NAMD-L: By Date

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NAMD-L: By Date

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

Re: Problem with TclBC when run in more than one processor Alexandre A. Vakhrouchev (Wed Jun 04 2008 - 22:52:43 CDT)
Re: Avoiding alpha-helix distortions Eric H. Lee (Sat Jul 05 2008 - 12:22:24 CDT)
Re: Avoiding alpha-helix distortions Praveen Agrawal (Sat Jul 05 2008 - 00:38:45 CDT)
Implementation of TCL script in NAMD .conf file sudipta sinha (Sat Jul 05 2008 - 00:18:25 CDT)
Re: won't launch on linux ubuntu cluster for a parallel run Peter Freddolino (Fri Jul 04 2008 - 22:34:03 CDT)
won't launch on linux ubuntu cluster for a parallel run LinJia Qi (Fri Jul 04 2008 - 21:23:45 CDT)
won't launch on linux ubuntu cluster for a parallel run accomp lin (Fri Jul 04 2008 - 12:21:18 CDT)
Re: ABF Method digenova (Thu Jul 03 2008 - 08:52:29 CDT)
Re: drop in Temp from NVT to NVE Peter Freddolino (Wed Jul 02 2008 - 10:49:15 CDT)
Re: ABF Method Eric H. Lee (Wed Jul 02 2008 - 10:45:15 CDT)
Re: Avoiding alpha-helix distortions Eric H. Lee (Wed Jul 02 2008 - 10:41:01 CDT)
drop in Temp from NVT to NVE S.K. Ghosh (Wed Jul 02 2008 - 10:18:41 CDT)
ABF Method Bonnie A Merchant (Wed Jul 02 2008 - 09:19:39 CDT)
RE: carbohydrates: CHARMM versus AMBER Matthew Tessier (Wed Jul 02 2008 - 08:02:24 CDT)
Re: Avoiding alpha-helix distortions Peter Freddolino (Wed Jul 02 2008 - 07:59:15 CDT)
Topology cartoon of proteins DEEPESH AGARWAL (Wed Jul 02 2008 - 06:13:59 CDT)
Avoiding alpha-helix distortions Valeria Losasso (Wed Jul 02 2008 - 03:38:20 CDT)
RE: NAMD 2.7? Branduardi Davide (Wed Jul 02 2008 - 02:14:27 CDT)
Re: NAMD 2.7? Davide Branduardi (Tue Jul 01 2008 - 02:04:26 CDT)
Heat flux along CNT Andy Shelley (Tue Jul 01 2008 - 14:13:36 CDT)
2 dimension PBC politr_at_huji.ac.il (Tue Jul 01 2008 - 07:15:29 CDT)
Re: Large MD simulations and atom number limits with NAMD Peter Freddolino (Mon Jun 30 2008 - 14:43:08 CDT)
Re: NAMD 2.7? Chris Harrison (Mon Jun 30 2008 - 12:54:29 CDT)
Re: NAMD 2.7? Jerome Henin (Mon Jun 30 2008 - 15:52:29 CDT)
Re: NAMD 2.7? Peter Freddolino (Mon Jun 30 2008 - 14:40:39 CDT)
Re: NAMD 2.7? L. Michel Espinoza-Fonseca (Mon Jun 30 2008 - 14:15:38 CDT)
palmytoilated Balazs JOJART (Mon Jun 30 2008 - 07:09:03 CDT)
NAMD 2.7? L. Michel Espinoza-Fonseca (Mon Jun 30 2008 - 06:42:59 CDT)
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Re: carbohydrates: CHARMM versus AMBER L. Michel Espinoza-Fonseca (Fri Jun 27 2008 - 17:44:41 CDT)
carbohydrates: CHARMM versus AMBER Gianluca Interlandi (Fri Jun 27 2008 - 17:16:26 CDT)
carbohydrates: CHARMM versus AMBER Gianluca Interlandi (Fri Jun 27 2008 - 14:16:08 CDT)
Re: Problem in making cyclic peptide Peter Freddolino (Fri Jun 27 2008 - 16:11:21 CDT)
Re: Problem in making cyclic peptide JC Gumbart (Fri Jun 27 2008 - 16:01:27 CDT)
Problem in making cyclic peptide Narang, Pooja, Ph.D. (Fri Jun 27 2008 - 15:24:38 CDT)
Re: Output of forces. Hidekazu WATANABE (Fri Jun 27 2008 - 04:11:56 CDT)
Re: Running minimization, heating and FEP simulation within the same configuration file. Jawahar Neelankatan (Thu Jun 26 2008 - 21:44:25 CDT)
Re: Running minimization, heating and FEP simulation within the same configuration file. Floris Buelens (Thu Jun 26 2008 - 02:46:41 CDT)
Cannot spot error in namd config file Claw Isthelaw (Thu Jun 26 2008 - 10:41:53 CDT)
Re: Output of forces. Osman Yogurtcu (Thu Jun 26 2008 - 02:30:25 CDT)
Output of forces. Hidekazu WATANABE (Thu Jun 26 2008 - 00:26:51 CDT)
, Build your vocab (word power)-Get emails daily Fr.ee Deepesh (Thu Jun 26 2008 - 00:02:52 CDT)
MD for phospho-aspartate using NAMD sunita gupta (Wed Jun 25 2008 - 03:37:51 CDT)
Re: charmrun not found Alexandre A. Vakhrouchev (Tue Jun 24 2008 - 22:50:45 CDT)
Running minimization, heating and FEP simulation within the same configuration file. Jawahar Neelankatan (Tue Jun 24 2008 - 20:28:21 CDT)
charmrun not found Diego Alejandro Vargas (Tue Jun 24 2008 - 21:59:24 CDT)
Re: Problem regarding psfgen Peter Freddolino (Tue Jun 24 2008 - 21:18:33 CDT)
Problem regarding psfgen haosheng_at_hec.utah.edu (Tue Jun 24 2008 - 18:03:08 CDT)
Re: Incorrect PSF file for min.pme Peter Freddolino (Tue Jun 24 2008 - 10:37:34 CDT)
Re: Dihedral scan in NAMD? L. Michel Espinoza-Fonseca (Tue Jun 24 2008 - 02:23:53 CDT)
Re: Dihedral scan in NAMD? Peter Freddolino (Mon Jun 23 2008 - 15:02:14 CDT)
Re: Dihedral scan in NAMD? Chris Chipot (Mon Jun 23 2008 - 15:21:57 CDT)
problem with executing MPI program in NAMD simulation Yinglong Miao (Mon Jun 23 2008 - 17:12:56 CDT)
Incorrect PSF file for min.pme Eva Nong (Mon Jun 23 2008 - 15:32:58 CDT)
Re: Dihedral scan in NAMD? L. Michel Espinoza-Fonseca (Mon Jun 23 2008 - 10:47:07 CDT)
Dihedral scan in NAMD? Kamilla Kopec (Mon Jun 23 2008 - 10:06:30 CDT)
Re: psf file Peter Freddolino (Mon Jun 23 2008 - 06:54:08 CDT)
psf file Christine Horejs DI (Mon Jun 23 2008 - 06:22:48 CDT)
Impressive Glashutte timepieces Becky Peoples (Sat Jun 21 2008 - 22:17:24 CDT)
Re: Typical maximization steps JC Gumbart (Fri Jun 20 2008 - 21:23:44 CDT)
creation and equilibration of a monolayer creston . (Fri Jun 20 2008 - 16:01:06 CDT)
Typical maximization steps S.K. Ghosh (Fri Jun 20 2008 - 14:05:36 CDT)
error messages with "reinitvels" Yinglong Miao (Fri Jun 20 2008 - 13:56:25 CDT)
Re: PME and r-RESPA issue in NAMD Thomas C. Bishop (Fri Jun 20 2008 - 09:56:25 CDT)
mutate G->U? paco ty (Fri Jun 20 2008 - 11:16:13 CDT)
Large MD simulations and atom number limits with NAMD Andrew Thomas (Fri Jun 20 2008 - 09:53:50 CDT)
Re: problem compiling NAMD2.6 in a MacOSX-PPC Peter Freddolino (Fri Jun 20 2008 - 08:16:56 CDT)
(no subject) Ariovaldo de Souza Junior (Fri Jun 20 2008 - 05:27:36 CDT)
problem compiling NAMD2.6 in a MacOSX-PPC Andrea Diaz (Thu Jun 19 2008 - 10:15:27 CDT)
Force Calibration Interaction abhijit ramachandran (Thu Jun 19 2008 - 17:31:57 CDT)
Re: Simulation with non-periodic boundary condition Victor Ovchinnikov (Thu Jun 19 2008 - 15:15:47 CDT)
problem compiling NAMD2.6 in a MacOSX-PPC Andrea Diaz (Thu Jun 19 2008 - 16:30:57 CDT)
Simulation with non-periodic boundary condition S.K. Ghosh (Thu Jun 19 2008 - 13:36:50 CDT)
NVT simulation by NAMD sudipta sinha (Thu Jun 19 2008 - 08:06:50 CDT)
Re: amber parameters for congo red Shaheen Ahmed (Thu Jun 19 2008 - 02:19:08 CDT)
Time step is incompatible in the NAMD DCD file analyzed with CHARMM twshen (Wed Jun 18 2008 - 14:07:02 CDT)
Re: amber parameters for congo red L. Michel Espinoza-Fonseca (Thu Jun 19 2008 - 04:07:31 CDT)
Re: amber parameters for congo red L. Michel Espinoza-Fonseca (Wed Jun 18 2008 - 16:07:30 CDT)
Re: Time step is incompatible in the NAMD DCD file analyzed with CHARMM Victor Ovchinnikov (Wed Jun 18 2008 - 16:35:42 CDT)
amber parameters for congo red Shaheen Ahmed (Wed Jun 18 2008 - 15:29:22 CDT)
Time step is incompatible in the NAMD DCD file analyzed with CHARMM tw shen (Wed Jun 18 2008 - 14:42:32 CDT)
Time Step is Incompatible in the NAMD DCD Analyzed with CHARMM twshen (Wed Jun 18 2008 - 12:28:22 CDT)
Re: Trouble in energy minimization with warning to increase cutoff Peter Freddolino (Wed Jun 18 2008 - 00:01:29 CDT)
Trouble in energy minimization with warning to increase cutoff Eva Nong (Tue Jun 17 2008 - 18:57:49 CDT)
2D periodic boundary condn & PME Harindar Keer (Tue Jun 17 2008 - 14:12:28 CDT)
Re: NAMD & CUDA, still in development ? Peter Freddolino (Tue Jun 17 2008 - 14:43:55 CDT)
