26:30 CST)
- Peter Freddolino (Mon Mar 02 2009 - 10:51:44 CST)
- Leandro Martínez (Mon Mar 02 2009 - 11:02:08 CST)
- Hugh Martin (Mon Mar 02 2009 - 10:42:53 CST)
- Peter Freddolino (Mon Mar 02 2009 - 10:33:22 CST)
- Hugh Martin (Mon Mar 02 2009 - 10:09:56 CST)
coordinates and cells
- Andreas Förster (Thu Feb 18 2010 - 04:47:29 CST)
- Rogan Carr (Wed Feb 17 2010 - 11:25:06 CST)
- Andreas Förster (Wed Feb 17 2010 - 11:00:54 CST)
Coordinates go to zero!
- Alex Huang (Wed Feb 27 2008 - 14:52:28 CST)
CoordinateTransformation
- Sting (Sun Sep 03 2006 - 20:17:21 CDT)
- Neelanjana Sengupta (Sun Sep 03 2006 - 15:34:48 CDT)
- Neelanjana Sengupta (Sun Sep 03 2006 - 15:33:32 CDT)
coordination chemistry with NAMD
- L. Michel Espinoza-Fonseca (Fri Aug 04 2006 - 10:50:30 CDT)
- Jan Saam (Fri Aug 04 2006 - 03:16:28 CDT)
- Gaurav Sharma (Thu Aug 03 2006 - 21:06:33 CDT)
- Nitin Bhardwaj (Wed Aug 02 2006 - 14:40:55 CDT)
- L. Michel Espinoza-Fonseca (Wed Aug 02 2006 - 14:34:00 CDT)
- Gaurav Sharma (Wed Aug 02 2006 - 14:04:04 CDT)
coordNum colvar with dummyAtom
- Giacomo Fiorin (Thu Dec 22 2011 - 17:41:20 CST)
- Ernesto Vargas (Mon Dec 19 2011 - 18:56:40 CST)
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)
Copper and Zinc: top_all27_prot_lipid.inp
- Cesar Luis Avila (Mon Sep 03 2007 - 10:47:35 CDT)
- Deepangi Pandit (Fri Aug 24 2007 - 15:27:47 CDT)
- Harish Lnu (Fri Aug 24 2007 - 12:22:11 CDT)
- Deepangi Pandit (Fri Aug 24 2007 - 11:51:39 CDT)
Copper ion moving out of the protein towards bulk solvent
- poker_at_physics.usyd.edu.au (Wed Feb 08 2012 - 18:24:50 CST)
- SUBHA KALYAANAMOORTHY (Tue Feb 07 2012 - 19:16:26 CST)
Copper parameters for CHARMM
- Axel Kohlmeyer (Fri Apr 24 2009 - 11:37:09 CDT)
- DimitryASuplatov (Fri Apr 24 2009 - 11:02:50 CDT)
Correctness of Simulation Results
- Peter Freddolino (Tue Jun 10 2008 - 11:45:03 CDT)
- Rahul (Tue Jun 10 2008 - 10:15:56 CDT)
- Axel Kohlmeyer (Mon Jun 09 2008 - 12:03:06 CDT)
- Rahul (Mon Jun 09 2008 - 09:16:13 CDT)
correlation functions
- Thomas Bishop (Mon Dec 12 2011 - 07:54:06 CST)
- Boyang Wang (Sat Dec 10 2011 - 18:03:53 CST)
- Aron Broom (Sat Dec 10 2011 - 08:54:56 CST)
- Molecular Dynamics (Sat Dec 10 2011 - 05:18:50 CST)
- Juan Diaz (Tue Dec 12 2006 - 14:39:52 CST)
- Juan Diaz (Tue Dec 12 2006 - 14:24:47 CST)
Correlation matrix of the Ca atoms
- Nicholas M Glykos (Mon Feb 02 2009 - 02:17:39 CST)
- Joshua Adelman (Sun Feb 01 2009 - 23:56:04 CST)
- Joshua Adelman (Sun Feb 01 2009 - 23:22:07 CST)
- sripad chandan (Sun Feb 01 2009 - 22:46:14 CST)
corrupt DCD file
- Axel Kohlmeyer (Wed Aug 27 2008 - 18:56:20 CDT)
- Forbes, Jeff (NIH/NIAMS) [E] (Wed Aug 27 2008 - 16:54:07 CDT)
corrupt dcd file >2GB on PowerPc
- George Madalin Giambasu (Wed Oct 18 2006 - 10:09:48 CDT)
Corrupt dcd files
- Marc Baaden (Wed May 11 2011 - 11:15:55 CDT)
Could I do the equilibration again with the same dcd file obtained?
- Schreiner Eduard (Thu Oct 30 2008 - 21:42:54 CDT)
- wayj86 wayj86 (Thu Oct 30 2008 - 20:40:09 CDT)
Could namd realizes the QM-MM method?
- Aurum Bai (Fri Dec 04 2009 - 01:31:32 CST)
Could namd support the ATI-GPU
- Aurum Bai (Wed Mar 17 2010 - 07:35:34 CDT)
Could namd use the method ONIOM of Gaussian?
- Axel Kohlmeyer (Thu Jun 10 2010 - 05:36:00 CDT)
- Aurum Bai (Thu Jun 10 2010 - 04:51:29 CDT)
couldn´t find rsh program
- francesco oteri (Wed Jun 23 2010 - 14:22:43 CDT)
- Axel Kohlmeyer (Thu Jun 17 2010 - 15:36:10 CDT)
- jose correa (Thu Jun 17 2010 - 14:39:56 CDT)
Coulomb 1-4 interactions
- Axel Kohlmeyer (Fri Dec 02 2011 - 10:21:36 CST)
- oguz gurbulak (Fri Dec 02 2011 - 10:11:24 CST)
Coulombic component of configurational energy
- divya nayar (Tue May 24 2011 - 03:12:24 CDT)
Coulombic virials
- Benjamin Roberts (Mon Dec 08 2008 - 22:14:00 CST)
Count protein solvent HBs?
- Dong Luo (Thu Jul 05 2007 - 09:21:36 CDT)
- JC Gumbart (Tue Jul 03 2007 - 17:44:15 CDT)
- paco ty (Tue Jul 03 2007 - 13:10:51 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)
Counterions: how to decide how many to put it?
- jonathan_at_ibt.unam.mx (Tue Dec 13 2005 - 21:05:34 CST)
- Ching Wong (Tue Dec 13 2005 - 17:44:33 CST)
counting gas molecules inside the nanotube
- mishacat_at_udm.ru (Thu Sep 18 2008 - 06:52:51 CDT)
counting h-bond in system with vmd
- Axel Kohlmeyer (Sat Dec 18 2010 - 04:51:30 CST)
- sara (Fri Dec 17 2010 - 15:10:21 CST)
Counting H-bonds from a dcd file
- Gianluca Interlandi (Tue Aug 29 2006 - 18:48:29 CDT)
- Nitin Bhardwaj (Tue Aug 29 2006 - 17:00:51 CDT)
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)
CPU GPU comparison
- Axel Kohlmeyer (Fri Jul 16 2010 - 08:39:18 CDT)
- francesco oteri (Fri Jul 16 2010 - 03:13:17 CDT)
- francesco oteri (Tue Jul 13 2010 - 11:47:05 CDT)
CPU USAGE
- Axel Kohlmeyer (Sun Jul 19 2009 - 11:15:14 CDT)
- Nicholas M Glykos (Sun Jul 19 2009 - 06:57:56 CDT)
- Benjamin Bouvier (Sun Jul 19 2009 - 04:51:32 CDT)
- mahmoud (Sun Jul 19 2009 - 04:15:08 CDT)
- JC Gumbart (Sun Jul 19 2009 - 00:16:30 CDT)
- mahmoud mirzaei (Sat Jul 18 2009 - 23:07:26 CDT)
- Axel Kohlmeyer (Sat Jul 18 2009 - 11:50:25 CDT)
- mahmoud mirzaei (Sat Jul 18 2009 - 11:14:10 CDT)
CPU usage when exec function is used
- daniel aguayo (Fri Jan 08 2010 - 17:46:30 CST)
- Axel Kohlmeyer (Fri Jan 08 2010 - 15:31:16 CST)
- daniel aguayo (Fri Jan 08 2010 - 14:48:42 CST)
cpu-gpu vs cpu
- Axel Kohlmeyer (Tue Nov 29 2011 - 10:19:50 CST)
- Nicholas M Glykos (Tue Nov 29 2011 - 09:28:34 CST)
- Axel Kohlmeyer (Tue Nov 29 2011 - 07:41:51 CST)
- Francesco Pietra (Tue Nov 29 2011 - 00:44:10 CST)
crash
- jp2854_at_columbia.edu (Mon Nov 29 2010 - 11:18:24 CST)
Crash during free energy calculation (MCTI)
- Grzegorz Jezierski (Wed Aug 24 2005 - 02:47:07 CDT)
crash in FFT optimizing...
- Brian Bennion (Thu Feb 19 2004 - 15:44:28 CST)
crash with more than 96 processors (v2.7b1)
- Grace Brannigan (Fri May 01 2009 - 16:36:11 CDT)
- Grace Brannigan (Fri May 01 2009 - 09:58:56 CDT)
- George Madalin Giambasu (Fri May 01 2009 - 10:28:50 CDT)
- Grace Brannigan (Fri May 01 2009 - 09:48:09 CDT)
- Chris Harrison (Thu Apr 30 2009 - 19:41:55 CDT)
- Grace Brannigan (Thu Apr 30 2009 - 14:49:58 CDT)
- Chris Harrison (Tue Apr 28 2009 - 18:30:16 CDT)
- Grace Brannigan (Tue Apr 28 2009 - 17:36:23 CDT)
- Chris Harrison (Tue Apr 28 2009 - 16:50:57 CDT)
- Grace Brannigan (Tue Apr 28 2009 - 14:16:07 CDT)
Crashing ibverbs binary of NAMD_2.7b2
- Philipp M. (Thu Feb 11 2010 - 05:16:47 CST)
- Philipp M. (Thu Feb 11 2010 - 05:30:32 CST)
- snoze pa (Wed Feb 10 2010 - 17:44:24 CST)
- Philipp M. (Wed Feb 10 2010 - 10:58:03 CST)
Crazy defoliator
- Allison Chan (Sun Jun 10 2007 - 14:18:35 CDT)
create inositol molecule
- dimka (Thu Dec 04 2008 - 12:11:20 CST)
- politr_at_huji.ac.il (Wed Dec 03 2008 - 10:48:38 CST)
creating .psf file for a nanotube
- Axel Kohlmeyer (Fri Mar 11 2011 - 08:26:58 CST)
- sakthi kumaran (Fri Mar 11 2011 - 06:34:36 CST)
- Axel Kohlmeyer (Fri Mar 11 2011 - 05:18:57 CST)
- sakthi kumaran (Fri Mar 11 2011 - 05:13:34 CST)
- sakthi kumaran (Fri Mar 11 2011 - 02:36:02 CST)
Creating a NAMD Shared Library -> Undefined Symbols in Charm libs
- Michael S. Sellers (Cont, ARL/WMRD) (Mon Nov 29 2010 - 15:22:40 CST)
- Michael S. Sellers (Cont, ARL/WMRD) (Mon Nov 29 2010 - 15:07:21 CST)
creating a pdb file based on sequence and psi phi omega values only
- Matan Dishon (Sun Aug 28 2005 - 04:58:07 CDT)
creating an output file from a dcd file
- Axel Kohlmeyer (Thu Mar 04 2010 - 11:20:31 CST)
- Rabab Toubar (Thu Mar 04 2010 - 10:40:12 CST)
- Nicholas M Glykos (Tue Mar 02 2010 - 15:11:54 CST)
- Rabab Toubar (Tue Mar 02 2010 - 14:51:20 CST)
- Zumot, Elia Nabil (Tue Mar 02 2010 - 12:52:17 CST)
- Nicholas M Glykos (Tue Mar 02 2010 - 12:30:49 CST)
- Axel Kohlmeyer (Tue Mar 02 2010 - 11:27:20 CST)
- Rabab Toubar (Tue Mar 02 2010 - 10:34:15 CST)
Creating bonds during a run
- Praveen Agrawal (Wed Jan 21 2009 - 04:18:43 CST)
- Jerome Henin (Mon Jan 12 2009 - 11:25:43 CST)
- Axel Kohlmeyer (Mon Jan 12 2009 - 10:09:24 CST)
- Marcin S. (Mon Jan 12 2009 - 09:41:23 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)
Creating PDB from PSF and COOR files
- Peter Freddolino (Fri Mar 30 2007 - 17:20:19 CDT)
- Vamshi Gangupomu (Fri Mar 30 2007 - 16:08:16 CDT)
Creating topology for carbon nanotube / any new structure
- Peter Freddolino (Fri Feb 22 2008 - 07:03:16 CST)
- prateeksha s (Fri Feb 22 2008 - 00:17:12 CST)
- prateeksha s (Sat Jan 19 2008 - 23:05:28 CST)
- prateeksha s (Sat Jan 19 2008 - 23:02:22 CST)
- prateeksha s (Wed Dec 19 2007 - 22:21:44 CST)
- prateeksha s (Wed Dec 19 2007 - 22:24:49 CST)
- prateeksha s (Tue Dec 18 2007 - 22:41:04 CST)
creation and equilibration of a monolayer
- creston . (Fri Jun 20 2008 - 16:01:06 CDT)
cross products
- wmsmith (Mon Jun 27 2005 - 14:35:18 CDT)
crossing the border by protein/ion complex
- Axel Kohlmeyer (Tue Feb 07 2012 - 17:33:08 CST)
- Maria Bykhovskaia (Tue Feb 07 2012 - 17:16:30 CST)
Crystal Structure Analysis
- George Madalin Giambasu (Tue Feb 27 2007 - 18:51:21 CST)
- pedro.borkowski_at_utoronto.ca (Tue Feb 27 2007 - 12:02:23 CST)
CT1 terminal patch for THR
- GONZALEZ NOYA, EVA (Mon Mar 07 2011 - 14:47:57 CST)
CthCreate failed to create fiber
- Ajasja LjubetiÄ (Thu Jun 09 2011 - 15:29:25 CDT)
- Jim Phillips (Tue Jun 07 2011 - 18:02:21 CDT)
- Ajasja LjubetiÄ (Tue Jun 07 2011 - 13:57:00 CDT)
- Jim Phillips (Fri Jun 03 2011 - 11:42:44 CDT)
- Patriche Simona (Fri Jun 03 2011 - 08:52:28 CDT)
Cu+2 parameters
- jose correa (Wed Jan 26 2011 - 07:36:59 CST)
Cube vs. Truncated Octahedron Performance
- Axel Kohlmeyer (Thu Oct 21 2010 - 18:02:20 CDT)
- Alexander Predeus (Thu Oct 21 2010 - 17:04:42 CDT)
cubic periodic boundary box: what happen if I use a rectangular box?
- Margaret S. Cheung (Mon Apr 16 2007 - 15:22:25 CDT)
- JC Gumbart (Mon Apr 16 2007 - 15:48:09 CDT)
- Margaret S. Cheung (Mon Apr 16 2007 - 14:43:13 CDT)
cuda 1.0 binaries on cuda 1.1
- Roman Petrenko (Wed Feb 11 2009 - 13:47:32 CST)
Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware.
- Gianluca Interlandi (Sun Aug 30 2009 - 23:55:57 CDT)
- Gianluca Interlandi (Sun Aug 30 2009 - 18:41:41 CDT)
- Roman Petrenko (Sun Aug 30 2009 - 16:06:26 CDT)
- Axel Kohlmeyer (Sun Aug 30 2009 - 15:33:08 CDT)
- Gianluca Interlandi (Sun Aug 30 2009 - 14:11:25 CDT)
- Mike Kuiper (Sun Aug 30 2009 - 03:54:57 CDT)
CUDA compiled code for Windows HPC
- Chewning, Joseph (Wed Sep 28 2011 - 14:52:29 CDT)
cuda error cudastreamcreate
- Jim Phillips (Tue Jun 14 2011 - 11:02:33 CDT)
- Ajasja LjubetiÄ (Tue Jun 14 2011 - 08:23:23 CDT)
- Francesco Pietra (Tue Jun 14 2011 - 00:45:37 CDT)
cuda error cudastreamcreate. SOLVED (probably)
- Axel Kohlmeyer (Thu Jun 16 2011 - 04:40:03 CDT)
- Francesco Pietra (Thu Jun 16 2011 - 00:57:15 CDT)
- Axel Kohlmeyer (Wed Jun 15 2011 - 09:51:33 CDT)
CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS
- Amodeo, Pietro (Fri Nov 26 2010 - 11:21:22 CST)
- Pietro Amodeo (Fri Nov 26 2010 - 18:07:46 CST)
CUDA error memcpy to exclusions: invalid argument
- Priyan Amaras (Tue Mar 16 2010 - 09:37:28 CDT)
CUDA limitations
- Ajasja LjubetiÄ (Fri Jun 24 2011 - 07:37:13 CDT)
- Ajasja LjubetiÄ (Thu Jun 09 2011 - 15:32:09 CDT)
- Jim Phillips (Fri May 13 2011 - 09:02:36 CDT)
- Ajasja LjubetiÄ (Fri May 13 2011 - 07:00:49 CDT)
- Jim Phillips (Thu May 12 2011 - 12:45:44 CDT)
- Ajasja LjubetiÄ (Thu May 12 2011 - 03:07:02 CDT)
CUDA Linux-x86 doesn't compile
- Sadhu, Shubho (NIH/NCI) [F] (Thu Jul 30 2009 - 09:06:04 CDT)
CUDA on GPU Cluster
- Arvind Kannan (Fri Aug 19 2011 - 17:31:06 CDT)
CUDA on Win32 NAMD
- Priyan Amaras (Tue Dec 08 2009 - 14:19:07 CST)
CUDA simulation memory usage
- Jesper SÃ¸rensen (Thu May 19 2011 - 03:11:41 CDT)
- Jim Phillips (Wed May 18 2011 - 17:37:45 CDT)
- Jesper Sørensen (Wed May 18 2011 - 08:41:34 CDT)
- Axel Kohlmeyer (Wed May 18 2011 - 08:29:18 CDT)
- Jesper SÃ¸rensen (Wed May 18 2011 - 07:23:28 CDT)
- Jesper SÃ¸rensen (Wed May 18 2011 - 06:14:51 CDT)
- Jesper SÃ¸rensen (Wed May 18 2011 - 05:55:59 CDT)
- Jesper SÃ¸rensen (Wed May 18 2011 - 05:03:17 CDT)
CUDA version status
- Chris Harrison (Sat Jan 24 2009 - 16:36:34 CST)
- Axel Kohlmeyer (Fri Jan 23 2009 - 20:28:27 CST)
- Artem Zhmurov (Fri Jan 23 2009 - 19:09:47 CST)
- Dow_Hurst (Fri Jan 23 2009 - 13:44:07 CST)
- Peter Freddolino (Thu Jan 22 2009 - 15:40:54 CST)
- Dow_Hurst (Wed Jan 21 2009 - 13:12:32 CST)
- Dow Hurst (Tue Jan 20 2009 - 12:39:20 CST)
CUDA-accelarated NAMD does not use the video card?
- Lee Wei Yang (Fri Nov 13 2009 - 18:15:27 CST)
- Jim Phillips (Fri Nov 13 2009 - 17:06:48 CST)
- Lee Wei Yang (Fri Nov 13 2009 - 16:55:15 CST)
CUDA-accelerated NAMD does not support NBFIX parameters
- Axel Kohlmeyer (Sun Sep 13 2009 - 14:49:47 CDT)
- Héctor Urbina (Sun Sep 13 2009 - 13:47:33 CDT)
CUDA-accelerated NAMD does not support NBFIX parameters [RESOLVED]
- Axel Kohlmeyer (Mon Sep 14 2009 - 15:57:12 CDT)
- Héctor Urbina (Mon Sep 14 2009 - 07:24:35 CDT)
CUDA-NAMD hangs -- check the Northbridge temp!
- Paul Rigor (uci-ics) (Wed Jan 06 2010 - 17:12:54 CST)
- Biff Forbush (Wed Jan 06 2010 - 18:12:08 CST)
- Pu Tian (Wed Jan 06 2010 - 09:36:55 CST)
- Biff Forbush (Tue Jan 05 2010 - 21:51:51 CST)
Current status of polarizable force fields in NAMD
- lucie delemotte (Wed Feb 16 2011 - 04:37:03 CST)
Custom CHARMM forcefield usage problem
- JC Gumbart (Wed Aug 10 2011 - 00:00:55 CDT)
- Jernej Zidar (Tue Aug 09 2011 - 23:47:30 CDT)
- Jernej Zidar (Tue Aug 09 2011 - 23:12:04 CDT)
custom pulling path
- Raul Alcantara (Wed Apr 19 2006 - 17:07:05 CDT)
- Jérôme Hénin (Wed Apr 19 2006 - 16:20:29 CDT)
- Leandro Martínez (Wed Apr 19 2006 - 14:16:36 CDT)
- Peter Freddolino (Wed Apr 19 2006 - 14:00:56 CDT)
- LEWYN LI (Wed Apr 19 2006 - 13:52:00 CDT)
- Raul Alcantara (Wed Apr 19 2006 - 12:30:13 CDT)
cutoffs in direct and indirect space used in PME?
- dimka (Thu Aug 06 2009 - 23:13:05 CDT)
cvs logs
- BIN ZHANG (Fri Apr 17 2009 - 13:53:54 CDT)
cyclic peptides
- Peter Freddolino (Mon Nov 03 2008 - 20:13:14 CST)
- Austin B. Yongye (Mon Nov 03 2008 - 16:38:40 CST)
Cyclopeptide: connectivity between the first and last residues
- List (Mon Oct 06 2008 - 11:58:17 CDT)
- List (Tue Sep 30 2008 - 19:08:44 CDT)
- Jerome Henin (Mon Sep 29 2008 - 17:31:30 CDT)
- David Tanner (Mon Sep 29 2008 - 15:36:31 CDT)
- List (Mon Sep 29 2008 - 12:52:14 CDT)
cylindrical boundary conditions
- Jim Phillips (Mon Oct 27 2003 - 13:40:51 CST)
- Ioana Cozmuta (Wed Oct 15 2003 - 16:48:08 CDT)
Cylindrical harmonic BC and constraintScaling
- Elsa Fernanda de Sousa Henriques (Mon Apr 20 2009 - 08:25:20 CDT)
- Elsa Fernanda de Sousa Henriques (Mon Apr 20 2009 - 05:22:25 CDT)
D-amino acids
- Aaron Oakley (Tue Oct 26 2004 - 03:05:28 CDT)
- Giovanni Bellesia (Mon Oct 25 2004 - 07:00:46 CDT)
Dangling Bonds?
- atsuiai_at_aim.com (Thu Sep 29 2011 - 08:45:39 CDT)
- atsuiai_at_aim.com (Thu Sep 29 2011 - 06:23:55 CDT)
- Axel Kohlmeyer (Wed Sep 28 2011 - 17:58:18 CDT)
- atsuiai_at_aim.com (Wed Sep 28 2011 - 17:35:12 CDT)
Data from Output file
- Tamal Banerjee (Mon Jul 03 2006 - 03:01:48 CDT)
data structure of neighbor list
- bqluan (Tue Aug 08 2006 - 10:37:52 CDT)
dcd
- Ajasja LjubetiÄ (Mon Feb 01 2010 - 05:40:14 CST)
- Ajasja LjubetiÄ (Mon Feb 01 2010 - 04:25:25 CST)
- ipsita basu (Mon Feb 01 2010 - 03:27:17 CST)
dcd binary file format
- Peter Freddolino (Tue May 01 2007 - 17:34:27 CDT)
- Jeffrey A Tibbitt (Tue May 01 2007 - 16:57:47 CDT)
- Jianhui Tian (Tue May 01 2007 - 14:41:53 CDT)
DCD file
- Ayse Ozlem Sezerman (Thu May 18 2006 - 10:02:41 CDT)
- Ayse Ozlem Sezerman (Thu May 18 2006 - 10:02:43 CDT)
- Peter Freddolino (Thu May 18 2006 - 09:44:11 CDT)
- Jindal Shah (Thu May 18 2006 - 08:35:17 CDT)
- Ayse Ozlem Sezerman (Thu May 18 2006 - 07:06:44 CDT)
- SÅ‚awek OrÅ‚owski (Thu May 18 2006 - 03:40:05 CDT)
- Ayse Ozlem Sezerman (Thu May 18 2006 - 02:09:40 CDT)
DCD file format
- Andrew Emerson (Thu Oct 02 2008 - 02:32:08 CDT)
- Alexander A. Vakhrushev (Wed Oct 01 2008 - 23:43:12 CDT)
- Audrey Salazar (Wed Oct 01 2008 - 15:04:28 CDT)
- Jerome Henin (Wed Oct 01 2008 - 14:38:35 CDT)
- Dave Rogers (Wed Oct 01 2008 - 14:17:10 CDT)
- Santanu Chatterjee (Wed Oct 01 2008 - 13:35:25 CDT)
- Leandro Martínez (Sat Nov 25 2006 - 05:08:28 CST)
- Hyonseok Hwang (Fri Nov 24 2006 - 20:47:42 CST)
- Leandro Martínez (Fri Nov 24 2006 - 05:44:06 CST)
- Leandro Martínez (Fri Nov 24 2006 - 05:38:05 CST)
dcd file is too large
- taojinwuhan_at_sohu.com (Mon Nov 13 2006 - 02:52:41 CST)
dcd file produced with NAMD can be used with AMBER?
- Rita Cassia (Wed Mar 28 2007 - 04:11:56 CDT)
DCD file really corrupt?
- Joshua D. Moore (Wed Mar 29 2006 - 15:37:24 CST)
- jonathan_at_ibt.unam.mx (Wed Mar 29 2006 - 11:55:40 CST)
- Lea Thøgersen (Wed Mar 29 2006 - 06:27:09 CST)
DCD file size
- Joshua D. Moore (Tue May 13 2008 - 01:39:57 CDT)
- Alexandre A. Vakhrouchev (Mon May 12 2008 - 21:50:25 CDT)
- Peter Freddolino (Mon May 12 2008 - 21:56:26 CDT)
- JC Gumbart (Mon May 12 2008 - 15:08:48 CDT)
- Alexandre A. Vakhrouchev (Mon May 12 2008 - 14:19:57 CDT)
dcd files
- Artem Zhmurov (Sun May 22 2011 - 16:52:19 CDT)
- grazia cottone (Sun May 22 2011 - 15:14:41 CDT)
- Jim Phillips (Sun May 22 2011 - 14:53:45 CDT)
- PAUL NEWMAN (Sun May 22 2011 - 14:46:57 CDT)
- Jim Phillips (Sun May 22 2011 - 14:38:55 CDT)
- Axel Kohlmeyer (Sun May 22 2011 - 09:15:48 CDT)
- Axel Kohlmeyer (Sun May 22 2011 - 09:10:29 CDT)
- PAUL NEWMAN (Sun May 22 2011 - 08:24:15 CDT)
- Molecular Dynamics (Sun May 22 2011 - 08:02:48 CDT)
- 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 for windows
- Richard Wood (Tue Mar 06 2007 - 19:50:22 CST)
- Gianluca Interlandi (Tue Mar 06 2007 - 17:32:09 CST)
- lily jin (Tue Mar 06 2007 - 15:25:40 CST)
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)
dcd to pdb conversion
- Claw Isthelaw (Mon Oct 27 2008 - 04:35:26 CDT)
- Eric H. Lee (Mon Oct 27 2008 - 04:11:51 CDT)
- L. Michel Espinoza-Fonseca (Mon Oct 27 2008 - 04:05:12 CDT)
- AyÅŸe Ã–zlem Aykut (Mon Oct 27 2008 - 03:58:58 CDT)
- Eric H. Lee (Mon Oct 27 2008 - 03:39:09 CDT)
- AyÅŸe Ã–zlem Aykut (Mon Oct 27 2008 - 03:28:16 CDT)
- Giovanni Bellesia (Tue Jun 13 2006 - 18:47:01 CDT)
- snoze pa (Tue Jun 13 2006 - 17:10:37 CDT)
- Jindal Shah (Tue Jun 13 2006 - 14:15:47 CDT)
- Himanshu Khandelia (Thu Jun 08 2006 - 08:57:14 CDT)
- AyÅŸe Ã–zlem Sezerman (Thu Jun 08 2006 - 04:13:22 CDT)
- Edelmiro Moman (Thu Jun 08 2006 - 02:57:31 CDT)
dcd to trr using catdcd
- Anurag Sethi (Tue Mar 22 2011 - 02:03:56 CDT)
- Neelanjana Sengupta (Tue Mar 22 2011 - 00:11:33 CDT)
- Neelanjana Sengupta (Mon Mar 21 2011 - 05:44:39 CDT)
DCD trajectories produced by SMD simulation
- Peter Freddolino (Thu Nov 15 2007 - 09:46:47 CST)
- Vlad Cojocaru (Thu Nov 15 2007 - 07:49:58 CST)
- Marcos Sotomayor (Thu Nov 15 2007 - 00:23:02 CST)
- Peter Freddolino (Thu Nov 15 2007 - 00:17:01 CST)
- Vlad Cojocaru (Tue Nov 13 2007 - 04:05:14 CST)
- Peter Freddolino (Mon Nov 12 2007 - 11:32:09 CST)
- Vlad Cojocaru (Mon Nov 12 2007 - 07:43:55 CST)
dcd trajectory format
- Jianhui Tian (Mon Apr 30 2007 - 11:26:31 CDT)
dcd]
- snoze pa (Mon Feb 01 2010 - 11:33:56 CST)
- Branko (Mon Feb 01 2010 - 10:59:57 CST)
DCOLVARS_DEBUG
- Giacomo Fiorin (Tue May 05 2009 - 17:14:49 CDT)
- George Madalin Giambasu (Tue May 05 2009 - 16:46:59 CDT)
- Giacomo Fiorin (Tue May 05 2009 - 16:19:57 CDT)
- George Madalin Giambasu (Tue May 05 2009 - 15:29:43 CDT)
- Giacomo Fiorin (Tue May 05 2009 - 13:53:18 CDT)
- Giacomo Fiorin (Tue May 05 2009 - 10:23:33 CDT)
- George Madalin Giambasu (Tue May 05 2009 - 10:17:43 CDT)
- Jerome Henin (Tue May 05 2009 - 10:00:09 CDT)
- George Madalin Giambasu (Mon May 04 2009 - 22:49:17 CDT)
Dealing with hyperthreading
- Gadi Oron (Sun Mar 07 2004 - 04:43:09 CST)
Dear friend
- Niraj kumar (Sun May 22 2011 - 20:29:53 CDT)
Debug NAMD with CharmDebug
- Jaime Gonzalez (Tue Jul 20 2010 - 03:41:45 CDT)
deca-Ala simulations with different cutoff produce different results
- Jun Zhang (Mon May 16 2011 - 03:47:44 CDT)
- Norman Geist (Mon May 16 2011 - 02:12:40 CDT)
- Jun Zhang (Mon May 16 2011 - 00:48:36 CDT)
defenestrate
- Peter Freddolino (Sun Jun 28 2009 - 15:20:11 CDT)
define abf1 and abf2 for CM of water and CM of molecule
- Chris Chipot (Wed Dec 21 2005 - 12:18:36 CST)
- Manori Indira Jayasinghe (Wed Dec 21 2005 - 11:26:37 CST)
- Chris Chipot (Tue Dec 20 2005 - 01:28:32 CST)
- Manori Indira Jayasinghe (Mon Dec 19 2005 - 22:53:42 CST)
defined path for NAMD2
- Andreas Forster (Fri Dec 18 2009 - 06:35:29 CST)
- Leonardo Trabuco (Fri Dec 18 2009 - 02:41:12 CST)
- hamze rahimi (Thu Dec 17 2009 - 06:45:56 CST)
Defining a group of atoms in a simulation
- Ilja Khavrutskii (Sat Jan 19 2008 - 14:02:58 CST)
- Arneh Babakhani (Sat Jan 19 2008 - 11:15:03 CST)
Defining Temperature for Langevin for Namd restart.
- Roman Petrenko (Thu Aug 06 2009 - 05:41:17 CDT)
- Gianluca Interlandi (Wed Aug 05 2009 - 17:16:33 CDT)
- Gianluca Interlandi (Wed Aug 05 2009 - 16:35:14 CDT)
- Joshua Adelman (Wed Aug 05 2009 - 16:36:23 CDT)
- Amr Zeinalabideen Majul (Wed Aug 05 2009 - 16:20:41 CDT)
- Roman Petrenko (Wed Aug 05 2009 - 15:13:57 CDT)
- Amr Zeinalabideen Majul (Wed Aug 05 2009 - 14:20:15 CDT)
Definition of two colvars for ABF
- Branko (Tue Jan 05 2010 - 08:19:14 CST)
- Jérôme Hénin (Tue Jan 05 2010 - 08:12:47 CST)
- Jérôme Hénin (Mon Jan 04 2010 - 16:59:22 CST)
- Branko (Fri Jan 01 2010 - 09:58:30 CST)
- Branko (Wed Dec 30 2009 - 14:41:20 CST)
Definitions of certain routine names in source
- Bennion, Brian (Wed Feb 03 2010 - 17:01:52 CST)
deformations in a cubic water box during equilibration in NAMD
- JC Gumbart (Fri Nov 03 2006 - 01:53:23 CST)
- regafan_at_usc.es (Thu Nov 02 2006 - 08:52:39 CST)
deformations in a water box during equilibration in NAMD
- JC Gumbart (Fri Nov 03 2006 - 09:57:39 CST)
- Alessandro Cembran (Fri Nov 03 2006 - 09:42:52 CST)
- regafan_at_usc.es (Fri Nov 03 2006 - 04:28:01 CST)
Deformations under constant strain rates
- Andrea Diaz (Mon May 14 2007 - 12:28:18 CDT)
deformed water box after heating
- Jerome Henin (Tue Oct 24 2006 - 10:18:20 CDT)
- Neelanjana Sengupta (Tue Oct 24 2006 - 09:58:09 CDT)
- Dhiraj Srivastava (Tue Oct 24 2006 - 07:42:57 CDT)
- Dhiraj Srivastava (Mon Oct 23 2006 - 22:12:29 CDT)
- Neelanjana Sengupta (Mon Oct 23 2006 - 21:59:15 CDT)
- Dhiraj Srivastava (Mon Oct 23 2006 - 21:40:37 CDT)
deformed water box during equilibration.
- Neelanjana Sengupta (Sat Oct 21 2006 - 14:26:17 CDT)
- Leandro Martínez (Sat Oct 21 2006 - 10:45:09 CDT)
- Dhiraj Srivastava (Sat Oct 21 2006 - 05:19:33 CDT)
- Dhiraj Srivastava (Sat Oct 21 2006 - 05:13:35 CDT)
degrees of freedom
- Jorgen Simonsen (Sat Sep 11 2010 - 00:26:10 CDT)
DEN residue name in Amber
- prateeksha s (Wed Dec 05 2007 - 00:10:42 CST)
Denaturation via increased temperature
- Bjoern Olausson (Mon Aug 15 2011 - 06:11:17 CDT)
- Jernej Zidar (Mon Aug 15 2011 - 04:38:55 CDT)
- Bjoern Olausson (Mon Aug 15 2011 - 04:31:25 CDT)
- Bjoern Olausson (Mon Aug 15 2011 - 04:11:06 CDT)
Denied permission on dcd file preventing simulation
- Jim Phillips (Mon Oct 18 2010 - 11:40:28 CDT)
- Christian Jorgensen (Mon Oct 18 2010 - 09:32:07 CDT)
- Axel Kohlmeyer (Mon Oct 18 2010 - 10:06:45 CDT)
Density
- AHMET BAKAN (Tue Dec 16 2003 - 12:45:26 CST)
Density Calculation
- Nd S (Wed Oct 15 2008 - 22:25:57 CDT)
- Swarna Patra (Sun Apr 10 2005 - 20:24:51 CDT)
Density of water
- griadi_at_utalca.cl (Tue Jun 06 2006 - 09:41:56 CDT)
- santanu chatterjee (Tue May 30 2006 - 14:04:32 CDT)
density of water molecules in a water sphere
- Margaret Shun Cheung (Mon Apr 03 2006 - 13:56:42 CDT)
Density Profile in VMD
- oguz gurbulak (Mon Sep 05 2011 - 02:30:50 CDT)
deprotonated form of Proline molecule
- Dhiraj Srivastava (Tue Aug 15 2006 - 14:55:35 CDT)
Deprotonated Lys
- felmerino_at_uchile.cl (Thu Jul 22 2010 - 23:33:39 CDT)
- Dhiraj Srivastava (Thu Jul 22 2010 - 21:13:50 CDT)
Determining Equillibration of a membrane protein
- Ilya Chorny (Tue Jun 26 2007 - 18:57:32 CDT)
determining force constant in exterbonds (harmonic potential)
- Segun Jung (Sat Feb 05 2011 - 10:09:50 CST)
Determining Transition State from an Unfolding Simulation
- Eduardo Tejera (Thu Sep 27 2007 - 17:27:28 CDT)
- Richard Wood (Thu Sep 27 2007 - 16:34:20 CDT)
- Arun Krishnan (Thu Sep 27 2007 - 16:17:15 CDT)
- Christopher Harrison (Thu Sep 27 2007 - 15:43:54 CDT)
- Eduardo Tejera (Thu Sep 27 2007 - 15:09:41 CDT)
- Richard Wood (Thu Sep 27 2007 - 14:28:49 CDT)
- Neema Salimi (Thu Sep 27 2007 - 13:22:08 CDT)
- Richard Wood (Thu Sep 27 2007 - 13:24:13 CDT)
- Thomas Gaillard (Thu Sep 27 2007 - 12:29:08 CDT)
- Christopher Harrison (Thu Sep 27 2007 - 11:45:16 CDT)
- Richard Wood (Thu Sep 27 2007 - 11:22:57 CDT)
- Richard Wood (Thu Sep 27 2007 - 07:24:20 CDT)
- Richard Wood (Thu Sep 27 2007 - 07:34:06 CDT)
- paco ty (Thu Sep 27 2007 - 04:35:14 CDT)
- Peter Freddolino (Wed Sep 26 2007 - 23:12:43 CDT)
- Richard Wood (Wed Sep 26 2007 - 17:30:51 CDT)
- Richard Wood (Wed Sep 26 2007 - 15:30:58 CDT)
- E. Prabhu Raman (Wed Sep 26 2007 - 12:24:03 CDT)
- Richard Wood (Wed Sep 26 2007 - 11:13:40 CDT)
- Neelanjana Sengupta (Wed Sep 26 2007 - 10:44:58 CDT)
- E. Prabhu Raman (Wed Sep 26 2007 - 08:09:07 CDT)
- Arun Krishnan (Tue Sep 25 2007 - 23:56:52 CDT)
- E. Prabhu Raman (Sun Sep 23 2007 - 21:43:36 CDT)
- Neelanjana Sengupta (Sun Sep 23 2007 - 18:33:44 CDT)
- Neelanjana Sengupta (Sun Sep 23 2007 - 18:32:34 CDT)
- Arun Krishnan (Sun Sep 23 2007 - 15:57:17 CDT)
Developing a neutral arginine patch in a topology file
- urmit shah (Fri Jun 19 2009 - 17:54:19 CDT)
developing parameters for charmm
- snoze pa (Sat Oct 08 2005 - 19:40:54 CDT)
Developing topologies for modified NA residues?
- L. Michel Espinoza-Fonseca (Mon Apr 10 2006 - 12:00:55 CDT)
- Jan Saam (Mon Apr 10 2006 - 11:23:39 CDT)
- Jacob Pøhlsgaard (Mon Apr 10 2006 - 08:37:04 CDT)
Development plan of NAMD?
- Jim Phillips (Tue May 24 2011 - 13:54:09 CDT)
- Norman Geist (Tue May 24 2011 - 02:03:37 CDT)
dextran and or poly-D-glucosamine topology
- Raul Araya (Fri Nov 04 2011 - 16:58:34 CDT)
Did anybody really use TIP4P?
- Alessio Alexiadis (Mon Jul 09 2007 - 09:52:47 CDT)
dielectric
- Michael Grabe (Wed Dec 17 2003 - 11:30:59 CST)
Dielectric Constant
- David Hardy (Wed May 05 2010 - 21:16:06 CDT)
- ydhuang2727 (Wed May 05 2010 - 09:45:20 CDT)
- Axel Kohlmeyer (Tue May 04 2010 - 08:03:08 CDT)
- Axel Kohlmeyer (Sat May 01 2010 - 13:22:10 CDT)
- ydhuang2727 (Sat May 01 2010 - 08:03:01 CDT)
- Axel Kohlmeyer (Thu Apr 29 2010 - 21:34:42 CDT)
- ydhuang2727 (Thu Apr 29 2010 - 20:59:23 CDT)
- Jérôme Hénin (Thu Apr 29 2010 - 10:06:57 CDT)
- Axel Kohlmeyer (Thu Apr 29 2010 - 08:34:36 CDT)
- ydhuang2727 (Thu Apr 29 2010 - 07:39:49 CDT)
- Jérôme Hénin (Thu Apr 29 2010 - 02:59:42 CDT)
- ydhuang2727 (Thu Apr 29 2010 - 01:19:46 CDT)
- Axel Kohlmeyer (Thu Apr 29 2010 - 00:06:18 CDT)
- Axel Kohlmeyer (Wed Apr 28 2010 - 23:44:20 CDT)
- ydhuang2727 (Wed Apr 28 2010 - 22:54:30 CDT)
- Axel Kohlmeyer (Wed Apr 28 2010 - 11:17:58 CDT)
- ydhuang2727 (Tue Apr 27 2010 - 20:23:11 CDT)
- Leandro Martínez (Thu May 12 2005 - 13:24:10 CDT)
- Pijush Ghosh (Thu May 12 2005 - 12:53:32 CDT)
- Dong Luo (Thu May 12 2005 - 11:52:42 CDT)
dielectric constant assignment
- Axel Kohlmeyer (Mon Nov 09 2009 - 07:22:35 CST)
- Rajiv Abhyankar (Mon Nov 09 2009 - 06:22:04 CST)
dielectric parameter?
- Anton Arkhipov (Thu Jan 15 2009 - 10:00:04 CST)
- Peter Freddolino (Thu Jan 15 2009 - 09:24:11 CST)
- BIN ZHANG (Thu Jan 15 2009 - 01:10:36 CST)
Difference between cwd and cd
- Ajasja LjubetiÄ (Wed Jul 06 2011 - 08:59:30 CDT)
- Axel Kohlmeyer (Wed Jul 06 2011 - 07:49:18 CDT)
- Ajasja LjubetiÄ (Wed Jul 06 2011 - 04:43:43 CDT)
Difference between Linux-x86_64-TCP and Linux-x86_64
- Axel Kohlmeyer (Tue Nov 24 2009 - 07:53:57 CST)
- Lee Wei Yang (Mon Nov 23 2009 - 16:33:12 CST)
difference between reassignfreq and rescalefreq in temperature controls.
- Leonardo G. Trabuco (Sat Apr 08 2006 - 13:31:47 CDT)
- Margaret Shun Cheung (Fri Apr 07 2006 - 13:13:16 CDT)
difference between run and minimize
- snoze pa (Wed Sep 14 2011 - 10:05:56 CDT)
- snoze pa (Wed Sep 14 2011 - 10:02:03 CDT)
- snoze pa (Fri Sep 09 2011 - 16:01:55 CDT)
Difference between the two Dowsers
- Leonardo Trabuco (Fri Jun 04 2010 - 02:47:21 CDT)
- Ning Zhang (Fri May 21 2010 - 05:26:37 CDT)
difference between two kinds of dimers
- olivier Walker (Wed Mar 02 2005 - 06:19:56 CST)
difference in total energy values
- Osman Yogurtcu (Wed Mar 15 2006 - 13:59:44 CST)
Differences between 32bit and 64bit version of NAMD?
