NAMD-L: By Subject

NAMD

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NAMD-L: By Subject

By Subject

11227 messages sorted by: [ author ] [ date ] [ thread ] [ attachment ]
About this archive

Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Fri Nov 20 2009 - 20:07:14 CST

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)

"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)
"Hands-On" Workshop on Computational Biophysics, July 6-10 and August 10-14, 2009
- TCBG Workshop (Thu Feb 05 2009 - 15:52:30 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)
"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)
(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)
(no subject)
- 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)
(Á¦¸ñ ¾ø ½)
- Taeho Kim (Wed Feb 11 2009 - 22:29:19 CST)
*** 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)
.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)
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)
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)
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)
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)
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)
[***** 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)
_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 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 confused question on amber param and in charmm form~
- Îº¿ (Fri Nov 26 2004 - 07:41:55 CST)
a different bug alert
- Meric Ayse Ovacik (Sun Oct 17 2004 - 09:27:23 CDT)
- Meric Ayse Ovacik (Sun Oct 17 2004 - 09:21:47 CDT)
A 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 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)
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 '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 + 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 - 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 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 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 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 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 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 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 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 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: 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)
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 "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 '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 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 compile namd2.7
- Axel Kohlmeyer (Sun Jul 19 2009 - 11:18:33 CDT)
- liupeng012 (Sun Jul 19 2009 - 05:58:05 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 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 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 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 MCTI output
- mashaojie163 (Mon Dec 27 2004 - 01:29:36 CST)
about membrane protein
- mashaojie163 (Mon Jun 14 2004 - 09:39:41 CDT)
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 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 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 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
- 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
- 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 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 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)
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)
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)
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 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 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 specific forces between atoms
- Michael Zimmermann (Mon Sep 21 2009 - 15:44:48 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 van Hove
- Arturas Ziemys (Thu Jan 15 2009 - 12:08:40 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)
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)
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 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)
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)
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)
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)
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)
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 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 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
- Xxxxxxxx Xxxxxxx (Mon Feb 11 2008 - 23:09:38 CST)
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 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 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 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)
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)
ApoB structure
- Alexandre A. Vakhrouchev (Thu Jun 12 2008 - 01:12:02 CDT)
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 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)
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)
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)
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 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 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 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)
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)
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 namd 2.7b1 installation
- DimitryASuplatov (Mon Nov 09 2009 - 11:36:22 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)
Backbone dihedral ABF
- Sébastien Légaré (Tue Oct 28 2008 - 11:50:02 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)
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 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)
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)
Benchmark calculation
- rebeca_at_mmb.pcb.ub.es (Thu Aug 14 2008 - 12:36:55 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)
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, 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)
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)
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 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)
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)
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)
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)
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)
BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars)
- snoze pa (Tue May 06 2008 - 10:20:47 CDT)
- snoze pa (Mon May 05 2008 - 16:49:43 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 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 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 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 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)
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 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 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 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 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)
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 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 ¡°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 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 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 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 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 FE - S
- surendra negi (Fri Sep 02 2005 - 15:36:43 CDT)
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 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)
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-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)
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.
- 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)
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)
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 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 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 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)
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 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)
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 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 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 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)
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 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 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++ 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 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 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 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 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 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 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 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 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: 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)
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)
cis/trans prolyl
- sfrickenhaus (Sat Aug 11 2007 - 03:40:55 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)
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)
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 in CHARMM force field
- Jorge Pikunic (Fri Oct 08 2004 - 12:27:47 CDT)
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)
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-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)
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 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)
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: 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)
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 segments
- Robert Brunner (Mon Aug 10 2009 - 11:32:26 CDT)
- d b (Mon Aug 10 2009 - 09:06:51 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)
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 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)
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 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 from SRC: Tungsten@NCSA
