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NAMD-L: By Thread

By Thread

4370 messages sorted by: [ author ] [ date ] [ subject ] [ attachment ]
About this archive

Starting: Fri Jan 01 2010 - 09:55:54 CST
Ending: Sat Dec 31 2011 - 05:23:47 CST

• GPRESSURE becomes nan in TIP4P simulation Udaysankar Midya (Sat Dec 31 2011 - 05:23:35 CST)
• tabulatd potentials Arturas (Thu Dec 29 2011 - 13:09:17 CST)
  • Re: tabulatd potentials Arturas (Thu Dec 29 2011 - 14:11:43 CST)
• Coarse-Graining MD don't work perfect as expected ÐìÖÓºÓ (Thu Dec 29 2011 - 00:50:31 CST)
  • Re: Coarse-Graining MD don't work perfect as expected Boyang Wang (Fri Dec 30 2011 - 03:57:44 CST)
• scaling Neelanjana Sengupta (Wed Dec 28 2011 - 22:56:45 CST)
  • Re: scaling Boyang Wang (Fri Dec 30 2011 - 03:56:03 CST)
• Fwd: about md in npt Boyang Wang (Wed Dec 28 2011 - 02:54:01 CST)
• about md in npt Hasan haska (Wed Dec 28 2011 - 02:18:30 CST)
  • Re: about md in npt Joshua Adelman (Wed Dec 28 2011 - 07:55:02 CST)
• equilibrate the system in NPT Hasan haska (Mon Dec 26 2011 - 13:57:37 CST)
• Parse Fep plugin error Joseph Antoine Garate (Fri Dec 23 2011 - 08:27:39 CST)
  • Re: vmd-l: Parse Fep plugin error John Stone (Fri Dec 23 2011 - 10:47:56 CST)
• collective variable calculation from dcd file Giovanni Bellesia (Wed Dec 21 2011 - 14:44:47 CST)
  • Re: collective variable calculation from dcd file Branko (Wed Dec 21 2011 - 15:15:06 CST)
    • Re: collective variable calculation from dcd file Giovanni Bellesia (Wed Dec 21 2011 - 15:20:27 CST)
      • Re: collective variable calculation from dcd file Branko (Wed Dec 21 2011 - 15:38:39 CST)
  • Re: collective variable calculation from dcd file Jérôme Hénin (Thu Dec 22 2011 - 05:20:15 CST)
• AW: glycosaminoglycan with GLYCAM06 in amber format Norman Geist (Wed Dec 21 2011 - 00:54:50 CST)
  • Re: AW: glycosaminoglycan with GLYCAM06 in amber format felmerino_at_uchile.cl (Wed Dec 21 2011 - 12:44:08 CST)
    • Re: AW: glycosaminoglycan with GLYCAM06 in amber format Massimiliano Porrini (Thu Dec 22 2011 - 11:12:10 CST)
• AW: glycosaminoglycan with GLYCAM06 in amber format Norman Geist (Tue Dec 20 2011 - 06:45:32 CST)
• coordNum colvar with dummyAtom Ernesto Vargas (Mon Dec 19 2011 - 18:56:40 CST)
  • Re: coordNum colvar with dummyAtom Giacomo Fiorin (Thu Dec 22 2011 - 17:41:20 CST)
• Re: Generating .tpr file using NAMD files rajitha tatikonda (Mon Dec 19 2011 - 00:32:56 CST)
  • Re: Re: Generating .tpr file using NAMD files Axel Kohlmeyer (Mon Dec 19 2011 - 11:59:35 CST)
  • Re: Re: Generating .tpr file using NAMD files Jeffrey Potoff (Mon Dec 19 2011 - 12:05:56 CST)
• Re: glycosaminoglycan with GLYCAM06 in amber format Massimiliano Porrini (Mon Dec 19 2011 - 05:04:40 CST)
  • AW: glycosaminoglycan with GLYCAM06 in amber format Norman Geist (Mon Dec 19 2011 - 07:35:58 CST)
  • Re: glycosaminoglycan with GLYCAM06 in amber format Lachele Foley (Lists) (Tue Dec 20 2011 - 08:53:59 CST)
    • Re: glycosaminoglycan with GLYCAM06 in amber format Massimiliano Porrini (Tue Dec 20 2011 - 09:46:18 CST)
      • AW: glycosaminoglycan with GLYCAM06 in amber format Norman Geist (Wed Dec 21 2011 - 00:51:03 CST)
  • Re: glycosaminoglycan with GLYCAM06 in amber format Massimiliano Porrini (Tue Dec 20 2011 - 08:55:58 CST)
• Sticking TIP4P water molecules AMBER Norman Geist (Mon Dec 19 2011 - 04:33:25 CST)
  • Re: Sticking TIP4P water molecules AMBER Nicholas M Glykos (Mon Dec 19 2011 - 04:58:13 CST)
    • Re: Sticking TIP4P water molecules AMBER George M Giambasu (Mon Dec 19 2011 - 10:16:56 CST)
      • AW: Sticking TIP4P water molecules AMBER Norman Geist (Tue Dec 20 2011 - 00:33:08 CST)
• Fwd: Generating .tpr file using NAMD files rajitha rajeshwar (Mon Dec 19 2011 - 03:05:34 CST)
• glycosaminoglycan with GLYCAM06 in amber format Massimiliano Porrini (Sun Dec 18 2011 - 10:44:48 CST)
  • AW: glycosaminoglycan with GLYCAM06 in amber format Norman Geist (Mon Dec 19 2011 - 00:45:19 CST)
• Interfaces in NAMD Hasan haska (Sat Dec 17 2011 - 14:20:25 CST)
• New physical understanding. Boyang Wang (Fri Dec 16 2011 - 00:39:27 CST)
  • Re: New physical understanding. Axel Kohlmeyer (Fri Dec 16 2011 - 05:47:48 CST)
    • Re: New physical understanding. Boyang Wang (Fri Dec 16 2011 - 06:56:42 CST)
      • Re: New physical understanding. Chris Harrison (Fri Dec 16 2011 - 09:20:53 CST)
      • Re: New physical understanding. Boyang Wang (Sat Dec 17 2011 - 08:52:28 CST)
      • Re: New physical understanding. Axel Kohlmeyer (Sat Dec 17 2011 - 13:42:31 CST)
      • Re: New physical understanding. Boyang Wang (Sat Dec 17 2011 - 21:24:21 CST)
• Umbrella sampling-NAMD Parisa Akhski (Thu Dec 15 2011 - 09:24:36 CST)
  • Re: Umbrella sampling-NAMD Jérôme Hénin (Thu Dec 15 2011 - 11:07:04 CST)
  • Re: Umbrella sampling-NAMD Aron Broom (Thu Dec 15 2011 - 11:11:04 CST)
    • RE: Umbrella sampling-NAMD Parisa Akhski (Thu Dec 15 2011 - 12:51:57 CST)
      • Re: Umbrella sampling-NAMD Chris Harrison (Thu Dec 15 2011 - 14:07:36 CST)
      • RE: Umbrella sampling-NAMD Parisa Akhski (Fri Dec 16 2011 - 09:29:27 CST)
      • Re: Umbrella sampling-NAMD Aron Broom (Fri Dec 16 2011 - 09:46:39 CST)
      • Re: Umbrella sampling-NAMD Aron Broom (Thu Dec 15 2011 - 14:14:05 CST)
• cell size Hasan haska (Tue Dec 13 2011 - 08:10:49 CST)
  • Re: cell size Axel Kohlmeyer (Tue Dec 13 2011 - 08:21:18 CST)
    • Re: cell size Hasan haska (Tue Dec 13 2011 - 09:47:50 CST)
      • Re: cell size Axel Kohlmeyer (Tue Dec 13 2011 - 10:00:43 CST)
      • Re: cell size Hasan haska (Wed Dec 14 2011 - 06:41:10 CST)
      • AW: cell size Norman Geist (Thu Dec 15 2011 - 00:16:59 CST)
      • Re: cell size Aron Broom (Tue Dec 13 2011 - 10:03:58 CST)
• tclforces and extrabonds Jian Dai (Mon Dec 12 2011 - 10:13:16 CST)
  • Re: tclforces and extrabonds Aron Broom (Mon Dec 12 2011 - 11:30:36 CST)
  • Re: tclforces and extrabonds Jérôme Hénin (Mon Dec 12 2011 - 11:30:47 CST)
• correlation functions Molecular Dynamics (Sat Dec 10 2011 - 05:18:50 CST)
  • Re: correlation functions Aron Broom (Sat Dec 10 2011 - 08:54:56 CST)
    • Re: correlation functions Boyang Wang (Sat Dec 10 2011 - 18:03:53 CST)
      • Re: correlation functions Thomas Bishop (Mon Dec 12 2011 - 07:54:06 CST)
• MMTools for analysis Namd Namd (Sat Dec 10 2011 - 05:07:19 CST)
  • Re: MMTools for analysis Branko (Sat Dec 10 2011 - 10:21:06 CST)
• Peptide planarity Dihedral angle restraints Vijay Vammi (Thu Dec 08 2011 - 20:07:12 CST)
  • Re: Peptide planarity Dihedral angle restraints Boyang Wang (Thu Dec 08 2011 - 20:17:02 CST)
    • Re: Peptide planarity Dihedral angle restraints Aron Broom (Thu Dec 08 2011 - 21:11:20 CST)
      • Re: Peptide planarity Dihedral angle restraints Vijay Vammi (Thu Dec 08 2011 - 21:20:23 CST)
      • AW: Peptide planarity Dihedral angle restraints Norman Geist (Fri Dec 09 2011 - 00:18:47 CST)
