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NAMD-L: By Author

By Author

3455 messages sorted by: [ date ] [ thread ] [ subject ] [ attachment ]
About this archive

Starting: Sat Jan 01 2005 - 14:57:24 CST
Ending: Fri Dec 29 2006 - 23:10:16 CST

• 13200178 Hendra Tampang Allo
  • error running namd (Mon Aug 01 2005 - 04:39:38 CDT)
• \
  • Re: Another question about MD simulation of a domain. (Tue Sep 27 2005 - 14:15:59 CDT)
  • Re: energy values (Tue Sep 13 2005 - 13:30:50 CDT)
  • Re: moments of inertia, principal axes (Tue Aug 30 2005 - 20:29:08 CDT)
  • Re: Random forces in Langevin temperature control -- three questions (Sun Jul 17 2005 - 12:09:41 CDT)
  • Re: RE: [Scalex86 - linux] FW: segfaults in mm_malloc (Fri Jul 01 2005 - 11:40:25 CDT)
  • Re: solvate and write pdb, psf file. (Thu Apr 28 2005 - 11:33:40 CDT)
  • Re: Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 12:15:58 CST)
• _at_huji.ac.il
  • namd question (Tue Dec 26 2006 - 04:44:42 CST)
• a-yermakova_at_northwestern.edu
  • TeraGrid Efficiency (Mon Jul 31 2006 - 12:22:41 CDT)
  • topology files (Wed Jul 26 2006 - 12:54:21 CDT)
  • Autopsf (Fri Jul 21 2006 - 16:00:41 CDT)
  • (No subject) (Fri Jul 21 2006 - 15:04:47 CDT)
  • PME grid error during minimization (Fri Jul 21 2006 - 15:05:10 CDT)
  • #QNAN: Please help! (Wed Jul 19 2006 - 14:09:40 CDT)
  • Re: About the unit of "efield" (Wed Jul 19 2006 - 13:24:39 CDT)
  • Minimizing and Equilibrating (Mon Jul 17 2006 - 13:12:52 CDT)
  • log File - pressure not read (Thu Jul 13 2006 - 15:32:37 CDT)
  • NAMD on TeraGrid: OpenMP? (Thu Jul 13 2006 - 12:43:53 CDT)
  • solvating a protein (Thu Jul 13 2006 - 11:16:04 CDT)
  • NAMD on TeraGrid (Thu Jul 13 2006 - 11:04:17 CDT)
  • Re: (No subject) (Wed Jul 12 2006 - 11:46:35 CDT)
  • (No subject) (Mon Jul 10 2006 - 12:50:19 CDT)
• A. Ozlem T. Bishop
  • imprecision in table energy (Sun Sep 24 2006 - 09:57:50 CDT)
• Aaron Oakley
  • Re: many short runs or one long run? (Mon Jul 10 2006 - 21:17:19 CDT)
  • CHARMM compatible Methotrexate params (Thu Nov 24 2005 - 22:17:18 CST)
  • Class I vs Class II force fields (Tue Jul 26 2005 - 00:42:01 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Tue Jun 21 2005 - 01:48:52 CDT)
  • Re: about protonation of HIS in membrane protein (Wed Apr 13 2005 - 19:10:18 CDT)
  • Re: glucose CHARMM force field (Tue Mar 29 2005 - 23:34:00 CST)
  • multiple MD simulations (Mon Mar 28 2005 - 18:29:39 CST)
  • Re: parameters for NAD,NAG,NAP (Thu Feb 03 2005 - 21:14:14 CST)
  • Re: area of a hydrophobic patch (Thu Feb 03 2005 - 16:35:56 CST)
  • autocorrelation analysis in timeseries (Mon Jan 31 2005 - 16:21:56 CST)
• akash.khandelwal_at_ndsu.edu
  • reconstruct PMF (Sat Oct 08 2005 - 15:54:26 CDT)
  • electron density profiles (EDP) (Wed Jun 22 2005 - 14:25:23 CDT)
  • charmm paramter (Thu May 05 2005 - 20:57:34 CDT)
• Al-Rawi, Ahlam
  • external force (Thu Nov 02 2006 - 12:16:23 CST)
  • external force (Tue Oct 24 2006 - 17:30:43 CDT)
  • external force (Tue Oct 24 2006 - 14:39:42 CDT)
• Alessandro Cembran
  • Re: unequal PMEGridSizes (Fri Dec 29 2006 - 17:07:58 CST)
  • Re: Linux HP Itanium Quadrics (Tue Nov 14 2006 - 13:39:27 CST)
  • Linux HP Itanium Quadrics (Fri Nov 10 2006 - 17:04:45 CST)
  • Re: deformations in a water box during equilibration in NAMD (Fri Nov 03 2006 - 09:42:52 CST)
  • Re: Hexagonal boundary conditions (Thu Sep 21 2006 - 10:34:51 CDT)
  • Re: PBS & local (scratch) space (Wed Sep 20 2006 - 16:19:19 CDT)
  • Re: Altix Performance Tuning (Wed Sep 20 2006 - 11:03:53 CDT)
  • Altix Performance Tuning (Mon Sep 18 2006 - 13:18:52 CDT)
  • Re: Lipids into NAMD (Mon Aug 21 2006 - 13:54:30 CDT)
  • Re: Lipids into NAMD (Mon Aug 21 2006 - 10:21:02 CDT)
  • Ion Channel Jarzynski (Thu Aug 10 2006 - 17:56:29 CDT)
  • UseConstantRatio between "run" (Mon Jul 10 2006 - 18:37:38 CDT)
  • Altix performances (Tue Jun 13 2006 - 17:40:59 CDT)
  • Pairlist warnings (Sat Jun 10 2006 - 16:58:07 CDT)
• Alessandro Pedretti
  • Re: problems reading large dcd file (Sat Jan 07 2006 - 04:14:55 CST)
  • Re: removing water from DCD (Thu Jul 21 2005 - 01:55:34 CDT)
  • Re: about *.psf (Fri May 27 2005 - 05:30:10 CDT)
• Alex Vakhrouchev
  • Topology for nano tubes (Tue Apr 19 2005 - 06:59:04 CDT)
• Alexe Bojovschi
  • CHARMM top and par files for PO4 (Mon Aug 14 2006 - 03:53:20 CDT)
  • Configurational temperature - coordinates (Wed Jan 18 2006 - 21:11:32 CST)
  • How to patch segments of aminoacids (Wed Nov 02 2005 - 03:09:08 CST)
  • namd2.5 on linux-cluster (Wed Feb 09 2005 - 04:41:43 CST)
• Allan Haldane
  • Re: popc pressure profile (Wed Nov 15 2006 - 21:18:13 CST)
  • popc pressure profile (Tue Oct 10 2006 - 11:40:43 CDT)
• Amin R. Mazloom
  • Velocity unit ofvelocity in NAMD the binary files (Tue Jun 13 2006 - 15:43:09 CDT)
  • Unit of Velocity in the Velocity files (Tue Jun 13 2006 - 11:36:56 CDT)
  • getting #.IND #QNAN after phase 8 (Mon Jun 05 2006 - 14:25:25 CDT)
• Amir Shamloo
  • FEP alchemical (Fri Jul 15 2005 - 19:51:23 CDT)
• Ana Celia Araujo Vila Verde
  • RE: water box deformation (Thu Nov 30 2006 - 17:15:35 CST)
  • RE: is there any maximum limt of atom numbers in VMD or NAMD? (Wed Nov 29 2006 - 10:07:10 CST)
  • RE: NAMD for inorganics?? (Thu Nov 23 2006 - 10:39:05 CST)
  • RE: rmsd is not stabilizing even after 0.6 ns (Tue Oct 31 2006 - 14:27:23 CST)
  • RE: "reinitvel" parameter in config file (Thu Oct 12 2006 - 07:50:30 CDT)
  • RE: vmd-l: imposing period boundary conditions in a simulation with a crystal (Wed Sep 06 2006 - 08:31:59 CDT)
  • Do I need to use an xsc file to restart a simulation in NVT? (Wed Jun 28 2006 - 10:41:07 CDT)
  • Do I need to use an xsc file to restart a simulation in NVT? (Wed Jun 28 2006 - 14:05:27 CDT)
• Anahita Tafvizi
  • Re: adding extra ions to neutralize charge on protein (Thu Oct 19 2006 - 12:30:02 CDT)
  • Re: rigid protein (Thu Oct 19 2006 - 10:50:01 CDT)
  • Re: rigid protein (Thu Oct 19 2006 - 10:23:16 CDT)
  • Re: rigid protein (Thu Oct 19 2006 - 08:21:45 CDT)
  • constraining distance (Wed Oct 04 2006 - 13:16:29 CDT)
  • question regarding the use of reaction coordinate "distance-com" in ABF method (Sun Sep 10 2006 - 12:51:46 CDT)
  • History file of an ABF smiulation (Sat Sep 09 2006 - 13:55:58 CDT)
  • Re: questions regarding output data of an ABF simulation (Mon Aug 07 2006 - 17:52:11 CDT)
  • questions regarding output data of an ABF simulation (Mon Aug 07 2006 - 15:27:34 CDT)
• Andrew D. Fant
  • Re: simulation of membrane-protein systems (Mon Dec 18 2006 - 13:42:31 CST)
  • Re: Building PDB files for DNA. (Fri Dec 15 2006 - 12:08:23 CST)
• Angel Gonzalez Wong
  • Re: vmd-l: convert DCD files to CRD format (Mon Dec 26 2005 - 09:19:53 CST)
• Angelo R. Rossi
  • All or Nothing at All?? (Sat Oct 29 2005 - 11:41:32 CDT)
• Anna Modzelewska
  • nve ensemble (Thu Jan 19 2006 - 05:08:29 CST)
  • Re: help generating psf files (Fri Oct 07 2005 - 09:16:57 CDT)
  • Re: help generating psf files (Fri Oct 07 2005 - 02:58:19 CDT)
  • Re: help generating psf files (Thu Oct 06 2005 - 08:55:18 CDT)
  • Re: help generating psf files (Thu Oct 06 2005 - 02:37:14 CDT)
  • Re: rotating constraints (Wed Sep 21 2005 - 04:22:30 CDT)
  • energy values (Tue Sep 13 2005 - 06:29:27 CDT)
  • Re: pair interactions in NPT (Fri Sep 02 2005 - 03:58:05 CDT)
  • pair interactions in NPT (Thu Sep 01 2005 - 03:21:46 CDT)
  • Re: interactions in flexible cel (Wed Jun 29 2005 - 02:07:04 CDT)
  • interactions in flexible cel (Wed Jun 29 2005 - 00:34:51 CDT)
  • interactions in flexible cell (Fri Jun 24 2005 - 04:31:27 CDT)
  • Re: vmd-l: autoimd on windows (Wed Jun 22 2005 - 05:29:52 CDT)
  • autoimd on windows (Mon Jun 20 2005 - 06:40:29 CDT)
• Annalisa Marsico
  • problem reading topolgy files (Sun Dec 10 2006 - 06:14:51 CST)
  • combine.tcl (Tue Nov 21 2006 - 12:40:00 CST)
• Anuradha Mittal
  • PMEGridSize (Sun Apr 02 2006 - 21:18:38 CDT)
• apw397_at_soton.ac.uk
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Wed Jun 22 2005 - 10:42:04 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Wed Jun 22 2005 - 10:41:58 CDT)
  • Re: equilibrated the system (Tue Jan 11 2005 - 09:58:27 CST)
• arijit_r_at_chem.iitkgp.ernet.in
  • Re: charmm27 fatal error (Mon Dec 19 2005 - 22:24:36 CST)
  • parameter and topology for 4-MI (Mon Nov 14 2005 - 00:19:27 CST)
• Arneh Babakhani
  • Re: Simulation failed during the stage of heat (Fri Mar 24 2006 - 12:29:34 CST)
  • Re: Re:Re:error caused by lipid membrane (Tue Mar 21 2006 - 00:35:02 CST)
  • Re: error caused by atoms of lipid membrane (Mon Mar 20 2006 - 10:35:14 CST)
  • Re: question on membrane crushing (Tue Mar 14 2006 - 15:59:53 CST)
  • Re: question on membrane crushing (Mon Mar 13 2006 - 16:52:04 CST)
  • Re: question on membrane crushing (Fri Mar 03 2006 - 14:49:42 CST)
  • Re: gradually pressure change (increase/decrease) (Tue Feb 28 2006 - 12:44:58 CST)
  • Re: Rattle Error During Equilibration of Lipid Bilayer Membrane (Wed Feb 22 2006 - 14:09:23 CST)
  • Re: Rattle Error During Equilibration of Lipid Bilayer Membrane (Sun Feb 12 2006 - 21:11:29 CST)
  • Re: Rattle Error During Equilibration of Lipid Bilayer Membrane (Sun Feb 12 2006 - 15:40:20 CST)
  • Rattle Error During Equilibration of Lipid Bilayer Membrane (Fri Feb 10 2006 - 22:32:51 CST)
• Arturas Ziemys
  • loadforces problem (Thu Dec 21 2006 - 13:58:44 CST)
  • addforce (Wed Dec 13 2006 - 14:16:43 CST)
  • particle access in tclBC (Thu Dec 07 2006 - 13:24:05 CST)
  • Tcl_Forces / 'loadcoords' loads NOT wrapped coordinates ? (Thu Dec 07 2006 - 12:19:31 CST)
  • Re: Tcl_Forces = pressure shifts while Langevin Piston is ON (Tue Dec 05 2006 - 13:47:08 CST)
  • polyethylene topology (Tue Dec 05 2006 - 12:05:57 CST)
  • Tcl_Forces = pressure shifts while Langevin Piston is ON (Fri Dec 01 2006 - 16:53:01 CST)
  • getbond (Tcl forces) / PBC (Thu Nov 30 2006 - 10:12:32 CST)
  • Dummy particles (Wed Nov 22 2006 - 14:55:36 CST)
  • Re: How to create repulsive particle ? (Tue Nov 21 2006 - 15:45:01 CST)
  • How to create repulsive particle ? (Tue Nov 21 2006 - 13:47:51 CST)
  • LES / cLES (Mon Nov 13 2006 - 09:40:09 CST)
  • LES : size (Fri Nov 10 2006 - 12:09:50 CST)
  • Replica Exchange (Thu Oct 26 2006 - 10:53:16 CDT)
  • heat capacity: NPT vs. NVT (Wed Oct 25 2006 - 09:53:37 CDT)
  • Re: (Thu Sep 28 2006 - 08:10:19 CDT)
  • Qmeasure=22?= command (Wed Sep 27 2006 - 16:30:24 CDT)
  • PBS & local (scratch) space (Wed Sep 20 2006 - 15:42:18 CDT)
  • Re: Recentering the box on target molecule and wraping (Mon Sep 11 2006 - 11:56:59 CDT)
  • Recentering the box on target molecule and wraping (Mon Sep 11 2006 - 10:39:55 CDT)
  • charmm toppology : internal coordinates (Tue Aug 22 2006 - 16:39:00 CDT)
  • parallel NAMD output problem (Tue May 30 2006 - 11:27:36 CDT)
  • bulk density in RDF.tcl (Wed Mar 29 2006 - 10:28:44 CST)
  • System after pressure change - confirmation needed (Wed Mar 01 2006 - 09:30:20 CST)
  • gradually pressure change (increase/decrease) (Tue Feb 28 2006 - 11:44:08 CST)
  • how gradually change (increase/decrease) pressure ? (Mon Feb 27 2006 - 11:59:15 CST)
  • dublicated residue numbers in PDB/PSF (Wed Feb 01 2006 - 09:14:53 CST)
  • Tools to "open" domains (Tue Jan 31 2006 - 10:12:03 CST)
  • charmm27 fatal error (Mon Dec 19 2005 - 14:06:00 CST)
• ashwin joshi
  • Compilation of NAMD on 64-bit NUMA with icc (Tue Oct 18 2005 - 02:46:18 CDT)
• Axel Kohlmeyer
  • Re: vmd-l: imposing period boundary conditions in a simulation with a crystal (Tue Sep 05 2006 - 12:00:19 CDT)
  • Re: vmd-l: Problem with VMD 'animate' command (Sun Feb 12 2006 - 20:00:46 CST)
  • Re: Re: vmd-l: multiple automated calls to NAMD (Fri Jun 10 2005 - 02:17:32 CDT)
  • Re: vmd-l: multiple automated calls to NAMD (Thu Jun 09 2005 - 02:38:35 CDT)
• ayhan duzgun
  • how to add charged particles manually. (Wed Apr 26 2006 - 21:24:13 CDT)
• Ayse Ozlem Sezerman
  • re: DCD file (Thu May 18 2006 - 10:02:41 CDT)
  • re: DCD file (Thu May 18 2006 - 10:02:43 CDT)
  • re:DCD file (Thu May 18 2006 - 07:06:44 CDT)
  • DCD file (Thu May 18 2006 - 02:09:40 CDT)
• AYTUG TUNCEL
  • Reassigning Velocities (Thu Dec 07 2006 - 06:47:58 CST)
  • minimization temperature and constraints (Tue Dec 05 2006 - 17:20:22 CST)
  • Re: RE: water box deformation (Fri Dec 01 2006 - 10:10:15 CST)
  • Re: Re: high vdw energy (Fri Dec 01 2006 - 09:38:34 CST)
  • water box deformation (Thu Nov 30 2006 - 16:59:15 CST)
  • high vdw energy (Thu Nov 30 2006 - 16:44:39 CST)
  • caps (Mon Jul 10 2006 - 12:53:23 CDT)
  • NAMD to Amber (Tue Jul 04 2006 - 18:56:23 CDT)
  • part of a protein (Tue Apr 25 2006 - 02:58:42 CDT)
• AyÅŸe Özlem Sezerman
  • Re: DCD to PDB conversion (Thu Jun 08 2006 - 04:13:22 CDT)
• Ayþe Özlem Sezerman
  • g(r) (Wed Dec 20 2006 - 04:20:51 CST)
  • [Fwd: Re: Specific Heat Calculation with VMD] (Mon May 29 2006 - 08:31:31 CDT)
  • Re: Specific Heat Calculation with VMD (Mon May 29 2006 - 00:38:52 CDT)
  • [Fwd: Specific Heat Calculation with VMD] (Fri May 26 2006 - 09:29:31 CDT)
  • Specific Heat Calculation with VMD (Fri May 26 2006 - 08:46:02 CDT)
  • Saving the coordinates of DCD file in pdb format (Mon May 22 2006 - 04:50:45 CDT)
• Baoqiang Cao
  • about protonation of HIS in membrane protein (Wed Apr 13 2005 - 09:21:08 CDT)
  • Re: RE: RE: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C (Sat Apr 09 2005 - 22:46:44 CDT)
  • Re: RE: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C (Sat Apr 09 2005 - 21:26:03 CDT)
  • error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C (Sat Apr 09 2005 - 14:40:37 CDT)
  • any script to build membrane+protein+solvent? (Fri Apr 08 2005 - 10:02:36 CDT)
• Baudilio Tejerina
  • Problem with C++ libraries (Tue Jun 27 2006 - 10:29:32 CDT)
• Ben Roberts
  • Re: Unit cell information in binary output files (Tue Sep 05 2006 - 23:54:15 CDT)
  • Unit cell information in binary output files (Tue Sep 05 2006 - 22:23:13 CDT)
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 18:27:07 CDT)
  • Re: catdcd and dcdunitcell (Mon Jun 27 2005 - 07:47:39 CDT)
  • libimf.so error when compiling charm++ (Thu May 12 2005 - 01:09:36 CDT)
• bertrand russell
  • NAMD-2.6 Insatallation help (Tue Dec 05 2006 - 04:29:43 CST)
  • Installation Problem (Fri Oct 06 2006 - 06:52:00 CDT)
• Bing Xiong
  • namd2 compile linux-i686-mpi (Tue May 03 2005 - 15:38:27 CDT)
• Binquan luan
  • help on compiling error (Thu Jun 01 2006 - 11:32:44 CDT)
  • Re: Water simulation with namd (Fri May 26 2006 - 15:09:17 CDT)
  • Re: sound velocity of water (Fri May 05 2006 - 14:41:08 CDT)
  • Re: sound velocity of water (Fri May 05 2006 - 13:08:39 CDT)
  • Re: sound velocity of water (Fri May 05 2006 - 10:39:27 CDT)
  • sound velocity of water (Thu May 04 2006 - 18:10:53 CDT)
  • Re: why pressure is fluctuating so much (Wed May 03 2006 - 18:56:25 CDT)
  • help on NAMD code (Tue Apr 11 2006 - 13:12:12 CDT)
  • help on error message during compiling (Mon Apr 03 2006 - 19:43:14 CDT)
• Blake Charlebois
  • RE: moments of inertia, principal axes (Thu Aug 18 2005 - 05:30:37 CDT)
  • RE: Protonation state of HIS (Wed Aug 10 2005 - 17:44:11 CDT)
  • RE: add ions (Mon Aug 08 2005 - 09:34:41 CDT)
  • RE: running on two different machines.... (Sun Jul 31 2005 - 11:17:20 CDT)
  • Re: the difference between the min_nacl.vel and min_nacl.restart.vel (Sat Jul 23 2005 - 09:25:48 CDT)
  • RE: Help with SMD (Wed Jul 20 2005 - 11:10:47 CDT)
  • Random forces in Langevin temperature control -- three questions (Fri Jul 15 2005 - 00:05:03 CDT)
  • RE: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Tue Jun 21 2005 - 15:41:19 CDT)
  • RE: set center (Fri Jun 17 2005 - 00:03:24 CDT)
  • RE: tcl question (Thu Jun 16 2005 - 22:32:39 CDT)
  • RE: tcl question (Thu Jun 16 2005 - 21:15:59 CDT)
  • RE: changing default directory in VMD? (Wed Jun 15 2005 - 15:21:43 CDT)
  • RE: Number of Steps (Thu Jun 09 2005 - 11:53:35 CDT)
  • RE: Avoiding Rotation and translation of protein (Wed Jun 08 2005 - 12:39:06 CDT)
  • RE: how to apply a random force on a atom (Mon Jun 06 2005 - 16:06:44 CDT)
  • RE: SMD-drifting of center of mass (Sun May 01 2005 - 21:23:48 CDT)
  • RE: protein interact with its image (Tue Apr 19 2005 - 12:10:20 CDT)
• bo baker
  • unable to open charmm parameter file in Window (Tue Nov 14 2006 - 01:16:37 CST)
  • NAMD: run problem (Wed Jun 21 2006 - 14:53:41 CDT)
  • Re: NAMD: compile problem (Fri Jun 16 2006 - 11:49:12 CDT)
  • NAMD: compile problem (Thu Jun 15 2006 - 19:04:58 CDT)
  • NAMD compile in Mac OSX and IBM XL C/C++ (Thu Jun 15 2006 - 15:18:56 CDT)
  • namd: problem (Wed Jun 14 2006 - 12:04:47 CDT)
  • namd: problem (Tue Jun 13 2006 - 14:16:56 CDT)
  • setenv: command not found (Mon Jun 12 2006 - 18:55:39 CDT)
  • MD problem (Sun Mar 26 2006 - 16:54:38 CST)
  • MD Run frozen (Fri Mar 24 2006 - 15:42:47 CST)
  • run frozen (Thu Mar 23 2006 - 20:08:58 CST)
  • Re: velocity error, still (Wed Jan 11 2006 - 16:20:37 CST)
  • simulation and equilibration (Tue Jan 10 2006 - 16:00:19 CST)
  • simulation and equilibration (Tue Jan 10 2006 - 18:01:46 CST)
  • velocity error, still (Tue Jan 10 2006 - 15:20:58 CST)
  • Re: Simulation in vaccum (Sat Jan 07 2006 - 19:12:56 CST)
  • Re: Simulation in vaccum (Fri Jan 06 2006 - 22:12:40 CST)
  • Simulation in vaccum (Fri Jan 06 2006 - 19:17:03 CST)
  • Re: velocity error (Thu Jan 05 2006 - 18:02:35 CST)
  • Atom distance & ptraj (Thu Jan 05 2006 - 11:47:46 CST)
  • Re: atom distances (Wed Jan 04 2006 - 18:09:31 CST)
  • Re: Re velocity error (Wed Jan 04 2006 - 17:20:51 CST)
  • Re: Energy Plugin (Wed Jan 04 2006 - 16:26:24 CST)
  • Re: atom distances (Wed Jan 04 2006 - 15:22:59 CST)
  • atom distances (Wed Jan 04 2006 - 14:17:29 CST)
  • velocity error (Wed Jan 04 2006 - 13:12:45 CST)
  • Energy Plugin (Mon Jan 02 2006 - 18:54:12 CST)
  • NAMD Energy Plugin (Tue Dec 27 2005 - 18:15:40 CST)
  • Re: namdplot: command not found (Mon Oct 17 2005 - 19:50:01 CDT)
  • Re: namdplot: command not found (Fri Oct 14 2005 - 14:04:53 CDT)
  • Re: namdplot: command not found (Thu Oct 13 2005 - 14:26:47 CDT)
  • Re: namdplot: command not found (Wed Oct 12 2005 - 15:27:23 CDT)
  • Re: namdplot: command not found (Tue Oct 11 2005 - 18:56:10 CDT)
  • namdplot: command not found (Mon Oct 10 2005 - 17:36:32 CDT)
  • fix backbone atom (Sun Oct 09 2005 - 01:52:35 CDT)
  • Penetration of water (Fri Oct 07 2005 - 00:20:46 CDT)
  • Re: log file (Wed Sep 21 2005 - 18:49:38 CDT)
  • autoionize & namd2 (Tue Sep 20 2005 - 18:07:34 CDT)
  • Re: log file (Mon Sep 19 2005 - 18:38:35 CDT)
  • Re: log file (Mon Sep 19 2005 - 16:55:33 CDT)
  • log file (Mon Sep 19 2005 - 14:09:42 CDT)
  • vmdtext and .cshrc. (Fri Sep 02 2005 - 18:26:29 CDT)
  • Re: par_all27_prot_lipid.inp (Thu Aug 18 2005 - 19:44:03 CDT)
  • par_all27_prot_lipid.inp (Thu Aug 18 2005 - 16:29:15 CDT)
  • Re: errno = 2 (Thu Aug 18 2005 - 13:12:41 CDT)
  • Re: errno = 2 (Wed Aug 17 2005 - 20:09:43 CDT)
  • Re: errno = 2 (Wed Aug 17 2005 - 12:30:27 CDT)
  • Re: errno = 2 (Tue Aug 16 2005 - 19:04:49 CDT)
  • errno = 2 (Mon Aug 15 2005 - 19:05:21 CDT)
• Bogdan Costescu
  • Re: NAMD Linux LAM/MPI 7.1 execution error (Tue Mar 07 2006 - 10:30:13 CST)
  • Re: charm++ over MPI (Fri Feb 17 2006 - 06:27:52 CST)
  • Re: charm++ over MPI (Thu Feb 16 2006 - 08:48:43 CST)
  • charm++ over MPI (Tue Feb 14 2006 - 11:07:19 CST)
• bora erdemli
  • psfgen error "Missing atom for conformation definition" (Sat Feb 12 2005 - 06:16:30 CST)
  • XPLOR topology to CHARMM (Wed Feb 09 2005 - 03:01:15 CST)
  • parameters for NAD,NAG,NAP (Thu Feb 03 2005 - 03:39:00 CST)
  • Re: segmentation violation!! (Sun Jan 16 2005 - 03:59:08 CST)
  • Re: segmentation violation!! (Fri Jan 14 2005 - 03:06:55 CST)
  • segmentation violation!! (Thu Jan 13 2005 - 02:15:19 CST)
  • Re: Bug alert!!! (Tue Jan 04 2005 - 01:13:37 CST)
• Boyang Wang
  • question about RMSD defined in NAMD (Sat Dec 02 2006 - 19:46:40 CST)
  • Type of force values in the tclForces script. (Fri Aug 25 2006 - 11:34:44 CDT)
  • About pressureProfile command for non-equilibrium system. (Wed Jul 26 2006 - 19:50:20 CDT)
  • Re: Boiling temperature of water. (Thu Jun 22 2006 - 21:38:54 CDT)
  • Boiling temperature of water. (Thu Jun 22 2006 - 19:20:09 CDT)
  • A puzzling problem about adsorption energy in solution. (Thu Jun 01 2006 - 17:39:26 CDT)
  • About loadcoors -- is there a loadvelocity? (Fri May 19 2006 - 13:01:11 CDT)
  • Re: About timestep again. (Mon May 08 2006 - 17:38:07 CDT)
  • Timestep -- Can I use 2 fs timestep for 50 nanoseconds simulation? (Mon May 08 2006 - 10:22:05 CDT)
  • About timestep again. -- Fastest motion O-H streching period 10 fs. (Mon May 08 2006 - 11:14:37 CDT)
  • Timestep. (Mon May 08 2006 - 10:05:17 CDT)
  • Re: About the command "set z [lindex $coorList($i) 2]". (Sun Apr 16 2006 - 19:45:30 CDT)
  • About the command "set z [lindex $coorList($i) 2]". (Sat Apr 15 2006 - 19:47:04 CDT)
  • About restart.vel.old file. (Fri Apr 07 2006 - 22:15:58 CDT)
  • Re£º difference in total energy values (Wed Mar 15 2006 - 15:44:33 CST)
  • Re: About Langevin Dynamics. (Thu Mar 02 2006 - 11:30:46 CST)
  • About Langevin Dynamics. (Wed Mar 01 2006 - 12:18:30 CST)
  • About Langevin Damping Coefficient. (Fri Feb 24 2006 - 17:57:24 CST)
  • Modeling HCN. (Wed Feb 08 2006 - 18:47:14 CST)
  • How to model HCN gas molecule by NAMD? (Wed Feb 08 2006 - 18:44:42 CST)
  • Re: About "mutate" command in psfgen package. (Thu Feb 02 2006 - 22:56:17 CST)
  • About "mutate" command in psfgen package. (Thu Feb 02 2006 - 17:24:42 CST)
  • Re£º question on 1-4scaling factor (Mon Jan 23 2006 - 09:48:29 CST)
  • Re: Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file. (Sat Jan 21 2006 - 12:54:04 CST)
  • Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file. (Fri Jan 20 2006 - 10:44:36 CST)
  • About "get z" command in MD script language. (Sat Jan 07 2006 - 20:57:08 CST)
  • Re: Re velocity error (Wed Jan 04 2006 - 17:46:46 CST)
  • Re velocity error (Wed Jan 04 2006 - 15:57:44 CST)
  • How does NAMD calculate Electrostatic potential energy (no periodic boundary condition)? (Mon Dec 26 2005 - 17:46:55 CST)
  • About the Source code. (Mon Dec 26 2005 - 21:40:56 CST)
  • Re: About RMSD calculation. (Fri Oct 28 2005 - 16:56:09 CDT)
  • Re: About RMSD calculation. (Fri Oct 28 2005 - 15:55:41 CDT)
  • About RMSD calculation. (Fri Oct 28 2005 - 10:49:14 CDT)
  • Does NAMD calculate the potential energy of FIXED ATOMS? (Wed Oct 05 2005 - 12:14:36 CDT)
  • Re: Re water box and system charge (Fri Sep 30 2005 - 21:18:04 CDT)
  • About calculating RMSD with rmsd.tcl (Fri Sep 30 2005 - 19:55:26 CDT)
  • Re water box and system charge (Fri Sep 30 2005 - 19:47:16 CDT)
  • Re water box and system charge (Fri Sep 30 2005 - 14:22:12 CDT)
  • A question about MD simulation of peptide. (Tue Sep 27 2005 - 12:24:59 CDT)
  • Another question about MD simulation of a domain. (Tue Sep 27 2005 - 12:30:43 CDT)
  • RE: For help with .log file. (Sun Aug 07 2005 - 21:42:49 CDT)
  • For help with .log file. (Sun Aug 07 2005 - 14:13:33 CDT)
  • FATAL ERROR: child atom 39 bonded only to child H atoms (Wed Jul 13 2005 - 11:06:19 CDT)
  • Mother atom with hydrogenGroupSize of 0 (Mon Jul 11 2005 - 17:57:51 CDT)
  • Re. van der waals energy (Thu Jul 07 2005 - 13:23:52 CDT)
  • How to set a molecule to be rigid in NAMD? (Mon May 16 2005 - 14:37:44 CDT)
  • Tyrocine dynamics came out wrong. (Sun May 15 2005 - 20:08:08 CDT)
  • benzene in NAMD (Sat May 14 2005 - 15:33:13 CDT)
  • Trajectory file. (Fri May 13 2005 - 16:20:17 CDT)
  • Bad global exclusion count. (Tue May 10 2005 - 11:56:32 CDT)
  • Re: charmm paramter (Thu May 05 2005 - 22:23:56 CDT)
  • RE: Restartname (Thu May 05 2005 - 21:52:36 CDT)
  • Restartname (Thu May 05 2005 - 19:19:26 CDT)
  • About Restart (Thu May 05 2005 - 18:50:52 CDT)
  • How to change psf file in the half way of VMD simulation? (Tue May 03 2005 - 21:48:23 CDT)
  • Re: SMD-drifting of center of mass (Sun May 01 2005 - 22:21:46 CDT)
  • RE: Parameter file. (Sun May 01 2005 - 17:28:48 CDT)
  • Parameter file. (Fri Apr 29 2005 - 23:20:52 CDT)
  • Fwd: Parameter file. (Sat Apr 30 2005 - 12:15:45 CDT)
  • Parameter file again. (Sat Apr 30 2005 - 12:20:19 CDT)
  • solvate and write pdb, psf file. (Wed Apr 27 2005 - 19:16:28 CDT)
• bqluan
  • about diahedra entry in top_all22_sugar.inp (Fri Oct 13 2006 - 13:31:35 CDT)
  • sialic acid (Tue Oct 03 2006 - 15:36:00 CDT)
  • Urea parameter (Wed Sep 13 2006 - 21:20:05 CDT)
  • data structure of neighbor list (Tue Aug 08 2006 - 10:37:52 CDT)
• Brady Chang
  • Re: socket closed error (Thu May 05 2005 - 20:40:05 CDT)
  • namd and node freeze (Tue Apr 05 2005 - 03:39:26 CDT)
  • socket closed error (Fri Mar 25 2005 - 14:54:01 CST)
• brian
  • strange memory behavior (Thu Nov 16 2006 - 11:20:06 CST)
• Brian Bennion
  • Re: pressure calculation in applied field (Tue Nov 28 2006 - 16:06:10 CST)
  • Re: Fwd: GRADIENT TOLERANCE: nan (Thu Oct 26 2006 - 11:29:00 CDT)
  • Re: NAMD installation on Xeon64 cluster (Mon Sep 18 2006 - 18:34:38 CDT)
  • Re: FW: Compilation problems on intel woodcrest (Thu Sep 07 2006 - 12:59:52 CDT)
  • wall clock vs secs/step metrics (Tue Sep 05 2006 - 12:02:29 CDT)
  • Re: Simulation of a 1000 water molecules (Thu Aug 03 2006 - 15:05:16 CDT)
  • Re: help!!! (Wed Jul 19 2006 - 01:14:52 CDT)
  • Re: qsub on a linux cluster (Fri Jul 14 2006 - 10:38:06 CDT)
  • Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) (Wed Jun 21 2006 - 17:24:11 CDT)
  • Re: Angle CO2 Problem (Fri Jun 16 2006 - 10:28:49 CDT)
  • Re: Angle CO2 Problem (Fri Jun 16 2006 - 10:08:04 CDT)
  • Re: why pressure is fluctuating so much (Wed May 03 2006 - 21:19:45 CDT)
  • Re: High VDW energies during minimization and dynamics (Thu Apr 13 2006 - 12:47:30 CDT)
  • Re: Can someone PLEASE explain the "firsttimestep" parameter ? (Wed Mar 22 2006 - 16:43:18 CST)
  • Re: problems with .conf script (Fri Mar 17 2006 - 15:16:24 CST)
  • Re: during namd build / compile -ltcl8.4 linking error (Mon Mar 13 2006 - 17:56:41 CST)
  • Re: build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version (Mon Mar 13 2006 - 14:18:15 CST)
  • Re: namd2.6b1 has bad scaling (Wed Jan 25 2006 - 14:03:28 CST)
  • Re: Problem with NAMD and constraint failures (Fri Jan 20 2006 - 01:00:55 CST)
  • Re: Atoms moving too fast (Tue Dec 06 2005 - 15:28:50 CST)
  • Re: How to patch segments of aminoacids (Wed Nov 02 2005 - 10:35:19 CST)
  • Re: CA CL CA angle? (Tue Nov 01 2005 - 12:57:43 CST)
  • Re: Serious Steric Atom Clashes (Mon Oct 24 2005 - 15:01:41 CDT)
  • Re: Serious Steric Atom Clashes (Mon Oct 24 2005 - 13:48:23 CDT)
  • Re: Serious Steric Atom Clashes (Mon Oct 24 2005 - 10:41:05 CDT)
  • Re: Compilation of NAMD on 64-bit NUMA with icc (Tue Oct 18 2005 - 10:47:16 CDT)
  • Re: namdplot: command not found (Fri Oct 14 2005 - 14:44:14 CDT)
  • Re: namdplot: command not found (Thu Oct 13 2005 - 16:09:03 CDT)
  • Re: NAMD distribute (Thu Oct 13 2005 - 16:05:59 CDT)
  • Re: NAMD distribute (Thu Oct 13 2005 - 10:18:41 CDT)
  • Re: About the potential of NAMD (Fri Oct 07 2005 - 10:35:42 CDT)
  • Re: error parsing config file (Fri Sep 30 2005 - 10:30:30 CDT)
  • Fatal error on PE 0> FATAL ERROR: DIHEDRALS INDEX 150255520 (Fri Aug 19 2005 - 16:47:19 CDT)
  • Re: volume from VMD and NAMD different? (Fri Aug 05 2005 - 17:38:27 CDT)
  • volume from VMD and NAMD different? (Fri Aug 05 2005 - 16:12:34 CDT)
  • error in config file (Fri Aug 05 2005 - 11:28:14 CDT)
  • Re: psfgen patches (Thu Jul 14 2005 - 18:37:37 CDT)
  • sync buffer overflow (Wed Jul 13 2005 - 16:44:36 CDT)
  • segfaults in mm_malloc (Tue Jun 28 2005 - 10:27:31 CDT)
  • RE: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Tue Jun 21 2005 - 17:40:15 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Tue Jun 21 2005 - 10:08:32 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Mon Jun 20 2005 - 10:26:49 CDT)
  • libimf.so problems (Fri May 27 2005 - 15:22:07 CDT)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Thu Apr 28 2005 - 12:01:32 CDT)
  • Re: NANMD errors: PME, qsub (Mon Apr 18 2005 - 17:23:35 CDT)
  • RE: minimization problem (Thu Apr 14 2005 - 18:28:42 CDT)
  • Re: modifying cut off (Fri Apr 08 2005 - 09:59:37 CDT)
  • Re: Nanotube psf file. (Wed Apr 06 2005 - 13:28:34 CDT)
  • Re: problem running namd (Mon Apr 04 2005 - 15:26:06 CDT)
  • Re: problem running namd (Mon Apr 04 2005 - 13:12:08 CDT)
  • Re: socket closed error (Fri Mar 25 2005 - 16:25:48 CST)
  • Re: visualizing dynamics output (Tue Mar 22 2005 - 12:55:00 CST)
  • Re: psfgen for DNA (Mon Mar 21 2005 - 11:51:21 CST)
  • Re: namd2 mpi error (Fri Mar 11 2005 - 11:05:18 CST)
  • RE: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 10 2005 - 18:22:43 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 10 2005 - 15:59:33 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 10 2005 - 14:11:29 CST)
  • Re: Compiling NAMD with mpicc myrinet (Thu Mar 10 2005 - 14:08:44 CST)
  • Re: compiling Namd on amd64 (Thu Mar 10 2005 - 10:20:46 CST)
  • Re: NAMD attempting to read FFTW (Wed Mar 02 2005 - 13:22:00 CST)
  • Re: Complie NAMD on Suse Linux (Mon Feb 07 2005 - 11:56:01 CST)
  • Re: gradient nan (Mon Feb 07 2005 - 11:33:00 CST)
  • Re: qsub (Tue Jan 25 2005 - 10:11:54 CST)
  • Re: segmentation violation!! (Tue Jan 18 2005 - 10:34:47 CST)
  • Re: about rigid bonds (Tue Jan 18 2005 - 10:29:19 CST)
  • Re: hydrogens collapsing (Tue Jan 18 2005 - 10:23:40 CST)
  • Re: extracting time from DCDs (Fri Jan 14 2005 - 14:10:02 CST)
  • Re: segmentation violation!! (Fri Jan 14 2005 - 10:20:49 CST)
  • rattle errors. (Thu Jan 13 2005 - 10:56:25 CST)
  • Re: segmentation violation!! (Thu Jan 13 2005 - 10:48:11 CST)
  • Re: success with opteron myrinet mpi etc (Thu Jan 13 2005 - 10:16:54 CST)
  • Re: multiple jobs on a cluster (Wed Jan 12 2005 - 17:15:05 CST)
  • Re: Bug alert!!! (Tue Jan 04 2005 - 10:46:40 CST)
• Caio Julio Martins Veloso
  • Benzamidine parameters (Sat Mar 25 2006 - 12:54:52 CST)
• Cameron Mura
  • Re: namddat not working (Tue May 24 2005 - 17:30:33 CDT)
  • binary restraint reference coordinates? (Thu Mar 31 2005 - 20:31:42 CST)
• carles ferrer
  • problems NAMD_2.6 (fwd) (Thu Sep 29 2005 - 04:06:09 CDT)
• carlos n. a.
