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NAMD-L: By Thread

By Thread

7665 messages sorted by: [ author ] [ date ] [ subject ] [ attachment ]
About this archive

Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Sun May 11 2008 - 12:32:05 CDT

• puase MD integration to communicate between jobs Floris Buelens (Sun May 11 2008 - 12:31:50 CDT)
• Run NPT ensemble simulation with sphericalBC? Yinglong Miao (Fri May 09 2008 - 13:37:04 CDT)
• 2 pdb files Christine Horejs DI (Fri May 09 2008 - 06:58:01 CDT)
  • Re: 2 pdb files Peter Freddolino (Fri May 09 2008 - 07:15:00 CDT)
• spermine force field bqluan (Thu May 08 2008 - 18:47:54 CDT)
• spermine force field bqluan (Thu May 08 2008 - 17:24:01 CDT)
• Trajectory file formats & structural alignment Wei Huang (Thu May 08 2008 - 15:46:13 CDT)
  • Re: Trajectory file formats & structural alignment Giovanni Bellesia (Thu May 08 2008 - 18:00:18 CDT)
• running NAMD with ranger@tacc Lei Shi (Wed May 07 2008 - 13:08:50 CDT)
  • Re: running NAMD with ranger@tacc Peter Freddolino (Wed May 07 2008 - 13:23:36 CDT)
• recalculating energy using dcd file gurvisha_at_leadinvent.com (Wed May 07 2008 - 09:19:14 CDT)
  • Re: recalculating energy using dcd file JC Gumbart (Wed May 07 2008 - 17:08:16 CDT)
• pbc Ahlam Al-Rawi (Tue May 06 2008 - 18:41:33 CDT)
• Negative Pressure Fabio Zegarra (Tue May 06 2008 - 15:44:53 CDT)
  • Re: Negative Pressure Vlad Cojocaru (Wed May 07 2008 - 09:39:02 CDT)
• Question about a shift in rmsd using fixedatom off snoze pa (Tue May 06 2008 - 11:47:45 CDT)
• NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled Ghalib Bello (Mon May 05 2008 - 23:02:45 CDT)
  • Re: NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled Peter Freddolino (Tue May 06 2008 - 00:37:54 CDT)
• Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) snoze pa (Mon May 05 2008 - 16:49:43 CDT)
  • Re: Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) snoze pa (Tue May 06 2008 - 10:20:47 CDT)
• question related to rmsd snoze pa (Mon May 05 2008 - 15:03:07 CDT)
  • Re: question related to rmsd JC Gumbart (Mon May 05 2008 - 16:19:47 CDT)
    • Re: question related to rmsd snoze pa (Mon May 05 2008 - 16:35:21 CDT)
      • Re: question related to rmsd JC Gumbart (Mon May 05 2008 - 17:58:43 CDT)
• help with calcforces Prabhakar Bhimalapuram (Fri May 02 2008 - 13:32:22 CDT)
• error on installing ImageMagick Hero (Thu May 01 2008 - 13:54:57 CDT)
  • Re: error on installing ImageMagick Peter Freddolino (Thu May 01 2008 - 14:02:39 CDT)
  • Re: error on installing ImageMagick Richard Law (Thu May 01 2008 - 14:53:37 CDT)
• electrostatics NAMD vs CHARMM Arturas Ziemys (Thu May 01 2008 - 11:29:49 CDT)
• langevin dynamics and random seeds Peter Freddolino (Thu May 01 2008 - 11:44:40 CDT)
• How to save the animation movie into files? Hero (Thu May 01 2008 - 01:48:35 CDT)
  • Re: How to save the animation movie into files? Jianhui Tian (Thu May 01 2008 - 09:16:50 CDT)
• compilaton error Swarna Patra (Wed Apr 30 2008 - 23:32:45 CDT)
  • Re: compilaton error Leonardo Trabuco (Thu May 01 2008 - 11:32:22 CDT)
    • Re: compilaton error Swarna Patra (Thu May 01 2008 - 20:04:47 CDT)
      • Re: compilaton error Leonardo Trabuco (Thu May 01 2008 - 23:47:06 CDT)
      • Re: compilaton error Swarna Patra (Fri May 02 2008 - 01:06:48 CDT)
      • Re: compilaton error Leonardo Trabuco (Fri May 02 2008 - 01:25:35 CDT)
• Running NAMD on cluster sudipta sinha (Wed Apr 30 2008 - 04:41:53 CDT)
  • Re: Running NAMD on cluster Philip Peartree (Wed Apr 30 2008 - 07:21:28 CDT)
• Neutral arginine patch in topology file. Alexandre F. G. (Tue Apr 29 2008 - 16:45:29 CDT)
  • RE: Neutral arginine patch in topology file. JC Gumbart (Thu May 01 2008 - 00:15:28 CDT)
• NAMD on a remote UNIX and VMD on local Windows - does this work? S.K. Ghosh (Tue Apr 29 2008 - 13:40:29 CDT)
  • Re: NAMD on a remote UNIX and VMD on local Windows - does this work? Tao Wu (Tue Apr 29 2008 - 15:49:57 CDT)
• NAMD on a remote UNIX and VMD on local Windows - does this work? S.K. Ghosh (Tue Apr 29 2008 - 13:31:34 CDT)
• velocity units in .vel file Neelanjana Sengupta (Mon Apr 28 2008 - 15:21:06 CDT)
  • Re: velocity units in .vel file Joshua D. Moore (Mon Apr 28 2008 - 17:47:48 CDT)
• How to save the animation movie into files? Hero (Mon Apr 28 2008 - 00:23:49 CDT)
  • Re: How to save the animation movie into files? Low Soo Mei (Mon Apr 28 2008 - 00:51:37 CDT)
• A question about restaints force. Yang Gao (Fri Apr 25 2008 - 11:28:20 CDT)
• q=D8=B8=B4=A3=BA=20Re:=20=20nodelist=20being=20ignore?= d during paralleling cong chen (Sun Apr 27 2008 - 21:50:34 CDT)
• How to save vmd figures to jpg or tiff? Hero (Sun Apr 27 2008 - 16:18:35 CDT)
• help with TCL forces script Jim Pfaendtner (Sun Apr 27 2008 - 05:47:30 CDT)
• nodelist being ignored during paralleling cong chen (Sat Apr 26 2008 - 22:24:17 CDT)
• How to play molecule trajectory with VMD? Hero (Sat Apr 26 2008 - 20:00:52 CDT)
• tracing not available with CMK_OPTIMIZE! Semorale (Sat Apr 26 2008 - 16:26:13 CDT)
• How to run namd2 on ubuntu linux? Hero (Sat Apr 26 2008 - 14:45:01 CDT)
  • Re: How to run namd2 on ubuntu linux? Leandro Martínez (Sat Apr 26 2008 - 16:10:35 CDT)
• Re: install VMD on Ubuntu Hero (Sat Apr 26 2008 - 14:38:19 CDT)
• install VMD on Ubuntu Hero (Sat Apr 26 2008 - 14:09:39 CDT)
  • Re: install VMD on Ubuntu Low Soo Mei (Sat Apr 26 2008 - 14:25:32 CDT)
• Configurations-Statistical Mechanics Mert Gür (Sat Apr 26 2008 - 13:00:08 CDT)
• How to install VMD and NAMD on Ubuntu? Hero (Sat Apr 26 2008 - 12:55:17 CDT)
• FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 05:56:26 CDT)
  • Re: FEP triangular bracket average Jerome Henin (Sat Apr 26 2008 - 11:30:37 CDT)
    • Re: FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 13:14:29 CDT)
      • Re: FEP triangular bracket average Jerome Henin (Sat Apr 26 2008 - 13:54:31 CDT)
      • Re: FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 15:26:21 CDT)
• install NAMD on Ubuntu Hero (Fri Apr 25 2008 - 23:46:07 CDT)
  • Re: install NAMD on Ubuntu Alexandre A. Vakhrouchev (Sat Apr 26 2008 - 01:12:30 CDT)
• A question about restaints force. Yang Gao (Fri Apr 25 2008 - 15:23:01 CDT)
  • Re: A question about restaints force. Gungor Ozer (Fri Apr 25 2008 - 16:17:13 CDT)
    • Re: A question about restaints force. Victor Ovchinnikov (Fri Apr 25 2008 - 17:48:40 CDT)
• Time factor Alexandre A. Vakhrouchev (Thu Apr 24 2008 - 23:16:04 CDT)
• TMD AND RIGIDBONDS Samuel Morales (Wed Apr 23 2008 - 20:50:43 CDT)
• compiling namd: cannot find -lmodulecommlib Corenflos, Steven Charles (Wed Apr 23 2008 - 14:42:18 CDT)
• reversing constant velocity SMD Jeff Forbes (Wed Apr 23 2008 - 14:36:16 CDT)
  • Re: reversing constant velocity SMD Peter Freddolino (Thu Apr 24 2008 - 08:24:55 CDT)
• VMD-NAMD-commands Vivek Sharma (Fri Apr 18 2008 - 23:06:12 CDT)
  • Re: VMD-NAMD-commands Alexandre A. Vakhrouchev (Sat Apr 19 2008 - 00:16:08 CDT)
  • Re: VMD-NAMD-commands Peter Freddolino (Sun Apr 20 2008 - 20:20:27 CDT)
    • Re: VMD-NAMD-commands Vivek Sharma (Sun Apr 20 2008 - 21:06:36 CDT)
• Format of Binary Restart and Output Coordinate and Velocity Files Joshua D. Moore (Fri Apr 18 2008 - 19:34:20 CDT)
• RE: Reading and writing Binary Restart or Output files with Fortran Joshua D. Moore (Fri Apr 18 2008 - 19:25:55 CDT)
  • Re: RE: Reading and writing Binary Restart or Output files with Fortran V.Ovchinnikov (Sat Apr 19 2008 - 10:40:46 CDT)
    • Re: RE: Reading and writing Binary Restart or Output files with Fortran Leandro Martínez (Sat Apr 19 2008 - 12:51:58 CDT)
      • Re: RE: Reading and writing Binary Restart or Output files with Fortran V.Ovchinnikov (Sat Apr 19 2008 - 16:10:32 CDT)
• question on ABF L. Michel Espinoza-Fonseca (Fri Apr 18 2008 - 18:40:08 CDT)
  • Re: question on ABF Jerome Henin (Fri Apr 18 2008 - 22:14:45 CDT)
    • Re: question on ABF Chris Chipot (Mon Apr 21 2008 - 07:01:39 CDT)
      • Re: question on ABF L. Michel Espinoza-Fonseca (Mon May 05 2008 - 09:16:44 CDT)