  • Re: Peptide planarity Dihedral angle restraints Chris Harrison (Fri Dec 09 2011 - 00:27:29 CST)
    • Re: Peptide planarity Dihedral angle restraints Vijay Vammi (Fri Dec 09 2011 - 00:47:00 CST)
• NAMD FEP - Bad Hydrogen group size John Baker (Wed Dec 07 2011 - 05:38:11 CST)
  • Re: NAMD FEP - Bad Hydrogen group size Jérôme Hénin (Wed Dec 07 2011 - 06:54:01 CST)
• stochastical boundary conditions in NAMD mjyang (Tue Dec 06 2011 - 19:24:17 CST)
  • AW: stochastical boundary conditions in NAMD Norman Geist (Wed Dec 07 2011 - 00:38:58 CST)
  • Re: stochastical boundary conditions in NAMD Jérôme Hénin (Wed Dec 07 2011 - 04:39:41 CST)
• Re: xplor-formated parameters Chris Harrison (Tue Dec 06 2011 - 12:41:05 CST)
• Thermodynamic integration questions pepe barrientos (Tue Dec 06 2011 - 10:39:38 CST)
• mmView - a tool for mmCIF exploration Daniel Svozil (Tue Dec 06 2011 - 05:38:35 CST)
• Calculation of distance traveled by an atom M.Raviprasad (Mon Dec 05 2011 - 14:54:27 CST)
  • Re: Calculation of distance traveled by an atom Axel Kohlmeyer (Mon Dec 05 2011 - 17:36:58 CST)
    • RE: Calculation of distance traveled by an atom M.Raviprasad (Mon Dec 05 2011 - 23:11:19 CST)
      • Re: Calculation of distance traveled by an atom Axel Kohlmeyer (Mon Dec 05 2011 - 23:22:53 CST)
      • Re: Calculation of distance traveled by an atom Aron Broom (Tue Dec 06 2011 - 02:43:34 CST)
  • Re: Calculation of distance traveled by an atom Aron Broom (Mon Dec 05 2011 - 17:38:33 CST)
    • RE: Calculation of distance traveled by an atom M.Raviprasad (Mon Dec 05 2011 - 23:19:54 CST)
• AW: installing namd on ibm cluster (powerpc) Norman Geist (Mon Dec 05 2011 - 03:30:48 CST)
• AW: installing namd on ibm cluster (powerpc) Norman Geist (Mon Dec 05 2011 - 00:29:43 CST)
• Coulomb 1-4 interactions oguz gurbulak (Fri Dec 02 2011 - 10:11:24 CST)
  • Re: Coulomb 1-4 interactions Axel Kohlmeyer (Fri Dec 02 2011 - 10:21:36 CST)
• cpu-gpu vs cpu Francesco Pietra (Tue Nov 29 2011 - 00:44:10 CST)
  • Re: cpu-gpu vs cpu Axel Kohlmeyer (Tue Nov 29 2011 - 07:41:51 CST)
    • Re: cpu-gpu vs cpu Nicholas M Glykos (Tue Nov 29 2011 - 09:28:34 CST)
      • Re: cpu-gpu vs cpu Axel Kohlmeyer (Tue Nov 29 2011 - 10:19:50 CST)
• paper/articule on colvars module Leonardo Herrera (Mon Nov 28 2011 - 19:35:37 CST)
  • Re: paper/articule on colvars module Giacomo Fiorin (Tue Nov 29 2011 - 01:12:39 CST)
    • Re: paper/articule on colvars module Leonardo Herrera (Tue Nov 29 2011 - 13:59:02 CST)
  • Re: paper/articule on colvars module Branko (Tue Nov 29 2011 - 04:16:42 CST)
• help in a FEP restart? Bruno Luís Pinto de Oliveira (Sat Nov 26 2011 - 10:15:13 CST)
  • Re: help in a FEP restart? Chris Chipot (Sat Nov 26 2011 - 10:51:57 CST)
• charmrun constantly hanging jani vinod (Fri Nov 25 2011 - 00:59:35 CST)
  • Re: charmrun constantly hanging Axel Kohlmeyer (Fri Nov 25 2011 - 08:27:08 CST)
    • Re: charmrun constantly hanging jani vinod (Sat Nov 26 2011 - 01:06:22 CST)
      • Re: charmrun constantly hanging Axel Kohlmeyer (Sat Nov 26 2011 - 10:06:22 CST)
• equilibrate water molecules Hasan haska (Thu Nov 24 2011 - 01:43:38 CST)
• AW: AW: AW: AW: namd-ibverbs fails to start Norman Geist (Thu Nov 24 2011 - 00:15:52 CST)
• HEME and Cystein instead of His Raul Araya (Wed Nov 23 2011 - 13:10:36 CST)
  • Re: HEME and Cystein instead of His Aron Broom (Wed Nov 23 2011 - 14:02:42 CST)
    • Re: HEME and Cystein instead of His Raul Araya (Wed Nov 23 2011 - 14:25:37 CST)
  • RE: HEME and Cystein instead of His Bruno Luís Pinto de Oliveira (Wed Nov 23 2011 - 14:33:39 CST)
• Is it possible to print out the force of one specific atom? Wenhao Liu (Wed Nov 23 2011 - 08:29:23 CST)
  • Re: Is it possible to print out the force of one specific atom? Michelle Kuttel (Wed Nov 23 2011 - 08:45:22 CST)
    • Re: Is it possible to print out the force of one specific atom? Wenhao Liu (Wed Nov 23 2011 - 08:59:10 CST)
      • Re: Is it possible to print out the force of one specific atom? Ehsan Ban (Wed Nov 23 2011 - 15:45:49 CST)
• Re: Predicting the binding affinity and anion bharat gupta (Wed Nov 23 2011 - 07:23:29 CST)
  • Re: Re: Predicting the binding affinity and anion Axel Kohlmeyer (Wed Nov 23 2011 - 07:37:19 CST)
  • Re: Re: Predicting the binding affinity and anion Aron Broom (Wed Nov 23 2011 - 12:46:33 CST)
• AW: AW: Norman Geist (Wed Nov 23 2011 - 01:00:42 CST)
• AW: AW: Norman Geist (Wed Nov 23 2011 - 00:59:15 CST)
  • AW: AW: Norman Geist (Wed Nov 23 2011 - 01:25:12 CST)
• AW: AW: AW: namd-ibverbs fails to start Norman Geist (Wed Nov 23 2011 - 00:09:41 CST)
• OpenCL and AMD GPUs Aron Broom (Tue Nov 22 2011 - 22:04:13 CST)
  • Re: OpenCL and AMD GPUs Nicholas M Glykos (Wed Nov 23 2011 - 01:01:20 CST)
  • Re: OpenCL and AMD GPUs Axel Kohlmeyer (Wed Nov 23 2011 - 05:07:52 CST)
    • Re: OpenCL and AMD GPUs Aron Broom (Wed Nov 23 2011 - 09:06:13 CST)
      • Re: OpenCL and AMD GPUs Axel Kohlmeyer (Wed Nov 23 2011 - 09:52:47 CST)
      • Re: OpenCL and AMD GPUs Thomas Bishop (Wed Nov 23 2011 - 10:09:43 CST)
      • Re: OpenCL and AMD GPUs Axel Kohlmeyer (Wed Nov 23 2011 - 10:23:06 CST)
      • Re: OpenCL and AMD GPUs Aron Broom (Thu Nov 24 2011 - 15:53:33 CST)
• (no subject) Chandra Ramananjara (Tue Nov 22 2011 - 12:31:08 CST)
  • AW: Norman Geist (Wed Nov 23 2011 - 00:01:50 CST)
• Re: AW: namd-ibverbs fails to start Axel Kohlmeyer (Tue Nov 22 2011 - 08:02:12 CST)
  • AW: AW: namd-ibverbs fails to start Norman Geist (Wed Nov 23 2011 - 00:16:28 CST)
• (no subject) Chandra Ramananjara (Tue Nov 22 2011 - 06:53:15 CST)
  • (no subject) Gabriel Jara (Tue Nov 22 2011 - 06:59:12 CST)
• namd force field Molecular Dynamics (Tue Nov 22 2011 - 06:21:16 CST)
  • Re: namd force field Axel Kohlmeyer (Tue Nov 22 2011 - 08:05:08 CST)
    • Re: namd force field felmerino_at_uchile.cl (Tue Nov 22 2011 - 12:14:28 CST)
• AW: AW: namd-ibverbs fails to start Norman Geist (Tue Nov 22 2011 - 00:49:46 CST)
• AW: AW: namd-ibverbs fails to start Norman Geist (Tue Nov 22 2011 - 00:47:00 CST)
• Segmentation violation with adaptive tempering. Nicholas M Glykos (Sun Nov 20 2011 - 05:13:02 CST)
  • Re: Segmentation violation with adaptive tempering. johan strumpfer (Mon Nov 21 2011 - 12:04:38 CST)
    • Re: Segmentation violation with adaptive tempering. Nicholas M Glykos (Mon Nov 21 2011 - 12:11:45 CST)
      • Re: Segmentation violation with adaptive tempering. johan strumpfer (Mon Nov 21 2011 - 12:20:28 CST)
• Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Mon Nov 21 2011 - 04:45:39 CST)
  • Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Wed Nov 23 2011 - 08:16:58 CST)
    • Re: Scaled forces, colvars and harmonic con/restraints Giacomo Fiorin (Wed Nov 23 2011 - 09:28:50 CST)
      • Re: Scaled forces, colvars and harmonic con/restraints Jérôme Hénin (Wed Nov 23 2011 - 10:41:58 CST)
      • Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Wed Nov 23 2011 - 14:03:22 CST)
      • Re: Scaled forces, colvars and harmonic con/restraints Aron Broom (Wed Nov 23 2011 - 14:36:42 CST)
      • Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Wed Nov 23 2011 - 23:33:26 CST)
      • Re: Scaled forces, colvars and harmonic con/restraints Jérôme Hénin (Thu Nov 24 2011 - 03:51:51 CST)
      • Re: Scaled forces, colvars and harmonic con/restraints Jérôme Hénin (Thu Nov 24 2011 - 06:33:58 CST)
      • Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Thu Nov 24 2011 - 07:24:58 CST)
      • Re: Scaled forces, colvars and harmonic con/restraints Jérôme Hénin (Thu Nov 24 2011 - 08:18:07 CST)
      • Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Thu Nov 24 2011 - 09:39:56 CST)
      • Re: Scaled forces, colvars and harmonic con/restraints Giacomo Fiorin (Wed Nov 23 2011 - 14:40:34 CST)
      • Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Wed Nov 23 2011 - 23:31:14 CST)
• intermittent non-execution of NAMD on tesla P.-L. Chau (Mon Nov 21 2011 - 04:09:04 CST)
• fullSamples in ABF: applied at restart? Neelanjana Sengupta (Sun Nov 20 2011 - 22:14:15 CST)
  • fullSamples in ABF: applied at restart? Neelanjana Sengupta (Sun Nov 20 2011 - 22:19:00 CST)
    • Re: fullSamples in ABF: applied at restart? Jérôme Hénin (Mon Nov 21 2011 - 02:10:10 CST)
      • Re: fullSamples in ABF: applied at restart? Neelanjana Sengupta (Mon Nov 21 2011 - 02:51:55 CST)
      • Re: fullSamples in ABF: applied at restart? Jérôme Hénin (Mon Nov 21 2011 - 04:11:06 CST)
• problem regarding charmm parameter file of carbon nano tube kanchi subbarao rao (Sun Nov 20 2011 - 16:43:01 CST)
  • Fwd: problem regarding charmm parameter file of carbon nano tube kanchi subbarao rao (Mon Nov 21 2011 - 05:07:50 CST)
  • Re: problem regarding charmm parameter file of carbon nano tube kanchi subbarao rao (Mon Nov 21 2011 - 09:52:36 CST)
• Fwd: restrain on COM Swarna M Patra (Fri Nov 18 2011 - 23:33:09 CST)
  • Re: Fwd: restrain on COM Jérôme Hénin (Sat Nov 19 2011 - 10:48:41 CST)
• namd-ibverbs fails to start David Hemmendinger (Fri Nov 18 2011 - 21:39:20 CST)
• 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, February 11-15, 2012 in Urbana, Illinois David Brandon (Thu Nov 17 2011 - 13:46:56 CST)
• Umbrella sampling Parisa Akhski (Wed Nov 16 2011 - 15:12:17 CST)
  • Re: Umbrella sampling koushik.k (Wed Nov 16 2011 - 22:18:59 CST)
    • Re: Umbrella sampling Jérôme Hénin (Thu Nov 17 2011 - 03:29:23 CST)
• Resend - ERROR: Atoms moving too fast; Nikhil Kumar Mittal (Fri Nov 11 2011 - 19:56:39 CST)
  • RE: Resend - ERROR: Atoms moving too fast; Nikhil Kumar Mittal (Fri Nov 11 2011 - 20:02:51 CST)
• ERROR: Atoms moving too fast; Nikhil Kumar Mittal (Fri Nov 11 2011 - 12:10:52 CST)
  • Re: ERROR: Atoms moving too fast; Chris Harrison (Fri Nov 11 2011 - 13:03:52 CST)
• Steered dynamics Jacopo Sgrignani (Fri Nov 11 2011 - 04:56:32 CST)
  • RE: Steered dynamics JC Gumbart (Sat Nov 12 2011 - 01:18:06 CST)
• improper angle Marco Sant (Fri Nov 11 2011 - 02:34:42 CST)
  • Re: improper angle johan strumpfer (Fri Nov 11 2011 - 06:21:38 CST)
    • RE: improper angle JC Gumbart (Sat Nov 12 2011 - 01:14:09 CST)
• Assertion failed in file @ KRAKEN PAUL NEWMAN (Wed Nov 09 2011 - 10:07:07 CST)
  • Re: Assertion failed in file @ KRAKEN Axel Kohlmeyer (Wed Nov 09 2011 - 11:00:04 CST)
    • two NAMD questions Richard Wood (Wed Nov 09 2011 - 22:31:18 CST)
      • Re: two NAMD questions sajad falsafi (Wed Nov 09 2011 - 23:16:18 CST)
• PLUMED release 1.3 available Massimiliano Bonomi (Wed Nov 09 2011 - 09:05:09 CST)
• Pressure Problems, Excessively High Readings Rajan Vatassery (Tue Nov 08 2011 - 20:43:10 CST)
  • Re: Pressure Problems, Excessively High Readings Jeffrey Potoff (Wed Nov 09 2011 - 04:02:30 CST)
  • Re: Pressure Problems, Excessively High Readings johan strumpfer (Tue Nov 08 2011 - 21:13:23 CST)
    • Re: Pressure Problems, Excessively High Readings Rajan Vatassery (Mon Nov 14 2011 - 01:14:41 CST)
• Low global exclusion count matziast_at_med.uth.gr (Tue Nov 08 2011 - 04:23:47 CST)
• Extra bonds-ABF Parisa Akhski (Mon Nov 07 2011 - 10:53:18 CST)
  • Re: Extra bonds-ABF Giacomo Fiorin (Mon Nov 07 2011 - 11:01:22 CST)
• dextran and or poly-D-glucosamine topology Raul Araya (Fri Nov 04 2011 - 16:58:34 CDT)
• membrane simulation at high Temp Jiao, Dian NMN (-EXP) (Fri Nov 04 2011 - 16:50:20 CDT)
  • Re: membrane simulation at high Temp Giacomo Fiorin (Fri Nov 04 2011 - 16:56:12 CDT)
    • Re: membrane simulation at high Temp Jiao, Dian NMN (-EXP) (Fri Nov 04 2011 - 17:38:56 CDT)
      • Re: membrane simulation at high Temp Chris Harrison (Fri Nov 04 2011 - 18:58:11 CDT)
      • Re: membrane simulation at high Temp Chris Harrison (Fri Nov 04 2011 - 19:01:07 CDT)
      • Re: membrane simulation at high Temp Axel Kohlmeyer (Fri Nov 04 2011 - 19:08:22 CDT)
• Running NAMD CUDA Steven Cox (Fri Nov 04 2011 - 15:06:31 CDT)
  • Re: Running NAMD CUDA Axel Kohlmeyer (Fri Nov 04 2011 - 15:16:45 CDT)
• AW: Reading files for multiple threaded simulations Norman Geist (Fri Nov 04 2011 - 02:28:50 CDT)
• (no subject) Gurunath Katagi (Thu Nov 03 2011 - 03:01:19 CDT)
• (no subject) Gurunath Katagi (Thu Nov 03 2011 - 03:00:22 CDT)
• Re: Reading files for multiple threaded simulations Chris Harrison (Wed Nov 02 2011 - 01:57:36 CDT)
  • Re: Reading files for multiple threaded simulations Yi He (Wed Nov 02 2011 - 11:00:11 CDT)
    • AW: Reading files for multiple threaded simulations Norman Geist (Thu Nov 03 2011 - 02:26:05 CDT)
• selection of cholesterol molecules Swarna M Patra (Tue Nov 01 2011 - 23:54:06 CDT)
  • Re: selection of cholesterol molecules Chris Harrison (Wed Nov 02 2011 - 00:06:35 CDT)
• Use of RBCG to convert multiple frames from atomistic trajectory to Coarse grained rohan uttarwar (Tue Nov 01 2011 - 13:13:20 CDT)
  • Re: Use of RBCG to convert multiple frames from atomistic trajectory to Coarse grained Axel Kohlmeyer (Tue Nov 01 2011 - 14:59:27 CDT)
• Reading files for multiple threaded simulations Yi He (Tue Nov 01 2011 - 12:16:52 CDT)
  • AW: Reading files for multiple threaded simulations Norman Geist (Wed Nov 02 2011 - 01:45:32 CDT)
• Cluster on commodity hardware Thomas Albers (Mon Oct 31 2011 - 12:37:30 CDT)
• (no subject) Buddhadev Maiti (Fri Oct 28 2011 - 22:14:30 CDT)
  • Re: Chris Harrison (Mon Oct 31 2011 - 15:24:19 CDT)
• minimization and gradient trend Francesco Pietra (Mon Oct 31 2011 - 03:57:10 CDT)
• installing namd on ibm cluster (powerpc) Gurunath Katagi (Fri Oct 28 2011 - 15:14:02 CDT)
  • Re: installing namd on ibm cluster (powerpc) Chris Harrison (Fri Oct 28 2011 - 17:35:07 CDT)
• question about namd simulation on protein in tip4p water box Liqun Zhang (Fri Oct 28 2011 - 13:14:36 CDT)
  • Re: question about namd simulation on protein in tip4p water box Chris Harrison (Fri Oct 28 2011 - 13:43:51 CDT)