Simulation stalled at startup Sean Law (Mon Jun 16 2008 - 11:01:06 CDT)
Problem with .conf file of NAMD sudipta sinha (Mon Jun 16 2008 - 06:30:57 CDT)
NAMD & CUDA, still in development ? Michael Heymann (Mon Jun 16 2008 - 06:40:24 CDT)
Re: Charmm is not free so how to learn it jfgaff_at_ncsu.edu (Sun Jun 15 2008 - 18:51:19 CDT)
Re: NAMD log file analysis script problem (namdstats.tcl) Axel Kohlmeyer (Sun Jun 15 2008 - 13:09:50 CDT)
Re: Charmm is not free so how to learn it Philip Peartree (Sun Jun 15 2008 - 09:38:02 CDT)
Re: NAMD log file analysis script problem (namdstats.tcl) Demet Akten (Sun Jun 15 2008 - 03:35:49 CDT)
NAMD log file analysis script problem (namdstats.tcl) sudipta sinha (Sat Jun 14 2008 - 13:39:32 CDT)
Charmm is not free so how to learn it abhijit ramachandran (Fri Jun 13 2008 - 15:01:50 CDT)
Re: nonbonded interactions Victor Ovchinnikov (Fri Jun 13 2008 - 13:16:24 CDT)
Re: paramter snoze pa (Fri Jun 13 2008 - 10:37:55 CDT)
Re: use of 'measure hbonds' Axel Kohlmeyer (Fri Jun 13 2008 - 07:43:12 CDT)
use of 'measure hbonds' DEEPESH AGARWAL (Thu Jun 12 2008 - 23:54:34 CDT)
Re: paramter snoze pa (Thu Jun 12 2008 - 16:16:21 CDT)
Seeking suggestions to decide on realistic configuration values S.K. Ghosh (Thu Jun 12 2008 - 14:40:27 CDT)
Re: Language Used and Elementary doubts Peter Freddolino (Thu Jun 12 2008 - 12:26:50 CDT)
Re: Language Used and Elementary doubts Alexandre A. Vakhrouchev (Thu Jun 12 2008 - 12:15:43 CDT)
Re: use of 'measure hbonds' mon_sharma_at_research.iiit.ac.in (Thu Jun 12 2008 - 11:08:12 CDT)
Language Used and Elementary doubts abhijit ramachandran (Thu Jun 12 2008 - 00:08:27 CDT)
use of 'measure hbonds' DEEPESH AGARWAL (Thu Jun 12 2008 - 06:03:06 CDT)
ApoB structure Alexandre A. Vakhrouchev (Thu Jun 12 2008 - 01:12:02 CDT)
Re: paramter JC Gumbart (Wed Jun 11 2008 - 21:08:26 CDT)
paramter snoze pa (Wed Jun 11 2008 - 17:44:10 CDT)
Re: Velocity scaling and thermostatting both at a time Jerome Henin (Wed Jun 11 2008 - 17:37:24 CDT)
Velocity scaling and thermostatting both at a time sudipta sinha (Wed Jun 11 2008 - 13:36:46 CDT)
Re: Different Hbonds values on different machines using same script for same trajectories John Stone (Wed Jun 11 2008 - 03:11:11 CDT)
April promo on watches Priscilla Dahl (Tue Jun 10 2008 - 16:41:36 CDT)
Re: Correctness of Simulation Results Peter Freddolino (Tue Jun 10 2008 - 11:45:03 CDT)
Re: Different Hbonds values on different machines using same script for same trajectories John Stone (Tue Jun 10 2008 - 00:18:07 CDT)
Re: Correctness of Simulation Results Rahul (Tue Jun 10 2008 - 10:15:56 CDT)
Replica or Original? Terrence Hare (Tue Jun 10 2008 - 07:43:09 CDT)
Re: Temperature rescaling and reassignment parameters sudipta sinha (Tue Jun 10 2008 - 05:35:03 CDT)
Re: Classic timepieces replicas Axel Kohlmeyer (Tue Jun 10 2008 - 04:37:57 CDT)
Re: Temperature rescaling and reassignment parameters Alexandre A. Vakhrouchev (Tue Jun 10 2008 - 04:53:44 CDT)
Re: Classic timepieces replicas Alexandre A. Vakhrouchev (Tue Jun 10 2008 - 04:41:40 CDT)
Classic timepieces replicas Cole Cox (Mon Jun 09 2008 - 19:10:25 CDT)
Re: Temperature rescaling and reassignment parameters sudipta sinha (Mon Jun 09 2008 - 23:46:29 CDT)
capping of end residues sudipta sinha (Mon Jun 09 2008 - 23:55:56 CDT)
Re: Temperature rescaling and reassignment parameters Alexandre A. Vakhrouchev (Mon Jun 09 2008 - 23:20:38 CDT)
Re: psgfen patch Peter Freddolino (Mon Jun 09 2008 - 23:09:06 CDT)
psgfen patch Hatley, Jade M (Mon Jun 09 2008 - 12:05:15 CDT)
Re: S-OXY CYSTEINE parameter snoze pa (Mon Jun 09 2008 - 16:19:38 CDT)
Re: Which conformation is more proper for the SMD Eric H. Lee (Mon Jun 09 2008 - 13:47:27 CDT)
Re: Which conformation is more proper for the SMD Shulin Zhuang (Mon Jun 09 2008 - 13:21:57 CDT)
Re: Correctness of Simulation Results Axel Kohlmeyer (Mon Jun 09 2008 - 12:03:06 CDT)
Inexpensive IWC watches Janie Sweeney (Mon Jun 09 2008 - 12:47:28 CDT)
Which conformation is more proper for the SMD Shulin Zhuang (Mon Jun 09 2008 - 11:43:56 CDT)
FW: Hydroxylysine parameters Elham Hamed (Mon Jun 09 2008 - 10:53:08 CDT)
Temperature rescaling and reassignment parameters sudipta sinha (Mon Jun 09 2008 - 10:04:24 CDT)
Correctness of Simulation Results Rahul (Mon Jun 09 2008 - 09:16:13 CDT)
Temperature rescaling and reassignment parameters sudipta sinha (Mon Jun 09 2008 - 05:14:59 CDT)
Different Hbonds values on different machines using same script for same trajectories sunita gupta (Mon Jun 09 2008 - 02:29:57 CDT)
Re: NAMD compilation on linux cluster Axel Kohlmeyer (Sun Jun 08 2008 - 11:32:26 CDT)
NAMD compilation on linux cluster sudipta sinha (Sun Jun 08 2008 - 10:55:36 CDT)
Re: PME and r-RESPA issue in NAMD Axel Kohlmeyer (Sat Jun 07 2008 - 09:50:59 CDT)
PME and r-RESPA issue in NAMD sudipta sinha (Sat Jun 07 2008 - 07:05:37 CDT)
Re: Multiple successive addforce calls Benjamin Bouvier (Thu Jun 05 2008 - 15:05:40 CDT)
Re: output area JC Gumbart (Thu Jun 05 2008 - 17:35:17 CDT)
output area JARROD EDWARD CHARLES NICKEL (Thu Jun 05 2008 - 15:26:49 CDT)
Re: Multiple successive addforce calls Peter Freddolino (Thu Jun 05 2008 - 15:25:31 CDT)
Re: Multiple successive addforce calls Peter Freddolino (Thu Jun 05 2008 - 14:02:46 CDT)
Re: Multiple successive addforce calls Gungor Ozer (Thu Jun 05 2008 - 13:53:12 CDT)
Re: Multiple successive addforce calls Benjamin Bouvier (Thu Jun 05 2008 - 12:35:31 CDT)
free enrgy calculations - an additional information politr_at_huji.ac.il (Wed Jun 04 2008 - 07:07:01 CDT)
Re: Problem with TclBC when run in more than one processor Peter Freddolino (Thu Jun 05 2008 - 08:36:51 CDT)
Multiple successive addforce calls Benjamin Bouvier (Thu Jun 05 2008 - 08:18:16 CDT)
NAMD in water vs in vacuum Yang Gao (Thu Jun 05 2008 - 09:54:48 CDT)
Re: steepest descent technique Peter Freddolino (Thu Jun 05 2008 - 08:32:43 CDT)
Re: Bond energy become Zero!!! Peter Freddolino (Thu Jun 05 2008 - 08:25:55 CDT)
Bond energy become Zero!!! Ming (Thu Jun 05 2008 - 04:17:01 CDT)
steepest descent technique DEEPESH AGARWAL (Thu Jun 05 2008 - 00:53:30 CDT)
Re: molefacture in vmd Peter Freddolino (Wed Jun 04 2008 - 17:27:06 CDT)
Re: molefacture in vmd Subhashis Biswas (Wed Jun 04 2008 - 17:03:29 CDT)
Re: The correct topology/parameter file and pgn S.K. Ghosh (Wed Jun 04 2008 - 13:48:41 CDT)
Problem with TclBC when run in more than one processor fett_at_vtr.net (Wed Jun 04 2008 - 12:08:57 CDT)
Re: free energy calculations Peter Freddolino (Wed Jun 04 2008 - 11:52:02 CDT)
Re: free energy calculations Eric H. Lee (Wed Jun 04 2008 - 11:28:13 CDT)
free energy calculations politr_at_huji.ac.il (Wed Jun 04 2008 - 05:34:01 CDT)
Re: The correct topology/parameter file and pgn S.K. Ghosh (Wed Jun 04 2008 - 03:51:24 CDT)
Re: The correct topology/parameter file and pgn Peter Freddolino (Tue Jun 03 2008 - 21:56:24 CDT)
Re: The correct topology/parameter file and pgn S.K. Ghosh (Tue Jun 03 2008 - 18:15:44 CDT)
Re: The correct topology/parameter file and pgn Peter Freddolino (Tue Jun 03 2008 - 15:11:55 CDT)
Thank you for your advices feng jack (Tue Jun 03 2008 - 11:15:41 CDT)
Re: Mindboggling Problem Related To NAMD2 Code Rahul (Mon Jun 02 2008 - 23:02:42 CDT)
Re: Mindboggling Problem Related To NAMD2 Code Peter Freddolino (Mon Jun 02 2008 - 22:16:39 CDT)
Re: Mindboggling Problem Related To NAMD2 Code Axel Kohlmeyer (Mon Jun 02 2008 - 18:42:04 CDT)