- Carsten Olbrich (Mon Jun 18 2007 - 17:12:37 CDT)
- Carsten Olbrich (Mon Jun 18 2007 - 13:34:45 CDT)
- Carsten Olbrich (Mon Jun 18 2007 - 11:04:30 CDT)
Differences between ABF and metadynamics
- Jérôme Hénin (Tue Sep 13 2011 - 08:45:17 CDT)
- Jérôme Hénin (Tue Sep 13 2011 - 05:43:39 CDT)
- Alex (Tue Sep 13 2011 - 05:13:34 CDT)
differences in multiprocessor energy minimization results
- Markus Metz (Wed Aug 17 2011 - 11:44:19 CDT)
different 1-4scaling values for different atom types?
- cong chen (Sun Dec 02 2007 - 23:51:11 CST)
different cutoff for elecstrostatic and VDW interactions
- Hyonseok Hwang (Tue Apr 18 2006 - 12:53:29 CDT)
Different dcd files for minimize and MD
- Lam T Nguyen (Fri Jul 25 2008 - 07:50:38 CDT)
- Lam T Nguyen (Thu Jul 24 2008 - 15:20:17 CDT)
different dielectric constant during simulation
- Liu, Zhanwu (Wed Dec 17 2003 - 10:24:30 CST)
Different Dielectric constant value for different segment
- Madhurima Jana (Wed Nov 24 2010 - 05:25:06 CST)
- Axel Kohlmeyer (Mon Nov 22 2010 - 09:07:06 CST)
- Madhurima Jana (Mon Nov 22 2010 - 07:48:39 CST)
Different electrostatic and Van der Waals cutoff
- Peter Spijker (Fri Apr 08 2005 - 04:56:42 CDT)
Different ensembles in the same system
- Eric Perim (Wed Jul 29 2009 - 14:48:39 CDT)
Different Hbonds values on different machines using same script for same trajectories
- John Stone (Wed Jun 11 2008 - 03:11:11 CDT)
- John Stone (Tue Jun 10 2008 - 00:18:07 CDT)
- sunita gupta (Mon Jun 09 2008 - 02:29:57 CDT)
different output in processors
- Marcos Sotomayor (Wed Feb 28 2007 - 04:08:32 CST)
- dora guzman (Tue Feb 27 2007 - 14:18:24 CST)
different result from different cpu
- Xiaoqing Wang (Tue May 10 2005 - 19:59:45 CDT)
- Jérôme Hénin (Tue May 10 2005 - 11:40:25 CDT)
- Xiaoqing Wang (Tue May 10 2005 - 07:31:31 CDT)
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)
different results for parallel vs serial runs for NAMD
- Yousung Jung (Mon Apr 16 2007 - 23:04:56 CDT)
Different solvents
- Marc Baaden (Sun Nov 13 2005 - 07:49:19 CST)
- Gaurav Sharma (Tue Nov 08 2005 - 13:09:27 CST)
Different types of constraints at the same time
- Chao Zhang (Thu Jul 15 2010 - 14:05:30 CDT)
different values of "1-4scaling" in a system
- Chris Harrison (Fri Jun 18 2010 - 11:49:49 CDT)
- D70039 (Wed Jun 16 2010 - 06:00:06 CDT)
different velocities problem
- Jérôme Hénin (Tue Oct 25 2011 - 02:10:14 CDT)
- Hasan haska (Tue Oct 25 2011 - 01:28:22 CDT)
Difficulties is minimizing capped peptides
- Gianluca Interlandi (Tue Mar 06 2007 - 00:19:08 CST)
- kate.nairn_at_csiro.au (Mon Mar 05 2007 - 21:18:01 CST)
Difficulties is minimizing capped peptides - solution
- kate.nairn_at_csiro.au (Tue Mar 27 2007 - 19:59:03 CDT)
difficulties using SMD on atoms in large systems
- Philip Blood (Tue Oct 04 2005 - 12:42:01 CDT)
diffusion / fex peptide problem
- Roman Petrenko (Wed May 06 2009 - 12:33:49 CDT)
- Benjamin Stauch (Wed May 06 2009 - 10:24:16 CDT)
diffusion coefficient from rmsd
- bo liu (Thu Aug 28 2008 - 01:38:38 CDT)
- Axel Kohlmeyer (Wed Aug 27 2008 - 22:39:52 CDT)
- Rudra Banerjee (Wed Aug 27 2008 - 21:55:28 CDT)
Diffusion of Protein through the membrane
- Peter Freddolino (Wed Jun 27 2007 - 10:35:31 CDT)
- Peter Freddolino (Wed Jun 27 2007 - 10:32:49 CDT)
- Ilya Chorny (Wed Jun 27 2007 - 09:57:49 CDT)
- Alessandro Cembran (Wed Jun 27 2007 - 09:08:32 CDT)
- Peter Freddolino (Wed Jun 27 2007 - 08:51:04 CDT)
- Cesar Luis Avila (Wed Jun 27 2007 - 08:12:00 CDT)
- Ilya Chorny (Tue Jun 26 2007 - 22:12:22 CDT)
Dihedral and Improper, Nonbonded.
- Wang, Boyang (Sun May 01 2005 - 22:46:22 CDT)
Dihedral angle calculation over the trajectories
- Peter Freddolino (Wed Aug 13 2008 - 10:24:59 CDT)
- sunita gupta (Wed Aug 13 2008 - 10:17:14 CDT)
Dihedral angle energy in silica block
- Eduardo (Mon Mar 01 2010 - 15:46:54 CST)
- Jindal Shah (Mon Mar 01 2010 - 09:11:47 CST)
- Eduardo (Sun Feb 28 2010 - 22:41:09 CST)
- Jindal Shah (Sun Feb 28 2010 - 21:51:15 CST)
Dihedral angle potential energy function
- Ajasja LjubetiÄ (Fri Jul 02 2010 - 08:09:44 CDT)
- Jérôme Hénin (Fri Jul 02 2010 - 07:13:10 CDT)
- Ajasja LjubetiÄ (Thu Jul 01 2010 - 05:07:27 CDT)
Dihedral coordinate ABF scheme
- Jerome Henin (Tue Jan 29 2008 - 16:25:57 CST)
- Luca (Tue Jan 29 2008 - 15:32:01 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 energy not getting generated ( is zero )
- prateeksha s (Wed Dec 26 2007 - 01:58:15 CST)
- prateeksha s (Wed Dec 26 2007 - 02:01:50 CST)
dihedral force constant
- Jerome Henin (Tue May 27 2008 - 20:38:40 CDT)
- jfgaff_at_ncsu.edu (Tue May 27 2008 - 18:38:06 CDT)
Dihedral Parameterization
- Jan Saam (Mon Aug 27 2007 - 03:47:04 CDT)
- Venky (Mon Aug 20 2007 - 19:17:28 CDT)
Dihedral parameters for multiple minima
- Chang, Christopher (Wed Mar 15 2006 - 19:34:22 CST)
Dihedral parameters for side-chains?
- Igor Petrik (Mon Apr 26 2010 - 07:54:41 CDT)
- Jérôme Hénin (Mon Apr 26 2010 - 07:29:40 CDT)
- Igor Petrik (Sat Apr 24 2010 - 22:41:06 CDT)
- Jun Zhang (Sat Apr 24 2010 - 22:29:12 CDT)
- Igor Petrik (Fri Apr 23 2010 - 11:50:30 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)
dihedral restraints "on-the-fly"?
- JC Gumbart (Mon May 26 2008 - 22:06:46 CDT)
- Sebastian Stolzenberg (Mon May 26 2008 - 19:40:32 CDT)
Dihedral restraints do not work
- Neelanjana Sengupta (Tue Mar 20 2007 - 10:44:10 CDT)
Dihedral Restraints during MD simulation
- Matthieu Wilhelm (Thu Apr 16 2009 - 03:56:59 CDT)
- Leonardo Trabuco (Wed Apr 15 2009 - 14:03:22 CDT)
- Jerome Henin (Wed Apr 15 2009 - 13:49:29 CDT)
- Leonardo Trabuco (Wed Apr 15 2009 - 13:43:18 CDT)
- Sebastian Stolzenberg (Wed Apr 15 2009 - 13:18:47 CDT)
- Matthieu Wilhelm (Wed Apr 15 2009 - 12:33:04 CDT)
dihedral rotation with ABF
- kakali sen (Sun Apr 10 2011 - 12:48:17 CDT)
Dihedral scan in NAMD?
- L. Michel Espinoza-Fonseca (Tue Jun 24 2008 - 02:23:53 CDT)
- Chris Chipot (Mon Jun 23 2008 - 15:21:57 CDT)
- Peter Freddolino (Mon Jun 23 2008 - 15:02:14 CDT)
- L. Michel Espinoza-Fonseca (Mon Jun 23 2008 - 10:47:07 CDT)
- Kamilla Kopec (Mon Jun 23 2008 - 10:06:30 CDT)
dihedral terms for a parameter file
- Basak Isin (Sun Jul 25 2010 - 17:09:09 CDT)
dihedrals multiplicity in xplor psf file
- Giovanni Bellesia (Wed Jan 25 2006 - 15:12:16 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)
dimer minimization
- ayk_at_mail.ecc.u-tokyo.ac.jp (Wed Feb 28 2007 - 03:54:40 CST)
Direction of SMD force
- aida_at_mit.edu (Tue Feb 17 2004 - 09:06:16 CST)
Direction of steered molecular dynamics
- ÖÜÎÄ²ý (Sat Nov 22 2008 - 08:39:51 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)
discrete energy value after restart
- Chris Harrison (Sun Jan 23 2011 - 10:00:07 CST)
- Kang Hee Cho (Thu Jan 20 2011 - 21:25:46 CST)
display all frames simultaneously
- Luis Gracia (Fri Apr 17 2009 - 00:35:29 CDT)
- uu zhu (Thu Apr 16 2009 - 22:16:52 CDT)
- gaillard_at_chimie.u-strasbg.fr (Thu Apr 16 2009 - 22:20:37 CDT)
- Samuel Coulbourn Flores èŠ±å±± (Thu Apr 16 2009 - 21:35:59 CDT)
dissociated quartz SiO2 groups in surface
- Eduardo (Tue Dec 14 2010 - 11:01:13 CST)
- christos.lamprakis_at_dcb.unibe.ch (Tue Dec 14 2010 - 05:39:59 CST)
dissociation in NAMD
- Peter Freddolino (Mon Nov 06 2006 - 15:24:02 CST)
- sukesh shenoy (Mon Nov 06 2006 - 11:00:40 CST)
dissociation of water
- Cesar Luis Avila (Mon Oct 09 2006 - 11:33:52 CDT)
- Shenoy, Sukesh (Sun Oct 08 2006 - 18:06:56 CDT)
Distance Analysis for Constant Force Pulling for kinesin neck linker
- Patriche Simona (Fri Mar 05 2010 - 05:44:37 CST)
distance calculation between atoms of two segments
- Ajasja LjubetiÄ (Sat Jan 22 2011 - 13:48:54 CST)
- mjyang (Sat Jan 22 2011 - 10:51:00 CST)
distance colvar
- Jérôme Hénin (Mon Jun 07 2010 - 06:27:00 CDT)
- Branko (Mon Jun 07 2010 - 06:17:34 CDT)
- Neelanjana Sengupta (Mon Jun 07 2010 - 03:07:51 CDT)
Distance constraint
- Jérôme Hénin (Thu Jun 17 2010 - 06:31:23 CDT)
- Nicolas Floquet (Thu Jun 17 2010 - 03:30:45 CDT)
- 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 constraints with an upper bound
- Luca (Thu Mar 22 2007 - 04:20:27 CDT)
- Neema Salimi (Wed Mar 21 2007 - 13:19:19 CDT)
distance dependant dielectric constant
- Wagener, M. (Markus) (Fri Feb 27 2004 - 06:58:43 CST)
Distance Restraint
- felmerino_at_uchile.cl (Tue Nov 23 2010 - 13:12:23 CST)
- Jérôme Hénin (Tue Nov 23 2010 - 11:27:03 CST)
- Bo Liu (Tue Nov 23 2010 - 11:16:42 CST)
- Benjamin Bouvier (Tue Nov 23 2010 - 11:00:45 CST)
- Jacopo Sgrignani (Tue Nov 23 2010 - 10:23:27 CST)
- luca (Thu Nov 23 2006 - 02:22:23 CST)
- Yao Fan (Wed Nov 22 2006 - 16:50:04 CST)
distance restraint w/upper bound example
- Neema Salimi (Mon Mar 05 2007 - 15:27:05 CST)
distance restraints during a dynamic
- Nicolas Sapay (Mon Apr 11 2005 - 11:13:40 CDT)
Distance XY-colvars
- Giacomo Fiorin (Wed Jan 05 2011 - 16:12:32 CST)
- Alex Liu (Tue Jan 04 2011 - 15:56:56 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)
distanceXY colvar-ABF
- Giacomo Fiorin (Sun Aug 21 2011 - 12:28:07 CDT)
- Parisa Akhski (Sun Aug 21 2011 - 09:05:16 CDT)
distorsion in hydrogens added
- regafan_at_usc.es (Wed Nov 22 2006 - 12:18:15 CST)
- Jerome Henin (Tue Nov 21 2006 - 14:25:05 CST)
- Jerome Henin (Tue Nov 21 2006 - 09:47:17 CST)
- regafan_at_usc.es (Tue Nov 21 2006 - 05:47:58 CST)
distortion of some bonds during structure preparation
- bharat gupta (Mon Jul 04 2011 - 03:36:39 CDT)
Distribute Points Evenly on Surface of a Sphere
- Rajan Vatassery (Mon Oct 18 2010 - 13:57:53 CDT)
Dividing a 2D ABF simulations into regions (on nodes with different speeds)
- Ajasja LjubetiÄ (Fri Jul 29 2011 - 11:56:17 CDT)
- Axel Kohlmeyer (Fri Jul 29 2011 - 08:34:33 CDT)
- Ajasja LjubetiÄ (Fri Jul 29 2011 - 04:44:38 CDT)
Dixitpd wants to Share Favorites with you
- dixitpd_at_gmail.com (Tue Nov 20 2007 - 22:05:54 CST)
DMF solvent parameters
- Austin B. Yongye (Wed Dec 10 2008 - 16:08:17 CST)
DMPC Atoms moving too fast !
- mustapha.hamdi_at_ensi-bourges.fr (Sat Mar 10 2007 - 10:08:08 CST)
dmpc bilayer
- Syed Kashif Zafar (Mon Dec 28 2009 - 13:10:46 CST)
- Song, Hyundeok (songhk) (Mon Dec 28 2009 - 10:03:38 CST)
- Axel Kohlmeyer (Mon Dec 28 2009 - 02:59:07 CST)
- Syed Kashif Zafar (Sun Dec 27 2009 - 15:10:26 CST)
dmpc membrane
- Swarna Patra (Mon Jul 04 2005 - 20:17:43 CDT)
DMPC psf.
- mustapha.hamdi_at_ensi-bourges.fr (Fri Feb 09 2007 - 18:41:51 CST)
- Lea Thøgersen (Fri Feb 09 2007 - 16:33:01 CST)
- Cesar Luis Avila (Fri Feb 09 2007 - 12:36:40 CST)
- mustapha.hamdi_at_ensi-bourges.fr (Fri Feb 09 2007 - 10:10:24 CST)
DNA and low pH
- Gaurav Sharma (Wed Jan 31 2007 - 15:06:46 CST)
DNA H-bonds
- Maxim Karachevtsev (Thu Feb 01 2007 - 03:51:26 CST)
DNA helix model
- lily jin (Tue Jan 30 2007 - 13:26:26 CST)
DNA hydrogen bonds
- Peter Freddolino (Fri Feb 02 2007 - 09:08:06 CST)
- Maxim Karachevtsev (Fri Feb 02 2007 - 02:00:46 CST)
DNA pdb file
- xing jing (Tue Jul 29 2008 - 15:16:16 CDT)
DNA protonation
- mustapha.hamdi_at_ensi-bourges.fr (Mon Feb 06 2006 - 05:04:53 CST)
DNA simulation by NAMD
- sudipta sinha (Sun Jul 13 2008 - 06:07:20 CDT)
DNA terminal Patch / How could I retain the primes in DNA
- raghav singh (Tue Jul 05 2011 - 03:23:21 CDT)
Do I need to use an xsc file to restart a simulation in NVT?
- Ana Celia Araujo Vila Verde (Wed Jun 28 2006 - 10:41:07 CDT)
- Peter Freddolino (Wed Jun 28 2006 - 14:09:13 CDT)
- Ana Celia Araujo Vila Verde (Wed Jun 28 2006 - 14:05:27 CDT)
Do top_all27_prot_na.inp and cornell.prm share the same naming rules of atom types?
- ºÎØ¹»Ô (Tue Sep 22 2009 - 02:51:56 CDT)
Do we need to renumber atoms after solvate?
- Peter Freddolino (Mon Jul 09 2007 - 00:33:59 CDT)
- Arun Krishnan (Sun Jul 08 2007 - 20:31:20 CDT)
Dock a metal ion into a peptide/protein
- Branko (Thu Sep 01 2011 - 04:09:16 CDT)
- Andrea Holfelder (Wed Aug 31 2011 - 21:51:27 CDT)
- Branko (Wed Aug 31 2011 - 15:28:17 CDT)
- Andrea Holfelder (Wed Aug 31 2011 - 14:29:39 CDT)
documentation on parallel implementation
- Paul Rigor (uci) (Wed Dec 16 2009 - 08:33:03 CST)
Does "rigidbond off" work instead of "rigidbonds none"
- Mert Gür (Fri Sep 17 2010 - 14:44:14 CDT)
- Jim Phillips (Fri Sep 17 2010 - 14:19:26 CDT)
- Mert Gür (Fri Sep 03 2010 - 04:25:40 CDT)
- Leonardo Trabuco (Fri Sep 03 2010 - 01:21:01 CDT)
- Mert Gür (Thu Sep 02 2010 - 15:03:21 CDT)
Does amber force field in NAMD 2.7b2 work stable?
- yudaqi (Fri Dec 18 2009 - 21:02:50 CST)
does any body have the parameter file for aldehyde group?
- felmerino_at_uchile.cl (Fri Jul 08 2011 - 01:44:15 CDT)
- AlbertAlbert (Fri Jul 08 2011 - 01:34:22 CDT)
Does anybody have gromacs topology example, which works OK using NAMD??
- Armen Poghosyan (Tue Jun 01 2004 - 14:24:00 CDT)
Does anyone have a sample tcl file for counting H-bonds
- Yang Gao (Wed Jul 30 2008 - 09:33:18 CDT)
Does Berendsen increase viscosity of water?
- Gianluca Interlandi (Wed Aug 05 2009 - 13:19:25 CDT)
- Gianluca Interlandi (Tue Aug 04 2009 - 00:36:38 CDT)
Does CHARMM stabilize alpha helices?
- Nikolaos Glykos (Sun Aug 22 2010 - 03:57:22 CDT)
- Rabab Toubar (Sat Aug 21 2010 - 15:58:24 CDT)
Does GB Implicit Solvent handle explicit ions?
- Gianluca Interlandi (Sun Apr 17 2011 - 22:43:37 CDT)
- David Tanner (Sun Apr 17 2011 - 06:39:19 CDT)
Does NAMD calculate the potential energy of FIXED ATOMS?
- Boyang Wang (Wed Oct 05 2005 - 12:14:36 CDT)
Does NAMD have any capability to assign coordiantes to novel sequences?
- Eric H. Lee (Thu Jun 25 2009 - 11:16:16 CDT)
- Nicholas M Glykos (Thu Jun 25 2009 - 11:36:02 CDT)
- Amr Zeinalabideen Majul (Thu Jun 25 2009 - 10:34:43 CDT)
Does pair interaction calculations uses PBC ?
- Peter Freddolino (Wed Feb 21 2007 - 11:26:38 CST)
- Arturas Ziemys (Wed Feb 21 2007 - 11:18:22 CST)
Does rmsd is the judge of system equilibrium in all conditions?
- cong chen (Mon Nov 19 2007 - 06:08:12 CST)
Domain error ParseFEP
- Christian Jorgensen (Fri Mar 25 2011 - 09:42:29 CDT)
- Chris Chipot (Fri Mar 25 2011 - 09:57:19 CDT)
- Chris Chipot (Fri Mar 25 2011 - 09:41:25 CDT)
- Christian Jorgensen (Fri Mar 25 2011 - 09:14:02 CDT)
Don't get mad, get Val1um!
- Jarred Whitlock (Mon Aug 13 2007 - 22:47:48 CDT)
Dose restart frequently affect the results?
- liu xin (Fri Dec 23 2005 - 21:33:40 CST)
Double bond-pheyl group bonding parameters
- Kevser Göçmen Topal (Wed Apr 18 2007 - 01:19:03 CDT)
double precision numerical accuracy issue
- Himanshu Khandelia (Thu May 17 2007 - 08:51:36 CDT)
double-wide sampling with soft-core
- Floris Buelens (Thu Jan 22 2009 - 13:25:19 CST)
- Chris Chipot (Thu Jan 22 2009 - 12:23:55 CST)
- Floris Buelens (Thu Jan 22 2009 - 12:02:36 CST)
- Jerome Henin (Thu Jan 22 2009 - 11:35:39 CST)
- Peter Freddolino (Thu Jan 22 2009 - 11:34:07 CST)
- Chris Harrison (Thu Jan 22 2009 - 11:48:23 CST)
- Chris Harrison (Thu Jan 22 2009 - 11:21:15 CST)
- Floris Buelens (Thu Jan 22 2009 - 04:58:40 CST)
- Chris Chipot (Wed Jan 21 2009 - 17:32:52 CST)
- Jerome Henin (Wed Jan 21 2009 - 16:02:24 CST)
- Sébastien Légaré (Tue Jan 20 2009 - 14:27:32 CST)
Doubts and problem in ABF simulations
- Jerome Henin (Wed Sep 02 2009 - 15:34:54 CDT)
- Giacomo Fiorin (Wed Sep 02 2009 - 13:21:09 CDT)
- Paulo Cesar Telles de Souza (Wed Sep 02 2009 - 13:11:07 CDT)
- Paulo Cesar Telles de Souza (Wed Sep 02 2009 - 10:55:19 CDT)
- Jerome Henin (Mon Aug 31 2009 - 17:18:52 CDT)
- Paulo Cesar Telles de Souza (Mon Aug 31 2009 - 11:00:57 CDT)
Downloading CHARMM Parameter and Topology Files
- JC Gumbart (Fri Jul 27 2007 - 12:01:34 CDT)
- Audrey Salazar (Fri Jul 27 2007 - 11:31:54 CDT)
Dowser
- Song, Hyundeok (songhk) (Sat May 29 2010 - 22:22:15 CDT)
- Basak Isin (Sat May 29 2010 - 21:48:12 CDT)
- Felipe Merino (Sat May 29 2010 - 21:51:28 CDT)
- Song, Hyundeok (songhk) (Sat May 29 2010 - 20:42:49 CDT)
- Axel Kohlmeyer (Sat May 29 2010 - 20:09:24 CDT)
- Basak Isin (Sat May 29 2010 - 20:21:38 CDT)
- Basak Isin (Sat May 29 2010 - 19:25:37 CDT)
- Charles Danko (Wed Jan 19 2005 - 09:01:18 CST)
- Charles Danko (Tue Jan 18 2005 - 16:20:06 CST)
- Peter Jones (Mon Dec 08 2003 - 02:26:35 CST)
Dowser with RESIDUE LYR
- Ale Gomez (Mon Aug 16 2010 - 12:02:18 CDT)
DPMTA instead of PME without PBC possible?
- Philipp Schoen1 (Mon May 14 2007 - 07:15:52 CDT)
DPPC
- Jérôme Hénin (Mon Aug 30 2004 - 11:48:39 CDT)
- Eunice Ramirez Melendez (Mon Aug 30 2004 - 02:28:55 CDT)
DPPC membrane
- Andres Morales N (Fri Jul 29 2011 - 03:16:50 CDT)
- Ajasja LjubetiÄ (Thu Jul 28 2011 - 05:21:10 CDT)
- Andres Morales N (Thu Jul 28 2011 - 01:29:36 CDT)
DPPC.Pdb
- Lechuga, Javier (Wed Aug 30 2006 - 05:57:38 CDT)
DPPC.Pdb file needed
- Elsa S. Henriques (Tue Sep 05 2006 - 08:42:29 CDT)
- Lechuga, Javier (Mon Sep 04 2006 - 11:27:49 CDT)
dramatical standard deviation in the pressure profile
- Nicolas Sapay (Mon Aug 29 2005 - 07:12:27 CDT)
Dreiding parameters
- fereshteh moradi (Wed Jun 09 2010 - 07:17:21 CDT)
Drift in performance
- Peter Freddolino (Mon Oct 15 2007 - 14:07:49 CDT)
- Jerome Henin (Mon Oct 15 2007 - 12:02:32 CDT)
drift in protein membrane simulation. membrane and protein one way, water the other way
- maria goranovic (Mon Aug 20 2007 - 05:20:06 CDT)
Drift of the center of mass of lipid bilayer
- Dai, Jian1 (Mon May 24 2010 - 13:26:39 CDT)
drop in Temp from NVT to NVE
- Peter Freddolino (Wed Jul 02 2008 - 10:49:15 CDT)
- S.K. Ghosh (Wed Jul 02 2008 - 10:18:41 CDT)
Drude polarizability parameters
- David Hardy (Thu May 06 2010 - 18:12:58 CDT)
- Igor Petrik (Thu May 06 2010 - 17:35:20 CDT)
- David Hardy (Sat Feb 20 2010 - 10:17:55 CST)
- Igor Petrik (Fri Feb 19 2010 - 06:09:57 CST)
drude water simulation bug ?
- Sergey (Tue Feb 28 2012 - 14:35:26 CST)
drude water simulation bug ? radial distrubuion function
- Sergey (Wed Feb 29 2012 - 01:22:30 CST)
Drug design issue.
- Branko (Tue Feb 28 2012 - 05:39:26 CST)
- Boyang Wang (Tue Feb 28 2012 - 02:08:07 CST)
dual all-atom/coarse grain simulation
- Keith Battle (Tue Jul 20 2010 - 15:52:30 CDT)
dual core processors
- Jimmy Tang (Fri Mar 31 2006 - 12:38:24 CST)
- Leandro Martínez (Fri Mar 31 2006 - 11:04:01 CST)
dublicated residue numbers in PDB/PSF
- ARTURAS ZIEMYS (Wed Feb 01 2006 - 09:14:53 CST)
dummy atom mass changed
- Jerome Henin (Tue May 12 2009 - 11:51:55 CDT)
- yun luo (Tue May 12 2009 - 11:10:11 CDT)
- yun luo (Thu May 07 2009 - 11:18:43 CDT)
- Floris Buelens (Thu May 07 2009 - 05:09:36 CDT)
- Chris Harrison (Wed May 06 2009 - 13:09:26 CDT)
- yun luo (Wed May 06 2009 - 11:50:06 CDT)
- yun luo (Tue May 05 2009 - 15:26:46 CDT)
- Chris Harrison (Tue May 05 2009 - 12:53:00 CDT)
- yun luo (Tue May 05 2009 - 12:19:05 CDT)
- yun luo (Tue May 05 2009 - 11:49:06 CDT)
- Jerome Henin (Tue May 05 2009 - 10:43:48 CDT)
- daniel aguayo (Tue May 05 2009 - 10:18:39 CDT)
- Chris Harrison (Mon May 04 2009 - 22:24:32 CDT)
- daniel aguayo (Mon May 04 2009 - 19:53:14 CDT)
- Jerome Henin (Mon May 04 2009 - 17:39:22 CDT)
- yun luo (Mon May 04 2009 - 16:24:59 CDT)
- Chris Harrison (Mon May 04 2009 - 15:33:57 CDT)
- yun luo (Mon May 04 2009 - 14:54:27 CDT)
dummy atoms and FEP
- Christophe Chipot (Thu Apr 06 2006 - 12:19:06 CDT)
- Raul Araya Secchi (Thu Apr 06 2006 - 11:36:57 CDT)
Dummy particles
- Arturas Ziemys (Wed Nov 22 2006 - 14:55:36 CST)
dummyAtom-ABF
- Jérôme Hénin (Fri Aug 26 2011 - 10:32:20 CDT)
- Parisa Akhski (Fri Aug 26 2011 - 09:57:13 CDT)
Dumy atoms in FEP
- Raul Araya Secchi (Mon Mar 13 2006 - 09:13:22 CST)
Duplicate lines in the output file !
- Rene Salmon (Thu Apr 07 2005 - 10:13:59 CDT)
- Parag Adhangale (Wed Apr 06 2005 - 11:52:56 CDT)
duplicate residue key ALA will be ignored
- Mert Gür (Tue May 18 2010 - 11:37:57 CDT)
- flavio seixas (Tue May 18 2010 - 11:21:07 CDT)
- ehenriques_at_qui.uc.pt (Tue May 18 2010 - 04:28:24 CDT)
- Mert Gür (Mon May 17 2010 - 16:42:59 CDT)
duplicated key CA in psfgen
- mustapha.hamdi_at_ensi-bourges.fr (Wed Apr 20 2005 - 07:12:36 CDT)
- mustapha.hamdi_at_ensi-bourges.fr (Wed Apr 20 2005 - 07:13:24 CDT)
- Pijush Ghosh (Tue Apr 19 2005 - 13:04:48 CDT)
- mustapha.hamdi_at_ensi-bourges.fr (Tue Apr 19 2005 - 12:49:33 CDT)
during namd build / compile -ltcl8.4 linking error
- Sabuj Pattanayek (Wed Mar 15 2006 - 13:17:49 CST)
- Sabuj Pattanayek (Wed Mar 15 2006 - 09:50:11 CST)
- Brian Bennion (Mon Mar 13 2006 - 17:56:41 CST)
- Sabuj Pattanayek (Mon Mar 13 2006 - 15:41:29 CST)
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)
Dynamics with a glycerol molecule
- Lucio Montero (Mon Apr 07 2008 - 17:34:39 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)
effects of box size
- Narender Singh Maan (Thu Sep 20 2007 - 10:31:02 CDT)
eigenvector projections
- Peter Jones (Mon Nov 08 2004 - 23:41:36 CST)
elastic network
- BIN ZHANG (Tue Apr 14 2009 - 18:10:37 CDT)
ELECT energy
- Michel Espinoza-Fonseca (Mon Apr 11 2005 - 16:18:10 CDT)
- Stern, Julie (Mon Apr 11 2005 - 14:37:57 CDT)
electric field
- Todd Trimble (Tue Nov 21 2006 - 15:08:11 CST)
- Todd Trimble (Thu Nov 16 2006 - 11:57:25 CST)
- Peter Freddolino (Sun Sep 03 2006 - 08:10:10 CDT)
- Neelanjana Sengupta (Sun Sep 03 2006 - 07:38:38 CDT)
- Ekta Khurana (Sat Sep 02 2006 - 20:17:21 CDT)
- jcm203_at_soton.ac.uk (Wed Feb 22 2006 - 10:17:39 CST)
- Swarna Patra (Wed Jan 12 2005 - 16:57:02 CST)
electric field along z-direction
- Roman Petrenko (Wed May 27 2009 - 16:21:27 CDT)
electric field and MISC
- Todd Trimble (Wed Nov 15 2006 - 18:20:54 CST)
electric field and MISC energy
- Todd Trimble (Tue Nov 14 2006 - 10:46:19 CST)
- curcio (Tue Nov 14 2006 - 02:55:04 CST)
- Todd Trimble (Mon Nov 13 2006 - 10:44:29 CST)
- Todd Trimble (Wed Nov 08 2006 - 16:19:02 CST)
electric field unit conversion
- Roman Petrenko (Wed Feb 17 2010 - 11:53:02 CST)
- Mikhail Suyetin (Wed Feb 17 2010 - 11:27:25 CST)
- Ziemys, Arturas (Wed Feb 17 2010 - 09:45:46 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)
Electron density profile?
- Leonardo Trabuco (Fri Dec 05 2008 - 01:59:05 CST)
- BIN ZHANG (Fri Dec 05 2008 - 01:40:53 CST)
electron density profiles (EDP)
- akash.khandelwal_at_ndsu.edu (Wed Jun 22 2005 - 14:25:23 CDT)
Electrostatic Potential Problems, WRT Minimizations
- Rajan Vatassery (Thu Oct 21 2010 - 21:34:23 CDT)
electrostatic vs van der waals
- Rabab Toubar (Tue Mar 02 2010 - 08:16:20 CST)
- David Tanner (Mon Mar 01 2010 - 11:49:07 CST)
- Mark M Huntress (Mon Mar 01 2010 - 09:57:35 CST)
Electrostatics cutoff with PME
- Christopher Gillespie (Tue Apr 15 2008 - 15:21:06 CDT)
- Peter Freddolino (Tue Apr 15 2008 - 14:31:35 CDT)
- L. Michel Espinoza-Fonseca (Tue Apr 15 2008 - 14:00:03 CDT)
- Gianluca Interlandi (Tue Apr 15 2008 - 13:01:48 CDT)
Electrostatics energy calculation
- Ben Roberts (Wed May 26 2004 - 20:09:43 CDT)
electrostatics NAMD vs CHARMM
- Arturas Ziemys (Thu May 01 2008 - 11:29:49 CDT)
electrostatics under spherical harmonic conditions
- Giovanni Bellesia (Fri Jan 28 2005 - 13:59:57 CST)
EM and MD of GPCRs
- Kalyan chaitanya (Thu Mar 20 2008 - 12:34:23 CDT)
embedding protein in membrane
- jose correa (Fri Oct 10 2008 - 07:24:36 CDT)
- Chris Harrison (Fri Oct 10 2008 - 00:49:44 CDT)
- jose correa (Wed Oct 08 2008 - 09:08:12 CDT)
END: No log file
- Luis Agullo (LAB) (Mon Jul 06 2009 - 09:56:15 CDT)
energy
- Swarna Patra (Thu Feb 17 2005 - 16:58:36 CST)
energy calculation in VMD
- lily jin (Wed Mar 22 2006 - 16:41:45 CST)
Energy conversation
- Alexander A. Vakhrushev (Sat Dec 06 2008 - 01:23:26 CST)
- Peter Freddolino (Sat Dec 06 2008 - 00:39:56 CST)
- Alexander A. Vakhrushev (Fri Dec 05 2008 - 23:06:30 CST)
- Roman Petrenko (Fri Dec 05 2008 - 20:48:24 CST)
- Alexander A. Vakhrushev (Fri Dec 05 2008 - 07:51:06 CST)
Energy Determination
- mdcooper (Wed Sep 15 2004 - 17:48:11 CDT)
Energy drif in NVE ensemble
- Peter Freddolino (Thu Jan 15 2009 - 11:56:33 CST)
- eprates_at_iqm.unicamp.br (Thu Jan 15 2009 - 11:51:54 CST)
energy drift in NVE
- David Hardy (Mon Aug 20 2007 - 22:12:54 CDT)
- Victor Ovchinnikov (Mon Aug 20 2007 - 08:24:51 CDT)
- Peter Freddolino (Mon Aug 20 2007 - 08:35:02 CDT)
- Vincent Kraeutler (Mon Aug 20 2007 - 02:22:49 CDT)
- Peter Freddolino (Mon Aug 20 2007 - 02:15:11 CDT)
- David Hardy (Mon Aug 20 2007 - 01:27:14 CDT)
- Peter Freddolino (Sun Aug 19 2007 - 15:53:58 CDT)
- Victor Ovchinnikov (Sun Aug 19 2007 - 15:21:22 CDT)
Energy due to electric field
- curcio (Tue Apr 04 2006 - 10:37:28 CDT)
- jcm203_at_soton.ac.uk (Tue Apr 04 2006 - 09:09:18 CDT)
- jcm203_at_soton.ac.uk (Wed Mar 08 2006 - 11:45:52 CST)
Energy for part of system
- Ralph Jimenez (Wed Nov 09 2005 - 16:55:14 CST)
energy jump between minimization and simulation
- Eva Gonzalez Noya (Wed Feb 16 2011 - 13:15:01 CST)
- Bennion, Brian (Wed Feb 16 2011 - 10:58:33 CST)
- Eva Gonzalez Noya (Wed Feb 16 2011 - 10:14:45 CST)
- Ajasja LjubetiÄ (Wed Feb 16 2011 - 03:27:53 CST)
- Eva Gonzalez Noya (Tue Feb 15 2011 - 18:06:25 CST)
energy jump running a simulation after minimization
- Eva Gonzalez Noya (Tue Feb 15 2011 - 17:23:07 CST)
- Eva Gonzalez Noya (Tue Feb 15 2011 - 16:37:59 CST)
Energy minimization
- bharat gupta (Tue Jun 28 2011 - 18:49:01 CDT)
- sripad chandan (Sat Feb 16 2008 - 10:11:22 CST)
- Leandro Martínez (Sat Feb 03 2007 - 06:35:32 CST)
- Peter Freddolino (Fri Feb 02 2007 - 22:06:50 CST)
- Shirley Hui (Fri Feb 02 2007 - 14:23:01 CST)
- xiaojing gong (Sun Sep 25 2005 - 22:05:32 CDT)
- xiaojing gong (Sun Sep 25 2005 - 21:57:00 CDT)
- Nicolas Sapay (Wed May 11 2005 - 11:06:15 CDT)
- mustapha.hamdi_at_ensi-bourges.fr (Wed May 11 2005 - 12:33:01 CDT)
- mustapha.hamdi_at_ensi-bourges.fr (Wed May 11 2005 - 09:46:40 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 minimization failure
- DimitryASuplatov (Thu Apr 30 2009 - 05:23:31 CDT)
energy minimization help
- sripad chandan (Sat Feb 09 2008 - 09:03:50 CST)
Energy minimization of membrane
- Boyang Wang (Thu Feb 02 2012 - 23:31:28 CST)
- R. Charbel Maroun (Thu Feb 02 2012 - 06:37:42 CST)
Energy Order of Magnitude
- Jérôme Hénin (Mon Jul 11 2005 - 14:49:49 CDT)
- s.bora erdemli (Mon Jul 11 2005 - 11:20:15 CDT)
energy per residue
- Peter Freddolino (Sat Nov 24 2007 - 08:38:48 CST)
- Xavier GALLET (Fri Nov 23 2007 - 09:15:49 CST)
Energy plot script
- bo liu (Thu May 15 2008 - 13:00:23 CDT)
- Subramanian Vaitheeswaran (Thu May 15 2008 - 07:28:20 CDT)
- Alexandre A. Vakhrouchev (Wed May 14 2008 - 22:11:19 CDT)
Energy Plugin
- Peter Freddolino (Thu Jan 05 2006 - 13:46:24 CST)
- bo baker (Wed Jan 04 2006 - 16:26:24 CST)
- Peter Freddolino (Mon Jan 02 2006 - 21:46:10 CST)
- bo baker (Mon Jan 02 2006 - 18:54:12 CST)
Energy Problem (Order of Magnitude)
- s.bora erdemli (Wed Jul 20 2005 - 15:05:03 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 shift during simulation
- Cesar Luis Avila (Tue May 29 2007 - 16:45:17 CDT)
- JC Gumbart (Tue May 29 2007 - 16:10:33 CDT)
- Cesar Luis Avila (Tue May 29 2007 - 15:51:55 CDT)
- Cesar Luis Avila (Tue May 29 2007 - 09:53:31 CDT)
- Cesar Luis Avila (Mon May 28 2007 - 18:26:29 CDT)
- hl332_at_drexel.edu (Mon May 28 2007 - 17:47:44 CDT)
- Cesar Luis Avila (Mon May 28 2007 - 16:21:29 CDT)
Energy units
- Brian Bennion (Tue Dec 30 2003 - 13:53:17 CST)
- Sundaramoorthy, Munirathinam (Tue Dec 30 2003 - 12:21:59 CST)
energy values
- LEWYN LI (Tue Sep 13 2005 - 15:16:48 CDT)
- \ (Tue Sep 13 2005 - 13:30:50 CDT)
- Leonardo Sepulveda Durán (Tue Sep 13 2005 - 11:38:21 CDT)
- Peter Freddolino (Tue Sep 13 2005 - 11:31:22 CDT)
- paul.dalhaimer_at_yale.edu (Tue Sep 13 2005 - 11:13:44 CDT)
- Anna Modzelewska (Tue Sep 13 2005 - 06:29:27 CDT)
enery evaluation inside Tcl-Forces?
- harish vashisth (Fri Dec 21 2007 - 16:16:23 CST)
- harish vashisth (Thu Dec 20 2007 - 10:14:48 CST)
Enhance electrostatic interactions?
- daniel aguayo (Fri Oct 22 2010 - 16:34:19 CDT)
- Wendy González (Thu Oct 21 2010 - 07:32:46 CDT)
ensemble
- Wei Chen (Wed Oct 05 2005 - 16:34:12 CDT)
Enthalpy calculation
- Jérôme Hénin (Thu Oct 28 2010 - 11:58:00 CDT)
- divya nayar (Thu Oct 28 2010 - 10:12:00 CDT)
Enthalpy calculation from NPT simulation
- sudipta (Wed Aug 11 2010 - 13:54:16 CDT)
entropy calculation
- Nicholas M Glykos (Sat Dec 20 2008 - 04:26:26 CST)
- hodak_at_chips.ncsu.edu (Fri Dec 19 2008 - 15:18:28 CST)
entropy calculations
- Ioana Cozmuta (Mon Feb 23 2004 - 17:41:54 CST)
Epsilon, Rmin for copper ions
- Francesco Pietra (Sat Sep 24 2011 - 03:55:34 CDT)
eq. info.
- shivam ghosh (Fri Jul 13 2007 - 00:53:05 CDT)
equilibrate the system in NPT
- Hasan haska (Mon Dec 26 2011 - 13:57:37 CST)
equilibrate water molecules
- Hasan haska (Thu Nov 24 2011 - 01:43:38 CST)
equilibrated the system
- Luis Rosales (Tue Jan 11 2005 - 17:49:16 CST)
- apw397_at_soton.ac.uk (Tue Jan 11 2005 - 09:58:27 CST)
- Xiaoqing Wang (Tue Jan 11 2005 - 08:43:17 CST)
equilibrating the system with constrained Protein
- Peter Freddolino (Thu Sep 14 2006 - 13:40:37 CDT)
- Dhiraj Srivastava (Thu Sep 14 2006 - 13:12:31 CDT)
Equilibration
- Erik Nordgren (Thu Jul 21 2011 - 20:44:38 CDT)
- Chris Harrison (Tue Jul 19 2011 - 14:42:06 CDT)
- Andres Morales N (Tue Jul 19 2011 - 13:39:37 CDT)
- Jim Phillips (Mon Jul 18 2011 - 16:01:26 CDT)
- saman amiri (Thu Jun 30 2011 - 02:53:42 CDT)
- snoze pa (Wed Jun 29 2011 - 18:00:48 CDT)
- saman amiri (Wed Jun 29 2011 - 16:05:11 CDT)
- johan strumpfer (Wed Jun 29 2011 - 01:25:35 CDT)
- Norman Geist (Wed Jun 29 2011 - 04:08:26 CDT)
- Norman Geist (Wed Jun 29 2011 - 04:04:42 CDT)
- Norman Geist (Wed Jun 29 2011 - 01:39:13 CDT)
- bharat gupta (Wed Jun 29 2011 - 01:06:10 CDT)
- amit dong (Fri Mar 23 2007 - 11:30:06 CDT)
Equilibration "substraction" from obtained PMF from MD
- Jerome Henin (Sat Aug 15 2009 - 16:01:01 CDT)
- Branko (Tue Jul 28 2009 - 16:32:00 CDT)
Equilibration - NVT & NPT
- bharat gupta (Thu Jun 30 2011 - 01:36:56 CDT)
equilibration at three different temperature
- Dhiraj Srivastava (Tue Oct 10 2006 - 18:00:52 CDT)
equilibration of "big" membrane
- L. Michel Espinoza-Fonseca (Mon Apr 09 2007 - 07:42:09 CDT)
- Richard Law (Sun Apr 08 2007 - 19:21:34 CDT)
- L. Michel Espinoza-Fonseca (Sun Apr 08 2007 - 14:02:44 CDT)
- Richard Law (Sat Apr 07 2007 - 17:34:44 CDT)
- L. Michel Espinoza-Fonseca (Sat Apr 07 2007 - 13:49:05 CDT)
equilibration of protein
- Dhiraj Srivastava (Wed Nov 01 2006 - 12:31:17 CST)
equilibration of protein in water box
- Valodymyr Nechyporuk-Zloy (Tue Jun 29 2004 - 09:08:01 CDT)
equilibration of solvent box and pressure
- Peter Freddolino (Mon Oct 06 2008 - 15:24:08 CDT)
- Hiroaki Maekawa (Sun Oct 05 2008 - 22:10:49 CDT)
Equilibration problem
- pedro mansilla (Wed Jul 26 2006 - 13:47:44 CDT)
equilibration script from restart files
- matziast_at_med.uth.gr (Sun Dec 26 2010 - 06:24:16 CST)
Equilibration simulation too slow.