    • RE: question on ABF Xu, Jiancong (Mon Apr 21 2008 - 10:35:16 CDT)
• What does "cellOrigin" really mean? bo liu (Fri Apr 18 2008 - 09:38:56 CDT)
  • What does "cellOrigin" really mean? bo liu (Wed Apr 23 2008 - 05:48:45 CDT)
    • Re: What does "cellOrigin" really mean? Alexandre A. Vakhrouchev (Wed Apr 23 2008 - 08:36:51 CDT)
• Multiple Different Harmonic Restraint Defitions Joshua Adelman (Thu Apr 17 2008 - 20:13:23 CDT)
• 2 molecule pair interactions Arturas Ziemys (Wed Apr 16 2008 - 16:26:27 CDT)
  • Re: 2 molecule pair interactions Peter Freddolino (Wed Apr 16 2008 - 17:11:52 CDT)
    • Re: 2 molecule pair interactions Ben Chern (Wed Apr 16 2008 - 23:49:33 CDT)
• Which namd on amd64? Corenflos, Steven Charles (Tue Apr 15 2008 - 15:26:25 CDT)
  • Re: Which namd on amd64? V.Ovchinnikov (Tue Apr 15 2008 - 17:19:43 CDT)
• binary install question winsvern_at_isu.edu (Tue Apr 15 2008 - 15:23:29 CDT)
• How to write different DCD files for separate MD runs in one simulation? Yinglong Miao (Tue Apr 15 2008 - 13:55:14 CDT)
  • Re: How to write different DCD files for separate MD runs in one simulation? Peter Freddolino (Tue Apr 15 2008 - 14:07:03 CDT)
  • Re: How to write different DCD files for separate MD runs in one simulation? V.Ovchinnikov (Tue Apr 15 2008 - 15:14:20 CDT)
    • Re: How to write different DCD files for separate MD runs in one simulation? Peter Freddolino (Tue Apr 15 2008 - 15:34:11 CDT)
      • Re: How to write different DCD files for separate MD runs in one simulation? V.Ovchinnikov (Tue Apr 15 2008 - 15:52:07 CDT)
      • Re: How to write different DCD files for separate MD runs in one simulation? Yinglong Miao (Tue Apr 15 2008 - 16:22:18 CDT)
• Electrostatics cutoff with PME Gianluca Interlandi (Tue Apr 15 2008 - 13:01:48 CDT)
  • Re: Electrostatics cutoff with PME L. Michel Espinoza-Fonseca (Tue Apr 15 2008 - 14:00:03 CDT)
    • Re: Electrostatics cutoff with PME Christopher Gillespie (Tue Apr 15 2008 - 15:21:06 CDT)
  • Re: Electrostatics cutoff with PME Peter Freddolino (Tue Apr 15 2008 - 14:31:35 CDT)
• temperature stepping during heating Low Soo Mei (Tue Apr 15 2008 - 05:21:43 CDT)
  • Re: temperature stepping during heating JC Gumbart (Thu Apr 17 2008 - 16:35:13 CDT)
    • Re: temperature stepping during heating Low Soo Mei (Thu Apr 17 2008 - 21:14:34 CDT)
      • Re: temperature stepping during heating Low Soo Mei (Fri Apr 18 2008 - 04:00:41 CDT)
• Problem with NAMD crashing without warning or error messages Jacob Durrant (Mon Apr 14 2008 - 20:36:25 CDT)
• help regarding NAMD equilibration snoze pa (Mon Apr 14 2008 - 18:11:46 CDT)
  • Re: help regarding NAMD equilibration Low Soo Mei (Tue Apr 15 2008 - 01:05:25 CDT)
    • Re: help regarding NAMD equilibration snoze pa (Tue Apr 15 2008 - 10:39:54 CDT)
    • Re: help regarding NAMD equilibration Dr. Luis Rosales León (Tue Apr 15 2008 - 12:39:24 CDT)
• NAMD CVS RUN ERROR Samuel Morales (Mon Apr 14 2008 - 16:13:31 CDT)
• rmsd_RNA_DNA sripad chandan (Mon Apr 14 2008 - 05:27:45 CDT)
• restarting ABF simulation Luca Bellucci (Mon Apr 14 2008 - 04:14:19 CDT)
  • Re: restarting ABF simulation Jerome Henin (Mon Apr 14 2008 - 06:43:40 CDT)
    • Re: restarting ABF simulation Luca Bellucci (Mon Apr 14 2008 - 08:04:01 CDT)
      • Re: restarting ABF simulation Jerome Henin (Mon Apr 14 2008 - 08:54:07 CDT)
      • Re: restarting ABF simulation Luca Bellucci (Mon Apr 14 2008 - 10:00:21 CDT)
    • Re: restarting ABF simulation Subramanian Vaitheeswaran (Mon Apr 14 2008 - 12:21:43 CDT)
      • Re: restarting ABF simulation Jerome Henin (Mon Apr 14 2008 - 13:58:57 CDT)
    • Re: restarting ABF simulation Subramanian Vaitheeswaran (Tue Apr 15 2008 - 11:16:36 CDT)
      • Re: restarting ABF simulation Jerome Henin (Tue Apr 15 2008 - 13:16:28 CDT)
• problem with VMD installation- libstdc++.so.5 => not found steve_at_phas.ubc.ca (Sat Apr 12 2008 - 22:03:05 CDT)
  • Re: problem with VMD installation- libstdc++.so.5 => not found Jerome Henin (Sun Apr 13 2008 - 14:59:21 CDT)
• spawn_namd_command How to properly execute this command bptilaka_at_mail.uh.edu (Sat Apr 12 2008 - 17:32:17 CDT)
• langevin dynamics Dibyadeep Paul (Sat Apr 12 2008 - 14:21:52 CDT)
  • Re: langevin dynamics Giovanni Bellesia (Sat Apr 12 2008 - 15:20:20 CDT)
    • Re: langevin dynamics Giovanni Bellesia (Sat Apr 12 2008 - 18:03:35 CDT)
• TclForces Vivek Sharma (Fri Apr 11 2008 - 05:42:50 CDT)
  • Re: TclForces JC Gumbart (Mon Apr 14 2008 - 10:21:22 CDT)
• Questions about equilibration pellegrini (Thu Apr 10 2008 - 10:19:57 CDT)
• PMF calculation floating-point error will (Thu Apr 10 2008 - 08:12:41 CDT)
• periodic cell conditions for membrane simulation Low Soo Mei (Thu Apr 10 2008 - 03:54:07 CDT)
• Replica Exchange Method bptilaka_at_mail.uh.edu (Wed Apr 09 2008 - 23:08:43 CDT)
• bug in NAMD CVS starting March 7, now fixed Jim Phillips (Tue Apr 08 2008 - 14:22:55 CDT)
• Dynamics with a glycerol molecule Lucio Montero (Mon Apr 07 2008 - 17:34:39 CDT)
• How to circumvent: FATAL ERROR: Periodic cell has become too small for original patch grid! Maxim Paliy (Mon Apr 07 2008 - 14:36:09 CDT)
  • Re: How to circumvent: FATAL ERROR: Periodic cell has become too small for original patch grid! L. Michel Espinoza-Fonseca (Mon Apr 07 2008 - 15:10:43 CDT)
• add calcium chloride Christine Horejs DI (Mon Apr 07 2008 - 03:21:59 CDT)
  • Re: add calcium chloride Peter Freddolino (Mon Apr 07 2008 - 08:09:58 CDT)
    • Re: add calcium chloride Christine Horejs DI (Wed Apr 16 2008 - 07:30:41 CDT)
      • Re: add calcium chloride Christine Horejs DI (Wed Apr 16 2008 - 08:22:28 CDT)
      • Re: add calcium chloride Thomas C. Bishop (Wed Apr 16 2008 - 10:12:24 CDT)
• Kinetic Momentum of Translation and/or Rotation Joshua D. Moore (Mon Apr 07 2008 - 01:54:38 CDT)
  • Re: Kinetic Momentum of Translation and/or Rotation Peter Freddolino (Mon Apr 07 2008 - 08:09:44 CDT)
• Calculating PMF from a constant velocity SMD simulation! Gungor Ozer (Sat Apr 05 2008 - 19:10:06 CDT)
• How to read specific DCD frames directly in Fortran? Yinglong Miao (Sat Apr 05 2008 - 13:21:53 CDT)
  • Re: vmd-l: How to read specific DCD frames directly in Fortran? Peter Freddolino (Sat Apr 05 2008 - 13:38:39 CDT)
    • Re: vmd-l: How to read specific DCD frames directly in Fortran? Yinglong Miao (Sun Apr 06 2008 - 10:51:40 CDT)
  • Re: vmd-l: How to read specific DCD frames directly in Fortran? John Stone (Sat Apr 05 2008 - 13:43:21 CDT)
• Rigid body effect, translational kinetic momentum Joshua D. Moore (Fri Apr 04 2008 - 19:40:35 CDT)
• problems sourcing namdstats in vmd Shaheen Ahmed (Fri Apr 04 2008 - 09:37:15 CDT)
  • Re: problems sourcing namdstats in vmd Jim Phillips (Fri Apr 04 2008 - 12:09:43 CDT)
• TMD bug correction??? Samuel Morales (Wed Apr 02 2008 - 13:28:35 CDT)
  • Re: TMD bug correction??? Peter Freddolino (Wed Apr 02 2008 - 14:39:37 CDT)
  • Re: TMD bug correction??? Samuel Morales (Mon Apr 14 2008 - 15:55:04 CDT)
    • Re: Re: TMD bug correction??? Peter Freddolino (Mon Apr 14 2008 - 16:15:44 CDT)
• MacOSX net version segmentation fault Joshua Adelman (Mon Mar 31 2008 - 18:25:29 CDT)
• Running NAMD at TACC (Ranger) Jim Pfaendtner (Sun Mar 30 2008 - 07:16:57 CDT)
  • Re: Running NAMD at TACC (Ranger) Peter Freddolino (Sun Mar 30 2008 - 09:28:06 CDT)
    • Re: Running NAMD at TACC (Ranger) JC Gumbart (Sun Mar 30 2008 - 13:20:45 CDT)
      • RE: Running NAMD at TACC (Ranger) Richard Swenson (Fri Apr 04 2008 - 12:42:49 CDT)
  • RE: Running NAMD at TACC (Ranger) Richard Swenson (Thu Apr 03 2008 - 18:09:22 CDT)
• coarse grained simulation Demet Akten (Fri Mar 28 2008 - 09:11:19 CDT)
• Pressure oscillation in NPT Xinguang Cheng (Thu Mar 27 2008 - 10:14:38 CDT)
  • Re: Pressure oscillation in NPT Peter Freddolino (Thu Mar 27 2008 - 11:07:02 CDT)
    • Re: Re: Pressure oscillation in NPT lcr312 (Thu Mar 27 2008 - 21:53:07 CDT)
  • Re: Pressure oscillation in NPT Per Jr. Greisen (Thu Mar 27 2008 - 11:30:04 CDT)
• NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Maxim Paliy (Wed Mar 26 2008 - 16:28:52 CDT)
• NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Maxim Paliy (Wed Mar 26 2008 - 16:37:01 CDT)
• NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Maxim Paliy (Wed Mar 26 2008 - 16:30:41 CDT)
  • Re: NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Peter Freddolino (Wed Mar 26 2008 - 16:38:23 CDT)
• FATAL ERROR: Periodic cell has become too small for original patch grid! Seth Lilavivat (Wed Mar 26 2008 - 15:36:48 CDT)
  • Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Jeffrey J. Potoff (Wed Mar 26 2008 - 18:27:05 CDT)
• abf and tcl scripting in NAMD Vlad Cojocaru (Wed Mar 26 2008 - 11:18:15 CDT)
• TMD SCRIPT Samuel Morales (Sat Mar 22 2008 - 17:30:59 CDT)
• FEP output dEavg and dG Payel Das (Fri Mar 21 2008 - 16:26:02 CDT)
  • Re: FEP output dEavg and dG Jerome Henin (Fri Mar 21 2008 - 17:16:18 CDT)
• NAMD+MPI on AMD64 Artem Zhmurov (Fri Mar 21 2008 - 12:30:29 CDT)
• ABF tutorial; updated FEP tutorial Jerome Henin (Thu Mar 20 2008 - 15:55:10 CDT)
  • Re: ABF tutorial; updated FEP tutorial Lei Shi (Thu Mar 20 2008 - 17:38:40 CDT)
    • Re: ABF tutorial; updated FEP tutorial Jerome Henin (Fri Mar 21 2008 - 18:53:58 CDT)
• Parallelism issue Artem Zhmurov (Thu Mar 20 2008 - 15:45:15 CDT)
• EM and MD of GPCRs Kalyan chaitanya (Thu Mar 20 2008 - 12:34:23 CDT)
• namd: ABF query gurvisha_at_leadinvent.com (Thu Mar 20 2008 - 05:12:55 CDT)
  • Re: namd: ABF query Peter Freddolino (Thu Mar 20 2008 - 11:16:50 CDT)
    • Re: namd: ABF query Peter Freddolino (Thu Mar 20 2008 - 11:49:33 CDT)
  • Re: namd: ABF query Jerome Henin (Thu Mar 20 2008 - 11:29:30 CDT)
• namd: ABF query gurvisha_at_leadinvent.com (Thu Mar 20 2008 - 05:12:30 CDT)
• Generating PSF from modified AMBER ff Seth Lilavivat (Wed Mar 19 2008 - 12:30:03 CDT)
  • Re: Generating PSF from modified AMBER ff Peter Freddolino (Wed Mar 19 2008 - 12:39:50 CDT)
    • Re: Generating PSF from modified AMBER ff Seth Lilavivat (Wed Mar 19 2008 - 12:53:27 CDT)
• using Amber paramter snoze pa (Tue Mar 18 2008 - 13:23:31 CDT)
• Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Kamilla Kopec (Mon Mar 17 2008 - 13:50:45 CDT)
  • Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Kamilla Kopec (Tue Mar 18 2008 - 07:49:24 CDT)
    • Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Peter Freddolino (Wed Mar 19 2008 - 10:38:21 CDT)
      • Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Kamilla Kopec (Wed Mar 19 2008 - 12:38:24 CDT)
      • Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Peter Freddolino (Wed Mar 19 2008 - 15:41:14 CDT)
• TARGETED MD - GRADUAL INCREASE OF FORCE Samuel Morales (Fri Mar 14 2008 - 15:21:51 CDT)
  • Re: TARGETED MD - GRADUAL INCREASE OF FORCE lcr312 (Sat Mar 15 2008 - 11:45:24 CDT)
• TARGETED MD - GRADUAL INCREASE OF FORCE Samuel Morales Navarro (Fri Mar 14 2008 - 14:20:06 CDT)
• quartz slab / pairInteractionSelf / Bad global exclusion count! Arturas Ziemys (Fri Mar 14 2008 - 12:55:11 CDT)
  • Re: quartz slab / pairInteractionSelf / Bad global exclusion count! Peter Freddolino (Sun Mar 16 2008 - 09:06:25 CDT)
• langevinHydrogen off with rigidBonds all? Low Soo Mei (Fri Mar 14 2008 - 04:57:27 CDT)
  • Re: langevinHydrogen off with rigidBonds all? Peter Freddolino (Sun Mar 16 2008 - 08:55:42 CDT)
• Free Energy of Conformational Change PMF - documentation on method? David Sivak (Thu Mar 13 2008 - 18:07:56 CDT)
• Re: TARGETED MD ERROR Jerome Henin (Thu Mar 13 2008 - 00:54:49 CDT)
  • Re: TARGETED MD ERROR mon_sharma_at_research.iiit.ac.in (Thu Mar 13 2008 - 01:52:57 CDT)
• FEP: FATAL ERROR: Periodic cell has become too small for original patch grid! List (Wed Mar 12 2008 - 13:29:38 CDT)
  • Re: FEP: FATAL ERROR: Periodic cell has become too small for original patch grid! Jeffrey J. Potoff (Thu Mar 13 2008 - 10:22:18 CDT)
    • Re: FEP: FATAL ERROR: Periodic cell has become too small for original patch grid! List (Thu Mar 13 2008 - 16:16:04 CDT)
    • FEP + MCTI in one MD simulation List (Thu Mar 13 2008 - 16:25:36 CDT)
• Question about 'NAMD TUTORIAL' Ben Chern (Wed Mar 12 2008 - 07:21:50 CDT)
  • Re: Question about 'NAMD TUTORIAL' Peter Freddolino (Wed Mar 12 2008 - 18:46:55 CDT)
    • Re: Question about 'NAMD TUTORIAL' Ben Chern (Thu Mar 13 2008 - 00:18:21 CDT)
  • TARGETED MD ERROR Samuel Morales Navarro (Wed Mar 12 2008 - 13:33:56 CDT)
• variation between results on different OSes Dibyadeep Paul (Wed Mar 12 2008 - 02:31:40 CDT)
  • Re: variation between results on different OSes Peter Freddolino (Wed Mar 12 2008 - 18:48:00 CDT)
• fixed atoms / pressure Arturas Ziemys (Mon Mar 10 2008 - 12:31:27 CDT)
  • Re: fixed atoms / pressure Peter Freddolino (Wed Mar 12 2008 - 18:55:07 CDT)
    • Re: fixed atoms / pressure Arturas Ziemys (Thu Mar 13 2008 - 10:52:41 CDT)
      • Re: fixed atoms / pressure Peter Freddolino (Sun Mar 16 2008 - 09:19:53 CDT)
• merge dcd files ,catdcd sripad chandan (Mon Mar 10 2008 - 06:45:58 CDT)
  • Re: merge dcd files ,catdcd sripad chandan (Mon Mar 10 2008 - 06:47:10 CDT)
• (no subject) me01136_at_cc.uoi.gr (Fri Mar 07 2008 - 12:29:57 CST)
• unsubscribe-namd Bertrand P. S. Russell (Fri Mar 07 2008 - 06:19:02 CST)
• clarification needed for wrapAll and wrapWater Yinglong Miao (Thu Mar 06 2008 - 08:13:40 CST)
• change segID using segment command in psfgen Low Soo Mei (Thu Mar 06 2008 - 03:01:18 CST)
  • RE: change segID using segment command in psfgen JC Gumbart (Thu Mar 06 2008 - 08:28:12 CST)
    • Re: change segID using segment command in psfgen Low Soo Mei (Thu Mar 06 2008 - 19:33:33 CST)
• Replica Server Tutorial Joshua Adelman (Thu Mar 06 2008 - 00:23:02 CST)
• TCL/NAMD: FATAL ERROR: error reading output from command: interrupted system call Corenflos, Steven Charles (Wed Mar 05 2008 - 15:03:47 CST)
• Restarting simulation goes the different temperature Magnus Heltstrom (Wed Mar 05 2008 - 10:19:53 CST)
  • Re: Restarting simulation goes the different temperature JC Gumbart (Wed Mar 05 2008 - 18:08:30 CST)
    • Re: Restarting simulation goes the different temperature Magnus Heltstrom (Mon Apr 14 2008 - 04:55:57 CDT)
      • Re: Restarting simulation goes the different temperature JC Gumbart (Mon Apr 14 2008 - 10:18:08 CDT)
• How to analyze? Namdstats, namdplots, etc. Seth Lilavivat (Tue Mar 04 2008 - 11:55:19 CST)
• NAMD stops running without error messages or termination Yinglong Miao (Mon Mar 03 2008 - 17:18:12 CST)
• solvate replicates water box (2 by 2 by 2) and segments (8X) for no apparent reason Steven Samuel Plotkin (Sun Mar 02 2008 - 22:56:20 CST)
  • Re: solvate replicates water box (2 by 2 by 2) and segments (8X) for no apparent reason L. Michel Espinoza-Fonseca (Sun Mar 02 2008 - 23:53:14 CST)
    • Re: solvate replicates water box (2 by 2 by 2) and segments (8X) for no apparent reason Steven Samuel Plotkin (Mon Mar 03 2008 - 00:26:11 CST)
• protein_RNA simulation sripad chandan (Sat Mar 01 2008 - 08:43:22 CST)
• ABF error calculation Xu, Jiancong (Fri Feb 29 2008 - 14:47:48 CST)
  • Re: ABF error calculation Jerome Henin (Fri Feb 29 2008 - 16:16:29 CST)
  • Re: ABF error calculation Chris Chipot (Fri Feb 29 2008 - 16:26:00 CST)
• Periodic Box Size vs. Water Box Size Seth Lilavivat (Thu Feb 28 2008 - 10:33:04 CST)
  • Re: Periodic Box Size vs. Water Box Size Peter Freddolino (Thu Feb 28 2008 - 11:10:44 CST)
  • Re: Periodic Box Size vs. Water Box Size Jeffrey J. Potoff (Thu Feb 28 2008 - 11:07:50 CST)
    • Re: Periodic Box Size vs. Water Box Size Seth Lilavivat (Thu Feb 28 2008 - 11:13:45 CST)
• Waterbox unexpectedly deformed after minimization. Kamilla Kopec (Thu Feb 28 2008 - 10:22:38 CST)
  • Re: Waterbox unexpectedly deformed after minimization. Peter Freddolino (Thu Feb 28 2008 - 11:08:09 CST)
• NAMD 2.6 - PME Error on Large Protein-DNA System! Sean Law (Wed Feb 27 2008 - 18:03:44 CST)
  • Re: NAMD 2.6 - PME Error on Large Protein-DNA System! Peter Freddolino (Wed Feb 27 2008 - 23:59:41 CST)