• ForceConstant in Umbrella Sampling Buddhadev Maiti (Fri Oct 28 2011 - 12:38:24 CDT)
  • Re: ForceConstant in Umbrella Sampling Chris Harrison (Fri Oct 28 2011 - 18:10:40 CDT)
• NAMD on KRAKEN PAUL NEWMAN (Fri Oct 28 2011 - 02:04:00 CDT)
  • Re: NAMD on KRAKEN Axel Kohlmeyer (Fri Oct 28 2011 - 04:43:59 CDT)
    • Re: NAMD on KRAKEN PAUL NEWMAN (Fri Oct 28 2011 - 07:55:01 CDT)
      • Re: NAMD on KRAKEN Axel Kohlmeyer (Fri Oct 28 2011 - 08:03:35 CDT)
• Carma v.1.1 released. Nicholas M Glykos (Thu Oct 27 2011 - 12:54:24 CDT)
• PME and net charge in the system Salvatore Mario Cosseddu (Thu Oct 27 2011 - 12:00:12 CDT)
  • Re: PME and net charge in the system Chris Harrison (Thu Oct 27 2011 - 12:12:46 CDT)
    • Re: PME and net charge in the system Salvatore Mario Cosseddu (Thu Oct 27 2011 - 12:20:26 CDT)
• Evaluated heat capacities via NAMD are larger than experimental values Mert Gür (Wed Oct 26 2011 - 13:44:35 CDT)
  • Re: Evaluated heat capacities via NAMD are larger than experimental values Jun Zhang (Wed Oct 26 2011 - 19:00:18 CDT)
• Error with "namd" Bob Masong (Wed Oct 26 2011 - 00:01:21 CDT)
  • AW: Error with "namd" Norman Geist (Wed Oct 26 2011 - 02:05:17 CDT)
• Accelerated Molecular Dynamics Vijay Vammi (Tue Oct 25 2011 - 16:11:54 CDT)
  • Re: Accelerated Molecular Dynamics Yi Wang (Tue Oct 25 2011 - 18:03:33 CDT)
    • Re: Accelerated Molecular Dynamics Vijay Vammi (Tue Oct 25 2011 - 21:04:49 CDT)
      • Re: Accelerated Molecular Dynamics Vijay Vammi (Tue Oct 25 2011 - 23:45:32 CDT)
      • Re: Accelerated Molecular Dynamics Vijay Vammi (Wed Nov 02 2011 - 20:42:07 CDT)
• PMF jafar azamat (Tue Oct 25 2011 - 06:52:28 CDT)
  • Re: PMF Axel Kohlmeyer (Tue Oct 25 2011 - 07:23:21 CDT)
• different velocities problem Hasan haska (Tue Oct 25 2011 - 01:28:22 CDT)
  • Re: different velocities problem Jérôme Hénin (Tue Oct 25 2011 - 02:10:14 CDT)
• Error with ubqp.pdb in NAMD tutorial Bob Masong (Mon Oct 24 2011 - 22:43:46 CDT)
  • Re: Error with ubqp.pdb in NAMD tutorial Jens K. Munk (Tue Oct 25 2011 - 02:10:22 CDT)
• What is the proper value of TMDk in TMD simulations? 常姗燕 (Sun Oct 23 2011 - 23:21:19 CDT)
  • Re: What is the proper value of TMDk in TMD simulations? Jérôme Hénin (Mon Oct 24 2011 - 03:02:43 CDT)
    • Re: What is the proper value of TMDk in TMD simulations? Gianluca Interlandi (Mon Oct 24 2011 - 11:03:37 CDT)
• FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100) Jens K. Munk (Sun Oct 23 2011 - 14:39:24 CDT)
  • Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100) Jernej Zidar (Sun Oct 23 2011 - 19:45:56 CDT)
  • Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100) johan strumpfer (Sun Oct 23 2011 - 16:42:07 CDT)
• GBIS and hydrophobic term, in replay to Jerome and David discussion Branko (Sun Oct 23 2011 - 09:36:17 CDT)
  • Re: GBIS and hydrophobic term, in replay to Jerome and David discussion Jérôme Hénin (Sun Oct 23 2011 - 09:43:08 CDT)
    • Re: GBIS and hydrophobic term, in replay to Jerome and David discussion Branko (Sun Oct 23 2011 - 09:55:27 CDT)
• * CGtool force field * HAMID - (Sat Oct 22 2011 - 12:00:19 CDT)
  • Re: * CGtool force field * Axel Kohlmeyer (Sat Oct 22 2011 - 12:47:47 CDT)
    • Re: * CGtool force field * HAMID - (Sat Oct 22 2011 - 14:11:14 CDT)
      • Re: * CGtool force field * Axel Kohlmeyer (Sat Oct 22 2011 - 14:36:38 CDT)
  • Re: * CGtool force field * Chris Harrison (Sat Oct 22 2011 - 17:02:37 CDT)
    • Re: * CGtool force field * HAMID - (Sun Oct 23 2011 - 03:09:03 CDT)
      • Re: * CGtool force field * Axel Kohlmeyer (Sun Oct 23 2011 - 16:16:47 CDT)
      • Re: * CGtool force field * HAMID - (Wed Oct 26 2011 - 08:47:39 CDT)
• About "alchDecouple" in FEP wenhao_at_uchicago.edu (Sat Oct 22 2011 - 10:47:14 CDT)
  • Re: About "alchDecouple" in FEP Jérôme Hénin (Sat Oct 22 2011 - 11:51:27 CDT)
    • Re: About "alchDecouple" in FEP wenhao_at_uchicago.edu (Sun Oct 23 2011 - 07:47:26 CDT)
• Problems Bionanotechnology Tutorial Salvador H-V (Fri Oct 21 2011 - 22:19:01 CDT)
• cellBasisvectors/.xsc fixing/colvars while running amber ff Francesco Pietra (Fri Oct 21 2011 - 13:13:57 CDT)
  • Re: cellBasisvectors/.xsc fixing/colvars while running amber ff Giacomo Fiorin (Fri Oct 21 2011 - 17:06:43 CDT)
• Error with tclBC to induce shear flow KONG Xian (Thu Oct 20 2011 - 20:59:42 CDT)
• coloring method in VMD lam nguyen (Thu Oct 20 2011 - 18:19:14 CDT)
  • Re: coloring method in VMD Axel Kohlmeyer (Thu Oct 20 2011 - 18:21:30 CDT)
• RBCG electrostatic term HAMID - (Thu Oct 20 2011 - 12:43:33 CDT)
• rigid body Dimitrios Tragoudaras (Thu Oct 20 2011 - 12:33:45 CDT)
• Sampling schemes with FEP Patargias, George (Thu Oct 20 2011 - 08:13:19 CDT)
  • Re: Sampling schemes with FEP Chris Chipot (Thu Oct 20 2011 - 09:16:34 CDT)
• how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 06:27:47 CDT)
  • Re: how to visualize an alchemical FEP transformation?? Axel Kohlmeyer (Thu Oct 20 2011 - 09:02:34 CDT)
    • RE: how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 13:28:13 CDT)
      • Re: how to visualize an alchemical FEP transformation?? Axel Kohlmeyer (Thu Oct 20 2011 - 14:02:59 CDT)
      • RE: how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 15:10:28 CDT)
      • Re: how to visualize an alchemical FEP transformation?? Chris Harrison (Thu Oct 20 2011 - 15:21:59 CDT)
      • RE: how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 16:19:38 CDT)
      • Re: how to visualize an alchemical FEP transformation?? Axel Kohlmeyer (Thu Oct 20 2011 - 16:42:02 CDT)
      • Re: how to visualize an alchemical FEP transformation?? Chris Harrison (Thu Oct 20 2011 - 18:02:32 CDT)
      • RE: how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Sat Oct 22 2011 - 09:58:42 CDT)
      • Re: how to visualize an alchemical FEP transformation?? Axel Kohlmeyer (Sat Oct 22 2011 - 11:33:47 CDT)
      • RE: how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Sat Oct 22 2011 - 12:31:01 CDT)
      • Re: how to visualize an alchemical FEP transformation?? Chris Harrison (Sat Oct 22 2011 - 12:48:16 CDT)
• TClforce Swarna M Patra (Thu Oct 20 2011 - 03:11:01 CDT)
  • Re: TClforce harish vashisth (Thu Oct 20 2011 - 12:29:14 CDT)
  • Re: TClforce poker_at_physics.usyd.edu.au (Thu Oct 20 2011 - 21:22:25 CDT)
• fftw libraries for ppc Gurunath Katagi (Wed Oct 19 2011 - 22:04:42 CDT)
• Using CHARMM Compatible Amber Parameters Ehsan Ban (Wed Oct 19 2011 - 20:10:30 CDT)
  • Re: Using CHARMM Compatible Amber Parameters Jernej Zidar (Wed Oct 19 2011 - 20:22:46 CDT)
    • Re: Using CHARMM Compatible Amber Parameters johan strumpfer (Wed Oct 19 2011 - 22:57:48 CDT)
  • Re: Using CHARMM Compatible Amber Parameters Axel Kohlmeyer (Thu Oct 20 2011 - 11:34:33 CDT)
    • Re: Using CHARMM Compatible Amber Parameters Ehsan Ban (Sun Oct 23 2011 - 12:57:03 CDT)