Postdoctoral Position in Scientific Computing David Brandon (Mon Jun 02 2008 - 15:08:45 CDT)
Re: Mindboggling Problem Related To NAMD2 Code Graham Jenkins (Mon Jun 02 2008 - 17:43:27 CDT)
The correct topology/parameter file and pgn S.K. Ghosh (Mon Jun 02 2008 - 15:55:06 CDT)
Re: Average energy in NAMD Axel Kohlmeyer (Sun Jun 01 2008 - 16:51:15 CDT)
Re: Average energy in NAMD JC Gumbart (Sun Jun 01 2008 - 21:02:40 CDT)
Re: Average energy in NAMD Axel Kohlmeyer (Sun Jun 01 2008 - 19:22:51 CDT)
Re: Average energy in NAMD JC Gumbart (Sun Jun 01 2008 - 18:06:29 CDT)
Average energy in NAMD feng jack (Sun Jun 01 2008 - 16:31:16 CDT)
Re: Mindboggling Problem Related To NAMD2 Code Peter Freddolino (Sun Jun 01 2008 - 09:56:21 CDT)
Re: Mindboggling Problem Related To NAMD2 Code Axel Kohlmeyer (Sun Jun 01 2008 - 08:01:34 CDT)
Mindboggling Problem Related To NAMD2 Code Rahul (Sun Jun 01 2008 - 04:19:13 CDT)
Re: Building Namd on a linux cluster. Axel Kohlmeyer (Fri May 30 2008 - 19:25:00 CDT)
Re: Building Namd on a linux cluster. Khaled Barakat (Fri May 30 2008 - 19:30:23 CDT)
(no subject) feng jack (Fri May 30 2008 - 16:04:44 CDT)
Re: NAMD trajectory format Konrad Hinsen (Fri May 30 2008 - 15:33:40 CDT)
Re: Building Namd on a linux cluster. Axel Kohlmeyer (Fri May 30 2008 - 14:41:27 CDT)
Re: Building Namd on a linux cluster. Khaled Barakat (Fri May 30 2008 - 14:32:09 CDT)
Re: Building Namd on a linux cluster. Axel Kohlmeyer (Fri May 30 2008 - 07:38:12 CDT)
Re: NAMD trajectory format Peter Freddolino (Fri May 30 2008 - 09:24:17 CDT)
Re: NAMD trajectory format Peter Freddolino (Fri May 30 2008 - 09:15:48 CDT)
Re: NAMD trajectory format Axel Kohlmeyer (Fri May 30 2008 - 08:29:26 CDT)
Re: NAMD trajectory format Peter Freddolino (Fri May 30 2008 - 08:28:08 CDT)
Re: constraintScaling - FOR LOOP Peter Freddolino (Fri May 30 2008 - 08:30:07 CDT)
Re: NAMD trajectory format Axel Kohlmeyer (Fri May 30 2008 - 07:34:52 CDT)
Re: aromatic-aromatic interaction L. Michel Espinoza-Fonseca (Fri May 30 2008 - 06:57:51 CDT)
Re: Building Namd on a linux cluster. Alexandre A. Vakhrouchev (Fri May 30 2008 - 00:38:25 CDT)
Re: NAMD trajectory format Konrad Hinsen (Thu May 29 2008 - 11:43:13 CDT)
Building Namd on a linux cluster. Khaled Barakat (Thu May 29 2008 - 21:39:53 CDT)
changing dcd output file DURING run? Sebastian Stolzenberg (Thu May 29 2008 - 12:49:36 CDT)
Re: benchmarking of NAMD: sustained performance (TF) Axel Kohlmeyer (Thu May 29 2008 - 09:05:40 CDT)
Re: benchmarking of NAMD: sustained performance (TF) Philip Peartree (Thu May 29 2008 - 04:35:50 CDT)
aromatic-aromatic interaction ramya narasimhan (Thu May 29 2008 - 00:20:43 CDT)
benchmarking of NAMD: sustained performance (TF) satya work (Wed May 28 2008 - 22:47:30 CDT)
constraintScaling - FOR LOOP Semorale (Wed May 28 2008 - 20:29:23 CDT)
Re: NAMD trajectory format John Stone (Wed May 28 2008 - 11:18:26 CDT)
Re: NAMD trajectory format Axel Kohlmeyer (Wed May 28 2008 - 09:05:46 CDT)
Re: NAMD trajectory format Konrad Hinsen (Wed May 28 2008 - 07:35:17 CDT)
Re: dihedral force constant Jerome Henin (Tue May 27 2008 - 20:38:40 CDT)
dihedral force constant jfgaff_at_ncsu.edu (Tue May 27 2008 - 18:38:06 CDT)
Re: Error Parsing Config File MIke S (Tue May 27 2008 - 14:27:47 CDT)
Re: Acceptable pressure values Peter Freddolino (Tue May 27 2008 - 14:33:00 CDT)
Re: Error Parsing Config File MIke S (Tue May 27 2008 - 09:07:03 CDT)
Re: charmm parameter and topology files Jerome Henin (Tue May 27 2008 - 11:20:30 CDT)
charmm parameter and topology files me00109_at_cc.uoi.gr (Tue May 27 2008 - 10:17:52 CDT)
Re: NAMD trajectory format Axel Kohlmeyer (Tue May 27 2008 - 05:27:04 CDT)
NAMD trajectory format Konrad Hinsen (Tue May 27 2008 - 02:41:29 CDT)
Charm++ compilation sudipta sinha (Tue May 27 2008 - 01:51:12 CDT)
Re: dihedral restraints "on-the-fly"? JC Gumbart (Mon May 26 2008 - 22:06:46 CDT)
Re: Acceptable pressure values Fabio Zegarra (Mon May 26 2008 - 19:32:21 CDT)
dihedral restraints "on-the-fly"? Sebastian Stolzenberg (Mon May 26 2008 - 19:40:32 CDT)
Re: Error Parsing Config File Peter Freddolino (Mon May 26 2008 - 19:03:55 CDT)
Re: Error Parsing Config File MIke S (Mon May 26 2008 - 15:46:19 CDT)
Re: harmonic restraint between two atoms Leonardo Trabuco (Mon May 26 2008 - 12:01:15 CDT)
Re: harmonic restraint between two atoms Leonardo Trabuco (Mon May 26 2008 - 11:34:27 CDT)
harmonic restraint between two atoms Esben A. Gad (Mon May 26 2008 - 03:55:16 CDT)
Re: REMD Khaled Barakat (Sun May 25 2008 - 18:43:11 CDT)
Re: PROTEIN VACUUM MINIMIZATION ERROR Peter Freddolino (Sat May 24 2008 - 20:46:34 CDT)
Re: REMD Peter Freddolino (Sat May 24 2008 - 20:45:00 CDT)
Re: REMD Khaled Barakat (Sat May 24 2008 - 15:02:00 CDT)
PROTEIN VACUUM MINIMIZATION ERROR Semorale (Sat May 24 2008 - 10:24:47 CDT)
Re: Acceptable pressure values Peter Freddolino (Sat May 24 2008 - 09:27:24 CDT)
Re: REMD Peter Freddolino (Sat May 24 2008 - 09:01:10 CDT)
Re: Error Parsing Config File Alexandre A. Vakhrouchev (Sat May 24 2008 - 03:06:29 CDT)
REMD Khaled Barakat (Sat May 24 2008 - 02:58:54 CDT)
Error Parsing Config File MIke S (Sat May 24 2008 - 00:01:43 CDT)
Acceptable pressure values Fabio Zegarra (Fri May 23 2008 - 17:24:22 CDT)
Re: ABF:reversibility and number of samples Jerome Henin (Fri May 23 2008 - 17:21:35 CDT)
Re: ABF:reversibility and number of samples Subramanian Vaitheeswaran (Fri May 23 2008 - 16:55:53 CDT)
Re: ABF:reversibility and number of samples Eric Cyr (Fri May 23 2008 - 15:11:29 CDT)
Re: ABF:reversibility and number of samples Luca (Fri May 23 2008 - 14:26:03 CDT)
Re: ABF:reversibility and number of samples Jerome Henin (Fri May 23 2008 - 12:15:11 CDT)
Re: ABF:reversibility and number of samples Chris Chipot (Fri May 23 2008 - 10:43:59 CDT)
ABF:reversibility and number of samples Luca Bellucci (Fri May 23 2008 - 07:33:27 CDT)
Re: Unable to edit files in NAMD folder. Diego Alejandro Vargas (Thu May 22 2008 - 13:31:59 CDT)
Re: Applying weak harmonic force between two proteins Floris Buelens (Thu May 22 2008 - 09:06:57 CDT)
Re: a question about equilibrium Joshua Adelman (Wed May 21 2008 - 21:07:35 CDT)
a question about equilibrium taojinwuhan_at_sohu.com (Wed May 21 2008 - 20:32:14 CDT)
Re: Applying weak harmonic force between two proteins Joshua Adelman (Wed May 21 2008 - 11:42:15 CDT)
Re: Simulation of Thiolated Biotin-Streptavidin on Gold Jerome Henin (Wed May 21 2008 - 11:29:42 CDT)
Applying weak harmonic force between two proteins greddy1_at_umd.edu (Wed May 21 2008 - 11:12:18 CDT)
Re: Simulation of Thiolated Biotin-Streptavidin on Gold S.K. Ghosh (Wed May 21 2008 - 08:16:24 CDT)
scaling the interaction energy Krishnan, Marimuthu (Wed May 21 2008 - 07:21:20 CDT)
Re: Unable to edit files in NAMD folder. Low Soo Mei (Wed May 21 2008 - 05:40:21 CDT)
Unable to edit files in NAMD folder. Alexandre A. Vakhrouchev (Wed May 21 2008 - 03:37:52 CDT)
Unable to edit files in NAMD folder. Diego Alejandro Vargas (Tue May 20 2008 - 23:39:51 CDT)
Re: Simulation of Thiolated Biotin-Streptavidin on Gold Axel Kohlmeyer (Tue May 20 2008 - 08:27:50 CDT)
Re: minimization of the squared gradient Peter Freddolino (Tue May 20 2008 - 08:19:58 CDT)
Simulation of Thiolated Biotin-Streptavidin on Gold S.K. Ghosh (Tue May 20 2008 - 07:11:36 CDT)
running namd with condor emir mahmut bahsi (Mon May 19 2008 - 15:42:38 CDT)