  • Re: Space environment simulations (Wed May 11 2005 - 11:11:29 CDT)
  • Re: Space environment simulations (Tue May 10 2005 - 16:02:28 CDT)
• Carlos Simoes
  • Re: Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file. (Sat Jan 21 2006 - 11:04:54 CST)
  • wrong simulation times or misleading time counting? (Wed Jan 18 2006 - 17:48:59 CST)
• casoni\_at_libero\.it
  • calculate potential energy from DCD file (Tue Sep 05 2006 - 07:21:57 CDT)
• Cesar Avila
  • Re: Possible bug on NAMD 2.6B1? (Tue Jul 18 2006 - 09:46:02 CDT)
  • Possible bug on NAMD 2.6B1? (Sat Jul 15 2006 - 11:06:23 CDT)
• Cesar Luis Avila
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 09:14:07 CST)
  • Help. Parameters for PSGL needed (Thu Dec 07 2006 - 09:49:48 CST)
  • Re: dissociation of water (Mon Oct 09 2006 - 11:33:52 CDT)
  • Re: vmd-l: trace to newcartoon inconsistent display problem (Thu Oct 05 2006 - 15:58:11 CDT)
  • Namd list administration (Tue Sep 26 2006 - 10:13:58 CDT)
  • Re: load balancer, athlon 64 dual core (Wed Sep 13 2006 - 07:54:48 CDT)
  • Accelerating groups of atoms (Tue Sep 05 2006 - 15:18:59 CDT)
  • Re: Re: vmd-l: Angles and dihedral generation (Tue Sep 05 2006 - 08:15:18 CDT)
  • Re: Re: vmd-l: Angles and dihedral generation (Mon Sep 04 2006 - 10:00:35 CDT)
  • Angles and dihedral generation (Fri Sep 01 2006 - 20:02:36 CDT)
  • Re: Segmentation violation from APOA1 simulation on AMD64 (Thu Aug 31 2006 - 10:42:41 CDT)
  • Re: Using PsfGen (Mon Aug 28 2006 - 15:23:05 CDT)
  • Segmentation violation from APOA1 simulation on AMD64 (Mon Aug 28 2006 - 13:49:25 CDT)
  • Re: Re: Info: Adjusted background load on 11 nodes. (Sat Aug 26 2006 - 17:00:08 CDT)
  • Re: Re: Info: Adjusted background load on 11 nodes. (Sat Aug 26 2006 - 16:40:15 CDT)
  • Linking with -memory paranoid (Thu Aug 10 2006 - 10:49:43 CDT)
  • Running NAMD on debug mode (Wed Aug 09 2006 - 09:46:06 CDT)
  • Re: Possible bug on NAMD 2.6B1? (Tue Jul 25 2006 - 09:39:02 CDT)
  • Re: Compiling NAMD on AMD64 dual core (Mon Jul 10 2006 - 10:57:59 CDT)
  • Compiling NAMD on AMD64 dual core (Tue Jul 04 2006 - 10:46:58 CDT)
  • Simulation Hangs during minimization (Mon Jul 03 2006 - 15:20:38 CDT)
  • Heating Up a system. (Thu Jun 29 2006 - 16:06:21 CDT)
  • Re: Generating lipid bilayer model (Mon Mar 27 2006 - 13:23:06 CST)
  • Gigabit ethernet switch for cluster (Tue Mar 21 2006 - 14:43:45 CST)
  • Building cluster (Sat Mar 18 2006 - 12:54:38 CST)
• Cetin Baloglu
  • Re: namdplot, graph is empty (Tue Jun 21 2005 - 15:44:29 CDT)
  • Re: namddat not working (Tue May 24 2005 - 20:31:02 CDT)
  • Re: regenerating PSF file (Wed May 18 2005 - 02:50:38 CDT)
  • regenerating PSF file (Wed May 18 2005 - 01:07:05 CDT)
  • Heat Capacity & Relaxation Functions (Mon Apr 25 2005 - 03:22:11 CDT)
• Chandra Ramananjara
  • namdenergy plugin (Sun Jul 09 2006 - 23:47:10 CDT)
  • Question about Van der Waals radii (Mon Jun 26 2006 - 09:14:10 CDT)
  • Re: vmd-l: error using Namdenergy (Wed Jun 21 2006 - 21:17:13 CDT)
  • error using Namdenergy (Wed Jun 21 2006 - 15:04:19 CDT)
  • NAMD support for MNDO semi-empirical model (Mon May 15 2006 - 10:34:07 CDT)
  • Tcl scripting within NAMD configuration file (Fri Mar 24 2006 - 09:26:18 CST)
  • TCL scripting within NAMD Configuration File (Thu Mar 23 2006 - 09:12:56 CST)
  • Re: vmd-l: Problem with VMD 'animate' command (Mon Feb 13 2006 - 01:37:31 CST)
  • Problem with VMD 'animate' command (Sun Feb 12 2006 - 10:12:36 CST)
• Chang, Christopher
  • RE: Bizarre atom behavior (Thu Apr 06 2006 - 16:40:04 CDT)
  • Bizarre atom behavior (Wed Apr 05 2006 - 11:35:54 CDT)
  • Dihedral parameters for multiple minima (Wed Mar 15 2006 - 19:34:22 CST)
  • Recalculating energies from DCD file (Fri Oct 07 2005 - 18:05:37 CDT)
  • catdcd-generated files and CHARMM (Thu Jul 21 2005 - 11:55:25 CDT)
  • Gradient tolerance--total or per atom? (Tue Apr 26 2005 - 11:46:07 CDT)
  • Setting target minimization gradient? (Fri Apr 22 2005 - 13:15:01 CDT)
• Charles Danko
  • Re: How to make a disulphide bond (Tue May 16 2006 - 13:47:37 CDT)
  • POPC or POPE? (Tue Nov 01 2005 - 22:20:04 CST)
  • Re: Incorrect periodic box imaging with AMBER parameters (Mon Jul 25 2005 - 08:32:20 CDT)
  • Re: Periodic cell has become too small for original patch grid (Thu Apr 14 2005 - 10:48:52 CDT)
  • Re: Re[2]: ERROR: Constraint failure in RATTLE algorithm for atom 127! (Thu Apr 14 2005 - 10:40:10 CDT)
  • Re: Periodic cell has become too small for original patch grid (Wed Apr 13 2005 - 09:32:03 CDT)
  • Re: DOWSER (Wed Jan 19 2005 - 09:01:18 CST)
  • DOWSER (Tue Jan 18 2005 - 16:20:06 CST)
  • Re: restarting a simulation accurately (Sat Jan 08 2005 - 15:06:24 CST)
  • Harmonic restraints for moving residue positions?? (Sat Jan 08 2005 - 15:03:50 CST)
• Charles McCallum
  • Re: PSFGEN (Sun May 29 2005 - 12:48:59 CDT)
• Charles Moad
  • Generating psf for a drug, trimethoprim (Sat May 14 2005 - 18:00:08 CDT)
• Cheri M Turman
  • multiple jobs on a cluster (Wed Jan 12 2005 - 15:55:42 CST)
• Ching Wong
  • running 2 jobs simutaneously? (Mon Oct 23 2006 - 21:14:41 CDT)
  • bulid psf for structure already with hydrogens (Wed Jul 19 2006 - 14:02:32 CDT)
  • any SD minimization in NAMD? (Thu Jul 13 2006 - 14:59:57 CDT)
  • many short runs or one long run? (Mon Jul 10 2006 - 15:04:42 CDT)
  • Protonation state (Mon Jul 10 2006 - 14:49:57 CDT)
  • Protonation states (Fri Jun 30 2006 - 19:04:32 CDT)
  • support TIP5? doubt on high temperature MD (Mon Jun 19 2006 - 20:31:52 CDT)
  • extended system or Basis Vector (Mon Jun 19 2006 - 20:29:01 CDT)
  • Tpr (Tue Apr 04 2006 - 10:55:33 CDT)
  • Use extendedSystem or cellBasisVector? (Wed Mar 22 2006 - 16:45:45 CST)
  • Counterions: how to decide how many to put it? (Tue Dec 13 2005 - 17:44:33 CST)
  • Water Box Shrinks (Fri Nov 25 2005 - 19:10:46 CST)
  • Na ions got into the catalytic site during Production Run (Sun Nov 20 2005 - 17:34:01 CST)
• Chona S. Guiang
  • Charm++ problem on EM64T/Myrinet cluster (Thu Mar 31 2005 - 16:08:38 CST)
• Chris Chipot
  • Re: question on free energy pert. (Wed Nov 22 2006 - 14:05:58 CST)
  • Re: ABF - zCoord for more than one monomer (Mon Nov 13 2006 - 07:47:30 CST)
  • Re: ABF on a single molecule (Mon Nov 06 2006 - 15:19:17 CST)
  • Re: ABF on a single molecule (Sun Nov 05 2006 - 03:26:53 CST)
  • Re: error estimate in FEP calculation (Sun Oct 29 2006 - 09:51:43 CST)
  • Re: question about total charge change in FEP calculation (Fri Jun 09 2006 - 02:05:46 CDT)
  • Re: question about total charge change in FEP calculation (Thu Jun 08 2006 - 14:47:27 CDT)
  • Re: FEP error "atoms moving too fast" (Sun Jun 04 2006 - 16:01:23 CDT)
  • Re: questions regrading ABF (Tue May 30 2006 - 01:04:28 CDT)
  • Re: questions regrading ABF (Mon May 29 2006 - 16:50:46 CDT)
  • Re: How to deal with a long path in ABF simulation? (Wed Apr 26 2006 - 15:01:10 CDT)
  • Re: FEP, IONS, DUMMY atoms, LARGE numbers (Tue Apr 18 2006 - 08:57:03 CDT)
  • Re: question about total charge change in FEP calculation (Sun Mar 05 2006 - 05:04:43 CST)
  • Re: how to make dual-hybrid topology? (Mon Feb 13 2006 - 08:31:45 CST)
  • Re: FEP setup (Wed Dec 28 2005 - 17:21:28 CST)
  • Re: Re: FATAL ERROR: unknown floating-point error, errno = 4 (Mon Dec 26 2005 - 10:52:40 CST)
  • Re: FATAL ERROR: unknown floating-point error, errno = 4 (Fri Dec 23 2005 - 01:22:32 CST)
  • Re: define abf1 and abf2 for CM of water and CM of molecule (Wed Dec 21 2005 - 12:18:36 CST)
  • Re: define abf1 and abf2 for CM of water and CM of molecule (Tue Dec 20 2005 - 01:28:32 CST)
  • Re: freeEnergy of conformational change of a test molecule (Thu Nov 17 2005 - 11:37:07 CST)
  • Re: freeEnergy of conformational change of a test molecule (Thu Nov 17 2005 - 03:44:55 CST)
  • Re: FEP.... (Fri Nov 11 2005 - 10:35:19 CST)
  • Re: PMF calculation using fixed restraints (Sun Nov 06 2005 - 14:54:16 CST)
  • Re: ABF Simulation (Wed Oct 05 2005 - 07:58:57 CDT)
  • Re: fep (Sat Jul 16 2005 - 04:48:02 CDT)
  • Re: free energy pertubation,binding energy and constant (Wed Jun 29 2005 - 08:14:27 CDT)
  • Re: binding free energy , binding constant (Fri Jun 17 2005 - 11:07:11 CDT)
  • Re: Reverse Free Energy perturbation (FEP)? (Wed Jun 08 2005 - 17:59:42 CDT)
  • Re: FEP charge perturbation (Fri Jun 03 2005 - 12:08:13 CDT)
  • FEP (Wed May 11 2005 - 17:34:47 CDT)
• Chris Samuel
  • Re: FATAL ERROR: Stale NFS file handle (Wed Apr 06 2005 - 22:29:59 CDT)
  • Re: NMAD job abnormally killed with PBS (Wed Apr 06 2005 - 22:32:01 CDT)
  • Re: problem running namd (Mon Apr 04 2005 - 18:10:58 CDT)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Wed Mar 30 2005 - 00:05:44 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Sun Mar 20 2005 - 20:04:50 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 17 2005 - 23:23:24 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Wed Mar 16 2005 - 04:37:07 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Wed Mar 16 2005 - 00:06:21 CST)
• Christophe Chipot
  • Re: dummy atoms and FEP (Thu Apr 06 2006 - 12:19:06 CDT)
• Christophe Combet [PBIL/IBCP/CNRS]
  • Re: linux cluster problems (Mon Jul 17 2006 - 05:38:04 CDT)
  • Re: NAMD Linux LAM/MPI 7.1 execution error (Thu Mar 09 2006 - 05:26:24 CST)
  • NAMD Linux LAM/MPI 7.1 execution error (Tue Mar 07 2006 - 07:45:35 CST)
• Christopher Calderon
  • SMD temperature scaling (Wed Mar 22 2006 - 17:09:44 CST)
• cunning cunning
  • Complie NAMD on Suse Linux (Thu Feb 03 2005 - 08:18:46 CST)
• curcio
  • Re: electric field and MISC energy (Tue Nov 14 2006 - 02:55:04 CST)
  • forward and backward pulling (Thu Oct 05 2006 - 10:59:10 CDT)
  • Re: Energy due to electric field (Tue Apr 04 2006 - 10:37:28 CDT)
  • LES with PME and neutralizing charges (Thu Mar 09 2006 - 11:48:41 CST)
  • temperature "coupling coefficient" in NAMD (Fri Nov 18 2005 - 11:09:13 CST)
• Damon Smith
  • Re: success with opteron myrinet mpi etc (Thu Jan 13 2005 - 18:24:24 CST)
  • success with opteron myrinet mpi etc (Thu Jan 13 2005 - 01:28:30 CST)
  • Compiling (Thu Jan 06 2005 - 19:02:04 CST)
• Dan Bolintineanu
  • Re: Issue with rhombic dodecahedron / CHARMM compatibility (Mon Dec 04 2006 - 17:12:58 CST)
  • Issue with rhombic dodecahedron / CHARMM compatibility (Mon Dec 04 2006 - 17:03:21 CST)
• Dan Strahs
  • checkpoint software for NAMD? (Thu Sep 21 2006 - 15:37:47 CDT)
  • Win64 version (Wed Sep 06 2006 - 14:50:25 CDT)
  • Re: Rattle Error During Equilibration of Lipid Bilayer Membrane (Mon Feb 13 2006 - 11:30:35 CST)
  • Re: extra lines in PSF !!! (Fri Feb 10 2006 - 13:32:07 CST)
  • Re: unusual, periodic crash in Linux FC3/GM/MPI/CHARM/NAMD (Thu Feb 09 2006 - 20:09:02 CST)
  • Re: unusual, periodic crash in Linux FC3/GM/MPI/CHARM/NAMD (Thu Feb 09 2006 - 18:41:29 CST)
  • unusual, periodic crash in Linux FC3/GM/MPI/CHARM/NAMD (Thu Feb 09 2006 - 17:01:30 CST)
  • Re: updating TCL version for NAMD? (Mon Jan 09 2006 - 11:18:16 CST)
  • updating TCL version for NAMD? (Fri Jan 06 2006 - 17:42:35 CST)
  • Re: NAMD distribute (Thu Oct 13 2005 - 15:46:42 CDT)
  • NAMD distribute (Wed Oct 12 2005 - 20:28:49 CDT)
• Darren Anderson
  • Re: How to "extract" coordinates from a DCD trajectory file? (Tue Aug 09 2005 - 07:54:51 CDT)
  • Re: pka calculations and their use in simulations (Mon Jul 11 2005 - 08:49:20 CDT)
• Dave Venky
  • clustering conformations (Mon Nov 20 2006 - 12:42:58 CST)
• David Brandon
  • "Hands-On" Workshop on Computational Biophysics (Fri Mar 11 2005 - 15:23:27 CST)
• David Kunzman
  • Re: segfaults in mm_malloc (Tue Jun 28 2005 - 12:29:01 CDT)
• David Sept
  • InfiniPath and NAMD (Mon Jul 24 2006 - 14:57:03 CDT)
• debashis.sikdar_at_ndsu.edu
  • velocity file of atoms at each time step (Sun Jun 19 2005 - 22:28:14 CDT)
  • saving picture from namdplot (Tue May 10 2005 - 11:31:04 CDT)
  • pairlist distance (Wed Mar 23 2005 - 09:32:48 CST)
  • pairlist distance (Tue Mar 22 2005 - 14:28:20 CST)
  • peridic boundary condition (Fri Mar 11 2005 - 09:08:37 CST)
  • Influence of PME grid size and cell basis vectors over simulation result (Mon Mar 07 2005 - 13:01:19 CST)
• Deborah Jameson
  • fep file (Mon Jul 25 2005 - 11:10:54 CDT)
  • changing file (Wed Jul 20 2005 - 03:18:12 CDT)
  • setting configuration file for free energy perturbation (Mon Jul 18 2005 - 10:25:02 CDT)
• Deva Priyakumar
  • Re: High VDW energies during minimization and dynamics (Thu Apr 13 2006 - 14:41:22 CDT)
  • High VDW energies during minimization and dynamics (Thu Apr 13 2006 - 10:23:38 CDT)
• Dhiraj Srivastava
  • Re: RE: about topology generation (Tue Dec 05 2006 - 01:34:08 CST)
  • atomlist command in matdcd (Sun Nov 12 2006 - 02:20:25 CST)
  • how to remove translational and rotational motion from dcd file (Thu Nov 09 2006 - 14:59:28 CST)
  • protein is moving from center to one corner of water box. (Mon Nov 06 2006 - 01:06:53 CST)
  • Warning: 1 processors are overloaded due to high background load (Fri Nov 03 2006 - 11:30:34 CST)
  • production in NVE ensemble after equilibration in NPT ensemble (Thu Nov 02 2006 - 23:54:30 CST)
  • equilibration of protein (Wed Nov 01 2006 - 12:31:17 CST)
  • rmsd is not stabilizing even after 0.6 ns (Tue Oct 31 2006 - 13:41:54 CST)
  • Re: Atoms moving too fast error (Fri Oct 27 2006 - 18:01:00 CDT)
  • constrained simulation (Fri Oct 27 2006 - 03:32:15 CDT)
  • Re: NPT ensemble with Periodic boundary condition (Wed Oct 25 2006 - 01:40:11 CDT)
  • NPT ensemble with Periodic boundary condition (Tue Oct 24 2006 - 17:07:38 CDT)
  • Re: deformed water box after heating (Tue Oct 24 2006 - 07:42:57 CDT)
  • Re: deformed water box after heating (Mon Oct 23 2006 - 22:12:29 CDT)
  • deformed water box after heating (Mon Oct 23 2006 - 21:40:37 CDT)
  • temperature reassignment (Mon Oct 23 2006 - 03:07:28 CDT)
  • Re: deformed water box during equilibration. (Sat Oct 21 2006 - 05:19:33 CDT)
  • deformed water box during equilibration. (Sat Oct 21 2006 - 05:13:35 CDT)
  • Re: charge on protein (Thu Oct 19 2006 - 13:50:59 CDT)
  • adding extra ions to neutralize charge on protein (Thu Oct 19 2006 - 11:42:48 CDT)
  • charge on protein (Wed Oct 18 2006 - 21:57:28 CDT)
  • NAMD on Dual processor computer (Sun Oct 15 2006 - 14:28:31 CDT)
  • Re: problem with reassigning temperature (Sun Oct 15 2006 - 14:08:31 CDT)
  • problem with reassigning temperature (Sat Oct 14 2006 - 21:55:15 CDT)
  • simulation in nve ensemble (Fri Oct 13 2006 - 21:45:37 CDT)
  • Re: "reinitvel" parameter in config file (Thu Oct 12 2006 - 13:03:38 CDT)
  • "reinitvel" parameter in config file (Wed Oct 11 2006 - 18:34:21 CDT)
  • Re: line too long in pdb file restart.coor (Wed Oct 11 2006 - 18:12:54 CDT)
  • line too long in pdb file restart.coor (Wed Oct 11 2006 - 14:28:41 CDT)
  • equilibration at three different temperature (Tue Oct 10 2006 - 18:00:52 CDT)
  • Re: restraining the protein not to move during equilibration (Sun Oct 08 2006 - 23:36:41 CDT)
  • restraining the protein not to move during equilibration (Sun Oct 08 2006 - 23:30:39 CDT)
  • restarting the simulation (Sun Oct 08 2006 - 16:17:38 CDT)
  • Re: value of B column is zero (Sun Oct 08 2006 - 12:26:57 CDT)
  • Re: zero kinetic energy during minimization (Sun Oct 08 2006 - 12:23:31 CDT)
  • value of B column is zero (Sun Oct 08 2006 - 00:34:16 CDT)
  • zero kinetic energy during minimization (Sun Oct 08 2006 - 00:12:39 CDT)
  • Re: How can I do protein complex's simulation? (Mon Oct 02 2006 - 19:58:29 CDT)
  • Re: "measure" command (Wed Sep 27 2006 - 17:56:50 CDT)
  • equilibrating the system with constrained Protein (Thu Sep 14 2006 - 13:12:31 CDT)
  • combined QM/MM calculation with NAMD (Thu Sep 14 2006 - 10:35:28 CDT)
  • assigning atom type for parameterization (Fri Sep 08 2006 - 15:23:02 CDT)
  • no parameter for CN8-ON6 (Wed Sep 06 2006 - 19:45:59 CDT)
  • parameterizing novel molecule (Wed Sep 06 2006 - 01:52:47 CDT)
  • error in loading "import hessian/charge from single point calculation" in paratool (Mon Aug 28 2006 - 17:53:11 CDT)
  • bad global exclusion count in LES (Fri Aug 18 2006 - 02:11:11 CDT)
  • topology and parameter file for non aromatic nitrogen in ring system. (Thu Aug 17 2006 - 22:15:57 CDT)
  • deprotonated form of Proline molecule (Tue Aug 15 2006 - 14:55:35 CDT)
  • Re: n terminal patch on proline (Tue Aug 15 2006 - 14:09:24 CDT)
  • Re: n terminal patch on proline (Tue Aug 15 2006 - 12:53:37 CDT)
  • n terminal patch on proline (Tue Aug 15 2006 - 11:53:47 CDT)
  • negatively charged proline as substrate (Mon Aug 14 2006 - 11:08:40 CDT)
  • atom type HZ4 not found (Sat Aug 05 2006 - 13:27:12 CDT)
  • fad topology and parameter file (Thu Aug 03 2006 - 02:11:45 CDT)
  • two chain in pdb file (Tue Aug 01 2006 - 01:46:01 CDT)
  • missing atoms in pdb file. (Tue Aug 01 2006 - 01:36:04 CDT)
  • collision correction of Locally Enhanced Sampling (Sun Jul 30 2006 - 15:14:52 CDT)
• dimka
  • PME for a hexagonal system (Fri Dec 22 2006 - 15:17:16 CST)
  • Re: Is the GBSA model in NAMD ? (Tue Jun 13 2006 - 15:17:55 CDT)
  • Re: Unit of harmonic restraint force constant (Fri Feb 24 2006 - 18:31:27 CST)
  • Re: Can extending MIN solve the problem of "Constraint failure in RATTLE algorithm" (Sat Dec 24 2005 - 19:51:31 CST)
  • Re: segmentation fault on Linux (Mon Nov 28 2005 - 12:41:25 CST)
  • Re: running NAMD2 in parallel (Mon Oct 10 2005 - 23:33:59 CDT)
  • namd 2.6b1 job crash error (Fri Sep 30 2005 - 16:18:43 CDT)
  • segmentation fault on Linux (Mon Sep 19 2005 - 16:48:02 CDT)
• Dong Luo
  • Re: Compile NAMD on Bluegene (Fri Jun 16 2006 - 13:56:46 CDT)
  • Re: Compile NAMD on Bluegene (Thu Jun 15 2006 - 14:16:30 CDT)
  • Re: Compile NAMD on Bluegene (Thu Jun 15 2006 - 11:35:18 CDT)
  • Re: Compile NAMD on Bluegene (Thu Jun 15 2006 - 09:48:32 CDT)
  • Compile NAMD on Bluegene (Wed Jun 14 2006 - 16:17:13 CDT)
  • Re: NAMD configuration files for NVT ensemble (Mon Apr 24 2006 - 15:10:11 CDT)
  • Re: simulated annealing with explicit water (Mon Apr 24 2006 - 13:05:31 CDT)
  • Re: Aligning structures (Fri Mar 10 2006 - 11:11:03 CST)
  • What's the highest temperature I can go? (Thu Jan 05 2006 - 13:11:19 CST)
  • Re: "Segmentation violation" on running namd2.6b1 (Mon Sep 19 2005 - 13:09:38 CDT)
  • "Segmentation violation" on running namd2.6b1 (Mon Sep 19 2005 - 10:36:30 CDT)
  • namd2.6b1 hang on IBM p-690 (Thu Sep 08 2005 - 10:50:21 CDT)
  • RE: shape change of water box and peptide move out (Mon Aug 15 2005 - 10:46:48 CDT)
  • shape change of water box and peptide move out (Fri Jul 29 2005 - 12:09:58 CDT)
  • Re: NAMD on IBM pSeries (690, 655) (Tue Jun 07 2005 - 14:01:54 CDT)
  • NAMD on IBM pSeries (690, 655) (Tue Jun 07 2005 - 11:45:53 CDT)
  • dielectric constant (Thu May 12 2005 - 11:52:42 CDT)
  • Re: hanging at startup phase 0 (Thu May 05 2005 - 13:59:37 CDT)
  • hanging at startup phase 0 (Thu May 05 2005 - 10:47:31 CDT)
• dora guzman
  • forming disulfide after equilibrating system (Fri Dec 22 2006 - 17:24:10 CST)
  • Re: Autoionize error: spontaneously quits (Fri Jun 23 2006 - 12:18:02 CDT)
  • Autoionize error: spontaneously quits (Wed Jun 21 2006 - 18:38:51 CDT)
  • [Fwd: Re: SMD of small molecule dimer] (Tue May 02 2006 - 11:59:32 CDT)
  • SMD of small molecule dimer (Fri Apr 28 2006 - 12:05:39 CDT)
  • SMD of small molecule dimer (Thu Apr 27 2006 - 19:28:20 CDT)
  • [Fwd: SMD of titin domain] (Wed Feb 08 2006 - 17:05:34 CST)
  • [Fwd: increasing RMSD after 2 ns minimization-equilibration] (Wed Feb 08 2006 - 17:05:51 CST)
  • error parsing config file (Thu Sep 29 2005 - 14:00:00 CDT)
• Doug Moby
  • Constraining a molecule and measuring the corresponding constraint force (Sat Sep 30 2006 - 08:36:31 CDT)
• Dow Hurst
  • Ammasso interconnect performance, LDB question (Mon Sep 05 2005 - 23:21:12 CDT)
  • Re: mpi problems on opteron (Wed Aug 03 2005 - 22:39:35 CDT)
  • Re: Re: charm++ 5.9 megatest failure too (Wed Aug 03 2005 - 22:11:54 CDT)
  • Re: Re: charm++ 5.9 megatest failure too (Wed Aug 03 2005 - 07:37:49 CDT)
  • NAMD and dual core Opterons, thoughts? (Tue Apr 26 2005 - 11:36:02 CDT)
  • Re: Not getting good speed up (Sun Mar 20 2005 - 02:22:00 CST)
• Dow_Hurst
  • Re: Gigabit ethernet switch for cluster (Wed Mar 22 2006 - 21:33:57 CST)
  • charm++ 5.9 megatest failure too (Tue Aug 02 2005 - 17:25:38 CDT)
  • charm++ 5.9 build fails, NAMD 2.6b1 make fails (Tue Aug 02 2005 - 17:16:55 CDT)
  • 2.6b1 source missing file (Tue Aug 02 2005 - 16:58:30 CDT)
  • Link Ammasso MPI with NAMD (Tue Aug 02 2005 - 14:46:59 CDT)
  • Link Ammasso MPI with NAMD (Tue Aug 02 2005 - 14:43:17 CDT)
  • Checkpoint on IRIX of namd 2.5 job not MPI enabled (Thu Apr 07 2005 - 09:40:55 CDT)
  • Re: Not getting good speed up (Tue Mar 15 2005 - 12:31:11 CST)
• E. Davis Oldham
  • NANMD errors: PME, qsub (Sat Apr 16 2005 - 12:37:37 CDT)
• E. Prabhu Raman
  • Replica-Exchange MD (Mon Oct 23 2006 - 13:53:41 CDT)
  • trajectory extension (Fri Sep 29 2006 - 13:39:55 CDT)
  • parameter file name (Fri Sep 08 2006 - 18:46:41 CDT)
  • atom name based paremeters (Tue Sep 05 2006 - 14:31:30 CDT)
  • mass of atoms changable? (Wed Aug 30 2006 - 16:19:46 CDT)
• Edelmiro Moman
  • Re: two chain in pdb file (Tue Aug 01 2006 - 03:40:12 CDT)
  • Re: third time..can someone help!! (Wed Jul 12 2006 - 03:13:58 CDT)
  • Re: third time..can someone help!! (Wed Jul 12 2006 - 02:40:03 CDT)
  • Tcl, minimization and MD (Warning: I am a lazy ignorant) (Tue Jun 20 2006 - 10:20:09 CDT)
  • Interrupted system call (Fri Jun 09 2006 - 02:21:25 CDT)
  • DCD to PDB conversion (Thu Jun 08 2006 - 02:57:31 CDT)
  • Factorization in PMEGridSize (Wed Jun 07 2006 - 04:36:54 CDT)
  • Where to put the "nodelist" file (Wed Jun 07 2006 - 02:45:37 CDT)
  • RE: Sybyl trajectory (Tue Sep 06 2005 - 10:33:37 CDT)
  • How to "extract" coordinates from a DCD trajectory file? (Tue Aug 09 2005 - 07:10:00 CDT)
• edu
  • Re: Time of MD (Mon Jul 03 2006 - 12:05:44 CDT)
  • Time of MD (Fri Jun 30 2006 - 11:18:16 CDT)
  • Re: Time of MD (Thu Jun 29 2006 - 10:02:26 CDT)
  • Time of MD (Fri Jun 23 2006 - 13:59:54 CDT)
  • calculation (continue) (Wed Jun 21 2006 - 16:03:40 CDT)
  • Re: Re. Namd window network problem (Fri Jun 16 2006 - 14:08:09 CDT)
  • chage free energy (Fri Jun 16 2006 - 13:58:08 CDT)
  • Re. Namd window network problem (Fri Jun 16 2006 - 10:33:25 CDT)
  • Namd window network problem (Thu Jun 15 2006 - 13:55:51 CDT)
• Edward Patrick Obrien
  • NAMD Myrinet issue - Strange behavior (Thu Apr 07 2005 - 12:04:31 CDT)
  • Re: Trouble with NAMD on Myrinet (Wed Mar 16 2005 - 10:04:20 CST)
  • Trouble with NAMD on Myrinet (Tue Mar 15 2005 - 14:02:40 CST)
  • Submitting jobs on myrinet...problem (Fri Mar 11 2005 - 18:29:19 CST)
  • Re: peridic boundary condition (Fri Mar 11 2005 - 13:09:43 CST)
  • Compiling NAMD with mpicc myrinet (Thu Mar 10 2005 - 12:19:50 CST)
  • Re: Problems with the nodelist file ! (Wed Mar 02 2005 - 17:22:02 CST)
  • FATAL ERROR: Stale NFS file handle (Fri Feb 18 2005 - 15:51:53 CST)
  • Re: pmf (Tue Jan 11 2005 - 19:24:04 CST)
  • Re: increase in energy over time (Tue Jan 04 2005 - 11:01:53 CST)
  • Re: increase in energy over time (Mon Jan 03 2005 - 18:29:46 CST)
• Ekta Khurana
  • electric field (Sat Sep 02 2006 - 20:17:21 CDT)
  • Fix distance (Tue Sep 20 2005 - 18:11:06 CDT)
  • SMD-drifting of center of mass (Sun May 01 2005 - 16:47:19 CDT)
  • SMD by pulling two groups apart (Fri Feb 04 2005 - 16:27:06 CST)
• eladp_at_hplus.tau.ac.il
  • How to have neutral terminal ends (Sat Oct 15 2005 - 04:15:01 CDT)
• Elijah Roberts
  • Re: Simulation in vaccum (Sun Jan 08 2006 - 10:53:43 CST)
• Elsa F. Sousa Henriques
  • Re: psfgen and charmm19: is there any inconsistency? (Thu Jun 29 2006 - 03:33:59 CDT)
  • Re: Vibrational mode analysis (Fri Jun 16 2006 - 02:11:55 CDT)
  • Re: Where to put the "nodelist" file (Wed Jun 07 2006 - 04:24:33 CDT)
  • Re: namd: adding water molecules (Thu May 11 2006 - 02:11:32 CDT)
  • Re: Heme - Cysteine link (Tue May 09 2006 - 09:09:33 CDT)
  • Asymmetric water molecule found??? (Wed May 03 2006 - 02:59:26 CDT)
• Elsa S. Henriques
  • Re: DPPC.Pdb file needed (Tue Sep 05 2006 - 08:42:29 CDT)
• EPF \(Esben Peter Friis\)
  • RE: Aligning structures (Fri Mar 10 2006 - 01:34:40 CST)
  • RE: starting simulation in charmm, continuing in NAMD ? (Mon Mar 06 2006 - 03:48:06 CST)
  • RE: starting simulation in charmm, continuing in NAMD ? (Sun Mar 05 2006 - 14:35:18 CST)
• Eric Bohm
  • Re: charm++ 5.9 megatest failure too (Tue Aug 02 2005 - 17:49:31 CDT)
• Eric Cyr
  • Potential energies in TCL interface (Mon Mar 07 2005 - 15:36:09 CST)
• Eric Perim
  • Constant Energy Simulations (Fri Jun 30 2006 - 08:42:48 CDT)
  • Atoms moving too fast (Tue Dec 06 2005 - 13:05:10 CST)
  • Problems opening the Extended Trajectory File (Thu Dec 01 2005 - 13:36:36 CST)
• Eric Peterson
  • Question about pair interaction feature (Thu Jan 20 2005 - 17:43:49 CST)
  • Re: Error in when using charmrun (Sat Jan 08 2005 - 22:24:11 CST)
  • Re: Error in when using charmrun (Sat Jan 08 2005 - 21:16:47 CST)
  • Error in when using charmrun (Sat Jan 08 2005 - 20:39:45 CST)
• Eunice Ramirez
  • Ferric heme (Mon Apr 25 2005 - 11:54:41 CDT)
• Eunice Ramirez Melendez
  • Re: RE: Help with SMD (Wed Jul 20 2005 - 03:37:44 CDT)
  • Help with SMD (Tue Jul 19 2005 - 12:08:34 CDT)
  • hbonds output!!! (Tue Jul 19 2005 - 11:59:30 CDT)
• Fabien Cailliez
  • namd and amber force field (Thu Feb 23 2006 - 11:38:01 CST)
• Fam Eklund
  • Re: Re: slow NAMD simulations on a AMD athlon64 in SUSE linux (Thu Jun 15 2006 - 02:19:34 CDT)
  • slow NAMD simulations on a AMD athlon64 in SUSE linux (Wed Jun 14 2006 - 16:28:38 CDT)
• floquet_at_icsn.cnrs-gif.fr
  • NAMD on SUN (Thu Sep 29 2005 - 01:31:03 CDT)
  • MDenergy error (Wed Jul 13 2005 - 14:43:15 CDT)
  • Segmentation fault with two processors (Fri Jul 01 2005 - 04:12:57 CDT)
  • Problem with mdenergy (Fri Jun 17 2005 - 08:05:41 CDT)
  • Multiple dihedral multiplicity (Fri May 27 2005 - 08:09:14 CDT)
• Floris Buelens
  • NAMD constraint force and energy (Wed Dec 20 2006 - 04:53:12 CST)
  • Re: Re: fep (Wed Jul 27 2005 - 04:41:06 CDT)
  • Re: FEP - one long simulation vs many short ones (Mon Jul 04 2005 - 07:22:55 CDT)
  • FEP - one long simulation vs many short ones (Fri Jul 01 2005 - 07:07:14 CDT)
  • new approach to counter FEP end-point VDW clashes (Sun Jun 26 2005 - 07:41:14 CDT)
  • optimisation for dual CPU sytem (Sat Jun 18 2005 - 08:25:39 CDT)
  • relating FEP-derived ddG values to experimental IC50 (Mon Jun 06 2005 - 17:49:54 CDT)
  • Re: FEP charge perturbation (Mon Jun 06 2005 - 17:40:44 CDT)
  • FEP charge perturbation (Sun May 29 2005 - 17:50:28 CDT)
• Francesco Iori
  • bad exclusion count (Fri Nov 17 2006 - 15:19:37 CST)
• Francisco Castro
  • Atom Positions during simulation (Wed Dec 14 2005 - 16:27:12 CST)
• Frank Yong Jiang
  • questions about anisotropic pressure coupling (Sat May 28 2005 - 10:34:45 CDT)
  • how to use gromacs force field in NAMD? (Tue May 24 2005 - 15:50:05 CDT)
• fu guoxing
  • Problem with compiling NAMD on Suse 9.3 (Tue Nov 08 2005 - 06:23:10 CST)
• gamini_at_ncbs.res.in
  • Re: Queries on patches, GDP-topology (Tue Jul 25 2006 - 03:16:20 CDT)
  • Re: Queries on patches, GDP-topology (Mon Jul 24 2006 - 14:13:41 CDT)
  • Queries on patches, GDP-topology (Sat Jul 22 2006 - 07:36:15 CDT)
  • Re: Computing Potential of Mean Force --SMD-cv (Thu Jul 13 2006 - 07:58:37 CDT)
  • Computing Potential of Mean Force --SMD-cv (Tue Jul 11 2006 - 15:36:45 CDT)
• Gan, Yong
  • VDW energy in CHARMM force field (Tue Jul 25 2006 - 15:49:37 CDT)
  • Generating lipid bilayer model (Sat Mar 25 2006 - 23:31:18 CST)
• Gan, Yong \(UMC-Student\)
  • fixed atoms (Tue Oct 25 2005 - 23:18:59 CDT)
  • Box size (Tue Oct 25 2005 - 11:50:06 CDT)
  • running NAMD2 in parallel (Tue Oct 11 2005 - 10:42:42 CDT)
  • RE: running NAMD2 in parallel (Mon Oct 10 2005 - 22:34:32 CDT)
  • running NAMD2 in parallel (Mon Oct 10 2005 - 21:23:46 CDT)
  • Running NAMD 2.6b1 on Linux Networks (Fri Oct 07 2005 - 16:44:53 CDT)
  • namd 2.6b1 (Wed Oct 05 2005 - 20:50:57 CDT)
  • surface density of lipid bilayer (Thu Sep 08 2005 - 12:42:21 CDT)
  • NAMD on PSC (Sun Aug 28 2005 - 12:26:30 CDT)
  • Pressure Profile Simulation (Wed Aug 24 2005 - 21:36:51 CDT)
  • Running NAMD on a multiprocessor computer (Tue Aug 02 2005 - 19:00:05 CDT)
  • velocity unit (Sun Jun 12 2005 - 21:49:52 CDT)
  • Periodic Boundary Condition (Wed Jun 01 2005 - 16:56:41 CDT)
  • Combine pdb and psf files (Fri Apr 29 2005 - 16:04:23 CDT)
  • RE: Generate psf file of DMPC membrane (Thu Apr 28 2005 - 11:58:02 CDT)
  • Generate psf file of DMPC membrane (Wed Apr 27 2005 - 22:10:34 CDT)
  • NAMD on new P4 (Fri Mar 18 2005 - 13:04:54 CST)
  • isotropic pressure tensor (Wed Mar 16 2005 - 21:56:49 CST)
  • membrane files (Tue Mar 15 2005 - 20:54:41 CST)
  • Patch (Thu Mar 03 2005 - 17:28:35 CST)
  • Kinetic energy (Fri Feb 25 2005 - 12:55:09 CST)
  • Pressure tensor and periodic boundary condition (Mon Feb 21 2005 - 21:40:58 CST)
  • Lipid membrane simulation by NAMD (Fri Feb 18 2005 - 17:40:25 CST)
• Gaurav Sharma
  • Re: small query... (Fri Nov 17 2006 - 21:15:50 CST)
  • Re: small query... (Wed Nov 15 2006 - 19:56:07 CST)
  • Question about ABF (Wed Oct 25 2006 - 18:03:13 CDT)
  • mechanical force calculation (Thu Aug 31 2006 - 22:23:55 CDT)
  • Re: coordination chemistry with NAMD (Thu Aug 03 2006 - 21:06:33 CDT)
  • coordination chemistry with NAMD (Wed Aug 02 2006 - 14:04:04 CDT)
  • force calculation during to conformational change (Tue Jul 11 2006 - 11:38:15 CDT)
  • force-field parameters for TOAC (Mon Mar 27 2006 - 17:02:31 CST)
  • Different solvents (Tue Nov 08 2005 - 13:09:27 CST)
  • Metal Ion and Protein binding (Thu Oct 13 2005 - 12:23:23 CDT)
  • Calculating forces (Thu Sep 01 2005 - 12:32:59 CDT)
  • Re: vmd-l: Nanotube Simulations (Tue Aug 02 2005 - 13:56:15 CDT)
  • Nanotube Simulations (Tue Aug 02 2005 - 08:51:14 CDT)
  • Parameter files for Nanotube Simulation (Thu Jul 28 2005 - 16:26:49 CDT)
  • PDB files for carbon nanotubes (Thu Jul 14 2005 - 14:33:05 CDT)
  • Space environment simulations (Fri May 06 2005 - 13:36:40 CDT)
  • Space environment simulations (Fri May 06 2005 - 13:20:53 CDT)
  • Unprotonating GLU, ASP (Sun Feb 13 2005 - 18:14:31 CST)
• gbellesia_at_chem.ucsb.edu
  • about TCL boundary forces (Sat Apr 29 2006 - 17:16:54 CDT)
  • still on tcl boundary forces (Tue Apr 25 2006 - 12:34:52 CDT)
  • error related to tcl boundary forces (Tue Apr 25 2006 - 00:52:38 CDT)
• Gengbin Zheng
  • Re: problems with paralellism (Tue Nov 28 2006 - 13:44:45 CST)
  • Re: problems for runing NAMD on parallel computers (Wed Jun 28 2006 - 22:08:02 CDT)
  • Re: Re: Is clock skew a problem for charm++ (Wed Jun 21 2006 - 23:17:07 CDT)
  • Re: Re: Is clock skew a problem for charm++ (Wed Jun 21 2006 - 02:08:08 CDT)
  • Re: Re. Namd window network problem (Fri Jun 16 2006 - 10:52:23 CDT)
  • Re: NAMD: compile problem (Thu Jun 15 2006 - 19:21:19 CDT)
  • Re: Namd window network problem (Thu Jun 15 2006 - 14:58:08 CDT)
  • Re: Compile NAMD on Bluegene (Thu Jun 15 2006 - 12:16:40 CDT)
  • Re: Compile NAMD on Bluegene (Thu Jun 15 2006 - 12:04:49 CDT)
  • Re: Compile NAMD on Bluegene (Thu Jun 15 2006 - 01:11:34 CDT)
  • Re: running NAMD on beowulf cluster (Thu Apr 06 2006 - 00:09:18 CDT)
  • Re: running NAMD on beowulf cluster (Wed Apr 05 2006 - 16:30:27 CDT)
  • Re: help on error message during compiling (Wed Apr 05 2006 - 11:32:45 CDT)
  • Re: compile error on amd64 in src/ComputeTclBC.C (Wed Mar 15 2006 - 14:38:19 CST)
  • Re: build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version (Tue Mar 14 2006 - 00:02:33 CST)
  • Re: charm++ over MPI (Fri Feb 17 2006 - 10:30:18 CST)