    • RE: NAMD 2.6 - PME Error on Large Protein-DNA System! Sean Law (Thu Feb 28 2008 - 11:35:42 CST)
      • Re: NAMD 2.6 - PME Error on Large Protein-DNA System! Peter Freddolino (Thu Feb 28 2008 - 14:27:20 CST)
• Coordinates go to zero! Alex Huang (Wed Feb 27 2008 - 14:52:28 CST)
  • Inorganic Builder Plugin Subhashis Biswas (Wed Feb 27 2008 - 17:57:12 CST)
• PME Grid Size - how far to deviate from cell basis vectors. Kamilla Kopec (Wed Feb 27 2008 - 10:05:47 CST)
  • Re: PME Grid Size - how far to deviate from cell basis vectors. George Madalin Giambasu (Wed Feb 27 2008 - 11:04:08 CST)
  • Re: PME Grid Size - how far to deviate from cell basis vectors. JC Gumbart (Thu Feb 28 2008 - 18:48:48 CST)
• Protein moving out of water-box after 10 ns simulation Jie-rong Huang (Wed Feb 27 2008 - 08:13:24 CST)
  • Re: Protein moving out of water-box after 10 ns simulation Per Jr. Greisen (Wed Feb 27 2008 - 09:40:49 CST)
    • Re: Protein moving out of water-box after 10 ns simulation Jie-rong Huang (Wed Feb 27 2008 - 10:34:15 CST)
      • Re: Protein moving out of water-box after 10 ns simulation JC Gumbart (Thu Feb 28 2008 - 18:45:54 CST)
      • Re: Protein moving out of water-box after 10 ns simulation snoze pa (Fri Feb 29 2008 - 10:55:32 CST)
• Question regarding ABF simulations bptilaka_at_mail.uh.edu (Tue Feb 26 2008 - 14:50:14 CST)
• unsubscribe namd-l Alessandro Cembran (Tue Feb 26 2008 - 14:11:36 CST)
• RNA_minimization sripad chandan (Tue Feb 26 2008 - 12:04:50 CST)
  • Re: RNA_minimization jrui_at_ci.uc.pt (Tue Feb 26 2008 - 13:45:04 CST)
• implicit solvent energy calculation regafan_at_usc.es (Tue Feb 26 2008 - 04:03:49 CST)
  • RE: implicit solvent energy calculation Chang, Christopher (Tue Feb 26 2008 - 13:51:26 CST)
  • Re: implicit solvent energy calculation Neema Salimi (Tue Feb 26 2008 - 15:10:25 CST)
• umbrella sampling of decalanine using the ABF module Philip Fowler (Mon Feb 25 2008 - 06:21:56 CST)
  • Re: umbrella sampling of decalanine using the ABF module Jerome Henin (Mon Feb 25 2008 - 10:44:24 CST)
    • RE: Re: umbrella sampling of decalanine using the ABF module Xu, Jiancong (Mon Feb 25 2008 - 12:37:02 CST)
      • Re: Re: umbrella sampling of decalanine using the ABF module George Madalin Giambasu (Mon Feb 25 2008 - 13:48:55 CST)
      • Re: umbrella sampling of decalanine using the ABF module Ilja Khavrutskii (Mon Feb 25 2008 - 16:34:41 CST)
    • Building NAMD on SGI Altix Rogan Carr (Mon Apr 14 2008 - 15:04:27 CDT)
• useGroupPressure with no RigidBonds ? Niels Christensen (Sun Feb 24 2008 - 16:50:55 CST)
• center-of-mass tcl and coordinate wrapping Ilja Khavrutskii (Sun Feb 24 2008 - 15:45:15 CST)
• namd_minimize sripad chandan (Sun Feb 24 2008 - 10:51:47 CST)
• subscribe namd-l Magnus Heltstrom (Fri Feb 22 2008 - 14:47:26 CST)
• restarting calc giving new temperatures Magnus Heltstrom (Fri Feb 22 2008 - 14:39:58 CST)
• Soft core potential - tested or not? Pawel Weronski (Fri Feb 22 2008 - 13:45:22 CST)
  • Re: Soft core potential - tested or not? Chris Chipot (Tue Feb 26 2008 - 15:24:57 CST)
• langevinHydrogen off with rigidbonds off? Justine Taylor (Fri Feb 22 2008 - 08:36:25 CST)
• problem in NAMD minimized structure when viewed in VMD ramaplot ramya narasimhan (Fri Feb 22 2008 - 04:41:23 CST)
• phosphohistidine parameters ??? paco ty (Thu Feb 21 2008 - 12:33:10 CST)
  • Re: phosphohistidine parameters ??? L. Michel Espinoza-Fonseca (Thu Feb 21 2008 - 13:45:27 CST)
• A difficult problem to explain the SMD force difference Shulin Zhuang (Wed Feb 20 2008 - 22:36:15 CST)
  • Re: A difficult problem to explain the SMD force difference Lewyn Li (Thu Feb 21 2008 - 06:59:26 CST)
• The correlation of SMD force vs. AFM data Shulin Zhuang (Wed Feb 20 2008 - 14:51:15 CST)
• Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Wed Feb 20 2008 - 13:59:44 CST)
  • Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Wed Feb 20 2008 - 15:55:23 CST)
  • Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Thu Feb 21 2008 - 08:24:55 CST)
    • Re: How to run NVT simulations without applying periodic boundary conditions? Leandro Martínez (Thu Feb 21 2008 - 08:34:49 CST)
      • Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Thu Feb 21 2008 - 09:44:45 CST)
• MD analysis Seth Lilavivat (Wed Feb 20 2008 - 13:46:42 CST)
• How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Wed Feb 20 2008 - 12:16:13 CST)
• Pair Interaction Calculations to get Charmm Charges? Kamilla Kopec (Tue Feb 19 2008 - 10:23:24 CST)
  • Re: Pair Interaction Calculations to get Charmm Charges? Jan Saam (Tue Feb 19 2008 - 17:55:30 CST)
• Alchemical FEP NAMD tutorial - problems with reproducing the results Jawahar Neelankatan (Mon Feb 18 2008 - 21:25:54 CST)
  • Re: Alchemical FEP NAMD tutorial - problems with reproducing the results Chris Chipot (Tue Feb 19 2008 - 07:14:13 CST)
    • Re: Alchemical FEP NAMD tutorial - problems with reproducing the results Jawahar Neelankatan (Wed Feb 20 2008 - 14:48:54 CST)
      • Re: Alchemical FEP NAMD tutorial - problems with reproducing the results Chris Chipot (Thu Feb 21 2008 - 03:19:42 CST)
• ptraj --- 2drms Philip Peartree (Mon Feb 18 2008 - 09:52:46 CST)
• PSFGEN Warnings about H positions on standard amino acids Bo Zhang (Mon Feb 18 2008 - 07:07:39 CST)
  • RE: PSFGEN Warnings about H positions on standard amino acids Chang, Christopher (Mon Feb 18 2008 - 18:17:48 CST)
• Tcl "loadtotalforces" question (forces never seem to be saved) Christopher Calderon (Sun Feb 17 2008 - 11:51:23 CST)
  • Re: Tcl "loadtotalforces" question (forces never seem to be saved) Jerome Henin (Sun Feb 17 2008 - 12:39:01 CST)
    • Re: Tcl "loadtotalforces" question (forces never seem to be saved) Christopher Calderon (Sun Feb 17 2008 - 13:06:31 CST)
      • Re: Tcl "loadtotalforces" question (forces never seem to be saved) Jerome Henin (Sun Feb 17 2008 - 13:52:28 CST)
      • Re: Tcl "loadtotalforces" question (forces never seem to be saved) Christopher Calderon (Sun Feb 17 2008 - 14:52:23 CST)
      • Re: Tcl "loadtotalforces" question (forces never seem to be saved) Jerome Henin (Sun Feb 17 2008 - 15:13:42 CST)
• energy minimization sripad chandan (Sat Feb 16 2008 - 10:11:22 CST)
• Question about catdcd and DCDunitcell Joshua D. Moore (Fri Feb 15 2008 - 05:16:21 CST)
• Converting PSF *BACK* to CHARMM Philip Peartree (Fri Feb 15 2008 - 03:17:12 CST)
• ABF question Matthew Davies (Wed Feb 13 2008 - 11:00:44 CST)
• restarting files converge to new temperature Jorgen Simonsen (Tue Feb 12 2008 - 05:21:09 CST)
  • Re: restarting files converge to new temperature Peter Freddolino (Tue Feb 12 2008 - 13:34:55 CST)
    • Re: restarting files converge to new temperature Jorgen Simonsen (Wed Feb 13 2008 - 02:13:09 CST)
      • Re: restarting files converge to new temperature Peter Freddolino (Wed Feb 13 2008 - 07:55:48 CST)
      • Re: restarting files converge to new temperature Jorgen Simonsen (Wed Feb 13 2008 - 10:08:24 CST)
      • Re: restarting files converge to new temperature Peter Freddolino (Wed Feb 13 2008 - 10:13:55 CST)
• To incorporate an energy term ramya narasimhan (Tue Feb 12 2008 - 04:32:54 CST)
• an aptamer and a lot of stupid problems Fridolin Treindl (Mon Feb 11 2008 - 23:09:38 CST)
• PCA calculation ramya narasimhan (Mon Feb 11 2008 - 01:49:06 CST)
  • RE: PCA calculation Xu, Jiancong (Mon Feb 11 2008 - 10:21:08 CST)
    • Re: PCA calculation Peter Freddolino (Mon Feb 11 2008 - 10:38:15 CST)
      • Re: PCA calculation NAVEEN P MICHAUD AGRAWAL (Mon Feb 11 2008 - 11:58:34 CST)
      • Re: PCA calculation Peter Freddolino (Mon Feb 11 2008 - 12:09:16 CST)
      • Re: PCA calculation NAVEEN P MICHAUD AGRAWAL (Mon Feb 11 2008 - 12:37:07 CST)
      • Re: PCA calculation L. Michel Espinoza-Fonseca (Mon Feb 11 2008 - 11:34:07 CST)
      • Re: PCA calculation Richard Wood (Tue Feb 12 2008 - 09:57:42 CST)
      • Re: PCA calculation Peter Freddolino (Tue Feb 12 2008 - 10:24:33 CST)
      • Re: PCA calculation ramya narasimhan (Tue Feb 12 2008 - 22:59:49 CST)