• Multiple dihedral parameters in X-PLOR format Joe Yelk (Tue Oct 18 2011 - 17:46:57 CDT)
• Question about silver nanoparticle simulation Yao Xiao (Wed Oct 19 2011 - 08:37:23 CDT)
  • Re: Question about silver nanoparticle simulation Axel Kohlmeyer (Wed Oct 19 2011 - 09:26:27 CDT)
• Running AMBER FF with NAMD 2.8-CUDA Francesco Pietra (Wed Oct 19 2011 - 08:14:59 CDT)
  • Re: Running AMBER FF with NAMD 2.8-CUDA Nicholas M Glykos (Wed Oct 19 2011 - 08:37:15 CDT)
    • Re: Running AMBER FF with NAMD 2.8-CUDA Francesco Pietra (Wed Oct 19 2011 - 09:23:32 CDT)
      • Re: Running AMBER FF with NAMD 2.8-CUDA Nicholas M Glykos (Wed Oct 19 2011 - 10:06:08 CDT)
• Area per lipid error Andres Morales N (Mon Oct 17 2011 - 21:12:33 CDT)
• tclforces- tcl extension written in c and built with swig Eva Gonzalez Noya (Mon Oct 17 2011 - 18:30:33 CDT)
  • Re: tclforces- tcl extension written in c and built with swig Axel Kohlmeyer (Mon Oct 17 2011 - 18:43:08 CDT)
  • Re: tclforces- tcl extension written in c and built with swig Chris Harrison (Mon Oct 17 2011 - 18:46:36 CDT)
• membrane moving up in simulation box kanchi subbarao rao (Mon Oct 17 2011 - 01:09:17 CDT)
  • Re: membrane moving up in simulation box Marcos Sotomayor (Mon Oct 17 2011 - 01:58:17 CDT)
• RE: Hello imran.1.618_at_gmail.com (Sat Oct 15 2011 - 00:32:59 CDT)
• Re: what is wrong with this pdb to simulate with NAMD raghav singh (Fri Oct 14 2011 - 12:04:20 CDT)
• rigid bonds Francesco Pietra (Fri Oct 14 2011 - 09:24:41 CDT)
  • Re: rigid bonds Axel Kohlmeyer (Fri Oct 14 2011 - 09:27:34 CDT)
  • Fwd: rigid bonds Francesco Pietra (Fri Oct 14 2011 - 09:44:14 CDT)
• RBCG water HAMID - (Thu Oct 13 2011 - 17:45:14 CDT)
• unit of force constant for dihedral angle restrain with extrabonds command Ling Wu (Thu Oct 13 2011 - 15:43:13 CDT)
• Restarting protein system simulation using different ligand Kevin Kastner (Thu Oct 13 2011 - 12:22:41 CDT)
  • Re: Restarting protein system simulation using different ligand Chris Harrison (Sun Oct 16 2011 - 18:41:55 CDT)
• Re: iron sulphur cluster parametrization francesco oteri (Thu Oct 13 2011 - 09:03:43 CDT)
• membrane moving up in simulation box kanchi subbarao rao (Thu Oct 13 2011 - 01:54:32 CDT)
  • Fwd: membrane moving up in simulation box kanchi subbarao rao (Thu Oct 13 2011 - 04:54:15 CDT)
    • Fwd: membrane moving up in simulation box kanchi subbarao rao (Thu Oct 13 2011 - 06:26:12 CDT)
• Boundary potential of colvar alpha not working? Yun Luo (Wed Oct 12 2011 - 09:34:27 CDT)
  • Re: Boundary potential of colvar alpha not working? Jérôme Hénin (Thu Oct 13 2011 - 07:14:53 CDT)
    • Re: Boundary potential of colvar alpha not working? Yun Luo (Thu Oct 13 2011 - 08:21:15 CDT)
      • Re: Boundary potential of colvar alpha not working? Jérôme Hénin (Thu Oct 13 2011 - 08:54:35 CDT)
      • Re: Boundary potential of colvar alpha not working? Yun Luo (Thu Oct 13 2011 - 09:03:46 CDT)
      • Re: Boundary potential of colvar alpha not working? Jérôme Hénin (Thu Oct 13 2011 - 10:23:41 CDT)
• rsh not working Neelanjana Sengupta (Tue Oct 11 2011 - 00:58:27 CDT)
  • Re: rsh not working Matteo Rotter (Tue Oct 11 2011 - 13:37:26 CDT)
    • Re: rsh not working Neelanjana Sengupta (Wed Oct 12 2011 - 02:29:16 CDT)
      • Re: rsh not working Chris Harrison (Wed Oct 12 2011 - 10:08:27 CDT)
• Questions Kevin Littrell (Mon Oct 10 2011 - 21:20:37 CDT)
  • Re: Questions Joshua Adelman (Mon Oct 10 2011 - 21:54:49 CDT)
• PBC Wrap + TMD Gianluca Interlandi (Mon Oct 10 2011 - 14:02:58 CDT)
• GBIS and hydrophobic solvation Jérôme Hénin (Mon Oct 10 2011 - 07:24:50 CDT)
  • Re: GBIS and hydrophobic solvation Branko (Mon Oct 10 2011 - 10:11:42 CDT)
    • Re: GBIS and hydrophobic solvation David Tanner (Thu Oct 13 2011 - 13:40:32 CDT)
• install NAMD 2.8 v Namd Namd (Mon Oct 10 2011 - 05:50:53 CDT)
• Force Vector Between Two Atoms Ehsan Ban (Fri Oct 07 2011 - 17:14:02 CDT)
  • RE: Force Vector Between Two Atoms Bruno Luís Pinto de Oliveira (Sat Oct 08 2011 - 04:25:40 CDT)
    • Re: Force Vector Between Two Atoms Ehsan Ban (Mon Oct 10 2011 - 01:19:55 CDT)
• namd log file Namd Namd (Fri Oct 07 2011 - 07:20:02 CDT)
  • Re: namd log file Jian Liu (Fri Oct 07 2011 - 19:14:39 CDT)
• Re: Minimization doesn't stop when converged Boyang Wang (Fri Oct 07 2011 - 03:56:01 CDT)
  • AW: Minimization doesn't stop when converged Norman Geist (Fri Oct 07 2011 - 04:54:47 CDT)
  • Re: Minimization doesn't stop when converged Jérôme Hénin (Fri Oct 07 2011 - 05:27:13 CDT)
  • Re: Minimization doesn't stop when converged Boyang Wang (Sat Oct 08 2011 - 01:25:24 CDT)
• Minimization doesn't stop when converged Norman Geist (Fri Oct 07 2011 - 03:48:36 CDT)
• iron sulphur cluster parametrization francesco oteri (Thu Oct 06 2011 - 09:24:31 CDT)
• Compiled Windows HPC version. Chewning, Joseph (Tue Oct 04 2011 - 07:04:31 CDT)
• Restart from anywhere in DCD trajectory Zack Scholl (Mon Oct 03 2011 - 13:19:41 CDT)
  • Re: Restart from anywhere in DCD trajectory johan strumpfer (Mon Oct 03 2011 - 17:16:57 CDT)
• How to write a dcd in fortran? lam nguyen (Mon Oct 03 2011 - 13:21:36 CDT)
  • Re: How to write a dcd in fortran? Axel Kohlmeyer (Mon Oct 03 2011 - 13:26:54 CDT)
    • Re: How to write a dcd in fortran? lam nguyen (Mon Oct 03 2011 - 14:07:47 CDT)
      • Re: How to write a dcd in fortran? Axel Kohlmeyer (Mon Oct 03 2011 - 14:13:03 CDT)
      • Re: How to write a dcd in fortran? Joshua D. Moore (Mon Oct 03 2011 - 15:56:57 CDT)
      • Re: How to write a dcd in fortran? lam nguyen (Mon Oct 03 2011 - 18:03:37 CDT)
      • Re: How to write a dcd in fortran? Axel Kohlmeyer (Mon Oct 03 2011 - 18:13:20 CDT)
• Help in reverse Free Energy perturbation - hysteresis Bruno Luís Pinto de Oliveira (Mon Oct 03 2011 - 05:24:58 CDT)
  • Re: Help in reverse Free Energy perturbation - hysteresis Jérôme Hénin (Mon Oct 03 2011 - 06:49:46 CDT)
    • Re: Help in reverse Free Energy perturbation - hysteresis Chris Chipot (Mon Oct 03 2011 - 07:05:16 CDT)
      • RE: Help in reverse Free Energy perturbation - hysteresis Bruno Luís Pinto de Oliveira (Tue Oct 04 2011 - 14:29:34 CDT)
      • Re: Help in reverse Free Energy perturbation - hysteresis Chris Chipot (Wed Oct 05 2011 - 01:10:24 CDT)
• script for equilibration matziast_at_med.uth.gr (Sun Oct 02 2011 - 04:19:19 CDT)
  • AW: script for equilibration Norman Geist (Tue Oct 04 2011 - 00:18:04 CDT)
• refphrasing of the question for equilibration script matziast_at_med.uth.gr (Fri Sep 30 2011 - 04:16:27 CDT)
• refphrasing of the question for equilibration script matziast_at_med.uth.gr (Fri Sep 30 2011 - 03:43:13 CDT)
  • Re: refphrasing of the question for equilibration script Jernej Zidar (Fri Sep 30 2011 - 03:50:35 CDT)
• Periodic cell has become too small for original patch grid!â€� Andres Morales N (Thu Sep 29 2011 - 23:52:39 CDT)