  • Re: charm++ over MPI (Thu Feb 16 2006 - 15:40:18 CST)
  • Re: charm++ over MPI (Wed Feb 15 2006 - 11:00:53 CST)
  • Re: NAMD with Myrinet MX on MacOS X (Fri Feb 03 2006 - 17:38:53 CST)
  • Re: NAMD fails on Altix (Fri Jan 13 2006 - 02:15:56 CST)
  • Re: Some problem on compiling NAMD (Thu Dec 15 2005 - 22:04:28 CST)
  • Re: NAMD on Win64 (Mon Dec 12 2005 - 21:04:07 CST)
  • Re: NAMD 2.6 in IBM SP (Sat Nov 05 2005 - 09:55:13 CST)
  • Re: questions about running namd on NCSA cluster tungsten (Sat Oct 29 2005 - 12:11:50 CDT)
  • Re: gcc4 (Fri Oct 14 2005 - 14:21:57 CDT)
  • Re: unexpected end with NAMD on quad-dual core opteron machine (Thu Sep 29 2005 - 13:39:22 CDT)
  • Re: log file (Mon Sep 19 2005 - 16:58:43 CDT)
  • Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Sun Sep 04 2005 - 11:08:03 CDT)
  • Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Fri Sep 02 2005 - 00:34:03 CDT)
  • Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Wed Aug 31 2005 - 14:18:07 CDT)
  • Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Wed Aug 31 2005 - 12:32:56 CDT)
  • Re: undefined symbol errors:__builtin_bzero and _alloca building mpi-ppc-darwin version of namd2.6b1 (Wed Aug 17 2005 - 14:14:43 CDT)
  • Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Tue Aug 09 2005 - 11:59:15 CDT)
  • Re: charm++ 5.9 megatest failure too (Tue Aug 02 2005 - 18:21:51 CDT)
  • Re: how to use the dual-processor machines (Sat Jul 30 2005 - 17:52:42 CDT)
  • Re: mpi problems on opteron (Wed Jul 27 2005 - 00:08:32 CDT)
  • Re: sync buffer overflow (Wed Jul 13 2005 - 22:32:31 CDT)
  • Re: config files (Tue Jun 07 2005 - 14:23:31 CDT)
  • Re: NAMD on IBM pSeries (690, 655) (Tue Jun 07 2005 - 14:05:07 CDT)
  • Re: NAMD on IBM pSeries (690, 655) (Tue Jun 07 2005 - 14:00:04 CDT)
  • Re: Installing NAMD on beowulf cluster, 64 bit, opteron, 4 processors. (Tue Jun 07 2005 - 13:58:15 CDT)
  • Re: NAMD on fedora 3 core? (Tue Jun 07 2005 - 12:00:22 CDT)
  • Re: Compilation of Charm++ on Linux opteron cluster with MPICH-GM installed (Wed May 25 2005 - 23:05:47 CDT)
  • Re: Megatest fails on Linux cluster (Wed May 25 2005 - 22:54:23 CDT)
  • Re: CHARM/NAMD network problems on amd64 Clustermatic (Wed May 11 2005 - 22:21:36 CDT)
  • Re: Compliling NAMD in RedHat9 (Wed May 11 2005 - 22:09:15 CDT)
  • Re: Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Wed May 11 2005 - 22:07:13 CDT)
  • Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Tue May 10 2005 - 09:57:04 CDT)
  • Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Tue May 10 2005 - 01:45:25 CDT)
  • Re: compile "mpi" charm++ on amd64 (Tue May 10 2005 - 01:31:51 CDT)
  • Re: hanging at startup phase 0 (Thu May 05 2005 - 11:00:22 CDT)
  • Re: Errors compiling NAMD 2.5 (Mon Apr 04 2005 - 03:13:33 CDT)
  • Re: Charm++ problem on EM64T/Myrinet cluster (Fri Apr 01 2005 - 01:23:51 CST)
  • Re: NAMD recognizes only one MPI process (Thu Mar 31 2005 - 17:41:20 CST)
  • Re: path problems (Tue Mar 22 2005 - 01:37:52 CST)
  • Re: strange behaviour when running apoa1 on 1 processor (Thu Mar 17 2005 - 13:56:03 CST)
  • Re: Re: Trouble with NAMD on Myrinet (Wed Mar 16 2005 - 11:27:19 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Wed Mar 16 2005 - 00:24:54 CST)
  • Re: Trouble with NAMD on Myrinet (Tue Mar 15 2005 - 14:14:14 CST)
  • Re: Not getting good speed up (Fri Mar 11 2005 - 16:04:53 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 10 2005 - 15:54:56 CST)
  • Re: namd on Altix (Wed Mar 09 2005 - 13:36:21 CST)
  • Re: namd on Altix (Tue Mar 08 2005 - 16:54:16 CST)
  • Re: namd on Altix (Tue Mar 08 2005 - 18:43:47 CST)
  • Re: namd on Altix (Tue Mar 08 2005 - 17:21:13 CST)
  • Re: namd on Altix (Tue Mar 08 2005 - 17:09:47 CST)
  • Re: namd on Altix (Tue Mar 08 2005 - 17:00:05 CST)
  • Re: G5 cluster (Tue Mar 08 2005 - 16:41:06 CST)
  • Re: G5 clusters (Tue Mar 08 2005 - 12:44:25 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 19:11:33 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 18:59:02 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 18:28:20 CST)
  • Re: question (fwd) (Mon Mar 07 2005 - 15:51:50 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 15:03:07 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 14:22:53 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 13:39:49 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 13:33:40 CST)
  • Re: installing NAMD on opteron cluster with MPI (Fri Mar 04 2005 - 01:00:59 CST)
  • Re: Not getting good speed up (Thu Mar 03 2005 - 13:34:56 CST)
  • Re: Not getting good speed up (Wed Mar 02 2005 - 21:42:39 CST)
  • Re: clustermatic nodelist file (Wed Mar 02 2005 - 21:29:40 CST)
  • Re: Problems with the nodelist file ! (Wed Mar 02 2005 - 21:15:41 CST)
  • Re: Re: Complie NAMD on Suse Linux (Wed Feb 09 2005 - 17:53:10 CST)
  • Re: Complie NAMD on Suse Linux (Mon Feb 07 2005 - 13:02:32 CST)
  • Re: NAMD on IBM cluster AIX-RS6000 (Mon Jan 24 2005 - 15:17:14 CST)
  • Re: NAMD on IBM cluster AIX-RS6000 (Fri Jan 21 2005 - 22:06:32 CST)
  • Re: Compiling the NAMD on HPUX-ia64 system Error! (Sat Jan 15 2005 - 11:03:51 CST)
  • Re: charm++ compile problem on x86_64 (Fri Jan 14 2005 - 15:32:10 CST)
  • Re: scyld no longer a supported option for building charm++ ? (Fri Jan 14 2005 - 14:43:56 CST)
  • Re: How to Compile NAMD on HPUX-ia64 system~ (Fri Jan 14 2005 - 12:36:56 CST)
  • Re: Compiling (Sun Jan 09 2005 - 11:00:43 CST)
  • Re: Error in when using charmrun (Sat Jan 08 2005 - 22:50:24 CST)
  • Re: Error in when using charmrun (Sat Jan 08 2005 - 21:20:08 CST)
  • Re: Error in when using charmrun (Sat Jan 08 2005 - 21:00:03 CST)
  • Re: About charm++/namd on AMD64 cluster (Mon Jan 03 2005 - 14:46:58 CST)
  • Re: About charm++/namd on AMD64 cluster (Sun Jan 02 2005 - 02:50:56 CST)
  • Re: clustermatic 4 and 5 Namd/charm (Sat Jan 01 2005 - 15:15:45 CST)
• genie lfs
  • periodic cell too small (Wed May 10 2006 - 04:48:44 CDT)
  • simulated annealing (Mon May 01 2006 - 11:04:35 CDT)
  • how long should the simulation be run (Sat Apr 29 2006 - 04:33:50 CDT)
• George M. Giambasu
  • non-cubic boxes for Periodic Boundary Conditions (Mon Jun 19 2006 - 17:38:31 CDT)
• George Madalin Giambasu
  • corrupt dcd file >2GB on PowerPc (Wed Oct 18 2006 - 10:09:48 CDT)
• Georgios Papadopoulos
  • top par for NAG, BMA ? (Mon Sep 11 2006 - 11:47:38 CDT)
  • user defined restraints? (Fri Aug 11 2006 - 04:41:17 CDT)
  • HD speed ?? (Sun Apr 30 2006 - 03:13:36 CDT)
  • Continue a run ? (Mon Mar 13 2006 - 11:27:52 CST)
  • tutorial address (Sat Feb 25 2006 - 03:16:25 CST)
  • extra lines in PSF !!! (Fri Feb 10 2006 - 11:47:10 CST)
  • pairInteraction energies? (Fri Sep 30 2005 - 01:32:46 CDT)
  • calculate enthalpy of binding (Tue Sep 27 2005 - 11:33:33 CDT)
  • Fluorophors ? (Wed Jun 22 2005 - 00:27:25 CDT)
  • plugins.tar.gz & charm_src.tar.gz !!! (Sat Jun 11 2005 - 05:38:27 CDT)
  • NAMD on fedora 3 core? (Tue Jun 07 2005 - 01:33:49 CDT)
  • Fe2+ parameters? (Sun Jun 05 2005 - 04:52:09 CDT)
• ghg_at_xalt.am
  • Lipid bilayer center go away from center of system. (Sun Jun 18 2006 - 10:10:38 CDT)
• Gianluca Interlandi
  • Re: SMD on center of mass (Thu Nov 02 2006 - 21:27:41 CST)
  • Re: SMD on center of mass (Thu Nov 02 2006 - 17:22:45 CST)
  • SMD on center of mass (Thu Nov 02 2006 - 15:40:40 CST)
  • Re: external force (Thu Nov 02 2006 - 13:55:24 CST)
  • Re: rigid protein (Thu Oct 19 2006 - 13:12:53 CDT)
  • Scale (Tue Oct 17 2006 - 00:36:56 CDT)
  • Re: NAMD on Dual processor computer (Sun Oct 15 2006 - 17:35:46 CDT)
  • Re: NAMD timestep and numsteps (Tue Oct 03 2006 - 14:19:10 CDT)
  • "wrapAll on" with a complex (Tue Oct 03 2006 - 00:01:37 CDT)
  • Re: Qmeasure=22?= command (Wed Sep 27 2006 - 17:56:56 CDT)
  • Re: redirecting stdout to a file (Tue Sep 26 2006 - 11:05:18 CDT)
  • Re: checkpoint software for NAMD? (Thu Sep 21 2006 - 16:55:46 CDT)
  • Poisson Boltzmann with NAMD (Wed Sep 06 2006 - 19:47:49 CDT)
  • Re: Counting H-bonds from a dcd file (Tue Aug 29 2006 - 18:48:29 CDT)
  • SMD and restart (Mon Aug 14 2006 - 01:01:50 CDT)
  • Conversion for forces (Tue Jun 20 2006 - 14:05:28 CDT)
  • Re: Vibrational mode analysis (Thu Jun 15 2006 - 21:01:04 CDT)
  • Re: Vibrational mode analysis (Thu Jun 15 2006 - 20:08:05 CDT)
  • Vibrational mode analysis (Thu Jun 15 2006 - 19:31:40 CDT)
  • Clustermatic and NFS mount (Sun May 07 2006 - 15:49:40 CDT)
  • TRIO (Tue May 02 2006 - 16:55:09 CDT)
  • RE: NAMD-L: question about harmonic constraints (Wed Apr 12 2006 - 17:05:24 CDT)
  • Multimeric protein (Sat Apr 08 2006 - 16:57:28 CDT)
  • langevinHydrogen off? (Mon Apr 03 2006 - 18:15:23 CDT)
  • gcc4 (Tue Oct 11 2005 - 16:34:32 CDT)
  • Re: About ions Representation in NAMD (Wed Sep 28 2005 - 07:33:39 CDT)
  • SHAKE or not? (Tue Sep 27 2005 - 14:42:43 CDT)
  • Compiling charm++-5.9: Problems with g++ (Sat Aug 20 2005 - 05:36:26 CDT)
  • shmget error (Mon Jun 20 2005 - 07:46:28 CDT)
  • Re: Trajectory file. (Fri May 13 2005 - 16:39:37 CDT)
  • NOE constraints with NAMD (Tue May 10 2005 - 09:25:35 CDT)
  • Re: Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 08:07:49 CST)
• Giovanni Bellesia
  • Re: help!!! (Wed Jul 19 2006 - 00:38:18 CDT)
  • Re: solvating a protein (Thu Jul 13 2006 - 11:54:36 CDT)
  • Re: ABF Simulation (Mon Jun 26 2006 - 21:29:24 CDT)
  • Re: Angle 2, Where is the problem [IMPORTANT] (Tue Jun 20 2006 - 01:15:37 CDT)
  • Re: DCD to PDB conversion (Tue Jun 13 2006 - 18:47:01 CDT)
  • Re: about TCL boundary forces (Mon May 22 2006 - 14:31:14 CDT)
  • amidated C-terminus (NH2) with OPLS force field (Mon Apr 17 2006 - 17:34:57 CDT)
  • OPLS-AA/L (Mon Apr 17 2006 - 15:53:34 CDT)
  • tcl boundary forces (Fri Apr 14 2006 - 13:26:16 CDT)
  • Re: math formula for spherical boundary conditions. (Mon Apr 03 2006 - 13:17:46 CDT)
  • Re: (Thu Feb 23 2006 - 12:45:28 CST)
  • NBFix not working with charmm par file (Wed Jan 25 2006 - 17:36:03 CST)
  • dihedrals multiplicity in xplor psf file (Wed Jan 25 2006 - 15:12:16 CST)
  • peptides confined in a water sphere (Thu Jan 19 2006 - 09:37:01 CST)
  • Re: trying to generate a peptide (Wed Oct 26 2005 - 11:27:43 CDT)
  • Re: moments of inertia, principal axes (Thu Aug 18 2005 - 04:42:20 CDT)
  • (no subject) (Thu Aug 11 2005 - 15:50:38 CDT)
  • rescaling of coordinates in PBC simulations (Thu Aug 11 2005 - 12:41:52 CDT)
  • Re: changing file (Wed Jul 20 2005 - 04:57:29 CDT)
  • Re: namddat: Command not found (Thu May 12 2005 - 13:49:45 CDT)
  • Re: namddat: Command not found (Thu May 12 2005 - 13:48:10 CDT)
  • Re: Molecular Dynamics or Langevin Dynamics (Wed Apr 27 2005 - 19:18:58 CDT)
  • Re: Molecular Dynamics or Langevin Dynamics (Wed Apr 27 2005 - 10:59:27 CDT)
  • Re: conformational alignment (Wed Mar 30 2005 - 16:40:36 CST)
  • electrostatics under spherical harmonic conditions (Fri Jan 28 2005 - 13:59:57 CST)
• Glenn Johnson
  • Re: bonding to image (Mon Apr 11 2005 - 16:02:28 CDT)
  • bonding to image (Mon Apr 11 2005 - 13:56:33 CDT)
  • temperature autocorrelation (Thu Apr 07 2005 - 17:39:28 CDT)
  • Modeling a polymer (Thu Mar 24 2005 - 13:44:29 CST)
  • convert namd structure/coordinate files to gromacs topology file (Fri Mar 18 2005 - 14:00:54 CST)
  • modeling sucrose (Wed Mar 09 2005 - 17:19:12 CST)
  • PMEGridSize (Thu Feb 24 2005 - 15:25:03 CST)
  • RE: conditional statements in conf files (Mon Feb 14 2005 - 15:49:46 CST)
  • conditional statements in conf files (Mon Feb 14 2005 - 14:59:02 CST)
  • Complementary programs for NAMD (Mon Feb 14 2005 - 13:32:24 CST)
  • RE: namdplot not working (Fri Feb 11 2005 - 17:30:33 CST)
  • namdplot not working (Fri Feb 11 2005 - 14:39:45 CST)
• Goran Krilov
  • NAMD with Myrinet MX on MacOS X (Fri Jan 27 2006 - 11:35:54 CST)
• Gordon Wells
  • system rotates after equilibration (Fri Mar 03 2006 - 03:21:30 CST)
• Grace Shen
  • Some warnings from log file after minimization (Fri Dec 16 2005 - 13:05:53 CST)
  • A question regarding generate pdb and psf file (Tue Dec 06 2005 - 11:06:27 CST)
  • The psf format conversion (Wed Nov 16 2005 - 16:54:42 CST)
  • The vector direction in SMD (Fri Nov 04 2005 - 15:01:51 CST)
  • RE: namd: advice (Fri Nov 04 2005 - 09:20:13 CST)
  • Increasing temp during MD (Thu Nov 03 2005 - 12:11:27 CST)
  • How to atomselect several residues (Wed Nov 02 2005 - 17:28:50 CST)
  • RE: About ADP (Tue Nov 01 2005 - 10:15:47 CST)
  • About ADP (Tue Nov 01 2005 - 09:48:43 CST)
  • Question regarding SMD (Mon Oct 31 2005 - 15:11:01 CST)
  • How to append charmm stream file (Wed Oct 26 2005 - 12:01:23 CDT)
  • Assign the ligand force field parameters (Mon Oct 24 2005 - 16:32:13 CDT)
• greisen_at_binf.ku.dk
  • ATP nucleotides using NAMD (Fri Oct 14 2005 - 04:56:45 CDT)
  • CMAP in VMD error (Thu Oct 13 2005 - 15:58:33 CDT)
• griadi_at_utalca.cl
  • Re: Simulation of a 1000 water molecules (Thu Aug 03 2006 - 15:12:37 CDT)
  • Re: RDF.tcl (Fri Jul 28 2006 - 17:01:24 CDT)
  • Re: solvating a protein (Thu Jul 13 2006 - 13:08:00 CDT)
  • Re: Density of water (Tue Jun 06 2006 - 09:41:56 CDT)
  • Re: Error on renaming file (Fri Jun 02 2006 - 13:14:01 CDT)
  • Re: bulk density in RDF.tcl (Wed Mar 29 2006 - 16:55:07 CST)
  • Re: is possible to remove the waterbox before running VMD (Thu Mar 09 2006 - 12:56:38 CST)
  • Re: radial distribution function (Wed Mar 01 2006 - 08:25:45 CST)
  • Fwd: All or Nothing at All?? (Sat Oct 29 2005 - 14:02:12 CDT)
• Grzegorz Jezierski
  • Re: Reproducing free energy profile for acetate-guanidinium association (Wed Nov 29 2006 - 06:01:07 CST)
  • Re: Reproducing free energy profile for acetate-guanidinium association (Wed Nov 29 2006 - 06:00:45 CST)
  • Reproducing free energy profile for acetate-guanidinium association (Tue Nov 14 2006 - 06:40:04 CST)
  • Re: Sybyl trajectory (Tue Sep 06 2005 - 08:32:17 CDT)
  • vectorized NAMD version? (Thu Sep 01 2005 - 09:42:35 CDT)
  • Crash during free energy calculation (MCTI) (Wed Aug 24 2005 - 02:47:07 CDT)
  • Extra terms in the expression for potential energy (Tue Aug 23 2005 - 12:04:35 CDT)
  • Re: Incorrect periodic box imaging with AMBER parameters (Mon Aug 08 2005 - 12:43:20 CDT)
  • Re: Incorrect periodic box imaging with AMBER parameters (Fri Aug 05 2005 - 06:23:57 CDT)
  • Re: Incorrect periodic box imaging with AMBER parameters (Thu Aug 04 2005 - 13:04:05 CDT)
  • Incorrect periodic box imaging with AMBER parameters (Mon Jul 25 2005 - 04:11:20 CDT)
• Guo Zhi
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 22:00:03 CST)
• hamdi
  • Constant electric field to selected atoms. (Wed Jun 07 2006 - 09:08:32 CDT)
• HAMON véronique
  • "Adaptive" force direction in SMD? (Tue Oct 03 2006 - 10:00:28 CDT)
• Hamsa Priya Mohana sundaram
  • why this error? (Mon Aug 21 2006 - 10:20:46 CDT)
  • unit cell information from dcd file (Thu Jul 20 2006 - 11:34:51 CDT)
• Harald Tepper
  • Problem with NAMD on Opteron cluster (Sat Nov 12 2005 - 05:29:33 CST)
• Harindar Keer
  • Rigid body minimization (Wed Sep 13 2006 - 23:27:51 CDT)
  • Hexagonal boundary conditions (Mon Jul 31 2006 - 13:23:50 CDT)
  • Pair interaction calculation for large number different pairs (Wed Mar 02 2005 - 22:26:06 CST)
  • Re: NAMD on IBM cluster AIX-RS6000 (Mon Jan 24 2005 - 14:38:47 CST)
  • NAMD on IBM cluster AIX-RS6000 (Fri Jan 21 2005 - 18:46:29 CST)
• Hemant Kushwaha
  • Transition path sampling (Tue May 23 2006 - 09:11:17 CDT)
  • NADP hydrogen zero (Fri Jun 03 2005 - 22:30:08 CDT)
  • Re: NADP problem (Fri Jun 03 2005 - 22:07:08 CDT)
  • Re: NADP problem (Fri Jun 03 2005 - 08:28:56 CDT)
  • psfgen problem (Fri May 20 2005 - 23:41:13 CDT)
  • NADP problem (Tue May 17 2005 - 07:12:29 CDT)
  • NADP topology (Mon May 02 2005 - 04:40:58 CDT)
  • gradient nan (Mon Feb 07 2005 - 00:17:04 CST)
• Hidekazu WATANABE
  • patch failed (Fri Jul 15 2005 - 05:19:19 CDT)
  • RE: About PDB file with fixed atom flags. (Thu May 05 2005 - 12:36:21 CDT)
  • About PDB file with fixed atom flags. (Wed May 04 2005 - 16:40:23 CDT)
• Himanshu Khandelia
  • Re: clustering conformations (Mon Nov 20 2006 - 15:05:09 CST)
  • Re: DCD to PDB conversion (Thu Jun 08 2006 - 08:57:14 CDT)
  • system calls inside namd script (Sat Apr 08 2006 - 16:42:46 CDT)
  • other crystal types in NAMD ? (Tue Apr 04 2006 - 10:17:40 CDT)
  • Re: Can someone PLEASE explain the "firsttimestep" parameter ? (Wed Mar 22 2006 - 16:45:17 CST)
  • Can someone PLEASE explain the "firsttimestep" parameter ? (Wed Mar 22 2006 - 14:49:03 CST)
  • the "firsttimestep" conundrum (Sun Mar 19 2006 - 15:20:47 CST)
  • Re: timestep in namd (Thu Mar 16 2006 - 13:26:53 CST)
  • command line arguments in NAMD ? (Tue Mar 14 2006 - 17:49:31 CST)
  • Re: question on membrane crushing (Tue Mar 14 2006 - 16:07:32 CST)
  • Re: MD in a loop with different names for dcd files (Tue Mar 14 2006 - 13:18:04 CST)
  • Re: question on membrane crushing (Tue Mar 14 2006 - 12:05:13 CST)
  • Re: MD in a loop with different names for dcd files (Tue Mar 14 2006 - 11:44:46 CST)
  • MD in a loop with different names for dcd files (Tue Mar 14 2006 - 10:56:21 CST)
  • Parameter resetting in NAMD (Thu Mar 09 2006 - 10:26:55 CST)
  • constraining water so that it does not get inside bilayer (Mon Mar 06 2006 - 14:06:35 CST)
  • RE: starting simulation in charmm, continuing in NAMD ? (Sun Mar 05 2006 - 14:50:39 CST)
  • starting simulation in charmm, continuing in NAMD ? (Sun Mar 05 2006 - 11:23:15 CST)
  • Re: question on membrane crushing (Thu Mar 02 2006 - 08:57:12 CST)
  • Re: peridic boundary condition (Fri Mar 11 2005 - 13:57:23 CST)
  • example scripts (Thu Mar 10 2005 - 10:03:53 CST)
• hl332_at_drexel.edu
  • small query... (Wed Nov 15 2006 - 13:48:39 CST)
  • small query... (Fri Aug 18 2006 - 11:17:25 CDT)
  • simple query.. (Thu Jul 27 2006 - 11:06:39 CDT)
  • help!!! (Wed Jul 19 2006 - 00:12:23 CDT)
  • plz help!! (Tue Jul 18 2006 - 10:30:07 CDT)
  • third time..can someone help!! (Tue Jul 11 2006 - 22:09:22 CDT)
  • autoionize plugin.. (Mon Jul 10 2006 - 11:32:18 CDT)
  • Repeating again: Periodic velocity pulls (Tue May 30 2006 - 09:51:14 CDT)
  • Periodic velcoity pulls (Fri May 26 2006 - 12:15:55 CDT)
• hodak_at_chips.ncsu.edu
  • RMSD increases after restarts, decreases at the end of run (Thu Aug 24 2006 - 17:16:03 CDT)
• Holly Freedman
  • pair interaction cutoff (Mon Aug 21 2006 - 21:51:30 CDT)
  • pairinteractionSelf (Thu Aug 03 2006 - 21:41:55 CDT)
  • need pair interaction energies, not forces (Wed Jul 19 2006 - 22:20:06 CDT)
  • Re: NAMDenergy (Wed Jul 05 2006 - 12:12:04 CDT)
  • NAMDenergy (Tue Jul 04 2006 - 12:44:59 CDT)
  • PME pair interaction analysis (Sun Jun 25 2006 - 16:17:41 CDT)
• Hrant Gharabekyan
  • Re[2]: ERROR: Constraint failure in RATTLE algorithm for atom 127! (Thu Apr 14 2005 - 05:48:08 CDT)
  • Re: Periodic cell has become too small for original patch grid (Thu Apr 14 2005 - 05:25:01 CDT)
  • Question about Constraint failure in RATTLE algorithm for atom (Tue Feb 08 2005 - 05:06:46 CST)
• hrh
  • Re: Re: Is clock skew a problem for charm++ (Wed Jun 21 2006 - 06:33:05 CDT)
• Hugo Azurmendi
  • variable cellOrigin (Wed Jan 11 2006 - 15:49:30 CST)
• Hui-Hsu Tsai
  • capping using Amber FF (Tue Mar 01 2005 - 12:32:24 CST)
• Hyonseok Hwang
  • Re: dcd file format (Fri Nov 24 2006 - 20:47:42 CST)
  • Re: Using NBFIX (Tue Oct 31 2006 - 16:41:11 CST)
  • Re: Using NBFIX (Mon Oct 30 2006 - 01:05:03 CST)
  • Re: Using NBFIX (Sun Oct 29 2006 - 20:44:30 CST)
  • Urey-Bradley term and VDW energy (Wed Oct 25 2006 - 22:41:36 CDT)
  • Re: NBFix and NAMD (Tue Jul 25 2006 - 21:33:14 CDT)
  • Re: NBFix and NAMD (Tue Jul 25 2006 - 16:35:23 CDT)
  • Re: question on the charged system (Wed May 17 2006 - 22:25:04 CDT)
  • question on the charged system (Wed May 17 2006 - 01:31:08 CDT)
  • Re: Nose-Hoover langevin piston pressure control and target surface tension (Mon May 15 2006 - 23:09:34 CDT)
  • Nose-Hoover langevin piston pressure control and target surface tension (Thu May 11 2006 - 23:04:55 CDT)
  • different cutoff for elecstrostatic and VDW interactions (Tue Apr 18 2006 - 12:53:29 CDT)
  • question on 1-4scaling factor (Sun Jan 22 2006 - 22:58:24 CST)
  • question on the format of adding Lennard-Jones parameters (Thu Jan 19 2006 - 19:06:54 CST)
  • Re: How to run namd on NCSA Tungsten (Wed Oct 19 2005 - 16:56:30 CDT)
  • NAMD on myrinet (Tue Oct 18 2005 - 16:12:36 CDT)
  • Re: glucose CHARMM force field (Thu Mar 31 2005 - 12:29:13 CST)
  • glucose CHARMM force field (Tue Mar 29 2005 - 21:37:34 CST)
• Idit Buch
  • minimization of a cyclic peptide with NAMD (Mon Sep 04 2006 - 04:22:03 CDT)
• Imran Khan
  • problem while running NAMD (Wed Sep 14 2005 - 11:25:56 CDT)
  • Compilation of NAMD on 64-bit NUMA (Wed Aug 17 2005 - 04:58:23 CDT)
• Indrajaya
  • how to make dual-hybrid topology? (Mon Feb 13 2006 - 06:47:21 CST)
• interesting.contraceptive_at_gmail.com
  • NVT nose-hoover hamiltonian in SMD? (Mon Jul 10 2006 - 19:30:56 CDT)
• Ioana Cozmuta
  • two references- I got them, thank you! (Wed Apr 26 2006 - 16:15:11 CDT)
  • two references (Wed Apr 26 2006 - 15:18:28 CDT)
  • Re: reconstructing PMF (Thu Apr 13 2006 - 13:58:09 CDT)
  • reconstructing PMF (Tue Apr 11 2006 - 16:57:02 CDT)
  • Re: NAMD-L: question about harmonic constraints (Mon Apr 10 2006 - 12:29:14 CDT)
  • Re: restart a simulation (Mon Apr 03 2006 - 13:37:36 CDT)
  • force over selection (Wed Mar 22 2006 - 23:51:46 CST)
  • c-shell into NAMD configuration file (Mon Jun 13 2005 - 02:02:48 CDT)
• ioana_at_pegasus.arc.nasa.gov
  • random seed (Tue Sep 27 2005 - 20:14:25 CDT)
• ir7_at_njit.edu
  • Packaging 100 cations and anions in a box (Tue Dec 06 2005 - 22:47:56 CST)
• Irene Newhouse
  • preparing a dimeric protein for NAMD (Thu Dec 22 2005 - 21:28:21 CST)
• Ivan Ufimtsev
  • RE: Periodic cell has become too small for original patch grid! (Fri Apr 14 2006 - 00:08:32 CDT)
  • FATAL ERROR: Tried to find atom type on node other than node 0 (Sat Dec 24 2005 - 17:26:26 CST)
• Jack
  • VMD solvate in CCl4 (Tue Jul 26 2005 - 08:37:08 CDT)
• Jackie
  • simulation crashing with nan (Wed Jul 26 2006 - 08:49:56 CDT)
  • LES (Tue Jul 25 2006 - 11:54:51 CDT)
  • total mol calculation (Wed Jul 19 2006 - 14:08:07 CDT)
  • total mol calculation (Wed Jul 19 2006 - 14:07:57 CDT)
• Jacob Poehlsgaard
  • Problem with equilibration and pressure (Wed Dec 13 2006 - 05:31:49 CST)
  • Generalized solvent boundary potential or similar tricks for huge systems in NAMD?? (Thu Nov 30 2006 - 03:15:35 CST)
  • Using/converting old extended top and par files? (Thu Oct 26 2006 - 05:34:31 CDT)
  • Re: Intel Woodcrest version? (Wed Oct 18 2006 - 03:01:33 CDT)
  • Intel Woodcrest version? (Tue Oct 17 2006 - 05:50:16 CDT)
  • re: water hole (Wed Sep 20 2006 - 04:54:37 CDT)
  • Water Hole (Tue Sep 19 2006 - 03:00:54 CDT)
  • FW: Compilation problems on intel woodcrest (Thu Sep 07 2006 - 06:51:41 CDT)
  • RE: Starting out with NAMD/VMD (Tue Jun 06 2006 - 04:38:53 CDT)
  • RE: Computing cost of frozen atoms (Wed Apr 19 2006 - 04:03:53 CDT)
• Jacob Pøhlsgaard
  • RE: Computing cost of frozen atoms (Wed Apr 19 2006 - 03:33:28 CDT)
  • Computing cost of frozen atoms (Tue Apr 18 2006 - 04:39:20 CDT)
  • Developing topologies for modified NA residues? (Mon Apr 10 2006 - 08:37:04 CDT)
• Jake Michaelson
  • namdstats gives nan's in tutorial output (Wed Mar 01 2006 - 10:40:48 CST)
  • hybrid qm/mm (Wed Jan 25 2006 - 15:14:47 CST)
• James W
  • The problem of "SMD and smd.tcl" (Mon Jul 03 2006 - 20:33:57 CDT)
• Jan Kosinski
  • Re: modeling zinc binding site (Fri Apr 28 2006 - 10:25:20 CDT)
  • modeling zinc binding site (Tue Apr 25 2006 - 07:46:30 CDT)
• Jan Saam
  • Re: assigning atom type for parameterization (Fri Sep 08 2006 - 20:21:32 CDT)
  • Re: error in loading "import hessian/charge from single point calculation" in paratool (Tue Aug 29 2006 - 03:58:15 CDT)
  • Re: About CHARMM charge (Mon Aug 28 2006 - 05:46:22 CDT)
  • Re: Stretching Deca-Alanine (Fri Aug 11 2006 - 00:01:50 CDT)
  • Re: coordination chemistry with NAMD (Fri Aug 04 2006 - 03:16:28 CDT)
  • Re: TCL Forces and Help on Script (Thu Jul 06 2006 - 14:27:46 CDT)
  • Re: Re: Is clock skew a problem for charm++ (Thu Jun 22 2006 - 12:54:47 CDT)
  • Re: Re: Is clock skew a problem for charm++ (Thu Jun 22 2006 - 06:56:26 CDT)
  • Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) (Thu Jun 22 2006 - 06:45:47 CDT)
  • Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) (Thu Jun 22 2006 - 06:36:50 CDT)
  • Re: NAMD results depend on # of processors!!?? (Wed Jun 21 2006 - 16:25:21 CDT)
  • NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) (Wed Jun 21 2006 - 15:55:13 CDT)
  • Re: Re: Is clock skew a problem for charm++ (Wed Jun 21 2006 - 14:38:09 CDT)
  • Re: Re: Is clock skew a problem for charm++ (Wed Jun 21 2006 - 09:24:10 CDT)
  • Re: Re: Is clock skew a problem for charm++ (Wed Jun 21 2006 - 08:52:54 CDT)
  • Re: Is clock skew a problem for charm++ (Tue Jun 20 2006 - 17:50:46 CDT)
  • Is clock skew a problem for charm++ (Tue Jun 20 2006 - 17:37:19 CDT)
  • Re: Re: ABF: example works; more questions. (Wed May 31 2006 - 17:27:03 CDT)
  • Re: ABF: example works; more questions. (Tue May 30 2006 - 12:38:05 CDT)
  • Re: ABF: example works; more questions. (Tue May 30 2006 - 11:01:29 CDT)
  • ABF: example works now; more questions. (Tue May 30 2006 - 08:57:15 CDT)
  • questions regrading ABF (Mon May 29 2006 - 10:47:48 CDT)
  • Re: Developing topologies for modified NA residues? (Mon Apr 10 2006 - 11:23:39 CDT)
  • Re: Charmm 1,4 Interactions - Scaling Question (Thu Jun 16 2005 - 18:20:22 CDT)
  • Re: Hexagonal cell and PME grid. (Tue Mar 01 2005 - 05:34:17 CST)
  • Re: using namd to compute energies (Thu Feb 17 2005 - 15:44:57 CST)
  • tclForces - addforce to group of atoms (Fri Jan 07 2005 - 17:27:40 CST)
  • tclForces - addforce to group of atoms (Fri Jan 07 2005 - 17:01:13 CST)
• jas theway
  • How to create psf for carbohydrate (Mon Jan 23 2006 - 19:02:13 CST)
• Jason Lee
  • Question on simulation energy output (Sun Mar 12 2006 - 21:33:28 CST)
  • Problem on NAMD simulation energy output (Sun Mar 12 2006 - 21:17:12 CST)
  • Question on the bond energy of NAMD tutorial (Mon Feb 06 2006 - 15:51:22 CST)
  • Berendsen pressure control problem (Thu Jan 26 2006 - 14:15:29 CST)
  • RE: Myrinet NAMD (Mon Oct 31 2005 - 15:00:25 CST)
  • NAMD running problem (Tue Sep 27 2005 - 15:02:27 CDT)
  • Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Fri Sep 02 2005 - 10:55:13 CDT)
  • Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Thu Sep 01 2005 - 16:46:24 CDT)
  • RE: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Tue Aug 30 2005 - 18:04:43 CDT)
  • Charmm++5.9 build on Mac OS X by IB xlc compiler (Mon Aug 08 2005 - 14:58:21 CDT)
  • Re: LDB question (Sun Aug 07 2005 - 11:32:08 CDT)
  • RE: Nanotube Simulations (Tue Aug 02 2005 - 14:23:32 CDT)
  • LDB question (Mon Aug 01 2005 - 21:06:19 CDT)
  • CCS ERROR during simulation (Mon Jul 25 2005 - 08:52:16 CDT)
  • Segment atom number limitation (Wed Jun 29 2005 - 11:18:50 CDT)
  • RESTARTING CONJUGATE GRADIENT ALGORITHM (Fri Jun 10 2005 - 10:18:33 CDT)
  • Nanotube simulation in water problem (Mon May 30 2005 - 09:30:12 CDT)
  • Re: Complie NAMD on Suse Linux (Wed Feb 09 2005 - 16:51:28 CST)
  • Complie NAMD on Suse Linux (Mon Feb 07 2005 - 09:32:02 CST)
• Javad Azadi
  • Re: Trouble with Charmm/PDB? (Tue Nov 07 2006 - 12:12:49 CST)
  • Trouble with Charmm/PDB? (Mon Nov 06 2006 - 23:33:21 CST)
• Jawahar Neelankatan
  • Re: Problem with Alchemical FEP (Wed Aug 09 2006 - 19:56:19 CDT)
  • Problem with Alchemical FEP (Mon Aug 07 2006 - 09:24:55 CDT)
  • Alchemical Free Energy Perturbation Simulation (Fri Jul 28 2006 - 11:18:20 CDT)
  • Alchemical Free Energy Perturbation (Sat Feb 25 2006 - 00:40:02 CST)
  • Alchemical Free Energy Perturbation (Sat Feb 25 2006 - 01:36:29 CST)
• jbelof_at_mail.usf.edu
  • TCL energy variables (Sat Apr 01 2006 - 11:29:14 CST)
• JC Gumbart
  • Re: forming disulfide after equilibrating system (Sat Dec 23 2006 - 12:55:40 CST)
  • Re: outputPressure (Fri Dec 15 2006 - 21:34:21 CST)
  • Re: Parallelization method (Thu Dec 14 2006 - 11:45:45 CST)
  • RE: simulation of membrane-protein systems (Wed Dec 13 2006 - 22:28:17 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 14:42:24 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 13:59:27 CST)
  • Re: about topology generation (Tue Dec 05 2006 - 13:07:43 CST)
  • Re: Harmonic Constraint: 2 types (Sun Nov 26 2006 - 23:21:21 CST)
  • RE: LINE=*CMAP* (Wed Nov 22 2006 - 08:39:10 CST)
  • Re: combine.tcl (Tue Nov 21 2006 - 22:44:51 CST)
  • Re: System of POPC bilayer (Fri Nov 10 2006 - 08:09:19 CST)
  • Re: how long is enough to heat up and equilibrate (Fri Nov 10 2006 - 08:06:21 CST)
  • Re: PME GridSize (Wed Nov 08 2006 - 10:40:51 CST)
  • Re: PME GridSize (Tue Nov 07 2006 - 23:28:50 CST)
  • RE: deformations in a water box during equilibration in NAMD (Fri Nov 03 2006 - 09:57:39 CST)
  • RE: external force (Fri Nov 03 2006 - 02:08:09 CST)
  • RE: deformations in a cubic water box during equilibration in NAMD (Fri Nov 03 2006 - 01:53:23 CST)
  • Re: constrained simulation (Fri Oct 27 2006 - 11:15:04 CDT)
  • Re: Replica-Exchange MD (Mon Oct 23 2006 - 14:49:01 CDT)
  • Re: Equilibriation Info (Mon Oct 23 2006 - 14:45:27 CDT)
  • Re: rigid protein (Thu Oct 19 2006 - 11:04:37 CDT)
  • Re: changing velocity during simulation (Wed Oct 11 2006 - 15:05:44 CDT)
  • Re: line too long in pdb file restart.coor (Wed Oct 11 2006 - 15:04:10 CDT)
  • Re: restarting the simulation (Sun Oct 08 2006 - 19:16:13 CDT)
  • Re: missing info from NAMD output (Tue Oct 03 2006 - 14:43:46 CDT)
  • Re: How can I do protein complex's simulation? (Mon Oct 02 2006 - 19:57:54 CDT)
  • RE: Constraining a molecule and measuring the corresponding constraint force (Sat Sep 30 2006 - 09:20:47 CDT)
  • Re: mDyne/A to kcal/mol/A2 (Tue Sep 05 2006 - 14:46:55 CDT)
  • Re: SMD of TFIIB! (Fri Aug 25 2006 - 19:43:34 CDT)
  • Re: Pulling of Center of Mass (Tue Aug 15 2006 - 13:43:07 CDT)
  • Re: Ion Channel Jarzynski (Thu Aug 10 2006 - 20:28:55 CDT)
  • Re: Queries on patches, GDP-topology (Sun Jul 23 2006 - 20:11:54 CDT)
  • Re: temp autocorrelation (Sun Jul 23 2006 - 20:04:52 CDT)
  • Re: Torque aplication with SMD (Sun Jul 23 2006 - 20:02:31 CDT)
  • Re: bulid psf for structure already with hydrogens (Sun Jul 23 2006 - 19:47:03 CDT)
  • Re: splitting up long run leads to very different DNA conformation in E field (Fri Jul 14 2006 - 11:49:28 CDT)
  • Re: splitting up long run leads to very different DNA conformation in E field (Thu Jul 13 2006 - 20:55:43 CDT)
  • Re: (No subject) (Mon Jul 10 2006 - 20:11:31 CDT)
  • RE: OXT in pdb file (Sat Jul 08 2006 - 01:32:31 CDT)
  • Re: Time of MD (Mon Jun 26 2006 - 16:33:54 CDT)
  • Re: Conversion for forces (Tue Jun 20 2006 - 14:28:10 CDT)
  • RE: Tcl, minimization and MD (Warning: I am a lazy ignorant) (Tue Jun 20 2006 - 10:38:17 CDT)
  • RE: extended system or Basis Vector (Tue Jun 20 2006 - 01:05:54 CDT)
  • RE: Angle 2, Where is the problem [IMPORTANT] (Tue Jun 20 2006 - 01:00:09 CDT)
  • Re: Lipid bilayer center go away from center of system. (Sun Jun 18 2006 - 20:55:11 CDT)
  • RE: Factorization in PMEGridSize (Wed Jun 07 2006 - 09:25:24 CDT)
  • RE: Basic question about steered moledular dynamic(SMD) simulation (Wed May 31 2006 - 09:19:11 CDT)
  • Re: Basic question about steered moledular dynamic(SMD) simulation (Tue May 30 2006 - 11:47:58 CDT)
  • RE: Basic question about steered moledular dynamic(SMD) simulation (Mon May 29 2006 - 12:01:21 CDT)
  • RE: Basic question about steered moledular dynamic(SMD) simulation (Mon May 29 2006 - 09:51:02 CDT)
  • Re: Basic question about steered moledular dynamic(SMD) simulation (Mon May 29 2006 - 00:36:34 CDT)