      • Re: PCA calculation Peter Freddolino (Wed Feb 13 2008 - 07:11:27 CST)
      • Re: PCA calculation Himanshu Khandelia (Wed Feb 13 2008 - 09:00:45 CST)
      • Re: PCA calculation Richard Wood (Wed Feb 13 2008 - 10:00:19 CST)
      • RE: PCA calculation Chang, Christopher (Thu Feb 14 2008 - 12:58:55 CST)
    • RE: PCA calculation Nicholas M Glykos (Tue Feb 12 2008 - 02:03:04 CST)
    • RE: PCA calculation Chang, Christopher (Thu Feb 14 2008 - 13:31:03 CST)
• Re: rigid body model Hidekazu WATANABE (Mon Feb 11 2008 - 01:19:23 CST)
• HSE and gromacs patrick wintrode (Sun Feb 10 2008 - 10:41:01 CST)
  • Re: HSE and gromacs Peter Freddolino (Sun Feb 10 2008 - 10:47:19 CST)
    • Re: HSE and gromacs Peter Freddolino (Sun Feb 10 2008 - 10:49:46 CST)
• HP-MPI on Xeon Infiniband Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 06:43:58 CST)
  • Re: HP-MPI on Xeon Infiniband Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 08:26:25 CST)
    • Re: HP-MPI on Xeon Infiniband Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 10:10:22 CST)
• energy minimization help sripad chandan (Sat Feb 09 2008 - 09:03:50 CST)
• quartz / FF(Lopez&MacKerrel) Arturas Ziemys (Fri Feb 08 2008 - 15:00:36 CST)
• rigid body model Hidekazu WATANABE (Fri Feb 08 2008 - 02:24:30 CST)
• NAMD 2.6 dcd and breaking XPLOR Neema Salimi (Thu Feb 07 2008 - 17:15:10 CST)
  • Re: NAMD 2.6 dcd and breaking XPLOR Neema Salimi (Wed Feb 13 2008 - 19:50:38 CST)
    • Re: NAMD 2.6 dcd and breaking XPLOR Peter Freddolino (Thu Feb 14 2008 - 07:14:02 CST)
• how to minimize the energy of a protein using CHARMM FF in NAMD Kalyan chaitanya (Thu Feb 07 2008 - 09:29:08 CST)
• Re: Constrain=?ISO-8859-1?Q? centers of mass for ?= selected atoms michael_at_perfect-kreim.de (Thu Feb 07 2008 - 07:03:17 CST)
  • Re: Constrain centers of mass for selected atoms poker_at_physics.usyd.edu.au (Thu Feb 07 2008 - 18:36:00 CST)
• Constrain centers of mass for selected atoms michael_at_perfect-kreim.de (Thu Feb 07 2008 - 04:12:39 CST)
• water models supported in NAMD L. Michel Espinoza-Fonseca (Wed Feb 06 2008 - 10:26:09 CST)
  • Re: water models supported in NAMD Philip Peartree (Wed Feb 06 2008 - 12:33:19 CST)
    • Re: water models supported in NAMD Jeffrey J. Potoff (Wed Feb 06 2008 - 14:14:27 CST)
  • Re: water models supported in NAMD Peter Freddolino (Wed Feb 06 2008 - 12:48:38 CST)
    • Re: water models supported in NAMD L. Michel Espinoza-Fonseca (Wed Feb 06 2008 - 18:18:34 CST)
• TCL forces mon_sharma_at_research.iiit.ac.in (Wed Feb 06 2008 - 10:11:45 CST)
• TCL forces Monika Sharma (Wed Feb 06 2008 - 07:15:13 CST)
• namd energy Leandro Martínez (Tue Feb 05 2008 - 03:39:30 CST)
  • Re: namd energy Peter Freddolino (Tue Feb 05 2008 - 06:40:09 CST)
• NAMD: constraints while heating Seth Lilavivat (Mon Feb 04 2008 - 15:35:46 CST)
  • Re: NAMD: constraints while heating Peter Freddolino (Tue Feb 05 2008 - 06:53:23 CST)
• python vs tcl Dibyadeep Paul (Mon Feb 04 2008 - 11:14:56 CST)
• FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HN Andrea Diaz (Sun Feb 03 2008 - 16:29:59 CST)
• OPLS-AA toppar files John R. Dowdle (Sat Feb 02 2008 - 08:20:46 CST)
  • Re: OPLS-AA toppar files John R. Dowdle (Mon Feb 04 2008 - 11:48:07 CST)
• ABF with different bin size Xu, Jiancong (Fri Feb 01 2008 - 11:11:58 CST)
• FATAL ERROR: Periodic cell Jorgen Simonsen (Fri Feb 01 2008 - 04:50:34 CST)
  • Re: FATAL ERROR: Periodic cell Jianhui Tian (Fri Feb 01 2008 - 08:44:54 CST)
• Applying SMD to a domain of protein Monika (Fri Feb 01 2008 - 00:49:37 CST)
  • Re: Applying SMD to a domain of protein harish vashisth (Fri Feb 01 2008 - 11:13:58 CST)
• FEP configuration file List (Mon Jan 28 2008 - 10:55:21 CST)
• NAMDENERGY in parellel Ghalib Bello (Thu Jan 31 2008 - 11:30:18 CST)
  • Re: NAMDENERGY in parellel Peter Freddolino (Thu Jan 31 2008 - 13:13:19 CST)
• Re: catDCD 32 bit Vs. 64 bit Version Monika Sharma (Thu Jan 31 2008 - 08:09:46 CST)
  • Re: catDCD 32 bit Vs. 64 bit Version juneja_at_speakeasy.net (Thu Jan 31 2008 - 11:51:28 CST)
  • Re: catDCD 32 bit Vs. 64 bit Version juneja_at_speakeasy.net (Fri Feb 01 2008 - 04:00:51 CST)
    • Re: catDCD 32 bit Vs. 64 bit Version Peter Freddolino (Fri Feb 01 2008 - 09:56:19 CST)
  • Re: catDCD 32 bit Vs. 64 bit Version juneja_at_speakeasy.net (Fri Feb 01 2008 - 10:59:52 CST)
    • Re: catDCD 32 bit Vs. 64 bit Version Philip Peartree (Sat Feb 02 2008 - 10:21:44 CST)
  • Re: catDCD 32 bit Vs. 64 bit Version Philip Peartree (Thu Feb 07 2008 - 09:28:15 CST)
• catDCD 32 bit Vs. 64 bit Version Alok Juneja (Thu Jan 31 2008 - 03:51:40 CST)
  • Re: catDCD 32 bit Vs. 64 bit Version Peter Freddolino (Thu Jan 31 2008 - 13:26:09 CST)
• FATAL ERROR: Periodic cell has become too small for original patch grid! Joshua Adelman (Wed Jan 30 2008 - 10:42:06 CST)
  • Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Peter Freddolino (Wed Jan 30 2008 - 10:52:48 CST)
    • Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Joshua Adelman (Wed Jan 30 2008 - 11:47:16 CST)
      • Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Peter Freddolino (Wed Jan 30 2008 - 11:55:21 CST)
      • Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Joshua Adelman (Wed Jan 30 2008 - 15:50:10 CST)
      • Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Peter Freddolino (Wed Jan 30 2008 - 15:57:53 CST)
• About ref frame for rmsd vs time Francesco Pietra (Wed Jan 30 2008 - 00:52:48 CST)
• Appending to the existing dcd file after restart Andrei Istomin (Wed Jan 30 2008 - 02:06:55 CST)
• Dihedral coordinate ABF scheme Luca (Tue Jan 29 2008 - 15:32:01 CST)
  • Re: Dihedral coordinate ABF scheme Jerome Henin (Tue Jan 29 2008 - 16:25:57 CST)
• Re: Cholesterol structure Richard Wood (Tue Jan 29 2008 - 09:19:07 CST)
  • Re: Cholesterol structure Alexandre A. Vakhrouchev (Thu Jan 31 2008 - 00:50:13 CST)
    • Re: Cholesterol structure Per Jr. Greisen (Thu Jan 31 2008 - 01:29:52 CST)
      • Re: Cholesterol structure Alexandre A. Vakhrouchev (Thu Jan 31 2008 - 01:38:03 CST)
      • Re: Cholesterol structure Alexandre A. Vakhrouchev (Thu Jan 31 2008 - 02:02:46 CST)
      • Re: Cholesterol structure Alexandre A. Vakhrouchev (Thu Jan 31 2008 - 08:06:03 CST)
• Cholesterol structure Alexandre A. Vakhrouchev (Tue Jan 29 2008 - 04:48:07 CST)
• Sudden expansion of box when continuing NPT simulation Jawahar Neelankatan (Mon Jan 28 2008 - 12:11:52 CST)
  • Re: Sudden expansion of box when continuing NPT simulation Peter Freddolino (Tue Jan 29 2008 - 12:24:46 CST)
• Grand canonical ensemble michael_at_perfect-kreim.de (Mon Jan 28 2008 - 07:20:11 CST)
  • Re: Grand canonical ensemble Peter Freddolino (Mon Jan 28 2008 - 08:51:09 CST)
• How can I set Tcouple ? mashaojie163 (Fri Jan 25 2008 - 20:13:26 CST)
• Re: SMD vs RAMD / TMD Vlad Cojocaru (Fri Jan 25 2008 - 04:00:10 CST)
• Re: Fwd: Re: SMD vs RAMD Vlad Cojocaru (Fri Jan 25 2008 - 03:37:46 CST)
• SMD vs RAMD Francesco Pietra (Thu Jan 24 2008 - 11:22:18 CST)
  • Re: SMD vs RAMD harish vashisth (Thu Jan 24 2008 - 12:25:20 CST)
  • Re: SMD vs RAMD Vlad Cojocaru (Thu Jan 24 2008 - 12:28:37 CST)
• Tests not running for Charm++ Myrinet with MPICH-MX brmorgan_at_clarku.edu (Wed Jan 23 2008 - 14:35:05 CST)
• minimization command Sourmaidou, Damiani (Wed Jan 23 2008 - 12:35:49 CST)
• can we run EM of 2 or more proteins simultaneously Kalyan chaitanya (Tue Jan 22 2008 - 08:47:16 CST)
• is there any informatn on callback??= michael_at_perfect-kreim.de (Tue Jan 22 2008 - 08:31:59 CST)
• Is it better to align all the trajectory before calculating rmsd? dongsheng lei (Tue Jan 22 2008 - 03:05:47 CST)
  • Re: Is it better to align all the trajectory before calculating rmsd? Ana Vila Verde (Tue Jan 22 2008 - 05:31:12 CST)
• Inconsistencies in NAMD simulations Chandra Ramananjara (Tue Jan 22 2008 - 02:49:53 CST)
  • Re: Inconsistencies in NAMD simulations Ana Vila Verde (Tue Jan 22 2008 - 06:14:52 CST)
• What is the unit of coupling coefficient when using tCouple to control temperatue? mashaojie163 (Mon Jan 21 2008 - 06:42:42 CST)