- Christopher Gillespie (Sun Dec 07 2008 - 10:43:17 CST)
- Diego Alejandro Vargas (Sun Dec 07 2008 - 09:59:35 CST)
Equilibration when splitting an ABF calculation
- Jérôme Hénin (Fri Jan 28 2011 - 06:44:32 CST)
- Ajasja LjubetiÄ (Fri Jan 28 2011 - 06:26:58 CST)
- Ajasja LjubetiÄ (Thu Jan 27 2011 - 08:48:48 CST)
- Jérôme Hénin (Thu Jan 27 2011 - 08:08:12 CST)
- Ajasja LjubetiÄ (Thu Jan 27 2011 - 06:25:04 CST)
Equilibration with constant temperature and pressure
- santanu chatterjee (Tue Mar 14 2006 - 19:07:09 CST)
Equilibriation Info
- JC Gumbart (Mon Oct 23 2006 - 14:45:27 CDT)
- Mark Abraham (Mon Oct 23 2006 - 14:06:04 CDT)
- tamal_at_iitk.ac.in (Mon Oct 23 2006 - 13:52:14 CDT)
erergy gradient tolerance in Configuration Files
- Jim Phillips (Wed Apr 08 2009 - 13:51:15 CDT)
- uu zhu (Wed Apr 08 2009 - 05:55:49 CDT)
Errata to: Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly
- Pietro Amodeo (Tue Dec 28 2010 - 05:45:16 CST)
- Axel Kohlmeyer (Tue Dec 28 2010 - 03:46:37 CST)
- Pietro Amodeo (Mon Dec 27 2010 - 14:20:03 CST)
Erratic behavior of TclBC in parallel
- Jérôme Hénin (Fri Jan 22 2010 - 11:08:02 CST)
- Jérôme Hénin (Thu Jan 21 2010 - 08:38:35 CST)
errno = 2
- Jerry Ebalunode (Thu Aug 18 2005 - 14:02:21 CDT)
- bo baker (Thu Aug 18 2005 - 13:12:41 CDT)
- bo baker (Wed Aug 17 2005 - 20:09:43 CDT)
- Jerry Ebalunode (Wed Aug 17 2005 - 16:08:51 CDT)
- Jerry Ebalunode (Wed Aug 17 2005 - 14:05:48 CDT)
- bo baker (Wed Aug 17 2005 - 12:30:27 CDT)
- bo baker (Tue Aug 16 2005 - 19:04:49 CDT)
- bo baker (Mon Aug 15 2005 - 19:05:21 CDT)
error
- Zumot, Elia Nabil (Wed Mar 03 2010 - 08:23:41 CST)
- jbp087_at_gmail.com (Tue Mar 02 2010 - 23:48:53 CST)
- Amit Paliwal (Mon May 24 2004 - 04:29:43 CDT)
error : atom moving too fast
- francesco oteri (Mon Jun 14 2010 - 02:32:07 CDT)
- ipsita basu (Mon Jun 14 2010 - 01:52:37 CDT)
- francesco oteri (Fri Jun 11 2010 - 01:26:57 CDT)
- ipsita basu (Fri Jun 11 2010 - 00:19:15 CDT)
- muniyamuthu.raviprasad_at_ndsu.edu (Wed May 19 2010 - 09:40:00 CDT)
- muniyamuthu.raviprasad_at_ndsu.edu (Fri May 14 2010 - 14:20:42 CDT)
- ipsita basu (Fri May 14 2010 - 00:14:30 CDT)
- muniyamuthu.raviprasad_at_ndsu.edu (Thu May 06 2010 - 09:35:02 CDT)
- Bjoern Olausson (Thu May 06 2010 - 06:34:45 CDT)
- ipsita basu (Thu May 06 2010 - 05:32:13 CDT)
- muniyamuthu.raviprasad_at_ndsu.edu (Wed May 05 2010 - 09:58:50 CDT)
- ipsita basu (Wed May 05 2010 - 01:10:33 CDT)
Error : DIDN'T FIND vdW PARAMETER FOR ATOM TYPE C11
- Chris Harrison (Sat Apr 11 2009 - 10:20:44 CDT)
- Goutham (Sat Apr 11 2009 - 00:54:22 CDT)
error about tclForcesScript
- xiaojing gong (Mon Apr 10 2006 - 09:21:13 CDT)
Error bad vdW format in Charmm parameter file
- Subramanian Vaitheeswaran (Fri Aug 24 2007 - 07:54:41 CDT)
- shyamala iyer (Thu Aug 23 2007 - 14:09:30 CDT)
error caused by atoms of lipid membrane
- Arneh Babakhani (Mon Mar 20 2006 - 10:35:14 CST)
- xiaojing gong (Mon Mar 20 2006 - 06:27:07 CST)
error caused by lipid membrane
- Arneh Babakhani (Tue Mar 21 2006 - 00:35:02 CST)
- xiaojing gong (Mon Mar 20 2006 - 20:33:42 CST)
error codes in charmrun/namd?
- J. Rui Rodrigues (Wed Feb 25 2004 - 14:02:43 CST)
error codes: 255
- Jim Phillips (Wed Oct 20 2010 - 14:35:05 CDT)
- hgrabner (Wed Oct 20 2010 - 03:57:07 CDT)
Error compile charm++
- Jianhui Tian (Thu Feb 15 2007 - 12:40:22 CST)
error compiling charm-6.2.2 for bluegenep-xlc
- hannes.loeffler_at_stfc.ac.uk (Tue Oct 26 2010 - 14:22:50 CDT)
Error compiling NAMD with MPI
- Kevin Jander (Mon Jul 09 2007 - 16:07:16 CDT)
error during charm-6.1.3 building
- Mikhail Suyetin (Mon Jun 21 2010 - 13:40:04 CDT)
error during heating of the minimized system: (please reply!)
- Chris Harrison (Wed Jan 14 2009 - 23:11:31 CST)
- Falgun Shah (Wed Jan 14 2009 - 01:08:28 CST)
error estimate in FEP calculation
- Chris Chipot (Sun Oct 29 2006 - 09:51:43 CST)
- jz7_at_duke.edu (Tue Oct 24 2006 - 23:18:27 CDT)
Error generating file.psf for cholesterol, missing coordinates in file.pdb.
- Leonardo Herrera (Sun Mar 29 2009 - 14:56:20 CDT)
error in atom type
- Rudra Banerjee (Thu Oct 02 2008 - 23:03:30 CDT)
error in config file
- Jim Phillips (Fri Aug 05 2005 - 12:36:07 CDT)
- Brian Bennion (Fri Aug 05 2005 - 11:28:14 CDT)
Error in configuration file
- JC Gumbart (Tue Nov 02 2010 - 11:46:34 CDT)
- Christian Jorgensen (Tue Nov 02 2010 - 11:33:12 CDT)
Error in equlibration
- Wei Liu (Tue Jun 19 2007 - 06:50:12 CDT)
error in explicit membrane protein simulations
- gurvisha_at_leadinvent.com (Sat Dec 06 2008 - 04:11:50 CST)
error in install NAMD_2.7b2_Linux-x86_64-CUDA
- hamze rahimi (Fri Dec 18 2009 - 06:59:43 CST)
error in loading "import hessian/charge from single point calculation" in paratool
- Jan Saam (Tue Aug 29 2006 - 03:58:15 CDT)
- Dhiraj Srivastava (Mon Aug 28 2006 - 17:53:11 CDT)
error in membrane producing
- xiaojing gong (Sun Mar 19 2006 - 18:00:04 CST)
- xiaojing gong (Fri Mar 17 2006 - 21:21:15 CST)
- xiaojing gong (Fri Mar 17 2006 - 19:30:25 CST)
Error in Minimization
- Ale Gomez (Wed Nov 11 2009 - 22:58:18 CST)
- Roman Petrenko (Tue Nov 10 2009 - 14:00:53 CST)
- Axel Kohlmeyer (Tue Nov 10 2009 - 13:30:10 CST)
- Ale Gomez (Mon Nov 09 2009 - 21:19:06 CST)
- Ale Gomez (Sun Nov 08 2009 - 11:19:28 CST)
- Axel Kohlmeyer (Sun Nov 08 2009 - 11:05:47 CST)
- Roman Petrenko (Sun Nov 08 2009 - 10:29:47 CST)
- Joshua Adelman (Sun Nov 08 2009 - 08:05:11 CST)
- Ale Gomez (Sat Nov 07 2009 - 10:45:24 CST)
Error in NAMD 2.8 function
- Sereda, Yuriy Vladimirovich (Wed Feb 22 2012 - 11:02:09 CST)
Error in NAMD Time Steps
- Hsing Pao (Tue Jul 15 2008 - 14:29:36 CDT)
error in notes on compiling namd2.5b2 with plugins
- Jerry Ebalunode (Tue Sep 16 2003 - 13:06:20 CDT)
Error in running minimization
- m.raviprasad_at_ndsu.edu (Fri May 21 2010 - 09:27:08 CDT)
- Prija Ponnan (Fri May 21 2010 - 05:24:58 CDT)
Error in running tutorial files
- Ragothaman Yennamalli (Mon May 23 2005 - 02:00:38 CDT)
- Pijush Ghosh (Wed May 18 2005 - 13:55:31 CDT)
- Ragothaman Yennamalli (Wed May 18 2005 - 12:20:50 CDT)
error in scripting
- ipsita basu (Wed Feb 17 2010 - 23:09:16 CST)
- Jeffrey J. Potoff (Tue Feb 16 2010 - 11:51:03 CST)
- Axel Kohlmeyer (Tue Feb 16 2010 - 06:28:55 CST)
- ipsita basu (Tue Feb 16 2010 - 05:26:07 CST)
- Axel Kohlmeyer (Wed Nov 25 2009 - 01:08:21 CST)
- ipsita basu (Wed Nov 25 2009 - 00:08:04 CST)
- Axel Kohlmeyer (Mon Nov 16 2009 - 07:36:50 CST)
- ipsita basu (Mon Nov 16 2009 - 00:47:57 CST)
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 in the orientationAngle
- Ajasja LjubetiÄ (Sun May 22 2011 - 05:48:29 CDT)
- Prathit Chatterjee (Sun May 22 2011 - 05:01:55 CDT)
- Giacomo Fiorin (Sat May 21 2011 - 09:47:49 CDT)
- Prathit Chatterjee (Sat May 21 2011 - 03:51:10 CDT)
Error in when using charmrun
- Gengbin Zheng (Sat Jan 08 2005 - 22:50:24 CST)
- Eric Peterson (Sat Jan 08 2005 - 22:24:11 CST)
- Gengbin Zheng (Sat Jan 08 2005 - 21:20:08 CST)
- Eric Peterson (Sat Jan 08 2005 - 21:16:47 CST)
- Gengbin Zheng (Sat Jan 08 2005 - 21:00:03 CST)
- Eric Peterson (Sat Jan 08 2005 - 20:39:45 CST)
error in writing restart files
- Ruchi Sachdeva (Fri Feb 27 2009 - 03:55:30 CST)
error message
- Ahlam Al-Rawi (Wed Aug 22 2007 - 19:49:12 CDT)
- snoze pa (Thu Apr 27 2006 - 17:37:09 CDT)
- snoze pa (Thu Apr 27 2006 - 16:15:35 CDT)
- surendra negi (Fri May 06 2005 - 10:22:55 CDT)
error message in free energy pert.
- OMAR NABEEL ALY DEMERDASH (Sun Nov 26 2006 - 23:36:23 CST)
error messages in log file
- Stern, Julie (Fri May 04 2007 - 10:41:14 CDT)
error messages with "reinitvels"
- Yinglong Miao (Fri Jun 20 2008 - 13:56:25 CDT)
error of the energy output when equilibration
- xyhu1127 (Thu Jan 14 2010 - 19:17:18 CST)
Error on closing binary file
- Seren Soner (Thu Jan 13 2011 - 06:42:50 CST)
error on installing ImageMagick
- Richard Law (Thu May 01 2008 - 14:53:37 CDT)
- Peter Freddolino (Thu May 01 2008 - 14:02:39 CDT)
- Hero (Thu May 01 2008 - 13:54:57 CDT)
Error on renaming file
- griadi_at_utalca.cl (Fri Jun 02 2006 - 13:14:01 CDT)
- Morad Alawneh (Fri Jun 02 2006 - 10:31:21 CDT)
Error on renaming file: Permission denied
- Stephen Hicks (Mon Jun 04 2007 - 00:38:28 CDT)
error on running NAMD on a large cluster with prun
- Vlad Cojocaru (Thu Apr 05 2007 - 04:14:33 CDT)
Error on Solaris
- Tirath Ramdas (Sat Jun 25 2005 - 20:10:21 CDT)
- Marcos Sotomayor (Sat Jun 25 2005 - 17:53:52 CDT)
- Tirath Ramdas (Sat Jun 25 2005 - 12:57:53 CDT)
Error on the constraints
- Jianping Lin (Tue Jun 05 2007 - 16:27:10 CDT)
Error opening XSC output file...Invalid argument
- Randy Crawford (Thu Aug 26 2004 - 13:48:38 CDT)
Error Parsing Config File
- MIke S (Tue May 27 2008 - 14:27:47 CDT)
- MIke S (Tue May 27 2008 - 09:07:03 CDT)
- Peter Freddolino (Mon May 26 2008 - 19:03:55 CDT)
- MIke S (Mon May 26 2008 - 15:46:19 CDT)
- Alexandre A. Vakhrouchev (Sat May 24 2008 - 03:06:29 CDT)
- MIke S (Sat May 24 2008 - 00:01:43 CDT)
- Brian Bennion (Fri Sep 30 2005 - 10:30:30 CDT)
- Pijush Ghosh (Thu Sep 29 2005 - 21:52:09 CDT)
- dora guzman (Thu Sep 29 2005 - 14:00:00 CDT)
error related to tcl boundary forces
- gbellesia_at_chem.ucsb.edu (Tue Apr 25 2006 - 00:52:38 CDT)
error running namd
- Robert Brunner (Mon Jul 27 2009 - 20:44:15 CDT)
- Giacomo Fiorin (Mon Jul 27 2009 - 18:07:12 CDT)
- Bernardo Sosa Padilla Araujo (Mon Jul 27 2009 - 16:37:17 CDT)
- Jim Phillips (Fri Aug 05 2005 - 12:48:40 CDT)
- 13200178 Hendra Tampang Allo (Mon Aug 01 2005 - 04:39:38 CDT)
- Jim Phillips (Wed Oct 08 2003 - 11:04:41 CDT)
- Raymond C. Fort Jr. (Wed Oct 08 2003 - 08:18:00 CDT)
Error running NAMD on CUDA
- Axel Kohlmeyer (Mon May 18 2009 - 08:44:05 CDT)
- jani sahil (Mon May 18 2009 - 03:34:11 CDT)
Error running simulation on KRAKEN XT5
- Peter Freddolino (Tue Mar 10 2009 - 23:32:45 CDT)
- harish vashisth (Tue Mar 10 2009 - 18:49:03 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 termination
- Sridhar Vaddadi (Fri Oct 02 2009 - 11:08:02 CDT)
error using Namdenergy
- Chandra Ramananjara (Wed Jun 21 2006 - 15:04:19 CDT)
Error when run Replica Exchange Method on Ranger
- Guoxiong Su (Thu May 12 2011 - 14:13:59 CDT)
Error when running NAMD at SDSC
- Joshua D. Moore (Sun Jun 19 2005 - 22:13:20 CDT)
Error when running NAMD_2.5 on mytinet
- Cesar Delgado (Sat Oct 04 2003 - 18:20:13 CDT)
error while running config file
- muniyamuthu.raviprasad_at_ndsu.edu (Thu Apr 22 2010 - 16:01:30 CDT)
- Asmita Gupta (Thu Apr 22 2010 - 13:41:29 CDT)
Error while running NPT Simulation
- Peter Freddolino (Thu Oct 16 2008 - 14:07:26 CDT)
- Audrey Salazar (Thu Oct 16 2008 - 13:51:30 CDT)
- Audrey Salazar (Thu Oct 16 2008 - 13:55:55 CDT)
- Axel Kohlmeyer (Thu Oct 16 2008 - 13:27:24 CDT)
- Nd S (Thu Oct 16 2008 - 12:44:50 CDT)
Error while using larger timesteps in Coarse grained Simulation of Polymer
- rohan uttarwar (Fri Mar 04 2011 - 15:53:56 CST)
Error while using NAMD
- Axel Kohlmeyer (Sun Nov 09 2008 - 16:16:32 CST)
- Eric H. Lee (Sun Nov 09 2008 - 16:00:57 CST)
- Marcus Batista (Sun Nov 09 2008 - 15:54:38 CST)
Error with "namd"
- Bob Masong (Wed Oct 26 2011 - 00:01:21 CDT)
error with calling exec: child process exited abnormally
- Yinglong Miao (Tue Aug 26 2008 - 16:22:21 CDT)
- Peter Freddolino (Tue Aug 26 2008 - 14:38:52 CDT)
- Yinglong Miao (Tue Aug 26 2008 - 10:37:25 CDT)
Error with External Electric Filed module
- Devendra (Wed Oct 15 2008 - 12:29:56 CDT)
- Ramya Gamini (Tue Oct 14 2008 - 17:08:39 CDT)
- Devendra (Tue Oct 14 2008 - 10:39:05 CDT)
Error with GUI NAMD Energy
- snoze pa (Mon Aug 10 2009 - 11:32:53 CDT)
- Elia Zumot (Sat Aug 08 2009 - 12:10:31 CDT)
- Peter Freddolino (Fri Aug 07 2009 - 19:16:53 CDT)
- Elia Zumot (Fri Aug 07 2009 - 16:45:23 CDT)
Error with Shape Based CG Model
- Anton Arkhipov (Wed Aug 06 2008 - 11:39:38 CDT)
- Anirban Ghosh (Wed Aug 06 2008 - 05:04:27 CDT)
Error with tclBC to induce shear flow
- KONG Xian (Thu Oct 20 2011 - 20:59:42 CDT)
Error with ubqp.pdb in NAMD tutorial
- Jens K. Munk (Tue Oct 25 2011 - 02:10:22 CDT)
- Bob Masong (Mon Oct 24 2011 - 22:43:46 CDT)
ERROR! Explicit exclusions or fluctuating charges not supported, atom ignored.
- Leonardo Trabuco (Thu Jul 02 2009 - 19:09:23 CDT)
- Leonardo Trabuco (Thu Jul 02 2009 - 18:55:23 CDT)
- emilia wu (Thu Jul 02 2009 - 18:35:32 CDT)
ERROR(S) IN THE CONFIGURATION FILE when running on a cluster.
- Axel Kohlmeyer (Fri Jul 18 2008 - 14:18:02 CDT)
- Joaquim Rui Rodrigues (Fri Jul 18 2008 - 14:17:43 CDT)
- Lam T Nguyen (Fri Jul 18 2008 - 13:32:14 CDT)
ERROR: 0031-250 task 0: Terminated
- Gurunath Katagi (Mon Jan 09 2012 - 23:42:53 CST)
Error: atom group "group1" is set, but has no definition
- Jagan Mohan (Mon Mar 08 2010 - 00:34:43 CST)
- Jagan Mohan (Mon Mar 08 2010 - 00:05:08 CST)
ERROR: Atoms moving too fast with RBCG model
- Jeffrey Potoff (Wed Nov 24 2010 - 15:21:48 CST)
- wenchangyu2006_at_gmail.com (Wed Nov 24 2010 - 10:00:57 CST)
ERROR: Atoms moving too fast;
- Chris Harrison (Fri Nov 11 2011 - 13:03:52 CST)
- Nikhil Kumar Mittal (Fri Nov 11 2011 - 12:10:52 CST)
Error: Compile charm-5.9 on Fedora core 6?
- Qiang Zhong (Fri Jun 15 2007 - 22:13:19 CDT)
ERROR: Constraint failure in RATTLE algorithm for atom
- snoze pa (Sun Jan 31 2010 - 12:41:16 CST)
ERROR: Constraint failure in RATTLE algorithm for atom 127!
- Charles Danko (Thu Apr 14 2005 - 10:40:10 CDT)
- Hrant Gharabekyan (Thu Apr 14 2005 - 05:48:08 CDT)
- Michel Espinoza-Fonseca (Wed Apr 13 2005 - 16:20:53 CDT)
- Shahid Qamar (Wed Apr 13 2005 - 14:20:16 CDT)
ERROR: Constraint failure in RATTLE algorithm for atom 1880!
- jinhyo_at_comcast.net (Mon May 18 2009 - 11:19:04 CDT)
ERROR: Constraint failure in RATTLE algorithm for atom 598!
- Raul Araya Secchi (Wed Nov 02 2005 - 08:17:29 CST)
ERROR: Constraint failure in RATTLE algorithm for atom 872
- ydhuang2727 (Thu Nov 20 2008 - 19:49:08 CST)
ERROR: Constraint failure in RATTLE algorithm for atom 9080!
- gurunath katagi (Fri Aug 28 2009 - 00:16:01 CDT)
ERROR: CUDA-enabled NAMD requires at least one patch per process
- Arash Azari (Wed Apr 27 2011 - 23:49:56 CDT)
error: DID NOT FIND NIMPHI AFTER ATOM LIST IN PSF
- Karol Kaszuba (Wed Jul 04 2007 - 14:10:12 CDT)
ERROR: DIDN'T FIND "NATOM" IN PSF FILE
- jose correa (Thu Oct 16 2008 - 07:19:50 CDT)
- Diego Alejandro Vargas (Wed Oct 15 2008 - 23:12:01 CDT)
error: expected floating-point number but got
- Axel Kohlmeyer (Thu Aug 04 2011 - 10:29:08 CDT)
- Shen, Han (Thu Aug 04 2011 - 10:21:32 CDT)
Error: failed on end of segment with RBCG
- Francesco Pietra (Sun Nov 15 2009 - 03:18:57 CST)
Error: keyword "group1" is not supported, or not recognized in this context.
- Giacomo Fiorin (Fri Apr 15 2011 - 11:02:03 CDT)
- Shen, Han (Fri Apr 15 2011 - 09:14:11 CDT)
ERROR: Margin is too small (BUG?)
- nordgren_at_sas.upenn.edu (Thu Aug 04 2005 - 17:52:49 CDT)
- Mauricio Carrillo Tripp (Wed Aug 03 2005 - 10:02:42 CDT)
ERROR: Multiple definitions of 'LangevinPiston'
- Peter Freddolino (Wed May 20 2009 - 09:59:45 CDT)
- roberta.rostagno (Wed May 20 2009 - 09:44:02 CDT)
- Peter Freddolino (Fri May 15 2009 - 05:54:11 CDT)
- Roberta Rostagno (Fri May 15 2009 - 02:19:09 CDT)
- Peter Freddolino (Thu May 14 2009 - 10:19:28 CDT)
- roberta.rostagno (Thu May 14 2009 - 04:02:29 CDT)
- Peter Freddolino (Tue May 12 2009 - 06:41:29 CDT)
- roberta.rostagno (Tue May 12 2009 - 03:02:45 CDT)
- Peter Freddolino (Mon May 11 2009 - 12:11:57 CDT)
- roberta.rostagno (Mon May 11 2009 - 07:15:42 CDT)
- roberta.rostagno (Mon May 11 2009 - 08:20:29 CDT)
- roberta.rostagno (Mon May 11 2009 - 07:38:38 CDT)
- Peter Freddolino (Mon May 11 2009 - 08:09:40 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)
ERROR: Number of pdb and psf atoms are not the same!
- Peter Freddolino (Mon Mar 26 2007 - 14:16:37 CDT)
- Arturas Ziemys (Mon Mar 26 2007 - 14:08:36 CDT)
Error: parameter multiplicity.plz reply.
- hl332_at_drexel.edu (Sat Feb 03 2007 - 12:36:45 CST)
ERROR: Stray PME grid charges detected
- roberta.rostagno (Mon May 25 2009 - 04:34:11 CDT)
Error: This application has requested the Runtime to terminate it in an unusual way: Please contact the application's support team for more information" after specifying the namd2.exe path
- Richard Owczarzy (Fri Mar 19 2010 - 17:13:53 CDT)
- Mary Newcomb (Fri Mar 19 2010 - 16:17:27 CDT)
Error: transport retry exceeded error
- Axel Kohlmeyer (Sat May 17 2008 - 15:37:12 CDT)
- Alexandre A. Vakhrouchev (Sat May 17 2008 - 00:03:03 CDT)
- Axel Kohlmeyer (Fri May 16 2008 - 10:49:46 CDT)
- Alexandre A. Vakhrouchev (Thu May 15 2008 - 13:41:21 CDT)
error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C
- Baoqiang Cao (Sat Apr 09 2005 - 22:46:44 CDT)
- Michel Espinoza-Fonseca (Sat Apr 09 2005 - 20:31:18 CDT)
- Baoqiang Cao (Sat Apr 09 2005 - 21:26:03 CDT)
- Michel Espinoza-Fonseca (Sat Apr 09 2005 - 15:41:45 CDT)
- Baoqiang Cao (Sat Apr 09 2005 - 14:40:37 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)
Errors compiling NAMD 2.5
- Gengbin Zheng (Mon Apr 04 2005 - 03:13:33 CDT)
- Koo Kee Kiat (Mon Apr 04 2005 - 01:46:34 CDT)
Errors during equilibration: segmentation fault and bad global exclusion count
- Ambrish (Tue Oct 23 2007 - 01:45:05 CDT)
errors in energy minimization
- Peter Freddolino (Tue Apr 24 2007 - 09:49:59 CDT)
- Wei Liu (Tue Apr 24 2007 - 05:27:52 CDT)
Errors on Missing Atoms for Some Bonds
- Taekyung Kwon (Sun Nov 30 2008 - 22:19:29 CST)
Errors: Periodic cell became too small for original patch grid & Setting parameter binaryoutput from script failed!
- Nitin Bhardwaj (Sun Nov 13 2005 - 12:26:35 CST)
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)
eucb - beta testers wanted for trajectory analysis program
- Athanassios Stavrakoudis (Thu Feb 05 2009 - 18:18:08 CST)
Euro QSAR 2004
- Ahmet Bakan (Sun Sep 05 2004 - 15:42:27 CDT)
Evaluated heat capacities via NAMD are larger than experimental values
- Jun Zhang (Wed Oct 26 2011 - 19:00:18 CDT)
- Mert Gür (Wed Oct 26 2011 - 13:44:35 CDT)
evaluating energy in a trajectory of variable box size?
- Jose Borreguero (Tue Apr 27 2010 - 14:04:11 CDT)
Evaluating kinetic energy from a modified DCD file
- Mert Gür (Sun Apr 12 2009 - 08:11:21 CDT)
- JT (Sat Apr 11 2009 - 03:47:57 CDT)
- Tibbitt, Jeffrey A. (Fri Apr 10 2009 - 15:03:24 CDT)
- Mert Gür (Fri Apr 10 2009 - 12:52:08 CDT)
- JT (Fri Apr 10 2009 - 11:36:52 CDT)
- JT (Wed Apr 08 2009 - 22:04:20 CDT)
- JT (Wed Apr 08 2009 - 19:59:48 CDT)
- Peter Freddolino (Wed Apr 08 2009 - 19:17:16 CDT)
- Mert Gür (Wed Apr 08 2009 - 16:57:01 CDT)
- Peter Freddolino (Wed Apr 08 2009 - 15:15:00 CDT)
- Mert Gür (Wed Apr 08 2009 - 14:33:05 CDT)
Ewald contribution to pressure profile only working on single core
- Bjoern Olausson (Tue Feb 07 2012 - 06:59:43 CST)
ewald method
- David Hardy (Fri Mar 25 2011 - 10:27:11 CDT)
- Hasan haska (Fri Mar 25 2011 - 09:49:57 CDT)
- Hasan haska (Fri Mar 25 2011 - 09:45:45 CDT)
ewald self energy
- Chen, Zhihong (chenz2) (Thu Sep 16 2010 - 15:12:07 CDT)
example psf and pdb files for simulations with tip4p
- Peter Freddolino (Wed Mar 02 2011 - 13:28:48 CST)
- Ana Celia Vila Verde (Wed Mar 02 2011 - 12:21:44 CST)
example scripts
- Himanshu Khandelia (Thu Mar 10 2005 - 10:03:53 CST)
exclude 1-2
- Peter Freddolino (Fri May 15 2009 - 06:55:37 CDT)
- doty alexiou (Fri May 15 2009 - 01:55:09 CDT)
exclude 1-2 or 1-4?
- doty alexiou (Tue May 12 2009 - 09:56:31 CDT)
- Peter Freddolino (Tue May 12 2009 - 10:07:42 CDT)
Excluding interactions?
- Jérôme Hénin (Thu Jan 21 2010 - 08:17:26 CST)
- Charles Zhao (Wed Jan 20 2010 - 13:44:47 CST)
- Jérôme Hénin (Sat Jan 16 2010 - 12:37:26 CST)
- Charles Zhao (Fri Jan 15 2010 - 21:12:23 CST)
- Jérôme Hénin (Fri Jan 15 2010 - 06:53:51 CST)
- Charles Zhao (Thu Jan 14 2010 - 19:46:57 CST)
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)
Exclusions and CUDA
- Axel Kohlmeyer (Thu Jun 04 2009 - 09:03:24 CDT)
- Benjamin Bouvier (Thu Jun 04 2009 - 03:40:22 CDT)
Exiting prematurely
- BIN ZHANG (Fri Apr 03 2009 - 11:10:04 CDT)
- Giacomo Fiorin (Fri Apr 03 2009 - 10:21:40 CDT)
- BIN ZHANG (Fri Apr 03 2009 - 02:22:28 CDT)
Expansion of DCD
- tamal_at_iitk.ac.in (Mon Nov 20 2006 - 23:20:04 CST)
expansion of solvation box at high temperature
- mjyang (Mon Oct 18 2010 - 22:31:13 CDT)
- Jim Phillips (Mon Oct 18 2010 - 11:32:18 CDT)
- Joshua Adelman (Sun Oct 17 2010 - 12:25:19 CDT)
- Jeffrey Potoff (Sun Oct 17 2010 - 11:44:53 CDT)
- mjyang (Sun Oct 17 2010 - 10:56:15 CDT)
- Nicholas Musolino (Sun Oct 17 2010 - 10:27:40 CDT)
- mjyang (Sun Oct 17 2010 - 10:18:26 CDT)
- Nicholas Musolino (Sun Oct 17 2010 - 08:29:06 CDT)
- mjyang (Sun Oct 17 2010 - 04:41:25 CDT)
- mjyang (Sun Oct 17 2010 - 02:03:31 CDT)
expect NAMD survey emails this week
- Jim Phillips (Tue Jul 19 2011 - 11:51:22 CDT)
experimental phi-values as restraints
- regafan_at_usc.es (Wed Jan 10 2007 - 10:08:42 CST)
explicit hydrogen bonds
- Sterling Paramore (Thu May 11 2006 - 10:41:56 CDT)
- Matthew Wilce (Thu May 11 2006 - 00:54:20 CDT)
Explicit Membrane Protein Simulations in NAMD/VMD
- Richard Law (Thu Aug 28 2008 - 15:40:10 CDT)
- Shultz, Jack (Thu Aug 28 2008 - 15:07:24 CDT)
- Jerome Henin (Thu Aug 28 2008 - 14:57:07 CDT)
- Shultz, Jack (Thu Aug 28 2008 - 12:25:23 CDT)
Explicit Solvent Sytem (40% Ethanol + 60% Water)
- Babban Mia (Wed Aug 10 2011 - 04:49:20 CDT)
- Branko (Tue Aug 09 2011 - 13:29:52 CDT)
- Ismail, Mohd F. (Tue Aug 09 2011 - 13:02:19 CDT)
- Babban Mia (Tue Aug 09 2011 - 09:42:26 CDT)
- Babban Mia (Tue Aug 09 2011 - 01:20:20 CDT)
Explicit Water System Condensing
- Jeffrey J. Potoff (Thu Feb 25 2010 - 10:13:43 CST)
- Keith Battle (Thu Feb 25 2010 - 09:17:53 CST)
Extended System Conservation
- David Hardy (Wed Jul 18 2007 - 15:36:37 CDT)
- Peter Freddolino (Wed Jul 18 2007 - 14:23:07 CDT)
- jadelman_at_berkeley.edu (Wed Jul 18 2007 - 13:02:31 CDT)
extended system or Basis Vector
- JC Gumbart (Tue Jun 20 2006 - 01:05:54 CDT)
- Ching Wong (Mon Jun 19 2006 - 20:29:01 CDT)
extending namd / shared library build (UNCLASSIFIED)
- Ajasja LjubetiÄ (Tue Nov 09 2010 - 08:39:47 CST)
- Jim Phillips (Mon Nov 01 2010 - 15:05:07 CDT)
- Sellers, Michael S. (Cont, ARL/WMRD) (Fri Oct 29 2010 - 08:23:41 CDT)
external force
- JC Gumbart (Fri Nov 03 2006 - 02:08:09 CST)
- Gianluca Interlandi (Thu Nov 02 2006 - 13:55:24 CST)
- Al-Rawi, Ahlam (Thu Nov 02 2006 - 12:16:23 CST)
- Al-Rawi, Ahlam (Tue Oct 24 2006 - 17:30:43 CDT)
- Al-Rawi, Ahlam (Tue Oct 24 2006 - 14:39:42 CDT)
external forces
- Jim Phillips (Wed Apr 13 2011 - 09:47:03 CDT)
- johan strumpfer (Mon Apr 04 2011 - 11:07:02 CDT)
- Matteo Rotter (Mon Apr 04 2011 - 08:13:24 CDT)
Extra bonds-ABF
- Giacomo Fiorin (Mon Nov 07 2011 - 11:01:22 CST)
- Parisa Akhski (Mon Nov 07 2011 - 10:53:18 CST)
extra lines in PSF !!!
- Dan Strahs (Fri Feb 10 2006 - 13:32:07 CST)
- Georgios Papadopoulos (Fri Feb 10 2006 - 11:47:10 CST)
extra points in NAMD
- Mgr. Lubos Vrbka (Sat Dec 17 2005 - 06:51:46 CST)
Extra terms in the expression for potential energy
- Grzegorz Jezierski (Tue Aug 23 2005 - 12:04:35 CDT)
Extract trajectory from replica exchange simulation
- Shi, Chuanyin (Mon Jul 19 2010 - 09:19:21 CDT)
extracting coordinates from dcd file
- M. Madhu (Mon Jul 30 2007 - 23:31:27 CDT)
- JC Gumbart (Mon Jul 30 2007 - 17:09:17 CDT)
- M. Madhu (Mon Jul 30 2007 - 13:50:00 CDT)
extracting forces from dcd files
- Peter Freddolino (Wed Jun 20 2007 - 13:44:46 CDT)
- Todd Trimble (Wed Jun 20 2007 - 12:31:49 CDT)
extracting info from output files
- Zumot, Elia Nabil (Tue Sep 22 2009 - 16:22:40 CDT)
- Rajiv Abhyankar (Tue Sep 22 2009 - 17:56:19 CDT)
- Giacomo Fiorin (Tue Sep 22 2009 - 15:12:05 CDT)
- Axel Kohlmeyer (Tue Sep 22 2009 - 14:03:12 CDT)
- Rajiv Abhyankar (Tue Sep 22 2009 - 13:26:08 CDT)
extracting interaction energies
- Peter Freddolino (Mon Oct 01 2007 - 15:38:57 CDT)
- Narender Singh Maan (Mon Oct 01 2007 - 15:20:36 CDT)
extracting time from DCDs
- Brian Bennion (Fri Jan 14 2005 - 14:10:02 CST)
- nordgren_at_sas.upenn.edu (Thu Jan 13 2005 - 19:54:30 CST)
extracting waters from DCD
- yi wang (Wed Aug 09 2006 - 10:38:00 CDT)
- Jerome Henin (Wed Aug 09 2006 - 10:26:26 CDT)
- Joshua A. Speidel (Wed Aug 09 2006 - 09:42:34 CDT)
- Marc Baaden (Wed Aug 09 2006 - 08:36:03 CDT)
- Nicholas M Glykos (Wed Aug 09 2006 - 06:54:44 CDT)
- Neelanjana Sengupta (Tue Aug 08 2006 - 17:24:42 CDT)
- Neelanjana Sengupta (Tue Aug 08 2006 - 17:08:50 CDT)
- Neelanjana Sengupta (Tue Aug 08 2006 - 15:57:56 CDT)
- Jerome Henin (Tue Aug 08 2006 - 15:55:01 CDT)
- Narender Singh Maan (Tue Aug 08 2006 - 14:04:04 CDT)
Extraction of force data
- JC Gumbart (Fri Mar 23 2007 - 23:36:03 CDT)
- Viral D. Tejani (Fri Mar 23 2007 - 13:00:51 CDT)
- Marcos Sotomayor (Thu Mar 22 2007 - 22:30:35 CDT)
- JC Gumbart (Thu Mar 22 2007 - 22:29:20 CDT)
- Viral D. Tejani (Thu Mar 22 2007 - 22:12:02 CDT)
Factorization in PMEGridSize
- JC Gumbart (Wed Jun 07 2006 - 09:25:24 CDT)
- Edelmiro Moman (Wed Jun 07 2006 - 04:36:54 CDT)
fad topology and parameter file
- Dhiraj Srivastava (Thu Aug 03 2006 - 02:11:45 CDT)
FAD topology and parameters of FAD
- jose correa (Wed Sep 16 2009 - 11:21:58 CDT)
FAD-parameters
- jose correa (Thu Sep 10 2009 - 13:50:33 CDT)
fail to run replica exchange on more than one node
- Linchen Gong (Wed Feb 18 2009 - 01:31:24 CST)
Fail to Run VMD
- Axel Kohlmeyer (Tue May 31 2011 - 13:57:24 CDT)
- Àî¼Ñ¼ü (Tue May 31 2011 - 13:53:07 CDT)
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)
failure in RATTLE
- Sangamesh B (Thu Dec 18 2008 - 03:51:54 CST)
- Axel Kohlmeyer (Wed Dec 17 2008 - 09:52:13 CST)
- Sangamesh B (Wed Dec 17 2008 - 03:02:38 CST)
- Axel Kohlmeyer (Tue Dec 16 2008 - 13:26:09 CST)
- Sangamesh B (Tue Dec 16 2008 - 08:20:24 CST)
failure in RATTLE algorithm using the adaptive biasing force method
- Jerome Henin (Wed Nov 12 2008 - 08:43:56 CST)
- steve.kaminski_at_mail.tu-berlin.de (Wed Nov 12 2008 - 03:37:11 CST)
- Giacomo Fiorin (Tue Nov 11 2008 - 14:52:19 CST)
- Jerome Henin (Tue Nov 11 2008 - 14:19:01 CST)
- steve.kaminski_at_mail.tu-berlin.de (Tue Nov 11 2008 - 13:43:51 CST)
Failure to run namd-cuda with gtx-470
- Francesco Pietra (Thu Jul 07 2011 - 01:57:25 CDT)
- Francesco Pietra (Wed Jul 06 2011 - 16:18:53 CDT)
- Francesco Pietra (Wed Jul 06 2011 - 10:44:38 CDT)
Faltal Error. reassignFreq fails
- Marc Q. Ma (Mon Apr 24 2006 - 10:53:46 CDT)
- Margaret Shun Cheung (Mon Apr 24 2006 - 10:24:48 CDT)
- Martin Loewer (Mon Apr 24 2006 - 09:18:02 CDT)
- Marcos Sotomayor (Fri Apr 21 2006 - 09:17:00 CDT)
- Martin Loewer (Fri Apr 21 2006 - 05:50:28 CDT)
Famous repl1ca w4tches r0lex Cartier Bvlgari
- Goldie Huffman (Sat Aug 11 2007 - 01:24:31 CDT)
FAO developers: vdW energies, forces and derivatives
- Jim Phillips (Mon Jan 29 2007 - 16:55:40 CST)
- Floris Buelens (Mon Jan 29 2007 - 05:23:43 CST)
farnesyl&retinal
- Magda W (Thu Mar 16 2006 - 02:44:08 CST)
Fast routines for distance evaluations using PBC.
- Arturas Ziemys (Fri May 11 2007 - 11:52:49 CDT)
Fat node
- jonathan_at_ibt.unam.mx (Fri Sep 22 2006 - 21:47:32 CDT)
- Jim Phillips (Tue Aug 29 2006 - 14:19:47 CDT)
- jonathan_at_ibt.unam.mx (Mon Aug 28 2006 - 21:02:13 CDT)
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 by charmc - Compiling NAMD_2.7b2_Source
- philipp.coloc_at_gmx.de (Wed Feb 10 2010 - 04:59:30 CST)
Fatal Error Help
- Narender Singh Maan (Thu Jul 09 2009 - 10:47:11 CDT)
- Chris Harrison (Thu Jul 09 2009 - 09:49:25 CDT)
- Goutham (Mon Jul 06 2009 - 16:10:18 CDT)
Fatal error in configuration file
- Chris Harrison (Thu Feb 05 2009 - 23:51:39 CST)
- BIN ZHANG (Thu Feb 05 2009 - 22:28:26 CST)
- Chris Harrison (Thu Feb 05 2009 - 20:27:23 CST)
- BIN ZHANG (Wed Feb 04 2009 - 22:12:55 CST)
- Corey Fugate (Wed Feb 04 2009 - 21:05:36 CST)
Fatal error on PE 0> FATAL ERROR: DIHEDRALS INDEX 150255520
- Brian Bennion (Fri Aug 19 2005 - 16:47:19 CDT)
Fatal Error Periodic cell has become too small for original patch grid
- bharat gupta (Fri Jul 01 2011 - 00:59:56 CDT)
fatal error running namd
- Brian Bennion (Mon Nov 15 2004 - 10:52:34 CST)
- Enrico Piccinini (Mon Nov 15 2004 - 04:30:06 CST)
FATAL error when run Replica Exchange Method on Franklin
- Guoxiong Su (Thu May 12 2011 - 14:03:58 CDT)
Fatal error when running ABF simulation
- Giacomo Fiorin (Tue Jun 08 2010 - 08:45:10 CDT)
- crazylyf (Tue Jun 08 2010 - 01:00:01 CDT)
Fatal error:
- Jim Phillips (Fri Aug 05 2005 - 11:17:30 CDT)
- vivek sharma (Thu Aug 04 2005 - 09:04:30 CDT)
- JC Gumbart (Thu Aug 04 2005 - 08:50:01 CDT)
- vivek sharma (Thu Aug 04 2005 - 07:58:30 CDT)
FATAL ERROR: ABNORMAL EOF FOUND - buffer=*0 0 0*
- FengXian Zheng (Fri Aug 21 2009 - 10:14:38 CDT)
FATAL ERROR: ABNORMAL EOF FOUND-buffer
- Jignesh Patel (Thu Apr 15 2010 - 15:11:55 CDT)
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: Asymmetric water molecule found??? This can't be right.