  • Re: Periodic cell has become too small for original patch grid! (Thu Apr 13 2006 - 13:21:15 CDT)
  • RE: NAMD-L: question about harmonic constraints (Tue Apr 11 2006 - 23:43:40 CDT)
  • Re: NAMD-L: question about harmonic constraints (Tue Apr 11 2006 - 17:41:08 CDT)
  • Re: NAMD-L: question about harmonic constraints (Mon Apr 10 2006 - 17:50:58 CDT)
  • Re: NAMD-L: question about harmonic constraints (Mon Apr 10 2006 - 17:21:27 CDT)
  • RE: NAMD-L: question about harmonic constraints (Mon Apr 10 2006 - 00:49:47 CDT)
  • RE: NAMD-L: question about harmonic constraints (Sat Apr 08 2006 - 13:52:02 CDT)
  • Re: Topology file for Building Gramicidin A (tutorial) (Tue Feb 07 2006 - 13:20:06 CST)
  • RE: About "mutate" command in psfgen package. (Thu Feb 02 2006 - 23:06:44 CST)
  • Re: About "mutate" command in psfgen package. (Thu Feb 02 2006 - 18:47:10 CST)
  • RE: wrong simulation times or misleading time counting? (Wed Jan 18 2006 - 23:27:28 CST)
  • RE: help-minimization and equilibration of Ubiquitin in a water box (Wed Jan 11 2006 - 19:52:10 CST)
  • RE: Simulation in vaccum (Sun Jan 08 2006 - 02:05:07 CST)
  • RE: same random numbers?? (Fri Jan 06 2006 - 23:40:53 CST)
  • RE: Simulation in vaccum (Fri Jan 06 2006 - 23:35:23 CST)
  • Re: A question regarding generate pdb and psf file (Tue Dec 06 2005 - 11:37:55 CST)
  • Re: pair.pdb and cutoff for pairInteraction (Wed Nov 30 2005 - 00:10:44 CST)
  • Re: pair.pdb and cutoff for pairInteraction (Tue Nov 29 2005 - 23:52:51 CST)
  • Re: temperature "coupling coefficient" in NAMD (Fri Nov 18 2005 - 12:02:37 CST)
  • Re: The vector direction in SMD (Fri Nov 04 2005 - 15:16:30 CST)
  • Re: How to atomselect several residues (Wed Nov 02 2005 - 18:38:27 CST)
  • RE: A question on psfgen (Tue Oct 18 2005 - 02:09:05 CDT)
  • Re: CMAP in VMD error (Thu Oct 13 2005 - 16:16:04 CDT)
  • Re: namdplot: command not found (Wed Oct 12 2005 - 15:41:43 CDT)
  • Re: problem with PSFGEN (Tue Oct 11 2005 - 11:54:42 CDT)
  • Re: fix backbone atom (Sun Oct 09 2005 - 02:29:57 CDT)
  • RE: water box and the procedure (Fri Oct 07 2005 - 20:38:26 CDT)
  • Re: ion concentration (Thu Oct 06 2005 - 20:21:20 CDT)
  • Re: autoionize and psfgen, which one first? (Thu Oct 06 2005 - 16:11:43 CDT)
  • Re: VMD scripting (Thu Oct 06 2005 - 14:39:51 CDT)
  • RE: random seed (Tue Sep 27 2005 - 20:30:05 CDT)
  • Re: It is posible to allow Bond and angle degrees of freedom in tip3 water?? (Mon Sep 26 2005 - 22:27:04 CDT)
  • Re: problem when do equilibration (Sun Aug 21 2005 - 14:14:12 CDT)
  • Re: par_all27_prot_lipid.inp (Thu Aug 18 2005 - 17:26:08 CDT)
  • RE: PSF file generation (Tue Aug 16 2005 - 01:00:32 CDT)
  • RE: For help with .log file. (Sun Aug 07 2005 - 14:57:58 CDT)
  • RE: Fatal error: (Thu Aug 04 2005 - 08:50:01 CDT)
  • RE: restarting SMD jobs (Tue Jul 26 2005 - 21:07:17 CDT)
  • RE: constrain or fix the system only in Z direction (Thu Jul 21 2005 - 09:34:22 CDT)
  • Re: removing water from DCD (Wed Jul 20 2005 - 20:50:49 CDT)
  • RE: cellBasisVectors and xsc files (Tue Jul 19 2005 - 21:03:07 CDT)
  • Re: Velocity after heating (Mon Jul 18 2005 - 13:35:44 CDT)
  • Re: Velocity after heating (Mon Jul 18 2005 - 12:18:52 CDT)
  • Re: psfgen patches (Thu Jul 14 2005 - 17:10:06 CDT)
  • Re: Unable to Generate PSF file ! (Mon Jul 04 2005 - 14:01:14 CDT)
  • RE: Unable to Generate PSF file ! (Mon Jul 04 2005 - 11:42:44 CDT)
  • RE: Unable to Generate PSF file ! (Mon Jul 04 2005 - 10:06:46 CDT)
  • RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) (Wed Jun 29 2005 - 11:18:23 CDT)
  • RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) (Wed Jun 29 2005 - 09:40:41 CDT)
• jcm203_at_soton.ac.uk
  • Energy due to electric field (Tue Apr 04 2006 - 09:09:18 CDT)
  • energy due to electric field (Wed Mar 08 2006 - 11:45:52 CST)
  • Electric Field (Wed Feb 22 2006 - 10:17:39 CST)
• Jerome Henin
  • Re: FEP & different ligands (Mon Dec 11 2006 - 11:29:59 CST)
  • Re: Tcl_Forces = pressure shifts while Langevin Piston is ON (Tue Dec 05 2006 - 12:19:31 CST)
  • Re: problem w/ free energy perturbation (Wed Nov 29 2006 - 20:04:53 CST)
  • Re: distorsion in hydrogens added (Tue Nov 21 2006 - 14:25:05 CST)
  • Re: distorsion in hydrogens added (Tue Nov 21 2006 - 09:47:17 CST)
  • Re: ABF (fwd) (Tue Nov 14 2006 - 18:52:10 CST)
  • Re: ABF (fwd) (Tue Nov 14 2006 - 08:49:03 CST)
  • Re: Reproducing free energy profile for acetate-guanidinium association (Tue Nov 14 2006 - 08:21:38 CST)
  • Re: Question about ABF (Wed Oct 25 2006 - 19:01:33 CDT)
  • Re: deformed water box after heating (Tue Oct 24 2006 - 10:18:20 CDT)
  • Re: problem with reassigning temperature (Sun Oct 15 2006 - 11:29:54 CDT)
  • Re: simulation in nve ensemble (Sat Oct 14 2006 - 10:07:51 CDT)
  • Re: "wrapAll on" with a complex (Thu Oct 05 2006 - 22:08:18 CDT)
  • Re: "measure" command (Wed Sep 27 2006 - 19:30:44 CDT)
  • Re: about abf (Wed Sep 27 2006 - 15:31:02 CDT)
  • Re: how add bond in psf file? (Mon Sep 25 2006 - 10:16:03 CDT)
  • Re: combined QM/MM calculation with NAMD (Thu Sep 14 2006 - 11:49:41 CDT)
  • Re: History file of an ABF smiulation (Sat Sep 09 2006 - 15:16:55 CDT)
  • Re: alchemical transformation (Thu Aug 17 2006 - 14:44:27 CDT)
  • Re: extracting waters from DCD (Wed Aug 09 2006 - 10:26:26 CDT)
  • Re: extracting waters from DCD (Tue Aug 08 2006 - 15:55:01 CDT)
  • Re: questions regarding output data of an ABF simulation (Mon Aug 07 2006 - 18:50:20 CDT)
  • Re: questions regarding output data of an ABF simulation (Mon Aug 07 2006 - 17:02:43 CDT)
  • Re: Problem with Alchemical FEP (Mon Aug 07 2006 - 15:24:03 CDT)
  • Re: Simulation of a 1000 water molecules (Thu Aug 03 2006 - 16:35:29 CDT)
  • Re: FEP implementation in NAMD - ERRATUM (Thu Aug 03 2006 - 11:01:54 CDT)
  • New alchemical FEP tutorial (Fri Jul 28 2006 - 14:13:40 CDT)
  • Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) (Wed Jun 21 2006 - 17:34:23 CDT)
  • Re: question about total charge change in FEP calculation (Fri Jun 09 2006 - 10:20:01 CDT)
  • Re: Repeating again: Periodic velocity pulls (Tue May 30 2006 - 19:00:02 CDT)
  • Re: Re: ABF: example works; more questions. (Tue May 30 2006 - 16:31:58 CDT)
  • Re: box size changes under anisotropic pressure coupling (Fri Apr 08 2005 - 13:44:19 CDT)
  • Re: FEP output in NAMD (Fri Apr 08 2005 - 13:37:41 CDT)
• Jerry Ebalunode
  • RE: Clustering of conformation (Tue Apr 18 2006 - 11:12:22 CDT)
  • Re: NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers (Fri Aug 19 2005 - 13:33:42 CDT)
  • RE: par_all27_prot_lipid.inp (Fri Aug 19 2005 - 10:59:10 CDT)
  • RE: errno = 2 (Thu Aug 18 2005 - 14:02:21 CDT)
  • RE: errno = 2 (Wed Aug 17 2005 - 16:08:51 CDT)
  • RE: errno = 2 (Wed Aug 17 2005 - 14:05:48 CDT)
  • undefined symbol errors:__builtin_bzero and _alloca building mpi-ppc-darwin version of namd2.6b1 (Wed Aug 17 2005 - 13:58:40 CDT)
  • Re: MM/PBSA (Mon Jun 13 2005 - 18:22:51 CDT)
  • Re: problem running namd (Mon Apr 04 2005 - 16:44:44 CDT)
  • Re: problem running namd (Mon Apr 04 2005 - 15:21:38 CDT)
  • Re: problem running namd (Mon Apr 04 2005 - 14:15:19 CDT)
  • Re: Submitting jobs on myrinet...problem (Fri Mar 11 2005 - 22:21:55 CST)
  • Re: Compiling NAMD with mpicc myrinet (Thu Mar 10 2005 - 15:45:54 CST)
  • atom specification in smd/tclforces for amber topology/parameter based systems (Mon Mar 07 2005 - 14:50:20 CST)
• Jerry Parks
  • RE: removing water from DCD (Thu Jul 21 2005 - 11:27:43 CDT)
  • NAMD/iAPBS (Fri Jul 08 2005 - 16:19:15 CDT)
• Jerry Xu
  • how to restart/continue NAMD run (Fri May 06 2005 - 11:28:33 CDT)
  • Hi, call NAMD from C (Mon Jan 31 2005 - 09:28:44 CST)
• Jianping Wang
  • Re: Radial Distribution Function (Fri Jun 17 2005 - 13:55:40 CDT)
• Jim Kress
  • It appears that the Claim that NAMD works with gromacs is false (Sat Jul 16 2005 - 19:43:42 CDT)
• Jim Phillips
  • Free Linux Cluster-Building Workshop - 30 Nov 2006 - 01 Dec 2006 (Mon Oct 16 2006 - 16:13:52 CDT)
  • Re: how add bond in psf file? (Thu Oct 05 2006 - 15:18:57 CDT)
  • Re: imprecision in table energy (Mon Sep 25 2006 - 14:10:00 CDT)
  • Re: how add bond in psf file? (Mon Sep 25 2006 - 14:05:27 CDT)
  • Re: NAMD installation on Cray XD1 (AMD opteron 64-bit) (Mon Sep 25 2006 - 14:02:20 CDT)
  • Re: Altix Performance Tuning (Wed Sep 20 2006 - 00:07:00 CDT)
  • Re: NAMD installation on Xeon64 cluster (Tue Sep 19 2006 - 23:53:08 CDT)
  • Re: Water Hole (Tue Sep 19 2006 - 23:47:10 CDT)
  • Re: NAMD installation on Xeon64 cluster (Sun Sep 17 2006 - 01:03:04 CDT)
  • Re: load balancer, athlon 64 dual core (Thu Sep 14 2006 - 23:15:51 CDT)
  • Re: Rigid body minimization (Thu Sep 14 2006 - 23:04:47 CDT)
  • Re: load balancer, athlon 64 dual core (Wed Sep 13 2006 - 15:33:49 CDT)
  • Re: parameter file name (Sun Sep 10 2006 - 14:53:20 CDT)
  • Re: Constraining angles ?? (Fri Sep 08 2006 - 17:42:19 CDT)
  • Re: Morse potential? (Fri Sep 08 2006 - 17:25:32 CDT)
  • Re: clarification(s) Re: namd 2.62b FATAL ERROR: Memory allocation failed on processor 0 or higher (Fri Sep 08 2006 - 17:23:12 CDT)
  • Re: namd 2.62b FATAL ERROR: Memory allocation failed on processor 0 or higher (Thu Sep 07 2006 - 01:54:39 CDT)
  • Re: Win64 version (Thu Sep 07 2006 - 01:45:46 CDT)
  • Re: atom name based paremeters (Tue Sep 05 2006 - 23:40:58 CDT)
  • Re: Re: vmd-l: Angles and dihedral generation (Mon Sep 04 2006 - 16:44:44 CDT)
  • Re: minimization of a cyclic peptide with NAMD (Mon Sep 04 2006 - 16:20:42 CDT)
  • Re: problem with Dihedral Restraints (Mon Sep 04 2006 - 16:17:31 CDT)
  • Re: namd 2.62b FATAL ERROR: Memory allocation failed on processor 0 or higher (Sun Sep 03 2006 - 22:30:13 CDT)
  • Re: vmd-l: CoordinateTransformation (Sun Sep 03 2006 - 21:59:46 CDT)
  • Re: vmd-l: Angles and dihedral generation (Sat Sep 02 2006 - 15:25:12 CDT)
  • Re: Minimization algorithms (Thu Aug 31 2006 - 15:38:49 CDT)
  • Re: Patches & psfgen (Thu Aug 31 2006 - 15:24:36 CDT)
  • Re: mass of atoms changable? (Wed Aug 30 2006 - 19:52:50 CDT)
  • NAMD 2.6 released (Wed Aug 30 2006 - 15:18:36 CDT)
  • Re: NAMD2.6b2: Segmentation fault (Tue Aug 29 2006 - 16:13:45 CDT)
  • Re: NAMD2.6b2: Segmentation fault (Tue Aug 29 2006 - 15:01:42 CDT)
  • Re: Segmentation violation from APOA1 simulation on AMD64 (Tue Aug 29 2006 - 14:51:41 CDT)
  • Re: Fat node (Tue Aug 29 2006 - 14:19:47 CDT)
  • Re: Type of force values in the tclForces script. (Fri Aug 25 2006 - 14:25:52 CDT)
  • Re: NAMD2.6b2: Segmentation fault (Mon Aug 21 2006 - 15:05:37 CDT)
  • Re: why this error? (Mon Aug 21 2006 - 14:55:04 CDT)
  • NAMD 2.6b1 released (Thu Aug 17 2006 - 18:24:22 CDT)
  • Re: slow NAMD simulations on a AMD athlon64 in SUSE linux (Wed Jun 14 2006 - 18:24:28 CDT)
  • Re: Velocity unit ofvelocity in NAMD the binary files (Wed Jun 14 2006 - 18:13:49 CDT)
  • RE: trying to generate a peptide (Wed Oct 26 2005 - 09:39:56 CDT)
  • Re: SGE (Grid Engine) on Rocks Cluster (Wed Oct 19 2005 - 17:42:20 CDT)
  • Re: NAMD2.6b1 on an OSX cluster (Thu Aug 25 2005 - 18:36:34 CDT)
  • Re: About the command "loadtotalforces" (Thu Aug 25 2005 - 18:14:34 CDT)
  • Re: peptide out of the water-box (Thu Aug 25 2005 - 18:08:52 CDT)
  • Re: Pressure Profile Simulation (Thu Aug 25 2005 - 18:00:25 CDT)
  • Re: namd 6-1- abf (Mon Aug 22 2005 - 18:35:49 CDT)
  • Re: NBFix command to apply Lorentz-Berthelot mixing rules (Mon Aug 22 2005 - 18:33:41 CDT)
  • Re: NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers (Mon Aug 22 2005 - 18:23:48 CDT)
  • Re: Compilation of NAMD on 64-bit NUMA (Mon Aug 22 2005 - 17:47:52 CDT)
  • Re: vdwGeometricSigma for OPLS in NAMD 2.6b1 Release (Mon Aug 22 2005 - 17:40:53 CDT)
  • Re: volume from VMD and NAMD different? (Fri Aug 05 2005 - 17:46:25 CDT)
  • 4th Annual Workshop on Charm++ and its Applications 2005 (Fri Aug 05 2005 - 17:40:30 CDT)
  • Re: volume from VMD and NAMD different? (Fri Aug 05 2005 - 17:34:45 CDT)
  • Re: error running namd (Fri Aug 05 2005 - 12:48:40 CDT)
  • Re: Running NAMD on a multiprocessor computer (Fri Aug 05 2005 - 12:44:31 CDT)
  • Re: error in config file (Fri Aug 05 2005 - 12:36:07 CDT)
  • Re: LDB question (Fri Aug 05 2005 - 12:28:10 CDT)
  • Re: Fatal error: (Fri Aug 05 2005 - 11:17:30 CDT)
  • Re: H-H bond in TIP3 water (Fri Aug 05 2005 - 11:11:15 CDT)
  • Re: shake and minimzation, equilibration (Fri Aug 05 2005 - 10:58:09 CDT)
  • Re: rigidBond water (Fri Aug 05 2005 - 10:54:44 CDT)
  • Re: velocity quenching (Fri Aug 05 2005 - 10:52:37 CDT)
  • Re: 2.6b1 source missing file (Fri Aug 05 2005 - 10:42:38 CDT)
  • NAMD 2.6b1 Released (Fri Jul 29 2005 - 18:55:59 CDT)
• JIMENEZ Ralph
  • successive minimization with different sets of fixed atoms (Tue Dec 06 2005 - 11:14:25 CST)
  • more heme troubles (Thu Oct 06 2005 - 16:14:45 CDT)
  • psfgen trouble with heme (Wed Oct 05 2005 - 14:54:26 CDT)
  • unexpected end with NAMD on quad-dual core opteron machine (Thu Sep 29 2005 - 12:59:42 CDT)
• Jimmy Tang
  • Re: namd/charm infiniband build (Tue Nov 07 2006 - 10:17:37 CST)
  • Re: dual core processors (Fri Mar 31 2006 - 12:38:24 CST)
  • Re: Building cluster (Sun Mar 19 2006 - 05:01:17 CST)
  • NAMD not starting calculations... (Thu Feb 16 2006 - 08:00:34 CST)
• Jindal Shah
  • calculation of non-bonded interactions (Mon Oct 23 2006 - 09:55:59 CDT)
  • Re: vdW parameters (Wed Aug 30 2006 - 15:04:16 CDT)
  • vdW parameters (Wed Aug 30 2006 - 10:38:19 CDT)
  • Re: DCD to PDB conversion (Tue Jun 13 2006 - 14:15:47 CDT)
  • Re: DCD file (Thu May 18 2006 - 08:35:17 CDT)
  • Water liquid-vapor interface (Thu May 11 2006 - 13:24:43 CDT)
  • PSF file (Tue Jan 17 2006 - 13:21:49 CST)
  • PSF file format (Tue Dec 20 2005 - 15:55:23 CST)
  • Re: vmd-l: Script for calculating energy of a water molecule (Wed Aug 17 2005 - 17:07:12 CDT)
  • Script for calculating energy of a water molecule (Wed Aug 17 2005 - 11:41:23 CDT)
• Joachim Hein
  • Re: namd2 on IBM P5 hangs (Mon Apr 24 2006 - 12:26:30 CDT)
  • Building NAMD 2.6b1 on IBM Power5 (Tue Dec 06 2005 - 03:49:53 CST)
  • Re: Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4 (Mon Nov 21 2005 - 04:12:05 CST)
  • Re: namd and fftw (Tue Mar 15 2005 - 03:56:13 CST)
• John Eargle
  • Re: HIS to HSD, HSE, and HSP (Tue Feb 14 2006 - 17:05:33 CST)
  • HIS to HSD, HSE, and HSP (Tue Feb 14 2006 - 14:48:05 CST)
• John Kerrigan
  • Re: peridic boundary condition (Fri Mar 11 2005 - 15:18:48 CST)
• John Saeger
  • Re: installing NAMD on opteron cluster with MPI (Wed Mar 09 2005 - 15:12:08 CST)
  • Re: clustermatic 4 and 5 Namd/charm (Sun Jan 02 2005 - 14:18:31 CST)
• John Stone
  • Re: vmd-l: error using Namdenergy (Thu Jun 22 2006 - 15:06:12 CDT)
  • Re: vmd-l: one residue rmsd (Tue May 02 2006 - 11:00:59 CDT)
  • Re: vmd-l: boubt about consistency of measures (Mon Mar 27 2006 - 00:47:16 CST)
  • Re: vmd-l: force over selection (Thu Mar 23 2006 - 10:26:50 CST)
  • Re: vmd-l: energy calculation in VMD (Wed Mar 22 2006 - 16:48:08 CST)
  • Re: vmd-l: VMD Command (Tue Mar 21 2006 - 01:17:36 CST)
  • Re: vmd-l: is possible to remove the waterbox before running VMD (Thu Mar 09 2006 - 10:39:27 CST)
  • Re: vmd-l: is possible to remove the waterbox before running VMD (Thu Mar 09 2006 - 10:40:39 CST)
  • Re: vmd-l: a display problem (Thu Mar 09 2006 - 10:33:27 CST)
  • Re: vmd-l: Problem with VMD 'animate' command (Tue Feb 14 2006 - 10:32:20 CST)
  • Re: vmd-l: Problem with VMD 'animate' command (Sun Feb 12 2006 - 16:02:36 CST)
  • Re: vmd-l: 64 bit NAMD on AIX and CatDCD (Mon Jan 23 2006 - 13:21:14 CST)
  • Re: vmd-l: CMAP problem (Tue Jan 03 2006 - 14:39:37 CST)
  • Re: vmd-l: CMAP problem (Tue Jan 03 2006 - 14:05:32 CST)
  • Re: vmd-l: ptraj (Tue Sep 27 2005 - 09:57:34 CDT)
  • Re: vmd-l: Sybyl trajectory (Tue Sep 06 2005 - 09:43:23 CDT)
  • Re: vmd-l: Script for calculating energy of a water molecule (Wed Aug 17 2005 - 14:32:41 CDT)
  • Re: vmd-l: Nanotube Simulations (Tue Aug 02 2005 - 12:34:58 CDT)
  • Re: vmd-l: Re: catdcd and dcdunitcell (Mon Jul 25 2005 - 13:50:03 CDT)
  • Re: vmd-l: autoimd on windows (Tue Jun 21 2005 - 15:43:11 CDT)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Thu Apr 28 2005 - 13:05:40 CDT)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Thu Apr 28 2005 - 10:08:17 CDT)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Thu Apr 21 2005 - 16:28:08 CDT)
  • Re: vmd-l: Interactive Simulations, ligand size limits.... (Wed Apr 20 2005 - 16:12:20 CDT)
  • Re: vmd-l: conformational alignment (Wed Mar 30 2005 - 15:30:26 CST)
• John Wise
  • Re: psfgen gets ATP chiral atoms wrong (Tue Jul 25 2006 - 14:46:35 CDT)
  • psfgen gets ATP chiral atoms wrong (Mon Jul 24 2006 - 15:43:23 CDT)
• jonas condes
  • SMD of TFIIB! (Thu Aug 24 2006 - 13:57:52 CDT)
  • SMD of TFIIB (Fri Aug 18 2006 - 14:40:46 CDT)
• Jonathan D. Proulx
  • Building for SunGrid (Tue Aug 15 2006 - 09:05:38 CDT)
• jonathan_at_ibt.unam.mx
  • Re: Warnings of psfgen (Wed Oct 25 2006 - 15:30:30 CDT)
  • Re: Fat node (Fri Sep 22 2006 - 21:47:32 CDT)
  • Fat node (Mon Aug 28 2006 - 21:02:13 CDT)
  • Re: other crystal types in NAMD ? (Tue Apr 04 2006 - 15:24:31 CDT)
  • Re: other crystal types in NAMD ? (Tue Apr 04 2006 - 13:53:00 CDT)
  • Re: DCD file really corrupt? (Wed Mar 29 2006 - 11:55:40 CST)
  • Re: Counterions: how to decide how many to put it? (Tue Dec 13 2005 - 21:05:34 CST)
• Jordi Camps
  • RE: Parallelization method (Thu Dec 14 2006 - 12:04:34 CST)
  • Parallelization method (Thu Dec 14 2006 - 11:33:38 CST)
  • RE: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 10 2005 - 18:08:02 CST)
  • Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 10 2005 - 12:57:47 CST)
• Jordi Cohen
  • Re: vmd-l: Nanotube Simulations (Tue Aug 02 2005 - 14:41:03 CDT)
• Jorge Pikunic
  • RE: problems reading large dcd file (Wed Jan 11 2006 - 09:06:59 CST)
  • RE: problems reading large dcd file (Tue Jan 10 2006 - 10:20:35 CST)
  • problems reading large dcd file (Fri Jan 06 2006 - 10:45:54 CST)
  • H-H bond in TIP3 water (Mon Aug 01 2005 - 17:21:26 CDT)
  • Re: H-H bond in solvate (Sat Jul 30 2005 - 09:35:13 CDT)
  • H-H bond in solvate (Sat Jul 30 2005 - 08:57:59 CDT)
  • concatenating two or more dcd files (Mon Apr 18 2005 - 10:44:07 CDT)
• Josef Scheiber
  • Re: vmd-l: Sybyl trajectory (Tue Sep 06 2005 - 05:38:38 CDT)
  • Sybyl trajectory (Mon Sep 05 2005 - 01:56:04 CDT)
  • Re: socket closed error (Tue Mar 29 2005 - 01:01:34 CST)
• Joshua A. Speidel
  • Re: extracting waters from DCD (Wed Aug 09 2006 - 09:42:34 CDT)
• Joshua D. Moore
  • Update on NAMD on BlueGene/TCL (Tue Dec 19 2006 - 15:20:47 CST)
  • TCL Forces and Help on Script (Thu Jul 06 2006 - 13:52:00 CDT)
  • Re: Calculating or Outputing Forces (Thu Jun 29 2006 - 12:55:38 CDT)
  • Re: Calculating or Outputing Forces (Wed Jun 28 2006 - 14:18:56 CDT)
  • Calculating or Outputing Forces (Mon Jun 26 2006 - 21:00:44 CDT)
  • Re: Is the GBSA model in NAMD ? (Tue Jun 13 2006 - 12:32:49 CDT)
  • NDON! and NACC! in Parameter Files (Thu May 18 2006 - 19:10:28 CDT)
  • Rigid bonds for United Atom Methylene Chloride CH2Cl2 (Wed May 17 2006 - 15:22:41 CDT)
  • Re: Simulation with denaturants? (Sat Apr 29 2006 - 15:56:10 CDT)
  • RE: restart a simulation (Mon Apr 03 2006 - 14:17:39 CDT)
  • Re: DCD file really corrupt? (Wed Mar 29 2006 - 15:37:24 CST)
  • Question about memory usage (Fri Mar 17 2006 - 12:03:59 CST)
  • Re: Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file. (Sat Jan 21 2006 - 18:32:58 CST)
  • 64 bit NAMD on AIX and CatDCD (Sat Jan 21 2006 - 13:22:11 CST)
  • Re: question on the format of adding Lennard-Jones parameters (Thu Jan 19 2006 - 21:30:12 CST)
  • RE: problems reading large dcd file (Fri Jan 13 2006 - 21:32:42 CST)
  • RE: problems reading large dcd file (Tue Jan 10 2006 - 19:35:55 CST)
  • Re: problems reading large dcd file (Fri Jan 06 2006 - 23:22:43 CST)
  • ABSOLUTE IMPRECISION and RELATIVE IMPRECISION IN TABLE FORCE (Fri Dec 23 2005 - 03:01:17 CST)
  • Re: UNABLE TO OPEN .psf FILE (Fri Dec 23 2005 - 02:56:34 CST)
  • UNABLE TO OPEN .psf FILE (Fri Dec 23 2005 - 02:53:00 CST)
  • Re: Question about Generating DCD files with only specified atoms (Thu Dec 22 2005 - 22:23:02 CST)
  • Re: Besides PSFGEN, are there any other good ways of generating .psf file (Thu Dec 22 2005 - 21:01:31 CST)
  • Question about Generating DCD files with only specified atoms (Thu Dec 22 2005 - 18:06:09 CST)
  • Re: The HT-HT-OT angle parameter for TIP3? (Thu Dec 22 2005 - 18:03:57 CST)
  • Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7 (Wed Dec 21 2005 - 16:57:37 CST)
  • flipDCD and Unit Cell information? (Mon Dec 19 2005 - 17:54:06 CST)
  • Re: Packaging 100 cations and anions in a box (Wed Dec 07 2005 - 02:25:23 CST)
  • Re: merge trajectory from NAMD (Wed Nov 30 2005 - 21:43:13 CST)
  • Update on Implicit Solvent Models in NAMD? (Fri Nov 25 2005 - 14:01:31 CST)
  • Using an arbitrary tabulated potential in NAMD (Tue Sep 27 2005 - 21:44:26 CDT)
  • Re: Free Energy of Conformational Change Calculations Error: "Problem parsing input parameters Error: Invalid AtomID" (Sat Sep 10 2005 - 17:49:26 CDT)
  • Free Energy of Conformational Change Calculations Error: "Problem parsing input parameters Error: Invalid AtomID" (Thu Sep 08 2005 - 22:13:17 CDT)
  • Re: pair interactions in NPT (Sun Sep 04 2005 - 18:12:59 CDT)
  • NAMD 2.6b1 Skipped Writing Velocity Restart File (Tue Aug 30 2005 - 01:09:20 CDT)
  • NBFix command to apply Lorentz-Berthelot mixing rules (Sun Aug 21 2005 - 14:45:59 CDT)
  • Re: Large Box Sizes and Total Energies Observed in NAMD 2.6b1 Binaries of AIX-POWER-MPI and Origin2000-MPI (Fri Aug 19 2005 - 14:42:02 CDT)
  • Re: Large Box Sizes and Total Energies Observed in NAMD 2.6b1 Binaries of AIX-POWER-MPI and Origin2000-MPI (Fri Aug 19 2005 - 06:38:04 CDT)
  • Large Box Sizes and Total Energies Observed in NAMD 2.6b1 Binaries of AIX-POWER-MPI and Origin2000-MPI (Thu Aug 18 2005 - 17:35:21 CDT)
  • Linux-MPI binary of NAMD 2.6b1 (Thu Aug 18 2005 - 06:09:41 CDT)
  • Re: vdwGeometricSigma for OPLS in NAMD 2.6b1 Release (Sat Aug 13 2005 - 03:21:44 CDT)
  • vdwGeometricSigma for OPLS in NAMD 2.6b1 Release (Wed Aug 10 2005 - 18:59:45 CDT)
  • Re: For help with .log file. (Sun Aug 07 2005 - 23:43:30 CDT)
  • Re: VMD solvate in CCl4 (Tue Jul 26 2005 - 20:55:03 CDT)
  • Re: vmd-l: Re: catdcd and dcdunitcell (Mon Jul 25 2005 - 14:16:16 CDT)
  • Fixed atoms and dcd file with DCDunitCell on (Fri Jul 22 2005 - 16:46:15 CDT)
  • Re: catdcd and dcdunitcell (Fri Jul 22 2005 - 16:04:00 CDT)
  • SPC/E Water Model and RigidBonds (Fri Jul 08 2005 - 15:46:41 CDT)
  • Periodic Boundary Conditions and Wrap (Tue Jun 28 2005 - 03:31:38 CDT)
  • Zeros at the beginning of each line in the output (Thu Jun 23 2005 - 19:17:43 CDT)
  • RE: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Wed Jun 22 2005 - 00:58:48 CDT)
  • Error when running NAMD at SDSC (Sun Jun 19 2005 - 22:13:20 CDT)
  • rigidBonds water (Sun Jun 05 2005 - 21:39:09 CDT)
  • Re: Converting Gromacs OPLS parameters to Charmm format (Tue May 17 2005 - 17:35:18 CDT)
• jsachs_at_mail.csb.yale.edu
  • Re: Alchemical Free Energy Perturbation (Wed Mar 01 2006 - 15:31:07 CST)
  • Re: Alchemical Free Energy Perturbation (Tue Feb 28 2006 - 10:00:13 CST)
  • atom restraints (Wed Jan 18 2006 - 15:02:26 CST)
• Juan Diaz
  • Correlation Functions (Tue Dec 12 2006 - 14:39:52 CST)
  • Correlation Functions (Tue Dec 12 2006 - 14:24:47 CST)
• junwang
  • the lastest version of NAMD source (Sun May 29 2005 - 12:29:35 CDT)
  • Compilation of NAMD on opteron cluster with myrinet (Mon May 23 2005 - 19:44:41 CDT)
• Jyh-Shyong Ho
  • FFTW problem (Wed Sep 27 2006 - 04:02:57 CDT)
  • NAMD/CHARM source installation option (Sat Dec 17 2005 - 23:36:55 CST)
• jz7_at_duke.edu
  • error estimate in FEP calculation (Tue Oct 24 2006 - 23:18:27 CDT)
  • Re: question about total charge change in FEP calculation (Thu Jun 08 2006 - 15:28:21 CDT)
  • please help-large energy change during FEP calculation (Thu Jun 08 2006 - 12:13:31 CDT)
  • Re: question about total charge change in FEP calculation (Thu Jun 08 2006 - 10:16:23 CDT)
  • Re: FEP error "atoms moving too fast" (Mon Jun 05 2006 - 12:25:08 CDT)
  • FEP error "atoms moving too fast" (Sun Jun 04 2006 - 10:39:37 CDT)
  • question about total charge change in FEP calculation (Thu Mar 02 2006 - 10:01:23 CST)
  • question about FEP calculation (Wed Mar 01 2006 - 11:11:37 CST)
  • how to do free energy perturbation calculation in NAMD? (Tue Feb 07 2006 - 11:21:39 CST)
  • question about patch (Thu Mar 24 2005 - 09:33:04 CST)
• Jérôme Hénin
  • Re: unit cell information from dcd file (Thu Jul 20 2006 - 13:39:27 CDT)
  • Re: Help on mutation (Wed Jul 05 2006 - 16:36:22 CDT)
  • Re: smd dimer dissociation (Thu Apr 27 2006 - 12:21:30 CDT)
• Jérôme Hénin
  • Re: FEP implementation in NAMD (Wed Aug 02 2006 - 21:16:17 CDT)
  • Re: TCL Forces and Help on Script (Thu Jul 06 2006 - 15:41:32 CDT)
  • Re: smd dimer dissociation (Tue Apr 25 2006 - 13:32:10 CDT)
  • Re: custom pulling path (Wed Apr 19 2006 - 16:20:29 CDT)
  • Re: reconstructing PMF (Thu Apr 13 2006 - 04:10:48 CDT)
  • Re: FEP in vacuum (Fri Mar 10 2006 - 11:36:03 CST)
  • Re: Pressure -ve (Wed Mar 08 2006 - 11:32:21 CST)
  • Re: Alchemical Free Energy Perturbation (Thu Mar 02 2006 - 07:39:16 CST)
  • Re: Alchemical Free Energy Perturbation (Tue Feb 28 2006 - 12:50:00 CST)
  • Re: Alchemical Free Energy Perturbation (Tue Feb 28 2006 - 09:03:55 CST)
  • Re: how to do free energy perturbation calculation in NAMD? (Mon Feb 13 2006 - 07:23:50 CST)
  • Re: Reading from DCD file and running MD (Wed Dec 07 2005 - 16:19:08 CST)
  • Re: ABF for conformational analysis (Mon Nov 14 2005 - 03:34:21 CST)
  • Re: ABF Simulation (Fri Oct 28 2005 - 04:05:52 CDT)
  • Re: ABF Simulation (Wed Oct 19 2005 - 04:11:17 CDT)
  • Re: ABF Simulation (Wed Oct 05 2005 - 11:35:25 CDT)
  • Re: abf (Tue Sep 06 2005 - 08:48:25 CDT)
  • Re: changing file (Wed Jul 20 2005 - 05:07:19 CDT)
  • Re: setting configuration file for free energy perturbation (Mon Jul 18 2005 - 12:18:39 CDT)
  • Re: Energy Order of Magnitude (Mon Jul 11 2005 - 14:49:49 CDT)
  • Re: FEP - one long simulation vs many short ones (Sat Jul 02 2005 - 18:45:11 CDT)
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 10:54:09 CDT)
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 09:14:32 CDT)
  • Re: Accessing beta / occupancy values from NAMD tcl (Mon Jun 27 2005 - 11:52:05 CDT)
  • Re: Using FEP as non-disruptive mutation procedure (Mon Jun 27 2005 - 05:19:37 CDT)
  • Re: new approach to counter FEP end-point VDW clashes (Mon Jun 27 2005 - 03:31:34 CDT)
  • Re: Tcl forces (Thu Jun 16 2005 - 07:19:13 CDT)
  • Re: non-repeatability NAMD simulations (Wed May 11 2005 - 03:00:55 CDT)
  • Re: different result from different cpu (Tue May 10 2005 - 11:40:25 CDT)
  • Re: addforce (Tue Apr 19 2005 - 11:21:21 CDT)
  • Re: peridic boundary condition (Fri Mar 11 2005 - 15:31:47 CST)
  • Re: CAN'T FIND BOND PARAMETERS FOR BOND (error) (Thu Mar 10 2005 - 07:59:14 CST)
  • Re: CAN'T FIND BOND PARAMETERS FOR BOND (error) (Thu Mar 10 2005 - 05:16:35 CST)
  • Re: writeback periodic cell info in dcd output (Mon Feb 21 2005 - 17:49:55 CST)
  • Re: alchemify FEP (Thu Feb 17 2005 - 15:04:18 CST)
  • Re: Protein moving out of PBC water box (Tue Feb 08 2005 - 17:08:05 CST)
  • Re: FEP (Tue Feb 01 2005 - 13:14:05 CST)
  • Re: thermodynamic integration and NAMD: soft-core or "separation-shifted" vdw potentials (Mon Jan 10 2005 - 15:57:01 CST)
  • Re: parameters for NVT ensemble (Fri Jan 07 2005 - 07:58:12 CST)
• Karina Martinez
  • Compliling NAMD in RedHat9 (Wed May 11 2005 - 21:59:28 CDT)
• Karunesh Arora
  • NAMD crashes with LES option ON (Mon Feb 07 2005 - 14:07:18 CST)
• Kasson
  • Gromacs parameters in NAMD (Thu Oct 20 2005 - 13:21:06 CDT)
• Klon, Anthony
  • Tcl parsing of NAMD config file does not work. (Thu Jul 20 2006 - 07:43:09 CDT)
• Koo Kee Kiat
  • Errors compiling NAMD 2.5 (Mon Apr 04 2005 - 01:46:34 CDT)
• Kramer Campen
  • Cham++ errors (Tue Aug 08 2006 - 15:01:07 CDT)
  • Using LES with AMBER parm files (Wed Aug 02 2006 - 14:35:05 CDT)
• Kyle Gustafson
  • volume exclusion (Thu Mar 09 2006 - 09:51:30 CST)
  • rigid bonds for other atoms (Thu Oct 06 2005 - 13:40:23 CDT)
  • Re: mpi problems on opteron (Thu Aug 04 2005 - 07:54:20 CDT)
  • Re: shape change of water box and peptide move out (Fri Jul 29 2005 - 16:46:11 CDT)
  • opteron 64bit installation (Fri Jul 29 2005 - 10:29:11 CDT)
  • compiling NAMD: plugins (Mon Jul 25 2005 - 19:53:01 CDT)
  • Re: mpi problems on opteron (Mon Jul 25 2005 - 19:04:56 CDT)
  • mpi problems on opteron (Mon Jul 25 2005 - 16:05:02 CDT)
  • NAMD on dual opterons (Mon Jul 25 2005 - 13:30:44 CDT)
• L. Michel Espinoza-Fonseca
  • simulation of membrane-protein systems (Mon Dec 18 2006 - 10:16:08 CST)
  • Re: simulation of membrane-protein systems (Fri Dec 15 2006 - 02:24:01 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 11:38:11 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 11:19:01 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 11:12:13 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 08:23:15 CST)
  • simulation of membrane-protein systems (Wed Dec 13 2006 - 02:01:41 CST)
  • Re: clustering conformations (Mon Nov 20 2006 - 14:49:16 CST)
  • Re: rigid protein (Thu Oct 19 2006 - 10:38:33 CDT)
  • Re: rigid protein (Thu Oct 19 2006 - 10:14:21 CDT)
  • Re: Poisson Boltzmann with NAMD (Wed Sep 06 2006 - 20:34:49 CDT)
  • Re: About CHARMM charge (Mon Aug 28 2006 - 10:10:05 CDT)
  • Re: Lipid into NAMD (Sun Aug 20 2006 - 18:44:38 CDT)
  • Re: Problem with Alchemical FEP (Mon Aug 07 2006 - 11:38:09 CDT)
  • Re: atom type HZ4 not found (Sat Aug 05 2006 - 16:10:33 CDT)
  • Re: coordination chemistry with NAMD (Fri Aug 04 2006 - 10:50:30 CDT)
  • Re: Simulation of a 1000 water molecules (Thu Aug 03 2006 - 14:34:47 CDT)
  • Re: coordination chemistry with NAMD (Wed Aug 02 2006 - 14:34:00 CDT)
  • Re: Autopsf (Fri Jul 21 2006 - 16:49:34 CDT)
  • Re: any SD minimization in NAMD? (Fri Jul 14 2006 - 11:36:09 CDT)
  • Re: many short runs or one long run? (Mon Jul 10 2006 - 15:29:02 CDT)
  • Re: Vibrational mode analysis (Thu Jun 15 2006 - 20:52:28 CDT)
  • Re: Vibrational mode analysis (Thu Jun 15 2006 - 19:47:29 CDT)
  • CMAP and NAMD (Mon Jun 05 2006 - 19:16:21 CDT)
  • Re: namd: adding water molecules (Thu May 11 2006 - 01:34:12 CDT)
  • Re: CMAP (Wed May 10 2006 - 14:52:43 CDT)
  • les + conformational free energy (Tue May 09 2006 - 08:31:51 CDT)
  • Re: convert .dcd into .trr (Tue May 02 2006 - 13:07:47 CDT)
  • Re: minimum energy frame (Wed Apr 26 2006 - 10:01:01 CDT)
  • smd dimer dissociation (Tue Apr 25 2006 - 11:24:12 CDT)
  • simulated annealing with explicit water (Mon Apr 24 2006 - 05:37:30 CDT)
  • Re: Clustering of conformation (Tue Apr 18 2006 - 05:08:07 CDT)
  • Re: Developing topologies for modified NA residues? (Mon Apr 10 2006 - 12:00:55 CDT)
  • namd + opteron/xeon (Mon Apr 10 2006 - 11:55:56 CDT)
  • Re: a display problem (Thu Mar 09 2006 - 10:53:08 CST)
  • Re: starting simulation in charmm, continuing in NAMD ? (Sun Mar 05 2006 - 15:19:44 CST)
  • Re: tutorial address (Sat Feb 25 2006 - 08:06:21 CST)
  • Re: Fwd: Water Box size (Thu Feb 16 2006 - 12:23:23 CST)
  • Re: Fwd: Water Box size (Wed Feb 15 2006 - 12:23:26 CST)
  • Re: Fwd: Water Box size (Wed Feb 15 2006 - 12:00:51 CST)
• Lacramioara Negureanu
  • topology file with CT carbon (Thu Aug 03 2006 - 19:46:59 CDT)
• laura
  • target molecular moves away from water box (Sun Oct 22 2006 - 20:18:11 CDT)
• Laurent Leger
  • Problem to run IMD simulation (Fri Feb 24 2006 - 04:29:29 CST)
• lc_at_chem.au.dk