- Vani Krishna (Fri Sep 10 2004 - 19:54:55 CDT)
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 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 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 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)
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 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)
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)
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
- 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)
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 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 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 3205
- ydhuang2727 (Fri Nov 14 2008 - 19:42:20 CST)
- Schreiner Eduard (Fri Nov 14 2008 - 20:13:30 CST)
constraint failure problem.
- ydhuang2727 (Wed Nov 26 2008 - 20:54:30 CST)
constraints
- 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 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)
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)
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 monitoring...
- Raul Araya Secchi (Tue Jun 05 2007 - 14:52:57 CDT)
convergence of abf
- 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_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 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 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)
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 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
- 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)
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)
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-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 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)
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)
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 a pdb file based on sequence and psi phi omega values only
- Matan Dishon (Sun Aug 28 2005 - 04:58:07 CDT)
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)
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)
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 Linux-x86 doesn't compile
- Sadhu, Shubho (NIH/NCI) [F] (Thu Jul 30 2009 - 09:06:04 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)
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)
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 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
- 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 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)
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)
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)
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)
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)
DEN residue name in Amber
- prateeksha s (Wed Dec 05 2007 - 00:10:42 CST)
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)
deprotonated form of Proline molecule
- Dhiraj Srivastava (Tue Aug 15 2006 - 14:55:35 CDT)
Determining Equillibration of a membrane protein
- Ilya Chorny (Tue Jun 26 2007 - 18:57:32 CDT)
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)
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
- 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 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 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)
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 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)
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 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 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 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)
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)
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)
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 constraint
- Jim Phillips (Fri Feb 06 2004 - 14:34:50 CST)
- Hyonseok Hwang (Wed Feb 04 2004 - 17:56:20 CST)
distance constraints in NAMD
- tsaih_at_ncifcrf.gov (Fri Mar 19 2004 - 07:06:34 CST)
distance 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
- 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-dependent dielectrics in NAMD
- Jim Phillips (Thu Nov 13 2003 - 15:52:31 CST)
- Sarah Harris (Mon Nov 10 2003 - 05:05:36 CST)
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)
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 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)
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)
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 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)
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
- 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)
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.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)
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)
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)
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)
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)
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)
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)
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 minimization
- 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 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)
ensemble
- Wei Chen (Wed Oct 05 2005 - 16:34:12 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)
eq. info.
- shivam ghosh (Fri Jul 13 2007 - 00:53:05 CDT)
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
- 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 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 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 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)
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
- Amit Paliwal (Mon May 24 2004 - 04:29:43 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 compile charm++
- Jianhui Tian (Thu Feb 15 2007 - 12:40:22 CST)
Error compiling NAMD with MPI
- Kevin Jander (Mon Jul 09 2007 - 16:07:16 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 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 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 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 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
- 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 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 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 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 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 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 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! 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: 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 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: 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: failed on end of segment with RBCG
- Francesco Pietra (Sun Nov 15 2009 - 03:18:57 CST)
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: 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)
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)
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 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)
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)
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)
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)
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)
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)
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)
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 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 running namd
- Brian Bennion (Mon Nov 15 2004 - 10:52:34 CST)
- Enrico Piccinini (Mon Nov 15 2004 - 04:30:06 CST)
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: 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??
- Richard Law (Thu Jul 21 2005 - 20:21:40 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: 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 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: 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: 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: 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 HT HT OT
- 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 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 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)
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 alchemical
- Amir Shamloo (Fri Jul 15 2005 - 19:51:23 CDT)
FEP and restraints
- Jérôme Hénin (Tue Mar 23 2004 - 14:42:12 CST)
- Michael Grabe (Tue Mar 23 2004 - 13:45:32 CST)
FEP 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 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 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 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 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, 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)
Ferric heme
- Eunice Ramirez (Mon Apr 25 2005 - 11:54:41 CDT)
FFTW problem
- Jyh-Shyong Ho (Wed Sep 27 2006 - 04:02:57 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)
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)
Finer details of an ABF/colvar simulation
- 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 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 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)
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 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 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)
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)
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 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)
- 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 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 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 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 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 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 shifted cutoff
- Stern, Julie (Tue Jul 19 2005 - 18:37:10 CDT)
- Stern, Julie (Thu Jul 07 2005 - 18:06:15 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)
forces calculation
- peach gil (Tue Sep 26 2006 - 13:12:16 CDT)
forces during SMD
- zhilei chen

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