- Jorgen Simonsen (Wed Jul 07 2010 - 17:34:44 CDT)
FATAL ERROR: Asymmetric water molecule??
- Richard Law (Thu Jul 21 2005 - 20:21:40 CDT)
FATAL ERROR: Bad global angle count!
- johan strumpfer (Sun Apr 24 2011 - 16:16:52 CDT)
- PAUL NEWMAN (Sat Apr 23 2011 - 22:04:37 CDT)
- PAUL NEWMAN (Fri Apr 22 2011 - 19:42:02 CDT)
FATAL ERROR: Bad global exclusion count
- Peter Freddolino (Tue Jun 12 2007 - 20:48:31 CDT)
- Huy N. Ha (Tue Jun 12 2007 - 19:24:27 CDT)
- Idit Buch (Tue Jun 12 2007 - 09:04:17 CDT)
FATAL ERROR: Bad global exclusion count!
- Axel Kohlmeyer (Mon Jun 01 2009 - 13:05:24 CDT)
- KIRTANA S (Mon Jun 01 2009 - 12:37:38 CDT)
FATAL ERROR: Bad global improper count!
- andrea carotti (Mon Jul 23 2007 - 03:47:16 CDT)
FATAL ERROR: called "save_callback" with too many arguments when running replica exchange
- Ana Vila Verde (Wed Sep 19 2007 - 11:23:50 CDT)
FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR CC NH1 CT1 C NH1 CT1 C NH1
- Gurunath Katagi (Sat Nov 06 2010 - 02:41:31 CDT)
FATAL ERROR: chdir() failed!
- LAM NGUYEN (Sat Sep 06 2008 - 14:56:57 CDT)
FATAL ERROR: child atom 39 bonded only to child H atoms
- Boyang Wang (Wed Jul 13 2005 - 11:06:19 CDT)
FATAL ERROR: Couldn't open DCD file equil0.dcd: No such file or directory
- henri mone (Sun Sep 05 2010 - 10:16:27 CDT)
FATAL ERROR: Couldn't open DCD file ubq_wb_eq.dcd: No such file or directory
- Bernardo Sosa Padilla Araujo (Tue Sep 15 2009 - 18:26:25 CDT)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CAI
- Per Jr. Greisen (Tue May 30 2006 - 04:08:56 CDT)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HN
- Andrea Diaz (Sun Feb 03 2008 - 16:29:59 CST)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HT1
- ramya narasimhan (Tue Nov 11 2008 - 22:18:25 CST)
- Giacomo Fiorin (Tue Nov 11 2008 - 08:58:10 CST)
- ramya narasimhan (Tue Nov 11 2008 - 03:23:43 CST)
FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs.
- Jérôme Hénin (Sat Sep 11 2010 - 04:02:52 CDT)
- dhacademic (Fri Sep 10 2010 - 14:11:23 CDT)
- Jérôme Hénin (Thu Sep 09 2010 - 11:06:33 CDT)
- dhacademic (Wed Sep 08 2010 - 17:07:09 CDT)
- dhacademic (Wed Sep 08 2010 - 16:46:37 CDT)
- Giacomo Fiorin (Wed Sep 08 2010 - 16:28:50 CDT)
- dhacademic (Tue Sep 07 2010 - 15:31:07 CDT)
- Giacomo Fiorin (Tue Sep 07 2010 - 11:23:35 CDT)
- dhacademic (Mon Sep 06 2010 - 17:26:29 CDT)
- Giacomo Fiorin (Mon Sep 06 2010 - 14:10:06 CDT)
- dhacademic (Mon Sep 06 2010 - 10:29:38 CDT)
- Jérôme Hénin (Mon Sep 06 2010 - 10:14:25 CDT)
- dhacademic (Mon Sep 06 2010 - 03:29:31 CDT)
- Jérôme Hénin (Sat Sep 04 2010 - 02:50:54 CDT)
- dhacademic (Fri Sep 03 2010 - 23:26:49 CDT)
- dhacademic (Fri Sep 03 2010 - 12:30:57 CDT)
- Jérôme Hénin (Tue Aug 31 2010 - 10:22:06 CDT)
- dhacademic (Tue Aug 31 2010 - 08:25:35 CDT)
FATAL ERROR: Duplicate bond
- Chris Harrison (Wed Mar 11 2009 - 17:48:13 CDT)
- JC Gumbart (Wed Mar 11 2009 - 17:17:36 CDT)
- ç’€ æŽ (Wed Mar 11 2009 - 02:45:17 CDT)
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
- Joachim Hein (Fri May 29 2009 - 11:07:56 CDT)
- Joachim Hein (Fri May 29 2009 - 11:40:41 CDT)
- Axel Kohlmeyer (Fri May 29 2009 - 10:59:30 CDT)
- Yogesh Aher (Fri May 29 2009 - 09:34:13 CDT)
FATAL ERROR: FixedAtoms may not be enabled in a script
- Dolan, Michael (NIH/NIAID) [C] (Fri Mar 06 2009 - 11:32:52 CST)
FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small.
- Chris Harrison (Mon Aug 29 2011 - 20:07:33 CDT)
- Chris Harrison (Mon Aug 29 2011 - 19:35:42 CDT)
- Massimiliano Porrini (Mon Aug 29 2011 - 14:26:06 CDT)
- Chris Harrison (Mon Aug 29 2011 - 11:50:00 CDT)
- Massimiliano Porrini (Mon Aug 29 2011 - 09:36:55 CDT)
FATAL ERROR: pairlist i_upper mismatch!
- xiaojing gong (Mon Jul 17 2006 - 21:43:46 CDT)
FATAL ERROR: Patch needed for tuple is missing
- rebeca_at_mmb.pcb.ub.es (Wed Aug 13 2008 - 17:31:27 CDT)
FATAL ERROR: Patch needed for tuple is missing.
- Armen Poghosyan (Thu May 06 2004 - 07:21:57 CDT)
FATAL ERROR: Periodic cell
- Jianhui Tian (Fri Feb 01 2008 - 08:44:54 CST)
- Jorgen Simonsen (Fri Feb 01 2008 - 04:50:34 CST)
FATAL ERROR: Periodic cell has become too small for original patch grid!
- Jerome Henin (Wed Apr 22 2009 - 10:11:15 CDT)
- Peter Freddolino (Wed Apr 22 2009 - 09:27:37 CDT)
- DimitryASuplatov (Wed Apr 22 2009 - 01:44:45 CDT)
- Jeffrey J. Potoff (Wed Mar 26 2008 - 18:27:05 CDT)
- Seth Lilavivat (Wed Mar 26 2008 - 15:36:48 CDT)
- Peter Freddolino (Wed Jan 30 2008 - 15:57:53 CST)
- Joshua Adelman (Wed Jan 30 2008 - 15:50:10 CST)
- Joshua Adelman (Wed Jan 30 2008 - 11:47:16 CST)
- Peter Freddolino (Wed Jan 30 2008 - 11:55:21 CST)
- Peter Freddolino (Wed Jan 30 2008 - 10:52:48 CST)
- Joshua Adelman (Wed Jan 30 2008 - 10:42:06 CST)
FATAL ERROR: Setting parameter constraints from script failed!
- Do Nhu Trang (Fri Jan 09 2009 - 10:17:02 CST)
- Axel Kohlmeyer (Fri Jan 09 2009 - 08:54:26 CST)
- Do Nhu Trang (Fri Jan 09 2009 - 08:31:02 CST)
- Joshua Adelman (Thu Jan 08 2009 - 11:14:24 CST)
- Axel Kohlmeyer (Thu Jan 08 2009 - 10:58:05 CST)
- Do Nhu Trang (Thu Jan 08 2009 - 09:57:28 CST)
FATAL ERROR: Setting parameter fixedAtomsFile from script failed!
- Rajan Vatassery (Fri Jul 15 2011 - 16:43:04 CDT)
- Jorgen Simonsen (Fri Jul 15 2011 - 15:55:26 CDT)
FATAL ERROR: Sorry, combined TI and FEP is not implemented
- Axel Kohlmeyer (Thu Jul 09 2009 - 06:38:57 CDT)
- Vlad Cojocaru (Thu Jul 09 2009 - 03:22:44 CDT)
- Chris Harrison (Wed Jul 08 2009 - 09:58:51 CDT)
- Vlad Cojocaru (Wed Jul 08 2009 - 05:41:00 CDT)
FATAL ERROR: Stale NFS file handle
- Chris Samuel (Wed Apr 06 2005 - 22:29:59 CDT)
- Edward Patrick Obrien (Fri Feb 18 2005 - 15:51:53 CST)
fatal error: tried to assign bond index before all parameter files were read
- Jorgen Simonsen (Wed May 06 2009 - 05:36:16 CDT)
FATAL ERROR: Tried to find atom type on node other than node 0
- Chris Harrison (Mon Aug 17 2009 - 09:44:35 CDT)
- Narender Singh Maan (Mon Aug 17 2009 - 08:43:41 CDT)
- Yoav Beck (Mon Aug 17 2009 - 05:04:48 CDT)
- yzliu (Sat Aug 15 2009 - 11:06:10 CDT)
- Yoav Beck (Thu Aug 13 2009 - 09:21:38 CDT)
- Jeffrey J. Potoff (Wed Jul 11 2007 - 11:28:31 CDT)
- Ivan Ufimtsev (Sat Dec 24 2005 - 17:26:26 CST)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7
- Joshua D. Moore (Wed Dec 21 2005 - 16:57:37 CST)
- Shirley Li (Wed Dec 21 2005 - 14:56:36 CST)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100)
- johan strumpfer (Sun Oct 23 2011 - 16:42:07 CDT)
- Jernej Zidar (Sun Oct 23 2011 - 19:45:56 CDT)
- Jens K. Munk (Sun Oct 23 2011 - 14:39:24 CDT)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
- johan strumpfer (Thu Apr 07 2011 - 09:23:02 CDT)
- Gary M. Skinner (Thu Apr 07 2011 - 07:17:14 CDT)
- gurunath katagi (Tue Nov 10 2009 - 12:08:13 CST)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3
- Chris Harrison (Sun Jun 21 2009 - 19:11:54 CDT)
- Chris Harrison (Sat Jun 20 2009 - 13:35:08 CDT)
- gurunath katagi (Sun Jun 21 2009 - 16:35:42 CDT)
- Axel Kohlmeyer (Sun Jun 21 2009 - 12:54:51 CDT)
- gurunath katagi (Sat Jun 20 2009 - 12:59:51 CDT)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1)
- Ajasja LjubetiÄ (Fri Jun 24 2011 - 03:46:18 CDT)
- JC Gumbart (Thu Jun 23 2011 - 16:17:59 CDT)
- Jorgen Simonsen (Thu Jun 23 2011 - 08:51:52 CDT)
FATAL ERROR: Unable to open binary file
- sibel.cakan (Thu Jul 14 2011 - 05:34:57 CDT)
FATAL ERROR: Unable to open extended system file.
- Jianhui Tian (Mon Jul 30 2007 - 08:58:58 CDT)
- Arun Krishnan (Mon Jul 30 2007 - 02:27:49 CDT)
FATAL ERROR: unknown floating-point error, errno = 4
- Chris Chipot (Mon Dec 26 2005 - 10:52:40 CST)
- Manori Indira Jayasinghe (Fri Dec 23 2005 - 11:47:10 CST)
- Chris Chipot (Fri Dec 23 2005 - 01:22:32 CST)
- Manori Indira Jayasinghe (Thu Dec 22 2005 - 23:16:41 CST)
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
- JC Gumbart (Thu Jan 11 2007 - 20:13:41 CST)
- Alexander Vaughn (Thu Jan 11 2007 - 19:37:34 CST)
FATAL ERROR:BAD GLOBAL EXCLUSION COUNT:Please help
- Werner Crous (Thu Mar 18 2010 - 04:29:55 CDT)
- Werner Crous (Thu Mar 18 2010 - 04:23:55 CDT)
- Chris Harrison (Wed Mar 17 2010 - 00:13:12 CDT)
- Werner Crous (Sat Mar 13 2010 - 10:22:47 CST)
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)
faulty kernel?
- Leandro Martínez (Fri Jun 01 2007 - 12:21:24 CDT)
- Brian Bennion (Fri Jun 01 2007 - 10:59:39 CDT)
Fe-S cluster topology parameters
- Chang, Christopher (Wed Aug 27 2008 - 11:51:45 CDT)
- jose correa (Wed Aug 27 2008 - 09:20:58 CDT)
Fe2+ parameters?
- Georgios Papadopoulos (Sun Jun 05 2005 - 04:52:09 CDT)
Feature request for the colvars module -- TCL syntax
- Ajasja LjubetiÄ (Mon Jan 24 2011 - 08:16:01 CST)
- Ajasja LjubetiÄ (Tue Jan 18 2011 - 11:44:54 CST)
- Axel Kohlmeyer (Tue Jan 18 2011 - 09:09:54 CST)
- Ajasja LjubetiÄ (Tue Jan 18 2011 - 07:17:54 CST)
- Chris Harrison (Mon Jan 17 2011 - 11:00:22 CST)
- Jérôme Hénin (Mon Jan 17 2011 - 11:52:23 CST)
- Ajasja LjubetiÄ (Mon Jan 17 2011 - 09:26:47 CST)
Fedora Core 4 problems (?) ...
- Nicholas M Glykos (Sat Oct 01 2005 - 08:08:55 CDT)
Fedora Core 4 problems [2] ...
- Nicholas M Glykos (Sat Oct 01 2005 - 08:42:21 CDT)
Feedback on "alchemify" tool
- Jérôme Hénin (Thu Apr 08 2004 - 10:52:31 CDT)
fep
- Floris Buelens (Wed Jul 27 2005 - 04:41:06 CDT)
- Wei Chen (Tue Jul 26 2005 - 17:05:39 CDT)
- Chris Chipot (Sat Jul 16 2005 - 04:48:02 CDT)
- Wei Chen (Thu May 12 2005 - 11:19:48 CDT)
- Philip Fowler (Thu May 12 2005 - 04:37:31 CDT)
- Chris Chipot (Wed May 11 2005 - 17:34:47 CDT)
- Wei Chen (Wed May 11 2005 - 13:49:53 CDT)
- Jérôme Hénin (Tue Feb 01 2005 - 13:14:05 CST)
- Wei Chen (Tue Feb 01 2005 - 11:15:24 CST)
FEP & different ligands
- Jerome Henin (Mon Dec 11 2006 - 11:29:59 CST)
- satya work (Mon Dec 11 2006 - 01:20:06 CST)
FEP + MCTI in one MD simulation
- List (Thu Mar 13 2008 - 16:25:36 CDT)
FEP - one long simulation vs many short ones
- Floris Buelens (Mon Jul 04 2005 - 07:22:55 CDT)
- Jérôme Hénin (Sat Jul 02 2005 - 18:45:11 CDT)
- Mauricio Carrillo Tripp (Fri Jul 01 2005 - 18:27:24 CDT)
- Wei Chen (Sat Jul 02 2005 - 12:13:51 CDT)
- Floris Buelens (Fri Jul 01 2005 - 07:07:14 CDT)
FEP - Protein binding to Membrane surface
- Bjoern Olausson (Thu Feb 10 2011 - 03:50:37 CST)
FEP alchemical
- Amir Shamloo (Fri Jul 15 2005 - 19:51:23 CDT)
FEP and GPU
- TJ Mustard (Mon Nov 08 2010 - 15:06:51 CST)
FEP and restraints
- Jérôme Hénin (Tue Mar 23 2004 - 14:42:12 CST)
- Michael Grabe (Tue Mar 23 2004 - 13:45:32 CST)
FEP and solvent
- Surjit Dixit (Thu Jun 16 2005 - 09:06:17 CDT)
- Matthew Wilce (Sun Jun 12 2005 - 22:35:32 CDT)
FEP and TI
- Matthew Wilce (Sun Jun 12 2005 - 22:42:05 CDT)
FEP anomaly?
- Jerome Henin (Tue Feb 24 2009 - 09:37:14 CST)
- Floris Buelens (Wed Feb 25 2009 - 09:13:22 CST)
- Christopher Hartshorn (Mon Feb 23 2009 - 12:53:15 CST)
FEP calculation is doing nothing
- Chris Chipot (Tue Aug 10 2010 - 11:06:11 CDT)
- sudipta (Tue Aug 10 2010 - 10:09:29 CDT)
FEP calculation of dimerization
- Christopher Hartshorn (Sun Nov 16 2008 - 23:45:05 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)
FEP charge perturbation
- Floris Buelens (Mon Jun 06 2005 - 17:40:44 CDT)
- Chris Chipot (Fri Jun 03 2005 - 12:08:13 CDT)
- Floris Buelens (Sun May 29 2005 - 17:50:28 CDT)
FEP configuration file
- List (Mon Jan 28 2008 - 10:55:21 CST)
FEP Energy very high: Mutual exclusion of atoms
- Nitin Bhardwaj (Tue Nov 07 2006 - 17:28:58 CST)
FEP error "atoms moving too fast"
- jz7_at_duke.edu (Mon Jun 05 2006 - 12:25:08 CDT)
- Chris Chipot (Sun Jun 04 2006 - 16:01:23 CDT)
- jz7_at_duke.edu (Sun Jun 04 2006 - 10:39:37 CDT)
FEP error: Rattle atom constriant
- Shahid Qamar (Thu Jun 09 2005 - 15:59:11 CDT)
fep file
- Deborah Jameson (Mon Jul 25 2005 - 11:10:54 CDT)
FEP for GLY and PRO Mutations
- Jérôme Hénin (Tue Jul 27 2010 - 05:01:36 CDT)
- Michael LeVine (Mon Jul 26 2010 - 10:10:28 CDT)
FEP implementation in NAMD
- Jérôme Hénin (Wed Aug 02 2006 - 21:16:17 CDT)
- nmichaud_at_jhu.edu (Wed Aug 02 2006 - 18:17:53 CDT)
FEP implementation in NAMD - ERRATUM
- Jerome Henin (Thu Aug 03 2006 - 11:01:54 CDT)
FEP implementation in NAMD 2.6 vs. 2.7b1
- Chris Harrison (Wed Jul 29 2009 - 06:11:33 CDT)
- Floris Buelens (Wed Jul 29 2009 - 01:50:40 CDT)
- Dan Bolintineanu (Tue Jul 28 2009 - 16:50:37 CDT)
FEP in vacuum
- Jérôme Hénin (Fri Mar 10 2006 - 11:36:03 CST)
- Raul Araya Secchi (Fri Mar 10 2006 - 08:48:52 CST)
FEP on 2.7b1
- Christopher Hartshorn (Mon May 11 2009 - 15:38:37 CDT)
FEP on charged residue mutation
- Jerome Henin (Tue Nov 25 2008 - 20:26:41 CST)
- Sebastian Stolzenberg (Tue Nov 25 2008 - 19:48:21 CST)
- Sebastian Stolzenberg (Tue Nov 25 2008 - 19:30:08 CST)
- Jerome Henin (Sat Nov 22 2008 - 16:30:52 CST)
- Sebastian Stolzenberg (Sat Nov 22 2008 - 13:48:14 CST)
- Jerome Henin (Sat Nov 22 2008 - 12:27:19 CST)
- Sebastian Stolzenberg (Sat Nov 22 2008 - 12:14:57 CST)
- Jerome Henin (Sat Nov 22 2008 - 11:57:11 CST)
- Sebastian Stolzenberg (Sat Nov 22 2008 - 11:34:10 CST)
- Jerome Henin (Fri Nov 21 2008 - 16:54:40 CST)
- Sebastian Stolzenberg (Fri Nov 21 2008 - 16:22:45 CST)
FEP on NAMD2.6 versus latest CVS NAMD build
- Floris Buelens (Fri Jan 30 2009 - 03:36:00 CST)
- Christopher Hartshorn (Fri Jan 30 2009 - 00:54:54 CST)
FEP output dEavg and dG
- Jerome Henin (Fri Mar 21 2008 - 17:16:18 CDT)
- Payel Das (Fri Mar 21 2008 - 16:26:02 CDT)
FEP output in NAMD
- Jerome Henin (Fri Apr 08 2005 - 13:37:41 CDT)
- Vani Krishna (Tue Apr 05 2005 - 11:26:39 CDT)
Fep performance
- matteo.rotter (Thu Sep 17 2009 - 08:43:00 CDT)
- Floris Buelens (Wed Aug 26 2009 - 01:26:49 CDT)
- matteo.rotter (Mon Aug 24 2009 - 10:51:27 CDT)
FEP question
- luca (Fri Sep 07 2007 - 12:43:24 CDT)
- Jerome Henin (Fri Sep 07 2007 - 10:33:47 CDT)
- luca (Fri Sep 07 2007 - 03:26:24 CDT)
- Jerome Henin (Thu Sep 06 2007 - 14:00:05 CDT)
- Victor Ovchinnikov (Thu Sep 06 2007 - 11:29:23 CDT)
- Jerome Henin (Thu Sep 06 2007 - 09:28:20 CDT)
- Matthew WIlce (Thu Sep 06 2007 - 08:32:09 CDT)
Fep questions about FepEquilSteps
- Chris Chipot (Wed Apr 25 2007 - 16:25:11 CDT)
- alex digenova bravo (Wed Apr 25 2007 - 14:50:43 CDT)
FEP restart?
- Christopher Hartshorn (Thu Mar 12 2009 - 00:35:02 CDT)
- Chris Harrison (Thu Mar 12 2009 - 07:14:23 CDT)
- Chris Harrison (Wed Mar 11 2009 - 19:53:09 CDT)
- Christopher Hartshorn (Wed Mar 11 2009 - 19:34:59 CDT)
FEP setup
- Chris Chipot (Wed Dec 28 2005 - 17:21:28 CST)
- Richard Wood (Tue Dec 27 2005 - 11:43:53 CST)
FEP simulations?
- Chris Chipot (Mon Jan 05 2009 - 05:24:00 CST)
- Christopher Hartshorn (Mon Jan 05 2009 - 03:20:53 CST)
- Jerome Henin (Tue Nov 18 2008 - 15:43:42 CST)
- Christopher Hartshorn (Tue Nov 18 2008 - 13:19:13 CST)
FEP substrate transformation with common moiety
- Jérôme Hénin (Sat Aug 28 2010 - 08:52:46 CDT)
- Chris Harrison (Fri Aug 27 2010 - 21:47:26 CDT)
- Sebastian Stolzenberg (Fri Aug 27 2010 - 20:35:01 CDT)
FEP to replace a PMF calculation?
- Jerome Henin (Sun Sep 27 2009 - 16:27:52 CDT)
- Sebastian Stolzenberg (Fri Sep 18 2009 - 18:26:42 CDT)
FEP triangular bracket average
- Mert Gür (Sat Apr 26 2008 - 15:26:21 CDT)
- Jerome Henin (Sat Apr 26 2008 - 13:54:31 CDT)
- Mert Gür (Sat Apr 26 2008 - 13:14:29 CDT)
- Jerome Henin (Sat Apr 26 2008 - 11:30:37 CDT)
- Mert Gür (Sat Apr 26 2008 - 05:56:26 CDT)
FEP tutorial graph question
- Jerome Henin (Fri May 01 2009 - 14:28:24 CDT)
- Christopher Hartshorn (Fri May 01 2009 - 12:05:21 CDT)
- Chris Harrison (Thu Apr 30 2009 - 10:23:25 CDT)
- Christopher Hartshorn (Wed Apr 29 2009 - 19:52:28 CDT)
- Jerome Henin (Wed Apr 29 2009 - 18:36:35 CDT)
- Chris Harrison (Wed Apr 29 2009 - 16:17:07 CDT)
- Christopher Hartshorn (Wed Apr 29 2009 - 15:35:27 CDT)
FEP VdW and electrostatic decoupling parameters
- Christian Jorgensen (Fri Dec 17 2010 - 10:21:39 CST)
FEP with fixed explicit environment?
- Peter Freddolino (Tue Mar 17 2009 - 14:10:07 CDT)
- Sebastian Stolzenberg (Tue Mar 17 2009 - 13:21:12 CDT)
- Sebastian Stolzenberg (Sun Mar 15 2009 - 12:03:28 CDT)
- Sebastian Stolzenberg (Fri Mar 13 2009 - 16:42:35 CDT)
- Sebastian Stolzenberg (Fri Mar 13 2009 - 10:58:32 CDT)
- Chris Harrison (Thu Mar 12 2009 - 22:05:24 CDT)
- Sebastian Stolzenberg (Thu Mar 12 2009 - 18:51:05 CDT)
- Sebastian Stolzenberg (Thu Mar 12 2009 - 18:50:32 CDT)
FEP with flattened free energy surface?
- Jérôme Hénin (Sat Apr 09 2011 - 01:18:19 CDT)
- Ivan Vyalov (Fri Apr 08 2011 - 15:48:09 CDT)
- Jérôme Hénin (Fri Apr 08 2011 - 15:05:30 CDT)
- Ivan Vyalov (Fri Apr 08 2011 - 14:12:38 CDT)
- Jérôme Hénin (Wed Apr 06 2011 - 11:45:29 CDT)
- Ivan Vyalov (Wed Apr 06 2011 - 04:49:50 CDT)
FEP yields the same results for forward and backward computation!
- Lela Vukovic (Tue May 18 2010 - 13:08:02 CDT)
- Jun Zhang (Thu May 13 2010 - 08:48:42 CDT)
- Felipe Merino (Thu May 13 2010 - 01:24:37 CDT)
- Jun Zhang (Wed May 12 2010 - 22:38:44 CDT)
FEP, IONS, DUMMY atoms, LARGE numbers
- Chris Chipot (Tue Apr 18 2006 - 08:57:03 CDT)
- Raul Araya Secchi (Mon Apr 17 2006 - 12:32:55 CDT)
FEP....
- Wei Chen (Fri Nov 11 2005 - 11:28:20 CST)
- Chris Chipot (Fri Nov 11 2005 - 10:35:19 CST)
- Raul Araya Secchi (Fri Nov 11 2005 - 09:39:41 CST)
FEP/binding free energy difference WT vs Mut
- Luis Cunha (Tue Feb 17 2009 - 11:50:20 CST)
- Jerome Henin (Mon Feb 16 2009 - 11:18:50 CST)
- Chris Chipot (Sun Feb 15 2009 - 20:03:27 CST)
- Jerome Henin (Fri Feb 13 2009 - 18:08:24 CST)
- Chris Harrison (Fri Feb 13 2009 - 17:57:21 CST)
- Luis Cunha (Fri Feb 13 2009 - 16:43:27 CST)
FEP: delta_G, memory of Hamiltonians corresponding to last G value?
- Jerome Henin (Thu Oct 09 2008 - 19:29:03 CDT)
- Sebastian Stolzenberg (Thu Oct 09 2008 - 18:01:13 CDT)
- Jerome Henin (Thu Oct 09 2008 - 17:49:05 CDT)
- Sebastian Stolzenberg (Thu Oct 09 2008 - 14:10:20 CDT)
FEP: FATAL ERROR: Periodic cell has become too small for original patch grid!
- List (Thu Mar 13 2008 - 16:16:04 CDT)
- Jeffrey J. Potoff (Thu Mar 13 2008 - 10:22:18 CDT)
- List (Wed Mar 12 2008 - 13:29:38 CDT)
FEP: How check equilibration sufficiency? calculate dG?
- Jerome Henin (Tue Oct 14 2008 - 16:00:24 CDT)
- L. Michel Espinoza-Fonseca (Tue Oct 14 2008 - 15:11:50 CDT)
- Sebastian Stolzenberg (Tue Oct 14 2008 - 11:44:51 CDT)
- Chris Chipot (Tue Oct 14 2008 - 04:12:43 CDT)
- Floris Buelens (Tue Oct 14 2008 - 02:45:50 CDT)
- Sebastian Stolzenberg (Mon Oct 13 2008 - 23:50:43 CDT)
Fermi NVidia
- Jim Phillips (Thu Oct 07 2010 - 15:36:47 CDT)
- jose correa (Thu Sep 30 2010 - 09:13:47 CDT)
Ferric heme
- Eunice Ramirez (Mon Apr 25 2005 - 11:54:41 CDT)
ffTK in the just released VMD 1.9.1
- JC Gumbart (Mon Feb 06 2012 - 01:15:52 CST)
- JC Gumbart (Sat Feb 04 2012 - 15:04:05 CST)
FFTW and NAMD problems during compiling on BluegeneL
- Axel Kohlmeyer (Wed Sep 29 2010 - 05:52:15 CDT)
- I. Vyalov (Wed Sep 29 2010 - 05:00:55 CDT)
fftw libraries for ppc
- Gurunath Katagi (Wed Oct 19 2011 - 22:04:42 CDT)
FFTW problem
- Jyh-Shyong Ho (Wed Sep 27 2006 - 04:02:57 CDT)
file writing stopped
- francesco oteri (Mon Apr 19 2010 - 10:47:30 CDT)
- Nicholas M Glykos (Wed Apr 14 2010 - 05:01:06 CDT)
- francesco oteri (Wed Apr 14 2010 - 03:34:59 CDT)
files for air
- Jeffrey J. Potoff (Fri May 11 2007 - 07:21:20 CDT)
- SMAHANE CHALABI (Fri May 11 2007 - 04:01:27 CDT)
filling hydrophobic cavity with... methane?
- Axel Kohlmeyer (Thu Dec 18 2008 - 17:44:23 CST)
- Sebastian Stolzenberg (Thu Dec 18 2008 - 16:10:00 CST)
Filtered mail?
- Jérôme Hénin (Tue Jul 12 2011 - 10:19:41 CDT)
- Austin B. Yongye (Tue Jul 12 2011 - 09:04:32 CDT)
Final production run in MD
- Jérôme Hénin (Fri Jul 01 2011 - 02:31:04 CDT)
- bharat gupta (Thu Jun 30 2011 - 18:42:23 CDT)
finding appropriate topology file for polymers
- Axel Kohlmeyer (Sun Nov 07 2010 - 12:29:28 CST)
- masoumeh ozmaeian (Sun Nov 07 2010 - 08:45:23 CST)
finding free energy at a time step using abf
- Jerome Henin (Wed Jun 27 2007 - 13:56:14 CDT)
- rmsmith_at_iastate.edu (Wed Jun 27 2007 - 13:24:47 CDT)
Finding size of water box
- Audrey Salazar (Mon Aug 06 2007 - 11:15:41 CDT)
finding water around protein
- divya nayar (Thu Jun 23 2011 - 00:59:56 CDT)
Finer details of an ABF/colvar simulation
- Hugh Martin (Tue Nov 24 2009 - 10:07:46 CST)
- Jerome Henin (Sun Nov 22 2009 - 13:37:32 CST)
- Hugh Martin (Fri Nov 20 2009 - 09:10:08 CST)
Finished install
- beckloni_at_umdnj.edu (Tue Apr 20 2004 - 00:53:09 CDT)
first aid
- Francesco Pietra (Fri May 11 2007 - 16:14:06 CDT)
- Peter Freddolino (Tue May 08 2007 - 17:06:43 CDT)
- JC Gumbart (Tue May 08 2007 - 17:01:40 CDT)
- Francesco Pietra (Tue May 08 2007 - 16:46:29 CDT)
firstLdbStep and ldbPeriod
- Gianluca Interlandi (Wed Mar 07 2007 - 13:11:37 CST)
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 in NAMD
- snoze pa (Mon Feb 01 2010 - 11:31:42 CST)
firsttimestep question
- Chris Harrison (Mon Oct 06 2008 - 07:32:25 CDT)
- Dong Xu (Mon Oct 06 2008 - 13:00:08 CDT)
- Dong Xu (Mon Oct 06 2008 - 00:00:46 CDT)
firsttimestep: simple question
- Brian Bennion (Fri Oct 29 2004 - 17:34:53 CDT)
- Sascha Tayefeh (Fri Oct 29 2004 - 16:16:56 CDT)
fix atoms in minimisation
- Maria Gonzalez (Tue May 02 2006 - 20:18:50 CDT)
- Leandro Martínez (Mon May 01 2006 - 15:20:56 CDT)
- Leonardo G. Trabuco (Mon May 01 2006 - 15:58:26 CDT)
- Maria Gonzalez (Mon May 01 2006 - 10:14:35 CDT)
Fix atoms-Colvars
- Jérôme Hénin (Fri Jan 07 2011 - 13:04:10 CST)
- Alex Liu (Thu Jan 06 2011 - 15:46:14 CST)
fix backbone atom
- JC Gumbart (Sun Oct 09 2005 - 02:29:57 CDT)
- bo baker (Sun Oct 09 2005 - 01:52:35 CDT)
Fix distance
- Ekta Khurana (Tue Sep 20 2005 - 18:11:06 CDT)
fix or Harmonic constraint ?
- li (Wed Apr 14 2004 - 02:05:19 CDT)
Fixatoms minimization problem!!
- Ranyere Deyler (Mon Mar 29 2010 - 18:41:29 CDT)
- Ranyere Deyler (Mon Mar 29 2010 - 09:14:13 CDT)
- Chris Harrison (Wed Mar 17 2010 - 00:27:37 CDT)
- Ranyere Deyler (Tue Mar 16 2010 - 12:45:57 CDT)
fixed atoms
- wzhuang_at_uci.edu (Wed Oct 26 2005 - 11:12:25 CDT)
- Gan, Yong $UMC-Student$ (Tue Oct 25 2005 - 23:18:59 CDT)
fixed atoms / pressure
- Peter Freddolino (Sun Mar 16 2008 - 09:19:53 CDT)
- Arturas Ziemys (Thu Mar 13 2008 - 10:52:41 CDT)
- Peter Freddolino (Wed Mar 12 2008 - 18:55:07 CDT)
- Arturas Ziemys (Mon Mar 10 2008 - 12:31:27 CDT)
Fixed atoms and dcd file with DCDunitCell on
- nordgren_at_sas.upenn.edu (Sat Jul 23 2005 - 12:11:46 CDT)
- Joshua D. Moore (Fri Jul 22 2005 - 16:46:15 CDT)
fixed atoms appearing on the other side of simulation box
- Ana Celia Araujo Vila Verde (Tue Jan 16 2007 - 13:38:33 CST)
FIXED atoms not included as described in the documentation
- Joshua D. Moore (Mon Aug 13 2007 - 04:55:35 CDT)
- Joshua D. Moore (Mon Aug 13 2007 - 04:49:03 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 atoms pdb
- Mark M Huntress (Mon Aug 24 2009 - 17:13:20 CDT)
Fixed COM
- Ajasja LjubetiÄ (Tue Jul 12 2011 - 08:11:04 CDT)
- Ajasja LjubetiÄ (Mon Jul 11 2011 - 14:37:43 CDT)
- Parisa Akhski (Mon Jul 11 2011 - 13:52:21 CDT)
- Ali Khanlarkhani (Mon Jul 11 2011 - 13:30:32 CDT)
fixed particles
- Kamp, Marc vander (Sat Jul 17 2004 - 03:20:33 CDT)
- AMIT PALIWAL (Fri Jul 16 2004 - 18:22:23 CDT)
fixed residue
- Gianluca Interlandi (Tue Jul 29 2008 - 01:03:40 CDT)
- Joshua Adelman (Mon Jul 28 2008 - 23:16:41 CDT)
- Roman Petrenko (Mon Jul 28 2008 - 23:36:45 CDT)
- Roman Petrenko (Mon Jul 28 2008 - 23:38:10 CDT)
- Rudra Banerjee (Mon Jul 28 2008 - 22:49:36 CDT)
Fixed restraint
- Leonardo Sepulveda Durán (Tue Jun 21 2005 - 18:56:45 CDT)
- Shahid Qamar (Tue Jun 21 2005 - 17:56:09 CDT)
fixed system just in Z direction
- Himanshu Khandelia (Thu May 10 2007 - 06:15:49 CDT)
- ali alizadeh (Thu May 10 2007 - 03:36:04 CDT)
FixedAtomForces and ExcludeFromPressure
- Vishal Kopardé (Thu Nov 30 2006 - 19:39:49 CST)
fixedAtoms may not be enabled in a script
- Christopher Hartshorn (Tue Oct 21 2008 - 10:54:17 CDT)
Fixing atoms during simulation
- nordgren_at_sas.upenn.edu (Sat May 07 2005 - 23:17:30 CDT)
- Uma Mahankali (Sat May 07 2005 - 19:33:49 CDT)
fixing group of atoms, Proper for manipualation
- M Mahjour (Wed Apr 13 2011 - 17:06:43 CDT)
fixing internal coordinates
- Jerome Henin (Mon Feb 05 2007 - 14:32:57 CST)
- Martin McCullagh (Mon Feb 05 2007 - 14:01:55 CST)
fixing parts of an equilibrated protein's environment
- Sebastian Stolzenberg (Wed Sep 09 2009 - 10:26:17 CDT)
Fixing position of COM
- Mauricio Carrillo Tripp (Wed Jun 30 2004 - 10:42:10 CDT)
fixing the protein during minimization
- Mert Gür (Mon Nov 09 2009 - 08:22:24 CST)
FK506 ligand topology file(1FKF)
- MERIC AYSE OVACIK (Thu Oct 28 2004 - 05:29:21 CDT)
flashmob namd
- Ramon Rocha (Tue Aug 03 2010 - 10:52:15 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)
flexible cell for MD simulations
- Michel Espinoza-Fonseca (Thu Mar 10 2005 - 16:25:17 CST)
flexible-cell constant pressure not supported in CUDA
- JC Gumbart (Mon Sep 27 2010 - 18:45:26 CDT)
- Jianing Song (Fri Sep 24 2010 - 19:50:26 CDT)
flexiblecell and constant ratio
- Peter Freddolino (Fri Feb 02 2007 - 09:26:48 CST)
- regafan_at_usc.es (Fri Feb 02 2007 - 06:09:00 CST)
flipdcd
- Axel Kohlmeyer (Mon Jun 01 2009 - 12:05:35 CDT)
- Michael Kreim (Sat May 30 2009 - 07:12:34 CDT)
flipDCD and Unit Cell information?
- Joshua D. Moore (Mon Dec 19 2005 - 17:54:06 CST)
fluorescent probes
- jayant james (Wed Dec 19 2007 - 20:08:33 CST)
Fluorophors ?
- Georgios Papadopoulos (Wed Jun 22 2005 - 00:27:25 CDT)
Flushing memory into output file
- Parisa Akhski (Fri Oct 08 2010 - 09:04:37 CDT)
- Jim Phillips (Thu Oct 07 2010 - 17:06:26 CDT)
- Axel Kohlmeyer (Thu Oct 07 2010 - 16:30:44 CDT)
- Nicholas M Glykos (Thu Oct 07 2010 - 14:39:25 CDT)
- Axel Kohlmeyer (Thu Oct 07 2010 - 12:42:50 CDT)
- Parisa Akhski (Thu Oct 07 2010 - 11:58:46 CDT)
Flushing output: MPI version of NAMD on AMD64
- Vani Krishna (Tue Oct 10 2006 - 00:00:31 CDT)
Flying ions
- jia (Tue Nov 27 2007 - 21:00:32 CST)
follow up question about heating the system
- surendra negi (Wed Feb 15 2006 - 16:18:30 CST)
- patrick wintrode (Wed Feb 15 2006 - 15:51:55 CST)
followup question on error calculation in ABF
- Jerome Henin (Thu Oct 08 2009 - 04:04:51 CDT)
- Ramya Gamini (Wed Oct 07 2009 - 16:41:57 CDT)
- Ramya Gamini (Wed Oct 07 2009 - 15:26:15 CDT)
- Giovanni Bellesia (Wed Oct 07 2009 - 15:35:39 CDT)
- Giovanni Bellesia (Wed Oct 07 2009 - 13:50:55 CDT)
for help from all!
- Lv Shouqin (Sat Feb 14 2004 - 23:14:38 CST)
For help with .log file.
- Boyang Wang (Sun Aug 07 2005 - 21:42:49 CDT)
- nmichaud_at_jhu.edu (Mon Aug 08 2005 - 09:38:02 CDT)
- Joshua D. Moore (Sun Aug 07 2005 - 23:43:30 CDT)
- JC Gumbart (Sun Aug 07 2005 - 14:57:58 CDT)
- Boyang Wang (Sun Aug 07 2005 - 14:13:33 CDT)
For slowly heating, temperature reassignment or Temperature coupling
- Shulin Zhuang (Tue Oct 16 2007 - 14:41:41 CDT)
for the isntall and run NAMD soft on 8 core (dual quad-core Xeons) system
- Sabuj Pattanayek (Thu Sep 27 2007 - 23:47:21 CDT)
- Victor Ovchinnikov (Thu Sep 27 2007 - 21:28:46 CDT)
- Ilya Chorny (Thu Sep 27 2007 - 20:48:10 CDT)
- Victor Ovchinnikov (Thu Sep 27 2007 - 19:11:27 CDT)
- Ilya Chorny (Wed Sep 26 2007 - 18:20:36 CDT)
- Shulin Zhuang (Wed Sep 26 2007 - 17:08:20 CDT)
for your suggestions on Pressure Control of transmembrane protein (GPCR)
- ÅÓÑ©ÇÛ Pang Xueqin (Wed Apr 07 2010 - 03:30:20 CDT)
- pxq ÅÓÑ©ÇÛ (Sun Aug 30 2009 - 22:18:47 CDT)
force calculation
- peach gil (Tue Sep 26 2006 - 14:03:10 CDT)
- Manuela Cavallari (Thu Jun 16 2005 - 11:53:13 CDT)
force calculation during to conformational change
- Pijush Ghosh (Tue Jul 11 2006 - 17:37:51 CDT)
- Gaurav Sharma (Tue Jul 11 2006 - 11:38:15 CDT)
Force Calculation in NAMD
- Gadi Oron (Sun May 23 2004 - 02:37:27 CDT)
- Xin Chen (Fri May 21 2004 - 13:02:09 CDT)
Force Calibration Interaction
- abhijit ramachandran (Thu Jun 19 2008 - 17:31:57 CDT)
Force constant for Umbrella Sampling
- Buddhadev Maiti (Mon Feb 14 2011 - 19:19:02 CST)
force constant for zer-velocity SMD
- namd vmd (Thu Feb 08 2007 - 06:35:53 CST)
force constant from gaussian to namd
- Mark Abraham (Wed Sep 20 2006 - 14:00:05 CDT)
- Shenoy, Sukesh (Wed Sep 20 2006 - 13:44:12 CDT)
force constant in abf configuration file
- Madhurima Jana (Tue Dec 15 2009 - 23:01:02 CST)
force constant matrix
- Ahlam Al-Rawi (Thu Dec 06 2007 - 14:20:07 CST)
- JC Gumbart (Thu Nov 01 2007 - 16:03:21 CDT)
- Ahlam Al-Rawi (Thu Nov 01 2007 - 08:29:23 CDT)
Force constant of harmonic restraint
- picot.delphine_at_neuf.fr (Thu May 12 2005 - 03:50:11 CDT)
Force constant scaling
- Jérôme Hénin (Wed Sep 01 2010 - 06:11:58 CDT)
- guardiani_at_fi.infn.it (Tue Aug 31 2010 - 09:45:14 CDT)
Force Constant Units
- Ramya Gamini (Wed Jun 10 2009 - 14:01:28 CDT)
- Kamilla Kopec (Wed Jun 10 2009 - 12:08:24 CDT)
force constraints
- Swarna Patra (Mon Jan 31 2005 - 19:49:07 CST)
force dcd files??