  • Re: Periodic cell has become too small for original patch grid!â€� Axel Kohlmeyer (Fri Sep 30 2011 - 08:06:26 CDT)
• an important question for equilibration script matziast_at_med.uth.gr (Thu Sep 29 2011 - 15:44:58 CDT)
  • Re: an important question for equilibration script Jernej Zidar (Thu Sep 29 2011 - 18:42:58 CDT)
• Dangling Bonds? atsuiai_at_aim.com (Wed Sep 28 2011 - 17:35:12 CDT)
  • Re: Dangling Bonds? Axel Kohlmeyer (Wed Sep 28 2011 - 17:58:18 CDT)
  • Re: Dangling Bonds? atsuiai_at_aim.com (Thu Sep 29 2011 - 06:23:55 CDT)
  • Re: Dangling Bonds? atsuiai_at_aim.com (Thu Sep 29 2011 - 08:45:39 CDT)
• TMD and binary coordinate files Bryan Roessler (Wed Sep 28 2011 - 16:40:49 CDT)
• ABF with Alpha colvar can't be used on supercomputer? Yun Luo (Wed Sep 28 2011 - 15:38:02 CDT)
  • Re: ABF with Alpha colvar can't be used on supercomputer? JC Gumbart (Thu Sep 29 2011 - 01:05:53 CDT)
    • Re: ABF with Alpha colvar can't be used on supercomputer? Jérôme Hénin (Thu Sep 29 2011 - 05:04:42 CDT)
      • RE: ABF with Alpha colvar can't be used on supercomputer? JC Gumbart (Thu Sep 29 2011 - 08:05:19 CDT)
      • Re: ABF with Alpha colvar can't be used on supercomputer? Jérôme Hénin (Thu Sep 29 2011 - 09:56:46 CDT)
      • Re: ABF with Alpha colvar can't be used on supercomputer? Chris Harrison (Thu Sep 29 2011 - 10:11:32 CDT)
      • Re: ABF with Alpha colvar can't be used on supercomputer? Yun Luo (Thu Sep 29 2011 - 14:25:57 CDT)
• Problem with NAMD2.8 & prmtop files made with AMBER11/AmberTools1.5 Irene Newhouse (Wed Sep 28 2011 - 15:40:24 CDT)
  • Re: Problem with NAMD2.8 & prmtop files made with AMBER11/AmberTools1.5 George Madalin Giambasu (Wed Sep 28 2011 - 19:04:22 CDT)
• CUDA compiled code for Windows HPC Chewning, Joseph (Wed Sep 28 2011 - 14:52:29 CDT)
• restraining residues in NAMD Haydee Valdes (Wed Sep 28 2011 - 10:59:20 CDT)
  • Re: restraining residues in NAMD flavio seixas (Wed Sep 28 2011 - 17:32:27 CDT)
    • Re: restraining residues in NAMD johan strumpfer (Wed Sep 28 2011 - 19:44:34 CDT)
• membrane simulation and mobility of lipids - blocking ion channel Jorgen Simonsen (Wed Sep 28 2011 - 09:07:50 CDT)
  • Re: membrane simulation and mobility of lipids - blocking ion channel HAMID - (Thu Sep 29 2011 - 04:33:48 CDT)
    • Re: membrane simulation and mobility of lipids - blocking ion channel HAMID - (Thu Sep 29 2011 - 04:57:10 CDT)
• Trouble running NAMD on win7 Haque-Student,STW, Farhadul (Sun Sep 25 2011 - 23:44:14 CDT)
  • Re: Trouble running NAMD on win7 Ajasja LjubetiÄ� (Mon Sep 26 2011 - 03:09:19 CDT)
  • Re: Trouble running NAMD on win7 Jernej Zidar (Mon Sep 26 2011 - 03:42:19 CDT)
• colvar and tclForces with CUDA Jiyong Park (Sun Sep 25 2011 - 02:02:29 CDT)
• Epsilon, Rmin for copper ions Francesco Pietra (Sat Sep 24 2011 - 03:55:34 CDT)
• how to use variables in colvar configuration file Ling Wu (Fri Sep 23 2011 - 12:26:08 CDT)
  • Re: how to use variables in colvar configuration file Jérôme Hénin (Fri Sep 23 2011 - 13:23:55 CDT)
• Fwd: Solved stream files and paratool Francesco Pietra (Fri Sep 23 2011 - 10:13:06 CDT)
• velocity information Molecular Dynamics (Fri Sep 23 2011 - 08:20:29 CDT)
• stream files and paratool Francesco Pietra (Fri Sep 23 2011 - 03:10:52 CDT)
• Help in FEP backward/reverse calculation Bruno Luís Pinto de Oliveira (Thu Sep 22 2011 - 14:36:38 CDT)
  • Re: Help in FEP backward/reverse calculation Jérôme Hénin (Fri Sep 23 2011 - 03:22:52 CDT)
• namd 2.8 new feature Hasan haska (Thu Sep 22 2011 - 08:37:27 CDT)
• ABF & distanceZ projection axis more HAMID - (Thu Sep 22 2011 - 03:05:07 CDT)
  • Re: ABF & distanceZ projection axis more Jérôme Hénin (Thu Sep 22 2011 - 04:33:02 CDT)
    • Re: ABF & distanceZ projection axis more HAMID - (Thu Sep 22 2011 - 05:36:32 CDT)
• force question Hasan haska (Thu Sep 22 2011 - 02:50:18 CDT)
  • Re: force question Jérôme Hénin (Thu Sep 22 2011 - 04:32:45 CDT)
    • Re: force question Ehsan Ban (Thu Sep 22 2011 - 05:18:34 CDT)
    • Re: force question Hasan haska (Thu Sep 22 2011 - 05:36:47 CDT)
• save the last frame as a pdb file using dcd file Namd Namd (Thu Sep 22 2011 - 02:02:53 CDT)
  • Re: save the last frame as a pdb file using dcd file HAMID - (Thu Sep 22 2011 - 03:08:25 CDT)
  • Re: save the last frame as a pdb file using dcd file Nicholas M Glykos (Thu Sep 22 2011 - 03:10:21 CDT)
  • AW: save the last frame as a pdb file using dcd file Norman Geist (Thu Sep 22 2011 - 03:15:43 CDT)
    • Re : AW: save the last frame as a pdb file using dcd file Namd Namd (Thu Sep 22 2011 - 03:33:05 CDT)
      • AW: AW: save the last frame as a pdb file using dcd file Norman Geist (Thu Sep 22 2011 - 04:33:07 CDT)
• Quick TCl scripting question Anthony Rey (Wed Sep 21 2011 - 20:57:07 CDT)
  • Re: Quick TCl scripting question Axel Kohlmeyer (Wed Sep 21 2011 - 21:09:50 CDT)
• ABF & distanceZ projection axis HAMID - (Wed Sep 21 2011 - 16:15:45 CDT)
  • Re: ABF & distanceZ projection axis Giacomo Fiorin (Wed Sep 21 2011 - 19:22:36 CDT)
    • Re: ABF & distanceZ projection axis HAMID - (Thu Sep 22 2011 - 01:20:02 CDT)
• ABF results interpretation HAMID - (Wed Sep 21 2011 - 10:22:38 CDT)
• membrane system ipsita basu (Wed Sep 21 2011 - 01:30:00 CDT)
  • Re: membrane system Jérôme Hénin (Wed Sep 21 2011 - 02:44:42 CDT)
    • Re: membrane system Jérôme Hénin (Wed Sep 21 2011 - 03:47:16 CDT)
    • Re: membrane system Bjoern Olausson (Thu Sep 22 2011 - 03:10:00 CDT)
  • Re: membrane system Bjoern Olausson (Wed Sep 21 2011 - 05:02:08 CDT)
• NAMD running on windows HPC question Chewning, Joseph (Tue Sep 20 2011 - 07:58:43 CDT)
  • Re: NAMD running on windows HPC question Nikolaos Glykos (Tue Sep 20 2011 - 08:23:34 CDT)
  • Re: NAMD running on windows HPC question johan strumpfer (Tue Sep 20 2011 - 08:30:51 CDT)
    • RE: NAMD running on windows HPC question Chewning, Joseph (Tue Sep 20 2011 - 08:34:51 CDT)
      • Re: NAMD running on windows HPC question johan strumpfer (Tue Sep 20 2011 - 08:46:51 CDT)
      • Re: NAMD running on windows HPC question Axel Kohlmeyer (Tue Sep 20 2011 - 11:27:23 CDT)
• NOE Jacopo Sgrignani (Tue Sep 20 2011 - 07:27:09 CDT)
  • Re: NOE Jérôme Hénin (Tue Sep 20 2011 - 08:17:30 CDT)
• Re: Fwd: Re : Setting up a membrane simulation Bjoern Olausson (Tue Sep 20 2011 - 04:27:23 CDT)
  • Re: Fwd: Re : Setting up a membrane simulation Bjoern Olausson (Tue Sep 20 2011 - 05:43:30 CDT)
• Heating in NPT Pellegrini Eric (Mon Sep 19 2011 - 07:44:04 CDT)
• Infiniband and commodity hardware Thomas Albers (Sat Sep 17 2011 - 14:59:20 CDT)
  • Re: Infiniband and commodity hardware Axel Kohlmeyer (Sun Sep 18 2011 - 02:38:48 CDT)
  • AW: Infiniband and commodity hardware Norman Geist (Mon Sep 19 2011 - 01:03:41 CDT)
• phosphorilated serine Branko (Sat Sep 17 2011 - 11:01:42 CDT)
• Setting up a membrane simulation Pellegrini Eric (Fri Sep 16 2011 - 02:52:05 CDT)