  • Re: hydrogens collapsing (Tue Jan 18 2005 - 12:12:04 CST)
  • hydrogens collapsing (Tue Jan 18 2005 - 08:46:23 CST)
  • namdstats (Tue Jan 11 2005 - 01:54:54 CST)
  • parameters for NVT ensemble (Fri Jan 07 2005 - 04:51:07 CST)
• Lea Thøgersen
  • DCD file really corrupt? (Wed Mar 29 2006 - 06:27:09 CST)
  • NAMD on Win64 (Mon Dec 12 2005 - 10:26:11 CST)
• Leandro Martinez
  • using namd to compute energies (Tue Feb 15 2005 - 13:24:20 CST)
  • smd and loadforces (Mon Jan 17 2005 - 11:06:50 CST)
• Leandro Martínez
  • Re: protein unfolding -- Phi MD (Wed Nov 29 2006 - 10:51:50 CST)
  • Re: dcd file format (Sat Nov 25 2006 - 05:08:28 CST)
  • dcd file format (Fri Nov 24 2006 - 05:44:06 CST)
  • dcd file format (Fri Nov 24 2006 - 05:38:05 CST)
  • problems with paralellism (Thu Nov 23 2006 - 12:49:39 CST)
  • Re: compiling charm++ with g++ 4.1 (Mon Nov 20 2006 - 14:27:43 CST)
  • compiling charm++ with g++ 4.1 (Mon Nov 20 2006 - 10:26:22 CST)
  • Re: LES : size (Fri Nov 10 2006 - 13:00:53 CST)
  • Re: Waiting for 0-th client to connect. (Tue Oct 24 2006 - 13:15:28 CDT)
  • Waiting for 0-th client to connect. (Tue Oct 24 2006 - 12:50:07 CDT)
  • Re: deformed water box during equilibration. (Sat Oct 21 2006 - 10:45:09 CDT)
  • Re: missing info from NAMD output (Tue Oct 03 2006 - 14:51:10 CDT)
  • Re: load balancer, athlon 64 dual core (Thu Sep 14 2006 - 14:51:07 CDT)
  • Re: load balancer, athlon 64 dual core (Wed Sep 13 2006 - 08:00:53 CDT)
  • load balancer, athlon 64 dual core (Wed Sep 13 2006 - 07:06:08 CDT)
  • Re: Re: Info: Adjusted background load on 11 nodes. (Tue Aug 29 2006 - 07:13:51 CDT)
  • Re: Re: Info: Adjusted background load on 11 nodes. (Mon Aug 28 2006 - 12:21:49 CDT)
  • Re: Info: Adjusted background load on 11 nodes. (Fri Aug 25 2006 - 08:01:53 CDT)
  • Info: Adjusted background load on 11 nodes. (Fri Aug 25 2006 - 07:42:28 CDT)
  • Re: fix atoms in minimisation (Mon May 01 2006 - 15:20:56 CDT)
  • Re: smd dimer dissociation (Tue Apr 25 2006 - 12:10:13 CDT)
  • Re: simulated annealing with explicit water (Mon Apr 24 2006 - 07:15:34 CDT)
  • Re: custom pulling path (Wed Apr 19 2006 - 14:16:36 CDT)
  • dual core processors (Fri Mar 31 2006 - 11:04:01 CST)
  • Re: MD in a loop with different names for dcd files (Tue Mar 14 2006 - 12:41:32 CST)
  • Re: (Thu Feb 23 2006 - 11:45:04 CST)
  • Socket closed before recv. (Tue Feb 07 2006 - 05:18:05 CST)
  • Re: reading a binary restart file (Tue Jan 10 2006 - 16:10:31 CST)
  • reading a binary restart file (Tue Jan 10 2006 - 13:09:18 CST)
  • pause simulation (Fri Dec 16 2005 - 12:53:23 CST)
  • Re: center of mass motion: problems (Thu Dec 08 2005 - 17:49:23 CST)
  • Re: Question regarding SMD (Mon Oct 31 2005 - 17:26:23 CST)
  • Re: Only part of the protein is moving in MD simulation (Wed Oct 26 2005 - 10:58:19 CDT)
  • Re: mpi problems on opteron (Mon Jul 25 2005 - 19:11:13 CDT)
  • Re: mpi problems on opteron (Mon Jul 25 2005 - 19:00:04 CDT)
  • addforce (Tue Jun 14 2005 - 10:02:28 CDT)
  • interface with external program (Fri Jun 10 2005 - 13:15:30 CDT)
  • Re: interface with external program (Fri Jun 10 2005 - 13:55:53 CDT)
  • Re: dielectric constant (Thu May 12 2005 - 13:24:10 CDT)
  • Re: addforce (Tue Apr 19 2005 - 11:37:55 CDT)
  • addforce (Tue Apr 19 2005 - 09:38:50 CDT)
  • Re: any script to build membrane+protein+solvent? (Sat Apr 09 2005 - 07:20:07 CDT)
  • Re: (Fri Apr 08 2005 - 13:50:34 CDT)
  • Re: question about par_all27_prot_lipid.inp (Sun Mar 20 2005 - 06:13:17 CST)
• Lechuga, Javier
  • DPPC.Pdb file needed (Mon Sep 04 2006 - 11:27:49 CDT)
  • DPPC.Pdb (Wed Aug 30 2006 - 05:57:38 CDT)
  • Using PsfGen (Mon Aug 28 2006 - 14:29:52 CDT)
  • Building molecule from topology file (Sat Aug 26 2006 - 06:57:40 CDT)
  • Lipids into NAMD (Mon Aug 21 2006 - 06:10:30 CDT)
  • Lipid into NAMD (Sat Aug 19 2006 - 09:33:26 CDT)
  • Cell membranes with lipids different from POPC and POPE (Mon Jul 31 2006 - 18:03:59 CDT)
  • NAMD configuration files for NVT ensemble (Sat Apr 22 2006 - 12:15:08 CDT)
  • Membrane configuration file (Fri Apr 08 2005 - 10:24:01 CDT)
• Lee Jason
  • RE: LDB question (Tue Aug 02 2005 - 08:01:52 CDT)
• Leo.Ghemtio_at_sanofi-aventis.com
  • Clustering of conformation (Tue Apr 18 2006 - 04:25:02 CDT)
  • radial distribution function (Wed Mar 01 2006 - 04:15:15 CST)
  • radial distribution function (Mon Feb 27 2006 - 08:23:42 CST)
• Leonardo G. Trabuco
  • Re: Superctitiacal CO2 (Wed Jun 14 2006 - 13:14:57 CDT)
  • Re: the patching problem in psfgen (Wed Jun 14 2006 - 13:09:36 CDT)
  • Re: the patch between segments for multiple chains molecule. (Wed Jun 14 2006 - 12:57:42 CDT)
  • Re: setenv: command not found (Mon Jun 12 2006 - 21:55:22 CDT)
  • Re: CMAP and NAMD (Mon Jun 05 2006 - 20:34:06 CDT)
  • Re: the patch between segments for multiple chains molecule. (Fri Jun 02 2006 - 13:09:23 CDT)
  • Re: fix atoms in minimisation (Mon May 01 2006 - 15:58:26 CDT)
  • Re: How to patch residues in different chains (Tue Apr 11 2006 - 20:28:25 CDT)
  • Re: How to patch residues in different chains (Mon Apr 10 2006 - 12:04:36 CDT)
  • Re: a name quesiton (Sat Apr 08 2006 - 14:34:11 CDT)
  • Re: difference between reassignfreq and rescalefreq in temperature controls. (Sat Apr 08 2006 - 13:31:47 CDT)
  • Re: How to patch residues in different chains (Sat Apr 08 2006 - 13:22:55 CDT)
  • Re: a name quesiton (Sat Apr 08 2006 - 13:15:56 CDT)
  • Re: CMAP in NAMD? (Wed Apr 05 2006 - 21:56:40 CDT)
  • Re: questions about the use of HIS residue (Sun Apr 02 2006 - 15:11:32 CDT)
  • Re: Molecular Volume (Thu Mar 30 2006 - 23:38:04 CST)
  • Re: 回å¤�： Re: Re： Re: how to constrain a dihedral angle? (Wed Mar 29 2006 - 13:19:53 CST)
  • Re: Re： Re: how to constrain a dihedral angle? (Tue Mar 28 2006 - 16:44:24 CST)
  • Re: how to constrain a dihedral angle? (Sat Mar 25 2006 - 17:48:57 CST)
  • Re: how to constrain a dihedral angle? (Fri Mar 24 2006 - 14:03:57 CST)
• Leonardo Sepulveda Durán
  • Question about cutoff distance (Tue Oct 11 2005 - 17:06:10 CDT)
  • Re: running NAMD2 in parallel (Mon Oct 10 2005 - 23:24:46 CDT)
  • Re: running NAMD2 in parallel (Mon Oct 10 2005 - 22:03:27 CDT)
  • Question about cutoff distance (Wed Oct 05 2005 - 12:56:24 CDT)
  • It is posible to allow Bond and angle degrees of freedom in tip3 water?? (Mon Sep 26 2005 - 16:52:55 CDT)
  • Re: energy values (Tue Sep 13 2005 - 11:38:21 CDT)
  • Re: problem when heating the system (Tue Aug 30 2005 - 07:53:49 CDT)
  • problems with autoionize total charge and minimization (Tue Jul 05 2005 - 14:18:25 CDT)
  • PMF force restraint question (Mon Jun 27 2005 - 19:11:11 CDT)
  • Using FEP as non-disruptive mutation procedure (Sun Jun 26 2005 - 17:10:17 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Sun Jun 26 2005 - 15:53:29 CDT)
  • changuing dihedral angle slowly (complete message) (Fri Jun 24 2005 - 17:47:02 CDT)
  • changuing dihedral angle slowly (Fri Jun 24 2005 - 17:35:20 CDT)
  • Re: Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS (Fri Jun 24 2005 - 10:33:40 CDT)
  • Re: Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS (Fri Jun 24 2005 - 09:30:26 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Wed Jun 22 2005 - 12:12:48 CDT)
  • Re: Fixed restraint (Tue Jun 21 2005 - 18:56:45 CDT)
  • Re: namdplot, graph is empty (Tue Jun 21 2005 - 15:10:22 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Tue Jun 21 2005 - 12:42:07 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Mon Jun 20 2005 - 12:53:09 CDT)
  • Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Sun Jun 19 2005 - 12:58:18 CDT)
  • How to conservate energy during NVE simulations??? (Wed Jun 15 2005 - 20:55:29 CDT)
  • Adjusting Density of waterbox used by solvate (Sun Jun 12 2005 - 21:51:51 CDT)
  • water density calculation (Fri Jun 10 2005 - 21:19:50 CDT)
  • it is posible to do NVE simulations in NAMD??? (Fri Jun 10 2005 - 18:04:16 CDT)
  • Re: implicit solvent (Thu Jun 09 2005 - 21:26:40 CDT)
  • Re: large vanderwalls energy during minimization (Thu Jun 09 2005 - 16:42:15 CDT)
  • Re: large vanderwalls energy during minimization (Thu Jun 09 2005 - 14:50:31 CDT)
  • Avoiding Rotation and translation of protein (Wed Jun 08 2005 - 10:58:33 CDT)
  • ligands in VMD (Wed Jun 01 2005 - 20:20:02 CDT)
  • Generating a lot of segments in proper order and selection around a center of mass (Wed Jun 01 2005 - 16:13:35 CDT)
  • question about nonnbonded parameters (Tue May 31 2005 - 11:04:23 CDT)
  • Problem with solvate and PSF files in CHARMM format (Mon May 30 2005 - 18:37:05 CDT)
  • Re: namddat not working (Wed May 25 2005 - 15:43:28 CDT)
  • namddat not working (Tue May 24 2005 - 16:34:24 CDT)
  • Re: Re: Simulated Annealing Config (Tue May 24 2005 - 14:55:49 CDT)
• Leonardo Trabuco
  • Re: charge on protein (Wed Oct 18 2006 - 22:17:56 CDT)
  • Re: CMAP in NAMD simulation (Sat Oct 14 2006 - 17:34:51 CDT)
  • Re: about diahedra entry in top_all22_sugar.inp (Fri Oct 13 2006 - 15:14:58 CDT)
  • Re: vmd-l: small query... (Fri Aug 18 2006 - 15:25:34 CDT)
  • Re: where is PSUL? Heme cystein link question? (Thu Aug 10 2006 - 16:50:03 CDT)
  • Re: Queries on patches, GDP-topology (Mon Jul 24 2006 - 14:20:17 CDT)
  • Re: total mol calculation (Wed Jul 19 2006 - 19:08:59 CDT)
  • Re: RNA to DNA (Mon Jul 10 2006 - 10:51:21 CDT)
  • Re: Hi (Fri Jun 30 2006 - 13:39:52 CDT)
• Lewyn Li
  • Re: "reinitvel" parameter in config file (Thu Oct 12 2006 - 08:12:12 CDT)
  • Re: Re: restraining the protein not to move during equilibration (Mon Oct 09 2006 - 10:52:55 CDT)
  • Re: Minimizing and Equilibrating (Mon Jul 17 2006 - 13:52:54 CDT)
  • Re: (No subject) (Wed Jul 12 2006 - 14:00:37 CDT)
  • Re: SMD Energy (Wed May 31 2006 - 14:14:05 CDT)
  • Re: sound velocity of water (Fri May 05 2006 - 12:35:09 CDT)
  • Re: binary.coor to ascII.coor (Thu Apr 27 2006 - 12:49:45 CDT)
  • Re: minimum energy frame (Tue Apr 25 2006 - 12:39:23 CDT)
  • Re: custom pulling path (Wed Apr 19 2006 - 13:52:00 CDT)
  • Re: restart a simulation (Mon Apr 03 2006 - 12:53:57 CDT)
  • Re: only minimization (Fri Feb 24 2006 - 10:57:10 CST)
  • Re: Atoms moving too fast (Tue Dec 06 2005 - 13:55:24 CST)
  • Adding amino acids to an existing pdb structure (Sun Dec 04 2005 - 21:30:49 CST)
  • Re: Problems opening the Extended Trajectory File (Thu Dec 01 2005 - 14:57:42 CST)
  • Re: About RMSD calculation. (Fri Oct 28 2005 - 15:30:20 CDT)
  • Re: saving coordinates as a PDB file after minimization in NAMD (Tue Oct 25 2005 - 16:32:19 CDT)
  • Re: Metal Ion and Protein binding (Thu Oct 13 2005 - 13:38:07 CDT)
  • Re: NAMD restarts binary files (Wed Oct 12 2005 - 11:27:01 CDT)
  • Re: energy values (Tue Sep 13 2005 - 15:16:48 CDT)
  • Re: vmd-l: script (Tue Sep 06 2005 - 11:12:35 CDT)
  • NAMD running only at 40-50% CPU capacity (Fri Sep 02 2005 - 11:00:35 CDT)
  • About the command "loadtotalforces" (Mon Aug 22 2005 - 21:25:44 CDT)
  • Re: addforce (Tue Jun 14 2005 - 14:07:10 CDT)
  • Re: water density calculation (Fri Jun 10 2005 - 22:22:42 CDT)
• Leyla Celik
  • Unit of harmonic restraint force constant (Fri Feb 24 2006 - 07:21:39 CST)
  • Re: topology and parameter for acetylcholine (Mon Oct 10 2005 - 01:27:41 CDT)
  • Re: Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 09:44:53 CST)
  • Re: Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 07:48:28 CST)
  • Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 02:47:42 CST)
  • Protein moving out of PBC water box (Tue Feb 08 2005 - 15:23:31 CST)
• li jianguo
  • charmm parameters for PEG (Sat Jun 04 2005 - 23:42:26 CDT)
• lily jin
  • how long is enough to heat up and equilibrate (Wed Nov 08 2006 - 11:05:37 CST)
  • Re: make the helix longer (Mon May 22 2006 - 15:19:57 CDT)
  • make the helix longer (Mon May 22 2006 - 13:16:06 CDT)
  • SMD (Tue May 16 2006 - 19:18:28 CDT)
  • How to make a disulphide bond (Tue May 16 2006 - 13:02:51 CDT)
  • Periodic cell has become too small for original patch grid! (Thu Apr 13 2006 - 11:40:24 CDT)
  • a name quesiton (Fri Apr 07 2006 - 11:19:41 CDT)
  • restart a simulation (Mon Apr 03 2006 - 12:25:57 CDT)
  • parameter files (Tue Mar 28 2006 - 14:13:39 CST)
  • input file for PO3 (Tue Mar 28 2006 - 11:02:34 CST)
  • energy calculation in VMD (Wed Mar 22 2006 - 16:41:45 CST)
  • possible error warning (Mon Mar 13 2006 - 12:48:58 CST)
  • is possible to remove the waterbox before running VMD (Thu Mar 09 2006 - 10:34:02 CST)
  • a display problem (Thu Mar 09 2006 - 10:22:57 CST)
  • where to find the program DOWSER for setting water ? (Thu Mar 02 2006 - 15:33:03 CST)
  • only minimization (Thu Feb 23 2006 - 18:11:22 CST)
• Lin
  • unsubscribe (Mon Jun 12 2006 - 09:45:23 CDT)
  • vmd-l: Generating PSF for 1JNO.pdb chain A (Fri Apr 14 2006 - 10:29:07 CDT)
  • Fwd: Re: vmd-l: Generating PSF for 1JNO.pdb chain A (Mon Mar 27 2006 - 19:18:13 CST)
  • Re: Topology file for Building Gramicidin A (tutorial) (Tue Feb 07 2006 - 23:53:32 CST)
  • Problem with biotin autopsf (Tue Jan 24 2006 - 08:14:15 CST)
• Lina M Nilsson
  • installing NAMD on opteron cluster with MPI (Thu Mar 03 2005 - 16:06:13 CST)
• Lina Nilsson
  • unstable simulation with AMBER ff in AMBER! (Wed Apr 13 2005 - 04:05:36 CDT)
  • AMBER ff system has too high velocities in NAMD (Wed Apr 13 2005 - 03:16:45 CDT)
  • Re: installing NAMD on opteron cluster with MPI (Tue Mar 08 2005 - 02:27:25 CST)
• linefinc
  • RE: Angle 2, Where is the problem [IMPORTANT] (Tue Jun 20 2006 - 11:02:28 CDT)
  • Angle 2, Where is the problem [IMPORTANT] (Mon Jun 19 2006 - 11:50:41 CDT)
  • Angle CO2 Problem (Fri Jun 16 2006 - 06:08:23 CDT)
  • Re: Re:Superctitiacal CO2 (Thu Jun 15 2006 - 10:52:22 CDT)
  • Re:Superctitiacal CO2 (Thu Jun 15 2006 - 04:07:49 CDT)
  • Re: Superctitiacal CO2 (Thu Jun 15 2006 - 03:47:19 CDT)
  • Superctitiacal CO2 (Wed Jun 14 2006 - 09:58:58 CDT)
• Lionel Perrin
  • Re: ABF Simulation (Tue Jun 27 2006 - 03:47:16 CDT)
  • Re: ABF Simulation (Wed Nov 02 2005 - 08:28:25 CST)
  • Re: ABF Simulation (Wed Oct 26 2005 - 10:52:53 CDT)
  • Re: ABF Simulation (Fri Oct 21 2005 - 04:03:02 CDT)
  • Re: ABF Simulation (Thu Oct 06 2005 - 09:13:45 CDT)
  • ABF Simulation (Wed Oct 05 2005 - 06:41:44 CDT)
• List User
  • simulations of periodic lattice (Sun Apr 30 2006 - 02:38:00 CDT)
• liu liuxiandong
  • help with adding a new force filed into NAMD (Thu Jun 15 2006 - 10:44:10 CDT)
• liu xin
  • Dose restart frequently affect the results? (Fri Dec 23 2005 - 21:33:40 CST)
  • restart problem (Fri Dec 02 2005 - 00:01:26 CST)
• Longzhu Shen
  • question on membrane crushing (Thu Mar 02 2006 - 15:18:09 CST)
  • question on pairinteraction (Sun Feb 26 2006 - 12:03:52 CST)
  • question on mutate command in NAMD (Wed Feb 15 2006 - 16:49:19 CST)
  • question on membrane simulation (Tue Feb 07 2006 - 11:03:43 CST)
  • question on membrane protein simulation (Thu Jan 19 2006 - 11:04:17 CST)
  • question on membrane protein simulation (Wed Jan 18 2006 - 04:56:44 CST)
• Lorant Janosi
  • compute nonbonding interactions on bonded atoms (Fri Dec 29 2006 - 23:10:12 CST)
• luca
  • Re: Distance restraint (Thu Nov 23 2006 - 02:22:23 CST)
  • Re: phi and psi dihedral restraints (Tue Oct 24 2006 - 08:01:45 CDT)
  • Re: phi and psi dihedral restraints (Mon Oct 23 2006 - 15:07:25 CDT)
  • removing bonds in psf (Fri Sep 29 2006 - 05:44:13 CDT)
  • Re: how add bond in psf file? (Tue Sep 26 2006 - 08:09:09 CDT)
• Luca Bellucci
  • Re: rigid protein (Fri Oct 20 2006 - 05:08:50 CDT)
  • Atomic partial charge (Mon Oct 09 2006 - 05:35:36 CDT)
  • Re: how add bond in psf file? (Mon Sep 25 2006 - 11:09:11 CDT)
  • how add bond in psf file? (Mon Sep 25 2006 - 08:18:27 CDT)
  • Transition state (Thu Sep 21 2006 - 03:45:49 CDT)
  • Trajectory analysis (Thu Aug 31 2006 - 08:00:49 CDT)
  • About CHARMM charge (Mon Aug 28 2006 - 04:10:45 CDT)
  • namdenergy (Wed Jul 26 2006 - 10:02:58 CDT)
• Luis Gracia
  • Re: Aligning structures (Fri Mar 10 2006 - 08:45:18 CST)
  • Re: vmd-l: script (Tue Sep 06 2005 - 13:21:40 CDT)
• Luis Rosales
  • Re: basic: combining two pdb files? (Fri Jun 24 2005 - 03:25:46 CDT)
  • Re: set center (Tue Jun 21 2005 - 17:33:53 CDT)
  • Re: vmdtext? (Thu Jun 16 2005 - 15:09:01 CDT)
  • Re: Combine pdb and psf files (Fri Apr 29 2005 - 18:26:06 CDT)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Wed Apr 27 2005 - 21:29:51 CDT)
  • Re: Setting target minimization gradient? (Fri Apr 22 2005 - 19:49:18 CDT)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Wed Apr 20 2005 - 22:22:10 CDT)
  • Re: vmd-l: Interactive Simulations, ligand size limits.... (Wed Apr 20 2005 - 18:19:58 CDT)
  • Interactive Simulations, ligand size limits.... (Tue Apr 19 2005 - 22:51:52 CDT)
  • RE: equilibrated the system (Tue Jan 11 2005 - 17:49:16 CST)
• Lv Shouqin
  • Qestions about NPT simulations. (Wed Jan 26 2005 - 07:29:47 CST)
• lzshen
  • question on pulling direction (Wed Apr 26 2006 - 11:41:46 CDT)
• M. Madhu
  • across the nodes, namd jobs don't get enough CPU! (Fri Jul 07 2006 - 11:00:59 CDT)
  • Re: area per lipid for a protein embedded membrane system (Sun Mar 12 2006 - 09:44:59 CST)
  • Re: area per lipid for a protein embedded membrane system (Fri Mar 10 2006 - 12:25:51 CST)
  • area per lipid for a protein embedded membrane system (Fri Mar 10 2006 - 11:08:41 CST)
  • Re: Jump in Electrostatic Energy between two values (Fri Feb 10 2006 - 16:47:07 CST)
  • Jump in Electrostatic Energy between two values (Fri Feb 10 2006 - 14:33:17 CST)
  • Re: Topology file for Building Gramicidin A (tutorial) (Tue Feb 07 2006 - 15:56:47 CST)
  • Topology file for Building Gramicidin A (tutorial) (Tue Feb 07 2006 - 11:37:13 CST)
• Magali Cottevieille
  • psfgen and charmm19: is there any inconsistency? (Tue Jun 27 2006 - 03:18:20 CDT)
• Magda W
  • farnesyl&retinal (Thu Mar 16 2006 - 02:44:08 CST)
• Mahalakshmi Sahasranaman
  • add ions (Mon Aug 08 2005 - 07:41:33 CDT)
• Manori Indira Jayasinghe
  • Re: FATAL ERROR: unknown floating-point error, errno = 4 (Fri Dec 23 2005 - 11:47:10 CST)
  • FATAL ERROR: unknown floating-point error, errno = 4 (Thu Dec 22 2005 - 23:16:41 CST)
  • Re: define abf1 and abf2 for CM of water and CM of molecule (Wed Dec 21 2005 - 11:26:37 CST)
  • define abf1 and abf2 for CM of water and CM of molecule (Mon Dec 19 2005 - 22:53:42 CST)
• Manuela Cavallari
  • force calculation (Thu Jun 16 2005 - 11:53:13 CDT)
  • Tcl forces (Thu Jun 16 2005 - 05:51:05 CDT)
• Mao Xiang
  • question on phosphotyrosine parameters from charmm (Thu Jun 08 2006 - 22:32:06 CDT)
• Marc Baaden
  • Re: rigid protein (Thu Oct 19 2006 - 12:29:32 CDT)
  • Re: extracting waters from DCD (Wed Aug 09 2006 - 08:36:03 CDT)
  • Re: Turning off forces in VMD (Mon Jan 09 2006 - 01:01:03 CST)
  • Replica-Exchange MD (Fri Nov 18 2005 - 03:18:19 CST)
  • Re: Different solvents (Sun Nov 13 2005 - 07:49:19 CST)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Fri Apr 29 2005 - 04:01:27 CDT)
  • Bio-Image summer school in Paris this year (Wed Mar 16 2005 - 05:42:59 CST)
• Marc Q. Ma
  • Re: sound velocity of water (Fri May 05 2006 - 12:56:09 CDT)
  • Re: Cannot specify both an initial temperature and a velocity file (Thu May 04 2006 - 08:45:53 CDT)
  • Re: [Fwd: Re: SMD of small molecule dimer] (Tue May 02 2006 - 14:27:18 CDT)
  • Re: Faltal Error. reassignFreq fails (Mon Apr 24 2006 - 10:53:46 CDT)
  • Re: Computing cost of frozen atoms (Tue Apr 18 2006 - 12:50:59 CDT)
  • Re: waterbox (Wed Feb 22 2006 - 13:09:45 CST)
  • Re: Fwd: Water Box size (Fri Feb 10 2006 - 12:40:50 CST)
  • Re: successive minimization with different sets of fixed atoms (Tue Dec 06 2005 - 12:31:36 CST)
  • Re: Na ions got into the catalytic site during Production Run (Mon Nov 21 2005 - 09:29:51 CST)
  • Re: Problem with NAMD on Opteron cluster (Mon Nov 14 2005 - 08:37:55 CST)
  • wallclock and cputime (Thu Sep 01 2005 - 16:31:01 CDT)
  • Re: About the command "loadtotalforces" (Fri Aug 26 2005 - 09:25:58 CDT)
  • scripts for binding free energy calculation using SMD and Jarzynski's equality (Wed Aug 17 2005 - 09:45:12 CDT)
  • Re: rigidBond water (Wed Aug 03 2005 - 14:57:26 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Tue Jun 21 2005 - 14:11:43 CDT)
  • Re: Avoiding Rotation and translation of protein (Fri Jun 10 2005 - 11:35:04 CDT)
  • Re: implicit solvent (Fri Jun 10 2005 - 08:28:21 CDT)
  • Re: Avoiding Rotation and translation of protein (Wed Jun 08 2005 - 16:58:02 CDT)
  • Re: Molecular Dynamics or Langevin Dynamics (Wed Apr 27 2005 - 12:39:29 CDT)
  • Re: Molecular Dynamics or Langevin Dynamics (Wed Apr 27 2005 - 09:38:13 CDT)
  • Re: addforce (Tue Apr 19 2005 - 11:17:20 CDT)
  • Re: concatenating two or more dcd files (Mon Apr 18 2005 - 12:13:51 CDT)
  • Re: AMBER ff system has too high velocities in NAMD (Wed Apr 13 2005 - 08:59:31 CDT)
  • Re: RATTLE and DNA (Tue Apr 05 2005 - 09:01:35 CDT)
  • Re: multiple MD simulations (Wed Mar 30 2005 - 11:57:11 CST)
  • Re: multiple MD simulations (Tue Mar 29 2005 - 07:42:46 CST)
  • Re: peridic boundary condition (Fri Mar 11 2005 - 14:00:37 CST)
  • Re: peridic boundary condition (Fri Mar 11 2005 - 13:15:31 CST)
  • Re: peridic boundary condition (Fri Mar 11 2005 - 10:38:15 CST)
  • Re: Kinetic energy (Fri Feb 25 2005 - 15:24:33 CST)
  • Re: PMEGridSize (Thu Feb 24 2005 - 16:52:19 CST)
  • cellOrigin (Tue Feb 22 2005 - 14:06:04 CST)
  • writeback periodic cell info in dcd output (Mon Feb 21 2005 - 16:16:01 CST)
• Marcela P.Aliste
  • Amber and SHAKE algorimth (Thu Feb 24 2005 - 16:14:26 CST)
• Marcelo Puiatti
  • (no subject) (Wed Dec 20 2006 - 12:30:55 CST)
• Marcos Sotomayor
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 11:59:53 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 11:34:22 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 11:02:37 CST)
  • Re: rigid protein (Thu Oct 19 2006 - 10:55:07 CDT)
  • Re: popc pressure profile (Tue Oct 10 2006 - 12:10:29 CDT)
  • Re: Unit cell information in binary output files (Tue Sep 05 2006 - 23:41:42 CDT)
  • Patches & psfgen (Thu Aug 31 2006 - 11:04:03 CDT)
  • Re: SMD and restart (Mon Aug 14 2006 - 01:23:12 CDT)
  • Re: many short runs or one long run? (Mon Jul 10 2006 - 16:03:15 CDT)
  • Re: Re: Re: Large energy fluctuation (Thu Jun 01 2006 - 13:02:55 CDT)
  • Re: Re: Re: Large energy fluctuation (Wed May 31 2006 - 21:48:37 CDT)
  • Re: Cannot specify both an initial temperature and a velocity file (Thu May 04 2006 - 10:02:27 CDT)
  • Re: Faltal Error. reassignFreq fails (Fri Apr 21 2006 - 09:17:00 CDT)
  • Re: Re: water hole (Thu Apr 20 2006 - 21:47:40 CDT)
  • Re: About the command "set z [lindex $coorList($i) 2]". (Sun Apr 16 2006 - 18:33:04 CDT)
  • Re: General question about psfgen atoms. (Tue Apr 11 2006 - 12:38:18 CDT)
  • Re: Problem about the energy change of refold of SMD protein (Thu Apr 06 2006 - 00:30:44 CDT)
  • Re: A possibel wrong coding in Parameters::read_charmm_parameter_file(char *) (Wed Apr 05 2006 - 11:01:27 CDT)
  • Re: A possibel wrong coding in Parameters::read_charmm_parameter_file(char *) (Wed Apr 05 2006 - 10:54:40 CDT)
  • Re: Question on simulation energy output (Sat Mar 25 2006 - 16:43:22 CST)
  • Re: Re£º Re: how to constrain a dihedralqangle=3F?= (Sat Mar 25 2006 - 16:36:28 CST)
  • Re: SMD temperature scaling (Wed Mar 22 2006 - 17:41:32 CST)
  • Re: Can someone PLEASE explain the "firsttimestep" parameter ? (Wed Mar 22 2006 - 15:53:16 CST)
  • Re: question about the parameter "exclude" (Tue Mar 21 2006 - 10:28:25 CST)
  • Re: vmd-l: Aligning structures (Fri Mar 10 2006 - 10:19:43 CST)
  • Re: question on membrane crushing (Thu Mar 02 2006 - 08:32:34 CST)
  • Re: Jump in Electrostatic Energy between two values (Fri Feb 10 2006 - 14:49:44 CST)
  • Re: Atoms moving too fast (Tue Dec 06 2005 - 13:43:54 CST)
  • Re: restart problem (Fri Dec 02 2005 - 00:10:18 CST)
  • Re: A question on minimization (Fri Nov 04 2005 - 16:18:46 CST)
  • Re: The vector direction in SMD (Fri Nov 04 2005 - 15:29:52 CST)
  • Re: Size of water box (Fri Nov 04 2005 - 14:59:17 CST)
  • Re: Serious Steric Atom Clashes (Mon Oct 24 2005 - 13:51:13 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Sun Jun 26 2005 - 14:04:28 CDT)
  • Re: Error on Solaris (Sat Jun 25 2005 - 17:53:52 CDT)
  • Re: How to conservate energy during NVE simulations??? (Thu Jun 16 2005 - 10:30:28 CDT)
• Margaret Kahn
  • Re: NAMD memory problems on ASC's SGI Altix machine (Thu Jan 19 2006 - 17:25:47 CST)
  • Re: Compiled NAMD on SGI Altix (Mon Jan 16 2006 - 19:13:45 CST)
  • NAMD fails on Altix (Wed Jan 11 2006 - 19:50:44 CST)
• Margaret Shun Cheung
  • Re: Faltal Error. reassignFreq fails (Mon Apr 24 2006 - 10:24:48 CDT)
  • NAMD-L: question about SMDk, the force constant for SMD (Wed Apr 12 2006 - 23:27:27 CDT)
  • RE: NAMD-L: question about harmonic constraints (Wed Apr 12 2006 - 22:05:14 CDT)
  • RE: NAMD-L: question about harmonic constraints (Wed Apr 12 2006 - 17:29:50 CDT)
  • RE: NAMD-L: question about harmonic constraints (Wed Apr 12 2006 - 13:31:20 CDT)
  • RE: NAMD-L: question about harmonic constraints (Wed Apr 12 2006 - 11:25:23 CDT)
  • Re: NAMD-L: question about harmonic constraints (Tue Apr 11 2006 - 21:06:33 CDT)
  • Re: NAMD-L: question about harmonic constraints (Mon Apr 10 2006 - 18:26:27 CDT)
  • RE: NAMD-L: question about harmonic constraints (Mon Apr 10 2006 - 12:54:57 CDT)
  • RE: NAMD-L: question about harmonic constraints (Mon Apr 10 2006 - 09:52:05 CDT)
  • RE: NAMD-L: question about harmonic constraints (Sat Apr 08 2006 - 22:30:13 CDT)
  • NAMD-L: question about harmonic constraints (Sat Apr 08 2006 - 13:33:33 CDT)
  • difference between reassignfreq and rescalefreq in temperature controls. (Fri Apr 07 2006 - 13:13:16 CDT)
  • Re: vmd-l:namd-l; question about psfgen (param for CT1?) (Thu Apr 06 2006 - 16:42:41 CDT)
  • Re: vmd-l:namd-l; question about psfgen (param for CT1?) (Thu Apr 06 2006 - 16:08:25 CDT)
  • Re: vmd-l:namd-l; question about psfgen (param for CT1?) (Thu Apr 06 2006 - 15:53:20 CDT)
  • tcouple vs langevin (Thu Apr 06 2006 - 10:53:46 CDT)
  • NAMD-L:density of water molecules in a water sphere (Tue Apr 04 2006 - 12:08:01 CDT)
  • density of water molecules in a water sphere (Mon Apr 03 2006 - 13:56:42 CDT)
  • Re: math formula for spherical boundary conditions. (Mon Apr 03 2006 - 13:34:21 CDT)
  • math formula for spherical boundary conditions. (Sun Apr 02 2006 - 15:44:11 CDT)
• Maria Gonzalez
  • pbc_box (Sun Sep 03 2006 - 12:49:09 CDT)
  • Re: fix atoms in minimisation (Tue May 02 2006 - 20:18:50 CDT)
  • fix atoms in minimisation (Mon May 01 2006 - 10:14:35 CDT)
• Maria Lin
  • Poorly guessed coordinates (Tue Jun 14 2005 - 14:03:59 CDT)
  • Namd on Mac os X (Wed Jun 08 2005 - 18:57:10 CDT)
• Mark A. Hallman
  • restart syntax (Tue Jun 21 2005 - 13:23:16 CDT)
  • config files (Tue Jun 07 2005 - 12:17:35 CDT)
• Mark Abraham
  • Re: about counterions (Tue Dec 19 2006 - 21:46:23 CST)
  • Re: how to use reaction field in NAMD (Sun Dec 10 2006 - 21:44:50 CST)
  • Re: Urey-Bradley term and VDW energy (Wed Oct 25 2006 - 22:50:33 CDT)
  • Re: heat capacity: NPT vs. NVT (Wed Oct 25 2006 - 19:56:15 CDT)
  • Re: Equilibriation Info (Mon Oct 23 2006 - 14:06:04 CDT)
  • Re: rigid protein (Thu Oct 19 2006 - 20:20:09 CDT)
  • Re: rigid protein (Thu Oct 19 2006 - 10:44:27 CDT)
  • Re: charge on protein (Wed Oct 18 2006 - 22:16:02 CDT)
  • Re: United Atoms in NAMD (Fri Sep 29 2006 - 02:26:36 CDT)
  • Re: redirecting stdout to a file (Tue Sep 26 2006 - 08:25:29 CDT)
  • Re: force constant from gaussian to namd (Wed Sep 20 2006 - 14:00:05 CDT)
  • Re: Altix Performance Tuning (Mon Sep 18 2006 - 13:42:53 CDT)
  • Re: third time..can someone help!! (Wed Jul 12 2006 - 00:58:39 CDT)
  • Re: (No subject) (Mon Jul 10 2006 - 18:52:23 CDT)
  • Re: many short runs or one long run? (Mon Jul 10 2006 - 18:49:50 CDT)
  • Re: NAMDenergy (Wed Jul 05 2006 - 08:43:06 CDT)
  • Re: NAMDenergy (Tue Jul 04 2006 - 22:51:44 CDT)
  • Re: Box size (Mon Jul 03 2006 - 23:37:27 CDT)
  • Re: Problem equilibrating with low pressure (Sat Jul 01 2006 - 01:30:13 CDT)
  • Re: Protonation states (Sat Jul 01 2006 - 01:25:13 CDT)
  • Re: Time of MD (Sat Jul 01 2006 - 01:05:18 CDT)
  • Re: Boiling temperature of water. (Thu Jun 22 2006 - 21:48:16 CDT)
  • Re: free energy calculate (Fri Jun 16 2006 - 01:44:05 CDT)
  • Re: Is the GBSA model in NAMD ? (Wed Jun 14 2006 - 09:00:45 CDT)
  • Re: Is the GBSA model in NAMD ? (Tue Jun 13 2006 - 22:24:30 CDT)
  • Re: Is the GBSA model in NAMD ? (Tue Jun 13 2006 - 02:00:01 CDT)
  • Re: question on the charged system (Wed May 17 2006 - 19:57:08 CDT)
  • Re: why pressure is fluctuating so much (Wed May 03 2006 - 19:19:34 CDT)
  • [Fwd: HD speed ??] (Sun Apr 30 2006 - 12:28:04 CDT)
  • Re: starting simulation in charmm, continuing in NAMD ? (Mon Mar 06 2006 - 05:37:10 CST)
  • Re: [Fwd: increasing RMSD after 2 ns minimization-equilibration] (Wed Feb 08 2006 - 19:14:08 CST)
  • Re: IMD-host name-port number-connection problem. (Fri Jan 27 2006 - 09:22:41 CST)
  • Re: Replica-Exchange MD (Fri Nov 18 2005 - 08:00:36 CST)
  • Re: namd: advice (Fri Nov 04 2005 - 14:30:55 CST)
  • Re: Size of water box (Fri Nov 04 2005 - 14:29:36 CST)
  • Replica-Exchange MD (Mon Oct 31 2005 - 22:57:17 CST)
• Martin Loewer
  • Re: Faltal Error. reassignFreq fails (Mon Apr 24 2006 - 09:18:02 CDT)
  • Faltal Error. reassignFreq fails (Fri Apr 21 2006 - 05:50:28 CDT)
• mashaojie163
  • about rigid bonds (Mon Jan 17 2005 - 07:24:39 CST)
• Matan Dishon
  • creating a pdb file based on sequence and psi phi omega values only (Sun Aug 28 2005 - 04:58:07 CDT)
  • peptide simulation (Mon Jun 27 2005 - 03:28:18 CDT)
  • inorganic surface peptide simulation (Mon Jun 06 2005 - 07:13:07 CDT)
• Matt Harrington
  • performance differences on 2.4 vs. 2.6 Linux kernels (Thu Apr 07 2005 - 19:10:54 CDT)
• matteo
  • PMF Calculation (Tue Feb 08 2005 - 04:38:20 CST)
• matteo filandri
  • NAMD octahedron (Thu Mar 09 2006 - 07:57:54 CST)
• Matteo Masetti
  • POPC (Wed Nov 22 2006 - 04:43:08 CST)
• Matthew Davies
  • Re: ABF (fwd) (Tue Nov 14 2006 - 10:10:38 CST)
  • ABF (fwd) (Tue Nov 14 2006 - 07:40:30 CST)
• Matthew Wilce
  • NAMD OSX Xgrid (Thu Aug 17 2006 - 19:45:58 CDT)
  • explicit hydrogen bonds (Thu May 11 2006 - 00:54:20 CDT)
  • Bromine (Wed Jul 20 2005 - 01:43:43 CDT)
  • FEP and TI (Sun Jun 12 2005 - 22:42:05 CDT)
  • FEP and solvent (Sun Jun 12 2005 - 22:35:32 CDT)
  • protein/DNA complexes (Fri May 06 2005 - 00:27:34 CDT)
• Mauricio Arenas Salinas
  • Re: Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4 (Mon Nov 21 2005 - 09:10:16 CST)
• Mauricio Carrillo Tripp
  • SGE (Grid Engine) on Rocks Cluster (Wed Oct 19 2005 - 17:27:57 CDT)
  • Re: Penetration of water (Fri Oct 07 2005 - 10:40:13 CDT)
  • Re: About the potantial of IONS (Fri Oct 07 2005 - 10:29:17 CDT)
  • 1-4 interactions scaling (Mon Oct 03 2005 - 14:30:00 CDT)
  • NAMD & Gromacs FF (Thu Sep 01 2005 - 16:21:50 CDT)
  • ERROR: Margin is too small (BUG?) (Wed Aug 03 2005 - 10:02:42 CDT)
  • Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs (Fri Jul 29 2005 - 16:36:07 CDT)
  • Re: catdcd-generated files and CHARMM (Thu Jul 21 2005 - 16:10:11 CDT)
  • Re: catdcd-generated files and CHARMM (Thu Jul 21 2005 - 14:05:10 CDT)
  • Re: Runnig same config file many times (Fri Jul 15 2005 - 17:33:48 CDT)
  • Re: Runnig same config file many times (Fri Jul 15 2005 - 16:45:05 CDT)
  • Re: FEP - one long simulation vs many short ones (Fri Jul 01 2005 - 18:27:24 CDT)
  • hard wall (Thu Jun 23 2005 - 11:24:00 CDT)
  • unwrapping dcd trajectory (Mon Apr 25 2005 - 16:47:42 CDT)
  • Re: Not getting good speed up (Fri Mar 18 2005 - 16:12:30 CST)
  • strange behaviour when running apoa1 on 1 processor (Thu Mar 17 2005 - 13:36:47 CST)