- Joshua D. Moore (Mon Dec 10 2007 - 10:32:36 CST)
- Thomas C. Bishop (Thu Dec 06 2007 - 15:22:49 CST)
Force extension from SMD log file
- snoze pa (Thu Aug 20 2009 - 17:25:20 CDT)
force field
- Namd Namd (Mon Jun 13 2011 - 03:36:04 CDT)
force field for 2-methyl-2,4-pentanediol (MPD)
- Yang Gao (Tue May 10 2011 - 10:40:40 CDT)
Force field for coarse grained simulations (and other questions)
- Peter Freddolino (Thu Jul 12 2007 - 07:58:12 CDT)
- patrick wintrode (Wed Jul 11 2007 - 16:20:20 CDT)
force field for H2PO4- and HPO4(-2) ions
- Mark Abraham (Sun Feb 25 2007 - 00:35:35 CST)
- Richard Wood (Sat Feb 24 2007 - 20:35:13 CST)
- Mark Abraham (Sat Feb 24 2007 - 17:44:13 CST)
- Richard Wood (Sat Feb 24 2007 - 15:42:55 CST)
- George Madalin Giambasu (Sat Feb 24 2007 - 14:33:16 CST)
- Mark Abraham (Sat Feb 24 2007 - 10:20:05 CST)
- Pawel Weronski (Sat Feb 24 2007 - 10:01:43 CST)
Force field for PDMS
- Yingzhe Liu (Fri Dec 31 2010 - 20:32:20 CST)
Force field for replica
- Chris Harrison (Sun Oct 31 2010 - 08:47:09 CDT)
- Xiang Yu (Thu Oct 28 2010 - 09:12:25 CDT)
force field for replica exchange with NAMD
- ä¿žç¿” (Thu Oct 28 2010 - 17:56:58 CDT)
- S¨¢ndor Kov¨¢cs (Thu Oct 28 2010 - 17:47:21 CDT)
- Alexander Predeus (Thu Oct 28 2010 - 16:15:05 CDT)
- ÓáÏè (Thu Oct 28 2010 - 15:40:52 CDT)
- Jim Phillips (Thu Oct 28 2010 - 14:18:46 CDT)
- Xiang Yu (Wed Oct 27 2010 - 23:06:32 CDT)
Force field parameters
- Ramya Gamini (Wed Nov 12 2008 - 12:05:41 CST)
- Rabab Toubar (Wed Nov 12 2008 - 10:27:58 CST)
force field parameters for fullerenes
- Adam Fraser (Mon Dec 10 2007 - 13:18:16 CST)
Force Fields
- Goutham (Fri May 01 2009 - 00:36:09 CDT)
Force on multiple atoms in ABF
- Mert Gür (Sun May 24 2009 - 11:26:16 CDT)
force on SMD atom
- Moumita Maiti (Wed Jun 27 2007 - 01:10:06 CDT)
- Moumita Maiti (Fri Jun 22 2007 - 14:43:27 CDT)
force output of pairInteraction
- BIN ZHANG (Mon Jun 01 2009 - 17:20:07 CDT)
force over selection
- Ioana Cozmuta (Wed Mar 22 2006 - 23:51:46 CST)
force potentials for residue-based CG
- Dolan, Michael (NIH/NIAID) [C] (Wed Nov 26 2008 - 13:36:51 CST)
force question
- Hasan haska (Thu Sep 22 2011 - 05:36:47 CDT)
- Ehsan Ban (Thu Sep 22 2011 - 05:18:34 CDT)
- Jérôme Hénin (Thu Sep 22 2011 - 04:32:45 CDT)
- Hasan haska (Thu Sep 22 2011 - 02:50:18 CDT)
force shifted cutoff
- Stern, Julie (Tue Jul 19 2005 - 18:37:10 CDT)
- Stern, Julie (Thu Jul 07 2005 - 18:06:15 CDT)
Force Vector Between Two Atoms
- Ehsan Ban (Mon Oct 10 2011 - 01:19:55 CDT)
- Bruno Luís Pinto de Oliveira (Sat Oct 08 2011 - 04:25:40 CDT)
- Ehsan Ban (Fri Oct 07 2011 - 17:14:02 CDT)
force-field for ATP
- Leandro Martínez (Tue Apr 28 2009 - 20:05:54 CDT)
- gaillard_at_chimie.u-strasbg.fr (Tue Apr 28 2009 - 19:41:13 CDT)
- Roman Petrenko (Tue Apr 28 2009 - 19:20:57 CDT)
- Roman Petrenko (Tue Apr 28 2009 - 18:55:05 CDT)
force-field for cy3, cy5 dyes
- Roman Petrenko (Wed May 06 2009 - 19:26:54 CDT)
force-field parameters for glycoproteins
- Kramer Campen (Fri May 25 2007 - 15:54:11 CDT)
- Gaurav Sharma (Fri May 25 2007 - 13:14:33 CDT)
force-field parameters for TOAC
- Gaurav Sharma (Mon Mar 27 2006 - 17:02:31 CST)
ForceConstant in Umbrella Sampling
- Chris Harrison (Fri Oct 28 2011 - 18:10:40 CDT)
- Buddhadev Maiti (Fri Oct 28 2011 - 12:38:24 CDT)
Forcefield for simulating peptide with heparin!!!!
- Aditya Ranganathan (Mon May 02 2011 - 07:24:56 CDT)
forces calculation
- peach gil (Tue Sep 26 2006 - 13:12:16 CDT)
forces during SMD
- zhilei chen (Sun Dec 07 2003 - 10:16:43 CST)
forces on atom
- Victor Ovchinnikov (Sun Nov 04 2007 - 11:08:57 CST)
- Pijush Ghosh (Sun Nov 04 2007 - 09:22:00 CST)
Forces on Atoms and Potential Energy
- JC Gumbart (Tue Feb 17 2009 - 14:29:52 CST)
- Mohamed Seyam (Mon Feb 16 2009 - 13:57:01 CST)
forces on fixed atoms
- Jérôme Hénin (Thu Feb 17 2011 - 03:31:32 CST)
- Bennion, Brian (Wed Feb 16 2011 - 18:04:30 CST)
- Jérôme Hénin (Wed Feb 16 2011 - 17:58:28 CST)
- Bennion, Brian (Wed Feb 16 2011 - 16:01:44 CST)
Format of Binary Restart and Output Coordinate and Velocity Files
- Joshua D. Moore (Fri Apr 18 2008 - 19:34:20 CDT)
Format of namd restartfile *.coor, *.vel) (2nd try ;) )
- Joshua D. Moore (Thu Nov 18 2010 - 18:27:22 CST)
- henri mone (Thu Nov 18 2010 - 10:05:15 CST)
Formating of logfile
- Bjoern Olausson (Sat Nov 14 2009 - 20:42:37 CST)
- Axel Kohlmeyer (Sat Nov 14 2009 - 10:11:01 CST)
- Bjoern Olausson (Fri Nov 13 2009 - 21:47:31 CST)
- Axel Kohlmeyer (Fri Nov 13 2009 - 15:17:49 CST)
- Bjoern Olausson (Fri Nov 13 2009 - 14:31:22 CST)
- Bjoern Olausson (Fri Nov 13 2009 - 02:55:02 CST)
- Bjoern Olausson (Wed Nov 11 2009 - 07:07:34 CST)
- Bjoern Olausson (Wed Nov 11 2009 - 06:58:44 CST)
forming disulfide after equilibrating system
- JC Gumbart (Sat Dec 23 2006 - 12:55:40 CST)
- dora guzman (Fri Dec 22 2006 - 17:24:10 CST)
formyl and ethanolamide parameters and topology
- Branko (Fri Jun 24 2011 - 03:52:32 CDT)
- flavio seixas (Thu Jun 23 2011 - 21:58:27 CDT)
- poker_at_physics.usyd.edu.au (Thu Jun 23 2011 - 19:11:57 CDT)
- flavio seixas (Thu Jun 23 2011 - 12:08:58 CDT)
- Jorgen Simonsen (Thu Jun 23 2011 - 09:52:18 CDT)
Fortran and tclForces
- Peter Freddolino (Fri May 25 2007 - 13:02:50 CDT)
- Luca Bellucci (Fri May 25 2007 - 03:22:11 CDT)
forward and backward pulling
- curcio (Thu Oct 05 2006 - 10:59:10 CDT)
Free Cluster-Building Workshops - 16-17 Mar 2006, 20-21 Apr 2006
- Tim Skirvin (Mon Feb 13 2006 - 14:41:24 CST)
free energy calculate
- Taeho Kim (Fri Jun 16 2006 - 02:45:55 CDT)
- Mark Abraham (Fri Jun 16 2006 - 01:44:05 CDT)
- Taeho Kim (Fri Jun 16 2006 - 01:30:29 CDT)
- Taeho Kim (Fri Jun 16 2006 - 00:52:16 CDT)
Free energy calculation fixing the dihedrals
- Luca Bellucci (Tue Nov 25 2008 - 02:48:06 CST)
- Jagan Mohan (Tue Nov 25 2008 - 01:09:46 CST)
- Jagan Mohan (Tue Nov 25 2008 - 01:12:10 CST)
Free Energy Calculation of a protein
- Mert Gür (Wed Dec 16 2009 - 08:41:50 CST)
- Axel Kohlmeyer (Tue Dec 15 2009 - 03:40:07 CST)
- Mert Gür (Tue Dec 15 2009 - 02:48:31 CST)
- Sébastien Légaré (Thu Dec 10 2009 - 14:19:01 CST)
- Mert Gür (Thu Dec 10 2009 - 03:48:22 CST)
- Mert Gür (Thu Dec 10 2009 - 03:14:28 CST)
- Pu Tian (Wed Dec 09 2009 - 15:53:35 CST)
- Mert Gür (Wed Dec 09 2009 - 14:19:42 CST)
Free energy calculation yields strange results
- Jun Zhang (Tue May 11 2010 - 21:25:57 CDT)
- Jérôme Hénin (Mon May 10 2010 - 08:04:43 CDT)
- Jun Zhang (Sun May 09 2010 - 07:53:36 CDT)
free energy calculations
- Peter Freddolino (Wed Jun 04 2008 - 11:52:02 CDT)
- Eric H. Lee (Wed Jun 04 2008 - 11:28:13 CDT)
- politr_at_huji.ac.il (Wed Jun 04 2008 - 05:34:01 CDT)
- alex digenova bravo (Mon Oct 01 2007 - 17:59:34 CDT)
free energy changes of one subunit
- Giacomo Fiorin (Tue Mar 16 2010 - 15:43:52 CDT)
- felmerino_at_uchile.cl (Tue Mar 16 2010 - 15:29:17 CDT)
- Lixia Jin Day (Tue Mar 16 2010 - 13:39:55 CDT)
Free energy constraints and logfile
- David Chalmers (Mon Dec 01 2003 - 22:54:01 CST)
Free energy from MD Simulation
- Nitin Bhardwaj (Wed May 31 2006 - 17:13:51 CDT)
free energy of binding
- Richard Wood (Thu Jul 07 2011 - 18:56:48 CDT)
- Jeff Wereszczynski (Thu Jul 07 2011 - 18:27:55 CDT)
- Gianluca Interlandi (Thu Jul 07 2011 - 17:29:18 CDT)
- Jeffrey Potoff (Thu Jul 07 2011 - 17:16:02 CDT)
- Chris Harrison (Thu Jul 07 2011 - 17:12:34 CDT)
- Gianluca Interlandi (Thu Jul 07 2011 - 17:08:55 CDT)
- Francesco Pietra (Thu Jul 07 2011 - 16:50:12 CDT)
- Dong Luo (Thu Jul 07 2011 - 10:50:07 CDT)
- Francesco Pietra (Thu Jul 07 2011 - 04:52:38 CDT)
Free Energy of Conformation Change
- Arturas Ziemys (Mon Mar 12 2007 - 13:16:57 CDT)
Free Energy of Conformation Change Units
- Kramer Campen (Tue Jan 02 2007 - 15:45:23 CST)
Free energy of conformational change
- Jerome Henin (Fri May 29 2009 - 11:31:00 CDT)
- Branko (Fri May 29 2009 - 06:44:32 CDT)
- Giacomo Fiorin (Wed May 20 2009 - 11:22:38 CDT)
- Branko (Wed May 20 2009 - 06:15:57 CDT)
- Lixia Jin Day (Wed Mar 25 2009 - 18:04:37 CDT)
- Chris Harrison (Wed Mar 25 2009 - 17:51:17 CDT)
- Lixia Jin Day (Wed Mar 25 2009 - 15:21:19 CDT)
Free Energy of Conformational Change Calculations Error: "Problem parsing input parameters Error: Invalid AtomID"
- Joshua D. Moore (Sat Sep 10 2005 - 17:49:26 CDT)
- Joshua D. Moore (Thu Sep 08 2005 - 22:13:17 CDT)
Free Energy of Conformational Change PMF - documentation on method?
- David Sivak (Thu Mar 13 2008 - 18:07:56 CDT)
free energy pertubation,binding energy and constant
- Chris Chipot (Wed Jun 29 2005 - 08:14:27 CDT)
- s.bora erdemli (Tue Jun 28 2005 - 14:30:07 CDT)
free energy perturbation
- Jérôme Hénin (Wed Jan 05 2011 - 12:07:39 CST)
- Jérôme Hénin (Wed Jan 05 2011 - 07:39:37 CST)
- BIN ZHANG (Wed Jan 05 2011 - 02:07:57 CST)
Free energy perturbation (FEP) hybrid pdb file
- JC Gumbart (Tue Dec 07 2010 - 23:04:18 CST)
- Christian Jorgensen (Tue Dec 07 2010 - 21:36:31 CST)
Free energy perturbation of a double mutant
- Chris Chipot (Tue Nov 06 2007 - 17:03:51 CST)
- jia (Tue Nov 06 2007 - 16:37:35 CST)
Free energy with amber topology
- Stefano Corni (Fri May 26 2006 - 02:53:28 CDT)
free energy,energy,entropy calculation for pushing ATP to active site of kinase!
- Qiang Zhong (Fri Jul 20 2007 - 06:40:44 CDT)
- Dong Luo (Thu Jul 19 2007 - 09:15:13 CDT)
- Qiang Zhong (Thu Jul 19 2007 - 06:11:39 CDT)
Free Energy/ ERROR
- Kramer Campen (Tue Mar 13 2007 - 09:11:25 CDT)
- Arturas Ziemys (Mon Mar 12 2007 - 15:37:31 CDT)
free enrgy calculations - an additional information
- politr_at_huji.ac.il (Wed Jun 04 2008 - 07:07:01 CDT)
Free Linux Cluster-Building Workshop - 30 Nov 2006 - 01 Dec 2006
- Jim Phillips (Mon Oct 16 2006 - 16:13:52 CDT)
Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms
- felmerino_at_uchile.cl (Tue Nov 09 2010 - 10:26:55 CST)
- Christian Jorgensen (Tue Nov 09 2010 - 09:42:22 CST)
- felmerino_at_uchile.cl (Tue Nov 09 2010 - 00:38:58 CST)
- Christian Jorgensen (Mon Nov 08 2010 - 16:23:51 CST)
FreeEnergy and minimization
- Roman Petrenko (Thu Apr 30 2009 - 23:31:55 CDT)
freeEnergy of conformational change of a test molecule
- Chris Chipot (Thu Nov 17 2005 - 11:37:07 CST)
- Uma Mahankali (Thu Nov 17 2005 - 08:45:12 CST)
- Chris Chipot (Thu Nov 17 2005 - 03:44:55 CST)
- Uma Mahankali (Wed Nov 16 2005 - 13:33:18 CST)
freeEnergy parsing error
- Lada Biedermannová (Wed Apr 27 2011 - 09:08:46 CDT)
FreeEnergy: Not enough steps to complete pfm & mcti blocks
- priyodorshi satpati (Wed Dec 02 2009 - 10:28:44 CST)
- Jérôme Hénin (Fri Nov 27 2009 - 06:42:59 CST)
- priyodorshi satpati (Fri Nov 27 2009 - 03:26:01 CST)
- priyodorshi satpati (Thu Nov 26 2009 - 03:19:48 CST)
- priyodorshi satpati (Wed Nov 25 2009 - 09:31:15 CST)
Freezing point
- Dr. Tamal Banerjee (Fri Sep 07 2007 - 08:22:05 CDT)
fresh file not ready to read?
- BIN ZHANG (Thu Oct 22 2009 - 01:46:10 CDT)
from NPT to NVT
- Hiroaki Maekawa (Mon Oct 20 2008 - 12:00:46 CDT)
- Hiroaki Maekawa (Fri Oct 17 2008 - 16:37:16 CDT)
frozen water Oxygens
- Chris Harrison (Wed Aug 05 2009 - 09:01:24 CDT)
- Mark M Huntress (Tue Aug 04 2009 - 11:13:12 CDT)
Full Electrostatic Calculations on Protein in Vacuo
- MIke S (Fri Oct 24 2008 - 16:26:02 CDT)
- Brian Bennion (Thu Oct 16 2008 - 10:19:32 CDT)
- Axel Kohlmeyer (Thu Oct 16 2008 - 10:08:23 CDT)
- MIke S (Thu Oct 16 2008 - 02:07:29 CDT)
Fullerene topology
- Luca Muccioli (Wed Oct 28 2009 - 15:31:38 CDT)
- Austin B. Yongye (Wed Oct 28 2009 - 11:41:49 CDT)
- Luca Muccioli (Wed Oct 28 2009 - 10:55:11 CDT)
- Austin B. Yongye (Mon Oct 26 2009 - 13:40:17 CDT)
fullSamples in ABF: applied at restart?
- Jérôme Hénin (Mon Nov 21 2011 - 04:11:06 CST)
- Neelanjana Sengupta (Mon Nov 21 2011 - 02:51:55 CST)
- Jérôme Hénin (Mon Nov 21 2011 - 02:10:10 CST)
- Neelanjana Sengupta (Sun Nov 20 2011 - 22:19:00 CST)
- Neelanjana Sengupta (Sun Nov 20 2011 - 22:14:15 CST)
FullSamples variable in ABF
- Christophe.Chipot_at_edam.uhp-nancy.fr (Wed May 23 2007 - 02:04:37 CDT)
- alex digenova bravo (Tue May 22 2007 - 23:50:36 CDT)
Fwd:
- Madhulika Gupta (Mon Jan 30 2012 - 22:10:37 CST)
Fwd: "cuda error cudastreamcreate",
- Francesco Pietra (Fri Jun 17 2011 - 02:36:49 CDT)
- John Stone (Fri Jun 17 2011 - 01:22:50 CDT)
- Francesco Pietra (Fri Jun 17 2011 - 00:50:05 CDT)
Fwd: 99999999.9999 as vander waals energy
- Chris Harrison (Sat Jul 11 2009 - 19:38:30 CDT)
Fwd: about md in npt
- Boyang Wang (Wed Dec 28 2011 - 02:54:01 CST)
Fwd: All or Nothing at All??
- griadi_at_utalca.cl (Sat Oct 29 2005 - 14:02:12 CDT)
Fwd: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance
- Francesco Pietra (Mon Jun 06 2011 - 04:30:46 CDT)
- Francesco Pietra (Mon Jun 06 2011 - 04:15:44 CDT)
Fwd: binaryrestart/binaryoutput problem
- Francesco Pietra (Tue Mar 01 2011 - 02:56:29 CST)
Fwd: Coarse Graining Problem
- Anton Arkhipov (Wed Feb 24 2010 - 11:20:08 CST)
- Aditya Ranganathan (Wed Feb 24 2010 - 05:59:51 CST)
Fwd: conf file for coarse grained simulation
- Peter Freddolino (Wed Dec 16 2009 - 18:49:13 CST)
- Peter Freddolino (Wed Dec 16 2009 - 15:46:39 CST)
- Francesco Pietra (Wed Dec 16 2009 - 03:01:27 CST)
- Francesco Pietra (Wed Dec 16 2009 - 02:13:59 CST)
- Francesco Pietra (Tue Dec 15 2009 - 10:01:30 CST)
- Francesco Pietra (Tue Dec 15 2009 - 02:40:55 CST)
- Axel Kohlmeyer (Tue Dec 15 2009 - 11:16:14 CST)
- Peter Freddolino (Tue Dec 15 2009 - 10:45:27 CST)
- Axel Kohlmeyer (Tue Dec 15 2009 - 02:17:45 CST)
- Francesco Pietra (Mon Dec 14 2009 - 02:19:52 CST)
Fwd: convergence of abf
- Eric H. Lee (Mon Sep 08 2008 - 14:45:53 CDT)
Fwd: cuda error cudastreamcreate. SOLVED (probably)
- Francesco Pietra (Wed Jun 15 2011 - 09:43:28 CDT)
- Francesco Pietra (Wed Jun 15 2011 - 02:45:26 CDT)
Fwd: Determining Transition State from an Unfolding Simulation
- Arun Krishnan (Wed Sep 26 2007 - 08:19:13 CDT)
Fwd: electric field unit conversion
- Mikhail Suyetin (Wed Feb 17 2010 - 11:25:21 CST)
Fwd: error : atom moving too fast
- ipsita basu (Tue Jun 08 2010 - 00:20:24 CDT)
Fwd: Error in Minimization
- Ale Gomez (Sun Nov 08 2009 - 09:15:02 CST)
Fwd: error in scripting
- ipsita basu (Thu Nov 19 2009 - 23:33:25 CST)
- ipsita basu (Thu Nov 19 2009 - 03:28:03 CST)
Fwd: extracting waters from DCD
- yi wang (Tue Aug 08 2006 - 16:50:55 CDT)
Fwd: force constant in abf configuration file
- Madhurima Jana (Thu Dec 17 2009 - 11:29:50 CST)
Fwd: Fwd: hi
- Axel Kohlmeyer (Thu Jun 02 2011 - 12:52:25 CDT)
- kanchi subbarao rao (Thu Jun 02 2011 - 12:44:27 CDT)
- kanchi subbarao rao (Wed Jun 01 2011 - 13:32:41 CDT)
Fwd: Fwd: Water Box size
- snoze pa (Wed Feb 15 2006 - 11:29:19 CST)
Fwd: Generating .tpr file using NAMD files
- rajitha rajeshwar (Mon Dec 19 2011 - 03:05:34 CST)
Fwd: GRADIENT TOLERANCE: nan
- Brian Bennion (Thu Oct 26 2006 - 11:29:00 CDT)
Fwd: hBond component in colvars and patching
- Francesco Pietra (Sun Mar 06 2011 - 02:36:10 CST)
Fwd: help to improve the script to predict mean square displacement
- Luca Muccioli (Fri Mar 12 2010 - 17:08:31 CST)
- jampani srinivas (Fri Mar 12 2010 - 14:51:55 CST)
Fwd: hi
- kanchi subbarao rao (Tue May 31 2011 - 05:10:32 CDT)
Fwd: hi all
- kanchi subbarao rao (Thu Jun 16 2011 - 07:16:22 CDT)
- kanchi subbarao rao (Wed Jun 15 2011 - 11:46:09 CDT)
Fwd: How can I load two forcefied at the same time
- Leonardo Trabuco (Fri Nov 21 2008 - 11:16:34 CST)
- Wang,Ying (Thu Nov 20 2008 - 13:24:10 CST)
Fwd: Incompatibility between colvars and tclforces?
- Francesco Pietra (Wed Mar 30 2011 - 12:32:53 CDT)
- Vlad Cojocaru (Thu Mar 31 2011 - 05:12:10 CDT)
- Vlad Cojocaru (Thu Mar 31 2011 - 02:27:40 CDT)
- Jérôme Hénin (Thu Mar 31 2011 - 03:25:18 CDT)
- Francesco Pietra (Thu Mar 31 2011 - 02:45:10 CDT)
Fwd: Installing NAMD on windows
- Axel Kohlmeyer (Sat Dec 04 2010 - 13:51:41 CST)
- Branko2 (Sat Dec 04 2010 - 11:25:29 CST)
- Gianluca Interlandi (Sat Dec 04 2010 - 10:43:34 CST)
- bharat gupta (Sat Dec 04 2010 - 02:07:05 CST)
Fwd: Job submission to Lonestar on TACC
- Peter Freddolino (Thu Mar 05 2009 - 20:04:29 CST)
- Ali Emileh (Thu Mar 05 2009 - 13:13:38 CST)
Fwd: Keyword "lower" not supported...colvars
- Francesco Pietra (Sun Mar 13 2011 - 05:37:41 CDT)
Fwd: Laptop for Molecular Dynamics - Summary
- Deepangi Pandit (Fri May 25 2007 - 20:41:09 CDT)
Fwd: membrane moving up in simulation box
- kanchi subbarao rao (Thu Oct 13 2011 - 06:26:12 CDT)
- kanchi subbarao rao (Thu Oct 13 2011 - 04:54:15 CDT)
Fwd: minimization problem
- ipsita basu (Fri Oct 29 2010 - 00:25:58 CDT)
Fwd: Minimization problem of a protein-DNA complex with namd
- Chris Harrison (Sun Jul 12 2009 - 18:23:40 CDT)
Fwd: missing atom prob
- surendra negi (Mon Nov 01 2004 - 17:58:33 CST)
Fwd: namd2 installation..
- Gengbin Zheng (Wed Jul 11 2007 - 01:31:30 CDT)
- Arun Krishnan (Wed Jul 11 2007 - 01:26:58 CDT)
Fwd: nvidia 275.09.07 driver. SOLVED, NO DRIVER PROBLEM
- Francesco Pietra (Thu Jun 30 2011 - 14:49:56 CDT)
Fwd: one atom off in the minimization result
- Chris Harrison (Sun Jul 12 2009 - 18:23:10 CDT)
Fwd: Parameter file.
- Pijush Ghosh (Sun May 01 2005 - 16:39:10 CDT)
- Boyang Wang (Sat Apr 30 2005 - 12:15:45 CDT)
Fwd: Periodic cell has become too small
- Francesco Pietra (Thu Dec 24 2009 - 03:49:16 CST)
Fwd: phosphotyrosine
- poker_at_physics.usyd.edu.au (Mon Jun 20 2011 - 01:42:49 CDT)
- bharat gupta (Mon Jun 20 2011 - 00:29:04 CDT)
Fwd: PROBLEM OF INSTALLATION OF NAMD
- Sadhu, Shubho (NIH/NCI) [F] (Fri Jul 17 2009 - 08:07:36 CDT)
- ipsita basu (Sun Jul 12 2009 - 23:28:30 CDT)
Fwd: problem regarding charmm parameter file of carbon nano tube
- kanchi subbarao rao (Mon Nov 21 2011 - 05:07:50 CST)
Fwd: psf file creation
- gurunath katagi (Sun Apr 12 2009 - 19:43:48 CDT)
Fwd: PSFgen error
- Brian Bennion (Tue Nov 02 2004 - 10:14:50 CST)
- surendra negi (Mon Nov 01 2004 - 17:58:12 CST)
Fwd: ramd firstRamdAtom
- Francesco Pietra (Mon Mar 28 2011 - 03:15:56 CDT)
Fwd: ramd seed
- Francesco Pietra (Thu Apr 07 2011 - 08:41:08 CDT)
Fwd: RAMD Setting parameter TclForces from script failed
- Cojocaru, Vlad (Mon Mar 28 2011 - 16:55:44 CDT)
- Jim Phillips (Mon Mar 28 2011 - 16:49:25 CDT)
- Francesco Pietra (Mon Mar 28 2011 - 15:37:24 CDT)
- Francesco Pietra (Mon Mar 28 2011 - 15:19:57 CDT)
Fwd: RBCG tutorial
- Francesco Pietra (Wed Nov 11 2009 - 03:56:35 CST)
Fwd: Re : Setting up a membrane simulation
- Bjoern Olausson (Tue Sep 20 2011 - 05:43:30 CDT)
- Bjoern Olausson (Tue Sep 20 2011 - 04:27:23 CDT)
Fwd: reading prameter file
- ipsita basu (Mon Feb 22 2010 - 00:27:10 CST)
Fwd: regarding protein-dna complex simulation please reply.......
- JC Gumbart (Tue Dec 23 2008 - 01:21:11 CST)
- JC Gumbart (Mon Dec 22 2008 - 13:30:58 CST)
- prasun kumar (Mon Dec 22 2008 - 09:44:08 CST)
Fwd: RESP and CHARMM
- r charbel maroun (Tue Jun 02 2009 - 08:35:17 CDT)
Fwd: restrain on COM
- Jérôme Hénin (Sat Nov 19 2011 - 10:48:41 CST)
- Swarna M Patra (Fri Nov 18 2011 - 23:33:09 CST)
Fwd: rigid bonds
- Francesco Pietra (Fri Oct 14 2011 - 09:44:14 CDT)
Fwd: Running a simulation with coarse-grained protein in membrane
- Francesco Pietra (Tue Dec 08 2009 - 09:54:46 CST)
Fwd: Solved stream files and paratool
- Francesco Pietra (Fri Sep 23 2011 - 10:13:06 CDT)
Fwd: STRIDE Question from article "Interpeptide interactions induce helix to strand structural transition in Abeta peptides"
- Aditya Ranganathan (Tue Mar 23 2010 - 01:34:47 CDT)
Fwd: suitable motherboards for both graphical visualization and NAMD-CUDA computation?
- Biff Forbush (Wed Jan 20 2010 - 20:32:06 CST)
Fwd: Tried to find atom type on node other than node 0
- Chris Harrison (Thu Jul 09 2009 - 09:45:23 CDT)
Fwd: vmd-l: CG bead definition
- BIN ZHANG (Tue Oct 20 2009 - 11:19:30 CDT)
Fwd: vmd-l: MOE discussion
- Mike McCallum (Wed Apr 28 2004 - 23:11:43 CDT)
Fwd: vmd-l: Restraints on coarse grained model
- Francesco Pietra (Wed Dec 09 2009 - 03:07:36 CST)
Fwd: Water Box size
- L. Michel Espinoza-Fonseca (Thu Feb 16 2006 - 12:23:23 CST)
- snoze pa (Thu Feb 16 2006 - 10:59:46 CST)
- L. Michel Espinoza-Fonseca (Wed Feb 15 2006 - 12:23:26 CST)
- L. Michel Espinoza-Fonseca (Wed Feb 15 2006 - 12:00:51 CST)
- snoze pa (Wed Feb 15 2006 - 11:58:33 CST)
- Philip Blood (Fri Feb 10 2006 - 13:37:54 CST)
- snoze pa (Fri Feb 10 2006 - 13:49:07 CST)
- Marc Q. Ma (Fri Feb 10 2006 - 12:40:50 CST)
- snoze pa (Fri Feb 10 2006 - 10:58:27 CST)
Fwd: what restraint can I use to prevent membrane diffusion on the Z-axis?
- kanchi subbarao rao (Tue Feb 28 2012 - 13:50:50 CST)
Fwd: Wrong exit from RAMD runs
- Vlad Cojocaru (Thu Apr 14 2011 - 03:08:54 CDT)
- Jim Phillips (Wed Apr 13 2011 - 10:02:18 CDT)
- Jim Phillips (Wed Apr 13 2011 - 09:59:25 CDT)
- Francesco Pietra (Tue Apr 05 2011 - 15:34:19 CDT)
FYEO
- Zachary Tyson (Fri Jun 08 2007 - 13:28:09 CDT)
g(r)
- Philip Fowler (Thu Jul 31 2008 - 02:29:47 CDT)
- Rudra Banerjee (Thu Jul 31 2008 - 01:51:17 CDT)
- Alexandre A. Vakhrouchev (Thu Jul 31 2008 - 01:10:05 CDT)
- Rudra Banerjee (Thu Jul 31 2008 - 00:39:47 CDT)
- Ayþe Özlem Sezerman (Wed Dec 20 2006 - 04:20:51 CST)
g(r) calculation for CNT
- felmerino_at_uchile.cl (Thu Sep 02 2010 - 10:30:55 CDT)
- sara (Thu Sep 02 2010 - 04:34:48 CDT)
g(r) GUI Plugin problem
- Axel Kohlmeyer (Tue Sep 29 2009 - 14:02:16 CDT)
- Branko (Tue Sep 29 2009 - 05:32:03 CDT)
g(r) plugin
- Ayþe Özlem Sezerman (Mon Jan 15 2007 - 04:09:56 CST)
G5 cluster
- Gengbin Zheng (Tue Mar 08 2005 - 16:41:06 CST)
G5 clusters
- Gengbin Zheng (Tue Mar 08 2005 - 12:44:25 CST)
- Michael Grabe (Tue Mar 08 2005 - 11:17:42 CST)
G5 or P4 cluster
- Grischa R. Meyer (Tue Nov 11 2003 - 00:58:07 CST)
Gas phase minimization
- Purushottam Dixit (Fri Jun 15 2007 - 16:58:44 CDT)
GBIS and ABF
- Ajasja LjubetiÄ (Mon Mar 28 2011 - 11:34:07 CDT)
- Giacomo Fiorin (Mon Mar 28 2011 - 10:08:00 CDT)
- Giacomo Fiorin (Mon Mar 28 2011 - 10:09:55 CDT)
- Bjoern Olausson (Mon Mar 28 2011 - 09:56:41 CDT)
- Ajasja LjubetiÄ (Mon Mar 28 2011 - 08:37:36 CDT)
- Bjoern Olausson (Mon Mar 28 2011 - 02:45:46 CDT)
- Jérôme Hénin (Thu Mar 24 2011 - 10:01:43 CDT)
- Jérôme Hénin (Thu Mar 24 2011 - 05:39:52 CDT)
- Ajasja LjubetiÄ (Wed Mar 23 2011 - 14:17:48 CDT)
- Bjoern Olausson (Wed Mar 23 2011 - 06:57:32 CDT)
- Jérôme Hénin (Wed Mar 23 2011 - 12:10:15 CDT)
- Bjoern Olausson (Wed Mar 23 2011 - 09:32:43 CDT)
- Bjoern Olausson (Wed Mar 23 2011 - 07:04:29 CDT)
- Bjoern Olausson (Tue Mar 22 2011 - 18:13:18 CDT)
- Branko (Tue Mar 22 2011 - 17:16:54 CDT)
- Branko (Fri Mar 18 2011 - 04:53:00 CDT)
- Giacomo Fiorin (Thu Mar 17 2011 - 20:02:37 CDT)
- Branko (Thu Mar 17 2011 - 15:50:40 CDT)
GBIS and hydrophobic solvation
- Gianluca Interlandi (Wed Feb 15 2012 - 15:45:54 CST)
- David Tanner (Wed Feb 15 2012 - 15:36:31 CST)
- Gianluca Interlandi (Fri Jan 20 2012 - 18:41:27 CST)
- David Tanner (Thu Oct 13 2011 - 13:40:32 CDT)
- Branko (Mon Oct 10 2011 - 10:11:42 CDT)
- Jérôme Hénin (Mon Oct 10 2011 - 07:24:50 CDT)
GBIS and hydrophobic term, in replay to Jerome and David discussion
- Branko (Sun Oct 23 2011 - 09:55:27 CDT)
- Jérôme Hénin (Sun Oct 23 2011 - 09:43:08 CDT)
- Branko (Sun Oct 23 2011 - 09:36:17 CDT)
GBIS not compatible with CUDA at this time
- David Tanner (Tue Mar 22 2011 - 14:21:09 CDT)
- Michael S. Sellers (Cont, ARL/WMRD) (Tue Mar 22 2011 - 13:27:48 CDT)
GBIS on GPU?
- Danny Xu (Thu Aug 04 2011 - 11:51:57 CDT)
GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03
- Bjoern Olausson (Wed Mar 23 2011 - 07:06:21 CDT)
- Jérôme Hénin (Wed Mar 23 2011 - 05:39:51 CDT)
- Bjoern Olausson (Wed Mar 23 2011 - 03:18:22 CDT)
- Giacomo Fiorin (Tue Mar 22 2011 - 21:07:53 CDT)
- Bjoern Olausson (Tue Mar 22 2011 - 17:56:09 CDT)
GBIS synamics
- David Tanner (Wed Mar 02 2011 - 07:56:59 CST)
- Francesco Oteri (Wed Mar 02 2011 - 05:02:29 CST)
gcc and G5 Xserves
- Charles McCallum (Mon Nov 15 2004 - 23:07:17 CST)
- Michael Grabe (Mon Nov 15 2004 - 02:06:03 CST)
gcc4
- Gengbin Zheng (Fri Oct 14 2005 - 14:21:57 CDT)
- Gianluca Interlandi (Tue Oct 11 2005 - 16:34:32 CDT)
GdHCl parameters
- Brian Bennion (Thu Mar 18 2004 - 17:19:38 CST)
- Ruxandra Dima (Thu Mar 18 2004 - 16:18:16 CST)
GeForce vs Tesla GPUs for high performance computing
- Axel Kohlmeyer (Thu Apr 14 2011 - 14:57:16 CDT)
- Gianluca Interlandi (Thu Apr 14 2011 - 14:48:58 CDT)
- Axel Kohlmeyer (Thu Apr 14 2011 - 14:23:50 CDT)
- Salvador H-V (Thu Apr 14 2011 - 13:58:30 CDT)
GeForce vs. Tesla
- Tian, Pu (NIH/NIDDK) [C] (Thu Nov 26 2009 - 07:23:20 CST)
- Axel Kohlmeyer (Wed Nov 25 2009 - 17:07:27 CST)
- Biff Forbush (Wed Nov 25 2009 - 15:22:22 CST)
- Tian, Pu (NIH/NIDDK) [C] (Mon Nov 23 2009 - 10:01:13 CST)
General and specific atom types in NAMD?
- David Chalmers (Thu Mar 04 2004 - 18:21:42 CST)
General question about NAMD
- michael jerry (Tue Nov 08 2005 - 10:52:04 CST)
General question about psfgen atoms.
- snoze pa (Tue Apr 11 2006 - 14:51:09 CDT)
- snoze pa (Tue Apr 11 2006 - 14:48:12 CDT)
- Marcos Sotomayor (Tue Apr 11 2006 - 12:38:18 CDT)
- snoze pa (Tue Apr 11 2006 - 12:27:27 CDT)
general question on protein-membrane simulations
- L. Michel Espinoza-Fonseca (Wed Apr 18 2007 - 11:26:46 CDT)
general question on protein-membrane simulations -complete message!
- Luca (Thu Apr 19 2007 - 02:48:21 CDT)
- L. Michel Espinoza-Fonseca (Wed Apr 18 2007 - 11:38:10 CDT)
Generalized Born calcs
- Thomas Bishop (Tue Aug 16 2011 - 14:53:17 CDT)
Generalized Born implicit solvent model in 2.8b1
- David Tanner (Wed Mar 30 2011 - 12:04:20 CDT)
- Enrico Guarnera (Wed Mar 30 2011 - 09:40:45 CDT)
generalized born routine
- Rie Nygaard (Tue Jan 09 2007 - 07:10:18 CST)
Generalized solvent boundary potential or similar tricks for huge systems in NAMD??
- Jacob Poehlsgaard (Thu Nov 30 2006 - 03:15:35 CST)
Generate missing atoms of a coarse grained structure
- Mert Gür (Wed Apr 14 2010 - 03:34:41 CDT)
- Mert Gür (Wed Apr 14 2010 - 03:35:13 CDT)
- Ajasja LjubetiÄ (Tue Apr 06 2010 - 10:22:02 CDT)
- y_ja_at_163.com (Sun Apr 04 2010 - 08:25:06 CDT)
- Peter Freddolino (Sun Apr 04 2010 - 07:55:56 CDT)
- Mert Gür (Sun Apr 04 2010 - 04:40:13 CDT)
Generate psf file of DMPC membrane
- Gan, Yong $UMC-Student$ (Thu Apr 28 2005 - 11:58:02 CDT)
- Gan, Yong $UMC-Student$ (Wed Apr 27 2005 - 22:10:34 CDT)
Generate psf files from Scott Feller's lipid coordinates
- Ranyere Deyler (Mon May 17 2010 - 16:57:10 CDT)
- Jeffrey Potoff (Sun May 16 2010 - 01:35:23 CDT)
- Dai, Jian1 (Sat May 15 2010 - 13:46:36 CDT)
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 .tpr file using NAMD files
- Jeffrey Potoff (Mon Dec 19 2011 - 12:05:56 CST)
- Axel Kohlmeyer (Mon Dec 19 2011 - 11:59:35 CST)
- rajitha tatikonda (Mon Dec 19 2011 - 00:32:56 CST)
Generating a gromacs topology file for analyzing NAMD trajectories
- Giovanni Bellesia (Thu Dec 06 2007 - 12:25:37 CST)
- Richard Wood (Thu Dec 06 2007 - 11:51:03 CST)
- Xu, Jiancong (Thu Dec 06 2007 - 09:41:22 CST)
- L. Michel Espinoza-Fonseca (Thu Dec 06 2007 - 09:11:44 CST)
- patrick wintrode (Thu Dec 06 2007 - 08:54:25 CST)
- Ilya Chorny (Wed Dec 05 2007 - 16:13:31 CST)
- Giovanni Bellesia (Wed Dec 05 2007 - 15:25:42 CST)
- patrick wintrode (Wed Dec 05 2007 - 14:15:11 CST)
- L. Michel Espinoza-Fonseca (Wed Dec 05 2007 - 14:52:52 CST)
Generating a lot of segments in proper order and selection around a center of mass
- Leonardo Sepulveda Durán (Wed Jun 01 2005 - 16:13:35 CDT)
Generating binvelocities, bincoordinates, and extendedSystem files (AMBER)
- Axel Kohlmeyer (Sun Feb 14 2010 - 04:54:11 CST)
- Johann Morr (Sat Feb 13 2010 - 23:01:32 CST)
Generating lipid bilayer model
- Cesar Luis Avila (Mon Mar 27 2006 - 13:23:06 CST)
- Gan, Yong (Sat Mar 25 2006 - 23:31:18 CST)
Generating novel structure
- Fangqiang Zhu (Tue Mar 02 2004 - 13:38:12 CST)
generating psf & energy calculation for unusual amino acid - Aib
- JC Gumbart (Fri Nov 07 2008 - 00:43:29 CST)
- balaji nagarajan (Thu Nov 06 2008 - 21:57:17 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 a drug, trimethoprim
- Charles Moad (Sat May 14 2005 - 18:00:08 CDT)
Generating psf for NPC1
- Joshua Lioi (Thu Nov 19 2009 - 10:45:07 CST)
generating psf for RNA using psfgen
- MinSoo Kim (Fri Jan 30 2004 - 01:53:40 CST)
Generating PSF from modified AMBER ff
- Seth Lilavivat (Wed Mar 19 2008 - 12:53:27 CDT)
- Seth Lilavivat (Wed Mar 19 2008 - 12:30:03 CDT)
- Peter Freddolino (Wed Mar 19 2008 - 12:39:50 CDT)
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)
generating xsc and vel files
- David A. Horita (Mon Feb 02 2009 - 10:29:29 CST)
- Peter Freddolino (Mon Feb 02 2009 - 10:46:40 CST)
Generation of .psf file of DNA
- Chris Harrison (Thu Jul 09 2009 - 09:42:10 CDT)
- Jian Liu (Thu Jul 09 2009 - 07:43:21 CDT)
- sudipta (Thu Jul 09 2009 - 01:53:25 CDT)
Generation of average trajectory
- Roman Petrenko (Mon Oct 12 2009 - 21:02:03 CDT)
- Nicholas M Glykos (Mon Oct 12 2009 - 12:55:11 CDT)
- Axel Kohlmeyer (Mon Oct 12 2009 - 10:40:08 CDT)
- Joshua Adelman (Mon Oct 12 2009 - 09:43:56 CDT)
- Monika Sharma (Mon Oct 12 2009 - 09:24:16 CDT)
- Nicholas M Glykos (Mon Oct 12 2009 - 05:06:26 CDT)
- mon_sharma_at_research.iiit.ac.in (Mon Oct 12 2009 - 02:26:02 CDT)
generation of non-standart charmm topology
- ziemys_at_ecr6.ohio-state.edu (Wed Jan 11 2006 - 12:08:12 CST)
geometric mean
- Leandro Martinez (Thu Jan 29 2004 - 07:53:58 CST)
geomtery optimization with namd
- Roman Petrenko (Mon May 04 2009 - 16:18:03 CDT)
Get number of timesteps from DCD via script
- Bjoern Olausson (Thu Feb 10 2011 - 03:52:44 CST)
- Joshua D. Moore (Wed Feb 09 2011 - 08:40:27 CST)
- Joshua D. Moore (Wed Feb 09 2011 - 06:41:06 CST)
- Axel Kohlmeyer (Wed Feb 09 2011 - 08:43:21 CST)
- Bjoern Olausson (Wed Feb 09 2011 - 08:05:42 CST)
- Bjoern Olausson (Wed Feb 09 2011 - 08:32:13 CST)
- Axel Kohlmeyer (Wed Feb 09 2011 - 07:43:17 CST)
- Bjoern Olausson (Wed Feb 09 2011 - 06:37:20 CST)
- Joshua D. Moore (Tue Feb 08 2011 - 17:01:32 CST)
- Joshua D. Moore (Tue Feb 08 2011 - 16:56:02 CST)
- Andrew Emerson (Tue Feb 08 2011 - 08:00:07 CST)
- Bjoern Olausson (Tue Feb 08 2011 - 05:24:29 CST)
- Chris Harrison (Mon Feb 07 2011 - 12:34:25 CST)
- Bjoern Olausson (Mon Feb 07 2011 - 06:52:39 CST)
Get restart file (restart.coor) from DCD
- Joshua D. Moore (Mon Mar 28 2011 - 20:18:11 CDT)
- Ismail, Mohd F. (Mon Mar 28 2011 - 17:41:56 CDT)
get total force on a group of atoms within GlobalMasterSMD
- Liao Chen (Sun Apr 11 2010 - 19:02:16 CDT)
getbond (Tcl forces) / PBC
- Arturas Ziemys (Thu Nov 30 2006 - 10:12:32 CST)
getting #.IND #QNAN after phase 8
- Amin R. Mazloom (Mon Jun 05 2006 - 14:25:25 CDT)
Getting density of water..