  • Re: Setting up a membrane simulation Bjoern Olausson (Fri Sep 16 2011 - 07:13:56 CDT)
    • Re : Setting up a membrane simulation Pellegrini Eric (Mon Sep 19 2011 - 02:09:58 CDT)
• Invitation to connect on LinkedIn Ahlam Al-Rawi (Thu Sep 15 2011 - 16:11:12 CDT)
• SMD Jacopo Sgrignani (Thu Sep 15 2011 - 07:12:26 CDT)
  • Re: SMD Leandro Martínez (Thu Sep 15 2011 - 07:21:15 CDT)
• Na ion, Cl ion in TIP4P divya nayar (Thu Sep 15 2011 - 02:42:54 CDT)
• time step and total simulation time in conf file Namd Namd (Wed Sep 14 2011 - 09:41:00 CDT)
  • Re: time step and total simulation time in conf file Jérôme Hénin (Wed Sep 14 2011 - 10:53:43 CDT)
• Constraint failure during equalibration Jiao, Dian NMN (-EXP) (Tue Sep 13 2011 - 12:45:50 CDT)
  • Constraint failure during equalibration Jiao, Dian NMN (-EXP) (Tue Sep 13 2011 - 12:55:22 CDT)
  • AW: Constraint failure during equalibration Norman Geist (Wed Sep 14 2011 - 00:31:59 CDT)
• Differences between ABF and metadynamics Alex (Tue Sep 13 2011 - 05:13:34 CDT)
  • Re: Differences between ABF and metadynamics Jérôme Hénin (Tue Sep 13 2011 - 05:43:39 CDT)
    • Re: Differences between ABF and metadynamics Jérôme Hénin (Tue Sep 13 2011 - 08:45:17 CDT)
• question about Distance XY Song, Hyundeok (songhk) (Mon Sep 12 2011 - 23:27:05 CDT)
  • Re: question about Distance XY Jérôme Hénin (Tue Sep 13 2011 - 02:50:13 CDT)
    • RE: question about Distance XY Song, Hyundeok (songhk) (Tue Sep 13 2011 - 09:10:07 CDT)
• Unsubscribe Gmail (Mon Sep 12 2011 - 14:33:58 CDT)
• SMD Jacopo Sgrignani (Mon Sep 12 2011 - 02:53:30 CDT)
  • Re: SMD Ajasja LjubetiÄ� (Mon Sep 12 2011 - 04:07:52 CDT)
• restraint with colvars mocule Ling Wu (Sun Sep 11 2011 - 16:25:39 CDT)
  • Re: restraint with colvars mocule Jérôme Hénin (Mon Sep 12 2011 - 04:48:33 CDT)
    • Re: restraint with colvars mocule Ling Wu (Mon Sep 12 2011 - 09:53:21 CDT)
      • Re: restraint with colvars mocule Jérôme Hénin (Mon Sep 12 2011 - 10:08:47 CDT)
      • Re: restraint with colvars mocule Giacomo Fiorin (Mon Sep 12 2011 - 11:23:57 CDT)
• Nice paper on MD Simulations pawan raghav (Sat Sep 10 2011 - 13:37:00 CDT)
• difference between run and minimize snoze pa (Fri Sep 09 2011 - 16:01:55 CDT)
  • Re: difference between run and minimize snoze pa (Wed Sep 14 2011 - 10:02:03 CDT)
    • Re: difference between run and minimize snoze pa (Wed Sep 14 2011 - 10:05:56 CDT)
• TopoTools for tpr file Hasan haska (Fri Sep 09 2011 - 09:01:44 CDT)
  • Re: TopoTools for tpr file Axel Kohlmeyer (Fri Sep 09 2011 - 10:44:42 CDT)
  • Re: TopoTools for tpr file Daniel Aguayo (Fri Sep 09 2011 - 10:46:33 CDT)
  • Re: TopoTools for tpr file Jeffrey Potoff (Fri Sep 09 2011 - 11:09:22 CDT)
• can we run FEP calculation in water sphere? wenhao_at_uchicago.edu (Fri Sep 09 2011 - 03:21:01 CDT)
• RE: Temperature during membrane equilibration Andres Morales N (Thu Sep 08 2011 - 18:33:47 CDT)
  • Re: Temperature during membrane equilibration Erik Nordgren (Fri Sep 09 2011 - 11:17:53 CDT)
    • RE: Temperature during membrane equilibration Andres Morales N (Fri Sep 09 2011 - 20:57:36 CDT)
• help in FEP calculations : analysis/confirmation of results Bruno Luís Pinto de Oliveira (Thu Sep 08 2011 - 13:59:23 CDT)
• Temperature during membrane equilibration Andres Morales N (Wed Sep 07 2011 - 23:57:10 CDT)
• Bonds are too long after simulation Anthony Rey (Wed Sep 07 2011 - 10:32:11 CDT)
  • Re: Bonds are too long after simulation Markus K. Dahlgren (Wed Sep 07 2011 - 12:54:16 CDT)
    • Re: Bonds are too long after simulation Anthony Rey (Wed Sep 07 2011 - 22:48:37 CDT)
      • RMSD trajectory flavio seixas (Fri Nov 18 2011 - 14:09:15 CST)
      • Re: RMSD trajectory Joshua Adelman (Fri Nov 18 2011 - 14:21:46 CST)
      • Re: RMSD trajectory flavio seixas (Sat Nov 19 2011 - 08:44:40 CST)
      • Re: RMSD trajectory Nikolaos Glykos (Fri Nov 18 2011 - 14:32:41 CST)
  • Re: Bonds are too long after simulation flavio seixas (Wed Sep 07 2011 - 13:10:13 CDT)
  • Re: Bonds are too long after simulation Axel Kohlmeyer (Wed Sep 07 2011 - 13:18:26 CDT)
• namd2_ti.pl Modification of non-creatable array value attempted, subscript -49999 Pete Kekenes-Huskey (Tue Sep 06 2011 - 17:22:26 CDT)
• mean square displacement Molecular Dynamics (Mon Sep 05 2011 - 08:15:28 CDT)
  • Re: mean square displacement Ajasja LjubetiÄ� (Mon Sep 05 2011 - 08:22:55 CDT)
  • Re: mean square displacement Axel Kohlmeyer (Mon Sep 05 2011 - 08:42:03 CDT)
• Density Profile in VMD oguz gurbulak (Mon Sep 05 2011 - 02:30:50 CDT)
• Patch at AutoPsfBuilder flavio seixas (Sun Sep 04 2011 - 14:17:38 CDT)
• POPC membrane model in pH 4 zhjpan_at_mail.ustc.edu.cn (Sat Sep 03 2011 - 09:36:58 CDT)
  • Re: POPC membrane model in pH 4 Axel Kohlmeyer (Sat Sep 03 2011 - 09:50:08 CDT)
    • Re: Re: POPC membrane model in pH 4 zhjpan_at_mail.ustc.edu.cn (Sat Sep 03 2011 - 10:12:06 CDT)
• Hints for building namd2.8 on charm++ ibverbs layer? Bennion, Brian (Fri Sep 02 2011 - 18:06:15 CDT)
• (solved) charmrun: ssh_exchange_identification: Connection closed by remote host Leandro Martínez (Fri Sep 02 2011 - 14:44:24 CDT)
• Pressure Calculation Priyan Amaras (Fri Sep 02 2011 - 12:43:25 CDT)
• Component distanceZ-ABF Parisa Akhski (Fri Sep 02 2011 - 11:21:56 CDT)
  • Re: Component distanceZ-ABF Jérôme Hénin (Fri Sep 02 2011 - 16:19:53 CDT)
    • RE: Component distanceZ-ABF Parisa Akhski (Mon Sep 05 2011 - 09:42:17 CDT)
      • Re: Component distanceZ-ABF Jérôme Hénin (Mon Sep 05 2011 - 10:56:06 CDT)
      • RE: Component distanceZ-ABF Parisa Akhski (Mon Sep 05 2011 - 13:07:26 CDT)
      • Re: Component distanceZ-ABF Jérôme Hénin (Tue Sep 06 2011 - 04:27:44 CDT)
• Namd-I: A question about constant force pulling of a group of atoms Ye Yang (Thu Sep 01 2011 - 10:16:18 CDT)
• help in FEP calculations_binding free energy difference between 2 inhibitors Bruno Luís Pinto de Oliveira (Thu Sep 01 2011 - 10:04:41 CDT)
  • help in FEP calculations_binding free energy difference between 2 inhibitors Bruno Luís Pinto de Oliveira (Mon Sep 05 2011 - 13:08:58 CDT)
    • Re: help in FEP calculations_binding free energy difference between 2 inhibitors Chirag Vora (Mon Sep 05 2011 - 16:36:04 CDT)
• Margin Value in NAMD Andrea Holfelder (Wed Aug 31 2011 - 21:42:05 CDT)
  • Re: Margin Value in NAMD johan strumpfer (Wed Aug 31 2011 - 22:56:39 CDT)
    • Re: Margin Value in NAMD Andrea Holfelder (Wed Aug 31 2011 - 23:57:36 CDT)
      • Re: Margin Value in NAMD johan strumpfer (Thu Sep 01 2011 - 00:35:30 CDT)
    • Re: Margin Value in NAMD Andrea Holfelder (Thu Sep 01 2011 - 03:09:09 CDT)
• Keeping rigidBonds during Minimization David Huggins (Wed Aug 31 2011 - 19:05:05 CDT)
  • Re: Keeping rigidBonds during Minimization David Huggins (Mon Sep 12 2011 - 12:20:28 CDT)
    • Re: Keeping rigidBonds during Minimization Jérôme Hénin (Mon Sep 12 2011 - 18:09:58 CDT)