  • Re: Not getting good speed up (Tue Mar 15 2005 - 10:55:16 CST)
  • Re: Not getting good speed up (Sat Mar 12 2005 - 15:38:06 CST)
  • Re: Not getting good speed up (Fri Mar 11 2005 - 15:32:38 CST)
  • namd2 mpi error (Thu Mar 10 2005 - 14:58:37 CST)
  • Re: Not getting good speed up (Thu Mar 03 2005 - 13:44:55 CST)
  • Re: Not getting good speed up (Thu Mar 03 2005 - 13:16:24 CST)
  • Not getting good speed up (Wed Mar 02 2005 - 16:37:18 CST)
• Maxim Fedorov
  • How to turn off electrostatic interactions (PME). (Wed May 17 2006 - 15:58:07 CDT)
• Mehdi Bagheri-Hamaneh
  • net translation in long simulations (Tue Dec 19 2006 - 17:00:59 CST)
  • ZeroMomentum-Please help (Tue Dec 19 2006 - 08:20:04 CST)
  • ZeroMomentum (Mon Dec 18 2006 - 11:09:20 CST)
  • rigid protein (Mon Oct 16 2006 - 13:00:58 CDT)
• Meunier, Vincent
  • basic: combining two pdb files? (Thu Jun 23 2005 - 20:16:45 CDT)
• Mgr. Lubos Vrbka
  • Re: Compile NAMD on Bluegene (Thu Jun 15 2006 - 01:01:25 CDT)
  • Re: namd: adding water molecules (Fri May 12 2006 - 00:51:02 CDT)
  • Re: why pressure is fluctuating so much (Fri Apr 28 2006 - 00:40:45 CDT)
  • extra points in NAMD (Sat Dec 17 2005 - 06:51:46 CST)
• Michael A. Wilson
  • Re: minimization temperature and constraints (Tue Dec 05 2006 - 18:55:24 CST)
  • alchemical transformation (Thu Aug 17 2006 - 12:04:55 CDT)
• michael atkinson
  • abf (Sun Sep 04 2005 - 22:21:29 CDT)
  • namd 6-1- abf (Mon Aug 15 2005 - 01:38:36 CDT)
• Michael Grabe
  • Re: About the module of "External Electric Field " (Tue Jul 18 2006 - 20:50:29 CDT)
  • Re: Conversion for forces (Tue Jun 20 2006 - 15:42:50 CDT)
  • Re: Vibrational mode analysis (Thu Jun 15 2006 - 20:36:16 CDT)
  • (no subject) (Mon Jun 12 2006 - 20:38:48 CDT)
  • Re: Re: vmd-l: (Tue Jun 06 2006 - 19:29:25 CDT)
  • Re: minimize in FEP.... (Wed Apr 05 2006 - 12:56:36 CDT)
  • Re: Spherical harmonic restraint (Thu Mar 02 2006 - 13:19:53 CST)
  • (no subject) (Tue Feb 28 2006 - 20:37:42 CST)
  • NAMD2.6b1 on MAC cluster problems (Tue Feb 28 2006 - 01:32:22 CST)
  • Re: Alchemical Free Energy Perturbation (Tue Feb 28 2006 - 12:09:50 CST)
  • NAMD2.6b1 on MACOSX (Tue Feb 28 2006 - 12:04:12 CST)
  • (no subject) (Wed Feb 22 2006 - 19:47:43 CST)
  • NAMD hangs in parallel on OSX (Fri Jan 27 2006 - 12:37:38 CST)
  • (no subject) (Thu Oct 27 2005 - 22:39:35 CDT)
  • Re: urestraint doesn't work (Thu Oct 27 2005 - 20:55:49 CDT)
  • Re: urestraint doesn't work (Thu Oct 27 2005 - 19:06:01 CDT)
  • Re: (Fri Oct 21 2005 - 12:15:15 CDT)
  • (no subject) (Wed Oct 19 2005 - 19:09:19 CDT)
  • (no subject) (Wed Oct 19 2005 - 14:53:14 CDT)
  • Re: NAMD distribute (Wed Oct 12 2005 - 21:31:10 CDT)
  • Re: NAMD2.6b1 on an OSX cluster (Fri Sep 09 2005 - 15:39:15 CDT)
  • NAMD2.6b1 on an OSX cluster (Tue Aug 23 2005 - 17:16:56 CDT)
  • Re: Using FEP as non-disruptive mutation procedure (Mon Jun 27 2005 - 11:19:13 CDT)
  • Re: implicit solvent (Fri Jun 10 2005 - 11:18:34 CDT)
  • NAMD hangs (Sun May 29 2005 - 15:53:09 CDT)
  • Re: regenerating PSF file (Wed May 18 2005 - 02:11:41 CDT)
  • Re: (Fri Apr 08 2005 - 12:31:36 CDT)
  • (no subject) (Fri Apr 08 2005 - 12:04:37 CDT)
  • Re: modifying cut off (Thu Apr 07 2005 - 19:38:03 CDT)
  • Re: modifying cut off (Thu Apr 07 2005 - 19:00:31 CDT)
  • path problems (Tue Mar 22 2005 - 01:29:25 CST)
  • G5 clusters (Tue Mar 08 2005 - 11:17:42 CST)
  • Re: question (fwd) (Mon Mar 07 2005 - 15:30:48 CST)
  • Re: alchemify FEP (Fri Feb 18 2005 - 01:26:17 CST)
• michael jerry
  • merge trajectory from NAMD (Wed Nov 30 2005 - 16:19:57 CST)
  • General question about NAMD (Tue Nov 08 2005 - 10:52:04 CST)
• Michael.Grabe_at_ucsf.edu
  • Re: is possible to remove the waterbox before running VMD (Thu Mar 09 2006 - 12:29:00 CST)
• Michal Walczak
  • namd installation (Thu Nov 02 2006 - 03:56:21 CST)
  • compiling namd (Sat Oct 28 2006 - 09:43:11 CDT)
• Michel Espinoza-Fonseca
  • RE: problems reading large dcd file (Tue Jan 10 2006 - 10:59:14 CST)
  • RE: charmm27 fatal error (Mon Dec 19 2005 - 15:30:41 CST)
  • RE: NAMD on Win64 (Mon Dec 12 2005 - 10:53:19 CST)
  • RE: Na ions got into the catalytic site during Production Run (Mon Nov 21 2005 - 10:16:38 CST)
  • RE: About ADP (Tue Nov 01 2005 - 13:21:22 CST)
  • RE: About ADP (Tue Nov 01 2005 - 10:16:43 CST)
  • RE: How to append charmm stream file (Wed Oct 26 2005 - 12:36:01 CDT)
  • RE: trying to generate a peptide (Wed Oct 26 2005 - 09:19:08 CDT)
  • RE: trying to generate a peptide (Wed Oct 26 2005 - 03:35:23 CDT)
  • topology and parameter for acetylcholine (Fri Oct 07 2005 - 06:28:38 CDT)
  • ptraj (Tue Sep 27 2005 - 06:24:50 CDT)
  • RE: Constraint failure (Mon Sep 26 2005 - 13:54:52 CDT)
  • RE: autoionize & namd2 (Thu Sep 22 2005 - 02:51:08 CDT)
  • RE: autoionize & namd2 (Wed Sep 21 2005 - 09:57:17 CDT)
  • RE: autoionize & namd2 (Wed Sep 21 2005 - 09:32:45 CDT)
  • RE: autoionize & namd2 (Wed Sep 21 2005 - 02:24:09 CDT)
  • reconstructing backbone with psfgen (Tue Sep 20 2005 - 09:07:04 CDT)
  • reconstructing backbone with psfgen (Tue Sep 20 2005 - 05:45:10 CDT)
  • namd performance on altix machines (Fri Sep 09 2005 - 07:10:48 CDT)
  • RE: par_all27_prot_lipid.inp (Fri Aug 19 2005 - 11:28:07 CDT)
  • RE: Nanotube Simulations (Tue Aug 02 2005 - 09:50:18 CDT)
  • RE: shape change of water box and peptide move out (Fri Jul 29 2005 - 12:35:09 CDT)
  • RE: Help with SMD (Wed Jul 20 2005 - 11:18:31 CDT)
  • RE: pka calculations and their use in simulations (Mon Jul 11 2005 - 07:41:49 CDT)
  • RE: About Restart (Thu May 05 2005 - 21:50:29 CDT)
  • RE: Restartname (Thu May 05 2005 - 21:48:00 CDT)
  • RE: About PDB file with fixed atom flags. (Thu May 05 2005 - 14:29:01 CDT)
  • RE: NAMD: HEM residue (Wed May 04 2005 - 17:17:01 CDT)
  • RE: About PDB file with fixed atom flags. (Wed May 04 2005 - 17:07:13 CDT)
  • RE: NAMD: HEM residue (Wed May 04 2005 - 15:17:34 CDT)
  • RE: minimization problem (Thu Apr 14 2005 - 15:52:05 CDT)
  • RE: about protonation of HIS in membrane protein (Wed Apr 13 2005 - 19:47:52 CDT)
  • RE: ERROR: Constraint failure in RATTLE algorithm for atom 127! (Wed Apr 13 2005 - 16:20:53 CDT)
  • RE: Periodic cell has become too small for original patch grid (Wed Apr 13 2005 - 11:32:17 CDT)
  • RE: ELECT energy (Mon Apr 11 2005 - 16:18:10 CDT)
  • RE: RE: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C (Sat Apr 09 2005 - 20:31:18 CDT)
  • RE: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C (Sat Apr 09 2005 - 15:41:45 CDT)
  • RE: (Fri Apr 08 2005 - 12:27:54 CDT)
  • phosphoserine (Fri Apr 08 2005 - 12:18:35 CDT)
  • RE: Membrane configuration file (Fri Apr 08 2005 - 11:21:28 CDT)
  • RE: modifying cut off (Thu Apr 07 2005 - 19:45:30 CDT)
  • RE: modifying cut off (Thu Apr 07 2005 - 19:01:03 CDT)
  • modifying cut off (Thu Apr 07 2005 - 18:30:23 CDT)
  • RE: Nanotube psf file. (Wed Apr 06 2005 - 12:34:44 CDT)
  • RE: problem running namd (Mon Apr 04 2005 - 16:48:48 CDT)
  • RE: problem running namd (Mon Apr 04 2005 - 13:48:02 CDT)
  • problem running namd (Mon Apr 04 2005 - 11:54:45 CDT)
  • problem running namd (Mon Apr 04 2005 - 11:18:01 CDT)
  • RE: glucose CHARMM force field (Tue Mar 29 2005 - 22:13:35 CST)
  • RE: molecules distorted (Tue Mar 22 2005 - 15:37:19 CST)
  • RE: visualizing dynamics output (Tue Mar 22 2005 - 14:17:12 CST)
  • RE: question about par_all27_prot_lipid.inp (Sun Mar 20 2005 - 15:22:19 CST)
  • namd and fftw (Mon Mar 14 2005 - 18:11:43 CST)
  • flexible cell for MD simulations (Thu Mar 10 2005 - 16:25:17 CST)
  • RE: namd on Altix (Wed Mar 09 2005 - 13:33:35 CST)
  • RE: namd on Altix (Tue Mar 08 2005 - 17:31:15 CST)
  • RE: namd on Altix (Tue Mar 08 2005 - 17:17:46 CST)
  • RE: namd on Altix (Tue Mar 08 2005 - 17:05:52 CST)
  • RE: namd on Altix (Tue Mar 08 2005 - 16:57:08 CST)
  • RE: namd on Altix (Tue Mar 08 2005 - 15:03:49 CST)
  • RE: namd on Altix (Mon Mar 07 2005 - 19:06:35 CST)
  • RE: namd on Altix (Mon Mar 07 2005 - 18:43:25 CST)
  • Installing NAMD (Mon Mar 07 2005 - 18:18:43 CST)
  • RE: namd on Altix (Mon Mar 07 2005 - 15:00:02 CST)
  • RE: namd on Altix (Mon Mar 07 2005 - 14:16:16 CST)
  • RE: namd on Altix (Mon Mar 07 2005 - 13:37:11 CST)
  • namd on Altix (Mon Mar 07 2005 - 13:14:07 CST)
• Michel Seigneuret
  • TM protein in octane slab questions (Fri Jul 22 2005 - 03:52:50 CDT)
• Mikolai Fajer
  • Re: psfgen and charmm19: is there any inconsistency? (Wed Jun 28 2006 - 14:06:43 CDT)
  • Binary for MacOSX-i686 (Wed Jun 28 2006 - 13:53:00 CDT)
  • Kinetic Energy difference using restart binaries (Wed Dec 21 2005 - 12:54:13 CST)
  • Manipulating structure (Mon Aug 15 2005 - 09:57:03 CDT)
  • Psfgen within NAMD (Fri Aug 12 2005 - 12:01:37 CDT)
  • Re: namddat: Command not found (Thu May 12 2005 - 14:50:20 CDT)
  • namddat: Command not found (Thu May 12 2005 - 12:41:46 CDT)
• milton sonoda
  • sphericalBCk1 (Mon Oct 23 2006 - 19:50:01 CDT)
  • Locally Enhanced Sampling (Wed Dec 21 2005 - 17:34:23 CST)
• moman_at_titus.u-strasbg.fr
  • Re: Tcl, minimization and MD (Warning: I am a lazy ignorant) (Wed Jun 21 2006 - 03:32:52 CDT)
• Morad Alawneh
  • Re: outputPressure (Mon Dec 18 2006 - 12:47:01 CST)
  • outputPressure (Fri Dec 15 2006 - 20:50:13 CST)
  • Re: Harmonic Constraint: 2 types (Thu Nov 30 2006 - 14:32:27 CST)
  • Harmonic Constraint: 2 types (Sun Nov 26 2006 - 19:36:15 CST)
  • Multiple tclForcesScript (Sat Oct 14 2006 - 14:53:28 CDT)
  • Re: NAMD2.6b2: Segmentation fault (Tue Aug 29 2006 - 14:18:41 CDT)
  • Re: NAMD2.6b2: Segmentation fault (Tue Aug 22 2006 - 10:05:42 CDT)
  • NAMD2.6b2: Segmentation fault (Mon Aug 21 2006 - 12:00:47 CDT)
  • Re: Re: vmd-l: psfgen: last CTER does not work (Thu Jun 15 2006 - 14:46:24 CDT)
  • psfgen: last CTER does not work (Thu Jun 15 2006 - 14:30:14 CDT)
  • Error on renaming file (Fri Jun 02 2006 - 10:31:21 CDT)
  • Taurine parameters (Sat May 13 2006 - 10:13:50 CDT)
  • Re: Spherical harmonic restraint (Thu Mar 02 2006 - 13:25:39 CST)
  • Spherical harmonic restraint (Thu Mar 02 2006 - 11:39:48 CST)
  • Re: Rattle Error During Equilibration of Lipid Bilayer Membrane (Sun Feb 12 2006 - 18:17:00 CST)
  • Re: Rattle Error During Equilibration of Lipid Bilayer Membrane (Sat Feb 11 2006 - 09:49:07 CST)
  • How to get different kinds of harmonic constraints in one script? (Tue Jan 31 2006 - 09:48:21 CST)
  • Re: Can any one help me with this parallel issue (Tue Jan 31 2006 - 09:42:58 CST)
  • Re: Can any one help me with this parallel issue (Mon Jan 30 2006 - 14:35:09 CST)
  • Can any one help me with this parallel issue (Sun Jan 29 2006 - 18:17:06 CST)
  • namd2.6b1 has bad scaling (Wed Jan 25 2006 - 11:17:53 CST)
  • Multi Harmonic constrains (Mon Jan 16 2006 - 11:01:00 CST)
  • psfgen problem (Wed Jan 04 2006 - 17:34:46 CST)
  • Re: vmd-l: CMAP problem (Tue Jan 03 2006 - 14:28:22 CST)
  • CMAP problem (Tue Jan 03 2006 - 13:45:41 CST)
• Moumita Maiti
  • Hi (Fri Jun 30 2006 - 04:26:18 CDT)
  • Regarding box-size (Tue Jun 20 2006 - 06:32:43 CDT)
  • problem in minimization while running (Thu Jun 15 2006 - 15:59:50 CDT)
  • Re: the patch between segments for multiple chains molecule. (Wed Jun 14 2006 - 06:21:09 CDT)
  • the patching problem in psfgen (Wed Jun 14 2006 - 06:13:20 CDT)
  • the patch between segments for multiple chains molecule. (Fri Jun 02 2006 - 12:14:58 CDT)
• mpavlova_at_purdue.edu
  • CMAP in NAMD? (Wed Apr 05 2006 - 16:34:58 CDT)
  • return molecule to its principal axes (Wed Dec 14 2005 - 13:54:32 CST)
• Mu Gao
  • RE: [Fwd: SMD of titin domain] (Wed Feb 08 2006 - 19:23:29 CST)
• Muhittin Emre Özdemir
  • Re: Heme - Cysteine link (Thu May 11 2006 - 02:43:17 CDT)
  • Re: Heme - Cysteine link (Wed May 10 2006 - 05:42:19 CDT)
  • Heme - Cysteine link (Tue May 09 2006 - 04:06:46 CDT)
• mustapha.hamdi_at_ensi-bourges.fr
  • DNA protonation (Mon Feb 06 2006 - 05:04:53 CST)
  • Ca++ topology&param files (Fri Sep 30 2005 - 04:11:31 CDT)
  • Velocity after heating (Mon Jul 18 2005 - 06:56:03 CDT)
  • Energy minimization (Wed May 11 2005 - 12:33:01 CDT)
  • Energy minimization (Wed May 11 2005 - 09:46:40 CDT)
  • RE: duplicated key CA in psfgen (Wed Apr 20 2005 - 07:12:36 CDT)
  • RE: duplicated key CA in psfgen (Wed Apr 20 2005 - 07:13:24 CDT)
  • duplicated key CA in psfgen (Tue Apr 19 2005 - 12:49:33 CDT)
  • Nanotube psf file. (Wed Apr 06 2005 - 13:06:59 CDT)
• MW Van der Kamp, School of Chemistry
  • urestraint for minimizations and MD (no PMF) (Thu Nov 02 2006 - 05:46:21 CST)
  • Problem setting distance restraints (Fri Oct 20 2006 - 07:24:04 CDT)
• Nara Dashdorj
  • Re: How to atomselect several residues (Wed Nov 02 2005 - 19:12:10 CST)
  • IC Removal and Problem (Tue Nov 01 2005 - 22:31:53 CST)
  • Re: Serious Steric Atom Clashes (Mon Oct 24 2005 - 14:51:18 CDT)
  • Re: Serious Steric Atom Clashes (Mon Oct 24 2005 - 13:09:32 CDT)
  • Serious Steric Atom Clashes (Sun Oct 23 2005 - 13:45:43 CDT)
• Narender Singh Maan
  • extracting waters from DCD (Tue Aug 08 2006 - 14:04:04 CDT)
  • area of a hydrophobic patch (Wed Feb 02 2005 - 23:23:24 CST)
• Naresh
  • Memory requirements for clusters (Fri Mar 17 2006 - 18:24:57 CST)
• Nathalie Reuter
  • Re: Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 09:51:07 CST)
  • Re: Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 07:21:56 CST)
• Nathan H. Cho
  • Simulating the orientation of detergent and lipid molecules around a membrane protein, bacteriorhodopsin (Wed Dec 20 2006 - 20:59:20 CST)
• Naveen Michaud-Agrawal
  • PMEGridSize (Thu Feb 24 2005 - 16:02:10 CST)
  • Catdcd (Wed Jan 26 2005 - 08:44:45 CST)
• NAVEEN P MICHAUD AGRAWAL
  • Re: Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs (Fri Jul 29 2005 - 23:30:23 CDT)
  • Re: Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs (Sat Jul 30 2005 - 10:42:29 CDT)
• Navratna Vajpai
  • hi... (Mon May 08 2006 - 04:36:33 CDT)
  • change in Disulphide Patches (Mon May 08 2006 - 03:05:28 CDT)
  • patch in psfgen... (Mon Feb 06 2006 - 11:37:14 CST)
  • peptide out of the water-box (Mon Aug 22 2005 - 02:52:11 CDT)
  • Periodic boundary conditions (Mon Aug 08 2005 - 03:34:34 CDT)
  • running on two different machines.... (Sun Jul 31 2005 - 02:24:39 CDT)
  • running on two different machines.... (Sun Jul 31 2005 - 02:27:57 CDT)
• Neelanjana Sengupta
  • unequal PMEGridSizes (Fri Dec 29 2006 - 16:46:56 CST)
  • Re: vmd-l: PSF files append!! (Wed Nov 15 2006 - 14:24:57 CST)
  • Re: how to remove translational and rotational motion from dcd file (Thu Nov 09 2006 - 20:04:56 CST)
  • Re: Another question on Diffusion (Wed Nov 08 2006 - 15:58:09 CST)
  • Re: PME GridSize (Wed Nov 08 2006 - 10:45:40 CST)
  • Re: PME GridSize (Wed Nov 08 2006 - 10:26:15 CST)
  • PME GridSize (Tue Nov 07 2006 - 17:57:24 CST)
  • Re: Using NBFIX (Mon Oct 30 2006 - 00:17:50 CST)
  • Re: Using NBFIX (Sun Oct 29 2006 - 18:01:59 CST)
  • Re: Warnings of psfgen (Wed Oct 25 2006 - 11:30:56 CDT)
  • Re: deformed water box after heating (Tue Oct 24 2006 - 09:58:09 CDT)
  • Re: deformed water box after heating (Mon Oct 23 2006 - 21:59:15 CDT)
  • Re: phi and psi dihedral restraints (Mon Oct 23 2006 - 12:20:41 CDT)
  • phi and psi dihedral restraints (Sun Oct 22 2006 - 18:24:24 CDT)
  • Re: Re: deformed water box during equilibration. (Sat Oct 21 2006 - 14:26:17 CDT)
  • Hydroxyproline topology (Tue Oct 17 2006 - 21:15:25 CDT)
  • CMAP in NAMD simulation (Sat Oct 14 2006 - 17:26:23 CDT)
  • problem with dihedral restraint (Fri Oct 06 2006 - 16:11:43 CDT)
  • missing info from NAMD output (Tue Oct 03 2006 - 14:27:08 CDT)
  • problem with Dihedral Restraints (Mon Sep 04 2006 - 01:13:44 CDT)
  • CoordinateTransformation (Sun Sep 03 2006 - 15:34:48 CDT)
  • CoordinateTransformation (Sun Sep 03 2006 - 15:33:32 CDT)
  • Re: electric field (Sun Sep 03 2006 - 07:38:38 CDT)
  • prob. with constraints (Wed Aug 30 2006 - 11:08:56 CDT)
  • N-methylacetamide (Tue Aug 22 2006 - 19:21:39 CDT)
  • Changes to dihedral angles (Wed Aug 09 2006 - 17:14:36 CDT)
  • Re: extracting waters from DCD (Tue Aug 08 2006 - 17:24:42 CDT)
  • Re: extracting waters from DCD (Tue Aug 08 2006 - 17:08:50 CDT)
  • Re: extracting waters from DCD (Tue Aug 08 2006 - 15:57:56 CDT)
  • Re: Simulation of a 1000 water molecules (Thu Aug 03 2006 - 15:11:37 CDT)
  • Re: NBFix and NAMD (Tue Jul 25 2006 - 18:08:39 CDT)
  • NBFix and NAMD (Tue Jul 25 2006 - 13:53:48 CDT)
• Nicholas M Glykos
  • Re: PME for a hexagonal system (Sat Dec 23 2006 - 04:28:09 CST)
  • Re: Building PDB files for DNA. (Fri Dec 15 2006 - 11:42:03 CST)
  • PME processors (Thu Oct 05 2006 - 07:11:46 CDT)
  • Re: extracting waters from DCD (Wed Aug 09 2006 - 06:54:44 CDT)
  • Re: linux cluster problems (Sat Jul 15 2006 - 06:35:00 CDT)
  • beta-peptides ... (Mon Oct 31 2005 - 06:34:20 CST)
  • Fedora Core 4 problems [2] ... (Sat Oct 01 2005 - 08:42:21 CDT)
  • Fedora Core 4 problems (?) ... (Sat Oct 01 2005 - 08:08:55 CDT)
  • Re: RATTLE and DNA (Tue Apr 05 2005 - 10:02:24 CDT)
  • RATTLE and DNA (Tue Apr 05 2005 - 05:33:48 CDT)
  • psfgen for DNA (Mon Mar 21 2005 - 10:20:49 CST)
  • Hexagonal cell and PME grid. (Tue Mar 01 2005 - 05:17:44 CST)
• Nicolae-Viorel Buchete
  • NAMD2.6b1 (&2.5) binaries on Scyld (missing libbproc.so.2 lib?) (Thu Sep 15 2005 - 16:44:28 CDT)
• Nicolas Floquet
  • Condition for stopping MD sim. with NAMD (Tue May 17 2005 - 02:56:45 CDT)
• Nicolas SAPAY
  • (no subject) (Fri Dec 08 2006 - 16:40:54 CST)
  • Re: area per lipid for a protein embedded membrane system (Sat Mar 11 2006 - 04:42:32 CST)
  • Re: how is NAMD output written in parallel mode? (Mon Dec 05 2005 - 08:17:58 CST)
  • Chamrun/NAMD processes and PBS cluster (Mon Dec 05 2005 - 07:55:15 CST)
  • problem with the NAMD CPU time consumption on a batch queueing system (Mon Nov 28 2005 - 11:46:08 CST)
  • Re: ptraj (Tue Sep 27 2005 - 10:03:18 CDT)
  • dramatical standard deviation in the pressure profile (Mon Aug 29 2005 - 07:12:27 CDT)
  • Re: Pressure Profile Simulation (Thu Aug 25 2005 - 04:32:40 CDT)
  • Re: Energy minimization (Wed May 11 2005 - 11:06:15 CDT)
  • NAMD job abnormally killed with PBS (Tue Apr 26 2005 - 02:14:33 CDT)
  • distance restraints during a dynamic (Mon Apr 11 2005 - 11:13:40 CDT)
  • Re: running VMD from a script? (Mon Mar 21 2005 - 02:29:34 CST)
  • NMAD job abnormally killed with PBS (Thu Feb 24 2005 - 12:09:19 CST)
• Nicolas Winter
  • infinite nanotubes with PBC in NAMD? (Wed Nov 08 2006 - 10:33:11 CST)
• Niraj kumar
  • Re: Re: segfaults in mm_malloc (Thu Jun 30 2005 - 00:25:18 CDT)
  • Re: Re: segfaults in mm_malloc (Wed Jun 29 2005 - 05:48:20 CDT)
  • Understanding NAMD performance data (Wed Jun 22 2005 - 05:27:10 CDT)
  • Re: Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Mon May 16 2005 - 05:14:31 CDT)
  • Re: Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Wed May 11 2005 - 01:40:56 CDT)
  • Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Tue May 10 2005 - 04:48:59 CDT)
  • NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Mon May 09 2005 - 06:03:19 CDT)
• nisha_at_ncbs.res.in
  • RNA to DNA (Sat Jul 08 2006 - 00:29:24 CDT)
  • Re: OXT in pdb file (Fri Jul 07 2006 - 22:48:42 CDT)
  • OXT in pdb file (Tue Jul 04 2006 - 05:09:51 CDT)
  • Starting out with NAMD/VMD (Thu Jun 01 2006 - 02:22:21 CDT)
• Nitin Bhardwaj
  • FEP Energy very high: Mutual exclusion of atoms (Tue Nov 07 2006 - 17:28:58 CST)
  • Counting H-bonds from a dcd file (Tue Aug 29 2006 - 17:00:51 CDT)
  • Re: coordination chemistry with NAMD (Wed Aug 02 2006 - 14:40:55 CDT)
  • Free energy from MD Simulation (Wed May 31 2006 - 17:13:51 CDT)
  • Re: running NAMD on beowulf cluster (Wed Apr 05 2006 - 16:42:46 CDT)
  • running NAMD on beowulf cluster (Wed Apr 05 2006 - 14:17:31 CDT)
  • Errors: Periodic cell became too small for original patch grid & Setting parameter binaryoutput from script failed! (Sun Nov 13 2005 - 12:26:35 CST)
• nmichaud_at_jhu.edu
  • Re: long range electrostatics for alchemical transformation (Thu Aug 17 2006 - 20:38:13 CDT)
  • long range electrostatics for alchemical transformation (Thu Aug 17 2006 - 14:36:44 CDT)
  • FEP implementation in NAMD (Wed Aug 02 2006 - 18:17:53 CDT)
  • Re: velocity error (Thu Jan 05 2006 - 15:26:03 CST)
  • Re: atom distances (Wed Jan 04 2006 - 16:49:08 CST)
  • Re: merge trajectory from NAMD (Wed Nov 30 2005 - 21:05:19 CST)
  • Re: For help with .log file. (Mon Aug 08 2005 - 09:38:02 CDT)
• Noah Edelson
  • unsubscribe (Tue Jul 04 2006 - 15:12:53 CDT)
• nordgren_at_sas.upenn.edu
  • Re: ERROR: Margin is too small (BUG?) (Thu Aug 04 2005 - 17:52:49 CDT)
  • Re: Incorrect periodic box imaging with AMBER parameters (Thu Aug 04 2005 - 17:40:58 CDT)
  • Re: system becomes very large when set LangevinPiston on (Tue Jul 26 2005 - 12:20:50 CDT)
  • Re: Fixed atoms and dcd file with DCDunitCell on (Sat Jul 23 2005 - 12:11:46 CDT)
  • Re: velocity file of atoms at each time step (Mon Jun 20 2005 - 10:23:07 CDT)
  • Re: c-shell into NAMD configuration file (Wed Jun 15 2005 - 09:23:20 CDT)
  • Re: Script for MD in a loop? (Wed Jun 15 2005 - 09:13:44 CDT)
  • Re: Multiple Harmonic Constraints (Wed Jun 15 2005 - 08:37:34 CDT)
  • Re: Simulation terminating due to RATTLE constraint failure (Mon Jun 13 2005 - 01:51:35 CDT)
  • Re: Re: vmd-l: multiple automated calls to NAMD (Thu Jun 09 2005 - 21:56:31 CDT)
  • multiple automated calls to NAMD (Wed Jun 08 2005 - 20:57:56 CDT)
  • NAMD automation (Sat May 07 2005 - 23:39:16 CDT)
  • Re: Fixing atoms during simulation (Sat May 07 2005 - 23:17:30 CDT)
  • extracting time from DCDs (Thu Jan 13 2005 - 19:54:30 CST)
• nsapay_at_ibcp.fr
  • Re: area per lipid for a protein embedded membrane system (Fri Mar 10 2006 - 12:08:54 CST)
• olga hrydziuszko
  • useFlexibleCell (Sat Oct 28 2006 - 09:19:03 CDT)
  • changing velocity during simulation (Wed Oct 11 2006 - 09:05:28 CDT)
  • changing velocity during simulation (Wed Oct 11 2006 - 08:10:17 CDT)
  • reflective barrier (Fri Oct 06 2006 - 10:49:33 CDT)
  • periodic boundry conditions (Fri Oct 06 2006 - 05:58:45 CDT)
  • removing bonds in psf (Fri Sep 29 2006 - 03:45:27 CDT)
  • redirecting stdout to a file (Tue Sep 26 2006 - 08:11:57 CDT)
• olivier Walker
  • Re: compiling Namd on amd64 (Fri Mar 11 2005 - 02:42:30 CST)
  • Re: compiling Namd on amd64 (Thu Mar 10 2005 - 11:55:03 CST)
  • compiling Namd on amd64 (Thu Mar 10 2005 - 04:08:08 CST)
  • difference between two kinds of dimers (Wed Mar 02 2005 - 06:19:56 CST)
• Olya Kravchenko
  • question on tcl script for rmsd calculation (Mon Feb 14 2005 - 13:44:41 CST)
• OMAR NABEEL ALY DEMERDASH
  • problem w/ free energy perturbation (Wed Nov 29 2006 - 18:51:17 CST)
  • error message in free energy pert. (Sun Nov 26 2006 - 23:36:23 CST)
  • question on free energy pert. (Wed Nov 22 2006 - 11:54:21 CST)
• Osman Yogurtcu
  • Cannot specify both an initial temperature and a velocity file (Thu May 04 2006 - 06:44:03 CDT)
  • difference in total energy values (Wed Mar 15 2006 - 13:59:44 CST)
• Parag Adhangale
  • Segmentation violation in NAMD ! (Thu May 26 2005 - 11:04:41 CDT)
  • Problem using the GROMACS force field ! (Thu May 05 2005 - 16:23:52 CDT)
  • Duplicate lines in the output file ! (Wed Apr 06 2005 - 11:52:56 CDT)
  • Problems with the nodelist file ! (Wed Mar 02 2005 - 16:38:13 CST)
• Parminder Mankoo
  • NAMD time step: AKMA? (Mon Oct 17 2005 - 18:52:26 CDT)
• patrick wintrode
  • topology & parameters for urea (Mon Oct 09 2006 - 11:00:44 CDT)
  • Re: How to make a virtual bond? (Thu May 25 2006 - 09:06:34 CDT)
  • How to make a virtual bond? (Wed May 24 2006 - 13:27:24 CDT)
  • Simulation with denaturants? (Sat Apr 29 2006 - 14:00:02 CDT)
  • Still problems with heating (Sat Feb 25 2006 - 11:15:01 CST)
  • follow up question about heating the system (Wed Feb 15 2006 - 15:51:55 CST)
  • Problem heating the system (Wed Feb 15 2006 - 08:37:16 CST)
  • problem using visual_mdenergy: program has trouble reading the dat file (Sat Jul 30 2005 - 17:08:45 CDT)
  • removing a covalent bond during a simulation (Wed Jun 29 2005 - 12:10:56 CDT)
  • langevin vs coupling to a heat bath (Tue Jun 21 2005 - 15:25:29 CDT)
• Paul R Brenner
  • Re: Replica-Exchange MD (Fri Nov 18 2005 - 09:49:38 CST)
  • Re: Charmm 1,4 Interactions - Scaling Question (Fri Jun 17 2005 - 09:08:54 CDT)
  • Charmm 1,4 Interactions - Scaling Question (Thu Jun 16 2005 - 12:00:05 CDT)
• paul.dalhaimer_at_yale.edu
  • Re: solvating a protein (Thu Jul 13 2006 - 15:12:06 CDT)
  • binary.coor to ascII.coor (Thu Apr 27 2006 - 12:14:52 CDT)
  • ACE patch (Wed Apr 12 2006 - 10:56:46 CDT)
  • RE: autoionize & namd2 (Wed Sep 21 2005 - 09:47:37 CDT)
  • Re: energy values (Tue Sep 13 2005 - 11:13:44 CDT)
  • compiling NAMD on a redhat-pentium-dell workstation (Tue May 03 2005 - 11:54:56 CDT)
• Pawel Weronski
  • TIP3P or TIPS3P (Thu Nov 09 2006 - 22:12:41 CST)
  • Re: smd dimer dissociation (Wed Apr 26 2006 - 14:12:45 CDT)
  • which binaries are best for SGI-Altix shared-memory? (Mon Jan 30 2006 - 15:25:46 CST)
  • Re: namdplot: command not found (Wed Oct 12 2005 - 08:57:32 CDT)
  • Re: namdplot: command not found (Tue Oct 11 2005 - 08:22:18 CDT)
• peach gil
  • force calculation (Tue Sep 26 2006 - 14:03:10 CDT)
  • forces calculation (Tue Sep 26 2006 - 13:12:16 CDT)
• Pedro Borkowski
  • Re: problems with .conf script (Fri Mar 17 2006 - 20:46:59 CST)
  • Re: problems with .conf script (Fri Mar 17 2006 - 15:29:36 CST)
  • problems with .conf script (Fri Mar 17 2006 - 13:13:17 CST)
  • Re: problem when do equilibration (Sun Aug 21 2005 - 11:09:17 CDT)
  • ATP in the Topology file (Fri Jul 29 2005 - 11:31:27 CDT)
• pedro mansilla
  • Equilibration problem (Wed Jul 26 2006 - 13:47:44 CDT)
  • Torque aplication with SMD (Sun Jul 23 2006 - 11:38:44 CDT)
• pedro.borkowski_at_utoronto.ca
  • Re: problems with .conf script (Fri Mar 17 2006 - 15:24:58 CST)
• Peiquan Chen
  • Question about free energy of conformation change (Thu Nov 09 2006 - 02:26:46 CST)
• Per Jr. Greisen
  • Minimization algorithms (Thu Aug 31 2006 - 11:19:19 CDT)
  • linux cluster problems (Mon Jul 17 2006 - 04:20:57 CDT)
  • Restarting velocities (Sun Jul 16 2006 - 05:47:58 CDT)
  • linux cluster problems (Sat Jul 15 2006 - 05:44:28 CDT)
  • qsub on a linux cluster (Fri Jul 14 2006 - 02:12:54 CDT)
  • FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CAI (Tue May 30 2006 - 04:08:56 CDT)
  • Remove water to close to the protein? (Fri May 26 2006 - 07:59:27 CDT)
  • Spike during minimization of protein with water (Fri May 26 2006 - 02:47:01 CDT)
  • How to include more parameterfiles in NAMD (Thu May 11 2006 - 09:36:36 CDT)
  • CMAP (Wed May 10 2006 - 12:04:07 CDT)
  • CMAP (Tue May 09 2006 - 06:16:45 CDT)
  • NAD splits up into 3 pieces (Sun Apr 30 2006 - 07:13:02 CDT)
  • parameter and topology file for ethanol (Sat Apr 29 2006 - 03:32:42 CDT)
  • Periodic cell has become too small (Wed Mar 29 2006 - 06:28:28 CST)
  • Warning: add bond failed in patch of ACE (Wed Oct 19 2005 - 14:14:24 CDT)
  • PSF file ATP (Sat Oct 15 2005 - 15:01:36 CDT)
  • ATP PDB file (Fri Oct 14 2005 - 07:25:40 CDT)
• Peter Bazeley
  • simulated annealing step size (Fri Jan 28 2005 - 20:23:19 CST)
  • resetting restartfreq parameter (Thu Jan 20 2005 - 17:17:16 CST)
  • tcoupling coefficient (Wed Jan 05 2005 - 06:31:07 CST)
  • Re: increase in energy over time (Mon Jan 03 2005 - 21:19:33 CST)
  • increase in energy over time (Mon Jan 03 2005 - 17:27:45 CST)
• Peter Freddolino
  • Re: namd question (Wed Dec 27 2006 - 12:56:13 CST)
  • Re: (Wed Dec 20 2006 - 13:59:28 CST)
  • Re: NAMD constraint force and energy (Wed Dec 20 2006 - 10:13:41 CST)
  • Re: about counterions (Wed Dec 20 2006 - 10:07:29 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 11:30:51 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 11:16:21 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 08:25:07 CST)
  • Re: Problem with equilibration and pressure (Wed Dec 13 2006 - 07:56:37 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 07:49:30 CST)
  • Re: bug in pressure calculation with E field? (Sat Dec 09 2006 - 14:19:01 CST)
  • Re: (Sat Dec 09 2006 - 12:40:48 CST)
  • Re: NAMD pairInteraction - huge VDW and TOTAL3 (Wed Dec 06 2006 - 21:21:32 CST)
  • Re: NAMD pairInteraction - huge VDW and TOTAL3 (Wed Dec 06 2006 - 19:44:07 CST)
  • Re: water box deformation (Fri Dec 01 2006 - 11:13:04 CST)
  • Re: help:autopsf changed the structure! (Sun Nov 26 2006 - 22:13:22 CST)
  • Re: How to create repulsive particle ? (Tue Nov 21 2006 - 16:05:18 CST)
  • Re: How to create repulsive particle ? (Tue Nov 21 2006 - 15:52:57 CST)
  • Re: How to create repulsive particle ? (Tue Nov 21 2006 - 15:13:40 CST)
  • Re: combine.tcl (Tue Nov 21 2006 - 15:12:55 CST)
  • Re: Another question on Diffusion (Wed Nov 08 2006 - 17:14:08 CST)
  • Re: Another question on Diffusion (Wed Nov 08 2006 - 17:12:23 CST)
  • Re: dissociation in NAMD (Mon Nov 06 2006 - 15:24:02 CST)
  • [Fwd: Re: SMD on center of mass] (Fri Nov 03 2006 - 14:05:47 CST)
  • Re: Rigid bonds (Tue Oct 24 2006 - 17:33:14 CDT)
  • Re: NPT ensemble with Periodic boundary condition (Tue Oct 24 2006 - 17:30:57 CDT)
  • Re: Trajectory analysis (Wed Oct 18 2006 - 12:06:57 CDT)
  • Re: zero kinetic energy during minimization (Sun Oct 08 2006 - 13:37:16 CDT)
  • Re: value of B column is zero (Sun Oct 08 2006 - 13:29:13 CDT)
  • Re: zero kinetic energy during minimization (Sun Oct 08 2006 - 12:13:26 CDT)
  • Re: value of B column is zero (Sun Oct 08 2006 - 12:14:41 CDT)
  • Re: equilibrating the system with constrained Protein (Thu Sep 14 2006 - 13:40:37 CDT)
  • Re: wall clock vs secs/step metrics (Tue Sep 05 2006 - 12:15:36 CDT)
  • Re: wall clock vs secs/step metrics (Tue Sep 05 2006 - 12:14:49 CDT)
  • Re: electric field (Sun Sep 03 2006 - 08:10:10 CDT)
  • Re: Trajectory analysis (Thu Aug 31 2006 - 09:35:57 CDT)
  • Re: Building molecule from topology file (Sat Aug 26 2006 - 10:44:23 CDT)
  • Re: n terminal patch on proline (Tue Aug 15 2006 - 14:21:40 CDT)
  • Re: n terminal patch on proline (Tue Aug 15 2006 - 14:04:59 CDT)
  • Re: atom type HZ4 not found (Sat Aug 05 2006 - 16:31:20 CDT)
  • Re: simulation crashing with nan (Wed Jul 26 2006 - 10:12:52 CDT)
  • Re: namdenergy (Wed Jul 26 2006 - 10:10:55 CDT)
  • Re: psfgen gets ATP chiral atoms wrong (Tue Jul 25 2006 - 10:50:20 CDT)
  • Re: psfgen gets ATP chiral atoms wrong (Tue Jul 25 2006 - 10:44:11 CDT)
  • Re: psfgen gets ATP chiral atoms wrong (Mon Jul 24 2006 - 16:06:37 CDT)
  • Re: Autopsf (Fri Jul 21 2006 - 16:10:39 CDT)
  • Re: need pair interaction energies, not forces (Thu Jul 20 2006 - 08:45:29 CDT)
  • Re: #QNAN: Please help! (Thu Jul 20 2006 - 08:22:35 CDT)
  • Re: total mol calculation (Thu Jul 20 2006 - 08:18:00 CDT)
  • Re: plz help!! (Tue Jul 18 2006 - 10:36:28 CDT)
  • Re: (No subject) (Wed Jul 12 2006 - 14:15:06 CDT)
  • Re: Computing Potential of Mean Force --SMD-cv (Wed Jul 12 2006 - 02:25:53 CDT)
  • Re: About the module of "External Electric Field " (Wed Jul 12 2006 - 02:02:03 CDT)
  • Re: (No subject) (Mon Jul 10 2006 - 20:15:33 CDT)
  • Re: vmd-l: namdenergy plugin (Mon Jul 10 2006 - 00:08:12 CDT)
  • Re: vmd-l: namdenergy plugin (Mon Jul 10 2006 - 00:02:33 CDT)
  • Re: NAMDenergy (Wed Jul 05 2006 - 17:14:42 CDT)
  • Re: Time of MD (Fri Jun 30 2006 - 11:11:03 CDT)
  • Re: Constant Energy Simulations (Fri Jun 30 2006 - 10:37:16 CDT)
  • Re: Do I need to use an xsc file to restart a simulation in NVT? (Wed Jun 28 2006 - 14:09:13 CDT)
  • Re: Binary for MacOSX-i686 (Wed Jun 28 2006 - 14:08:03 CDT)
  • Re: Question about Van der Waals radii (Mon Jun 26 2006 - 10:57:21 CDT)
  • Re: Question about Van der Waals radii (Mon Jun 26 2006 - 10:49:09 CDT)
  • Re: PME pair interaction analysis (Sun Jun 25 2006 - 16:35:34 CDT)
  • Re: Tcl, minimization and MD (Warning: I am a lazy ignorant) (Wed Jun 21 2006 - 20:17:10 CDT)
  • Re: NAMD: run problem (Wed Jun 21 2006 - 18:22:17 CDT)
  • Re: vmd-l: error using Namdenergy (Wed Jun 21 2006 - 17:17:17 CDT)
  • Re: Tcl, minimization and MD (Warning: I am a lazy ignorant) (Wed Jun 21 2006 - 12:34:40 CDT)
  • Re: Regarding box-size (Tue Jun 20 2006 - 10:51:04 CDT)
  • Re: Tcl, minimization and MD (Warning: I am a lazy ignorant) (Tue Jun 20 2006 - 10:40:52 CDT)
  • Re: chage free energy (Fri Jun 16 2006 - 13:11:52 CDT)
  • Re: NAMD: compile problem (Fri Jun 16 2006 - 12:02:01 CDT)
  • Re: vmd-l: problem in minimization while running (Thu Jun 15 2006 - 16:06:09 CDT)
  • Re: Re: vmd-l: psfgen: last CTER does not work (Thu Jun 15 2006 - 14:48:48 CDT)
  • Re: help with adding a new force filed into NAMD (Thu Jun 15 2006 - 14:37:45 CDT)
  • Re: vmd-l: psfgen: last CTER does not work (Thu Jun 15 2006 - 14:35:02 CDT)
  • Re: Is the GBSA model in NAMD ? (Wed Jun 14 2006 - 09:16:58 CDT)
  • Re: Specific Heat Calculation with VMD (Tue May 30 2006 - 14:02:22 CDT)
  • Re: Basic question. (Sat May 27 2006 - 15:20:56 CDT)
  • Re: Basic question. (Fri May 26 2006 - 21:41:43 CDT)
  • Re: Specific Heat Calculation with VMD (Fri May 26 2006 - 10:30:34 CDT)
  • Re: How to make a virtual bond? (Thu May 25 2006 - 09:56:47 CDT)
  • Re: How to make a virtual bond? (Wed May 24 2006 - 17:48:35 CDT)
  • Re: Water simulation with namd (Wed May 24 2006 - 17:45:30 CDT)
  • Re: DCD file (Thu May 18 2006 - 09:44:11 CDT)
  • Re: About timestep again. -- Fastest motion O-H streching period 10 fs. (Mon May 08 2006 - 16:09:25 CDT)
  • Re: how long should the simulation be run (Sat Apr 29 2006 - 16:22:11 CDT)
  • Re: parameter and topology file for ethanol (Sat Apr 29 2006 - 16:18:08 CDT)
  • Re: Simulation with denaturants? (Sat Apr 29 2006 - 16:11:16 CDT)
  • Re: NAMD configuration files for NVT ensemble (Mon Apr 24 2006 - 14:21:22 CDT)
  • Re: simulated annealing with explicit water (Mon Apr 24 2006 - 10:22:03 CDT)
  • Re: custom pulling path (Wed Apr 19 2006 - 14:00:56 CDT)
  • Re: vmd-l: Multiple residues at same position (Sun Apr 16 2006 - 08:38:30 CDT)
  • Re: High VDW energies during minimization and dynamics (Thu Apr 13 2006 - 13:24:35 CDT)
  • Re: High VDW energies during minimization and dynamics (Thu Apr 13 2006 - 13:22:07 CDT)
  • Re: vmd-l:namd-l; question about psfgen (param for CT1?) (Thu Apr 06 2006 - 16:25:30 CDT)
  • Re: vmd-l:namd-l; question about psfgen (param for CT1?) (Thu Apr 06 2006 - 15:56:07 CDT)
  • Re: vmd-l: dummy atoms and FEP (Thu Apr 06 2006 - 11:45:26 CDT)
  • Re: Bizarre atom behavior (Thu Apr 06 2006 - 00:39:41 CDT)
  • Re: vmd-l: parameter files (Tue Mar 28 2006 - 14:31:59 CST)
  • Re: no Na or CLA paramters in par_all22_prot.inp (Mon Mar 27 2006 - 09:39:30 CST)
  • Re: psfgen operation for the C terminal of HSE (Mon Mar 27 2006 - 08:43:22 CST)
  • Re: about the MSE residue (Mon Mar 27 2006 - 08:42:39 CST)
  • Re: MD problem (Sun Mar 26 2006 - 18:19:13 CST)
  • Re: problems with .conf script (Fri Mar 17 2006 - 15:44:25 CST)
  • Re: timestep in namd (Thu Mar 16 2006 - 13:32:22 CST)
  • Re: Aligning structures (Thu Mar 09 2006 - 21:37:05 CST)
  • Re: question on membrane crushing (Thu Mar 02 2006 - 08:54:05 CST)
  • Re: question on pairinteraction (Sun Feb 26 2006 - 11:25:50 CST)
  • Re: pairInteractionSelf (Fri Feb 10 2006 - 11:57:53 CST)
  • Re: Single point energy? (Tue Jan 31 2006 - 09:55:10 CST)
  • Re: velocity error, still (Thu Jan 12 2006 - 10:41:51 CST)
  • Re: velocity error, still (Tue Jan 10 2006 - 15:34:12 CST)
  • Re: velocity error (Thu Jan 05 2006 - 15:48:36 CST)
  • Re: Atom distance & ptraj (Thu Jan 05 2006 - 13:59:48 CST)
  • Re: Energy Plugin (Thu Jan 05 2006 - 13:46:24 CST)
  • Re: velocity error (Thu Jan 05 2006 - 13:38:13 CST)
  • Re: Energy Plugin (Mon Jan 02 2006 - 21:46:10 CST)
  • Re: preparing a dimeric protein for NAMD (Fri Dec 23 2005 - 22:00:55 CST)
  • Re: preparing a dimeric protein for NAMD (Fri Dec 23 2005 - 14:41:19 CST)
  • Re: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Thu Dec 22 2005 - 14:35:37 CST)
  • Re: pair.pdb and cutoff for pairInteraction (Tue Nov 29 2005 - 11:26:19 CST)
  • Re: Pair Interaction options (Thu Nov 10 2005 - 10:27:14 CST)
  • Re: Increasing temp during MD (Thu Nov 03 2005 - 12:43:33 CST)
  • Re: About RMSD calculation. (Fri Oct 28 2005 - 16:20:48 CDT)
  • Re: Running NAMD 2.6b1 on Linux Networks (Fri Oct 07 2005 - 17:09:31 CDT)
  • Re: help generating psf files (Fri Oct 07 2005 - 10:18:02 CDT)
  • Re: help generating psf files (Thu Oct 06 2005 - 15:22:01 CDT)
  • Re: About calculating RMSD with rmsd.tcl (Wed Oct 05 2005 - 22:22:23 CDT)
  • Re: pairInteraction energies? (Wed Oct 05 2005 - 22:19:30 CDT)
  • Re: 1-4 interactions scaling (Wed Oct 05 2005 - 22:15:36 CDT)
  • Re: help generating psf files (Wed Oct 05 2005 - 22:09:07 CDT)
  • Re: calculate enthalpy of binding (Tue Sep 27 2005 - 17:27:44 CDT)
  • Re: energy values (Tue Sep 13 2005 - 11:31:22 CDT)
• Peter Jones
  • Tcl Boundary Forces (Sat Nov 18 2006 - 20:31:29 CST)
• Peter Spijker
  • Different electrostatic and Van der Waals cutoff (Fri Apr 08 2005 - 04:56:42 CDT)
• Philip Blood
  • Re: Trajectory analysis (Tue Oct 17 2006 - 18:42:56 CDT)
  • Re: Re: NAMD with Myrinet MX on MacOS X (Wed Mar 01 2006 - 11:26:38 CST)
  • Re: Fwd: Water Box size (Fri Feb 10 2006 - 13:37:54 CST)
  • NAMD memory leaks on AMD Opterons using MPICH-MX (Fri Jan 27 2006 - 13:07:45 CST)
  • Re: NAMD memory problems on ASC's SGI Altix machine (Thu Jan 19 2006 - 18:02:37 CST)
  • Re: POPC or POPE? (Wed Nov 02 2005 - 18:16:19 CST)
  • NAMD 2.6b1 error writing DCD file on Cray XT3 (Fri Oct 07 2005 - 13:24:47 CDT)
  • difficulties using SMD on atoms in large systems (Tue Oct 04 2005 - 12:42:01 CDT)
  • Tcl interface--dynamically changing simulation parameters (Thu Apr 28 2005 - 17:19:42 CDT)
  • Re: box size changes under anisotropic pressure coupling (Fri Apr 08 2005 - 14:28:11 CDT)
  • box size changes under anisotropic pressure coupling (Fri Apr 08 2005 - 11:14:40 CDT)
• Philip Fowler
  • Re: pair interactions in NPT (Fri Sep 02 2005 - 02:22:21 CDT)
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 11:07:38 CDT)
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 09:27:06 CDT)
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 07:18:15 CDT)
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 07:15:36 CDT)
  • catdcd and dcdunitcell (Mon Jun 27 2005 - 05:07:01 CDT)
  • Re: FEP (Thu May 12 2005 - 04:37:31 CDT)
  • thermodynamic integration and NAMD: soft-core or "separation-shifted" vdw potentials (Mon Jan 10 2005 - 11:12:41 CST)
• Phoenix
  • Re: problem when heating the system (Tue Aug 30 2005 - 21:39:29 CDT)
  • problem when heating the system (Mon Aug 29 2005 - 23:07:42 CDT)
  • Re: Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS (Fri Jun 24 2005 - 09:59:13 CDT)
  • Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS (Fri Jun 24 2005 - 00:08:37 CDT)
  • Re: how to apply a random force on a atom (Tue Jun 07 2005 - 01:08:36 CDT)
• picot.delphine_at_neuf.fr
  • Force constant of harmonic restraint (Thu May 12 2005 - 03:50:11 CDT)
• Pijush Ghosh
  • Comments on 'restart' simulation (Thu Oct 12 2006 - 16:33:10 CDT)
  • MD in steps (Thu Oct 12 2006 - 11:21:39 CDT)
  • Water outside protein surface (Fri Sep 15 2006 - 00:06:39 CDT)
  • RE: force calculation during to conformational change (Tue Jul 11 2006 - 17:37:51 CDT)
  • RE: The problem of "SMD and smd.tcl" (Mon Jul 03 2006 - 22:43:57 CDT)
  • Help on mutation (Sun Jul 02 2006 - 01:24:19 CDT)
  • RE: SMD Energy (Tue May 30 2006 - 12:16:00 CDT)
  • RE: SMD Energy (Tue May 30 2006 - 12:04:34 CDT)
  • SMD Energy (Tue May 30 2006 - 10:47:32 CDT)
  • RE: Re: vmd-l: breaking the DCD file (Sun Apr 16 2006 - 19:35:18 CDT)
  • RE: High VDW energies during minimization and dynamics (Thu Apr 13 2006 - 11:52:35 CDT)
  • VMD Command (Tue Mar 21 2006 - 00:00:42 CST)
  • RE: atom distances (Wed Jan 04 2006 - 15:14:53 CST)
  • RE: error parsing config file (Thu Sep 29 2005 - 21:52:09 CDT)
  • Problem in restarting simulation (Fri Sep 02 2005 - 10:54:54 CDT)
  • RE: problem when heating the system (Tue Aug 30 2005 - 00:09:08 CDT)
  • RE: removing water from DCD (Wed Jul 20 2005 - 22:03:20 CDT)
  • Radial Distribution Function (Thu Jun 16 2005 - 10:43:18 CDT)
  • RE: addforce (Tue Jun 14 2005 - 14:23:05 CDT)
  • Number of Steps (Wed Jun 08 2005 - 13:39:34 CDT)
  • RE: PSFGEN (Fri May 27 2005 - 17:10:47 CDT)
  • RE: Error in running tutorial files (Wed May 18 2005 - 13:55:31 CDT)
  • RE: regenerating PSF file (Wed May 18 2005 - 10:01:51 CDT)
  • RE: dielectric constant (Thu May 12 2005 - 12:53:32 CDT)
  • RE: Bad global exclusion count. (Tue May 10 2005 - 14:12:06 CDT)
  • RE: Fwd: Parameter file. (Sun May 01 2005 - 16:39:10 CDT)
  • Regulating density of water (Thu Apr 28 2005 - 13:44:35 CDT)
  • RE: duplicated key CA in psfgen (Tue Apr 19 2005 - 13:04:48 CDT)
  • Re: minimization problem (Thu Apr 14 2005 - 14:52:05 CDT)
  • Rotating a structure about an atom (Wed Jan 19 2005 - 12:47:56 CST)
• pijush.ghosh_at_ndsu.edu
  • Re: Question about Generating DCD files with only specified atoms (Thu Dec 22 2005 - 19:36:07 CST)
  • Re: PSFGEN (Sun May 29 2005 - 15:50:15 CDT)
• Po Hu
  • Constraint failure (Sat Sep 24 2005 - 13:42:42 CDT)
  • How to use AMBER force field in NAMD? (Mon Sep 19 2005 - 20:31:13 CDT)
• prodakt_at_o2.pl
  • make namd2 problem (Wed Oct 12 2005 - 06:21:53 CDT)
• q=90=B4=E6=B4=AA=E6=98=8E?=
  • Re: Basic question about steered moledular dynamic(SMD) simulation (Wed May 31 2006 - 01:45:20 CDT)
  • Re: Basic question about steered moledular dynamic(SMD) simulation (Mon May 29 2006 - 03:54:12 CDT)
• q=CF=20=B3=C2?=
  • something about simulation of small molecules in NAMD (Thu May 25 2006 - 21:00:43 CDT)
• q=E2=BA=E9=C3=F7?=
  • Re: Interrupted system call (Sun Jun 11 2006 - 21:31:56 CDT)
  • Re: Interrupted system call (Sun Jun 11 2006 - 21:26:02 CDT)
  • Re: Basic question about steered moledular dynamic(SMD) simulation (Wed May 31 2006 - 03:48:41 CDT)
  • Re: Basic question about steered moledular dynamic(SMD) simulation (Wed May 31 2006 - 00:05:38 CDT)
  • Re: Basic question about steered moledular dynamic(SMD) simulation (Tue May 30 2006 - 11:22:42 CDT)
  • Basic question about steered moledular dynamic(SMD) simulation (Mon May 29 2006 - 00:49:42 CDT)
  • How to deal with this sugar residues though psfgen? (Tue Apr 18 2006 - 00:51:58 CDT)
  • Re: hi all, I want to know how to turn the debug mode on of the namd (Mon Sep 26 2005 - 23:43:25 CDT)
  • hi all, I want to know how to turn the debug mode on of the namd (Mon Sep 26 2005 - 09:56:17 CDT)
  • how to apply a random force on a atom (Mon Jun 06 2005 - 12:31:46 CDT)
  • hi ,everyone.I have a problem about random force (Mon Jun 06 2005 - 11:48:08 CDT)
• q=F5=D0=A1=C7=E5?=
  • Re: About charm++/namd on AMD64 cluster (Mon Jan 03 2005 - 04:15:19 CST)
  • About charm++/namd on AMD64 cluster (Sun Jan 02 2005 - 02:01:32 CST)
• Qikai Li
  • A possibel wrong coding in Parameters::read_charmm_parameter_file(char *) (Wed Apr 05 2006 - 10:25:56 CDT)
• Raeanne Napoleon
  • namdplot, grpah is empty (Mon Jun 27 2005 - 11:01:58 CDT)
  • namdplot, graph is empty (Tue Jun 21 2005 - 13:48:34 CDT)
• Ragothaman Yennamalli
  • RE: Error in running tutorial files (Mon May 23 2005 - 02:00:38 CDT)
  • Error in running tutorial files (Wed May 18 2005 - 12:20:50 CDT)
• Rahul Bhowmik
  • Pulling of Center of Mass (Tue Aug 15 2006 - 10:44:07 CDT)
  • Multiplicity of parameters (Tue Apr 18 2006 - 09:36:22 CDT)
• Raj NK
  • unsubscribe (Sat Jul 15 2006 - 21:46:00 CDT)
  • munch: The input file main.o is not valid in the current object mode (Mon Nov 14 2005 - 16:14:36 CST)
• Rajan Vatassery
  • Rigid bonds (Tue Oct 24 2006 - 14:26:47 CDT)
  • United Atoms in NAMD (Fri Sep 29 2006 - 02:08:12 CDT)
• rakesh...
  • Re: IMD-host name-port number-connection problem. (Fri Jan 27 2006 - 08:26:02 CST)
  • IMD-host name-port number-connection problem. (Thu Jan 26 2006 - 15:54:43 CST)
• Ralph Jimenez
  • checking for correct construction of dihedrals, etc. (Mon Dec 19 2005 - 16:51:52 CST)
  • Energy for part of system (Wed Nov 09 2005 - 16:55:14 CST)
  • questions about applying patches (Thu Nov 03 2005 - 14:23:27 CST)
  • RE: more Heme troubles (Thu Nov 03 2005 - 13:19:54 CST)
• Randy Crawford
  • NAMD recognizes only one MPI process (Thu Mar 31 2005 - 11:46:45 CST)
• Raul Alcantara
  • Re: custom pulling path (Wed Apr 19 2006 - 17:07:05 CDT)
  • custom pulling path (Wed Apr 19 2006 - 12:30:13 CDT)
• Raul Araya
  • minimize in FEP.... (Wed Apr 05 2006 - 10:55:56 CDT)
• Raul Araya Secchi
  • MMPBSA... (Wed May 03 2006 - 16:23:46 CDT)
  • FEP, IONS, DUMMY atoms, LARGE numbers (Mon Apr 17 2006 - 12:32:55 CDT)
  • dummy atoms and FEP (Thu Apr 06 2006 - 11:36:57 CDT)
  • minimize in FEP.... (Tue Apr 04 2006 - 13:53:41 CDT)
  • Dumy atoms in FEP (Mon Mar 13 2006 - 09:13:22 CST)
  • FEP in vacuum (Fri Mar 10 2006 - 08:48:52 CST)
  • FEP.... (Fri Nov 11 2005 - 09:39:41 CST)
  • ERROR: Constraint failure in RATTLE algorithm for atom 598! (Wed Nov 02 2005 - 08:17:29 CST)
  • Water Sphere (Mon Oct 24 2005 - 15:21:27 CDT)
• Ravinder Abrol
  • Re: NAMD pairInteraction - huge VDW and TOTAL3 (Thu Dec 07 2006 - 03:23:58 CST)
  • Re: NAMD pairInteraction - huge VDW and TOTAL3 (Wed Dec 06 2006 - 20:35:15 CST)
  • NAMD pairInteraction - huge VDW and TOTAL3 (Wed Dec 06 2006 - 18:10:23 CST)
  • Re: only minimization (Fri Feb 24 2006 - 12:59:52 CST)
  • Re: how is NAMD output written in parallel mode? (Tue Dec 06 2005 - 17:30:01 CST)
  • how is NAMD output written in parallel mode? (Mon Dec 05 2005 - 02:09:38 CST)
• regafan_at_usc.es
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 13:47:44 CST)
  • problems of RATTLE with big systems (Wed Dec 13 2006 - 12:46:22 CST)
  • RATTLE errors in equilibration (Wed Nov 29 2006 - 09:46:32 CST)
  • Re: distorsion in hydrogens added (Wed Nov 22 2006 - 12:18:15 CST)
  • LINE=*CMAP* (Wed Nov 22 2006 - 08:32:24 CST)
  • distorsion in hydrogens added (Tue Nov 21 2006 - 05:47:58 CST)
  • charges in topology (Wed Nov 15 2006 - 11:34:32 CST)
  • RE: deformations in a water box during equilibration in NAMD (Fri Nov 03 2006 - 04:28:01 CST)
  • deformations in a cubic water box during equilibration in NAMD (Thu Nov 02 2006 - 08:52:39 CST)
• Rene Salmon
  • namd/charm infiniband build (Mon Oct 30 2006 - 14:57:30 CST)
  • Re: namd2 on IBM P5 hangs (Mon Apr 24 2006 - 14:48:42 CDT)
  • namd2 on IBM P5 hangs (Wed Apr 19 2006 - 13:34:16 CDT)
  • compile NAMD/CHARM on infiniband cluster (Fri Feb 24 2006 - 16:20:16 CST)
  • Re: NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers (Wed Aug 24 2005 - 15:01:26 CDT)
  • NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers (Fri Aug 19 2005 - 10:38:20 CDT)
  • Namd hangs on Bproc cluster (Wed Jun 08 2005 - 11:55:00 CDT)
  • Re: CHARM/NAMD network problems on amd64 Clustermatic (Wed May 25 2005 - 12:12:05 CDT)
  • CHARM/NAMD network problems on amd64 Clustermatic (Wed May 11 2005 - 13:07:25 CDT)
  • Re: Duplicate lines in the output file ! (Thu Apr 07 2005 - 10:13:59 CDT)
  • Re: clustermatic nodelist file (Fri Mar 04 2005 - 14:53:47 CST)
  • Re: clustermatic 4 and 5 Namd/charm (Sat Jan 01 2005 - 14:56:56 CST)
• Richard Law
  • Re: Vibrational mode analysis (Thu Jun 15 2006 - 20:52:18 CDT)
  • Re: sound velocity of water (Thu May 04 2006 - 19:25:17 CDT)
  • Re: binary.coor to ascII.coor (Thu Apr 27 2006 - 12:51:03 CDT)
  • Re: saving coordinates as a PDB file after minimization in NAMD (Tue Oct 25 2005 - 16:14:18 CDT)
  • Re: saving coordinates as a PDB file after minimization in NAMD (Tue Oct 25 2005 - 15:44:17 CDT)
  • Re: par_all27_prot_lipid.inp (Thu Aug 18 2005 - 17:13:19 CDT)
  • Re: TM protein in octane slab questions (Fri Jul 22 2005 - 12:30:54 CDT)
  • Re: FATAL ERROR: Asymmetric water molecule?? (Thu Jul 21 2005 - 20:21:40 CDT)
  • Re: Help with SMD (Wed Jul 20 2005 - 10:54:50 CDT)
  • Re: psfgen and extending 5' end of DNA (Thu Jul 14 2005 - 17:45:48 CDT)
  • Re: psfgen patches (Thu Jul 14 2005 - 17:28:41 CDT)
  • pka calculations and their use in simulations (Sun Jul 10 2005 - 18:12:00 CDT)
• Richard Wood
  • Re: simulation of membrane-protein systems (Fri Dec 15 2006 - 05:12:26 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 14:21:25 CST)
  • Re: (No subject) (Mon Jul 10 2006 - 19:58:12 CDT)
  • Re: NAMDenergy (Wed Jul 05 2006 - 04:52:07 CDT)
  • Re: Is the GBSA model in NAMD ? (Wed Jun 14 2006 - 05:22:22 CDT)
  • Re: minimum energy frame (Wed Apr 26 2006 - 09:26:53 CDT)
  • minimum energy frame (Tue Apr 25 2006 - 10:45:33 CDT)
  • Aligning structures (Thu Mar 09 2006 - 21:20:45 CST)
  • Single point energy? (Mon Jan 30 2006 - 14:35:39 CST)
  • MMTools/PCA (Wed Jan 18 2006 - 12:13:00 CST)
  • Re: Turning off forces in VMD (Sun Jan 08 2006 - 17:03:28 CST)
  • Turning off forces in VMD (Sun Jan 08 2006 - 12:15:06 CST)
  • AutoIMD (Fri Jan 06 2006 - 12:36:03 CST)
  • FEP setup (Tue Dec 27 2005 - 11:43:53 CST)
  • Re: CA CL CA angle? (Wed Nov 02 2005 - 10:31:05 CST)
  • CA CL CA angle? (Tue Nov 01 2005 - 11:11:44 CST)
  • new problem (Thu Oct 27 2005 - 21:52:17 CDT)
  • Re: trying to generate a peptide (Wed Oct 26 2005 - 11:39:44 CDT)
  • RE: trying to generate a peptide (Wed Oct 26 2005 - 09:26:48 CDT)
  • RE: trying to generate a peptide (Wed Oct 26 2005 - 07:34:59 CDT)
  • Re: saving coordinates as a PDB file after minimization in NAMD (Tue Oct 25 2005 - 16:11:44 CDT)
  • trying to generate a peptide (Tue Oct 25 2005 - 20:07:01 CDT)
  • saving coordinates as a PDB file after minimization in NAMD (Tue Oct 25 2005 - 13:12:02 CDT)
  • help generating psf files (Tue Oct 04 2005 - 11:37:08 CDT)
• Rob
  • Can I use namd for carbon nanotubes? (Tue Mar 28 2006 - 22:16:44 CST)
• rob yang
  • membrane protein md protocol (Mon Jun 27 2005 - 10:36:15 CDT)
• Robert Bjornson
  • scaling issue (Fri Oct 21 2005 - 15:56:13 CDT)
  • Question about load balancing (Fri Oct 21 2005 - 15:44:46 CDT)
• Robert Brunner
  • Re: NAMD distribute (Thu Oct 13 2005 - 17:40:26 CDT)
  • Re: namdplot: command not found (Thu Oct 13 2005 - 15:11:37 CDT)
  • Re: namdplot: command not found (Tue Oct 11 2005 - 10:32:00 CDT)
  • New BioCoRE server released (Wed Aug 17 2005 - 12:00:16 CDT)
  • Re: Space environment simulations (Tue May 10 2005 - 11:41:37 CDT)
  • Re: segmentation violation!! (Tue Jan 18 2005 - 11:05:00 CST)
• roberte_at_organ.su.se
  • non-repeatability NAMD simulations (Tue May 10 2005 - 17:08:30 CDT)
  • Problems compiling NAMD on linux/clustermatic 5 (Sat May 07 2005 - 05:54:18 CDT)
• rossi_at_york.cuny.edu
  • NAMD 2.6b2 on IBM POWER5 with AIX 5.3 Operating System (Tue Aug 22 2006 - 12:45:59 CDT)
  • Binding Energies for a Peptide-RNA System (Sat Sep 17 2005 - 14:37:11 CDT)
• Ruxandra Dima
  • Re: Compiling (Thu Jan 06 2005 - 20:13:50 CST)
• rwiese_at_unr.edu
  • Problem with center of mass movement in simulation (Mon Feb 06 2006 - 12:01:21 CST)
  • Problem with NAMD and constraint failures (Thu Jan 19 2006 - 18:27:11 CST)
• s.bora erdemli
  • Re: removing water from DCD (Wed Jul 20 2005 - 21:06:53 CDT)
  • Energy Problem (Order of Magnitude) (Wed Jul 20 2005 - 15:05:03 CDT)
  • Energy Order of Magnitude (Mon Jul 11 2005 - 11:20:15 CDT)
  • free energy pertubation,binding energy and constant (Tue Jun 28 2005 - 14:30:07 CDT)
  • Re: Trajectory file. (Fri May 13 2005 - 17:30:58 CDT)
• sabri bora erdemli
  • Van Der Waals energy (Thu Jul 07 2005 - 09:07:44 CDT)
  • van der waals energy (Thu Jul 07 2005 - 09:25:45 CDT)
  • binding free energy , binding constant (Fri Jun 17 2005 - 08:11:33 CDT)
  • Molecular Dynamics or Langevin Dynamics (Tue Apr 26 2005 - 11:21:00 CDT)
  • Re: CAN'T FIND BOND PARAMETERS FOR BOND (error) (Thu Mar 10 2005 - 05:36:33 CST)
  • CAN'T FIND BOND PARAMETERS FOR BOND (error) (Thu Mar 10 2005 - 03:23:02 CST)
• Sabuj Pattanayek
  • Re: compile error on amd64 in src/ComputeTclBC.C (Wed Mar 15 2006 - 15:55:03 CST)
  • Re: compile error on amd64 in src/ComputeTclBC.C (Wed Mar 15 2006 - 15:54:02 CST)
  • compile error on amd64 in src/ComputeTclBC.C (Wed Mar 15 2006 - 14:27:53 CST)
  • Re: during namd build / compile -ltcl8.4 linking error (Wed Mar 15 2006 - 13:17:49 CST)
  • Re: during namd build / compile -ltcl8.4 linking error (Wed Mar 15 2006 - 09:50:11 CST)
  • during namd build / compile -ltcl8.4 linking error (Mon Mar 13 2006 - 15:41:29 CST)
  • Re: build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version (Mon Mar 13 2006 - 14:09:45 CST)
  • build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version (Mon Mar 13 2006 - 12:31:56 CST)
• samantha cox
  • output in tcl (Fri Jul 22 2005 - 15:06:06 CDT)
• Sameer Kumar
  • Re: Re: Is clock skew a problem for charm++ (Thu Jun 22 2006 - 08:04:11 CDT)
• Samuel Flores
  • RE: tcl question (Thu Jun 16 2005 - 22:01:23 CDT)
  • tcl question (Thu Jun 16 2005 - 20:03:29 CDT)
  • RE: vmdtext? (Thu Jun 16 2005 - 15:38:47 CDT)
  • aquaporin question (Thu Jun 16 2005 - 15:39:11 CDT)
  • RE: changing default directory in VMD? (Thu Jun 16 2005 - 14:20:31 CDT)
  • changing default directory in VMD? (Wed Jun 15 2005 - 14:09:25 CDT)
  • vmdtext? (Mon Jun 13 2005 - 11:41:12 CDT)
  • molecules distorted (Tue Mar 22 2005 - 15:35:03 CST)
  • RE: visualizing dynamics output (Tue Mar 22 2005 - 13:51:07 CST)
  • visualizing dynamics output (Tue Mar 22 2005 - 11:31:31 CST)
  • RE: running VMD from a script? -- oops, never mind! (Mon Mar 21 2005 - 19:49:50 CST)
  • RE: running VMD from a script? (Mon Mar 21 2005 - 19:28:41 CST)
  • running VMD from a script? (Sun Mar 20 2005 - 18:22:23 CST)
  • question about par_all27_prot_lipid.inp (Sun Mar 20 2005 - 01:34:58 CST)
• Sandeep Agrawal
  • Cannot open file 'pair.pdb' (Mon May 15 2006 - 07:32:42 CDT)
  • UNABLE TO OPEN XPLOR PARAMETER FILE alanin.params (Fri May 12 2006 - 04:17:06 CDT)
• santanu chatterjee
  • NAMD timestep and numsteps (Tue Oct 03 2006 - 12:39:26 CDT)
  • Box size (Mon Jul 03 2006 - 16:33:33 CDT)
  • Problem equilibrating with low pressure (Fri Jun 30 2006 - 16:31:55 CDT)
  • Pressure control (Wed Jun 28 2006 - 13:43:52 CDT)
  • Density of water (Tue May 30 2006 - 14:04:32 CDT)
  • Periodic cell has become too small (Sun May 28 2006 - 17:42:29 CDT)
  • Water simulation with namd (Wed May 24 2006 - 16:32:49 CDT)
  • Equilibration with constant temperature and pressure (Tue Mar 14 2006 - 19:07:09 CST)
  • A question on simulation with NPT ensemble (Fri Mar 03 2006 - 13:18:34 CST)
  • A question on minimization (Fri Nov 04 2005 - 15:44:32 CST)
  • Size of water box (Fri Nov 04 2005 - 13:06:07 CST)
  • A question on psfgen (Tue Oct 18 2005 - 01:55:39 CDT)
  • Help with psf and par for small molecules (Wed Aug 03 2005 - 15:12:40 CDT)
• Sascha Tayefeh
  • Re: Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4 (Mon Nov 21 2005 - 06:16:14 CST)
  • Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4 (Mon Nov 21 2005 - 02:56:34 CST)
  • Re: problem when heating the system (Tue Aug 30 2005 - 01:26:25 CDT)
  • NPT and FIXED atoms (Mon Aug 29 2005 - 02:14:28 CDT)
  • Re: PDB files for carbon nanotubes (Thu Jul 14 2005 - 16:13:25 CDT)
  • Re: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) (Wed Jun 29 2005 - 09:56:54 CDT)
  • Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) (Wed Jun 29 2005 - 09:31:23 CDT)
  • Re: Multiple Harmonic Constraints (Thu Jun 09 2005 - 08:28:52 CDT)
  • Multiple Harmonic Constraints (Thu Jun 09 2005 - 02:31:38 CDT)
• satya work
  • FEP & different ligands (Mon Dec 11 2006 - 01:20:06 CST)
• Scott Atchley
  • Re: NAMD memory leaks on AMD Opterons using MPICH-MX (Fri Jan 27 2006 - 19:32:28 CST)
  • Re: NAMD with Myrinet MX on MacOS X (Fri Jan 27 2006 - 13:23:29 CST)
  • Trying to profile namd to look for memory leaks (Fri Jan 27 2006 - 10:33:04 CST)
  • Re: NAMD memory problems on ASC's SGI Altix machine (Wed Jan 25 2006 - 09:37:24 CST)
• Sebastian Wasilewski
  • LDB problem on Dual Atlon64 X2 (Wed May 17 2006 - 17:07:17 CDT)
• seigneuret_at_cochin.inserm.fr
  • learning how to do a Cys palmitoyl patch (Tue Aug 02 2005 - 16:24:19 CDT)
• seonah kim
  • how to install rmsdtt in Windows... (Tue Jan 17 2006 - 09:52:00 CST)
• Sergio Anis
  • Re: namd: adding water molecules (Thu May 11 2006 - 21:52:18 CDT)
  • namd: adding water molecules (Wed May 10 2006 - 21:12:43 CDT)
  • namd: adding water molecules (Wed May 10 2006 - 21:52:33 CDT)
  • parameters for camphor (Mon May 01 2006 - 12:35:04 CDT)
  • vmd-l: boubt about consistency of measures (Thu Mar 23 2006 - 08:19:52 CST)
  • Re: RE: namd: advice (Fri Nov 04 2005 - 09:43:25 CST)
  • namd: advice (Fri Nov 04 2005 - 07:56:34 CST)
  • NAMD: error messages (Tue Oct 04 2005 - 06:21:31 CDT)
  • vmd-l: script (Tue Sep 06 2005 - 07:11:50 CDT)
  • Re: Ca trace only (Wed Jul 20 2005 - 06:52:05 CDT)
• Seungho Choe
  • output on Linux-amd64-MPI (Tue Jun 06 2006 - 15:47:33 CDT)
• sh
  • NAMD on Linux IBM PowerPC JS20 Cluster (Wed Nov 15 2006 - 10:32:59 CST)
• Shahid Qamar
  • same random numbers?? (Fri Jan 06 2006 - 15:49:01 CST)
  • Reading from DCD file and running MD (Wed Dec 07 2005 - 14:35:05 CST)
  • ABF.TCl file ??? (Tue Nov 01 2005 - 13:56:25 CST)
  • Can I miminimize some atoms in system (Tue Oct 25 2005 - 16:40:06 CDT)
  • (no subject) (Fri Oct 21 2005 - 11:20:08 CDT)
  • command to run MPI and ABF (Thu Oct 06 2005 - 18:10:39 CDT)
  • Partial charges for fluorescein/topology file (Thu Sep 15 2005 - 13:19:41 CDT)
  • Modified DNA bases PDB files (Wed Sep 07 2005 - 14:00:54 CDT)
  • Runnig same config file many times (Fri Jul 15 2005 - 14:38:38 CDT)
  • Some questions about TCL (Tue Jul 05 2005 - 16:38:28 CDT)
  • MD stops when COM or atom reaches a distance (Fri Jul 01 2005 - 11:34:39 CDT)
  • How MD stopes at a specific distance? (Thu Jun 30 2005 - 12:41:54 CDT)
  • Fixed restraint (Tue Jun 21 2005 - 17:56:09 CDT)
  • urestraint ? (Mon Jun 13 2005 - 13:12:22 CDT)
  • Script for MD in a loop? (Fri Jun 10 2005 - 10:05:34 CDT)
  • FEP error: Rattle atom constriant (Thu Jun 09 2005 - 15:59:11 CDT)
  • Reverse Free Energy perturbation (FEP)? (Wed Jun 08 2005 - 15:35:30 CDT)
  • Milestoning in NAMD (Wed May 18 2005 - 15:46:19 CDT)
  • ERROR: Constraint failure in RATTLE algorithm for atom 127! (Wed Apr 13 2005 - 14:20:16 CDT)
• shaila_at_biof.ufrj.br
  • Z-origin set to zero by Linux/Mac 2.5 binaries, Minimisation (Wed Jun 22 2005 - 07:01:14 CDT)
• Shantenu Jha
  • Re: NAMD distribute (Thu Oct 13 2005 - 18:08:56 CDT)
• Shaowen Hu
  • Compile charm++ with icc (Sat Nov 18 2006 - 15:42:36 CST)
• Shenoy, Sukesh
  • dissociation of water (Sun Oct 08 2006 - 18:06:56 CDT)
  • force constant from gaussian to namd (Wed Sep 20 2006 - 13:44:12 CDT)
  • Morse potential? (Thu Sep 07 2006 - 21:57:56 CDT)
  • mDyne/A to kcal/mol/A2 (Tue Sep 05 2006 - 14:29:59 CDT)
  • mDyne/A to kcal/mol/A2 (Tue Sep 05 2006 - 12:56:27 CDT)
  • Simulation of a 1000 water molecules (Thu Aug 03 2006 - 13:19:34 CDT)
• shgnwgn_at_eden.rutgers.edu
  • large vanderwalls energy during minimization (Thu Jun 09 2005 - 13:31:53 CDT)
• Shirley Hui
  • Re: removing water from DCD (Wed Jul 20 2005 - 20:25:51 CDT)
  • Ca trace only (Tue Jul 19 2005 - 18:37:11 CDT)
  • Fw: changing default directory in VMD? (Wed Jun 15 2005 - 15:34:51 CDT)
  • Simulation terminating due to RATTLE constraint failure (Sun Jun 12 2005 - 22:21:09 CDT)
  • RE: Avoiding Rotation and translation of protein (Wed Jun 08 2005 - 12:45:04 CDT)
  • Re: NAMD restarts binary files (Tue Mar 08 2005 - 10:26:59 CST)
  • NAMD restarts binary files (Tue Mar 08 2005 - 10:13:08 CST)
  • Re: NAMD attempting to read FFTW (Wed Mar 02 2005 - 13:27:57 CST)
  • NAMD attempting to read FFTW (Tue Mar 01 2005 - 13:59:21 CST)
  • Re: using namd to compute energies (Tue Feb 15 2005 - 14:24:46 CST)
• Shirley Li
  • pair interaction analysis of multiple trajectories with different timestep (Wed May 17 2006 - 10:18:03 CDT)
  • pair interaction (Mon May 15 2006 - 19:13:27 CDT)
  • Some basic questions about NAMD (Tue May 09 2006 - 15:01:37 CDT)
  • Re: protein moves away from water box (Fri May 05 2006 - 18:38:38 CDT)
  • protein moves away from water box (Fri May 05 2006 - 14:25:40 CDT)
  • convert .dcd into .trr (Tue May 02 2006 - 12:37:53 CDT)
  • gradient for minimization (Thu Mar 02 2006 - 12:59:40 CST)
  • PSFGEN for protein containing GTP (Wed Jan 04 2006 - 21:55:13 CST)
  • Re: preparing a dimeric protein for NAMD (Thank you) (Tue Dec 27 2005 - 12:38:15 CST)
  • Thanks a lot (Tue Dec 27 2005 - 12:28:52 CST)
  • Can extending MIN solve the problem of "Constraint failure in RATTLE algorithm" (Sat Dec 24 2005 - 12:58:55 CST)
  • Re: Re: Besides PSFGEN, (Thank you) (Fri Dec 23 2005 - 17:42:54 CST)
  • Re: preparing a dimeric protein for NAMD (Fri Dec 23 2005 - 17:35:59 CST)
  • Besides PSFGEN, are there any other good ways of generating .psf file (Thu Dec 22 2005 - 19:01:36 CST)
  • Re: ANGLE PARAMETERS (It works now) (Thu Dec 22 2005 - 16:54:06 CST)
  • The HT-HT-OT angle parameter for TIP3? (Thu Dec 22 2005 - 14:57:19 CST)
  • UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Thu Dec 22 2005 - 13:16:00 CST)
  • The angle parameters for CN7 are missing in NAMD? (Wed Dec 21 2005 - 18:02:07 CST)
  • FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7 (Wed Dec 21 2005 - 14:56:36 CST)
  • Re: pair.pdb and cutoff for pairInteraction (Tue Nov 29 2005 - 22:33:36 CST)
  • pair.pdb and cutoff for pairInteraction (Tue Nov 29 2005 - 11:00:02 CST)
  • restart a simulation (Fri Nov 04 2005 - 16:15:35 CST)
  • Autoionize: net charge NOT equal to zero (Wed Oct 19 2005 - 11:44:34 CDT)
  • problem with PSFGEN: the O3A atom cannot be recognized (Tue Oct 11 2005 - 12:52:49 CDT)
  • problem with PSFGEN (Mon Oct 10 2005 - 18:15:58 CDT)
  • RE: water box and the procedure (Mon Oct 10 2005 - 18:05:34 CDT)
  • water box and the procedure (Fri Oct 07 2005 - 09:50:15 CDT)
  • ion concentration (Thu Oct 06 2005 - 18:36:26 CDT)
  • autoionize and psfgen, which one first? (Thu Oct 06 2005 - 16:01:42 CDT)
  • Re: VMD scripting (Thanks a lot) (Thu Oct 06 2005 - 15:54:24 CDT)
  • VMD scripting (Thu Oct 06 2005 - 14:33:21 CDT)
• Shulin Zhuang
  • no Na or CLA paramters in par_all22_prot.inp (Mon Mar 27 2006 - 06:54:49 CST)
  • psfgen operation for the C terminal of HSE (Mon Mar 27 2006 - 01:46:57 CST)
  • about the MSE residue (Sun Mar 26 2006 - 23:42:16 CST)
  • Simulation failed during the stage of heat (Thu Mar 23 2006 - 23:58:15 CST)
• Shunzhou Wan
  • protein interact with its image (Tue Apr 19 2005 - 10:23:58 CDT)
• Slawomir Orlowski
  • AMD64 or PIV Prescott ... (Tue Jan 11 2005 - 05:52:48 CST)
• Snigdha Chakraborty
  • How to run for periodic boundary Conditions? (Wed Jul 20 2005 - 12:19:32 CDT)
• snowyowls
  • Re: a error during install charm-5.9 (Tue Jun 06 2006 - 08:13:49 CDT)
  • a error during install charm-5.9 (Mon Jun 05 2006 - 18:45:14 CDT)
• snoze pa
  • Re: DCD to PDB conversion (Tue Jun 13 2006 - 17:10:37 CDT)
  • Re: vmd-l: (Tue Jun 06 2006 - 17:47:34 CDT)
  • one residue rmsd (Mon May 01 2006 - 17:49:02 CDT)
  • Re: error message (Thu Apr 27 2006 - 17:37:09 CDT)
  • error message (Thu Apr 27 2006 - 16:15:35 CDT)
  • MD analysis (Mon Apr 17 2006 - 14:37:31 CDT)
  • Re: vmd-l: breaking the DCD file (Sun Apr 16 2006 - 17:08:31 CDT)
  • Multiple residues at same position (Sun Apr 16 2006 - 02:01:35 CDT)
  • Re: vmd-l: Generating PSF for 1JNO.pdb chain A (Fri Apr 14 2006 - 11:40:34 CDT)
  • Re: General question about psfgen atoms. (Tue Apr 11 2006 - 14:51:09 CDT)
  • Re: General question about psfgen atoms. (Tue Apr 11 2006 - 14:48:12 CDT)