- Arun Krishnan (Fri Nov 09 2007 - 02:08:39 CST)
- Arun Krishnan (Fri Nov 09 2007 - 01:24:36 CST)
getting desired angle
- Axel Kohlmeyer (Mon Oct 25 2010 - 08:08:30 CDT)
- Kwee Hong (Sun Oct 24 2010 - 22:06:33 CDT)
- Axel Kohlmeyer (Sun Oct 24 2010 - 18:06:00 CDT)
- Kwee Hong (Sat Oct 23 2010 - 03:49:23 CDT)
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)
Getting total energy of system + pressure and temperature bath.
- Jerome Henin (Thu Oct 16 2008 - 11:21:55 CDT)
- Audrey Salazar (Wed Oct 15 2008 - 16:23:12 CDT)
Gibbs potential
- sajad falsafi (Tue Jun 07 2011 - 02:14:40 CDT)
- Patriche Simona (Mon Jun 06 2011 - 10:10:01 CDT)
Gigabit ethernet switch for cluster
- Dow_Hurst (Wed Mar 22 2006 - 21:33:57 CST)
- Cesar Luis Avila (Tue Mar 21 2006 - 14:43:45 CST)
glibc detected : corrupted double-linked list: 0xa4657ad8
- Vlad Cojocaru (Wed Aug 19 2009 - 04:43:40 CDT)
- Vlad Cojocaru (Wed Aug 19 2009 - 02:17:55 CDT)
- Vlad Cojocaru (Wed Aug 19 2009 - 02:46:08 CDT)
- Cojocaru,Vlad (Tue Aug 18 2009 - 15:52:59 CDT)
- George Madalin Giambasu (Tue Aug 18 2009 - 12:05:22 CDT)
- Vlad Cojocaru (Tue Aug 18 2009 - 05:44:58 CDT)
- Vlad Cojocaru (Tue Aug 18 2009 - 05:15:55 CDT)
glibc runtime errors on BlueGeneP occur only if running the cvs code (18.08) and not namd 2.6
- Vlad Cojocaru (Wed Aug 19 2009 - 06:02:26 CDT)
- Vlad Cojocaru (Wed Aug 19 2009 - 05:38:47 CDT)
global and internal motion of protein
- Nicholas M Glykos (Wed Oct 27 2010 - 04:43:08 CDT)
- Ajasja LjubetiÄ (Wed Oct 27 2010 - 03:12:08 CDT)
- divya nayar (Wed Oct 27 2010 - 02:39:04 CDT)
Globus-WS Submission of a NAMD Job ..
- Graham Jenkins (Fri Sep 28 2007 - 02:19:28 CDT)
glucose CHARMM force field
- Hyonseok Hwang (Thu Mar 31 2005 - 12:29:13 CST)
- Aaron Oakley (Tue Mar 29 2005 - 23:34:00 CST)
- Wei Chen (Tue Mar 29 2005 - 23:05:06 CST)
- Michel Espinoza-Fonseca (Tue Mar 29 2005 - 22:13:35 CST)
- Hyonseok Hwang (Tue Mar 29 2005 - 21:37:34 CST)
glycosaminoglycan with GLYCAM06 in amber format
- Massimiliano Porrini (Tue Dec 20 2011 - 09:46:18 CST)
- Massimiliano Porrini (Tue Dec 20 2011 - 08:55:58 CST)
- Lachele Foley (Lists) (Tue Dec 20 2011 - 08:53:59 CST)
- Massimiliano Porrini (Mon Dec 19 2011 - 05:04:40 CST)
- Massimiliano Porrini (Sun Dec 18 2011 - 10:44:48 CST)
Gold nanoparticle and 1-octanethiol
- Edroaldo Lummertz da Rocha (Thu Apr 28 2011 - 19:07:44 CDT)
- Edroaldo Lummertz da Rocha (Wed Apr 27 2011 - 07:01:52 CDT)
- Edroaldo Lummertz da Rocha (Mon Apr 25 2011 - 13:14:22 CDT)
GPGPU Programming summer school at University of Tennessee, Aug 10-14.
- Axel Kohlmeyer (Mon Jun 29 2009 - 14:43:11 CDT)
GPRESSURE becomes nan in TIP4P simulation
- Udaysankar Midya (Sat Dec 31 2011 - 05:23:35 CST)
GPU acceleration press
- Jim Phillips (Fri May 25 2007 - 14:00:42 CDT)
GPU heavy models?
- Michael Di Domenico (Tue Dec 14 2010 - 08:03:52 CST)
gpu pressure control
- Chris Harrison (Sun Jan 04 2009 - 12:23:48 CST)
- JC Gumbart (Sun Dec 28 2008 - 23:27:07 CST)
- Daniel Miscevski (Sun Dec 28 2008 - 23:10:46 CST)
GPU Selection in NAMD CUDA
- Axel Kohlmeyer (Tue Sep 22 2009 - 04:39:59 CDT)
- Ron Stubbs (Mon Sep 21 2009 - 14:56:42 CDT)
GPU-CPU small-scale machine for NAMD
- Jim Phillips (Wed May 18 2011 - 12:48:52 CDT)
- Darko Stefanovski (Tue May 17 2011 - 12:10:31 CDT)
- Francesco Pietra (Mon May 16 2011 - 03:45:37 CDT)
gradient for minimization
- Shirley Li (Thu Mar 02 2006 - 12:59:40 CST)
gradient nan
- Brian Bennion (Mon Feb 07 2005 - 11:33:00 CST)
- Hemant Kushwaha (Mon Feb 07 2005 - 00:17:04 CST)
gradient tolerance
- Ramya Narasimhan (Tue Jun 08 2010 - 05:48:11 CDT)
- Brian Bennion (Wed Oct 13 2004 - 14:43:04 CDT)
- mdcooper (Tue Oct 12 2004 - 18:52:43 CDT)
Gradient tolerance nan for A three-atom simulation
- Peter Freddolino (Mon Jan 12 2009 - 12:17:49 CST)
- BIN ZHANG (Mon Jan 12 2009 - 12:03:52 CST)
- Peter Freddolino (Fri Jan 09 2009 - 16:14:48 CST)
- Peter Freddolino (Fri Jan 09 2009 - 16:14:33 CST)
- accomp lin (Fri Jan 09 2009 - 02:51:43 CST)
- Peter Freddolino (Thu Jan 08 2009 - 13:19:39 CST)
- accomp lin (Tue Jan 06 2009 - 22:20:18 CST)
- JC Gumbart (Mon Jan 05 2009 - 23:24:35 CST)
- accomp lin (Mon Jan 05 2009 - 23:09:41 CST)
Gradient tolerance--total or per atom?
- Chang, Christopher (Tue Apr 26 2005 - 11:46:07 CDT)
gradual increase in the temperature after minimization
- gurunath katagi (Wed Dec 09 2009 - 12:21:34 CST)
gradually pressure change (increase/decrease)
- Arneh Babakhani (Tue Feb 28 2006 - 12:44:58 CST)
- ARTURAS ZIEMYS (Tue Feb 28 2006 - 11:44:08 CST)
Gramicidin
- Swarna Patra (Mon Jun 20 2005 - 20:54:09 CDT)
Grand canonical ensemble
- Peter Freddolino (Mon Jan 28 2008 - 08:51:09 CST)
- michael_at_perfect-kreim.de (Mon Jan 28 2008 - 07:20:11 CST)
Graphene pdb/psf files cannot be read by psfgen
- Axel Kohlmeyer (Thu Feb 16 2012 - 07:39:36 CST)
- Wanzhi Qiu (Thu Feb 16 2012 - 00:36:20 CST)
- Axel Kohlmeyer (Thu Feb 16 2012 - 00:09:13 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 23:58:52 CST)
- Axel Kohlmeyer (Wed Feb 15 2012 - 23:13:47 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 23:04:53 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 22:41:23 CST)
- kanchi subbarao rao (Wed Feb 15 2012 - 21:48:00 CST)
- Axel Kohlmeyer (Wed Feb 15 2012 - 20:57:14 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 20:50:30 CST)
- Axel Kohlmeyer (Wed Feb 15 2012 - 20:13:44 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 20:12:05 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 20:06:01 CST)
- kanchi subbarao rao (Wed Feb 15 2012 - 08:11:10 CST)
- Cruz-Chu Eduardo Roberto (Wed Feb 15 2012 - 05:06:31 CST)
- Wanzhi Qiu (Wed Feb 15 2012 - 01:14:04 CST)
Grid Forces
- Chris Harrison (Sat Jun 27 2009 - 09:53:55 CDT)
- gbellesia_at_chem.ucsb.edu (Thu Jun 25 2009 - 15:31:19 CDT)
Grid Forces documentation
- Eduardo Cruz-Chu (Thu Jul 16 2009 - 14:20:11 CDT)
- Chris Harrison (Thu Jul 16 2009 - 12:24:00 CDT)
- Hugh Martin (Thu Jul 16 2009 - 08:02:04 CDT)
grid-based correction map
- yandong Huang (Thu Aug 12 2010 - 08:52:33 CDT)
GridForces methodology in NAMD 2.7b1
- Robert Brunner (Thu May 28 2009 - 16:46:16 CDT)
- Giovanni Bellesia (Fri May 22 2009 - 13:26:16 CDT)
gromacs analysis tools
- Axel Kohlmeyer (Sun Apr 03 2011 - 14:28:04 CDT)
- Francesco Oteri (Sun Apr 03 2011 - 13:47:19 CDT)
- Joshua Adelman (Sun Apr 03 2011 - 10:45:16 CDT)
- Molecular Dynamics (Sun Apr 03 2011 - 04:33:14 CDT)
- Molecular Dynamics (Sun Apr 03 2011 - 04:54:35 CDT)
Gromacs analysis tools for Namd output
- Axel Kohlmeyer (Wed Feb 01 2012 - 11:48:47 CST)
- PAUL NEWMAN (Wed Feb 01 2012 - 11:41:40 CST)
Gromacs force field paramets: Syntax error in ATOMS
- Sichun Yang (Wed Jun 23 2004 - 03:09:39 CDT)
Gromacs parameters in NAMD
- Kasson (Thu Oct 20 2005 - 13:21:06 CDT)
Gromacs simulation not running in NAMD
- abhijit ramachandran (Tue Mar 24 2009 - 10:44:47 CDT)
- Peter Freddolino (Mon Mar 23 2009 - 22:43:27 CDT)
- abhijit ramachandran (Mon Mar 23 2009 - 21:19:32 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)
Group forces in tclForces
- Benjamin Bouvier (Mon Jul 27 2009 - 06:02:12 CDT)
GTP topology file
- tiziano gallo cassarino (Fri Mar 20 2009 - 08:47:23 CDT)
guesscoord fails, hydrogen adding problem, output pdb is all zeros
- JC Gumbart (Sat Jul 28 2007 - 10:06:45 CDT)
- Venky (Sat Jul 28 2007 - 03:45:05 CDT)
gurukatagi@gmail.com
- Marcos Sotomayor (Thu Feb 23 2012 - 16:44:47 CST)
- Aron Broom (Wed Feb 22 2012 - 12:08:08 CST)
- Ajasja LjubetiÄ (Wed Feb 22 2012 - 11:51:51 CST)
- Gurunath Katagi (Wed Feb 22 2012 - 11:22:01 CST)
- Aron Broom (Mon Feb 06 2012 - 12:09:08 CST)
- Ajasja LjubetiÄ (Mon Feb 06 2012 - 11:05:26 CST)
- Gurunath Katagi (Mon Feb 06 2012 - 10:37:49 CST)
H-bond and salt bridge between protein dimer
- Eduard Schreiner (Sat Oct 30 2010 - 08:31:02 CDT)
- surendra jain (Sat Oct 30 2010 - 07:17:55 CDT)
H-bond energy
- amit dong (Thu Jan 11 2007 - 04:24:04 CST)
H-bond occupancy in nucleic acids
- Tianjiao Wang (Thu Nov 20 2008 - 10:08:27 CST)
H-H bond in solvate
- Jorge Pikunic (Sat Jul 30 2005 - 09:35:13 CDT)
- Jorge Pikunic (Sat Jul 30 2005 - 08:57:59 CDT)
H-H bond in TIP3 water
- Jim Phillips (Fri Aug 05 2005 - 11:11:15 CDT)
- Jorge Pikunic (Mon Aug 01 2005 - 17:21:26 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)
hanging at startup phase 0
- Dong Luo (Thu May 05 2005 - 13:59:37 CDT)
- surendra negi (Thu May 05 2005 - 12:25:06 CDT)
- Gengbin Zheng (Thu May 05 2005 - 11:00:22 CDT)
- Dong Luo (Thu May 05 2005 - 10:47:31 CDT)
Happy Viagra
- Brittany Collier (Tue Jun 12 2007 - 03:36:22 CDT)
- Natasha Kerr (Fri Jun 08 2007 - 07:54:55 CDT)
- Dustin Waller (Wed Jun 06 2007 - 12:48:07 CDT)
Haptic Device
- Uday Chippada (Fri Apr 02 2004 - 13:55:42 CST)
Hard sphere potential
- Axel Kohlmeyer (Thu Feb 02 2012 - 22:41:22 CST)
- M.Raviprasad (Thu Feb 02 2012 - 22:18:23 CST)
- Axel Kohlmeyer (Thu Feb 02 2012 - 20:56:09 CST)
- M.Raviprasad (Thu Feb 02 2012 - 20:20:14 CST)
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)
hard wall
- Mauricio Carrillo Tripp (Thu Jun 23 2005 - 11:24:00 CDT)
Hardware for NAMD / VMD machine
- Axel Kohlmeyer (Fri Jul 03 2009 - 11:56:08 CDT)
- Olve Peersen (Fri Jul 03 2009 - 01:26:11 CDT)
Harmonic Constrain like MMFP in CHARMM
- Giacomo Fiorin (Tue Jan 24 2012 - 09:40:08 CST)
- Vahid Mirjalili (Mon Jan 23 2012 - 14:56:55 CST)
- Giacomo Fiorin (Sat Jan 21 2012 - 01:24:14 CST)
- Vahid Mirjalili (Fri Jan 20 2012 - 19:41:28 CST)
- Giacomo Fiorin (Fri Jan 20 2012 - 18:42:26 CST)
- Vahid Mirjalili (Fri Jan 20 2012 - 17:52:14 CST)
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 constraint when equilibrate the system
- Naiyin Yu (Sun Jan 17 2010 - 00:32:57 CST)
Harmonic Constraint: 2 types
- Morad Alawneh (Thu Nov 30 2006 - 14:32:27 CST)
- JC Gumbart (Sun Nov 26 2006 - 23:21:21 CST)
- Morad Alawneh (Sun Nov 26 2006 - 19:36:15 CST)
Harmonic dihedral restraints
- Jeff Wereszczynski (Mon May 07 2007 - 19:15:30 CDT)
- Christopher Rowley (Mon May 07 2007 - 16:57:08 CDT)
harmonic distance restraint
- X Zheng (Tue Jan 16 2007 - 16:02:59 CST)
harmonic restraint
- Amit Paliwal (Tue Jun 15 2004 - 12:23:10 CDT)
harmonic restraint between two atoms
- Leonardo Trabuco (Mon May 26 2008 - 11:34:27 CDT)
- Leonardo Trabuco (Mon May 26 2008 - 12:01:15 CDT)
- Esben A. Gad (Mon May 26 2008 - 03:55:16 CDT)
Harmonic restraint parameters
- Bernardo Sosa Padilla Araujo (Mon Nov 09 2009 - 13:49:37 CST)
Harmonic restraints for moving residue positions??
- Charles Danko (Sat Jan 08 2005 - 15:03:50 CST)
Harmonically constrained simulations
- JT (Thu May 21 2009 - 11:25:55 CDT)
- Sumanth Jamadagni (Thu May 21 2009 - 11:47:26 CDT)
- Sumanth Jamadagni (Thu May 21 2009 - 10:00:13 CDT)
has anyone patched NAG to ASN?
- JC Gumbart (Tue Jun 26 2007 - 14:16:00 CDT)
- Irene Newhouse (Mon Jun 25 2007 - 20:57:03 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)
hBond colvars and patching
- Giacomo Fiorin (Fri Mar 11 2011 - 11:40:06 CST)
- Francesco Pietra (Fri Mar 11 2011 - 09:07:20 CST)
- Peter Freddolino (Tue Mar 08 2011 - 13:48:53 CST)
- Francesco Pietra (Tue Mar 08 2011 - 00:34:36 CST)
- Peter Freddolino (Mon Mar 07 2011 - 17:08:23 CST)
- Francesco Pietra (Mon Mar 07 2011 - 10:04:37 CST)
- Peter Freddolino (Mon Mar 07 2011 - 09:19:20 CST)
- Francesco Pietra (Mon Mar 07 2011 - 00:12:54 CST)
- Giacomo Fiorin (Sun Mar 06 2011 - 22:57:04 CST)
- Francesco Pietra (Sun Mar 06 2011 - 14:05:47 CST)
hBond component in colvars and patching
- Francesco Pietra (Sat Mar 05 2011 - 14:38:45 CST)
hbonds output!!!
- Eunice Ramirez Melendez (Tue Jul 19 2005 - 11:59:30 CDT)
HD speed ??
- Georgios Papadopoulos (Sun Apr 30 2006 - 03:13:36 CDT)
headgroup area calculation
- ipsita basu (Wed Jul 14 2010 - 02:05:22 CDT)
- Branko (Mon Jul 12 2010 - 08:14:19 CDT)
- ipsita basu (Mon Jul 12 2010 - 07:33:47 CDT)
heat annealing conf file
- Molecular Dynamics (Fri Jun 03 2011 - 09:57:07 CDT)
- Ada Zhan (Thu Jun 02 2011 - 14:02:06 CDT)
- Molecular Dynamics (Thu Jun 02 2011 - 05:26:17 CDT)
Heat Capacity & Relaxation Functions
- Cetin Baloglu (Mon Apr 25 2005 - 03:22:11 CDT)
heat capacity: NPT vs. NVT
- Mark Abraham (Wed Oct 25 2006 - 19:56:15 CDT)
- Arturas Ziemys (Wed Oct 25 2006 - 09:53:37 CDT)
heat diffusion
- Jonathan Lee (Mon Jun 25 2007 - 12:38:12 CDT)
- Jonathan Lee (Fri Jun 22 2007 - 11:36:55 CDT)
- Jonathan Lee (Wed Jun 20 2007 - 17:39:22 CDT)
heat diffusion calculation
- Jonathan Lee (Tue Jun 19 2007 - 15:13:12 CDT)
- Jonathan Lee (Mon Jun 18 2007 - 16:13:00 CDT)
- Victor Ovchinnikov (Mon Jun 18 2007 - 14:58:13 CDT)
- QJos=E9_R=2E_Sabino=22?= (Mon Jun 18 2007 - 14:11:17 CDT)
- Jonathan Lee (Mon Jun 18 2007 - 12:16:20 CDT)
- Jonathan Lee (Fri Jun 15 2007 - 17:40:52 CDT)
Heat flux along CNT
- Andy Shelley (Tue Jul 01 2008 - 14:13:36 CDT)
heat flux when using langevin dynamics
- Philipp Schön (Thu Nov 01 2007 - 09:12:56 CDT)
Heating /Equilibration
- Axel Kohlmeyer (Fri Aug 26 2011 - 08:16:29 CDT)
- Babban Mia (Fri Aug 26 2011 - 05:20:23 CDT)
- Babban Mia (Wed Aug 24 2011 - 02:56:37 CDT)
heating a system
- Bernardo Sosa Padilla Araujo (Thu Oct 01 2009 - 11:51:10 CDT)
heating and binvelocities
- Jim Phillips (Fri Aug 06 2010 - 09:30:38 CDT)
- Dhiraj Srivastava (Tue Aug 03 2010 - 11:26:36 CDT)
Heating in NAMD
- Babban Mia (Sun Aug 21 2011 - 06:06:25 CDT)
- Babban Mia (Sat Aug 20 2011 - 05:37:53 CDT)
- Erik Nordgren (Fri Aug 19 2011 - 12:52:31 CDT)
- Babban Mia (Thu Aug 18 2011 - 10:13:08 CDT)
Heating in NPT
- Pellegrini Eric (Mon Sep 19 2011 - 07:44:04 CDT)
heating system
- Luca Bellucci (Mon May 28 2007 - 03:01:38 CDT)
- baxy (Sun May 27 2007 - 13:45:44 CDT)
- Luca (Sun May 27 2007 - 04:16:36 CDT)
- baxy (Sat May 26 2007 - 05:09:20 CDT)
- Richard Law (Fri May 25 2007 - 14:52:31 CDT)
- baxy (Fri May 25 2007 - 13:06:50 CDT)
Heating Up a system.
- Cesar Luis Avila (Thu Jun 29 2006 - 16:06:21 CDT)
heating with restraints
- AYTUG TUNCEL (Fri Jan 19 2007 - 12:12:05 CST)
Helix tilt
- Thomas C Bishop (Tue Jul 13 2010 - 01:08:45 CDT)
- Nicholas M Glykos (Tue Jul 06 2010 - 11:48:22 CDT)
- Eduard Schreiner (Tue Jul 06 2010 - 12:27:50 CDT)
- Bjoern Olausson (Tue Jul 06 2010 - 10:59:54 CDT)
- stefhoor (Tue Jul 06 2010 - 09:29:42 CDT)
Hello
- imran.1.618_at_gmail.com (Sat Oct 15 2011 - 00:32:59 CDT)
- murffyp_at_gmail.com (Tue Jun 21 2011 - 07:54:59 CDT)
Hello!
- Eric Perim (Wed Mar 17 2010 - 07:45:19 CDT)
help
- Jérôme Hénin (Thu Apr 22 2010 - 16:44:58 CDT)
- snoze pa (Mon Jan 07 2008 - 13:41:47 CST)
- Sathish Kumar Gurupatham (Thu May 24 2007 - 11:31:39 CDT)
- RICARDO VAZQUEZ (Thu May 03 2007 - 18:26:06 CDT)
Help !!! ERROR: Atoms mooving too fast
- Luis Cunha (Tue Apr 03 2007 - 20:53:10 CDT)
- Jeff Wereszczynski (Tue Apr 03 2007 - 18:02:33 CDT)
- Andrea Diaz (Tue Apr 03 2007 - 14:46:36 CDT)
- Juan Diaz (Tue Mar 27 2007 - 18:21:05 CDT)
- Juan Diaz (Tue Mar 27 2007 - 18:17:29 CDT)
Help building a desktop for namd
- Axel Kohlmeyer (Thu Apr 14 2011 - 08:37:20 CDT)
- Jeffrey Potoff (Thu Apr 14 2011 - 00:07:16 CDT)
- Axel Kohlmeyer (Wed Apr 13 2011 - 17:22:03 CDT)
- Gianluca Interlandi (Wed Apr 13 2011 - 17:06:53 CDT)
- Salvador H-V (Wed Apr 13 2011 - 11:34:18 CDT)
- Jim Phillips (Wed Apr 13 2011 - 10:17:27 CDT)
- Axel Kohlmeyer (Mon Apr 11 2011 - 16:34:22 CDT)
- Gianluca Interlandi (Mon Apr 11 2011 - 16:25:26 CDT)
- Gianluca Interlandi (Mon Apr 11 2011 - 16:21:27 CDT)
- Axel Kohlmeyer (Mon Apr 11 2011 - 15:06:33 CDT)
- Gianluca Interlandi (Mon Apr 11 2011 - 14:41:28 CDT)
- Axel Kohlmeyer (Mon Apr 11 2011 - 12:55:34 CDT)
- Salvador H-V (Mon Apr 11 2011 - 12:22:01 CDT)
- Axel Kohlmeyer (Sun Apr 10 2011 - 12:52:59 CDT)
- Salvador H-V (Sun Apr 10 2011 - 12:40:05 CDT)
help generating psf files
- Peter Freddolino (Fri Oct 07 2005 - 10:18:02 CDT)
- Anna Modzelewska (Fri Oct 07 2005 - 09:16:57 CDT)
- Anna Modzelewska (Fri Oct 07 2005 - 02:58:19 CDT)
- Peter Freddolino (Thu Oct 06 2005 - 15:22:01 CDT)
- Anna Modzelewska (Thu Oct 06 2005 - 08:55:18 CDT)
- Anna Modzelewska (Thu Oct 06 2005 - 02:37:14 CDT)
- Peter Freddolino (Wed Oct 05 2005 - 22:09:07 CDT)
- Richard Wood (Tue Oct 04 2005 - 11:37:08 CDT)
help in a FEP restart?
- Chris Chipot (Sat Nov 26 2011 - 10:51:57 CST)
- Bruno Luís Pinto de Oliveira (Sat Nov 26 2011 - 10:15:13 CST)
Help in FEP backward/reverse calculation
- Jérôme Hénin (Fri Sep 23 2011 - 03:22:52 CDT)
- Bruno Luís Pinto de Oliveira (Thu Sep 22 2011 - 14:36:38 CDT)
help in FEP calculations : analysis/confirmation of results
- Bruno Luís Pinto de Oliveira (Thu Sep 08 2011 - 13:59:23 CDT)
help in FEP calculations_binding free energy difference between 2 inhibitors
- Chirag Vora (Mon Sep 05 2011 - 16:36:04 CDT)
- Bruno Luís Pinto de Oliveira (Mon Sep 05 2011 - 13:08:58 CDT)
- Bruno Luís Pinto de Oliveira (Thu Sep 01 2011 - 10:04:41 CDT)
Help in reverse Free Energy perturbation - hysteresis
- Chris Chipot (Wed Oct 05 2011 - 01:10:24 CDT)
- Bruno Luís Pinto de Oliveira (Tue Oct 04 2011 - 14:29:34 CDT)
- Chris Chipot (Mon Oct 03 2011 - 07:05:16 CDT)
- Jérôme Hénin (Mon Oct 03 2011 - 06:49:46 CDT)
- Bruno Luís Pinto de Oliveira (Mon Oct 03 2011 - 05:24:58 CDT)
help needed
- harish vashisth (Tue Mar 01 2011 - 10:00:46 CST)
- Richard Wood (Tue Mar 01 2011 - 09:25:51 CST)
help needed on node list
- srinivasa murthy (Tue Sep 16 2003 - 23:36:51 CDT)
Help Needed>Compiling source namd mpi enabled for a linux cluster
- Vincent Kraeutler (Fri Jul 27 2007 - 03:47:40 CDT)
- Daniel.G.Roberts_at_sanofi-aventis.com (Wed Jul 25 2007 - 16:31:35 CDT)
help on compiling error
- Binquan luan (Thu Jun 01 2006 - 11:32:44 CDT)
help on error message during compiling
- Gengbin Zheng (Wed Apr 05 2006 - 11:32:45 CDT)
- Binquan luan (Mon Apr 03 2006 - 19:43:14 CDT)
Help on mutation
- JÃ©rÃ´me HÃ©nin (Wed Jul 05 2006 - 16:36:22 CDT)
- surendra negi (Wed Jul 05 2006 - 15:21:16 CDT)
- Pijush Ghosh (Sun Jul 02 2006 - 01:24:19 CDT)
help on NAMD code
- Binquan luan (Tue Apr 11 2006 - 13:12:12 CDT)
Help pls: Got error on FEP calculation: ERROR: The following variables are NOT VALID lambda2...
- Li, Hongzhi (Mon Nov 09 2009 - 12:18:59 CST)
Help reg. input file
- snoze pa (Wed Jan 02 2008 - 12:35:19 CST)
help regarding NAMD equilibration
- Dr. Luis Rosales León (Tue Apr 15 2008 - 12:39:24 CDT)
- snoze pa (Tue Apr 15 2008 - 10:39:54 CDT)
- Low Soo Mei (Tue Apr 15 2008 - 01:05:25 CDT)
- snoze pa (Mon Apr 14 2008 - 18:11:46 CDT)
help requested
- Sridhar Vaddadi (Wed Sep 23 2009 - 11:23:36 CDT)
Help required for nanoscale simulation
- amit banerjee (Wed Jul 13 2011 - 03:03:45 CDT)
help running NAMD energy at multiple stable temperatures (newbie)
- Chris Harrison (Wed Mar 04 2009 - 11:12:52 CST)
- Eric H. Lee (Tue Mar 03 2009 - 00:05:58 CST)
- Peter Freddolino (Mon Mar 02 2009 - 23:37:11 CST)
- Marie N (Mon Mar 02 2009 - 23:32:04 CST)
help whit distance restraint
- Leonardo Herrera (Wed Jun 02 2010 - 17:37:57 CDT)
- Axel Kohlmeyer (Wed Jun 02 2010 - 18:11:00 CDT)
help with adding a new force filed into NAMD
- Peter Freddolino (Thu Jun 15 2006 - 14:37:45 CDT)
- liu liuxiandong (Thu Jun 15 2006 - 10:44:10 CDT)
help with calcforces
- Prabhakar Bhimalapuram (Fri May 02 2008 - 13:32:22 CDT)
Help With colvars/abf Please
- Angelo Rossi (Sun Jan 30 2011 - 11:00:38 CST)
- Jérôme Hénin (Sun Jan 30 2011 - 09:10:50 CST)
- Angelo Rossi (Sun Jan 30 2011 - 07:09:41 CST)
Help with cys unprotonated
- Leonardo Herrera (Tue Jun 15 2010 - 11:43:47 CDT)
- ehenriques_at_qui.uc.pt (Tue Jun 15 2010 - 05:08:55 CDT)
- Leonardo Herrera (Mon Jun 14 2010 - 20:24:39 CDT)
Help with NAMD + Clustermatic 4 please
- Mike Grommet (Sun Dec 14 2003 - 01:01:55 CST)
Help with psf and par for small molecules
- santanu chatterjee (Wed Aug 03 2005 - 15:12:40 CDT)
help with running namd-cuda for the tutorials
- Paul Rigor (uci) (Fri Nov 20 2009 - 21:05:48 CST)
- Axel Kohlmeyer (Fri Nov 20 2009 - 20:56:52 CST)
- Paul Rigor (uci) (Fri Nov 20 2009 - 20:06:38 CST)
- Axel Kohlmeyer (Fri Nov 20 2009 - 11:25:14 CST)
- Paul Rigor (uci) (Fri Nov 20 2009 - 10:24:20 CST)
Help with SMD
- Eunice Ramirez Melendez (Wed Jul 20 2005 - 03:37:44 CDT)
- Michel Espinoza-Fonseca (Wed Jul 20 2005 - 11:18:31 CDT)
- Blake Charlebois (Wed Jul 20 2005 - 11:10:47 CDT)
- Richard Law (Wed Jul 20 2005 - 10:54:50 CDT)
- Eunice Ramirez Melendez (Tue Jul 19 2005 - 12:08:34 CDT)
help with TCL forces script
- Jim Pfaendtner (Sun Apr 27 2008 - 05:47:30 CDT)
Help with TCl script
- Ilya Chorny (Fri Oct 26 2007 - 00:38:05 CDT)
- Ilya Chorny (Thu Oct 25 2007 - 23:44:49 CDT)
help with the equilibration script
- matziast_at_med.uth.gr (Tue Dec 28 2010 - 16:31:44 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! How to build charm++ on core 2 computer processor
- xiaojing gong (Tue Apr 10 2007 - 06:29:09 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!!
- JC Gumbart (Thu Jun 14 2007 - 14:07:59 CDT)
- shivam ghosh (Thu Jun 14 2007 - 06:43:31 CDT)
help!!!
- Brian Bennion (Wed Jul 19 2006 - 01:14:52 CDT)
- Giovanni Bellesia (Wed Jul 19 2006 - 00:38:18 CDT)
- hl332_at_drexel.edu (Wed Jul 19 2006 - 00:12:23 CDT)
Help, MD run errors
- Xiaobing Tian (Sun May 02 2004 - 21:06:58 CDT)
help-minimization and equilibration of Ubiquitin in a water box
- Zhi Qi (Thu Jan 12 2006 - 18:38:00 CST)
- JC Gumbart (Wed Jan 11 2006 - 19:52:10 CST)
- Zhi Qi (Wed Jan 11 2006 - 14:13:45 CST)
Help. Parameters for PSGL needed
- Cesar Luis Avila (Thu Dec 07 2006 - 09:49:48 CST)
Help: do you have the top parameter of Gla
- Wang,Ying (Tue Dec 02 2008 - 10:27:56 CST)
help: how to scale the velocities by a factor for a subset of the system?
- Yong Zhang (Tue Sep 05 2006 - 21:59:25 CDT)
Help: NAMD on cluster; nodes reject multiple connections
- David Kelly (Thu Jul 01 2010 - 00:33:11 CDT)
help:autopsf changed the structure!
- Peter Freddolino (Sun Nov 26 2006 - 22:13:22 CST)
- taojinwuhan_at_sohu.com (Sun Nov 26 2006 - 19:57:42 CST)
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 - Cysteine link
- Muhittin Emre Özdemir (Thu May 11 2006 - 02:43:17 CDT)
- Muhittin Emre Özdemir (Wed May 10 2006 - 05:42:19 CDT)
- Elsa F. Sousa Henriques (Tue May 09 2006 - 09:09:33 CDT)
- SÅ‚awek OrÅ‚owski (Tue May 09 2006 - 08:20:50 CDT)
- Muhittin Emre Özdemir (Tue May 09 2006 - 04:06:46 CDT)
Heme A topology?
- Olya Kravchenko (Thu Jan 22 2004 - 17:05:49 CST)
HEME and Cystein instead of His
- Bruno Luís Pinto de Oliveira (Wed Nov 23 2011 - 14:33:39 CST)
- Raul Araya (Wed Nov 23 2011 - 14:25:37 CST)
- Aron Broom (Wed Nov 23 2011 - 14:02:42 CST)
- Raul Araya (Wed Nov 23 2011 - 13:10:36 CST)
HEME patch
- surendra negi (Thu May 05 2005 - 13:38:37 CDT)
Hepl whit colvar subrutiene
- Giacomo Fiorin (Fri Jun 18 2010 - 20:11:10 CDT)
- Leonardo Herrera (Fri Jun 18 2010 - 16:11:19 CDT)
Hessian
- mdcooper (Mon Nov 01 2004 - 18:08:24 CST)
HETATM vs ATOM in .pdb file
- Bjoern Olausson (Wed Aug 31 2011 - 06:20:55 CDT)
- Axel Kohlmeyer (Wed Aug 31 2011 - 06:16:16 CDT)
- Andrea Holfelder (Wed Aug 31 2011 - 04:56:35 CDT)
Heteroatom entries
- Mithun Mitra (Tue Apr 27 2004 - 10:17:00 CDT)
Hexafluoro-2-propanol (HFIP) force parameters
- Dong Luo (Wed Jan 21 2009 - 15:04:43 CST)
Hexagonal boundary conditions
- Alessandro Cembran (Thu Sep 21 2006 - 10:34:51 CDT)
- Harindar Keer (Mon Jul 31 2006 - 13:23:50 CDT)
hexagonal box
- dimka (Tue Apr 17 2007 - 12:11:09 CDT)
Hexagonal cell and PME grid.
- Jan Saam (Tue Mar 01 2005 - 05:34:17 CST)
- Nicholas M Glykos (Tue Mar 01 2005 - 05:17:44 CST)
hexagonal crystal
- Allison Langham (Wed Mar 21 2007 - 11:22:26 CDT)
hexagonal unit cell
- Anna Modzelewska (Thu Jul 01 2004 - 03:49:56 CDT)
hexane
- lara lara (Sun Oct 17 2010 - 23:29:53 CDT)
- Jian Liu (Sun Oct 17 2010 - 23:10:34 CDT)
- Jian Liu (Sat Oct 16 2010 - 20:32:09 CDT)
- lara lara (Sat Oct 16 2010 - 04:00:09 CDT)
hi
- Sándor Kovács (Thu Jul 14 2011 - 14:19:52 CDT)
- kanchi subbarao rao (Thu Jul 14 2011 - 12:31:06 CDT)
- kanchi subbarao rao (Wed Jul 13 2011 - 13:47:30 CDT)
- murffyp_at_gmail.com (Sun May 22 2011 - 23:14:11 CDT)
- Bjoern Olausson (Thu May 19 2011 - 04:29:14 CDT)
- Jim Phillips (Wed May 18 2011 - 17:52:49 CDT)
- Giacomo Fiorin (Wed May 18 2011 - 10:28:48 CDT)
- kanchi subbarao rao (Wed May 18 2011 - 03:43:25 CDT)
- Segun Jung (Wed Dec 23 2009 - 00:59:44 CST)
- Leonardo Trabuco (Fri Jun 30 2006 - 13:39:52 CDT)
- Moumita Maiti (Fri Jun 30 2006 - 04:26:18 CDT)
- 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)
hi ,everyone.I have a problem about random force
- q=E2=BA=E9=C3=F7?= (Mon Jun 06 2005 - 11:48:08 CDT)
hi all
- Ajasja LjubetiÄ (Thu Jun 16 2011 - 07:29:53 CDT)
- kanchi subbarao rao (Wed Jun 15 2011 - 04:14:04 CDT)
hi all, I want to know how to turn the debug mode on of the namd
- q=E2=BA=E9=C3=F7?= (Mon Sep 26 2005 - 23:43:25 CDT)
- q=E2=BA=E9=C3=F7?= (Mon Sep 26 2005 - 09:56:17 CDT)
Hi, call NAMD from C
- Jerry Xu (Mon Jan 31 2005 - 09:28:44 CST)
Hi, I am a new user of Namd, and I met some problems using increment of temperature during simulation
- Ye Yang (Fri Feb 25 2011 - 13:40:43 CST)
Hi,all, the parameters for Strain
- uu zhu (Tue Jun 30 2009 - 01:32:26 CDT)
Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS
- Leonardo Sepulveda Durán (Fri Jun 24 2005 - 10:33:40 CDT)
- Phoenix (Fri Jun 24 2005 - 09:59:13 CDT)
- Leonardo Sepulveda Durán (Fri Jun 24 2005 - 09:30:26 CDT)
- Phoenix (Fri Jun 24 2005 - 00:08:37 CDT)
Hi,Thank you!
- Peter Murphy (Fri Jul 11 2008 - 03:46:57 CDT)
- Peter Murphy (Fri Jul 11 2008 - 03:35:29 CDT)
hi...
- Navratna Vajpai (Mon May 08 2006 - 04:36:33 CDT)
Hi: some doubt about nvt and npt equilibration
- johan strumpfer (Sun Jul 03 2011 - 20:53:47 CDT)
- bharat gupta (Sun Jul 03 2011 - 20:36:19 CDT)
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 atom velocity
- francesco oteri (Wed May 05 2010 - 14:12:49 CDT)
- francesco oteri (Tue May 04 2010 - 16:33:43 CDT)
- Mark M Huntress (Tue May 04 2010 - 14:36:56 CDT)
High background load warning message
- Cesar Luis Avila (Mon Jul 02 2007 - 14:48:33 CDT)
- Cesar Avila (Sun Jun 24 2007 - 13:56:24 CDT)
- Jerome Henin (Sat Jun 23 2007 - 20:57:37 CDT)
- Cesar Luis Avila (Sat Jun 23 2007 - 19:12:32 CDT)
high pressure
- tillmann.utesch_at_mail.tu-berlin.de (Tue Apr 20 2010 - 06:52:01 CDT)
- Giacomo Fiorin (Thu Mar 11 2010 - 13:00:56 CST)
- Tillmann Utesch (Thu Mar 11 2010 - 15:05:59 CST)
- Tillmann Utesch (Thu Mar 11 2010 - 10:29:22 CST)
- Dimitar V Pachov (Thu Mar 11 2010 - 09:09:56 CST)
- tillmann.utesch_at_mail.tu-berlin.de (Thu Mar 11 2010 - 06:01:06 CST)
High RMSD in Coarse Grain Simulation of Protein
- sunita gupta (Wed Oct 13 2010 - 03:06:22 CDT)
High RMSD of Coarse grain Protein
- Hannes Loeffler (Mon Oct 18 2010 - 09:01:20 CDT)
- sunita gupta (Mon Oct 18 2010 - 06:52:18 CDT)
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)
High VDW energies during minimization and dynamics
- Deva Priyakumar (Thu Apr 13 2006 - 14:41:22 CDT)
- Peter Freddolino (Thu Apr 13 2006 - 13:24:35 CDT)
- Peter Freddolino (Thu Apr 13 2006 - 13:22:07 CDT)
- Brian Bennion (Thu Apr 13 2006 - 12:47:30 CDT)
- Pijush Ghosh (Thu Apr 13 2006 - 11:52:35 CDT)
- Deva Priyakumar (Thu Apr 13 2006 - 10:23:38 CDT)
high vdw energy
- AYTUG TUNCEL (Fri Dec 01 2006 - 09:38:34 CST)
- Xiongce Zhao (Fri Dec 01 2006 - 07:44:12 CST)
- AYTUG TUNCEL (Thu Nov 30 2006 - 16:44:39 CST)
highthroughput NAMD
- Thomas C. Bishop (Thu Mar 11 2010 - 11:25:35 CST)
Hints for building namd2.8 on charm++ ibverbs layer?
- Bennion, Brian (Fri Sep 02 2011 - 18:06:15 CDT)
HIS modification
- yxiong_at_mail.ccnu.edu.cn (Wed Dec 17 2003 - 04:37:24 CST)
HIS to HSD, HSE, and HSP
- John Eargle (Tue Feb 14 2006 - 17:05:33 CST)
- John Eargle (Tue Feb 14 2006 - 14:48:05 CST)
Histamine topology file
- Peter Freddolino (Fri Jun 12 2009 - 13:52:12 CDT)
- r charbel maroun (Fri Jun 12 2009 - 11:32:35 CDT)
histidine protonation
- xiaojing gong (Thu Nov 02 2006 - 08:18:27 CST)
History file of an ABF smiulation
- Jerome Henin (Sat Sep 09 2006 - 15:16:55 CDT)
- Anahita Tafvizi (Sat Sep 09 2006 - 13:55:58 CDT)
Hoe to create psf file of C-terminous of protein?