CFP: 3rd Annual CMM Workshop on QM/MM Simulations CMM QM/MM Workshop (Mon May 19 2008 - 13:43:55 CDT)
RE: minimization of the squared gradient Krishnan, Marimuthu (Mon May 19 2008 - 13:36:01 CDT)
Re: minimization of the squared gradient Victor Ovchinnikov (Mon May 19 2008 - 10:24:28 CDT)
Re: minimization of the squared gradient Peter Freddolino (Mon May 19 2008 - 09:20:17 CDT)
RE: minimization of the squared gradient Krishnan, Marimuthu (Mon May 19 2008 - 08:56:31 CDT)
Re: minimization of the squared gradient Peter Freddolino (Mon May 19 2008 - 06:40:33 CDT)
minimization of the squared gradient Krishnan, Marimuthu (Mon May 19 2008 - 01:53:05 CDT)
scaling the interaction energy Krishnan, Marimuthu (Mon May 19 2008 - 01:41:53 CDT)
Re: Error: transport retry exceeded error Axel Kohlmeyer (Sat May 17 2008 - 15:37:12 CDT)
Re: pair interaction Osman Yogurtcu (Sat May 17 2008 - 05:54:14 CDT)
Re: Error: transport retry exceeded error Alexandre A. Vakhrouchev (Sat May 17 2008 - 00:03:03 CDT)
pair interaction Osman Yogurtcu (Fri May 16 2008 - 13:34:21 CDT)
Re: Error: transport retry exceeded error Axel Kohlmeyer (Fri May 16 2008 - 10:49:46 CDT)
Re: vmd-l: Re: Truncated Octahedron for VMD and NAMD simulation Vlad Cojocaru (Fri May 16 2008 - 09:51:44 CDT)
Re: NVE ENSEMBLE Vlad Cojocaru (Fri May 16 2008 - 03:36:38 CDT)
Re: Truncated Octahedron for VMD and NAMD simulation George Madalin Giambasu (Thu May 15 2008 - 15:23:51 CDT)
Truncated Octahedron for VMD and NAMD simulation Yinglong Miao (Thu May 15 2008 - 14:31:48 CDT)
Error: transport retry exceeded error Alexandre A. Vakhrouchev (Thu May 15 2008 - 13:41:21 CDT)
Re: Energy plot script bo liu (Thu May 15 2008 - 13:00:23 CDT)
NVE ENSEMBLE Semorale (Thu May 15 2008 - 10:24:21 CDT)
Re: Energy plot script Subramanian Vaitheeswaran (Thu May 15 2008 - 07:28:20 CDT)
Energy plot script Alexandre A. Vakhrouchev (Wed May 14 2008 - 22:11:19 CDT)
RE: Trajectory file formats & structural alignment JC Gumbart (Wed May 14 2008 - 00:15:17 CDT)
Re: Trajectory file formats & structural alignment Wei Huang (Tue May 13 2008 - 21:57:01 CDT)
Re: NAMD electrostatics no cutoff or switching Peter Freddolino (Tue May 13 2008 - 21:25:30 CDT)
how to prepare *.paramas file Kalyan chaitanya (Tue May 13 2008 - 17:48:54 CDT)
Re: ZINC parameter Jerome Henin (Tue May 13 2008 - 14:57:48 CDT)
S-OXY CYSTEINE parameter snoze pa (Tue May 13 2008 - 13:53:57 CDT)
NAMD electrostatics no cutoff or switching Alvaro Foletti (Tue May 13 2008 - 12:44:01 CDT)
ZINC parameter surendra negi (Tue May 13 2008 - 12:22:47 CDT)
Re: DCD file size Joshua D. Moore (Tue May 13 2008 - 01:39:57 CDT)
Re: DCD file size Peter Freddolino (Mon May 12 2008 - 21:56:26 CDT)
Re: DCD file size Alexandre A. Vakhrouchev (Mon May 12 2008 - 21:50:25 CDT)
Re: DCD file size JC Gumbart (Mon May 12 2008 - 15:08:48 CDT)
DCD file size Alexandre A. Vakhrouchev (Mon May 12 2008 - 14:19:57 CDT)
puase MD integration to communicate between jobs Floris Buelens (Sun May 11 2008 - 12:31:50 CDT)
Run NPT ensemble simulation with sphericalBC? Yinglong Miao (Fri May 09 2008 - 13:37:04 CDT)
Re: 2 pdb files Peter Freddolino (Fri May 09 2008 - 07:15:00 CDT)
2 pdb files Christine Horejs DI (Fri May 09 2008 - 06:58:01 CDT)
spermine force field bqluan (Thu May 08 2008 - 18:47:54 CDT)
Re: Trajectory file formats & structural alignment Giovanni Bellesia (Thu May 08 2008 - 18:00:18 CDT)
spermine force field bqluan (Thu May 08 2008 - 17:24:01 CDT)
Trajectory file formats & structural alignment Wei Huang (Thu May 08 2008 - 15:46:13 CDT)
Re: recalculating energy using dcd file JC Gumbart (Wed May 07 2008 - 17:08:16 CDT)
Re: running NAMD with ranger@tacc Peter Freddolino (Wed May 07 2008 - 13:23:36 CDT)
running NAMD with ranger@tacc Lei Shi (Wed May 07 2008 - 13:08:50 CDT)
Re: Negative Pressure Vlad Cojocaru (Wed May 07 2008 - 09:39:02 CDT)
recalculating energy using dcd file gurvisha_at_leadinvent.com (Wed May 07 2008 - 09:19:14 CDT)
pbc Ahlam Al-Rawi (Tue May 06 2008 - 18:41:33 CDT)
Negative Pressure Fabio Zegarra (Tue May 06 2008 - 15:44:53 CDT)
Question about a shift in rmsd using fixedatom off snoze pa (Tue May 06 2008 - 11:47:45 CDT)
Re: Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) snoze pa (Tue May 06 2008 - 10:20:47 CDT)
Re: NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled Peter Freddolino (Tue May 06 2008 - 00:37:54 CDT)
NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled Ghalib Bello (Mon May 05 2008 - 23:02:45 CDT)
Re: question related to rmsd JC Gumbart (Mon May 05 2008 - 17:58:43 CDT)
Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) snoze pa (Mon May 05 2008 - 16:49:43 CDT)
Re: question related to rmsd snoze pa (Mon May 05 2008 - 16:35:21 CDT)
Re: question related to rmsd JC Gumbart (Mon May 05 2008 - 16:19:47 CDT)
question related to rmsd snoze pa (Mon May 05 2008 - 15:03:07 CDT)
Re: question on ABF L. Michel Espinoza-Fonseca (Mon May 05 2008 - 09:16:44 CDT)
help with calcforces Prabhakar Bhimalapuram (Fri May 02 2008 - 13:32:22 CDT)
Re: compilaton error Leonardo Trabuco (Fri May 02 2008 - 01:25:35 CDT)
Re: compilaton error Swarna Patra (Fri May 02 2008 - 01:06:48 CDT)
Re: compilaton error Leonardo Trabuco (Thu May 01 2008 - 23:47:06 CDT)
Re: compilaton error Swarna Patra (Thu May 01 2008 - 20:04:47 CDT)
Re: error on installing ImageMagick Richard Law (Thu May 01 2008 - 14:53:37 CDT)
Re: error on installing ImageMagick Peter Freddolino (Thu May 01 2008 - 14:02:39 CDT)
error on installing ImageMagick Hero (Thu May 01 2008 - 13:54:57 CDT)
electrostatics NAMD vs CHARMM Arturas Ziemys (Thu May 01 2008 - 11:29:49 CDT)
langevin dynamics and random seeds Peter Freddolino (Thu May 01 2008 - 11:44:40 CDT)
Re: compilaton error Leonardo Trabuco (Thu May 01 2008 - 11:32:22 CDT)
Re: How to save the animation movie into files? Jianhui Tian (Thu May 01 2008 - 09:16:50 CDT)
How to save the animation movie into files? Hero (Thu May 01 2008 - 01:48:35 CDT)
RE: Neutral arginine patch in topology file. JC Gumbart (Thu May 01 2008 - 00:15:28 CDT)
compilaton error Swarna Patra (Wed Apr 30 2008 - 23:32:45 CDT)
Re: Running NAMD on cluster Philip Peartree (Wed Apr 30 2008 - 07:21:28 CDT)
Running NAMD on cluster sudipta sinha (Wed Apr 30 2008 - 04:41:53 CDT)
Neutral arginine patch in topology file. Alexandre F. G. (Tue Apr 29 2008 - 16:45:29 CDT)
Re: NAMD on a remote UNIX and VMD on local Windows - does this work? Tao Wu (Tue Apr 29 2008 - 15:49:57 CDT)
NAMD on a remote UNIX and VMD on local Windows - does this work? S.K. Ghosh (Tue Apr 29 2008 - 13:40:29 CDT)
NAMD on a remote UNIX and VMD on local Windows - does this work? S.K. Ghosh (Tue Apr 29 2008 - 13:31:34 CDT)
Re: velocity units in .vel file Joshua D. Moore (Mon Apr 28 2008 - 17:47:48 CDT)
velocity units in .vel file Neelanjana Sengupta (Mon Apr 28 2008 - 15:21:06 CDT)
Re: How to save the animation movie into files? Low Soo Mei (Mon Apr 28 2008 - 00:51:37 CDT)
How to save the animation movie into files? Hero (Mon Apr 28 2008 - 00:23:49 CDT)
A question about restaints force. Yang Gao (Fri Apr 25 2008 - 11:28:20 CDT)
q=D8=B8=B4=A3=BA=20Re:=20=20nodelist=20being=20ignore?= d during paralleling cong chen (Sun Apr 27 2008 - 21:50:34 CDT)
How to save vmd figures to jpg or tiff? Hero (Sun Apr 27 2008 - 16:18:35 CDT)
help with TCL forces script Jim Pfaendtner (Sun Apr 27 2008 - 05:47:30 CDT)
nodelist being ignored during paralleling cong chen (Sat Apr 26 2008 - 22:24:17 CDT)