• namd vs gromacs vs charmm vs amber Dibyadeep Paul (Sun Jan 20 2008 - 04:43:41 CST)
• Re: Shear flow: Lees-Edwards Boundary Conditions Richard Wood (Sat Jan 19 2008 - 12:57:12 CST)
• About Amber force fields Francesco Pietra (Sat Jan 19 2008 - 08:54:30 CST)
  • Defining a group of atoms in a simulation Arneh Babakhani (Sat Jan 19 2008 - 11:15:03 CST)
    • Re: Defining a group of atoms in a simulation Ilja Khavrutskii (Sat Jan 19 2008 - 14:02:58 CST)
  • Re: About Amber force fields Jan Saam (Sat Jan 19 2008 - 23:00:45 CST)
• Problems found --- [Fwd: Bad global dihedral count.] Wang, Boyang (Fri Jan 18 2008 - 19:56:22 CST)
• Shear flow: Lees-Edwards Boundary Conditions Prabhakar Bhimalapuram (Fri Jan 18 2008 - 17:44:10 CST)
• Bad global dihedral count. Wang, Boyang (Fri Jan 18 2008 - 14:44:11 CST)
• C NH1 C minimization error Sourmaidou, Damiani (Thu Jan 17 2008 - 06:43:18 CST)
  • Re: vmd-l: C NH1 C minimization error L. Michel Espinoza-Fonseca (Thu Jan 17 2008 - 07:13:33 CST)
    • RE: vmd-l: C NH1 C minimization error Sourmaidou, Damiani (Sat Jan 19 2008 - 03:28:51 CST)
• Problems restarting an amber simulation Seth Lilavivat (Wed Jan 16 2008 - 11:04:14 CST)
  • RE: Problems restarting an amber simulation Irene Newhouse (Wed Jan 16 2008 - 12:34:41 CST)
  • Re: Problems restarting an amber simulation Guanglei Cui (Wed Jan 16 2008 - 14:35:30 CST)
• Converting DCD file to XTC format Jianping Lin (Tue Jan 15 2008 - 17:09:39 CST)
  • Re: Converting DCD file to XTC format Alessandro Pedretti (Wed Jan 16 2008 - 02:11:20 CST)
• resonable dcdfreq Lixia Jin Day (Tue Jan 15 2008 - 16:21:58 CST)
• Characteristic time of atomic vibrations and collisions? Yinglong Miao (Mon Jan 14 2008 - 16:16:11 CST)
  • Re: Characteristic time of atomic vibrations and collisions? Victor Ovchinnikov (Mon Jan 14 2008 - 17:33:42 CST)
    • Re: Characteristic time of atomic vibrations and collisions? Yinglong Miao (Tue Jan 15 2008 - 10:06:29 CST)
• RE: ABF question jia (Sun Jan 13 2008 - 12:55:37 CST)
• changing position of atoms during NAMD simulation michael_at_perfect-kreim.de (Mon Jan 14 2008 - 07:11:52 CST)
• ABF using distance-com but with negative xiMin Philip Fowler (Fri Jan 11 2008 - 09:21:48 CST)
  • Re: ABF using distance-com but with negative xiMin Jerome Henin (Fri Jan 11 2008 - 17:19:32 CST)
• Question about Error Message Alex Huang (Thu Jan 10 2008 - 09:33:49 CST)
• ABF question Xu, Jiancong (Wed Jan 09 2008 - 10:04:19 CST)
  • Re: ABF question Jerome Henin (Wed Jan 09 2008 - 11:26:57 CST)
    • RE: ABF question Xu, Jiancong (Mon Jan 14 2008 - 10:14:07 CST)
      • Re: ABF question Jerome Henin (Mon Jan 14 2008 - 11:02:35 CST)
      • RE: ABF question Xu, Jiancong (Mon Jan 14 2008 - 11:19:27 CST)
      • Re: ABF question Jerome Henin (Mon Jan 14 2008 - 11:40:49 CST)
• Help snoze pa (Mon Jan 07 2008 - 13:41:47 CST)
• NAMD binaries Sangamesh B (Fri Jan 04 2008 - 22:50:58 CST)
• Coarse grained psf file and parameter luca (Fri Jan 04 2008 - 08:37:21 CST)
• Strange Input Error Jason Wyonn O'Young (Thu Jan 03 2008 - 02:05:37 CST)
• Help reg. input file snoze pa (Wed Jan 02 2008 - 12:35:19 CST)
• problems-periodic cell jose correa (Tue Jan 01 2008 - 09:30:10 CST)
  • Re: problems-periodic cell Christopher Gillespie (Tue Jan 01 2008 - 12:23:25 CST)
    • RE: problems-periodic cell Irene Newhouse (Tue Jan 01 2008 - 14:41:36 CST)
• charmm charge style carlos alberto gueto tettay (Thu Dec 27 2007 - 12:55:00 CST)
  • Re: charmm charge style Jan Saam (Wed Jan 02 2008 - 15:48:27 CST)
• Dihedral energy not getting generated ( is zero ) prateeksha s (Wed Dec 26 2007 - 01:58:15 CST)
  • Re: Dihedral energy not getting generated ( is zero ) prateeksha s (Wed Dec 26 2007 - 02:01:50 CST)
• Problems of mpi with namd 2.6 cong chen (Mon Dec 24 2007 - 00:53:25 CST)
• Compiling NAMD on PPC G4 w/Apple's Leopard Joshua Adelman (Sun Dec 23 2007 - 10:31:57 CST)
• (no subject) jfgaff_at_ncsu.edu (Sat Dec 22 2007 - 08:30:16 CST)
• Re: enery evaluation inside Tcl-Forces? harish vashisth (Fri Dec 21 2007 - 16:16:23 CST)
• ligand parameters... I know the next step carlos alberto gueto tettay (Fri Dec 21 2007 - 11:36:53 CST)
• ligands parameters carlos alberto gueto tettay (Fri Dec 21 2007 - 08:42:15 CST)
• Segmentation violation when running without an internet connection jadelman_at_berkeley.edu (Thu Dec 20 2007 - 12:20:51 CST)
  • Re: Segmentation violation when running without an internet connection Christopher Gillespie (Thu Dec 20 2007 - 13:53:30 CST)
  • Re: Segmentation violation when running without an internet connection Robert Brunner (Thu Dec 20 2007 - 14:45:41 CST)
• enery evaluation inside Tcl-Forces? harish vashisth (Thu Dec 20 2007 - 10:14:48 CST)
• Re: Creating topology for carbon nanotube / any new structure prateeksha s (Wed Dec 19 2007 - 22:21:44 CST)
• fluorescent probes jayant james (Wed Dec 19 2007 - 20:08:33 CST)
• psfgen for pre-equilibrated membrane bilayer Myunggi Yi (Wed Dec 19 2007 - 18:47:10 CST)
• Tcl-forces query Harish Lnu (Wed Dec 19 2007 - 10:23:01 CST)
• Creating topology for carbon nanotube / any new structure prateeksha s (Tue Dec 18 2007 - 22:41:04 CST)
  • Re: Creating topology for carbon nanotube / any new structure prateeksha s (Wed Dec 19 2007 - 22:24:49 CST)
    • Re: Re: Creating topology for carbon nanotube / any new structure prateeksha s (Sat Jan 19 2008 - 23:02:22 CST)
      • Re: Creating topology for carbon nanotube / any new structure prateeksha s (Sat Jan 19 2008 - 23:05:28 CST)
      • Re: Re: Creating topology for carbon nanotube / any new structure prateeksha s (Fri Feb 22 2008 - 00:17:12 CST)
      • Re: Re: Creating topology for carbon nanotube / any new structure Peter Freddolino (Fri Feb 22 2008 - 07:03:16 CST)
• Re: ABF: split reaction coordinate in widows Subramanian Vaitheeswaran (Tue Dec 18 2007 - 10:40:39 CST)
• ABF: split reaction coordinate in widows Vlad Cojocaru (Tue Dec 18 2007 - 08:01:55 CST)
• namd-l : Topology info - RESidue information for carbon nanotube prateeksha s (Sat Dec 15 2007 - 07:25:19 CST)
• Topology info - RESidue information for carbon nanotube prateeksha s (Sat Dec 15 2007 - 07:23:08 CST)
• ABF - PMF Calculation Jason O'Young (Fri Dec 14 2007 - 10:00:48 CST)
  • Re: ABF - PMF Calculation Jerome Henin (Fri Dec 14 2007 - 11:15:15 CST)
• add Mg2+ Lixia Jin Day (Thu Dec 13 2007 - 11:30:26 CST)
• Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portlandcompilers Philip Peartree (Wed Dec 12 2007 - 15:35:10 CST)
• Scripting: Handle for energy terms in the PSF file? Chang, Christopher (Mon Dec 10 2007 - 21:18:24 CST)
  • re: Scripting: Handle for energy terms in the PSF file? Chang, Christopher (Tue Dec 11 2007 - 19:19:02 CST)
  • Re: Scripting: Handle for energy terms in the PSF file? Peter Freddolino (Tue Dec 11 2007 - 20:30:22 CST)
    • RE: Scripting: Handle for energy terms in the PSF file? Chang, Christopher (Wed Dec 12 2007 - 15:32:56 CST)
  • re: Scripting: Handle for energy terms in the PSF file? Chang, Christopher (Thu Dec 13 2007 - 13:39:18 CST)
• force field parameters for fullerenes Adam Fraser (Mon Dec 10 2007 - 13:18:16 CST)
• SMD question Qiang Zhong (Sat Dec 08 2007 - 19:26:03 CST)
  • Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 09:20:23 CST)
    • Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 15:22:14 CST)
      • Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 16:54:09 CST)
      • Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 17:47:59 CST)
      • Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Fri Dec 14 2007 - 07:29:01 CST)
      • Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Fri Dec 14 2007 - 12:52:44 CST)
      • Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Fri Dec 14 2007 - 16:01:56 CST)
      • Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Dow_Hurst (Sat Dec 15 2007 - 21:49:11 CST)
      • Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Sat Dec 15 2007 - 22:04:08 CST)