- Qiang Zhong (Wed Aug 15 2007 - 02:48:53 CDT)
- JC Gumbart (Tue Aug 14 2007 - 19:49:33 CDT)
- Qiang Zhong (Tue Aug 14 2007 - 19:07:24 CDT)
- Peter Freddolino (Tue Aug 14 2007 - 09:00:20 CDT)
- Qiang Zhong (Mon Aug 13 2007 - 06:53:13 CDT)
hole on the surface of the waterbox
- Mert Gür (Fri Aug 28 2009 - 17:14:00 CDT)
- Mert Gür (Fri Aug 28 2009 - 13:45:03 CDT)
- Ana Vila Verde (Fri Aug 28 2009 - 07:48:35 CDT)
- Mert Gür (Fri Aug 28 2009 - 07:36:16 CDT)
- Nicholas M Glykos (Fri Aug 28 2009 - 07:38:00 CDT)
- Mert Gür (Fri Aug 28 2009 - 07:20:09 CDT)
- Ana Vila Verde (Fri Aug 28 2009 - 07:26:14 CDT)
- Ana Vila Verde (Fri Aug 28 2009 - 06:19:41 CDT)
- Mert Gür (Fri Aug 28 2009 - 06:12:25 CDT)
- Ana Vila Verde (Fri Aug 28 2009 - 05:54:06 CDT)
- Mert Gür (Fri Aug 28 2009 - 05:08:09 CDT)
how add bond in psf file?
- Jim Phillips (Thu Oct 05 2006 - 15:18:57 CDT)
- luca (Tue Sep 26 2006 - 08:09:09 CDT)
- Jim Phillips (Mon Sep 25 2006 - 14:05:27 CDT)
- Luca Bellucci (Mon Sep 25 2006 - 11:09:11 CDT)
- Jerome Henin (Mon Sep 25 2006 - 10:16:03 CDT)
- Luca Bellucci (Mon Sep 25 2006 - 08:18:27 CDT)
How are the SMD atoms connected to the center of mass
- Mert Gür (Wed Dec 02 2009 - 07:45:26 CST)
- Mert Gür (Tue Dec 01 2009 - 07:31:47 CST)
how best to build a GPU-accelerated desktop machine for NAMD?
- Axel Kohlmeyer (Fri Nov 19 2010 - 22:00:38 CST)
- Erik Nordgren (Fri Nov 19 2010 - 20:08:48 CST)
How can I calculate the distance between two atoms frame by frame?
- Jerome Henin (Sun Oct 19 2008 - 09:51:51 CDT)
- Grace Brannigan (Sun Oct 19 2008 - 01:39:03 CDT)
- Grace Brannigan (Sat Oct 18 2008 - 23:05:45 CDT)
- Axel Kohlmeyer (Sat Oct 18 2008 - 22:07:13 CDT)
- wayj86 wayj86 (Sat Oct 18 2008 - 21:15:25 CDT)
How can I connect different structures between them using VMD and NAMD?
- Patriche Simona (Sun Jul 04 2010 - 19:45:15 CDT)
how can i demonstrate that a chain-like molecule within a membrane.
- Chris Chipot (Wed Feb 15 2012 - 07:27:44 CST)
- superdirac (Wed Feb 15 2012 - 07:19:36 CST)
How can I do protein complex's simulation?
- JC Gumbart (Mon Oct 02 2006 - 19:57:54 CDT)
- Dhiraj Srivastava (Mon Oct 02 2006 - 19:58:29 CDT)
- Yuqi Liu (Mon Oct 02 2006 - 18:46:13 CDT)
How can I find topology and parameter files for heterocyclic, heteroaromatic, halogens and sugar compounds
- Lisa Brown (Fri Feb 27 2009 - 11:02:51 CST)
How can I fix lipid lateral area in membrane simulation?
- Leonardo Herrera (Tue Apr 14 2009 - 12:39:38 CDT)
How can I get parameters of unknown residues
- dongsheng lei (Wed Oct 31 2007 - 04:26:16 CDT)
how can i get the energy of a molecule of a whole system?
- JC Gumbart (Tue Feb 17 2009 - 14:28:36 CST)
- Wang,Ying (Tue Feb 17 2009 - 10:30:11 CST)
How can I increase the computing rate on the computer cluster
- xiaojing gong (Sun Oct 30 2005 - 05:44:24 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 monitor the force during constant velocity SMD?
- wayj86 wayj86 (Sat Nov 15 2008 - 07:26:02 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 can I set Tcouple ?
- mashaojie163 (Fri Jan 25 2008 - 20:13:26 CST)
How can I specify an exact initial velocity?
- Jerome Henin (Wed Nov 05 2008 - 03:56:46 CST)
- wayj86 wayj86 (Tue Nov 04 2008 - 20:01:09 CST)
- Jerome Henin (Tue Nov 04 2008 - 09:07:14 CST)
- wayj86 wayj86 (Tue Nov 04 2008 - 02:29:07 CST)
How can I use TIP4-P water model with NAMD?
- Nils Zimmermann (Fri Mar 30 2007 - 04:29:01 CDT)
How could I find which part of the protein became more flexible
- Yuxiao Wang (Tue Jun 19 2007 - 07:56:23 CDT)
How could I fixed the system just in Z-coordinate?
- Himanshu Khandelia (Wed May 23 2007 - 10:51:49 CDT)
- ali alizadeh (Wed May 23 2007 - 09:34:32 CDT)
How do I connect the non-overlwindows of ABF's results?
- Aurum Bai (Sun Jun 27 2010 - 23:14:38 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 debug tcl scripts in vmd ?
- Andriy Volynets (Mon Aug 04 2008 - 12:12:18 CDT)
How do you evaluate forces on a fixed atom?
- Bill K (Mon Nov 17 2008 - 15:33:38 CST)
How do you keep atoms a fixed distance apart?
- Leonardo Trabuco (Wed Nov 26 2008 - 01:23:18 CST)
- timko_at_physics.usyd.edu.au (Wed Nov 26 2008 - 00:59:47 CST)
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 does NAMD calculate Electrostatic potential energy (no periodic boundary condition)?
- Boyang Wang (Mon Dec 26 2005 - 17:46:55 CST)
How does NAMD count atoms in PDB files?
- Corenflos, Steven Charles (Thu Aug 21 2008 - 16:15:18 CDT)
how does namd handle violations of the minimum image convention?
- Boyang Wang (Tue Jan 10 2012 - 21:45:04 CST)
- Ana Celia Vila Verde (Mon Jan 09 2012 - 05:32:32 CST)
how gradually change (increase/decrease) pressure ?
- ARTURAS ZIEMYS (Mon Feb 27 2006 - 11:59:15 CST)
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 insert de harmonic restraint?
- Leonardo Herrera (Fri May 07 2010 - 15:33:18 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 is dG caluclated from dE during FEP?
- Floris Buelens (Fri Jun 19 2009 - 02:39:05 CDT)
- Michael Thomas (Wed Jun 17 2009 - 06:51:31 CDT)
how is NAMD output written in parallel mode?
- Ravinder Abrol (Tue Dec 06 2005 - 17:30:01 CST)
- Nicolas Sapay (Mon Dec 05 2005 - 08:17:58 CST)
- Ravinder Abrol (Mon Dec 05 2005 - 02:09:38 CST)
How is the maximum velocity limit set?
- Yinglong Miao (Fri Nov 30 2007 - 10:22:40 CST)
how long is enough to heat up and equilibrate
- JC Gumbart (Fri Nov 10 2006 - 08:06:21 CST)
- lily jin (Wed Nov 08 2006 - 11:05:37 CST)
how long should the simulation be run
- Peter Freddolino (Sat Apr 29 2006 - 16:22:11 CDT)
- genie lfs (Sat Apr 29 2006 - 04:33:50 CDT)
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 MD stopes at a specific distance?
- Shahid Qamar (Thu Jun 30 2005 - 12:41:54 CDT)
how obtain .xst form .dcd file?
- Erik Santiso (Wed Mar 23 2011 - 17:24:16 CDT)
- Ajasja LjubetiÄ (Wed Mar 23 2011 - 14:11:27 CDT)
- wood irene (Wed Mar 23 2011 - 12:59:01 CDT)
- wood irene (Mon Mar 21 2011 - 09:25:47 CDT)
how 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 the seed influences the molecular dynamics simulations?
- Agostino (Wed Sep 23 2009 - 04:15:26 CDT)
How to "extract" coordinates from a DCD trajectory file?
- Darren Anderson (Tue Aug 09 2005 - 07:54:51 CDT)
- Edelmiro Moman (Tue Aug 09 2005 - 07:10:00 CDT)
How to "twist" a molecule?
- Margaret S. Cheung (Thu Mar 22 2007 - 18:02:57 CDT)
How to "twist" a molecule? (resubmit)
- Margaret.Cheung_at_mail.uh.edu (Tue Jun 12 2007 - 11:19:36 CDT)
- Victor Ovchinnikov (Mon Jun 11 2007 - 20:21:35 CDT)
- Margaret S. Cheung (Mon Jun 11 2007 - 17:49:57 CDT)
- Grzegorz Jezierski (Wed Mar 28 2007 - 04:56:42 CDT)
- Margaret S. Cheung (Mon Mar 26 2007 - 14:09:33 CDT)
- Grzegorz Jezierski (Mon Mar 26 2007 - 04:46:53 CDT)
- Margaret S. Cheung (Mon Mar 26 2007 - 08:51:16 CDT)
- Margaret S. Cheung (Mon Mar 26 2007 - 08:49:42 CDT)
- JC Gumbart (Sun Mar 25 2007 - 00:33:00 CDT)
- Margaret S. Cheung (Fri Mar 23 2007 - 11:05:16 CDT)
How to access energies after MD step with Tcl ?
- Arturas Ziemys (Wed Sep 05 2007 - 11:30:31 CDT)
How to access velocity coordinates from within TclForces script
- Giacomo Fiorin (Thu Sep 17 2009 - 16:37:03 CDT)
- Patrick Hogan (Thu Sep 17 2009 - 14:43:21 CDT)
How to acetylate at the N terminus and amidate at the C terminus
- ydhuang2727 (Tue Dec 22 2009 - 21:10:45 CST)
how to add charged particles manually.
- ayhan duzgun (Wed Apr 26 2006 - 21:24:13 CDT)
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 add ions to a system
- jose correa (Wed Jan 28 2009 - 06:48:03 CST)
- uma mageshwari (Wed Jan 28 2009 - 03:18:19 CST)
- uma mageshwari (Wed Jan 28 2009 - 01:57:09 CST)
- uma mageshwari (Wed Jan 28 2009 - 01:08:12 CST)
how to add ions to a system/DASHOFSALT
- Thomas C. Bishop (Wed Jan 28 2009 - 09:10:23 CST)
How to analysis RAMD data?
- Vlad Cojocaru (Wed Sep 29 2010 - 02:26:28 CDT)
- asknamd asknamd (Tue Sep 28 2010 - 13:43:33 CDT)
How to analyze? Namdstats, namdplots, etc.
- Seth Lilavivat (Tue Mar 04 2008 - 11:55:19 CST)
How to append charmm stream file
- Michel Espinoza-Fonseca (Wed Oct 26 2005 - 12:36:01 CDT)
- Grace Shen (Wed Oct 26 2005 - 12:01:23 CDT)
how to apply a random force on a atom
- Phoenix (Tue Jun 07 2005 - 01:08:36 CDT)
- Blake Charlebois (Mon Jun 06 2005 - 16:06:44 CDT)
- q=E2=BA=E9=C3=F7?= (Mon Jun 06 2005 - 12:31:46 CDT)
How to apply an unsteady magnetic field?
- Axel Kohlmeyer (Fri Oct 30 2009 - 15:40:32 CDT)
- fereshteh moradi (Sun Oct 25 2009 - 01:52:29 CDT)
how to apply different damping coefficients simultaneously to different atoms in the same system.
- L. Michel Espinoza-Fonseca (Fri Oct 19 2007 - 00:09:06 CDT)
- Wang, Boyang (Thu Oct 18 2007 - 22:44:09 CDT)
- Jerome Henin (Thu Oct 18 2007 - 22:03:45 CDT)
- Wang, Boyang (Thu Oct 18 2007 - 20:25:36 CDT)
how to apply different temperature simultaneously to different atoms in the same system
- charlie (Wed Apr 27 2011 - 02:41:08 CDT)
how to apply restraints for phi and psi for alpha helix regions
- Chris Harrison (Sun Jan 04 2009 - 12:28:23 CST)
- Leonardo Trabuco (Fri Jan 02 2009 - 02:55:40 CST)
- Leonardo Trabuco (Thu Dec 11 2008 - 14:37:08 CST)
- Leonardo Trabuco (Thu Dec 11 2008 - 13:12:14 CST)
- Achani K. Yatawara (Thu Dec 11 2008 - 07:42:37 CST)
How to apply velocity to the entire system with COMmotion enabled
- Yinglong Miao (Mon Sep 29 2008 - 08:43:38 CDT)
How to atomselect several residues
- Nara Dashdorj (Wed Nov 02 2005 - 19:12:10 CST)
- JC Gumbart (Wed Nov 02 2005 - 18:38:27 CST)
- Grace Shen (Wed Nov 02 2005 - 17:28:50 CST)
How to avoid => ERROR: Step 100920 cell rescaling factor limited.
- Philipp Schön (Mon Aug 13 2007 - 07:28:39 CDT)
how to build AQP1 tetramer
- xiaojing gong (Thu Jun 23 2005 - 21:31:13 CDT)
How to build charm++ on core2 processor
- Gengbin Zheng (Wed Apr 11 2007 - 14:26:06 CDT)
- xiaojing gong (Tue Apr 10 2007 - 07:12:40 CDT)
How to build the psf file and the parameter file of a ligand
- taojinwuhan_at_sohu.com (Mon Jul 16 2007 - 03:08:33 CDT)
how to caculate the hydrogen bonds occupancy?
- Gianluca Interlandi (Sun May 13 2007 - 13:43:57 CDT)
- lnubiofox (Sun May 13 2007 - 09:36:35 CDT)
How to calculate Binding Free energy in NAMD
- Chris Chipot (Sat Jun 18 2011 - 07:51:20 CDT)
- jnsong (Sat Jun 18 2011 - 01:00:49 CDT)
How to calculate binding free energy of a protein-DNA complex by using NAMD?
- sudipta (Fri Jun 25 2010 - 11:14:38 CDT)
How to calculate free energy for conformational change
- gaurav bhatti (Thu Jul 30 2009 - 23:51:05 CDT)
- Lixia Jin Day (Thu Jul 30 2009 - 16:46:07 CDT)
how to calculate partial charge for ligand based on CHARMM principle?
- Jeffrey Potoff (Thu Jul 21 2011 - 12:02:49 CDT)
- AB (Thu Jul 21 2011 - 11:49:39 CDT)
How to calculate 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 calculate surface tension properly
- Bjoern Olausson (Wed Feb 08 2012 - 07:59:15 CST)
How to calculate the C alpha RMSD from NAMD trajectory
- priti arora (Fri Aug 03 2007 - 06:10:53 CDT)
- Shulin Zhuang (Fri Aug 03 2007 - 02:31:22 CDT)
how to cenvert NAMD binary coordinate file to text file
- Hannes Loeffler (Thu Oct 21 2010 - 04:48:59 CDT)
- jnsong (Thu Oct 21 2010 - 03:40:42 CDT)
- Ajasja LjubetiÄ (Thu Oct 21 2010 - 03:24:19 CDT)
- jnsong (Thu Oct 21 2010 - 03:34:11 CDT)
- OiniL (Thu Oct 21 2010 - 03:15:16 CDT)
- jnsong (Thu Oct 21 2010 - 02:27:06 CDT)
How to change psf file in the half way of VMD simulation?
- Boyang Wang (Tue May 03 2005 - 21:48:23 CDT)
How to chech the harmonic constraint work normally~
- Îº¿ (Thu Dec 16 2004 - 03:21:17 CST)
How to choose force field?
- Jerome Henin (Wed Oct 15 2008 - 11:11:16 CDT)
- Axel Kohlmeyer (Wed Oct 15 2008 - 10:57:01 CDT)
- Diego Alejandro Vargas (Tue Oct 14 2008 - 23:34:20 CDT)
How to circumvent: FATAL ERROR: Periodic cell has become too small for original patch grid!
- L. Michel Espinoza-Fonseca (Mon Apr 07 2008 - 15:10:43 CDT)
- Maxim Paliy (Mon Apr 07 2008 - 14:36:09 CDT)
How to Compile NAMD on HPUX-ia64 system~
- Gengbin Zheng (Fri Jan 14 2005 - 12:36:56 CST)
- Îº¿ (Fri Jan 14 2005 - 04:56:14 CST)
How to compile NAMD2.6 on core2 operons, x86_64-redhat-linux,which is the proper choice in Arch.
- xiaojing gong (Mon May 14 2007 - 21:41:43 CDT)
How to compute interaction energies between individual amino acid residues
- Vivek Sharma (Tue Sep 30 2008 - 22:20:18 CDT)
- harish vashisth (Tue Sep 30 2008 - 12:34:53 CDT)
- Jemmy Hu (Tue Sep 30 2008 - 11:24:33 CDT)
how to config two different files for fixed atoms
- karthik s (Tue Mar 31 2009 - 06:54:10 CDT)
How to confirm water box is big enough?
- Jin Liu (Tue Mar 30 2010 - 17:48:37 CDT)
- Giacomo Fiorin (Tue Mar 30 2010 - 17:36:12 CDT)
- Jin Liu (Tue Mar 30 2010 - 17:09:06 CDT)
- David Tanner (Tue Mar 30 2010 - 15:13:10 CDT)
- Giacomo Fiorin (Tue Mar 30 2010 - 16:38:00 CDT)
- Dimitar V Pachov (Tue Mar 30 2010 - 15:53:46 CDT)
- Jin Liu (Tue Mar 30 2010 - 15:44:26 CDT)
- snoze pa (Tue Mar 30 2010 - 15:11:44 CDT)
- Jin Liu (Tue Mar 30 2010 - 14:29:15 CDT)
How to conservate energy during NVE simulations???
- Marcos Sotomayor (Thu Jun 16 2005 - 10:30:28 CDT)
- Leonardo Sepulveda Durán (Wed Jun 15 2005 - 20:55:29 CDT)
how to constrain a dihedral angle?
- Leonardo G. Trabuco (Wed Mar 29 2006 - 13:19:53 CST)
- Leonardo G. Trabuco (Tue Mar 28 2006 - 16:44:24 CST)
- Leonardo G. Trabuco (Sat Mar 25 2006 - 17:48:57 CST)
- Leonardo G. Trabuco (Fri Mar 24 2006 - 14:03:57 CST)
- xiaojing gong (Thu Mar 23 2006 - 18:55:34 CST)
how to constrain a dihedralqangle=3F?=
- xiaojing gong (Tue Mar 28 2006 - 08:20:02 CST)
- Marcos Sotomayor (Sat Mar 25 2006 - 16:36:28 CST)
- xiaojing gong (Sat Mar 25 2006 - 08:17:29 CST)
how to constrains the smd atom on a line when do my smd simulation??
- ÎâºéÃ÷ (Mon Dec 05 2005 - 01:59:09 CST)
How to construct .prm file of phospho-THR?
- Qiang Zhong (Tue Aug 07 2007 - 18:34:25 CDT)
- Qiang Zhong (Tue Aug 07 2007 - 08:55:52 CDT)
- L. Michel Espinoza-Fonseca (Tue Aug 07 2007 - 09:09:19 CDT)
How to contract the PBC cell
- Tamal Banerjee (Mon Mar 27 2006 - 01:21:06 CST)
how to convert dcd files from namd to charmm
- L. Michel Espinoza-Fonseca (Thu Mar 15 2007 - 16:20:40 CDT)
- Peter Freddolino (Thu Mar 15 2007 - 15:49:06 CDT)
- Alessandro Cembran (Thu Mar 15 2007 - 15:38:37 CDT)
- regafan_at_usc.es (Thu Mar 15 2007 - 15:34:31 CDT)
- regafan_at_usc.es (Thu Mar 15 2007 - 15:33:41 CDT)
- Peter Freddolino (Thu Mar 15 2007 - 15:16:25 CDT)
- regafan_at_usc.es (Thu Mar 15 2007 - 15:06:16 CDT)
- regafan_at_usc.es (Thu Mar 15 2007 - 09:56:03 CDT)
- Alessandro Cembran (Thu Mar 15 2007 - 08:08:25 CDT)
- Alessandro Cembran (Thu Mar 15 2007 - 07:59:01 CDT)
- regafan_at_usc.es (Thu Mar 15 2007 - 06:50:45 CDT)
How to convert the GROMOS parameter unit into charmm22 style
- Axel Kohlmeyer (Wed Jan 20 2010 - 07:50:29 CST)
- Jérôme Hénin (Wed Jan 20 2010 - 07:05:37 CST)
- Jérôme Hénin (Wed Jan 20 2010 - 03:27:42 CST)
- Íõ—² (Wed Jan 20 2010 - 00:24:27 CST)
how to convert X_PLOR to CHARMM?
- Lisa Brown (Fri Mar 25 2011 - 11:01:26 CDT)
How to create a substrate parameter file ?
- Davit Hakobyan (Thu May 06 2004 - 15:09:00 CDT)
How to create psf for carbohydrate
- jas theway (Mon Jan 23 2006 - 19:02:13 CST)
How to create repulsive particle ?
- Peter Freddolino (Tue Nov 21 2006 - 16:05:18 CST)
- Peter Freddolino (Tue Nov 21 2006 - 15:52:57 CST)
- Arturas Ziemys (Tue Nov 21 2006 - 15:45:01 CST)
- Peter Freddolino (Tue Nov 21 2006 - 15:13:40 CST)
- Arturas Ziemys (Tue Nov 21 2006 - 13:47:51 CST)
How to deal with a long path in ABF simulation?
- Wenyu Zhong (Thu Apr 27 2006 - 07:28:34 CDT)
- Chris Chipot (Wed Apr 26 2006 - 15:01:10 CDT)
- Wenyu Zhong (Wed Apr 26 2006 - 09:34:31 CDT)
How to deal with this sugar residues though psfgen?
- q=E2=BA=E9=C3=F7?= (Tue Apr 18 2006 - 00:51:58 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 define a spatial grid for a temperature landscape/contour
- Philipp Schoen1 (Thu Apr 12 2007 - 04:36:31 CDT)
how to define the numsteps in ABF or metadynamics simulation?
- Jérôme Hénin (Sat Jul 16 2011 - 10:57:21 CDT)
- ÕÅÓÂ (Thu Jul 14 2011 - 19:48:32 CDT)
- Giacomo Fiorin (Tue Jul 12 2011 - 15:06:17 CDT)
- Clark Zhang (Wed Jul 06 2011 - 23:08:50 CDT)
how to 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 a complex dynamics simulation
- ydhuang2727 (Wed Aug 05 2009 - 03:25:10 CDT)
how to do a MD of small part of a protein, using namd?
- Giacomo Fiorin (Mon Feb 23 2009 - 11:53:43 CST)
- Lisa Brown (Mon Feb 23 2009 - 10:23:43 CST)
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 free energy perturbation calculation in NAMD?
- Jérôme Hénin (Mon Feb 13 2006 - 07:23:50 CST)
- jz7_at_duke.edu (Tue Feb 07 2006 - 11:21:39 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 do: FEP e2?, a protonating mutation?
- SÃ©bastien LÃ©garÃ© (Wed Apr 15 2009 - 22:32:27 CDT)
- Sébastien Légaré (Thu Apr 09 2009 - 10:48:06 CDT)
- Sebastian Stolzenberg (Tue Apr 07 2009 - 19:15:19 CDT)
how to ensure molecules adopt their favor orientations in SMD simulation
- crazylyf (Tue Apr 06 2010 - 22:39:11 CDT)
How to evaluate the area per lipid and thickness of a lipid bilayer?
- Ming (Thu Nov 01 2007 - 22:24:03 CDT)
How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system?
- Salvador H-V (Thu Aug 25 2011 - 11:12:49 CDT)
- Boyang Wang (Thu Aug 25 2011 - 02:32:01 CDT)
- å¼ å‹‡ (Thu Aug 25 2011 - 02:26:50 CDT)
- Boyang Wang (Thu Aug 25 2011 - 01:41:51 CDT)
- ÕÅÓÂ (Thu Aug 25 2011 - 01:32:33 CDT)
How to fix atoms during minimization?
- Anirban Ghosh (Wed Nov 19 2008 - 08:06:29 CST)
How to fix relative position of a group
- JC Gumbart (Tue Oct 13 2009 - 19:27:40 CDT)
- Yang (Tue Oct 13 2009 - 15:40:53 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 fix the Center of mass of protein when performing SMD?
- JC Gumbart (Thu Dec 18 2008 - 23:22:39 CST)
- ÕÅÓÂ (Wed Dec 17 2008 - 22:06:14 CST)
- ÕÅÓÂ (Mon Dec 15 2008 - 21:54:20 CST)
How to freeze some atoms
- cong chen (Tue Nov 20 2007 - 20:11:24 CST)
how to generate DNA psf files?
- Chris Harrison (Wed Aug 05 2009 - 09:10:25 CDT)
- Roman Petrenko (Fri Jul 31 2009 - 00:22:31 CDT)
- He Yuhui (Wed Jul 29 2009 - 21:04:27 CDT)
how to generate psf file using the AMBER topology file
- Peter Freddolino (Fri Jul 18 2008 - 15:30:45 CDT)
- Axel Kohlmeyer (Fri Jul 18 2008 - 12:09:48 CDT)
- tinni sona (Fri Jul 18 2008 - 05:38:45 CDT)
How to generate the tcouple file for NAMD runs?
- Chris Harrison (Sun Oct 31 2010 - 08:23:46 CDT)
- a a (Fri Oct 29 2010 - 22:45:42 CDT)
how to generate the topology and parameter file for ligand
- jnsong (Thu Dec 16 2010 - 07:45:52 CST)
how to generate topology and parameter file for ligand
- jnsong (Thu Dec 16 2010 - 07:40:38 CST)
how to generate transparent figures?
- Bjoern Olausson (Mon Jul 25 2011 - 04:04:58 CDT)
- Nicholas M Glykos (Sat Jul 23 2011 - 10:47:54 CDT)
- AB (Sat Jul 23 2011 - 09:59:07 CDT)
how to 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 .coor .vel and .xsc for a .dcd file
- Axel Kohlmeyer (Wed Jan 27 2010 - 09:13:17 CST)
- ÅÓÑ©ÇÛ Pang Xueqin (Wed Jan 27 2010 - 08:42:44 CST)
how to get 2 identical trajectories using NAMD in parallel
- David Hardy (Fri Dec 12 2008 - 11:25:25 CST)
- gaillard_at_chimie.u-strasbg.fr (Fri Dec 12 2008 - 11:03:26 CST)
- gaillard_at_chimie.u-strasbg.fr (Fri Dec 12 2008 - 10:49:47 CST)
- Vlad Cojocaru (Fri Dec 12 2008 - 09:33:44 CST)
How to get around with "atoms moving too fast"
- yi wang (Fri Oct 19 2007 - 22:34:32 CDT)
- Yinglong Miao (Fri Oct 19 2007 - 11:45:50 CDT)
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 different kinds of harmonic constraints in one script?
- Morad Alawneh (Tue Jan 31 2006 - 09:48:21 CST)
how to get hydrogen-bond energy?
- Lv Shouqin (Tue Aug 17 2004 - 21:34:17 CDT)
How to get information of computing time for LJ calculation and pair list generation
- Hideya Nakamura (Wed Mar 17 2010 - 03:32:31 CDT)
- Chris Harrison (Wed Mar 17 2010 - 00:06:07 CDT)
- Hideya Nakamura (Mon Mar 15 2010 - 12:08:20 CDT)
- Hideya Nakamura (Mon Mar 15 2010 - 12:15:18 CDT)
How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely
- Chris Harrison (Sun Jan 04 2009 - 12:03:37 CST)
- sunita gupta (Fri Jan 02 2009 - 03:58:37 CST)
How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely.
- jani sahil (Wed Dec 31 2008 - 05:25:10 CST)
- sunita gupta (Wed Dec 31 2008 - 00:27:08 CST)
How to get PMF from SMD with colvars
- Jian Liu (Sat Apr 10 2010 - 03:45:05 CDT)
how to get psf files of DNA but not RNA with psfgen?
- Xueqing Zou (Thu Sep 17 2009 - 09:52:19 CDT)
- ºÎØ¹»Ô (Thu Sep 17 2009 - 06:25:02 CDT)
how to get rid of TCL messages in namd.log from tclForcesScript
- Roman Petrenko (Fri Mar 13 2009 - 20:47:30 CDT)
- Axel Kohlmeyer (Fri Mar 13 2009 - 19:24:25 CDT)
- Roman Petrenko (Fri Mar 13 2009 - 18:45:21 CDT)
How to get the acceptance ratio in REMD
- Axel Kohlmeyer (Thu Mar 12 2009 - 08:22:38 CDT)
- Yunlang Li (Mon Mar 09 2009 - 16:59:50 CDT)
How to get the coordinate of a certain atom with tcl in the config file?
- Íõ—² (Mon Dec 28 2009 - 04:14:23 CST)
how to get the energy in vacuum of a molecule in NAMD
- Jim Phillips (Wed Jul 20 2011 - 11:25:59 CDT)
- jnsong (Wed Jun 22 2011 - 08:36:40 CDT)
how to 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 get the velocities from the dcd file
- Alessio Alexiadis (Mon Mar 05 2007 - 09:25:49 CST)
how to get topology and parameter file for ligand
- jnsong (Thu Dec 16 2010 - 08:58:07 CST)
How to have neutral terminal ends
- eladp_at_hplus.tau.ac.il (Sat Oct 15 2005 - 04:15:01 CDT)
how to image molecules back into a PBC box
- Xiongce Zhao (Tue Feb 15 2005 - 09:08:21 CST)
How to implement an additional interaction potential?
- Vincent Kraeutler (Thu Aug 23 2007 - 07:53:05 CDT)
- Philipp Schön (Thu Aug 23 2007 - 07:00:12 CDT)
how to improve the occupation of GPU with NAMD-2.7b3-CUDA
- Jianing Song (Wed Oct 13 2010 - 20:45:59 CDT)
- Axel Kohlmeyer (Mon Oct 11 2010 - 22:09:15 CDT)
- Axel Kohlmeyer (Mon Oct 11 2010 - 08:55:41 CDT)
- Jianing Song (Sun Oct 10 2010 - 09:43:58 CDT)
How to include more parameterfiles in NAMD
- Per Jr. Greisen (Thu May 11 2006 - 09:36:36 CDT)
How to include parameters from stream files in calculations
- Qiang Zhong (Tue Aug 21 2007 - 19:43:57 CDT)
- Spiro Pavlopoulos (Tue Aug 21 2007 - 15:02:39 CDT)
how to install namd in windows xp
- Eric H. Lee (Sat Apr 04 2009 - 01:29:58 CDT)
- balaji nagarajan (Sat Apr 04 2009 - 01:11:00 CDT)
how to install NAMD on suse10_ppc64 without xlc
- bay__gulf618_at_sina.com (Fri Apr 24 2009 - 05:18:04 CDT)
how to install rmsdtt in Windows...
- seonah kim (Tue Jan 17 2006 - 09:52:00 CST)
How to install VMD and NAMD on Ubuntu?
- Hero (Sat Apr 26 2008 - 12:55:17 CDT)
How to keep Total Energy constant when an external force is added?
- Fred (Rui FENG) (Thu Oct 23 2008 - 11:58:29 CDT)
- Jerome Henin (Thu Oct 23 2008 - 10:11:33 CDT)
- Axel Kohlmeyer (Thu Oct 23 2008 - 09:58:15 CDT)
- Fred (Rui FENG) (Wed Oct 22 2008 - 22:48:43 CDT)
how to kill namd job in TCL FORCES Script?
- Jerome Henin (Mon Jul 16 2007 - 12:41:59 CDT)
- hl332_at_drexel.edu (Mon Jul 16 2007 - 12:22:50 CDT)
how to kill namd2 child process after power cut
- Philipp Schoen1 (Fri Apr 13 2007 - 03:16:59 CDT)
How to link two proteins
- Peter Freddolino (Wed May 16 2007 - 07:25:26 CDT)
- olivier walker (Wed May 16 2007 - 02:50:00 CDT)
How to load velocities during simulations.
- Wang, Boyang (Sat Sep 08 2007 - 19:56:55 CDT)
How to make a disulphide bond
- SÅ‚awek OrÅ‚owski (Wed May 17 2006 - 03:36:44 CDT)
- Charles Danko (Tue May 16 2006 - 13:47:37 CDT)
- lily jin (Tue May 16 2006 - 13:02:51 CDT)
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 make a virtual bond?
- Peter Freddolino (Thu May 25 2006 - 09:56:47 CDT)
- patrick wintrode (Thu May 25 2006 - 09:06:34 CDT)
- Peter Freddolino (Wed May 24 2006 - 17:48:35 CDT)
- patrick wintrode (Wed May 24 2006 - 13:27:24 CDT)
How to make alkaline ph pgn file
- Gaurav Sharma (Mon Apr 16 2007 - 21:59:26 CDT)
- ravi sharma (Mon Apr 16 2007 - 14:11:47 CDT)
how to make dual-hybrid topology?
- Chris Chipot (Mon Feb 13 2006 - 08:31:45 CST)
- Indrajaya (Mon Feb 13 2006 - 06:47:21 CST)
How to measure of radius of a molecules?
- Taeho Kim (Mon Apr 10 2006 - 03:30:28 CDT)
How to minimize our model by SD using namd
- Ahmad Firoz (Tue May 19 2009 - 00:33:01 CDT)
how to minimize the energy of a protein using CHARMM FF in NAMD
- Kalyan chaitanya (Thu Feb 07 2008 - 09:29:08 CST)
How to model HCN gas molecule by NAMD?
- Boyang Wang (Wed Feb 08 2006 - 18:44:42 CST)
How to move COM during minimization?
- Shahid Qamar (Wed Dec 15 2004 - 12:03:12 CST)
How to obtain the system force on a fixed atom
- Axel Kohlmeyer (Tue Dec 22 2009 - 03:34:27 CST)
- chengh_at_ringo.chem.pitt.edu (Mon Dec 21 2009 - 15:18:47 CST)
- Jian Liu (Mon Dec 21 2009 - 07:34:30 CST)
- Jérôme Hénin (Wed Dec 16 2009 - 12:01:33 CST)
- Jérôme Hénin (Wed Dec 16 2009 - 10:38:55 CST)
- Roman Petrenko (Wed Dec 16 2009 - 09:34:36 CST)
- Roman Petrenko (Wed Dec 16 2009 - 09:41:57 CST)
- chengh_at_ringo.chem.pitt.edu (Wed Dec 16 2009 - 08:40:37 CST)
how to output the velocity for one selected atom in the system
- chengh_at_ringo.chem.pitt.edu (Sat Dec 19 2009 - 10:49:54 CST)
How to patch residues in different chains
- Leonardo G. Trabuco (Tue Apr 11 2006 - 20:28:25 CDT)
- snoze pa (Tue Apr 11 2006 - 11:25:13 CDT)
- Leonardo G. Trabuco (Mon Apr 10 2006 - 12:04:36 CDT)
- snoze pa (Mon Apr 10 2006 - 11:25:59 CDT)
- Leonardo G. Trabuco (Sat Apr 08 2006 - 13:22:55 CDT)
- snoze pa (Fri Apr 07 2006 - 18:32:38 CDT)
How to patch segments of aminoacids
- Brian Bennion (Wed Nov 02 2005 - 10:35:19 CST)
- Alexe Bojovschi (Wed Nov 02 2005 - 03:09:08 CST)
how to perform MD with two proteins
- Mert Gür (Wed Dec 05 2007 - 09:04:57 CST)
- Peter Freddolino (Sun Dec 02 2007 - 10:31:54 CST)
- Richard Wood (Sun Dec 02 2007 - 10:00:43 CST)
- Mert Gür (Sun Dec 02 2007 - 09:12:28 CST)
- Mert Gür (Sun Dec 02 2007 - 08:37:18 CST)
- Mert Gür (Sun Dec 02 2007 - 07:35:14 CST)
How to play molecule trajectory with VMD?
- Hero (Sat Apr 26 2008 - 20:00:52 CDT)
how to plugin catDCD into VMD of windows version
- xiaojing gong (Wed Mar 29 2006 - 07:07:02 CST)
how to plugin catDCD intoqVMD=20of=20windows=20version?=
- xiaojing gong (Wed Mar 29 2006 - 19:17:03 CST)
how to prepare *.paramas file
- Kalyan chaitanya (Tue May 13 2008 - 17:48:54 CDT)
How to prevent cg water entering a membrane
- Francesco Pietra (Fri Dec 18 2009 - 16:49:55 CST)
How to put a COM restraint on a membrane protein?
- A D (Tue Oct 06 2009 - 18:03:25 CDT)
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 read charmm binary trajectory file using home-made C/C++ code
- Wei Zhuang (Tue Mar 22 2005 - 14:39:15 CST)
How to read specific DCD frames directly in Fortran?
- Yinglong Miao (Sat Apr 05 2008 - 13:21:53 CDT)
How to read trajectory within CHARMM generated by NAMD
- Yang MIngjun (Thu Dec 31 2009 - 04:18:13 CST)
- Dimitar V Pachov (Mon Dec 28 2009 - 11:52:59 CST)
- David A. Horita (Mon Dec 28 2009 - 08:33:31 CST)
- gaillard_at_chimie.u-strasbg.fr (Mon Dec 28 2009 - 08:44:16 CST)
- Axel Kohlmeyer (Mon Dec 28 2009 - 02:46:34 CST)
- Yang MIngjun (Sun Dec 27 2009 - 20:06:44 CST)
- Axel Kohlmeyer (Sun Dec 27 2009 - 02:36:30 CST)
- Yang MIngjun (Sun Dec 27 2009 - 01:36:53 CST)
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 remove translational and rotational motion from dcd file
- Neelanjana Sengupta (Thu Nov 09 2006 - 20:04:56 CST)
- Dhiraj Srivastava (Thu Nov 09 2006 - 14:59:28 CST)
How to restart a simulation
- Audrey Salazar (Thu Sep 20 2007 - 10:28:06 CDT)
- Audrey Salazar (Thu Sep 20 2007 - 10:25:10 CDT)
how to restart FEP
- jia (Fri Oct 26 2007 - 15:29:12 CDT)
- Jerome Henin (Fri Oct 26 2007 - 14:32:38 CDT)
- jia (Fri Oct 26 2007 - 13:50:44 CDT)
how to restart/continue NAMD run
- maruthi_at_imsc.res.in (Thu Aug 02 2007 - 04:05:52 CDT)
- Wei Chen (Fri May 06 2005 - 15:47:25 CDT)
- Jerry Xu (Fri May 06 2005 - 11:28:33 CDT)
How to restraint angle in NAMD
- George Khelashvili (Fri Oct 01 2010 - 21:32:29 CDT)
How to retrieve IC50 of a specific compound from NCBI?
- L. Michel Espinoza-Fonseca (Tue Sep 09 2008 - 04:25:15 CDT)
- Ming (Tue Sep 09 2008 - 03:54:38 CDT)
How to reverse the smd pcv pulling simulation
- Wang,Ying (Tue Dec 09 2008 - 16:49:29 CST)
How to run for periodic boundary Conditions?
- Snigdha Chakraborty (Wed Jul 20 2005 - 12:19:32 CDT)
how to run namd in cluster
- Anupam Nath Jha (Sun Jul 27 2008 - 13:23:22 CDT)
How to run namd on NCSA Tungsten
- Hyonseok Hwang (Wed Oct 19 2005 - 16:56:30 CDT)
- snoze pa (Wed Oct 19 2005 - 14:38:58 CDT)
How to run namd2 on ubuntu linux?
- Leandro Martínez (Sat Apr 26 2008 - 16:10:35 CDT)
- Hero (Sat Apr 26 2008 - 14:45:01 CDT)
how to run namd2.7b1 on multiple nodes
- Roman Petrenko (Fri Jul 24 2009 - 11:13:22 CDT)
- Chris Harrison (Thu Jul 23 2009 - 18:16:08 CDT)
- Roman Petrenko (Thu Jul 23 2009 - 17:48:19 CDT)
How to run NVT simulations without applying periodic boundary conditions?
- Yinglong Miao (Thu Feb 21 2008 - 09:44:45 CST)
- Yinglong Miao (Thu Feb 21 2008 - 08:24:55 CST)
- Leandro Martínez (Thu Feb 21 2008 - 08:34:49 CST)
- Yinglong Miao (Wed Feb 20 2008 - 15:55:23 CST)
- Yinglong Miao (Wed Feb 20 2008 - 13:59:44 CST)
- Yinglong Miao (Wed Feb 20 2008 - 12:16:13 CST)
how to save a DCD file without water in NAMD ?
- Lisa Brown (Fri Aug 13 2010 - 11:02:36 CDT)
- Athanassios Stavrakoudis (Fri Aug 13 2010 - 10:23:01 CDT)
- Axel Kohlmeyer (Fri Aug 13 2010 - 08:54:51 CDT)
- Mert Gür (Fri Aug 13 2010 - 08:56:44 CDT)
- Lisa Brown (Fri Aug 13 2010 - 08:06:36 CDT)
- Zumot, Elia Nabil (Thu Aug 12 2010 - 16:52:51 CDT)
- Lisa Brown (Thu Aug 12 2010 - 15:00:40 CDT)
how to save a DCD file without water in NAMD: COMMAND LINE
- Thomas C Bishop (Fri Aug 13 2010 - 08:44:09 CDT)
how to save output file in plain text?
- JC Gumbart (Thu Jan 08 2009 - 16:30:58 CST)
- JC Gumbart (Thu Jan 08 2009 - 16:05:30 CST)
- Segun Jung (Thu Jan 08 2009 - 15:09:02 CST)
how to save pdb file after "moveby" command in VMD?
- Joshua Adelman (Tue Aug 18 2009 - 22:14:18 CDT)
- He Yuhui (Tue Aug 18 2009 - 21:33:42 CDT)
How to save the animation movie into files?
- Jianhui Tian (Thu May 01 2008 - 09:16:50 CDT)
- Hero (Thu May 01 2008 - 01:48:35 CDT)
- Low Soo Mei (Mon Apr 28 2008 - 00:51:37 CDT)
- Hero (Mon Apr 28 2008 - 00:23:49 CDT)
How to save vmd figures to jpg or tiff?
- Hero (Sun Apr 27 2008 - 16:18:35 CDT)
How to set a molecule to be rigid in NAMD?
- Boyang Wang (Mon May 16 2005 - 14:37:44 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 set improper dihedral for trans-double bond.
- Boyang Wang (Mon Nov 29 2010 - 06:15:16 CST)
how to set initial velocity?
- Joshua Adelman (Wed Apr 29 2009 - 15:09:34 CDT)
- uu zhu (Wed Apr 29 2009 - 01:58:13 CDT)
- Joshua Adelman (Tue Apr 28 2009 - 21:59:21 CDT)
- uu zhu (Tue Apr 28 2009 - 21:27:37 CDT)
How to set magnitude of cellBasisVector?
- Joshua Adelman (Fri Jul 24 2009 - 01:13:24 CDT)
- Aurum Bai (Fri Jul 24 2009 - 00:52:19 CDT)
how to set pH
- felmerino_at_uchile.cl (Wed Mar 31 2010 - 15:01:01 CDT)
- Ajasja LjubetiÄ (Wed Mar 31 2010 - 06:59:06 CDT)
- Jérôme Hénin (Wed Mar 31 2010 - 06:29:20 CDT)
- Axel Kohlmeyer (Wed Mar 31 2010 - 05:54:15 CDT)
- crazylyf (Wed Mar 31 2010 - 05:23:58 CDT)
How to set the parameters for C60?
- uu zhu (Thu Apr 16 2009 - 05:06:37 CDT)
How to set the parameters for two different baths in one molecule?
- uu zhu (Mon Jun 08 2009 - 20:14:36 CDT)
How to set the right PME parameters for amber's prmtop and inpcrd files?
- a a (Wed Jan 26 2011 - 04:34:33 CST)
- a a (Wed Jan 26 2011 - 04:17:32 CST)
how to set up force parameters of a novel residue?
- Axel Kohlmeyer (Thu Aug 27 2009 - 16:14:17 CDT)
- He Yuhui (Thu Aug 27 2009 - 02:37:12 CDT)
How to set values for cellBasisVector and PMEGridSize properly
- Anirban Ghosh (Mon Oct 20 2008 - 08:30:23 CDT)
- Peter Freddolino (Mon Oct 20 2008 - 07:06:16 CDT)
- ydhuang2727 (Mon Oct 20 2008 - 03:00:15 CDT)
How to simulate a charged surface
- Yingzhe Liu (Wed Jun 22 2011 - 02:53:56 CDT)
- Yingzhe Liu (Thu Jun 23 2011 - 05:43:49 CDT)
how to simulate a protein-ligand complex ?
- ydhuang2727 (Tue Aug 11 2009 - 08:29:25 CDT)
how to simulate sugars
- George Madalin Giambasu (Sun May 27 2007 - 19:51:35 CDT)
- Aaron Oakley (Sun May 27 2007 - 19:19:55 CDT)
- Richard Casey (Sun May 27 2007 - 12:21:26 CDT)
How to solve the out of cell box for long time in Periodic Boundary Conditions?
- Jérôme Hénin (Thu May 20 2010 - 10:00:08 CDT)
- Aurum Bai (Wed May 19 2010 - 21:06:38 CDT)
How to specify processors for running VMD on a cluster?
- Yinglong Miao (Tue Feb 10 2009 - 10:45:27 CST)
how to submit job on a HPC equipped with infiniband
- Bjoern Olausson (Mon Jul 26 2010 - 04:31:55 CDT)
- liupeng012 (Mon Jul 26 2010 - 02:59:34 CDT)
How to treat the terminal residue psfgen in NAMD~
- Îº¿ (Mon Nov 29 2004 - 20:11:37 CST)
How to turn off electrostatic interactions (PME).
- Maxim Fedorov (Wed May 17 2006 - 15:58:07 CDT)
how to understand vdwForceSwitching
- Chris Harrison (Wed Feb 15 2012 - 15:50:33 CST)
- Liqun Zhang (Sat Feb 11 2012 - 17:09:48 CST)
How to unsubscribe ?
- Gianluca Interlandi (Wed May 16 2007 - 14:43:41 CDT)
- Richard Law (Wed May 16 2007 - 13:41:30 CDT)
- Viswanadham Sridhara (Wed May 16 2007 - 12:30:38 CDT)
How to use AMBER force field in NAMD?
- Po Hu (Mon Sep 19 2005 - 20:31:13 CDT)
How to use bigdcd on a trajectory while skipping first 1000 frames
- Alexander A. Vakhrushev (Thu Sep 25 2008 - 06:14:35 CDT)
- Eric H. Lee (Thu Sep 25 2008 - 04:54:29 CDT)
- maria goranovic (Thu Sep 25 2008 - 04:42:29 CDT)
how to use constraints properly
- Joshua Adelman (Thu Mar 19 2009 - 13:53:09 CDT)
- Roman Petrenko (Thu Mar 19 2009 - 13:38:24 CDT)
how to use ethanol as solvent in namd for MD simulations ?
- Branko (Fri Jul 31 2009 - 04:50:17 CDT)
- Wang Yf (Fri Jul 31 2009 - 04:06:55 CDT)
how to use ethanol as solvent in namd for MD simulations?
- Branko (Fri Jul 31 2009 - 07:59:03 CDT)
- Jian Liu (Fri Jul 31 2009 - 07:33:35 CDT)
how to use gromacs force field in NAMD?
- Frank Yong Jiang (Tue May 24 2005 - 15:50:05 CDT)
- Armen Poghosyan (Mon May 31 2004 - 02:34:06 CDT)
How to use harmonic restraint parameter for 2 selection of atoms
- Íõ—² (Thu Apr 15 2010 - 02:00:06 CDT)
how to use hydrogen bond parameter during minimization and simulation
- prasun kumar (Thu Mar 05 2009 - 23:27:47 CST)
How to use lset inside tclforces/calc_forces
- Cameron Abrams (Mon Mar 09 2009 - 09:00:51 CDT)
how to use measure hbonds to calculate occupancy of all hbonds in simulation?
- lnubiofox (Wed May 16 2007 - 09:57:51 CDT)
- Dong Luo (Tue May 15 2007 - 18:27:01 CDT)
- lnubiofox (Tue May 15 2007 - 09:21:33 CDT)
How to use NPT ensemble to fix water density
- Jeffrey J. Potoff (Tue Aug 14 2007 - 15:01:35 CDT)
- Irene Newhouse (Tue Aug 14 2007 - 14:59:59 CDT)
- Adam Fraser (Tue Aug 14 2007 - 14:28:18 CDT)
how to use reaction field in NAMD
- Mark Abraham (Sun Dec 10 2006 - 21:44:50 CST)
- xiaojing gong (Sun Dec 10 2006 - 21:21:33 CST)
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)
how to use the dual-processor machines
- Gengbin Zheng (Sat Jul 30 2005 - 17:52:42 CDT)
- Xiaoqing Wang (Sat Jul 30 2005 - 08:37:39 CDT)
How to use the transformation matrix in VMD to obtain the tetramer
- JC Gumbart (Tue Mar 27 2007 - 14:17:46 CDT)
- xiaojing gong (Tue Mar 27 2007 - 07:22:47 CDT)
how to use variables in colvar configuration file
- Jérôme Hénin (Fri Sep 23 2011 - 13:23:55 CDT)
- Ling Wu (Fri Sep 23 2011 - 12:26:08 CDT)
how to use volmap analysing a series of dcd.
- liupeng012_at_mail.nankai.edu.cn (Wed Sep 16 2009 - 08:39:50 CDT)
how to visualize an alchemical FEP transformation??
- Chris Harrison (Sat Oct 22 2011 - 12:48:16 CDT)
- Bruno Luís Pinto de Oliveira (Sat Oct 22 2011 - 12:31:01 CDT)
- Axel Kohlmeyer (Sat Oct 22 2011 - 11:33:47 CDT)
- Bruno Luís Pinto de Oliveira (Sat Oct 22 2011 - 09:58:42 CDT)
- Chris Harrison (Thu Oct 20 2011 - 18:02:32 CDT)
- Axel Kohlmeyer (Thu Oct 20 2011 - 16:42:02 CDT)
- Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 16:19:38 CDT)
- Chris Harrison (Thu Oct 20 2011 - 15:21:59 CDT)
- Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 15:10:28 CDT)
- Axel Kohlmeyer (Thu Oct 20 2011 - 14:02:59 CDT)
- Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 13:28:13 CDT)
- Axel Kohlmeyer (Thu Oct 20 2011 - 09:02:34 CDT)
- Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 06:27:47 CDT)
how to write a command to close vmd in shell script?
- Schreiner Eduard (Sun Aug 09 2009 - 22:39:36 CDT)
- He Yuhui (Sun Aug 09 2009 - 22:21:34 CDT)
How to write a dcd in fortran?
- Axel Kohlmeyer (Mon Oct 03 2011 - 18:13:20 CDT)
- lam nguyen (Mon Oct 03 2011 - 18:03:37 CDT)
- Joshua D. Moore (Mon Oct 03 2011 - 15:56:57 CDT)
- Axel Kohlmeyer (Mon Oct 03 2011 - 14:13:03 CDT)
- lam nguyen (Mon Oct 03 2011 - 14:07:47 CDT)
- Axel Kohlmeyer (Mon Oct 03 2011 - 13:26:54 CDT)
- lam nguyen (Mon Oct 03 2011 - 13:21:36 CDT)
How to write a new dcd.file by using Tcl
- xiaojing gong (Thu Jan 25 2007 - 08:28:21 CST)
How to write different DCD files for separate MD runs in one simulation?
- Yinglong Miao (Tue Apr 15 2008 - 16:22:18 CDT)
- V.Ovchinnikov (Tue Apr 15 2008 - 15:52:07 CDT)
- Peter Freddolino (Tue Apr 15 2008 - 15:34:11 CDT)
- V.Ovchinnikov (Tue Apr 15 2008 - 15:14:20 CDT)
- Peter Freddolino (Tue Apr 15 2008 - 14:07:03 CDT)
- Yinglong Miao (Tue Apr 15 2008 - 13:55:14 CDT)
How to write gradual heating config file
- Hyundeok Song (Mon Aug 25 2008 - 19:30:26 CDT)
- Audrey Salazar (Mon Aug 25 2008 - 18:23:41 CDT)
- Audrey Salazar (Mon Aug 25 2008 - 17:41:59 CDT)
How to write gradual heating config files
- Cristina Rodríguez (Mon Feb 14 2011 - 19:08:07 CST)
how to write out the dcd file by vmd python command?
- mjyang (Mon Feb 21 2011 - 08:53:58 CST)
how to write the bond across the cell boundary
- Axel Kohlmeyer (Fri Mar 25 2011 - 08:17:05 CDT)
- Ajasja LjubetiÄ (Fri Mar 25 2011 - 03:44:41 CDT)
- Íõ—² (Fri Mar 25 2011 - 01:52:15 CDT)
How were the output files of the Replica Exchange Method sorted?
- Guoxiong Su (Sun Dec 12 2010 - 14:11:37 CST)
how work: harmonic position "constraints" module + "WrapAll on"?
- Sebastian Stolzenberg (Mon Jul 20 2009 - 12:52:06 CDT)
- Joshua Adelman (Mon Jul 20 2009 - 09:23:13 CDT)
- Sebastian Stolzenberg (Mon Jul 20 2009 - 07:12:04 CDT)
howcan I use amber forcefield in NAMD?
- mashaojie163 (Sat Nov 17 2007 - 01:28:51 CST)
- Floris Buelens (Fri Nov 16 2007 - 05:19:37 CST)
- Richard Wood (Thu Nov 15 2007 - 22:32:56 CST)
- JC Gumbart (Thu Nov 15 2007 - 22:01:54 CST)
- Richard Wood (Thu Nov 15 2007 - 21:33:00 CST)
- mashaojie163 (Thu Nov 15 2007 - 20:55:53 CST)
- Huy N. Ha (Thu Nov 15 2007 - 17:24:36 CST)
- mashaojie163 (Thu Nov 15 2007 - 06:23:49 CST)
- Irene Newhouse (Thu Nov 15 2007 - 00:51:41 CST)
- mashaojie163 (Wed Nov 14 2007 - 21:58:39 CST)
Howto lengthen a collagen strand (which tool to use)
- Peter Freddolino (Wed Oct 10 2007 - 10:09:52 CDT)
- QMarcus_R=F6lz=22?= (Wed Oct 10 2007 - 08:08:17 CDT)
- Peter Freddolino (Tue Oct 09 2007 - 09:47:28 CDT)
- QMarcus_R=F6lz=22?= (Tue Oct 09 2007 - 07:23:03 CDT)
HP Cluster Platform 4000
- Giacomo Fiorin (Fri Dec 05 2008 - 09:13:07 CST)
- Hannes Loeffler (Fri Dec 05 2008 - 07:52:02 CST)
HP-MPI on Xeon Infiniband
- Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 10:10:22 CST)
- Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 08:26:25 CST)
- Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 06:43:58 CST)
HSE and gromacs
- patrick wintrode (Sun Feb 10 2008 - 10:41:01 CST)
- Peter Freddolino (Sun Feb 10 2008 - 10:47:19 CST)
- Peter Freddolino (Sun Feb 10 2008 - 10:49:46 CST)
html manual 2.8, ref 46 and some GBIS questions
- Branko (Sun Mar 20 2011 - 09:05:27 CDT)
HW - HW IN PARAMETER FILES
- Axel Kohlmeyer (Thu May 07 2009 - 07:47:07 CDT)
- Jorgen Simonsen (Thu May 07 2009 - 06:17:19 CDT)
Hybond calulator and display
- John Stone (Fri Jan 16 2004 - 13:07:09 CST)
- Jerry Ebalunode (Fri Jan 16 2004 - 12:24:30 CST)
hybrid qm/mm
- Jake Michaelson (Wed Jan 25 2006 - 15:14:47 CST)
hydration in membrane-protein simulations
- Chris Harrison (Tue Jul 06 2010 - 09:36:22 CDT)
- dhacademic (Sat Jul 03 2010 - 10:20:23 CDT)
Hydrogen Atoms and Water Molecules
- Yu Liu (Mon Jul 09 2007 - 21:21:38 CDT)
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)
Hydrogen molecule model
- Axel Kohlmeyer (Fri Oct 30 2009 - 15:00:12 CDT)
- Mikhail Suyetin (Fri Oct 30 2009 - 10:42:19 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)
Hydrogens collapsing
- Vishal Kopardé (Wed Nov 01 2006 - 21:20:50 CST)
- lc_at_chem.au.dk (Tue Jan 18 2005 - 12:12:04 CST)
- Brian Bennion (Tue Jan 18 2005 - 10:23:40 CST)
- lc_at_chem.au.dk (Tue Jan 18 2005 - 08:46:23 CST)
hydroxyls in phosphate group collapsing
- Yvonne.Westermaier_at_unige.ch (Mon Jul 27 2009 - 09:41:20 CDT)
Hydroxylysine parameters
- Elham Hamed (Mon Jun 09 2008 - 10:53:08 CDT)
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)
Hydroxyproline topology
- Neelanjana Sengupta (Tue Oct 17 2006 - 21:15:25 CDT)
Hymen destroyer
- Barbara Riddle (Wed Jun 06 2007 - 19:31:28 CDT)
- George Benton (Mon Jun 04 2007 - 06:25:11 CDT)
Hymen penetrator
- Natasha Davidson (Sat Jun 09 2007 - 01:15:47 CDT)
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 can patch namd for amber ff on GPU
- Francesco Oteri (Sun Oct 17 2010 - 21:50:58 CDT)
I can't keep my pulling directions the same with the SMD vector
- Axel Kohlmeyer (Tue Apr 21 2009 - 07:27:50 CDT)
- Mert Gür (Tue Apr 21 2009 - 02:49:19 CDT)
- Axel Kohlmeyer (Mon Apr 20 2009 - 08:41:22 CDT)
- Mert Gür (Mon Apr 20 2009 - 03:16:39 CDT)
- Chris Harrison (Sun Apr 19 2009 - 18:27:24 CDT)
- Mert Gür (Sun Apr 19 2009 - 11:10:11 CDT)
- Chris Harrison (Sun Apr 19 2009 - 10:25:14 CDT)
- Mert Gür (Sun Apr 19 2009 - 07:56:00 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)
I M wants to share "legis_2011" with you
- Dropbox (Fri Jun 03 2011 - 15:20:24 CDT)
I need help with this
- Chris Harrison (Fri Feb 11 2011 - 12:08:56 CST)
- Chris Harrison (Fri Feb 11 2011 - 12:44:42 CST)
- Richard Wood (Fri Feb 11 2011 - 12:39:57 CST)
- Richard Wood (Fri Feb 11 2011 - 12:00:11 CST)
- Chris Harrison (Fri Feb 11 2011 - 11:42:41 CST)
- felmerino_at_uchile.cl (Fri Feb 11 2011 - 10:35:52 CST)
- Richard Wood (Fri Feb 11 2011 - 11:07:42 CST)
- Richard Wood (Fri Feb 11 2011 - 06:07:23 CST)
- Cruz-Chu Eduardo Roberto (Thu Feb 10 2011 - 02:51:43 CST)
- Richard Wood (Wed Feb 09 2011 - 13:01:25 CST)
I want to know how to make pdb file with 2d structrure file.
- Taeho Kim (Fri Feb 10 2006 - 02:14:31 CST)
I'm sorry ... please ignore the junk !!
- Vlad Cojocaru (Mon Apr 09 2007 - 05:50:54 CDT)
I: Running Charm++ over MPI does not work
- Chris Harrison (Thu Jan 22 2009 - 10:53:50 CST)
- andy.mastellone_at_alice.it (Thu Jan 22 2009 - 08:23:58 CST)
IA64 and MPICH and mpiexec runtime shmem errors
- Randy Crawford (Thu Aug 05 2004 - 14:38:06 CDT)
iAPBS 1.0.0 released
- Robert Konecny (Wed Nov 18 2009 - 22:55:24 CST)
IB fabrics
- Bennion, Brian (Fri Jan 06 2012 - 12:58:08 CST)
- Chris Harrison (Fri Jan 06 2012 - 12:52:21 CST)
- Bennion, Brian (Fri Jan 06 2012 - 12:39:04 CST)
- Axel Kohlmeyer (Fri Jan 06 2012 - 11:58:14 CST)
- Thomas Bishop (Fri Jan 06 2012 - 11:42:53 CST)
Ib version and nodelist
- Neelanjana Sengupta (Mon Aug 22 2011 - 00:36:09 CDT)
IBM SP build
- Jim Phillips (Thu Nov 13 2003 - 14:57:20 CST)
- David Skinner (Sun Nov 09 2003 - 00:21:31 CST)
IBverbs charmrun problem
- Seren Soner (Tue Mar 08 2011 - 05:41:33 CST)
ibverbs crash
- Bjoern Olausson (Wed Nov 04 2009 - 08:38:25 CST)
- Bjoern Olausson (Wed Nov 04 2009 - 04:06:48 CST)
- Bjoern Olausson (Wed Nov 04 2009 - 08:38:45 CST)
- David A. Horita (Tue Nov 03 2009 - 14:17:17 CST)
IBVerbs NAMD build segfaults
- Jason Russler (Wed Jan 21 2009 - 08:47:28 CST)
IC Removal and Problem
- Nara Dashdorj (Tue Nov 01 2005 - 22:31:53 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)
If I run NAMD on small computer, which processor is the best for NAMD under Linux?
- Wenyu Zhong (Fri Jul 14 2006 - 08:00:15 CDT)
- xiaojing gong (Fri Jul 14 2006 - 02:25:48 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)
image centering problem
- ipsita basu (Thu Aug 11 2011 - 00:41:20 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)
IMD VMD NAMD adding frames
- Scooter Willis (Mon Feb 01 2010 - 13:35:37 CST)
IMD, Hostname and Port
- Nano Group (Tue Jun 02 2009 - 07:40:01 CDT)
IMD-host name-port number-connection problem.
- Mark Abraham (Fri Jan 27 2006 - 09:22:41 CST)
- rakesh... (Fri Jan 27 2006 - 08:26:02 CST)
- rakesh... (Thu Jan 26 2006 - 15:54:43 CST)
Implementation of graphite walls
- Sabine Leroch (Mon Jul 13 2009 - 07:36:05 CDT)
Implementation of Martini CG FF in NAMD
- Liao Chuan (Wed Apr 14 2010 - 11:25:50 CDT)
Implementation of TCL script in NAMD .conf file
- Benjamin Bouvier (Mon Jul 07 2008 - 04:34:54 CDT)
- sudipta sinha (Sat Jul 05 2008 - 00:18:25 CDT)
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)
implementing RBCG
- Peter Freddolino (Wed Mar 23 2011 - 20:19:09 CDT)
- Peter Freddolino (Tue Mar 22 2011 - 21:17:32 CDT)
- Chris Harrison (Tue Mar 22 2011 - 21:25:54 CDT)
- Michael Zimmermann (Tue Mar 22 2011 - 15:11:30 CDT)
Implicit membrane models
- Austin B. Yongye (Wed Sep 09 2009 - 09:03:53 CDT)
Implicit solvent
- David Tanner (Mon Jun 27 2011 - 09:04:24 CDT)
- Massimiliano Porrini (Mon Jun 27 2011 - 06:35:00 CDT)
- Michael Grabe (Fri Jun 10 2005 - 11:18:34 CDT)
- Marc Q. Ma (Fri Jun 10 2005 - 08:28:21 CDT)
- Leonardo Sepulveda Durán (Thu Jun 09 2005 - 21:26:40 CDT)
- Wei Zhuang (Thu Jun 09 2005 - 17:47:48 CDT)
implicit solvent and cuda
- Jim Phillips (Tue May 10 2011 - 20:24:17 CDT)
- Francesco Oteri (Mon May 02 2011 - 16:03:15 CDT)
implicit solvent energy calculation
- Neema Salimi (Tue Feb 26 2008 - 15:10:25 CST)
- Chang, Christopher (Tue Feb 26 2008 - 13:51:26 CST)
- regafan_at_usc.es (Tue Feb 26 2008 - 04:03:49 CST)
implicit solvent job error in NAMD2.8b1
- David Tanner (Tue Apr 05 2011 - 11:35:49 CDT)
- David Tanner (Mon Apr 04 2011 - 16:34:11 CDT)
- harish vashisth (Mon Apr 04 2011 - 17:14:20 CDT)
- harish vashisth (Mon Apr 04 2011 - 15:47:33 CDT)
implicit solvent model
- Frances Leung (Mon Jan 19 2004 - 20:10:59 CST)
implicit solvent model in NAMD?
- David Tanner (Sat Jul 04 2009 - 06:50:14 CDT)
- Yinglong Miao (Fri Jul 03 2009 - 15:18:17 CDT)
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 solvent simulation
- Bjoern Olausson (Fri Jul 08 2011 - 05:57:03 CDT)
- jaya c.jose (Fri Jul 08 2011 - 05:35:40 CDT)
- Cesar Avila (Mon Sep 03 2007 - 08:45:16 CDT)
implicit solvent with iapbs
- Robert Konecny (Mon Feb 01 2010 - 17:30:09 CST)
- BIN ZHANG (Thu Jan 28 2010 - 01:33:38 CST)
Implicit water dielectric constant.
- Blake Charlebois (Tue Nov 16 2004 - 15:06:50 CST)
- Ivan Vinogradov (Wed Nov 10 2004 - 10:16:57 CST)
Importance of the Topology File, .rtf, and Other Files
- Rajan Vatassery (Sat Oct 16 2010 - 13:57:10 CDT)
impose restraint on the internal coordinate of protein
- Giacomo Fiorin (Mon Jun 21 2010 - 16:09:20 CDT)
- Eduard Schreiner (Mon Jun 21 2010 - 14:41:53 CDT)
- dhacademic (Mon Jun 21 2010 - 13:43:58 CDT)
imprecision in table energy
- Jim Phillips (Mon Sep 25 2006 - 14:10:00 CDT)
- A. Ozlem T. Bishop (Sun Sep 24 2006 - 09:57:50 CDT)
Impressive Glashutte timepieces
- Becky Peoples (Sat Jun 21 2008 - 22:17:24 CDT)
improper angle
- JC Gumbart (Sat Nov 12 2011 - 01:14:09 CST)
- johan strumpfer (Fri Nov 11 2011 - 06:21:38 CST)
- Marco Sant (Fri Nov 11 2011 - 02:34:42 CST)
improper torsion
- Hidekazu WATANABE (Fri May 18 2007 - 04:56:37 CDT)
impropers for aromatic residues
- Jerome Henin (Sun Nov 09 2008 - 15:37:43 CST)
- CHINDEA Vlad (Sat Nov 08 2008 - 15:17:44 CST)
Impropers in Charmm and OPLS
- johan strumpfer (Tue Jun 14 2011 - 10:01:13 CDT)
- Henriette Elisabeth Autzen (Tue Jun 14 2011 - 08:33:58 CDT)
Impropers in histidine residues
- Jerome Henin (Wed Aug 06 2008 - 16:54:15 CDT)
- Marc Baaden (Sat Aug 02 2008 - 03:56:17 CDT)
Improve your sexual life and save up to 80%
- Matthew Hughes (Tue Jun 05 2007 - 12:16:03 CDT)
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)
in NAMD tutorials: why "HSE" instead of "HSD"?
- Sebastian Stolzenberg (Mon Apr 26 2010 - 18:57:04 CDT)
Incompatibility between colvars and tclforces?
- Francesco Pietra (Wed Mar 30 2011 - 11:29:15 CDT)
- Giacomo Fiorin (Wed Mar 30 2011 - 11:20:08 CDT)
- Jérôme Hénin (Wed Mar 30 2011 - 10:23:45 CDT)
- Wang Yi (Wed Mar 30 2011 - 09:16:25 CDT)
- Francesco Pietra (Wed Mar 30 2011 - 09:06:13 CDT)
- Jérôme Hénin (Wed Mar 30 2011 - 06:23:42 CDT)
- Ajasja LjubetiÄ (Wed Mar 30 2011 - 06:21:23 CDT)
- Francesco Pietra (Wed Mar 30 2011 - 05:04:02 CDT)
incompatibility between NAMD and amber topology files
- Osman, Roman (Tue Jan 10 2012 - 15:33:43 CST)
- Osman, Roman (Mon Jan 09 2012 - 16:13:24 CST)
incompatibility between VMD & NAMD for reading Amber crd files
- Kamp, Marc vander (Mon Jun 21 2004 - 07:33:11 CDT)
inconsistence in NAMD and AMBER energy
- George Madalin Giambasu (Tue Jul 21 2009 - 11:27:03 CDT)
- Yi Shang (Tue Jul 21 2009 - 11:04:18 CDT)
- Thomas C. Bishop (Tue Jul 21 2009 - 11:11:39 CDT)
- Floris Buelens (Tue Jul 21 2009 - 10:57:41 CDT)
- Yi Shang (Tue Jul 21 2009 - 10:22:45 CDT)
- Thomas C. Bishop (Tue Jul 21 2009 - 10:14:28 CDT)
- Yi Shang (Tue Jul 21 2009 - 09:56:04 CDT)
- Thomas C. Bishop (Tue Jul 21 2009 - 09:33:35 CDT)
- Floris Buelens (Tue Jul 21 2009 - 02:11:51 CDT)
- Goutham (Tue Jul 21 2009 - 01:13:48 CDT)
- Yi Shang (Mon Jul 20 2009 - 18:31:47 CDT)
inconsistence in NAMD and AMBER energy: AMBER truncted octahedron
- Vlad Cojocaru (Wed Jul 22 2009 - 04:44:45 CDT)
- Thomas C. Bishop (Tue Jul 21 2009 - 11:30:35 CDT)
- Vlad Cojocaru (Tue Jul 21 2009 - 11:08:40 CDT)
Inconsistencies in NAMD simulations
- Ana Vila Verde (Tue Jan 22 2008 - 06:14:52 CST)
- Chandra Ramananjara (Tue Jan 22 2008 - 02:49:53 CST)
inconsistencies with amber force fields due to scnb and 1-4scalin g
- Stern, Julie (Wed May 18 2005 - 10:38:51 CDT)
Incorrect Atom Count
- Charles Zhao (Thu Dec 03 2009 - 01:26:32 CST)
- Charles Zhao (Wed Dec 02 2009 - 17:58:03 CST)
- BIN ZHANG (Wed Dec 02 2009 - 16:31:20 CST)
- Charles Zhao (Wed Dec 02 2009 - 15:53:51 CST)
- vivek behera (Tue Mar 13 2007 - 23:22:16 CDT)
- vivek behera (Tue Feb 27 2007 - 09:02:17 CST)
Incorrect Atom Count in binary file
- Ada Zhan (Wed Oct 20 2010 - 14:20:08 CDT)
- namd_chcwaaa_at_yahoo.com.cn (Tue Oct 13 2009 - 06:30:06 CDT)
- Yogesh Aher (Tue Oct 13 2009 - 03:42:44 CDT)
Incorrect periodic box imaging with AMBER parameters
- Grzegorz Jezierski (Mon Aug 08 2005 - 12:43:20 CDT)
- Grzegorz Jezierski (Fri Aug 05 2005 - 06:23:57 CDT)
- nordgren_at_sas.upenn.edu (Thu Aug 04 2005 - 17:40:58 CDT)
- surendra negi (Thu Aug 04 2005 - 16:11:15 CDT)
- Grzegorz Jezierski (Thu Aug 04 2005 - 13:04:05 CDT)
- Charles Danko (Mon Jul 25 2005 - 08:32:20 CDT)
- Grzegorz Jezierski (Mon Jul 25 2005 - 04:11:20 CDT)
Incorrect PSF file for min.pme
- Peter Freddolino (Tue Jun 24 2008 - 10:37:34 CDT)
- Eva Nong (Mon Jun 23 2008 - 15:32:58 CDT)
increase in energy over time
- Edward Patrick Obrien (Tue Jan 04 2005 - 11:01:53 CST)
- Peter Bazeley (Mon Jan 03 2005 - 21:19:33 CST)
- Edward Patrick Obrien (Mon Jan 03 2005 - 18:29:46 CST)
- Peter Bazeley (Mon Jan 03 2005 - 17:27:45 CST)
Increase the decimal points of energy output
- Yang, Lee Wei (Tue Dec 09 2008 - 20:26:16 CST)
- Robert Brunner (Tue Dec 09 2008 - 12:14:48 CST)
- Yang, Lee Wei (Tue Dec 09 2008 - 05:14:10 CST)
increase the temperature step by step after minimization
- Chris Harrison (Mon Aug 10 2009 - 05:01:08 CDT)
- gurunath katagi (Mon Aug 10 2009 - 00:27:03 CDT)
increasing MAX_EXCLUSIONS
- Francesco Oteri (Thu Jan 20 2011 - 09:56:35 CST)
- Axel Kohlmeyer (Wed Jan 19 2011 - 16:42:29 CST)
- Francesco Oteri (Wed Jan 19 2011 - 16:07:05 CST)
Increasing temp during MD
- Peter Freddolino (Thu Nov 03 2005 - 12:43:33 CST)
- Grace Shen (Thu Nov 03 2005 - 12:11:27 CST)
Inexpensive IWC watches
- Janie Sweeney (Mon Jun 09 2008 - 12:47:28 CDT)
Infiniband and commodity hardware
- Axel Kohlmeyer (Sun Sep 18 2011 - 02:38:48 CDT)
- Thomas Albers (Sat Sep 17 2011 - 14:59:20 CDT)
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)
InfiniPath and NAMD
- David Sept (Mon Jul 24 2006 - 14:57:03 CDT)
Infinite Armchair Single Wall Carbon Nanotubes and Periodic Boundary Conditions (PBC)
- Joshua D. Moore (Sat Aug 11 2007 - 15:21:44 CDT)
- Peter Freddolino (Sat Aug 11 2007 - 15:05:20 CDT)
- Joshua D. Moore (Sat Aug 11 2007 - 01:33:01 CDT)
infinite DNA
- Stern, Julie (Wed Jul 06 2005 - 11:52:17 CDT)
infinite layer
- Peter Freddolino (Tue May 01 2007 - 11:17:28 CDT)
- Nicolas Belloy (Tue May 01 2007 - 08:18:40 CDT)
- Nicolas Belloy (Wed Apr 18 2007 - 06:06:52 CDT)
- Peter Freddolino (Fri Apr 13 2007 - 21:57:58 CDT)
- Nicolas Belloy (Thu Apr 12 2007 - 11:59:26 CDT)
infinite nanotubes with PBC in NAMD?
- Nicolas Winter (Wed Nov 08 2006 - 10:33:11 CST)
Influence of PME grid size and cell basis vectors over simulation result
- debashis.sikdar_at_ndsu.edu (Mon Mar 07 2005 - 13:01:19 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)
Info: Adjusted background load on 11 nodes.
- Leandro Martínez (Tue Aug 29 2006 - 07:13:51 CDT)
- Leandro Martínez (Mon Aug 28 2006 - 12:21:49 CDT)
- Cesar Luis Avila (Sat Aug 26 2006 - 17:00:08 CDT)
- Cesar Luis Avila (Sat Aug 26 2006 - 16:40:15 CDT)
- Leandro Martínez (Fri Aug 25 2006 - 08:01:53 CDT)
- Leandro Martínez (Fri Aug 25 2006 - 07:42:28 CDT)
Info: Attempting to read FFTW data from FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt
- Richard Owczarzy (Mon Feb 01 2010 - 10:27:44 CST)
- Ajasja LjubetiÄ (Mon Feb 01 2010 - 04:09:24 CST)
- Bala subramanian (Mon Feb 01 2010 - 03:12:04 CST)
infrequent rattle failure with charmm36
- Edward Lyman (Wed Apr 20 2011 - 09:50:37 CDT)
- Markus K. Dahlgren (Wed Apr 20 2011 - 09:30:11 CDT)
- Edward Lyman (Wed Apr 20 2011 - 08:47:59 CDT)
Initial and final state fix MD
- JC Gumbart (Thu Oct 04 2007 - 16:56:58 CDT)
- Gungor Ozer (Thu Oct 04 2007 - 16:57:01 CDT)
- Ugur Akgun (Thu Oct 04 2007 - 16:21:25 CDT)
initial structures for md simulations
- Jeffrey J. Potoff (Wed Feb 16 2011 - 09:02:13 CST)
- oguz gurbulak (Wed Feb 16 2011 - 07:52:26 CST)
- oguz gurbulak (Wed Feb 16 2011 - 06:22:11 CST)
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)
Inorganic Builder Plugin
- Subhashis Biswas (Wed Feb 27 2008 - 17:57:12 CST)
Inorganic compounds
- Chris Harrison (Wed Jan 14 2009 - 23:25:19 CST)
- Casey,Richard (Thu Jan 08 2009 - 12:20:34 CST)
inorganic surface peptide simulation
- Matan Dishon (Mon Jun 06 2005 - 07:13:07 CDT)
input file for memory optimised version
- Stefano Pieraccini (Tue Dec 14 2010 - 03:43:12 CST)
input file for PO3
- lily jin (Tue Mar 28 2006 - 11:02:34 CST)
Input/output error
- Axel Kohlmeyer (Tue May 18 2010 - 04:18:20 CDT)
- Íõ—² (Tue May 18 2010 - 01:55:20 CDT)
Inquire on gradual temperature increase.
- jose correa (Mon Oct 20 2008 - 09:39:40 CDT)
- Diego Alejandro Vargas (Mon Oct 20 2008 - 08:59:46 CDT)
install NAMD 2.8 v
- Namd Namd (Mon Oct 10 2011 - 05:50:53 CDT)
install namd on dell power edge 1900
- Ramon Rocha (Thu Dec 04 2008 - 11:43:08 CST)
install NAMD on Ubuntu
- Alexandre A. Vakhrouchev (Sat Apr 26 2008 - 01:12:30 CDT)
- Hero (Fri Apr 25 2008 - 23:46:07 CDT)
install VMD on Ubuntu
- Low Soo Mei (Sat Apr 26 2008 - 14:25:32 CDT)
- Hero (Sat Apr 26 2008 - 14:38:19 CDT)
- Hero (Sat Apr 26 2008 - 14:09:39 CDT)
installation of charm-6.0 in ia-64 cluster machine
- Peter Freddolino (Fri Jul 11 2008 - 12:23:30 CDT)
- Anupam Nath Jha (Fri Jul 11 2008 - 06:49:34 CDT)
installation of namd
- Axel Kohlmeyer (Tue Feb 16 2010 - 06:40:06 CST)
- ipsita basu (Tue Feb 16 2010 - 04:00:23 CST)
Installation of NAMD & charm - fatal errors
- DimitryASuplatov (Sun Mar 28 2010 - 04:24:43 CDT)
- DDR (Sat Mar 27 2010 - 18:23:25 CDT)
installation of namd in parallel mode
- Andreas Förster (Mon Feb 15 2010 - 03:46:03 CST)
- Mert Gür (Sun Feb 14 2010 - 05:51:55 CST)
- ipsita basu (Sat Feb 13 2010 - 01:40:28 CST)
installation of namd without tcl and fftw
- ipsita basu (Tue May 11 2010 - 08:02:11 CDT)
- Axel Kohlmeyer (Tue May 11 2010 - 08:11:24 CDT)
- Axel Kohlmeyer (Tue May 11 2010 - 06:55:33 CDT)
- Jérôme Hénin (Tue May 11 2010 - 05:16:01 CDT)
- Jérôme Hénin (Tue May 11 2010 - 03:41:00 CDT)
- ipsita basu (Tue May 11 2010 - 00:40:59 CDT)
- Jérôme Hénin (Mon May 10 2010 - 07:51:53 CDT)
- Axel Kohlmeyer (Mon May 10 2010 - 06:58:59 CDT)
- ipsita basu (Mon May 10 2010 - 06:11:39 CDT)
Installation Problem
- bertrand russell (Fri Oct 06 2006 - 06:52:00 CDT)
Installation problem on Win64
- muniyamuthu.raviprasad_at_ndsu.edu (Fri Apr 02 2010 - 10:27:02 CDT)
- Richard Owczarzy (Fri Apr 02 2010 - 09:39:19 CDT)
- Giacomo Fiorin (Fri Apr 02 2010 - 09:11:02 CDT)
- Kwee Hong (Fri Apr 02 2010 - 04:46:28 CDT)
Installing NAMD
- brmorgan_at_clarku.edu (Tue Nov 20 2007 - 13:02:42 CST)
- Jason Russler (Tue Nov 20 2007 - 07:39:58 CST)
- brmorgan_at_clarku.edu (Fri Nov 16 2007 - 11:28:47 CST)
- Michel Espinoza-Fonseca (Mon Mar 07 2005 - 18:18:43 CST)
- Brian Bennion (Wed Apr 07 2004 - 16:56:14 CDT)
- beckloni_at_umdnj.edu (Wed Apr 07 2004 - 15:56:21 CDT)
Installing NAMD 2.6 on SMP machine... charm++ install errors
- Claudio Redaelli (Fri Jul 06 2007 - 04:14:39 CDT)
- Arun Krishnan (Fri Jul 06 2007 - 01:45:46 CDT)
- Arun Krishnan (Fri Jul 06 2007 - 01:29:25 CDT)
Installing NAMD on a 64-bit linux (NVIDIA CUDA)
- Axel Kohlmeyer (Mon Jan 30 2012 - 12:24:40 CST)
- Shyno Mathew (Mon Jan 30 2012 - 12:15:15 CST)
Installing NAMD on beowulf cluster, 64 bit, opteron, 4 processors.
- Gengbin Zheng (Tue Jun 07 2005 - 13:58:15 CDT)
- Wang, Boyang (Mon Jun 06 2005 - 22:23:59 CDT)
installing namd on ibm cluster (powerpc)
- Chris Harrison (Fri Oct 28 2011 - 17:35:07 CDT)
- Gurunath Katagi (Fri Oct 28 2011 - 15:14:02 CDT)
installing NAMD on opteron cluster with MPI
- John Saeger (Wed Mar 09 2005 - 15:12:08 CST)
- Lina Nilsson (Tue Mar 08 2005 - 02:27:25 CST)
- Gengbin Zheng (Fri Mar 04 2005 - 01:00:59 CST)
- Lina M Nilsson (Thu Mar 03 2005 - 16:06:13 CST)
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 11 compilers
- David A. Horita (Fri Jul 10 2009 - 13:37:54 CDT)
- Guanglei Cui (Fri Jul 10 2009 - 10:45:17 CDT)
- Nicholas M Glykos (Fri Jul 10 2009 - 10:01:59 CDT)
- Xavier Deupi (Fri Jul 10 2009 - 08:52:58 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)
Intel Woodcrest version?
- Jacob Poehlsgaard (Wed Oct 18 2006 - 03:01:33 CDT)
- Jacob Poehlsgaard (Tue Oct 17 2006 - 05:50:16 CDT)
Interaction between metal and metal-water.
- Taeho Kim (Fri Nov 25 2005 - 10:39:22 CST)
Interaction energy
- Peter Freddolino (Tue Jul 08 2008 - 21:07:10 CDT)
- abhijit ramachandran (Tue Jul 08 2008 - 15:57:47 CDT)
- 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 difference
- Nicholas J Musolino (Thu Jul 29 2010 - 10:42:35 CDT)
- Axel Kohlmeyer (Thu Jul 29 2010 - 00:08:52 CDT)
- m.raviprasad_at_ndsu.edu (Wed Jul 28 2010 - 22:42:07 CDT)
Interaction energy for fixed atoms
- AMIT PALIWAL (Fri Jan 09 2004 - 17:35:13 CST)
Interaction potentials W-S
- Axel Kohlmeyer (Thu Dec 16 2010 - 05:31:58 CST)
- Evgeniya Volkova (Wed Dec 15 2010 - 08:13:40 CST)
interaction-energy
- balaji nagarajan (Wed Aug 18 2010 - 05:15:03 CDT)
interactions in flexible cel
- Anna Modzelewska (Wed Jun 29 2005 - 02:07:04 CDT)
- Anna Modzelewska (Wed Jun 29 2005 - 00:34:51 CDT)
interactions in flexible cell
- Anna Modzelewska (Fri Jun 24 2005 - 04:31:27 CDT)
Interactive MD driver/controller software no longer in beta
- Axel Kohlmeyer (Fri Nov 12 2010 - 09:41:59 CST)
Interactive protonation
- Peter Freddolino (Sat Mar 28 2009 - 19:26:51 CDT)
- Giacomo Fiorin (Sat Mar 28 2009 - 18:48:43 CDT)
- DimitryASuplatov (Sat Mar 28 2009 - 16:46:51 CDT)
Interactive Simulations, ligand size limits....
- Luis Rosales (Tue Apr 19 2005 - 22:51:52 CDT)
Interface analisis
- Leonardo Herrera (Tue Aug 03 2010 - 12:20:00 CDT)
interface with external program
- Leandro Martínez (Fri Jun 10 2005 - 13:15:30 CDT)
- Leandro Martínez (Fri Jun 10 2005 - 13:55:53 CDT)
Interfaces in NAMD
- Hasan haska (Sat Dec 17 2011 - 14:20:25 CST)
intermittent non-execution of NAMD on tesla
- P.-L. Chau (Mon Nov 21 2011 - 04:09:04 CST)
interpretation of timing data in output
- Jim Phillips (Wed Jul 20 2011 - 11:47:04 CDT)
- Hannes Loeffler (Fri Jun 24 2011 - 04:29:42 CDT)
Interrupted system call
- claudia (Thu Oct 18 2007 - 08:25:22 CDT)
- q=E2=BA=E9=C3=F7?= (Sun Jun 11 2006 - 21:31:56 CDT)
- q=E2=BA=E9=C3=F7?= (Sun Jun 11 2006 - 21:26:02 CDT)
- Edelmiro Moman (Fri Jun 09 2006 - 02:21:25 CDT)
intramolecular LJ parameters
- Hamsa Priya Mohana sundaram (Wed Oct 01 2008 - 12:19:56 CDT)
Invalid cpus 2 in nodelist ignored
- Gianluca Interlandi (Fri Feb 16 2007 - 19:16:59 CST)
Invitation to connect on LinkedIn
- Ahlam Al-Rawi (Thu Sep 15 2011 - 16:11:12 CDT)
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)
Ion Channel Jarzynski
- JC Gumbart (Thu Aug 10 2006 - 20:28:55 CDT)
- Alessandro Cembran (Thu Aug 10 2006 - 17:56:29 CDT)
ion concentration
- JC Gumbart (Thu Oct 06 2005 - 20:21:20 CDT)
- Shirley Li (Thu Oct 06 2005 - 18:36:26 CDT)
ion concentration in residue-based coarse-grained model
- Demet Akten (Wed Sep 22 2010 - 02:49:01 CDT)
- Francesco Oteri (Wed Sep 22 2010 - 03:50:41 CDT)
Ion-protein and protein-protein interactions
- Vishal Kopardé (Thu Oct 26 2006 - 12:50:48 CDT)
Ionization with VMD
- Axel Kohlmeyer (Thu Oct 15 2009 - 09:48:29 CDT)
- Luis Agullo (LAB) (Thu Oct 15 2009 - 09:07:13 CDT)
ionize (big, big, big system!)
- Jacob Poehlsgaard (Tue Feb 13 2007 - 02:22:23 CST)
- Peter Freddolino (Mon Feb 12 2007 - 13:07:08 CST)
- Cesar Luis Avila (Mon Feb 12 2007 - 12:58:11 CST)
- L. Michel Espinoza-Fonseca (Mon Feb 12 2007 - 10:58:32 CST)
Ionize script
- Axel Kohlmeyer (Thu Apr 08 2010 - 11:52:45 CDT)
- ehenriques_at_qui.uc.pt (Thu Apr 08 2010 - 10:55:44

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