How to play molecule trajectory with VMD? Hero (Sat Apr 26 2008 - 20:00:52 CDT)
tracing not available with CMK_OPTIMIZE! Semorale (Sat Apr 26 2008 - 16:26:13 CDT)
Re: How to run namd2 on ubuntu linux? Leandro Martínez (Sat Apr 26 2008 - 16:10:35 CDT)
Re: FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 15:26:21 CDT)
How to run namd2 on ubuntu linux? Hero (Sat Apr 26 2008 - 14:45:01 CDT)
Re: install VMD on Ubuntu Hero (Sat Apr 26 2008 - 14:38:19 CDT)
Re: install VMD on Ubuntu Low Soo Mei (Sat Apr 26 2008 - 14:25:32 CDT)
install VMD on Ubuntu Hero (Sat Apr 26 2008 - 14:09:39 CDT)
Re: FEP triangular bracket average Jerome Henin (Sat Apr 26 2008 - 13:54:31 CDT)
Re: FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 13:14:29 CDT)
Configurations-Statistical Mechanics Mert Gür (Sat Apr 26 2008 - 13:00:08 CDT)
How to install VMD and NAMD on Ubuntu? Hero (Sat Apr 26 2008 - 12:55:17 CDT)
Re: FEP triangular bracket average Jerome Henin (Sat Apr 26 2008 - 11:30:37 CDT)
FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 05:56:26 CDT)
Re: install NAMD on Ubuntu Alexandre A. Vakhrouchev (Sat Apr 26 2008 - 01:12:30 CDT)
install NAMD on Ubuntu Hero (Fri Apr 25 2008 - 23:46:07 CDT)
Re: A question about restaints force. Victor Ovchinnikov (Fri Apr 25 2008 - 17:48:40 CDT)
Re: A question about restaints force. Gungor Ozer (Fri Apr 25 2008 - 16:17:13 CDT)
A question about restaints force. Yang Gao (Fri Apr 25 2008 - 15:23:01 CDT)
Time factor Alexandre A. Vakhrouchev (Thu Apr 24 2008 - 23:16:04 CDT)
Re: reversing constant velocity SMD Peter Freddolino (Thu Apr 24 2008 - 08:24:55 CDT)
TMD AND RIGIDBONDS Samuel Morales (Wed Apr 23 2008 - 20:50:43 CDT)
compiling namd: cannot find -lmodulecommlib Corenflos, Steven Charles (Wed Apr 23 2008 - 14:42:18 CDT)
reversing constant velocity SMD Jeff Forbes (Wed Apr 23 2008 - 14:36:16 CDT)
Re: What does "cellOrigin" really mean? Alexandre A. Vakhrouchev (Wed Apr 23 2008 - 08:36:51 CDT)
What does "cellOrigin" really mean? bo liu (Wed Apr 23 2008 - 05:48:45 CDT)
RE: question on ABF Xu, Jiancong (Mon Apr 21 2008 - 10:35:16 CDT)
Re: question on ABF Chris Chipot (Mon Apr 21 2008 - 07:01:39 CDT)
Re: VMD-NAMD-commands Vivek Sharma (Sun Apr 20 2008 - 21:06:36 CDT)
Re: VMD-NAMD-commands Peter Freddolino (Sun Apr 20 2008 - 20:20:27 CDT)
Re: RE: Reading and writing Binary Restart or Output files with Fortran V.Ovchinnikov (Sat Apr 19 2008 - 16:10:32 CDT)
Re: RE: Reading and writing Binary Restart or Output files with Fortran Leandro Martínez (Sat Apr 19 2008 - 12:51:58 CDT)
Re: RE: Reading and writing Binary Restart or Output files with Fortran V.Ovchinnikov (Sat Apr 19 2008 - 10:40:46 CDT)
Re: VMD-NAMD-commands Alexandre A. Vakhrouchev (Sat Apr 19 2008 - 00:16:08 CDT)
VMD-NAMD-commands Vivek Sharma (Fri Apr 18 2008 - 23:06:12 CDT)
Re: question on ABF Jerome Henin (Fri Apr 18 2008 - 22:14:45 CDT)
Format of Binary Restart and Output Coordinate and Velocity Files Joshua D. Moore (Fri Apr 18 2008 - 19:34:20 CDT)
RE: Reading and writing Binary Restart or Output files with Fortran Joshua D. Moore (Fri Apr 18 2008 - 19:25:55 CDT)
question on ABF L. Michel Espinoza-Fonseca (Fri Apr 18 2008 - 18:40:08 CDT)
What does "cellOrigin" really mean? bo liu (Fri Apr 18 2008 - 09:38:56 CDT)
Re: temperature stepping during heating Low Soo Mei (Fri Apr 18 2008 - 04:00:41 CDT)
Re: temperature stepping during heating Low Soo Mei (Thu Apr 17 2008 - 21:14:34 CDT)
Multiple Different Harmonic Restraint Defitions Joshua Adelman (Thu Apr 17 2008 - 20:13:23 CDT)
Re: temperature stepping during heating JC Gumbart (Thu Apr 17 2008 - 16:35:13 CDT)
Re: 2 molecule pair interactions Ben Chern (Wed Apr 16 2008 - 23:49:33 CDT)
Re: 2 molecule pair interactions Peter Freddolino (Wed Apr 16 2008 - 17:11:52 CDT)
2 molecule pair interactions Arturas Ziemys (Wed Apr 16 2008 - 16:26:27 CDT)
Re: add calcium chloride Thomas C. Bishop (Wed Apr 16 2008 - 10:12:24 CDT)
Re: add calcium chloride Christine Horejs DI (Wed Apr 16 2008 - 08:22:28 CDT)
Re: add calcium chloride Christine Horejs DI (Wed Apr 16 2008 - 07:30:41 CDT)
Re: Which namd on amd64? V.Ovchinnikov (Tue Apr 15 2008 - 17:19:43 CDT)
Re: How to write different DCD files for separate MD runs in one simulation? Yinglong Miao (Tue Apr 15 2008 - 16:22:18 CDT)
Re: How to write different DCD files for separate MD runs in one simulation? V.Ovchinnikov (Tue Apr 15 2008 - 15:52:07 CDT)
Re: How to write different DCD files for separate MD runs in one simulation? Peter Freddolino (Tue Apr 15 2008 - 15:34:11 CDT)
Which namd on amd64? Corenflos, Steven Charles (Tue Apr 15 2008 - 15:26:25 CDT)
binary install question winsvern_at_isu.edu (Tue Apr 15 2008 - 15:23:29 CDT)
Re: Electrostatics cutoff with PME Christopher Gillespie (Tue Apr 15 2008 - 15:21:06 CDT)
Re: How to write different DCD files for separate MD runs in one simulation? V.Ovchinnikov (Tue Apr 15 2008 - 15:14:20 CDT)
Re: Electrostatics cutoff with PME Peter Freddolino (Tue Apr 15 2008 - 14:31:35 CDT)
Re: How to write different DCD files for separate MD runs in one simulation? Peter Freddolino (Tue Apr 15 2008 - 14:07:03 CDT)
Re: Electrostatics cutoff with PME L. Michel Espinoza-Fonseca (Tue Apr 15 2008 - 14:00:03 CDT)
How to write different DCD files for separate MD runs in one simulation? Yinglong Miao (Tue Apr 15 2008 - 13:55:14 CDT)
Re: restarting ABF simulation Jerome Henin (Tue Apr 15 2008 - 13:16:28 CDT)
Electrostatics cutoff with PME Gianluca Interlandi (Tue Apr 15 2008 - 13:01:48 CDT)
Re: help regarding NAMD equilibration Dr. Luis Rosales León (Tue Apr 15 2008 - 12:39:24 CDT)
Re: restarting ABF simulation Subramanian Vaitheeswaran (Tue Apr 15 2008 - 11:16:36 CDT)
Re: help regarding NAMD equilibration snoze pa (Tue Apr 15 2008 - 10:39:54 CDT)
temperature stepping during heating Low Soo Mei (Tue Apr 15 2008 - 05:21:43 CDT)
Re: help regarding NAMD equilibration Low Soo Mei (Tue Apr 15 2008 - 01:05:25 CDT)
Problem with NAMD crashing without warning or error messages Jacob Durrant (Mon Apr 14 2008 - 20:36:25 CDT)
help regarding NAMD equilibration snoze pa (Mon Apr 14 2008 - 18:11:46 CDT)
Re: Re: TMD bug correction??? Peter Freddolino (Mon Apr 14 2008 - 16:15:44 CDT)
NAMD CVS RUN ERROR Samuel Morales (Mon Apr 14 2008 - 16:13:31 CDT)
Re: TMD bug correction??? Samuel Morales (Mon Apr 14 2008 - 15:55:04 CDT)
Building NAMD on SGI Altix Rogan Carr (Mon Apr 14 2008 - 15:04:27 CDT)
Re: restarting ABF simulation Jerome Henin (Mon Apr 14 2008 - 13:58:57 CDT)
Re: restarting ABF simulation Subramanian Vaitheeswaran (Mon Apr 14 2008 - 12:21:43 CDT)
Re: TclForces JC Gumbart (Mon Apr 14 2008 - 10:21:22 CDT)
Re: Restarting simulation goes the different temperature JC Gumbart (Mon Apr 14 2008 - 10:18:08 CDT)
Re: restarting ABF simulation Luca Bellucci (Mon Apr 14 2008 - 10:00:21 CDT)
Re: restarting ABF simulation Jerome Henin (Mon Apr 14 2008 - 08:54:07 CDT)
Re: restarting ABF simulation Luca Bellucci (Mon Apr 14 2008 - 08:04:01 CDT)
Re: restarting ABF simulation Jerome Henin (Mon Apr 14 2008 - 06:43:40 CDT)
rmsd_RNA_DNA sripad chandan (Mon Apr 14 2008 - 05:27:45 CDT)
Re: Restarting simulation goes the different temperature Magnus Heltstrom (Mon Apr 14 2008 - 04:55:57 CDT)
restarting ABF simulation Luca Bellucci (Mon Apr 14 2008 - 04:14:19 CDT)
Re: problem with VMD installation- libstdc++.so.5 => not found Jerome Henin (Sun Apr 13 2008 - 14:59:21 CDT)
problem with VMD installation- libstdc++.so.5 => not found steve_at_phas.ubc.ca (Sat Apr 12 2008 - 22:03:05 CDT)
Re: langevin dynamics Giovanni Bellesia (Sat Apr 12 2008 - 18:03:35 CDT)
spawn_namd_command How to properly execute this command bptilaka_at_mail.uh.edu (Sat Apr 12 2008 - 17:32:17 CDT)
Re: langevin dynamics Giovanni Bellesia (Sat Apr 12 2008 - 15:20:20 CDT)
langevin dynamics Dibyadeep Paul (Sat Apr 12 2008 - 14:21:52 CDT)
TclForces Vivek Sharma (Fri Apr 11 2008 - 05:42:50 CDT)
Questions about equilibration pellegrini (Thu Apr 10 2008 - 10:19:57 CDT)
PMF calculation floating-point error will (Thu Apr 10 2008 - 08:12:41 CDT)
periodic cell conditions for membrane simulation Low Soo Mei (Thu Apr 10 2008 - 03:54:07 CDT)
Replica Exchange Method bptilaka_at_mail.uh.edu (Wed Apr 09 2008 - 23:08:43 CDT)
bug in NAMD CVS starting March 7, now fixed Jim Phillips (Tue Apr 08 2008 - 14:22:55 CDT)
Dynamics with a glycerol molecule Lucio Montero (Mon Apr 07 2008 - 17:34:39 CDT)
Re: How to circumvent: FATAL ERROR: Periodic cell has become too small for original patch grid! L. Michel Espinoza-Fonseca (Mon Apr 07 2008 - 15:10:43 CDT)
How to circumvent: FATAL ERROR: Periodic cell has become too small for original patch grid! Maxim Paliy (Mon Apr 07 2008 - 14:36:09 CDT)
Re: vmd-l: How to read specific DCD frames directly in Fortran? John Stone (Sat Apr 05 2008 - 13:43:21 CDT)
Re: add calcium chloride Peter Freddolino (Mon Apr 07 2008 - 08:09:58 CDT)
Re: Kinetic Momentum of Translation and/or Rotation Peter Freddolino (Mon Apr 07 2008 - 08:09:44 CDT)
add calcium chloride Christine Horejs DI (Mon Apr 07 2008 - 03:21:59 CDT)
Kinetic Momentum of Translation and/or Rotation Joshua D. Moore (Mon Apr 07 2008 - 01:54:38 CDT)
Re: vmd-l: How to read specific DCD frames directly in Fortran? Yinglong Miao (Sun Apr 06 2008 - 10:51:40 CDT)
Calculating PMF from a constant velocity SMD simulation! Gungor Ozer (Sat Apr 05 2008 - 19:10:06 CDT)
Re: vmd-l: How to read specific DCD frames directly in Fortran? Peter Freddolino (Sat Apr 05 2008 - 13:38:39 CDT)
How to read specific DCD frames directly in Fortran? Yinglong Miao (Sat Apr 05 2008 - 13:21:53 CDT)
Rigid body effect, translational kinetic momentum Joshua D. Moore (Fri Apr 04 2008 - 19:40:35 CDT)
RE: Running NAMD at TACC (Ranger) Richard Swenson (Fri Apr 04 2008 - 12:42:49 CDT)
Re: problems sourcing namdstats in vmd Jim Phillips (Fri Apr 04 2008 - 12:09:43 CDT)
problems sourcing namdstats in vmd Shaheen Ahmed (Fri Apr 04 2008 - 09:37:15 CDT)
RE: Running NAMD at TACC (Ranger) Richard Swenson (Thu Apr 03 2008 - 18:09:22 CDT)
Re: TMD bug correction??? Peter Freddolino (Wed Apr 02 2008 - 14:39:37 CDT)
TMD bug correction??? Samuel Morales (Wed Apr 02 2008 - 13:28:35 CDT)
MacOSX net version segmentation fault Joshua Adelman (Mon Mar 31 2008 - 18:25:29 CDT)
Re: Running NAMD at TACC (Ranger) JC Gumbart (Sun Mar 30 2008 - 13:20:45 CDT)
Re: Running NAMD at TACC (Ranger) Peter Freddolino (Sun Mar 30 2008 - 09:28:06 CDT)
Running NAMD at TACC (Ranger) Jim Pfaendtner (Sun Mar 30 2008 - 07:16:57 CDT)
coarse grained simulation Demet Akten (Fri Mar 28 2008 - 09:11:19 CDT)
Re: Re: Pressure oscillation in NPT lcr312 (Thu Mar 27 2008 - 21:53:07 CDT)
Re: Pressure oscillation in NPT Per Jr. Greisen (Thu Mar 27 2008 - 11:30:04 CDT)
Re: Pressure oscillation in NPT Peter Freddolino (Thu Mar 27 2008 - 11:07:02 CDT)
Pressure oscillation in NPT Xinguang Cheng (Thu Mar 27 2008 - 10:14:38 CDT)
Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Jeffrey J. Potoff (Wed Mar 26 2008 - 18:27:05 CDT)
NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Maxim Paliy (Wed Mar 26 2008 - 16:28:52 CDT)
Re: NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Peter Freddolino (Wed Mar 26 2008 - 16:38:23 CDT)
NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Maxim Paliy (Wed Mar 26 2008 - 16:37:01 CDT)
NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Maxim Paliy (Wed Mar 26 2008 - 16:30:41 CDT)
FATAL ERROR: Periodic cell has become too small for original patch grid! Seth Lilavivat (Wed Mar 26 2008 - 15:36:48 CDT)
abf and tcl scripting in NAMD Vlad Cojocaru (Wed Mar 26 2008 - 11:18:15 CDT)
TMD SCRIPT Samuel Morales (Sat Mar 22 2008 - 17:30:59 CDT)
Re: ABF tutorial; updated FEP tutorial Jerome Henin (Fri Mar 21 2008 - 18:53:58 CDT)
Re: FEP output dEavg and dG Jerome Henin (Fri Mar 21 2008 - 17:16:18 CDT)
FEP output dEavg and dG Payel Das (Fri Mar 21 2008 - 16:26:02 CDT)
NAMD+MPI on AMD64 Artem Zhmurov (Fri Mar 21 2008 - 12:30:29 CDT)
Re: ABF tutorial; updated FEP tutorial Lei Shi (Thu Mar 20 2008 - 17:38:40 CDT)
ABF tutorial; updated FEP tutorial Jerome Henin (Thu Mar 20 2008 - 15:55:10 CDT)
Parallelism issue Artem Zhmurov (Thu Mar 20 2008 - 15:45:15 CDT)
EM and MD of GPCRs Kalyan chaitanya (Thu Mar 20 2008 - 12:34:23 CDT)
Re: namd: ABF query Peter Freddolino (Thu Mar 20 2008 - 11:49:33 CDT)
Re: namd: ABF query Jerome Henin (Thu Mar 20 2008 - 11:29:30 CDT)
Re: namd: ABF query Peter Freddolino (Thu Mar 20 2008 - 11:16:50 CDT)
namd: ABF query gurvisha_at_leadinvent.com (Thu Mar 20 2008 - 05:12:55 CDT)
namd: ABF query gurvisha_at_leadinvent.com (Thu Mar 20 2008 - 05:12:30 CDT)
Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Peter Freddolino (Wed Mar 19 2008 - 15:41:14 CDT)
Re: Generating PSF from modified AMBER ff Seth Lilavivat (Wed Mar 19 2008 - 12:53:27 CDT)
Re: Generating PSF from modified AMBER ff Peter Freddolino (Wed Mar 19 2008 - 12:39:50 CDT)
Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Kamilla Kopec (Wed Mar 19 2008 - 12:38:24 CDT)
Generating PSF from modified AMBER ff Seth Lilavivat (Wed Mar 19 2008 - 12:30:03 CDT)
Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Peter Freddolino (Wed Mar 19 2008 - 10:38:21 CDT)
using Amber paramter snoze pa (Tue Mar 18 2008 - 13:23:31 CDT)
Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Kamilla Kopec (Tue Mar 18 2008 - 07:49:24 CDT)
Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Kamilla Kopec (Mon Mar 17 2008 - 13:50:45 CDT)
Re: fixed atoms / pressure Peter Freddolino (Sun Mar 16 2008 - 09:19:53 CDT)
Re: quartz slab / pairInteractionSelf / Bad global exclusion count! Peter Freddolino (Sun Mar 16 2008 - 09:06:25 CDT)
Re: langevinHydrogen off with rigidBonds all? Peter Freddolino (Sun Mar 16 2008 - 08:55:42 CDT)
Re: TARGETED MD - GRADUAL INCREASE OF FORCE lcr312 (Sat Mar 15 2008 - 11:45:24 CDT)
TARGETED MD - GRADUAL INCREASE OF FORCE Samuel Morales (Fri Mar 14 2008 - 15:21:51 CDT)
TARGETED MD - GRADUAL INCREASE OF FORCE Samuel Morales Navarro (Fri Mar 14 2008 - 14:20:06 CDT)
quartz slab / pairInteractionSelf / Bad global exclusion count! Arturas Ziemys (Fri Mar 14 2008 - 12:55:11 CDT)
FEP + MCTI in one MD simulation List (Thu Mar 13 2008 - 16:25:36 CDT)
Re: FEP: FATAL ERROR: Periodic cell has become too small for original patch grid! List (Thu Mar 13 2008 - 16:16:04 CDT)
langevinHydrogen off with rigidBonds all? Low Soo Mei (Fri Mar 14 2008 - 04:57:27 CDT)
Free Energy of Conformational Change PMF - documentation on method? David Sivak (Thu Mar 13 2008 - 18:07:56 CDT)
Re: fixed atoms / pressure Arturas Ziemys (Thu Mar 13 2008 - 10:52:41 CDT)
Re: FEP: FATAL ERROR: Periodic cell has become too small for original patch grid! Jeffrey J. Potoff (Thu Mar 13 2008 - 10:22:18 CDT)
Re: TARGETED MD ERROR mon_sharma_at_research.iiit.ac.in (Thu Mar 13 2008 - 01:52:57 CDT)
Re: TARGETED MD ERROR Jerome Henin (Thu Mar 13 2008 - 00:54:49 CDT)
Re: Question about 'NAMD TUTORIAL' Ben Chern (Thu Mar 13 2008 - 00:18:21 CDT)
TARGETED MD ERROR Samuel Morales Navarro (Wed Mar 12 2008 - 13:33:56 CDT)
FEP: FATAL ERROR: Periodic cell has become too small for original patch grid! List (Wed Mar 12 2008 - 13:29:38 CDT)
Re: fixed atoms / pressure Peter Freddolino (Wed Mar 12 2008 - 18:55:07 CDT)
Re: variation between results on different OSes Peter Freddolino (Wed Mar 12 2008 - 18:48:00 CDT)
Re: Question about 'NAMD TUTORIAL' Peter Freddolino (Wed Mar 12 2008 - 18:46:55 CDT)
Question about 'NAMD TUTORIAL' Ben Chern (Wed Mar 12 2008 - 07:21:50 CDT)
variation between results on different OSes Dibyadeep Paul (Wed Mar 12 2008 - 02:31:40 CDT)
fixed atoms / pressure Arturas Ziemys (Mon Mar 10 2008 - 12:31:27 CDT)
Re: merge dcd files ,catdcd sripad chandan (Mon Mar 10 2008 - 06:47:10 CDT)
merge dcd files ,catdcd sripad chandan (Mon Mar 10 2008 - 06:45:58 CDT)
(no subject) me01136_at_cc.uoi.gr (Fri Mar 07 2008 - 12:29:57 CST)
unsubscribe-namd Bertrand P. S. Russell (Fri Mar 07 2008 - 06:19:02 CST)
Re: change segID using segment command in psfgen Low Soo Mei (Thu Mar 06 2008 - 19:33:33 CST)
RE: change segID using segment command in psfgen JC Gumbart (Thu Mar 06 2008 - 08:28:12 CST)
clarification needed for wrapAll and wrapWater Yinglong Miao (Thu Mar 06 2008 - 08:13:40 CST)
change segID using segment command in psfgen Low Soo Mei (Thu Mar 06 2008 - 03:01:18 CST)
Replica Server Tutorial Joshua Adelman (Thu Mar 06 2008 - 00:23:02 CST)
Re: Restarting simulation goes the different temperature JC Gumbart (Wed Mar 05 2008 - 18:08:30 CST)
TCL/NAMD: FATAL ERROR: error reading output from command: interrupted system call Corenflos, Steven Charles (Wed Mar 05 2008 - 15:03:47 CST)
Restarting simulation goes the different temperature Magnus Heltstrom (Wed Mar 05 2008 - 10:19:53 CST)
How to analyze? Namdstats, namdplots, etc. Seth Lilavivat (Tue Mar 04 2008 - 11:55:19 CST)
NAMD stops running without error messages or termination Yinglong Miao (Mon Mar 03 2008 - 17:18:12 CST)
Re: solvate replicates water box (2 by 2 by 2) and segments (8X) for no apparent reason Steven Samuel Plotkin (Mon Mar 03 2008 - 00:26:11 CST)
Re: solvate replicates water box (2 by 2 by 2) and segments (8X) for no apparent reason L. Michel Espinoza-Fonseca (Sun Mar 02 2008 - 23:53:14 CST)
solvate replicates water box (2 by 2 by 2) and segments (8X) for no apparent reason Steven Samuel Plotkin (Sun Mar 02 2008 - 22:56:20 CST)
protein_RNA simulation sripad chandan (Sat Mar 01 2008 - 08:43:22 CST)
Re: ABF error calculation Chris Chipot (Fri Feb 29 2008 - 16:26:00 CST)
Re: ABF error calculation Jerome Henin (Fri Feb 29 2008 - 16:16:29 CST)
ABF error calculation Xu, Jiancong (Fri Feb 29 2008 - 14:47:48 CST)
Re: Protein moving out of water-box after 10 ns simulation snoze pa (Fri Feb 29 2008 - 10:55:32 CST)
Re: PME Grid Size - how far to deviate from cell basis vectors. JC Gumbart (Thu Feb 28 2008 - 18:48:48 CST)
Re: Protein moving out of water-box after 10 ns simulation JC Gumbart (Thu Feb 28 2008 - 18:45:54 CST)
Re: NAMD 2.6 - PME Error on Large Protein-DNA System! Peter Freddolino (Thu Feb 28 2008 - 14:27:20 CST)
RE: NAMD 2.6 - PME Error on Large Protein-DNA System! Sean Law (Thu Feb 28 2008 - 11:35:42 CST)
Re: Periodic Box Size vs. Water Box Size Seth Lilavivat (Thu Feb 28 2008 - 11:13:45 CST)
Re: Periodic Box Size vs. Water Box Size Peter Freddolino (Thu Feb 28 2008 - 11:10:44 CST)
Re: Periodic Box Size vs. Water Box Size Jeffrey J. Potoff (Thu Feb 28 2008 - 11:07:50 CST)
Re: Waterbox unexpectedly deformed after minimization. Peter Freddolino (Thu Feb 28 2008 - 11:08:09 CST)
Periodic Box Size vs. Water Box Size Seth Lilavivat (Thu Feb 28 2008 - 10:33:04 CST)
Waterbox unexpectedly deformed after minimization. Kamilla Kopec (Thu Feb 28 2008 - 10:22:38 CST)
Re: NAMD 2.6 - PME Error on Large Protein-DNA System! Peter Freddolino (Wed Feb 27 2008 - 23:59:41 CST)
NAMD 2.6 - PME Error on Large Protein-DNA System! Sean Law (Wed Feb 27 2008 - 18:03:44 CST)
Inorganic Builder Plugin Subhashis Biswas (Wed Feb 27 2008 - 17:57:12 CST)
Coordinates go to zero! Alex Huang (Wed Feb 27 2008 - 14:52:28 CST)
Re: PME Grid Size - how far to deviate from cell basis vectors. George Madalin Giambasu (Wed Feb 27 2008 - 11:04:08 CST)
Re: Protein moving out of water-box after 10 ns simulation Jie-rong Huang (Wed Feb 27 2008 - 10:34:15 CST)
PME Grid Size - how far to deviate from cell basis vectors. Kamilla Kopec (Wed Feb 27 2008 - 10:05:47 CST)
Re: Protein moving out of water-box after 10 ns simulation Per Jr. Greisen (Wed Feb 27 2008 - 09:40:49 CST)
Protein moving out of water-box after 10 ns simulation Jie-rong Huang (Wed Feb 27 2008 - 08:13:24 CST)
Re: Soft core potential - tested or not? Chris Chipot (Tue Feb 26 2008 - 15:24:57 CST)
Re: implicit solvent energy calculation Neema Salimi (Tue Feb 26 2008 - 15:10:25 CST)
Question regarding ABF simulations bptilaka_at_mail.uh.edu (Tue Feb 26 2008 - 14:50:14 CST)
unsubscribe namd-l Alessandro Cembran (Tue Feb 26 2008 - 14:11:36 CST)
RE: implicit solvent energy calculation Chang, Christopher (Tue Feb 26 2008 - 13:51:26 CST)
Re: RNA_minimization jrui_at_ci.uc.pt (Tue Feb 26 2008 - 13:45:04 CST)
RNA_minimization sripad chandan (Tue Feb 26 2008 - 12:04:50 CST)
implicit solvent energy calculation regafan_at_usc.es (Tue Feb 26 2008 - 04:03:49 CST)
Re: umbrella sampling of decalanine using the ABF module Ilja Khavrutskii (Mon Feb 25 2008 - 16:34:41 CST)
Re: Re: umbrella sampling of decalanine using the ABF module George Madalin Giambasu (Mon Feb 25 2008 - 13:48:55 CST)
RE: Re: umbrella sampling of decalanine using the ABF module Xu, Jiancong (Mon Feb 25 2008 - 12:37:02 CST)
umbrella sampling of decalanine using the ABF module Philip Fowler (Mon Feb 25 2008 - 06:21:56 CST)
Re: umbrella sampling of decalanine using the ABF module Jerome Henin (Mon Feb 25 2008 - 10:44:24 CST)
useGroupPressure with no RigidBonds ? Niels Christensen (Sun Feb 24 2008 - 16:50:55 CST)
center-of-mass tcl and coordinate wrapping Ilja Khavrutskii (Sun Feb 24 2008 - 15:45:15 CST)
namd_minimize sripad chandan (Sun Feb 24 2008 - 10:51:47 CST)
subscribe namd-l Magnus Heltstrom (Fri Feb 22 2008 - 14:47:26 CST)
restarting calc giving new temperatures Magnus Heltstrom (Fri Feb 22 2008 - 14:39:58 CST)
Soft core potential - tested or not? Pawel Weronski (Fri Feb 22 2008 - 13:45:22 CST)
langevinHydrogen off with rigidbonds off? Justine Taylor (Fri Feb 22 2008 - 08:36:25 CST)
Re: Re: Creating topology for carbon nanotube / any new structure Peter Freddolino (Fri Feb 22 2008 - 07:03:16 CST)
problem in NAMD minimized structure when viewed in VMD ramaplot ramya narasimhan (Fri Feb 22 2008 - 04:41:23 CST)
Re: Re: Creating topology for carbon nanotube / any new structure prateeksha s (Fri Feb 22 2008 - 00:17:12 CST)
Re: phosphohistidine parameters ??? L. Michel Espinoza-Fonseca (Thu Feb 21 2008 - 13:45:27 CST)
phosphohistidine parameters ??? paco ty (Thu Feb 21 2008 - 12:33:10 CST)
Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Thu Feb 21 2008 - 09:44:45 CST)
Re: How to run NVT simulations without applying periodic boundary conditions? Leandro Martínez (Thu Feb 21 2008 - 08:34:49 CST)
Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Thu Feb 21 2008 - 08:24:55 CST)
Re: A difficult problem to explain the SMD force difference Lewyn Li (Thu Feb 21 2008 - 06:59:26 CST)