• Dock a metal ion into a peptide/protein Andrea Holfelder (Wed Aug 31 2011 - 14:29:39 CDT)
  • Re: Dock a metal ion into a peptide/protein Branko (Wed Aug 31 2011 - 15:28:17 CDT)
    • Re: Dock a metal ion into a peptide/protein Andrea Holfelder (Wed Aug 31 2011 - 21:51:27 CDT)
      • Re: Dock a metal ion into a peptide/protein Branko (Thu Sep 01 2011 - 04:09:16 CDT)
• HETATM vs ATOM in .pdb file Andrea Holfelder (Wed Aug 31 2011 - 04:56:35 CDT)
  • Re: HETATM vs ATOM in .pdb file Axel Kohlmeyer (Wed Aug 31 2011 - 06:16:16 CDT)
  • Re: HETATM vs ATOM in .pdb file Bjoern Olausson (Wed Aug 31 2011 - 06:20:55 CDT)
• about extrabonds restrain Ling Wu (Mon Aug 29 2011 - 16:22:53 CDT)
  • AW: about extrabonds restrain Norman Geist (Tue Aug 30 2011 - 01:18:37 CDT)
    • Re: AW: about extrabonds restrain Ling Wu (Tue Aug 30 2011 - 07:58:25 CDT)
      • AW: AW: about extrabonds restrain Norman Geist (Wed Aug 31 2011 - 00:05:47 CDT)
  • Re: about extrabonds restrain Axel Kohlmeyer (Tue Aug 30 2011 - 08:06:04 CDT)
  • Re: about extrabonds restrain JC Gumbart (Tue Aug 30 2011 - 08:41:35 CDT)
• FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. Massimiliano Porrini (Mon Aug 29 2011 - 09:36:55 CDT)
  • Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. Chris Harrison (Mon Aug 29 2011 - 11:50:00 CDT)
    • Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. Massimiliano Porrini (Mon Aug 29 2011 - 14:26:06 CDT)
      • Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. Chris Harrison (Mon Aug 29 2011 - 19:35:42 CDT)
      • Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. Chris Harrison (Mon Aug 29 2011 - 20:07:33 CDT)
• colvar restrain of water in lipid system Ling Wu (Mon Aug 29 2011 - 09:13:58 CDT)
  • Re: colvar restrain of water in lipid system Giacomo Fiorin (Mon Aug 29 2011 - 09:36:39 CDT)
    • Re: colvar restrain of water in lipid system Ling Wu (Mon Aug 29 2011 - 09:55:45 CDT)
      • Re: colvar restrain of water in lipid system Giacomo Fiorin (Mon Aug 29 2011 - 11:06:44 CDT)
      • Re: colvar restrain of water in lipid system Jérôme Hénin (Mon Aug 29 2011 - 11:17:47 CDT)
• Using 'Alignment to principal axes ' Andres Morales N (Mon Aug 29 2011 - 00:38:44 CDT)
• RNA simulation Juan Antonio Raygoza Garay (Fri Aug 26 2011 - 15:38:38 CDT)
  • Re: RNA simulation Chris Harrison (Mon Aug 29 2011 - 19:23:07 CDT)
• colvar restrain of water in lipid system Ling Wu (Fri Aug 26 2011 - 14:44:21 CDT)
• dummyAtom-ABF Parisa Akhski (Fri Aug 26 2011 - 09:57:13 CDT)
  • Re: dummyAtom-ABF Jérôme Hénin (Fri Aug 26 2011 - 10:32:20 CDT)
• combining metadynamics simulations Giovanni Bellesia (Fri Aug 26 2011 - 08:40:29 CDT)
  • Re: combining metadynamics simulations Giacomo Fiorin (Fri Aug 26 2011 - 09:18:01 CDT)
• Heating /Equilibration Babban Mia (Fri Aug 26 2011 - 05:20:23 CDT)
  • Re: Heating /Equilibration Axel Kohlmeyer (Fri Aug 26 2011 - 08:16:29 CDT)
• SMD-extension MOhan maruthi sena (Fri Aug 26 2011 - 05:18:25 CDT)
  • Re: SMD-extension Axel Kohlmeyer (Fri Aug 26 2011 - 08:20:28 CDT)
    • Re: SMD-extension Ehsan Ban (Fri Aug 26 2011 - 08:36:10 CDT)
  • Re: SMD-extension johan strumpfer (Fri Aug 26 2011 - 07:26:18 CDT)
• About Columb energy of 2 ions in Vacuum wenhao_at_uchicago.edu (Thu Aug 25 2011 - 18:02:04 CDT)
  • RE: About Columb energy of 2 ions in Vacuum JC Gumbart (Fri Aug 26 2011 - 01:37:05 CDT)
    • RE: About Columb energy of 2 ions in Vacuum wenhao_at_uchicago.edu (Fri Aug 26 2011 - 02:30:48 CDT)
      • Re: About Columb energy of 2 ions in Vacuum Jérôme Hénin (Fri Aug 26 2011 - 04:30:54 CDT)
• How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? ÕÅÓÂ (Thu Aug 25 2011 - 01:32:33 CDT)
  • Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? Boyang Wang (Thu Aug 25 2011 - 01:41:51 CDT)
    • Re: Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? 张勇 (Thu Aug 25 2011 - 02:26:50 CDT)
      • Re: Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? Boyang Wang (Thu Aug 25 2011 - 02:32:01 CDT)
  • Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? Salvador H-V (Thu Aug 25 2011 - 11:12:49 CDT)
• SWM4-NDP Simulation David Huggins (Wed Aug 24 2011 - 14:49:33 CDT)
  • Re: SWM4-NDP Simulation David Hardy (Wed Aug 24 2011 - 18:49:22 CDT)
• convert pdb format to normal pdb format hamze rahimi (Wed Aug 24 2011 - 04:48:09 CDT)
  • Re: convert pdb format to normal pdb format flavio seixas (Wed Aug 24 2011 - 18:05:18 CDT)
• Heating /Equilibration Babban Mia (Wed Aug 24 2011 - 02:56:37 CDT)
• About Columb energy of 2 ions in Vacuum wenhao_at_uchicago.edu (Tue Aug 23 2011 - 17:28:04 CDT)
  • Re: About Columb energy of 2 ions in Vacuum Edward Lyman (Tue Aug 23 2011 - 19:47:25 CDT)
    • Re: About Columb energy of 2 ions in Vacuum wenhao_at_uchicago.edu (Tue Aug 23 2011 - 22:30:29 CDT)
    • Re: About Columb energy of 2 ions in Vacuum wenhao_at_uchicago.edu (Tue Aug 23 2011 - 22:32:08 CDT)
• Memory leak patch Andy Somogyi (Tue Aug 23 2011 - 09:20:09 CDT)
• Logfile flooded with "The last position output [...]" when IMDon is used. Bjoern Olausson (Tue Aug 23 2011 - 04:32:47 CDT)
• 'firsttimestep' treated as signed integer ? Nicholas M Glykos (Mon Aug 22 2011 - 12:01:26 CDT)
• Ib version and nodelist Neelanjana Sengupta (Mon Aug 22 2011 - 00:36:09 CDT)
  • AW: Ib version and nodelist Norman Geist (Mon Aug 22 2011 - 00:50:56 CDT)
• distanceXY colvar-ABF Parisa Akhski (Sun Aug 21 2011 - 09:05:16 CDT)
  • Re: distanceXY colvar-ABF Giacomo Fiorin (Sun Aug 21 2011 - 12:28:07 CDT)
• SASA of PBD files Andrea Holfelder (Sat Aug 20 2011 - 04:11:25 CDT)
  • Re: SASA of PBD files David Tanner (Thu Aug 25 2011 - 08:47:31 CDT)
• CUDA on GPU Cluster Arvind Kannan (Fri Aug 19 2011 - 17:31:06 CDT)
  • AW: CUDA on GPU Cluster Norman Geist (Mon Aug 22 2011 - 00:47:16 CDT)
• PBB File Format/Setup for PBC Anna James (Fri Aug 19 2011 - 07:24:11 CDT)
  • Re: PBB File Format/Setup for PBC johan strumpfer (Fri Aug 19 2011 - 17:41:04 CDT)
• remove translation of protein under spherical boundary conditions kakali sen (Fri Aug 19 2011 - 04:39:24 CDT)
• Restarting MD (Disabling Checklist) Babban Mia (Thu Aug 18 2011 - 10:58:55 CDT)
  • Re: Restarting MD (Disabling Checklist) Babban Mia (Fri Aug 19 2011 - 06:50:04 CDT)
    • Re: Restarting MD (Disabling Checklist) Joshua Adelman (Fri Aug 19 2011 - 07:18:17 CDT)
• Re: Multinode NAMD CUDA GPU Selection Axel Kohlmeyer (Thu Aug 18 2011 - 10:39:18 CDT)
  • AW: Multinode NAMD CUDA GPU Selection Norman Geist (Fri Aug 19 2011 - 00:22:56 CDT)
    • Re: AW: Multinode NAMD CUDA GPU Selection Axel Kohlmeyer (Fri Aug 19 2011 - 06:33:28 CDT)
  • AW: Multinode NAMD CUDA GPU Selection Norman Geist (Fri Aug 19 2011 - 00:53:31 CDT)
• Heating in NAMD Babban Mia (Thu Aug 18 2011 - 10:13:08 CDT)
  • Re: Heating in NAMD Erik Nordgren (Fri Aug 19 2011 - 12:52:31 CDT)
    • Re: Heating in NAMD Babban Mia (Sat Aug 20 2011 - 05:37:53 CDT)
      • