• Home

• Overview

• Publications

• Research

• Software

• VMD Molecular Graphics Viewer

• NAMD Molecular Dynamics Simulator

• BioCoRE Collaboratory Environment

• MD Service Suite

• Structural Biology Software Database

• Computational Facility

• Outreach

NAMD-L: By Subject

By Subject

7965 messages sorted by: [ author ] [ date ] [ thread ] [ attachment ]
About this archive

Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Sun Jul 06 2008 - 07:51:49 CDT

• 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)
• Jérôme Hénin (Thu Jul 01 2004 - 04:47:55 CDT)
• Cable, Sam B ERDC-ITL-MS Contractor (Thu Apr 15 2004 - 15:44:57 CDT)
• Gengbin Zheng (Thu Apr 15 2004 - 12:14:36 CDT)
• Jim Phillips (Mon Jan 26 2004 - 17:51:12 CST)
• james tomomi macdonald (Mon Dec 08 2003 - 08:46:54 CST)
• Jim Phillips (Wed Dec 03 2003 - 15:03:46 CST)
• Cesar Delgado (Wed Dec 03 2003 - 08:46:12 CST)
• Fangqiang Zhu (Sat Nov 29 2003 - 00:41:44 CST)
• Ioana Cozmuta (Mon Oct 20 2003 - 12:32:02 CDT)
• Cesar Delgado (Mon Oct 20 2003 - 01:13:08 CDT)
• "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)
• "CWeb performance data sent to wrong processor..."
  • Jon Halverson (Thu Jan 11 2007 - 15:47:57 CST)
• "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)
• "Hands-On" Workshop on Computational Biophysics
  • David Brandon (Fri Mar 11 2005 - 15:23:27 CST)
• "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)
• "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)
• (no subject)
  • 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)
• *** 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)
• , 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)
• .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)
• 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)
• 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-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)
• 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 vs. 64 bits
  • Leandro Martinez (Fri May 14 2004 - 08:07:14 CDT)
• 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)
• <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)
• [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)
• [Periodic Boundary]: from charmm to namd
  • Sascha Tayefeh (Tue Nov 02 2004 - 12:46:02 CST)
  • Charles Danko (Tue Nov 02 2004 - 11:35:23 CST)
  • Sascha Tayefeh (Tue Nov 02 2004 - 09:08:42 CST)
• _alloca undefined symbol (OS X/XL compiler)
  • Gengbin Zheng (Mon Apr 05 2004 - 00:20:45 CDT)
  • Mike McCallum (Fri Apr 02 2004 - 18:29:26 CST)
• _NAMD_crashes?= on winx64 during parallel run.
  • Alexandre A. Vakhrouchev (Sun Jul 29 2007 - 00:42:38 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 confused question on amber param and in charmm form~
  • κ¿­ (Fri Nov 26 2004 - 07:41:55 CST)
• a different bug alert
  • Meric Ayse Ovacik (Sun Oct 17 2004 - 09:27:23 CDT)
  • Meric Ayse Ovacik (Sun Oct 17 2004 - 09:21:47 CDT)
• A 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 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 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 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 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 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 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~
  • κ¿­ (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 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)
• 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 (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 - 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 - 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 - 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 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 error calculation
  • 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 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 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 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 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 question
  • 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 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 Simulation
  • 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 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 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.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: 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: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)
• 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 '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)
  • ËïæÃæà (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)
  • ËïæÃæà (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 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 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 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 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 cutoff parameter for real space calculation in PME
  • xiaojing gong (Sun May 27 2007 - 06:47:26 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 ExcludeFromPressure
  • mashaojie163 (Tue Oct 26 2004 - 21:59:50 CDT)
  • mashaojie163 (Fri Oct 22 2004 - 03:52:15 CDT)
• about guesscoord
  • mashaojie (Wed Mar 03 2004 - 21:31:05 CST)
• about HIS residue
  • J. Rui Rodrigues (Sun Dec 21 2003 - 13:47:28 CST)
  • yxiong_at_mail.ccnu.edu.cn (Fri Dec 19 2003 - 20:40:35 CST)
• about internal coordinate IC statement of CHARMM force field
  • Brian Bennion (Tue Nov 25 2003 - 13:09:41 CST)
  • yxiong_at_mail.ccnu.edu.cn (Tue Nov 25 2003 - 01:24:23 CST)
• About 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 loadcoors -- is there a loadvelocity?
  • Boyang Wang (Fri May 19 2006 - 13:01:11 CDT)
• about MCTI output
  • mashaojie163 (Mon Dec 27 2004 - 01:29:36 CST)
• about membrane protein
  • mashaojie163 (Mon Jun 14 2004 - 09:39:41 CDT)
• about 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 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 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 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 ref frame for rmsd vs time
  • Francesco Pietra (Wed Jan 30 2008 - 00:52:48 CST)
• About Restart
  • 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
  • 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 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
  • 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 error of "Tcl interface"
  • wang (Thu Jul 06 2006 - 00:26:31 CDT)
  • wang (Wed Jul 05 2006 - 21:05:27 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 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 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)
• 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)
• 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)
• Accepted temperature and pressure oscillation
  • cong chen (Wed Oct 31 2007 - 03:14:55 CDT)
• 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)
• 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)
• AcetylProlineAmide topology
  • Neelanjana Sengupta (Wed Jan 17 2007 - 12:35:45 CST)
• across the nodes, namd jobs don't get enough CPU!
  • M. Madhu (Fri Jul 07 2006 - 11:00:59 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
  • 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)
• Adding amino acids to an existing pdb structure
  • LEWYN LI (Sun Dec 04 2005 - 21:30:49 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)
• 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)
• affecting the atom velocities
  • Luca Muccioli (Fri Jun 15 2007 - 04:02:01 CDT)
  • Philipp Schoen1 (Fri Jun 15 2007 - 02:20:55 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 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 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)
• 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)
• 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)
• 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)
• 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 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)
• 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)
• 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)
• an aptamer and a lot of stupid problems
  • Fridolin Treindl (Mon Feb 11 2008 - 23:09:38 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)
• 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 PARAMETERS (It works now)
  • Shirley Li (Thu Dec 22 2005 - 16:54:06 CST)
• 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)
• 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)
• 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)
• ApoB structure
  • Alexandre A. Vakhrouchev (Thu Jun 12 2008 - 01:12:02 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 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 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)
• 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)
• 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 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)
• 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)
• Asymmetric water molecule found???
  • Elsa F. Sousa Henriques (Wed May 03 2006 - 02:59:26 CDT)
• 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 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 specification in smd/tclforces for amber topology/parameter based systems
  • Jerry Ebalunode (Mon Mar 07 2005 - 14:50:20 CST)
• Atom type explaination for NAMD
  • myang (Wed May 26 2004 - 18:04:05 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)
• Atomic partial charge
  • Luca Bellucci (Mon Oct 09 2006 - 05:35:36 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)
• 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)
• 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)
• 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)
• 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)
• Avoiding alpha-helix distortions
  • 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)
• bad exclusion count
  • Francesco Iori (Fri Nov 17 2006 - 15:19:37 CST)
• Bad global dihedral count.
  • Wang, Boyang (Fri Jan 18 2008 - 14:44:11 CST)
• Bad global exclusion count
  • 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 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)
• 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)
• 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 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)
• 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)
• 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)
• 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)
• 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)
• beta-peptides ...
  • Nicholas M Glykos (Mon Oct 31 2005 - 06:34:20 CST)
• 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)
• 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)
• 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 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)
• 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)
• 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)
• 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)
• 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