Re: Alchemical FEP NAMD tutorial - problems with reproducing the results Chris Chipot (Thu Feb 21 2008 - 03:19:42 CST)
A difficult problem to explain the SMD force difference Shulin Zhuang (Wed Feb 20 2008 - 22:36:15 CST)
Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Wed Feb 20 2008 - 15:55:23 CST)
Re: Alchemical FEP NAMD tutorial - problems with reproducing the results Jawahar Neelankatan (Wed Feb 20 2008 - 14:48:54 CST)
The correlation of SMD force vs. AFM data Shulin Zhuang (Wed Feb 20 2008 - 14:51:15 CST)
Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Wed Feb 20 2008 - 13:59:44 CST)
MD analysis Seth Lilavivat (Wed Feb 20 2008 - 13:46:42 CST)
How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Wed Feb 20 2008 - 12:16:13 CST)
Re: Pair Interaction Calculations to get Charmm Charges? Jan Saam (Tue Feb 19 2008 - 17:55:30 CST)
Pair Interaction Calculations to get Charmm Charges? Kamilla Kopec (Tue Feb 19 2008 - 10:23:24 CST)
Re: Alchemical FEP NAMD tutorial - problems with reproducing the results Chris Chipot (Tue Feb 19 2008 - 07:14:13 CST)
Alchemical FEP NAMD tutorial - problems with reproducing the results Jawahar Neelankatan (Mon Feb 18 2008 - 21:25:54 CST)
RE: PSFGEN Warnings about H positions on standard amino acids Chang, Christopher (Mon Feb 18 2008 - 18:17:48 CST)
ptraj --- 2drms Philip Peartree (Mon Feb 18 2008 - 09:52:46 CST)
PSFGEN Warnings about H positions on standard amino acids Bo Zhang (Mon Feb 18 2008 - 07:07:39 CST)
Re: Tcl "loadtotalforces" question (forces never seem to be saved) Jerome Henin (Sun Feb 17 2008 - 15:13:42 CST)
Re: Tcl "loadtotalforces" question (forces never seem to be saved) Christopher Calderon (Sun Feb 17 2008 - 14:52:23 CST)
Re: Tcl "loadtotalforces" question (forces never seem to be saved) Jerome Henin (Sun Feb 17 2008 - 13:52:28 CST)
Re: Tcl "loadtotalforces" question (forces never seem to be saved) Christopher Calderon (Sun Feb 17 2008 - 13:06:31 CST)
Re: Tcl "loadtotalforces" question (forces never seem to be saved) Jerome Henin (Sun Feb 17 2008 - 12:39:01 CST)
Tcl "loadtotalforces" question (forces never seem to be saved) Christopher Calderon (Sun Feb 17 2008 - 11:51:23 CST)
energy minimization sripad chandan (Sat Feb 16 2008 - 10:11:22 CST)
Question about catdcd and DCDunitcell Joshua D. Moore (Fri Feb 15 2008 - 05:16:21 CST)
Converting PSF *BACK* to CHARMM Philip Peartree (Fri Feb 15 2008 - 03:17:12 CST)
RE: PCA calculation Chang, Christopher (Thu Feb 14 2008 - 13:31:03 CST)
RE: PCA calculation Chang, Christopher (Thu Feb 14 2008 - 12:58:55 CST)
Re: NAMD 2.6 dcd and breaking XPLOR Peter Freddolino (Thu Feb 14 2008 - 07:14:02 CST)
Re: NAMD 2.6 dcd and breaking XPLOR Neema Salimi (Wed Feb 13 2008 - 19:50:38 CST)
Re: restarting files converge to new temperature Peter Freddolino (Wed Feb 13 2008 - 10:13:55 CST)
Re: restarting files converge to new temperature Jorgen Simonsen (Wed Feb 13 2008 - 10:08:24 CST)
Re: PCA calculation Richard Wood (Wed Feb 13 2008 - 10:00:19 CST)
ABF question Matthew Davies (Wed Feb 13 2008 - 11:00:44 CST)
Re: PCA calculation Himanshu Khandelia (Wed Feb 13 2008 - 09:00:45 CST)
Re: restarting files converge to new temperature Peter Freddolino (Wed Feb 13 2008 - 07:55:48 CST)
Re: PCA calculation Peter Freddolino (Wed Feb 13 2008 - 07:11:27 CST)
Re: restarting files converge to new temperature Jorgen Simonsen (Wed Feb 13 2008 - 02:13:09 CST)
Re: PCA calculation ramya narasimhan (Tue Feb 12 2008 - 22:59:49 CST)
Re: restarting files converge to new temperature Peter Freddolino (Tue Feb 12 2008 - 13:34:55 CST)
Re: PCA calculation Peter Freddolino (Tue Feb 12 2008 - 10:24:33 CST)
Re: PCA calculation Richard Wood (Tue Feb 12 2008 - 09:57:42 CST)
restarting files converge to new temperature Jorgen Simonsen (Tue Feb 12 2008 - 05:21:09 CST)
To incorporate an energy term ramya narasimhan (Tue Feb 12 2008 - 04:32:54 CST)
RE: PCA calculation Nicholas M Glykos (Tue Feb 12 2008 - 02:03:04 CST)
an aptamer and a lot of stupid problems Fridolin Treindl (Mon Feb 11 2008 - 23:09:38 CST)
Re: PCA calculation NAVEEN P MICHAUD AGRAWAL (Mon Feb 11 2008 - 12:37:07 CST)
Re: PCA calculation Peter Freddolino (Mon Feb 11 2008 - 12:09:16 CST)
Re: PCA calculation NAVEEN P MICHAUD AGRAWAL (Mon Feb 11 2008 - 11:58:34 CST)
Re: PCA calculation L. Michel Espinoza-Fonseca (Mon Feb 11 2008 - 11:34:07 CST)
Re: PCA calculation Peter Freddolino (Mon Feb 11 2008 - 10:38:15 CST)
RE: PCA calculation Xu, Jiancong (Mon Feb 11 2008 - 10:21:08 CST)
PCA calculation ramya narasimhan (Mon Feb 11 2008 - 01:49:06 CST)
Re: rigid body model Hidekazu WATANABE (Mon Feb 11 2008 - 01:19:23 CST)
Re: HSE and gromacs Peter Freddolino (Sun Feb 10 2008 - 10:49:46 CST)
Re: HSE and gromacs Peter Freddolino (Sun Feb 10 2008 - 10:47:19 CST)
HSE and gromacs patrick wintrode (Sun Feb 10 2008 - 10:41:01 CST)
Re: HP-MPI on Xeon Infiniband Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 10:10:22 CST)
Re: HP-MPI on Xeon Infiniband Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 08:26:25 CST)
HP-MPI on Xeon Infiniband Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 06:43:58 CST)
energy minimization help sripad chandan (Sat Feb 09 2008 - 09:03:50 CST)
quartz / FF(Lopez&MacKerrel) Arturas Ziemys (Fri Feb 08 2008 - 15:00:36 CST)
rigid body model Hidekazu WATANABE (Fri Feb 08 2008 - 02:24:30 CST)
Re: Constrain centers of mass for selected atoms poker_at_physics.usyd.edu.au (Thu Feb 07 2008 - 18:36:00 CST)
NAMD 2.6 dcd and breaking XPLOR Neema Salimi (Thu Feb 07 2008 - 17:15:10 CST)
Re: catDCD 32 bit Vs. 64 bit Version Philip Peartree (Thu Feb 07 2008 - 09:28:15 CST)
how to minimize the energy of a protein using CHARMM FF in NAMD Kalyan chaitanya (Thu Feb 07 2008 - 09:29:08 CST)
Re: Constrain=?ISO-8859-1?Q? centers of mass for ?= selected atoms michael_at_perfect-kreim.de (Thu Feb 07 2008 - 07:03:17 CST)
Constrain centers of mass for selected atoms michael_at_perfect-kreim.de (Thu Feb 07 2008 - 04:12:39 CST)
Re: water models supported in NAMD L. Michel Espinoza-Fonseca (Wed Feb 06 2008 - 18:18:34 CST)
Re: water models supported in NAMD Jeffrey J. Potoff (Wed Feb 06 2008 - 14:14:27 CST)
Re: water models supported in NAMD Peter Freddolino (Wed Feb 06 2008 - 12:48:38 CST)
Re: water models supported in NAMD Philip Peartree (Wed Feb 06 2008 - 12:33:19 CST)
water models supported in NAMD L. Michel Espinoza-Fonseca (Wed Feb 06 2008 - 10:26:09 CST)
TCL forces mon_sharma_at_research.iiit.ac.in (Wed Feb 06 2008 - 10:11:45 CST)
TCL forces Monika Sharma (Wed Feb 06 2008 - 07:15:13 CST)
Re: NAMD: constraints while heating Peter Freddolino (Tue Feb 05 2008 - 06:53:23 CST)
Re: namd energy Peter Freddolino (Tue Feb 05 2008 - 06:40:09 CST)
namd energy Leandro Martínez (Tue Feb 05 2008 - 03:39:30 CST)
NAMD: constraints while heating Seth Lilavivat (Mon Feb 04 2008 - 15:35:46 CST)
Re: OPLS-AA toppar files John R. Dowdle (Mon Feb 04 2008 - 11:48:07 CST)
python vs tcl Dibyadeep Paul (Mon Feb 04 2008 - 11:14:56 CST)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HN Andrea Diaz (Sun Feb 03 2008 - 16:29:59 CST)
Re: catDCD 32 bit Vs. 64 bit Version Philip Peartree (Sat Feb 02 2008 - 10:21:44 CST)
OPLS-AA toppar files John R. Dowdle (Sat Feb 02 2008 - 08:20:46 CST)
Re: Applying SMD to a domain of protein harish vashisth (Fri Feb 01 2008 - 11:13:58 CST)
ABF with different bin size&n

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