  • General question about psfgen atoms. (Tue Apr 11 2006 - 12:27:27 CDT)
  • Re: How to patch residues in different chains (Tue Apr 11 2006 - 11:25:13 CDT)
  • Re: How to patch residues in different chains (Mon Apr 10 2006 - 11:25:59 CDT)
  • How to patch residues in different chains (Fri Apr 07 2006 - 18:32:38 CDT)
  • Re: Can someone PLEASE explain the "firsttimestep" parameter ? (Wed Mar 22 2006 - 16:24:49 CST)
  • timestep in namd (Thu Mar 16 2006 - 12:34:10 CST)
  • waterbox (Wed Feb 22 2006 - 10:57:12 CST)
  • Re: Fwd: Water Box size (Thu Feb 16 2006 - 10:59:46 CST)
  • useGroupPressure (Wed Feb 15 2006 - 15:48:55 CST)
  • Re: Fwd: Water Box size (Wed Feb 15 2006 - 11:58:33 CST)
  • Fwd: Fwd: Water Box size (Wed Feb 15 2006 - 11:29:19 CST)
  • computer network (Mon Feb 13 2006 - 11:26:51 CST)
  • Re: Jump in Electrostatic Energy between two values (Fri Feb 10 2006 - 15:24:25 CST)
  • Re: Fwd: Water Box size (Fri Feb 10 2006 - 13:49:07 CST)
  • Fwd: Water Box size (Fri Feb 10 2006 - 10:58:27 CST)
  • Amber Parameter in NAMD (Wed Feb 08 2006 - 18:42:00 CST)
  • Re: margin error message (Tue Jan 24 2006 - 11:11:12 CST)
  • NAMD at NCSA (Tue Jan 24 2006 - 11:09:31 CST)
  • How to run namd on NCSA Tungsten (Wed Oct 19 2005 - 14:38:58 CDT)
  • NAMD restarts binary files (Wed Oct 12 2005 - 10:21:46 CDT)
  • developing parameters for charmm (Sat Oct 08 2005 - 19:40:54 CDT)
  • namd cluster run, connection refused (Thu Sep 29 2005 - 20:06:57 CDT)
  • water box and system charge (Fri Sep 30 2005 - 11:44:21 CDT)
  • NAMD cluster run (Fri Sep 30 2005 - 10:35:22 CDT)
• Soumyasaswati Sarangi
  • Re: Trouble with Charmm/PDB? (Tue Nov 07 2006 - 02:47:37 CST)
• Stefano Corni
  • Free energy with amber topology (Fri May 26 2006 - 02:53:28 CDT)
• Sterling Paramore
  • Re: SMD Energy (Wed May 31 2006 - 11:41:57 CDT)
  • Re: SMD Energy (Tue May 30 2006 - 13:50:28 CDT)
  • Re: SMD Energy (Tue May 30 2006 - 11:46:57 CDT)
  • Re: question on the charged system (Wed May 17 2006 - 20:50:10 CDT)
  • Re: question on the charged system (Wed May 17 2006 - 09:02:47 CDT)
  • Re: explicit hydrogen bonds (Thu May 11 2006 - 10:41:56 CDT)
  • Re: protein moves away from water box (Fri May 05 2006 - 19:00:01 CDT)
  • Re: protein moves away from water box (Fri May 05 2006 - 15:46:06 CDT)
  • Re: Computing cost of frozen atoms (Tue Apr 18 2006 - 11:09:05 CDT)
  • Re: a name quesiton (Sat Apr 08 2006 - 14:13:35 CDT)
  • Re: other crystal types in NAMD ? (Tue Apr 04 2006 - 15:13:29 CDT)
  • Re: other crystal types in NAMD ? (Tue Apr 04 2006 - 14:16:07 CDT)
  • Re: Can someone PLEASE explain the "firsttimestep" parameter ? (Wed Mar 22 2006 - 15:40:02 CST)
  • Re: is possible to remove the waterbox before running VMD (Thu Mar 09 2006 - 11:50:08 CST)
  • Re: NAMD octahedron (Thu Mar 09 2006 - 10:44:56 CST)
  • Re: Pressure -ve (Wed Mar 08 2006 - 12:10:51 CST)
  • Re: (Thu Feb 23 2006 - 11:34:36 CST)
  • Re: Can any one help me with this parallel issue (Mon Jan 30 2006 - 14:42:42 CST)
  • Re: Can any one help me with this parallel issue (Mon Jan 30 2006 - 10:02:17 CST)
  • NAMD memory problems on ASC's SGI Altix machine (Thu Jan 19 2006 - 10:46:33 CST)
  • Re: Compiled NAMD on SGI Altix (Tue Jan 17 2006 - 11:44:33 CST)
  • Compiled NAMD on SGI Altix (Mon Jan 16 2006 - 18:51:18 CST)
  • Re: Question about Generating DCD files with only specified atoms (Thu Dec 22 2005 - 21:17:41 CST)
  • NAMD on Intel XEON EM64T (Mon Nov 14 2005 - 16:55:50 CST)
  • Re: namdplot: command not found (Thu Oct 13 2005 - 14:59:36 CDT)
  • Re: XPLOR psf format (Thu Jul 07 2005 - 14:40:01 CDT)
  • Megatest fails on Linux cluster (Fri May 13 2005 - 14:40:11 CDT)
• Stern, Julie
  • moments of inertia, principal axes (Wed Aug 17 2005 - 19:00:53 CDT)
  • wrap ions (Wed Aug 03 2005 - 23:13:05 CDT)
  • shake and minimzation, equilibration (Wed Aug 03 2005 - 14:56:13 CDT)
  • rigidBond water (Wed Aug 03 2005 - 13:45:07 CDT)
  • velocity quenching (Tue Aug 02 2005 - 23:15:45 CDT)
  • steepest descent minimization (Tue Aug 02 2005 - 22:35:00 CDT)
  • added more bases to DNA using psfgen (Thu Jul 21 2005 - 21:50:55 CDT)
  • namdplot error (Thu Jul 21 2005 - 20:06:53 CDT)
  • removing water from DCD (Wed Jul 20 2005 - 19:49:12 CDT)
  • cellBasisVectors and xsc files (Tue Jul 19 2005 - 20:53:01 CDT)
  • force shifted cutoff (Tue Jul 19 2005 - 18:37:10 CDT)
  • psfgen and poorly guessed coordinates (Fri Jul 15 2005 - 18:17:56 CDT)
  • patch PYRT and extending DNA (Thu Jul 14 2005 - 20:17:04 CDT)
  • psfgen and extending 5' end of DNA (Thu Jul 14 2005 - 17:07:23 CDT)
  • psfgen patches (Thu Jul 14 2005 - 17:04:51 CDT)
  • force shifted cutoff (Thu Jul 07 2005 - 18:06:15 CDT)
  • XPLOR psf format (Thu Jul 07 2005 - 14:16:48 CDT)
  • infinite DNA (Wed Jul 06 2005 - 11:52:17 CDT)
  • inconsistencies with amber force fields due to scnb and 1-4scalin g (Wed May 18 2005 - 10:38:51 CDT)
  • scnb scaling factor and compatibility with AMBER force fields (Thu May 12 2005 - 11:47:01 CDT)
  • RE: minimization problem (Thu Apr 14 2005 - 16:53:15 CDT)
  • RE: minimization problem (Thu Apr 14 2005 - 15:26:04 CDT)
  • minimization problem (Thu Apr 14 2005 - 13:41:19 CDT)
  • ELECT energy (Mon Apr 11 2005 - 14:37:57 CDT)
  • warning on unique coordinates (Wed Feb 23 2005 - 15:07:19 CST)
  • restarting a simulation accurately (Sat Jan 08 2005 - 14:32:41 CST)
  • namd on lemieux (Fri Jan 07 2005 - 11:51:53 CST)
  • prmtop reading error (Sun Jan 02 2005 - 15:35:42 CST)
• Steven A. DuChene
  • Re: charm++ compile problem on x86_64 (Fri Jan 14 2005 - 17:09:42 CST)
  • charm++ compile problem on x86_64 (Fri Jan 14 2005 - 15:24:02 CST)
  • scyld no longer a supported option for building charm++ ? (Fri Jan 14 2005 - 14:30:10 CST)
• Sting
  • Re: RE: about topology generation (Tue Dec 05 2006 - 01:03:56 CST)
  • about topology generation (Mon Dec 04 2006 - 22:18:26 CST)
  • Re: CoordinateTransformation (Sun Sep 03 2006 - 20:17:21 CDT)
  • Re: Some problem on pair force calculation (Thu Jun 08 2006 - 20:40:11 CDT)
  • Some problem on pair force calculation (Tue Jun 06 2006 - 22:27:30 CDT)
  • Some problem on pair force calculation (Tue Jun 06 2006 - 08:32:48 CDT)
  • Re: Re: Large energy fluctuation (Wed Jun 01 2005 - 02:34:35 CDT)
  • Re: Re: Large energy fluctuation (Tue May 31 2005 - 21:38:38 CDT)
  • Large energy fluctuation (Mon May 30 2005 - 21:44:44 CDT)
  • Large energy fluctuation (Fri Apr 08 2005 - 07:09:07 CDT)
  • Re: Re: water hole (Thu Apr 20 2006 - 22:15:42 CDT)
  • Re: Re: water hole (Sat Apr 20 2002 - 21:28:49 CDT)
  • water hole (Fri Apr 19 2002 - 21:45:40 CDT)
• Subhasish Chatterjee
  • autocorrelation function ! (Fri Mar 03 2006 - 20:17:56 CST)
  • radial distribution function (Wed Mar 01 2006 - 16:01:44 CST)
• sukesh shenoy
  • dissociation in NAMD (Mon Nov 06 2006 - 11:00:40 CST)
  • Using NBFIX (Sat Oct 28 2006 - 17:59:52 CDT)
  • changing parameter files during simulation run (Fri Oct 27 2006 - 10:18:55 CDT)
• surendra negi
  • RE: OXT in pdb file (Sun Jul 09 2006 - 11:09:38 CDT)
  • Re: Help on mutation (Wed Jul 05 2006 - 15:21:16 CDT)
  • Re: OXT in pdb file (Wed Jul 05 2006 - 15:16:12 CDT)
  • Re: Can someone PLEASE explain the "firsttimestep" parameter ? (Wed Mar 22 2006 - 18:19:39 CST)
  • Re: Problem heating the system (Thu Feb 16 2006 - 11:22:03 CST)
  • Re: follow up question about heating the system (Wed Feb 15 2006 - 16:18:30 CST)
  • Re: question on mutate command in NAMD (Wed Feb 15 2006 - 10:58:53 CST)
  • Re: Problem heating the system (Wed Feb 15 2006 - 10:50:10 CST)
  • margin error message (Sat Jan 21 2006 - 12:23:01 CST)
  • Re: NAMD ligand (Thu Jan 12 2006 - 12:19:26 CST)
  • CAN'T FIND BOND PARAMETERS FOR BOND FE - S (Fri Sep 02 2005 - 15:36:43 CDT)
  • Protonation state of HIS (Wed Aug 10 2005 - 16:57:06 CDT)
  • Re: Incorrect periodic box imaging with AMBER parameters (Thu Aug 04 2005 - 16:11:15 CDT)
  • Re: error message (Fri May 06 2005 - 10:22:55 CDT)
  • Re: HEME patch (Thu May 05 2005 - 13:38:37 CDT)
  • Re: hanging at startup phase 0 (Thu May 05 2005 - 12:25:06 CDT)
  • NAMD simulation: HEME (Wed May 04 2005 - 15:16:58 CDT)
  • NAMD: HEM residue (Wed May 04 2005 - 14:56:58 CDT)
• Surjit Dixit
  • Re: FEP and solvent (Thu Jun 16 2005 - 09:06:17 CDT)
• Swarna Patra
  • Stretching Deca-Alanine (Thu Aug 10 2006 - 23:41:47 CDT)
  • temp autocorrelation (Sun Jul 23 2006 - 20:00:09 CDT)
  • dmpc membrane (Mon Jul 04 2005 - 20:17:43 CDT)
  • Gramicidin (Mon Jun 20 2005 - 20:54:09 CDT)
  • set center (Thu Jun 16 2005 - 22:53:28 CDT)
  • density calculation (Sun Apr 10 2005 - 20:24:51 CDT)
  • mmtools (Thu Feb 17 2005 - 23:32:55 CST)
  • energy (Thu Feb 17 2005 - 16:58:36 CST)
  • force constraints (Mon Jan 31 2005 - 19:49:07 CST)
  • SMD (Wed Jan 26 2005 - 20:52:27 CST)
  • qsub (Mon Jan 24 2005 - 23:02:37 CST)
  • Re: pmf (Sun Jan 16 2005 - 20:17:55 CST)
  • Electric Field (Wed Jan 12 2005 - 16:57:02 CST)
  • pmf (Tue Jan 11 2005 - 18:55:44 CST)
• SÅ‚awek OrÅ‚owski
  • Re: DCD file (Thu May 18 2006 - 03:40:05 CDT)
  • Re: How to make a disulphide bond (Wed May 17 2006 - 03:36:44 CDT)
  • Re: Simulation on AMD64 Dual Core - threads lose connection (Tue May 16 2006 - 01:04:39 CDT)
  • Simulation on AMD64 Dual Core - threads lose connection (Thu May 11 2006 - 02:42:00 CDT)
  • Re: Heme - Cysteine link (Tue May 09 2006 - 08:20:50 CDT)
  • LES and minimalization (Tue Feb 21 2006 - 02:42:06 CST)
• Taeho Kim
  • Re: free energy calculate (Fri Jun 16 2006 - 02:45:55 CDT)
  • Re: free energy calculate (Fri Jun 16 2006 - 01:30:29 CDT)
  • free energy calculate (Fri Jun 16 2006 - 00:52:16 CDT)
  • Re: Basic question. (Fri May 26 2006 - 22:03:20 CDT)
  • Basic question. (Fri May 26 2006 - 20:24:54 CDT)
  • How to measure of radius of a molecules? (Mon Apr 10 2006 - 03:30:28 CDT)
  • I want to know how to make pdb file with 2d structrure file. (Fri Feb 10 2006 - 02:14:31 CST)
  • Interaction between metal and metal-water. (Fri Nov 25 2005 - 10:39:22 CST)
• Tamal Banerjee
  • restart the simulation (Fri Jul 14 2006 - 23:06:25 CDT)
  • Rattle Algorithm (Thu Jul 06 2006 - 01:52:49 CDT)
  • Data from Output file (Mon Jul 03 2006 - 03:01:48 CDT)
  • a basic question (Sun May 07 2006 - 12:04:31 CDT)
  • why pressure is fluctuating so much (Thu Apr 27 2006 - 22:40:28 CDT)
  • residue name and segment name (Thu Apr 06 2006 - 02:05:07 CDT)
  • Molecular Volume (Thu Mar 30 2006 - 22:22:26 CST)
  • How to contract the PBC cell (Mon Mar 27 2006 - 01:21:06 CST)
  • Pressure -ve (Wed Mar 08 2006 - 08:49:57 CST)
  • PSF file generation (Tue Aug 16 2005 - 00:16:46 CDT)
  • Unable to Generate PSF file ! (Mon Jul 04 2005 - 08:09:43 CDT)
• tamal_at_iitk.ac.in
  • Expansion of DCD (Mon Nov 20 2006 - 23:20:04 CST)
  • Equilibriation Info (Mon Oct 23 2006 - 13:52:14 CDT)
  • Constraining angles ?? (Fri Sep 08 2006 - 13:36:31 CDT)
• taojinwuhan_at_sohu.com
  • about counterions (Tue Dec 19 2006 - 21:18:19 CST)
  • Is it equilibrated? (Mon Dec 04 2006 - 01:45:49 CST)
  • help:autopsf changed the structure! (Sun Nov 26 2006 - 19:57:42 CST)
  • dcd file is too large (Mon Nov 13 2006 - 02:52:41 CST)
• Taras Pogorelov
  • Re: MMPBSA... (Wed May 03 2006 - 19:39:09 CDT)
• TCWu
  • Problem about the energy change of refold of SMD protein (Wed Apr 05 2006 - 18:53:35 CDT)
• tepper_at_amolf.nl
  • Problem with NAMD on Opteron cluster (Fri Nov 11 2005 - 10:36:39 CST)
• Thomas C. Bishop
  • scaling NAMD2.6B1 on IBM P5 (Tue Apr 25 2006 - 14:44:33 CDT)
• Thomas Caulfield
  • Re: namd 2.62b FATAL ERROR: Memory allocation failed on processor 0 or higher (Wed Sep 06 2006 - 11:55:15 CDT)
  • namd 2.62b FATAL ERROR: Memory allocation failed on processor 0 or higher (Sun Sep 03 2006 - 20:54:06 CDT)
• Tim Sirianni
  • RE: RE: [Scalex86 - linux] FW: segfaults in mm_malloc (Fri Jul 01 2005 - 17:46:03 CDT)
  • RE: [Scalex86 - linux] FW: segfaults in mm_malloc (Thu Jun 30 2005 - 18:20:44 CDT)
• Tim Skirvin
  • Free Cluster-Building Workshops - 16-17 Mar 2006, 20-21 Apr 2006 (Mon Feb 13 2006 - 14:41:24 CST)
• Timothy Isgro
  • Re: Minimizing and Equilibrating (Tue Jul 18 2006 - 12:19:50 CDT)
• Tirath Ramdas
  • Re: Error on Solaris (Sat Jun 25 2005 - 20:10:21 CDT)
  • Error on Solaris (Sat Jun 25 2005 - 12:57:53 CDT)
• Todd Trimble
  • RE: pressure calculation in applied field (Tue Nov 28 2006 - 17:30:21 CST)
  • RE: pressure calculation in applied field (Tue Nov 28 2006 - 17:18:24 CST)
  • pressure calculation in applied field (Tue Nov 28 2006 - 12:36:51 CST)
  • electric field (Tue Nov 21 2006 - 15:08:11 CST)
  • electric field (Thu Nov 16 2006 - 11:57:25 CST)
  • electric field and MISC (Wed Nov 15 2006 - 18:20:54 CST)
  • RE: electric field and MISC energy (Tue Nov 14 2006 - 10:46:19 CST)
  • electric field and MISC energy (Mon Nov 13 2006 - 10:44:29 CST)
  • electric field and MISC energy (Wed Nov 08 2006 - 16:19:02 CST)
  • splitting up long run leads to very different DNA conformation in E field (Thu Jul 13 2006 - 18:40:10 CDT)
• Tom Caulfield
  • Re: Re: Re: clarification(s) Re: namd 2.62b FATAL ERROR: Memory allocation failed on processor 0 or higher (Sat Sep 09 2006 - 16:35:50 CDT)
  • Re: clarification(s) Re: namd 2.62b FATAL ERROR: Memory allocation failed on processor 0 or higher (Thu Sep 07 2006 - 20:25:27 CDT)
  • tRNA simulation psf file generation explicit solvent and ions (Thu Jan 27 2005 - 02:29:47 CST)
• Troy Wymore
  • PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP (Fri Oct 14 2005 - 13:18:27 CDT)
  • PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP (Thu Sep 15 2005 - 11:22:29 CDT)
• Tru Huynh
  • Re: recompiling NAMD 2.6 from sources on CentOS-3 x86_64: Charm++ failing test (Tue Nov 21 2006 - 08:41:12 CST)
  • recompiling NAMD 2.6 from sources on CentOS-3 x86_64: Charm++ failing test (Mon Nov 13 2006 - 10:16:46 CST)
• Turman, Cheri M
  • RE: NAMD: HEM residue (Wed May 04 2005 - 17:07:50 CDT)
• Tyler Luchko
  • Re: ABF Simulation (Thu Jun 29 2006 - 00:11:42 CDT)
  • Re: ABF Simulation (Mon Jun 26 2006 - 19:45:02 CDT)
  • TCL forces and boundary conditions (Tue Jun 06 2006 - 18:23:27 CDT)
• TZU-LAN YEH
  • question about protein leaving water box (Fri Apr 14 2006 - 21:05:17 CDT)
• Ugur Akgun
  • ABF with z-coord (Fri Nov 24 2006 - 20:31:06 CST)
  • ABF - zCoord for more than one monomer (Thu Nov 09 2006 - 10:19:47 CST)
  • Re: ABF on a single molecule (Mon Nov 06 2006 - 16:33:24 CST)
  • Re: ABF on a single molecule (Mon Nov 06 2006 - 14:19:04 CST)
  • ABF on a single molecule (Thu Nov 02 2006 - 14:26:11 CST)
  • SMD From Force to Free Energy (Tue Oct 03 2006 - 09:54:07 CDT)
  • NAMD installation on Xeon64 cluster (Wed Sep 20 2006 - 16:21:16 CDT)
  • NAMD installation on Xeon64 cluster (Wed Sep 20 2006 - 16:08:07 CDT)
  • NAMD installation on Xeon64 cluster (Wed Sep 20 2006 - 15:40:16 CDT)
  • NAMD installation on Xeon64 cluster (Mon Sep 18 2006 - 16:20:42 CDT)
  • NAMD installation on Xeon64 cluster (Fri Sep 15 2006 - 16:50:14 CDT)
• Uma Mahankali
  • Warning in namd output file (Wed Nov 30 2005 - 18:27:48 CST)
  • Re: freeEnergy of conformational change of a test molecule (Thu Nov 17 2005 - 08:45:12 CST)
  • freeEnergy of conformational change of a test molecule (Wed Nov 16 2005 - 13:33:18 CST)
  • ABF for conformational analysis (Fri Nov 11 2005 - 16:54:11 CST)
  • Pair Interaction options (Thu Nov 10 2005 - 10:20:24 CST)
  • Only part of the protein is moving in MD simulation (Wed Oct 26 2005 - 10:12:13 CDT)
  • namd hangs (Mon Aug 08 2005 - 23:10:13 CDT)
  • Fixing atoms during simulation (Sat May 07 2005 - 19:33:49 CDT)
• valesrdp
  • Minimization with NAMD (Mon May 09 2005 - 09:17:57 CDT)
  • Minimization after a MD simulation (Tue May 03 2005 - 04:48:14 CDT)
  • (no subject) (Thu Apr 21 2005 - 03:54:58 CDT)
• Vani Krishna
  • Flushing output: MPI version of NAMD on AMD64 (Tue Oct 10 2006 - 00:00:31 CDT)
  • Re: about abf (Tue Sep 26 2006 - 22:41:06 CDT)
  • Re: NAMD installation on Cray XD1 (AMD opteron 64-bit) (Tue Sep 26 2006 - 22:36:21 CDT)
  • NAMD installation on Cray XD1 (AMD opteron 64-bit) (Wed Sep 20 2006 - 23:46:37 CDT)
  • center of mass motion: problems (Thu Dec 08 2005 - 16:27:06 CST)
  • PMF calculation using fixed restraints (Sun Nov 06 2005 - 12:26:22 CST)
  • restarting SMD jobs (Tue Jul 26 2005 - 20:25:38 CDT)
  • FEP output in NAMD (Tue Apr 05 2005 - 11:26:39 CDT)
  • constraining center of mass-constrained MD (Thu Feb 17 2005 - 02:51:12 CST)
• Vinit Rege
  • Unnatural Bond lengths (Sat Nov 11 2006 - 01:56:35 CST)
  • Re: System of POPC bilayer (Fri Nov 10 2006 - 12:53:06 CST)
  • Re: Another question on Diffusion (Wed Nov 08 2006 - 19:02:30 CST)
  • Another question on Diffusion (Wed Nov 08 2006 - 13:15:49 CST)
  • System of POPC bilayer (Wed Nov 08 2006 - 12:21:56 CST)
  • residue name LIP ... ! (Sat Nov 04 2006 - 19:52:26 CST)
• Vishal Kopardé
  • FixedAtomForces and ExcludeFromPressure (Thu Nov 30 2006 - 19:39:49 CST)
  • Re: RATTLE errors in equilibration (Wed Nov 29 2006 - 12:30:24 CST)
  • TIP4P water (Mon Nov 27 2006 - 17:53:34 CST)
  • positive VDW?? (Tue Nov 21 2006 - 15:34:31 CST)
  • NAMD for inorganics?? (Tue Nov 21 2006 - 15:18:47 CST)
  • Hydrogens collapsing (Wed Nov 01 2006 - 21:20:50 CST)
  • Atoms moving too fast error (Fri Oct 27 2006 - 17:12:23 CDT)
  • Ion-protein and protein-protein interactions (Thu Oct 26 2006 - 12:50:48 CDT)
  • Re: Warnings of psfgen (Wed Oct 25 2006 - 17:09:15 CDT)
  • Warnings of psfgen (Wed Oct 25 2006 - 08:37:30 CDT)
  • RATTLE Error (Wed Oct 25 2006 - 06:59:18 CDT)
• Viswanadham Sridhara
  • Re: VMD Command (Tue Mar 21 2006 - 12:31:23 CST)
• vivek sharma
  • RE: Fatal error: (Thu Aug 04 2005 - 09:04:30 CDT)
  • Fatal error: (Thu Aug 04 2005 - 07:58:30 CDT)
  • psfgen/auto none (Thu Jun 30 2005 - 02:50:30 CDT)
  • Re: namdplot not working (Fri Feb 11 2005 - 16:04:06 CST)
• Vlad Cojocaru
  • Re: LES : size (Mon Nov 13 2006 - 03:51:46 CST)
  • Re: is possible to remove the waterbox before running VMD (Thu Mar 09 2006 - 13:26:53 CST)
  • Re: LES with PME and neutralizing charges (Thu Mar 09 2006 - 13:03:10 CST)
  • last call for early registrations for "Horizons2005" (Fri Jan 14 2005 - 07:19:00 CST)
• wang
  • Re: two chain in pdb file (Tue Aug 01 2006 - 03:19:06 CDT)
  • Re: About the module of "External Electric Field " (Tue Jul 18 2006 - 19:50:43 CDT)
  • About the unit of "efield" (Tue Jul 18 2006 - 00:28:03 CDT)
  • About the module of "External Electric Field " (Wed Jul 12 2006 - 01:47:29 CDT)
  • Re: Rattle Algorithm (Thu Jul 06 2006 - 03:21:15 CDT)
  • Re: About the error of "Tcl interface" (Thu Jul 06 2006 - 00:26:31 CDT)
  • About the error of "Tcl interface" (Wed Jul 05 2006 - 21:05:27 CDT)
  • Re: The problem of "SMD and smd.tcl" (Mon Jul 03 2006 - 22:58:24 CDT)
  • Re: Is the GBSA model in NAMD ? (Tue Jun 13 2006 - 04:03:08 CDT)
  • Is the GBSA model in NAMD ? (Tue Jun 13 2006 - 01:42:14 CDT)
  • PMF error (Mon Jun 05 2006 - 21:38:18 CDT)
• Wang Tianhua
  • loodking or topology file for zinc finger (Tue Mar 08 2005 - 19:43:02 CST)
• Wang, Boyang
  • Building PDB files for DNA. (Fri Dec 15 2006 - 10:29:55 CST)
  • Pressure Driven flow of Water (Tue Feb 14 2006 - 15:14:02 CST)
  • Installing NAMD on beowulf cluster, 64 bit, opteron, 4 processors. (Mon Jun 06 2005 - 22:23:59 CDT)
  • Dihedral and Improper, Nonbonded. (Sun May 01 2005 - 22:46:22 CDT)
  • a target molecule in a water box. (Mon Apr 25 2005 - 21:12:02 CDT)
• Wei Chen
  • Re: FEP.... (Fri Nov 11 2005 - 11:28:20 CST)
  • ensemble (Wed Oct 05 2005 - 16:34:12 CDT)
  • Re: fep (Tue Jul 26 2005 - 17:05:39 CDT)
  • RE: cellBasisVectors and xsc files (Wed Jul 20 2005 - 10:47:21 CDT)
  • Re: changing file (Wed Jul 20 2005 - 10:43:24 CDT)
  • Re: FEP - one long simulation vs many short ones (Sat Jul 02 2005 - 12:13:51 CDT)
  • convert_from_namd_to_amber (Tue Jun 28 2005 - 22:02:18 CDT)
  • Re: basic: combining two pdb files? (Thu Jun 23 2005 - 21:03:30 CDT)
  • Re: restart syntax (Tue Jun 21 2005 - 16:26:19 CDT)
  • Pressure_control (Fri Jun 17 2005 - 21:41:19 CDT)
  • Re: binding free energy , binding constant (Fri Jun 17 2005 - 15:46:35 CDT)
  • MM/PBSA (Mon Jun 13 2005 - 15:41:45 CDT)
  • RE: PSFGEN (Sat May 28 2005 - 20:42:40 CDT)
  • PSFGEN (Fri May 27 2005 - 15:10:30 CDT)
  • pressure (Mon May 23 2005 - 19:50:28 CDT)
  • Re: FEP (Thu May 12 2005 - 11:19:48 CDT)
  • FEP (Wed May 11 2005 - 13:49:53 CDT)
  • Re: how to restart/continue NAMD run (Fri May 06 2005 - 15:47:25 CDT)
  • (no subject) (Wed Apr 27 2005 - 11:04:07 CDT)
  • Re: a target molecule in a water box. (Mon Apr 25 2005 - 22:33:54 CDT)
  • RE: glucose CHARMM force field (Tue Mar 29 2005 - 23:05:06 CST)
  • computing resource (Mon Mar 14 2005 - 23:08:48 CST)
  • NAMD_utilities (Tue Mar 01 2005 - 12:43:56 CST)
  • Re: alchemify FEP (Fri Feb 18 2005 - 12:54:44 CST)
  • alchemify FEP (Thu Feb 17 2005 - 13:14:20 CST)
  • FEP (Tue Feb 01 2005 - 11:15:24 CST)
• Wei Fu
  • protein unfolding -- Phi MD (Tue Nov 28 2006 - 13:59:29 CST)
• Wei Zhuang
  • which force field to choose (Sat Jan 14 2006 - 14:02:25 CST)
  • questions about running namd on NCSA cluster tungsten (Fri Oct 28 2005 - 17:09:22 CDT)
  • Myrinet NAMD (Fri Oct 28 2005 - 14:01:21 CDT)
  • Re: Re: urestraint doesn't work (Thu Oct 27 2005 - 21:45:37 CDT)
  • Re: Re: urestraint doesn't work (Thu Oct 27 2005 - 20:35:22 CDT)
  • urestraint doesn't work (Thu Oct 27 2005 - 16:56:55 CDT)
  • running NAMD on tungsten (Tue Oct 18 2005 - 01:59:57 CDT)
  • implicit solvent (Thu Jun 09 2005 - 17:47:48 CDT)
  • How to read charmm binary trajectory file using home-made C/C++ code (Tue Mar 22 2005 - 14:39:15 CST)
• weikai
  • Can NAMD control pressure gradually increase? (Fri Oct 21 2005 - 02:30:41 CDT)
  • Can NAMD deal with solid-state system? (Wed Aug 31 2005 - 21:57:21 CDT)
• Wen Li
  • Re: vmd-l: conformational alignment (Thu Mar 31 2005 - 12:26:20 CST)
  • Re: vmd-l: conformational alignment (Thu Mar 31 2005 - 10:32:51 CST)
  • Re: vmd-l: conformational alignment (Thu Mar 31 2005 - 10:24:18 CST)
  • conformational alignment (Wed Mar 30 2005 - 15:21:26 CST)
  • run NPT equilibration (Tue Feb 08 2005 - 11:30:07 CST)
  • Re: question on running NAMD2 using Amber files (Mon Feb 07 2005 - 12:15:41 CST)
  • question on running NAMD2 using Amber files (fwd) (Mon Feb 07 2005 - 10:25:32 CST)
  • question on running NAMD2 using Amber files (Mon Feb 07 2005 - 08:40:56 CST)
• Wenyu Zhong
  • Re: If I run NAMD on small computer, which processor is the best for NAMD under Linux? (Fri Jul 14 2006 - 08:00:15 CDT)
  • Re: How to deal with a long path in ABF simulation? (Thu Apr 27 2006 - 07:28:34 CDT)
  • How to deal with a long path in ABF simulation? (Wed Apr 26 2006 - 09:34:31 CDT)
• Westley A Sherman
  • Charged Atoms in External Magnetic Field (Thu Nov 16 2006 - 18:50:12 CST)
• wmsmith
  • RE: Velocity after heating (Mon Jul 18 2005 - 13:04:14 CDT)
  • RE: Some questions about TCL (Tue Jul 05 2005 - 17:20:54 CDT)
  • RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) (Wed Jun 29 2005 - 13:43:44 CDT)
  • cross products (Mon Jun 27 2005 - 14:35:18 CDT)
  • Accessing beta / occupancy values from NAMD tcl (Mon Jun 27 2005 - 10:24:47 CDT)
• Wolbach, Jeffrey P \(WOLBACH\)
  • RE: is possible to remove the waterbox before running VMD (Thu Mar 09 2006 - 13:45:20 CST)
  • RE: Adjusting Density of waterbox used by solvate (Mon Jun 13 2005 - 11:36:11 CDT)
  • RE: using namd to compute energies (Wed Feb 16 2005 - 07:30:41 CST)
• WONG Hua
  • steered molecular dynamics docking (Wed May 18 2005 - 04:55:37 CDT)
• wzhuang
  • OPLS force field for carbon tetrachloride ( ccl4 ) ? (Fri Apr 28 2006 - 02:15:44 CDT)
• wzhuang_at_uci.edu
  • Re: fixed atoms (Wed Oct 26 2005 - 11:12:25 CDT)
  • Myrinet vs. Infiniband (Wed Apr 06 2005 - 12:36:10 CDT)
• xiaojing gong
  • how to use reaction field in NAMD (Sun Dec 10 2006 - 21:21:33 CST)
  • histidine protonation (Thu Nov 02 2006 - 08:18:27 CST)
  • FATAL ERROR: pairlist i_upper mismatch! (Mon Jul 17 2006 - 21:43:46 CDT)
  • If I run NAMD on small computer, which processor is the best for NAMD under Linux? (Fri Jul 14 2006 - 02:25:48 CDT)
  • what does "syntax error" mean in VMD? and does confinment to some residue will cause error? (Thu Jun 29 2006 - 23:56:51 CDT)
  • RE£º Re: £º Re: problems for runing NAMD on parallel computers (Thu Jun 29 2006 - 23:32:46 CDT)
  • problems for runing NAMD on parallel computers (Wed Jun 28 2006 - 09:15:44 CDT)
  • NAMD is unstable on myrinet connecting cpus (Wed Apr 26 2006 - 09:15:21 CDT)
  • error about tclForcesScript (Mon Apr 10 2006 - 09:21:13 CDT)
  • Constrain only in Z direction (Sun Apr 09 2006 - 22:32:02 CDT)
  • questions about the use of HIS residue (Sun Apr 02 2006 - 08:05:53 CDT)
  • RE£º Re: how to plugin catDCD intoqVMD=20of=20windows=20version?= (Wed Mar 29 2006 - 19:17:03 CST)
  • how to plugin catDCD into VMD of windows version (Wed Mar 29 2006 - 07:07:02 CST)
  • q=D8=B8=B4=A3=BA=20=20Re:=20Re=A3=BA=20Re:=20?= qhow=20to=20constrain=20a=20dihedral=20angle=3F?= (Wed Mar 29 2006 - 06:31:46 CST)
  • Re£º Re: how to constrain a dihedralqangle=3F?= (Tue Mar 28 2006 - 08:20:02 CST)
  • Re£º Re: how to constrain a dihedralqangle=3F?= (Sat Mar 25 2006 - 08:17:29 CST)
  • re£º force over selection (Thu Mar 23 2006 - 19:12:22 CST)
  • how to constrain a dihedral angle? (Thu Mar 23 2006 - 18:55:34 CST)
  • using restart file or .coor/.vel file (Wed Mar 22 2006 - 08:44:57 CST)
  • question about the parameter "exclude" (Tue Mar 21 2006 - 07:20:31 CST)
  • Re:Re:error caused by lipid membrane (Mon Mar 20 2006 - 20:33:42 CST)
  • error caused by atoms of lipid membrane (Mon Mar 20 2006 - 06:27:07 CST)
  • what does "patch" mean? (Sun Mar 19 2006 - 20:04:25 CST)
  • Re: error in membrane producing (Sun Mar 19 2006 - 18:00:04 CST)
  • error in membrane producing (Fri Mar 17 2006 - 21:21:15 CST)
  • error in membrane producing (Fri Mar 17 2006 - 19:30:25 CST)
  • How can I increase the computing rate on the computer cluster (Sun Oct 30 2005 - 05:44:24 CST)
  • Is there a method to choose what is saved in DCD files (Sun Oct 02 2005 - 09:34:02 CDT)
  • temperature coupling and pressure coupling (Mon Sep 26 2005 - 01:44:16 CDT)
  • energy minimization (Sun Sep 25 2005 - 22:05:32 CDT)
  • energy minimization (Sun Sep 25 2005 - 21:57:00 CDT)
  • problem about equilibration (Mon Aug 15 2005 - 08:30:44 CDT)
  • constraint constant in equilibration (Sat Jul 30 2005 - 00:19:26 CDT)
  • the difference between the min_nacl.vel and min_nacl.restart.vel (Sat Jul 23 2005 - 07:59:48 CDT)
  • constrain or fix the system only in Z direction (Thu Jul 21 2005 - 07:01:33 CDT)
  • pressure control in config file (Sun Jul 17 2005 - 20:06:16 CDT)
  • how to build AQP1 tetramer (Thu Jun 23 2005 - 21:31:13 CDT)
• Xiaoqing Wang
  • how to use the dual-processor machines (Sat Jul 30 2005 - 08:37:39 CDT)
  • Re: system becomes very large when set LangevinPiston on (Wed Jul 27 2005 - 21:32:01 CDT)
  • Re: system becomes very large when set LangevinPiston on (Tue Jul 26 2005 - 22:02:34 CDT)
  • Re: system becomes very large when set LangevinPiston on (Tue Jul 26 2005 - 04:48:13 CDT)
  • system becomes very large when set LangevinPiston on (Sun Jul 24 2005 - 22:06:43 CDT)
  • Re: "make" Linux-amd64-g++ error (Mon May 16 2005 - 09:08:03 CDT)
  • Re: "make" Linux-amd64-g++ error (Mon May 16 2005 - 07:45:38 CDT)
  • "make" Linux-amd64-g++ error (Sun May 15 2005 - 22:31:47 CDT)
  • What's wrong with my namd2 (Sun May 15 2005 - 07:01:13 CDT)
  • Re: different result from different cpu (Tue May 10 2005 - 19:59:45 CDT)
  • different result from different cpu (Tue May 10 2005 - 07:31:31 CDT)
  • compile "mpi" charm++ on amd64 (Mon May 09 2005 - 22:09:32 CDT)
  • RE: Periodic cell has become too small for original patch grid (Thu Apr 14 2005 - 09:29:02 CDT)
  • Periodic cell has become too small for original patch grid (Wed Apr 13 2005 - 03:38:33 CDT)
  • Re: any script to build membrane+protein+solvent? (Fri Apr 08 2005 - 21:23:48 CDT)
  • add water on the top of the protein border (Wed Apr 06 2005 - 09:11:47 CDT)
  • BUG ALERT: Mother atom with hydrogenGroupSize of 0! (Mon Jan 24 2005 - 01:26:21 CST)
  • Obtain message from MD (Tue Jan 18 2005 - 01:30:23 CST)
  • constraint failure (Tue Jan 11 2005 - 21:07:08 CST)
  • equilibrated the system (Tue Jan 11 2005 - 08:43:17 CST)
• Xinghua Shi
  • RE: NAMD 2.6 in IBM SP (Sun Nov 06 2005 - 05:41:18 CST)
  • NAMD 2.6 in IBM SP (Sat Nov 05 2005 - 09:41:35 CST)
  • NAMD 2.6 in IBM SP (Sat Nov 05 2005 - 09:12:12 CST)
• Xiongce Zhao
  • Re: high vdw energy (Fri Dec 01 2006 - 07:44:12 CST)
  • 2D Ewald summation (Thu Aug 10 2006 - 10:08:46 CDT)
  • NAMD for Xeon clusters (Wed Sep 28 2005 - 17:13:06 CDT)
  • rotation constraint angular velocity (Wed Feb 16 2005 - 10:32:14 CST)
  • 1 D Periodic Boundary (Tue Feb 15 2005 - 14:43:42 CST)
  • how to image molecules back into a PBC box (Tue Feb 15 2005 - 09:08:21 CST)
• Xiuping Tao
  • (no subject) (Thu Feb 16 2006 - 15:49:52 CST)
• yangbing00_at_mails.tsinghua.edu.cn
  • About the potential of NAMD (Thu Oct 06 2005 - 22:53:46 CDT)
  • About the potantial of IONS (Thu Oct 06 2005 - 22:16:17 CDT)
  • About Potential Addition in NAMD (Wed Sep 28 2005 - 06:45:18 CDT)
  • About ions Representation in NAMD (Wed Sep 28 2005 - 06:40:45 CDT)
• Yao Fan
  • Distance restraint (Wed Nov 22 2006 - 16:50:04 CST)
• yi wang
  • Re: RMSD increases after restarts, decreases at the end of run (Fri Aug 25 2006 - 15:25:49 CDT)
  • Re: extracting waters from DCD (Wed Aug 09 2006 - 10:38:00 CDT)
  • Fwd: extracting waters from DCD (Tue Aug 08 2006 - 16:50:55 CDT)
  • Re:Alchemical Free Energy Perturbation Simulation (Wed Aug 02 2006 - 12:10:51 CDT)
• Yong Zhang
  • help: how to scale the velocities by a factor for a subset of the system? (Tue Sep 05 2006 - 21:59:25 CDT)
• youbin tu
  • is there any maximum limt of atom numbers in VMD or NAMD? (Tue Nov 28 2006 - 23:00:41 CST)
  • Re: where is PSUL? Heme cystein link question? (Fri Aug 11 2006 - 13:38:22 CDT)
  • where is PSUL? Heme cystein link question? (Thu Aug 10 2006 - 11:01:50 CDT)
• Yu Wang
  • parameter file for DAD (Fri Apr 07 2006 - 09:18:55 CDT)
  • pairInteractionSelf (Fri Feb 10 2006 - 03:19:34 CST)
• Yuqi Liu
  • How can I do protein complex's simulation? (Mon Oct 02 2006 - 18:46:13 CDT)
• Zach Hensel
  • Re: Buffering problems while attempting to read log file (Fri Feb 10 2006 - 14:20:11 CST)
  • Buffering problems while attempting to read log file (Fri Feb 10 2006 - 11:08:29 CST)
• Zhi Qi
  • help-minimization and equilibration of Ubiquitin in a water box (Thu Jan 12 2006 - 18:38:00 CST)
  • help-minimization and equilibration of Ubiquitin in a water box (Wed Jan 11 2006 - 14:13:45 CST)
• ziemys_at_ecr6.ohio-state.edu
  • cluster / scratch space (Thu May 11 2006 - 09:28:06 CDT)
  • generation of non-standart charmm topology (Wed Jan 11 2006 - 12:08:12 CST)
• ×Þ¿¡
  • Question about REMD (Wed Oct 25 2006 - 08:37:00 CDT)
• ËïæÃæÃ
  • about abf (Tue Sep 26 2006 - 08:30:24 CDT)
  • xplor parameter to charmm (Fri Jul 08 2005 - 03:54:19 CDT)
  • about *.psf (Thu May 26 2005 - 23:59:07 CDT)
• ËïÍ¥¹ã
  • A strange phenomenon in my dynamics system,any suggestion? (Fri Apr 07 2006 - 21:29:32 CDT)
  • Some problem on compiling NAMD (Thu Dec 15 2005 - 21:24:18 CST)
• Íõº£Ãû
  • parameter and topology for cyclodextrin! (Mon Apr 24 2006 - 23:58:57 CDT)
• κ¿­
  • Compiling the NAMD on HPUX-ia64 system Error! (Sat Jan 15 2005 - 08:35:00 CST)
  • How to Compile NAMD on HPUX-ia64 system~ (Fri Jan 14 2005 - 04:56:14 CST)
• ÎâºéÃ÷
  • how to constrains the smd atom on a line when do my smd simulation?? (Mon Dec 05 2005 - 01:59:09 CST)
  • problem when do equilibration (Sun Aug 21 2005 - 03:40:44 CDT)