• nonbonded interactions Xu, Jiancong (Fri Dec 07 2007 - 13:34:46 CST)
  • Re: nonbonded interactions Joseph Heil (Fri Dec 07 2007 - 20:42:24 CST)
• ABF - restricting reaction coordinate Subramanian Vaitheeswaran (Fri Dec 07 2007 - 08:55:48 CST)
  • Re: ABF - restricting reaction coordinate Subramanian Vaitheeswaran (Fri Dec 07 2007 - 09:38:36 CST)
    • Re: Re: ABF - restricting reaction coordinate Jerome Henin (Fri Dec 07 2007 - 10:43:49 CST)
  • Re: ABF - restricting reaction coordinate Jerome Henin (Fri Dec 07 2007 - 10:01:47 CST)
    • Re: ABF - restricting reaction coordinate Subramanian Vaitheeswaran (Fri Dec 07 2007 - 14:49:55 CST)
      • Re: ABF - restricting reaction coordinate Jerome Henin (Fri Dec 07 2007 - 15:04:21 CST)
• MD runs at different clusters Monika Sharma (Fri Dec 07 2007 - 04:04:35 CST)
  • Re: MD runs at different clusters JC Gumbart (Fri Dec 07 2007 - 14:53:56 CST)
• force dcd files?? Thomas C. Bishop (Thu Dec 06 2007 - 15:22:49 CST)
  • Re: force dcd files?? Joshua D. Moore (Mon Dec 10 2007 - 10:32:36 CST)
• SYSTEM ENERGY MINIMIZATION Samuel Morales (Thu Dec 06 2007 - 12:40:54 CST)
• Simple TCL (Forces) question - defining bond vector Jim Pfaendtner (Thu Dec 06 2007 - 09:33:59 CST)
  • Re: Simple TCL (Forces) question - defining bond vector Jeff Wereszczynski (Thu Dec 06 2007 - 11:43:45 CST)
  • Re: Simple TCL (Forces) question - defining bond vector Victor Ovchinnikov (Thu Dec 06 2007 - 12:53:37 CST)
• SYSTEM ENERGY MINIMIZATION El Escuchado por DIOS (Wed Dec 05 2007 - 15:06:48 CST)
• Generating a gromacs topology file for analyzing NAMD trajectories patrick wintrode (Wed Dec 05 2007 - 14:15:11 CST)
  • Re: Generating a gromacs topology file for analyzing NAMD trajectories L. Michel Espinoza-Fonseca (Wed Dec 05 2007 - 14:52:52 CST)
    • Re: Generating a gromacs topology file for analyzing NAMD trajectories patrick wintrode (Thu Dec 06 2007 - 08:54:25 CST)
      • Re: Generating a gromacs topology file for analyzing NAMD trajectories L. Michel Espinoza-Fonseca (Thu Dec 06 2007 - 09:11:44 CST)
    • Re: Generating a gromacs topology file for analyzing NAMD trajectories Richard Wood (Thu Dec 06 2007 - 11:51:03 CST)
      • Re: Generating a gromacs topology file for analyzing NAMD trajectories Giovanni Bellesia (Thu Dec 06 2007 - 12:25:37 CST)
  • Re: Generating a gromacs topology file for analyzing NAMD trajectories Giovanni Bellesia (Wed Dec 05 2007 - 15:25:42 CST)
    • Re: Generating a gromacs topology file for analyzing NAMD trajectories Ilya Chorny (Wed Dec 05 2007 - 16:13:31 CST)
  • RE: Generating a gromacs topology file for analyzing NAMD trajectories Xu, Jiancong (Thu Dec 06 2007 - 09:41:22 CST)
• simulation of fullerenes Adam Fraser (Wed Dec 05 2007 - 12:16:39 CST)
  • Re: simulation of fullerenes Adam Fraser (Wed Dec 05 2007 - 12:31:45 CST)
• Convergence of ABF calculation: n_samples Subramanian Vaitheeswaran (Wed Dec 05 2007 - 08:39:47 CST)
  • Re: Convergence of ABF calculation: n_samples Chris Chipot (Wed Dec 05 2007 - 09:53:39 CST)
  • Re: Convergence of ABF calculation: n_samples Jerome Henin (Wed Dec 05 2007 - 10:14:37 CST)
• DEN residue name in Amber prateeksha s (Wed Dec 05 2007 - 00:10:42 CST)
• Protein hydrogens causing "Atoms too fast" error Christopher Gillespie (Mon Dec 03 2007 - 18:03:59 CST)
• ABF fullsamples Jason O'Young (Mon Dec 03 2007 - 13:18:40 CST)
  • Re: ABF fullsamples Chris Chipot (Mon Dec 03 2007 - 15:47:06 CST)
  • Re: ABF fullsamples Jerome Henin (Mon Dec 03 2007 - 18:13:40 CST)
• different 1-4scaling values for different atom types? cong chen (Sun Dec 02 2007 - 23:51:11 CST)
• ABF Output File Jason Wyonn O'Young (Sun Dec 02 2007 - 12:47:26 CST)
  • Re: ABF Output File Chris Chipot (Sun Dec 02 2007 - 13:22:03 CST)
• Re: how to perform MD with two proteins Richard Wood (Sun Dec 02 2007 - 10:00:43 CST)
  • Re: how to perform MD with two proteins Peter Freddolino (Sun Dec 02 2007 - 10:31:54 CST)
    • Re: how to perform MD with two proteins Mert Gür (Wed Dec 05 2007 - 09:04:57 CST)
• how to perform MD with two proteins Mert Gür (Sun Dec 02 2007 - 09:12:28 CST)
• how to perform MD with two proteins Mert Gür (Sun Dec 02 2007 - 08:37:18 CST)
• how to perform MD with two proteins Mert Gür (Sun Dec 02 2007 - 07:35:14 CST)
• Re: tip4p - namd follwup luca (Sat Dec 01 2007 - 03:45:35 CST)
• About para file format cong chen (Sat Dec 01 2007 - 00:14:36 CST)
• Unsubscribe Raja Natesan (Fri Nov 30 2007 - 23:44:12 CST)
• Periodic boundary conditions Gianluca Interlandi (Fri Nov 30 2007 - 19:20:07 CST)
• paratool for MG Tianjiao Wang (Fri Nov 30 2007 - 12:48:05 CST)
  • Re: paratool for MG Philip Peartree (Fri Nov 30 2007 - 15:51:53 CST)
• tip4p - namd follwup Bishop, Thomas C (Fri Nov 30 2007 - 10:37:24 CST)
• Parameter or patch for thioester Jianping Lin (Fri Nov 30 2007 - 12:23:52 CST)
• Re: PME on a negatively charged system Hai Long (Fri Nov 30 2007 - 11:09:35 CST)
• SMD ensemble? gian peralta (Thu Nov 29 2007 - 17:49:09 CST)
• Pressure fluctuations Ayþe Özlem Sezerman (Fri Nov 30 2007 - 10:50:32 CST)
  • Re: Pressure fluctuations Peter Freddolino (Mon Dec 03 2007 - 22:01:04 CST)
• TMD and RMSD constrained dynamcs M. Madhu (Fri Nov 30 2007 - 10:22:48 CST)
• How is the maximum velocity limit set? Yinglong Miao (Fri Nov 30 2007 - 10:22:40 CST)
• Re: abf: multiple distance Jerome Henin (Fri Nov 30 2007 - 09:01:39 CST)
  • Re: abf: multiple distance luca (Fri Nov 30 2007 - 09:50:58 CST)
    • Re: abf: multiple distance Jerome Henin (Fri Nov 30 2007 - 11:34:09 CST)
  • Re: abf: multiple distance Vlad Cojocaru (Fri Nov 30 2007 - 10:05:43 CST)
    • Re: abf: multiple distance Jerome Henin (Fri Nov 30 2007 - 11:44:39 CST)
• PME on a negatively charged system. Richard Swenson (Thu Nov 29 2007 - 14:53:18 CST)
• tcl script for applying constraints Pijush Ghosh (Thu Nov 29 2007 - 14:35:13 CST)
  • Re: tcl script for applying constraints luca (Fri Nov 30 2007 - 02:20:50 CST)
• problems replicating a DOPC membrane regafan_at_usc.es (Thu Nov 29 2007 - 12:26:29 CST)
  • Re: problems replicating a DOPC membrane Richard Swenson (Thu Nov 29 2007 - 14:57:35 CST)
• abf: multiple distance Luca Bellucci (Thu Nov 29 2007 - 04:18:19 CST)
• Re: Parameters for NH3, NH4+, and CO2 Ilya Chorny (Wed Nov 28 2007 - 20:31:09 CST)
  • Re: Re: Parameters for NH3, NH4+, and CO2 Jeffrey J. Potoff (Wed Nov 28 2007 - 21:34:29 CST)
    • Re: Re: Parameters for NH3, NH4+, and CO2 Ilya Chorny (Wed Nov 28 2007 - 21:51:19 CST)
      • Re: Re: Parameters for NH3, NH4+, and CO2 Jeffrey J. Potoff (Wed Nov 28 2007 - 23:08:34 CST)
      • Re: Re: Parameters for NH3, NH4+, and CO2 Himanshu Khandelia (Thu Nov 29 2007 - 01:51:56 CST)
    • Re: Re: Parameters for NH3, NH4+, and CO2 Richard Wood (Wed Nov 28 2007 - 22:58:30 CST)
• uncharged ends Xavier GALLET (Wed Nov 28 2007 - 09:46:22 CST)
  • Re: uncharged ends L. Michel Espinoza-Fonseca (Wed Nov 28 2007 - 10:30:15 CST)
• problem with *.pdb and *.psf jose correa (Wed Nov 28 2007 - 08:16:38 CST)
  • RE: problem with *.pdb and *.psf Richard Swenson (Wed Nov 28 2007 - 09:18:30 CST)
• Flying ions jia (Tue Nov 27 2007 - 21:00:32 CST)
• REMD Dirar Homouz (Tue Nov 27 2007 - 14:33:46 CST)
• Is there solution to numerical inaccuracy Alok Juneja (Tue Nov 20 2007 - 06:07:57 CST)
• Re: SMD Constant Velocity: Force Vamshi Gangupomu (Mon Nov 26 2007 - 09:33:51 CST)
  • Re: SMD Constant Velocity: Force Peter Freddolino (Mon Nov 26 2007 - 14:03:38 CST)
• Avoiding self-interaction with PME. Niels Christensen (Sun Nov 25 2007 - 09:59:57 CST)
• SMD Constant Velocity: Force Vamshi Gangupomu (Sun Nov 25 2007 - 00:33:24 CST)
• replica exchange trajectories Raul Alcantara (Fri Nov 23 2007 - 13:12:48 CST)
• energy per residue Xavier GALLET (Fri Nov 23 2007 - 09:15:49 CST)
  • Re: energy per residue Peter Freddolino (Sat Nov 24 2007 - 08:38:48 CST)
• minimization-problem jose correa (Thu Nov 22 2007 - 08:13:51 CST)
  • Re: minimization-problem Karol Kaszuba (Thu Nov 22 2007 - 10:18:12 CST)
  • Re: minimization-problem Karol Kaszuba (Thu Nov 22 2007 - 10:20:41 CST)
• PO3 psf Ahlam Al-Rawi (Wed Nov 21 2007 - 16:06:22 CST)
• ABF : dihedral-com.tcl Subramanian Vaitheeswaran (Wed Nov 21 2007 - 09:59:37 CST)
  • Re: ABF : dihedral-com.tcl Chris Chipot (Wed Nov 21 2007 - 10:36:37 CST)
  • Re: ABF : dihedral-com.tcl Vlad Cojocaru (Wed Nov 21 2007 - 10:36:31 CST)
    • Re: ABF : dihedral-com.tcl Subramanian Vaitheeswaran (Wed Nov 21 2007 - 11:16:37 CST)
• SMD behavior Adam Fraser (Wed Nov 21 2007 - 09:47:54 CST)
  • Re: SMD behavior poker_at_physics.usyd.edu.au (Wed Nov 21 2007 - 18:18:13 CST)
    • Re: SMD behavior Adam Fraser (Sat Dec 01 2007 - 12:03:40 CST)
• Dixitpd wants to Share Favorites with you dixitpd_at_gmail.com (Tue Nov 20 2007 - 22:05:54 CST)
• How to freeze some atoms cong chen (Tue Nov 20 2007 - 20:11:24 CST)
• New ABF order parameters Subramanian Vaitheeswaran (Tue Nov 20 2007 - 15:56:20 CST)
  • Re: New ABF order parameters Jerome Henin (Tue Nov 20 2007 - 16:07:01 CST)
  • Re: New ABF order parameters Subramanian Vaitheeswaran (Tue Nov 20 2007 - 16:29:25 CST)
  • Re: New ABF order parameters Subramanian Vaitheeswaran (Tue Nov 20 2007 - 16:43:45 CST)
• MD of DNA lily jin (Tue Nov 20 2007 - 10:31:39 CST)
• RE: ABF calculations jia (Tue Nov 20 2007 - 09:14:42 CST)
  • Re: ABF calculations Chris Chipot (Wed Nov 21 2007 - 18:37:32 CST)
• Is there solution to numerical inaccuracy Alok Juneja (Tue Nov 20 2007 - 07:54:29 CST)
  • Re: Is there solution to numerical inaccuracy Peter Freddolino (Tue Nov 20 2007 - 09:14:47 CST)
    • Re: Is there solution to numerical inaccuracy Alok Juneja (Tue Nov 20 2007 - 10:53:04 CST)
      • Re: Is there solution to numerical inaccuracy Peter Freddolino (Tue Nov 20 2007 - 11:48:58 CST)
      • Re: Is there solution to numerical inaccuracy David Hardy (Wed Nov 21 2007 - 09:54:41 CST)
      • Re: Is there solution to numerical inaccuracy Himanshu Khandelia (Thu Nov 22 2007 - 02:19:55 CST)
      • Re: Is there solution to numerical inaccuracy David Hardy (Thu Nov 22 2007 - 07:35:01 CST)
      • Re: Is there solution to numerical inaccuracy Peter Freddolino (Thu Nov 22 2007 - 09:15:29 CST)
      • Re: Is there solution to numerical inaccuracy Alok Juneja (Mon Nov 26 2007 - 04:54:22 CST)
      • Re: Is there solution to numerical inaccuracy Peter Freddolino (Mon Nov 26 2007 - 14:08:16 CST)
      • Re: Is there solution to numerical inaccuracy Alok Juneja (Thu Nov 29 2007 - 12:04:50 CST)
      • Re: Is there solution to numerical inaccuracy Ilya Chorny (Thu Nov 29 2007 - 13:24:50 CST)
      • Re: Is there solution to numerical inaccuracy Ilya Chorny (Thu Nov 29 2007 - 13:53:47 CST)
      • Re: Is there solution to numerical inaccuracy Peter Freddolino (Thu Nov 29 2007 - 13:25:35 CST)
      • Re: Is there solution to numerical inaccuracy Alok Juneja (Mon Dec 03 2007 - 12:49:50 CST)
      • Re: Is there solution to numerical inaccuracy Peter Freddolino (Mon Dec 03 2007 - 17:02:51 CST)
      • Re: Is there solution to numerical inaccuracy Peter Freddolino (Mon Nov 26 2007 - 14:16:40 CST)
      • Re: Is there solution to numerical inaccuracy Alok Juneja (Fri Nov 23 2007 - 12:14:01 CST)
• About RMSD cong chen (Tue Nov 20 2007 - 03:29:32 CST)
• psfGen error Joseph Heil (Mon Nov 19 2007 - 22:00:57 CST)
  • Re: psfGen error Karol Kaszuba (Tue Nov 20 2007 - 03:44:41 CST)
  • Re: psfGen error Jeffrey J. Potoff (Tue Nov 20 2007 - 09:17:00 CST)
    • Re: psfGen error Joseph Heil (Tue Nov 20 2007 - 23:37:32 CST)
      • Re: psfGen error JC Gumbart (Wed Nov 21 2007 - 15:28:22 CST)
• ABF calculations jia (Mon Nov 19 2007 - 14:33:51 CST)
  • Re: ABF calculations Jerome Henin (Mon Nov 19 2007 - 15:56:17 CST)
  • Re: ABF calculations Chris Chipot (Mon Nov 19 2007 - 16:30:42 CST)
• Any flag values returned when executing "minimize" and "run"? Yinglong Miao (Mon Nov 19 2007 - 10:52:44 CST)
  • Re: Any flag values returned when executing "minimize" and "run"? Peter Freddolino (Tue Nov 20 2007 - 09:19:33 CST)
    • Re: Any flag values returned when executing "minimize" and "run"? Yinglong Miao (Tue Nov 20 2007 - 10:10:52 CST)
      • Re: Any flag values returned when executing "minimize" and "run"? Peter Freddolino (Tue Nov 20 2007 - 11:20:39 CST)
      • Re: Any flag values returned when executing "minimize" and "run"? Victor Ovchinnikov (Tue Nov 20 2007 - 11:35:51 CST)
      • Re: Any flag values returned when executing "minimize" and "run"? Yinglong Miao (Tue Nov 20 2007 - 12:46:10 CST)
• Does rmsd is the judge of system equilibrium in all conditions? cong chen (Mon Nov 19 2007 - 06:08:12 CST)
• Installing NAMD brmorgan_at_clarku.edu (Fri Nov 16 2007 - 11:28:47 CST)
  • Re: Installing NAMD Jason Russler (Tue Nov 20 2007 - 07:39:58 CST)
    • Re: Installing NAMD brmorgan_at_clarku.edu (Tue Nov 20 2007 - 13:02:42 CST)
• ABF or SMD jia (Fri Nov 16 2007 - 11:26:20 CST)
• Fw: What is an IC table in the .inp files char_at_ks.uiuc.edu (Thu Nov 15 2007 - 21:10:29 CST)
• [Fwd: Re: What is an IC table in the .inp files] Victor Ovchinnikov (Thu Nov 15 2007 - 21:00:51 CST)
• What is an IC table in the .inp files Ilya Chorny (Thu Nov 15 2007 - 19:02:07 CST)
  • Re: What is an IC table in the .inp files Chris Harrison (Thu Nov 15 2007 - 20:53:43 CST)
    • Re: What is an IC table in the .inp files Richard Wood (Thu Nov 15 2007 - 21:29:12 CST)
      • Re: What is an IC table in the .inp files Ilya Chorny (Fri Nov 16 2007 - 13:31:44 CST)
      • Re: What is an IC table in the .inp files Alessandro Cembran (Fri Nov 16 2007 - 14:23:08 CST)
      • RE: What is an IC table in the .inp files Richard Swenson (Fri Nov 16 2007 - 14:45:02 CST)
    • Re: What is an IC table in the .inp files Richard Wood (Fri Nov 16 2007 - 13:46:26 CST)
• Using NAMD DCD in CHARMM Ahlam Al-Rawi (Thu Nov 15 2007 - 13:38:58 CST)
  • Re: Using NAMD DCD in CHARMM Peter Freddolino (Thu Nov 15 2007 - 23:23:36 CST)
    • Re: Using NAMD DCD in CHARMM Himanshu Khandelia (Fri Nov 16 2007 - 01:19:21 CST)
• question switching function Peter Kiss (Thu Nov 15 2007 - 12:12:08 CST)
• user defined restraint in ABF Vlad Cojocaru (Thu Nov 15 2007 - 10:15:17 CST)
  • Re: user defined restraint in ABF Jerome Henin (Thu Nov 15 2007 - 12:09:29 CST)
• howcan I use amber forcefield in NAMD? mashaojie163 (Wed Nov 14 2007 - 21:58:39 CST)
  • RE: howcan I use amber forcefield in NAMD? Irene Newhouse (Thu Nov 15 2007 - 00:51:41 CST)
    • Re: howcan I use amber forcefield in NAMD? mashaojie163 (Thu Nov 15 2007 - 06:23:49 CST)
      • RE: howcan I use amber forcefield in NAMD? Huy N. Ha (Thu Nov 15 2007 - 17:24:36 CST)
      • Re: howcan I use amber forcefield in NAMD? mashaojie163 (Thu Nov 15 2007 - 20:55:53 CST)
      • Re: howcan I use amber forcefield in NAMD? Richard Wood (Thu Nov 15 2007 - 21:33:00 CST)
      • RE: howcan I use amber forcefield in NAMD? JC Gumbart (Thu Nov 15 2007 - 22:01:54 CST)
      • Re: howcan I use amber forcefield in NAMD? Richard Wood (Thu Nov 15 2007 - 22:32:56 CST)
      • Re: howcan I use amber forcefield in NAMD? Floris Buelens (Fri Nov 16 2007 - 05:19:37 CST)
      • Re: howcan I use amber forcefield in NAMD? mashaojie163 (Sat Nov 17 2007 - 01:28:51 CST)
• Ligand Bound. kparra_at_mail.usf.edu (Wed Nov 14 2007 - 12:30:27 CST)
• OPLS Lipid topology/potenital for NAMD Ilya Chorny (Tue Nov 13 2007 - 16:44:02 CST)
  • Re: OPLS Lipid topology/potenital for NAMD Himanshu Khandelia (Wed Nov 14 2007 - 02:36:07 CST)
    • Re: OPLS Lipid topology/potenital for NAMD Ilya Chorny (Wed Nov 14 2007 - 08:37:49 CST)
      • Re: OPLS Lipid topology/potenital for NAMD Himanshu Khandelia (Wed Nov 14 2007 - 11:12:37 CST)
      • Re: OPLS Lipid topology/potenital for NAMD Ilya Chorny (Wed Nov 14 2007 - 11:18:04 CST)
      • Re: OPLS Lipid topology/potenital for NAMD Himanshu Khandelia (Thu Nov 15 2007 - 02:12:50 CST)
• Replica Exchange NAMD Dirar Homouz (Tue Nov 13 2007 - 12:09:52 CST)
  • Re: Replica Exchange NAMD John R. Dowdle (Mon Nov 19 2007 - 20:16:43 CST)
  • Re: Replica Exchang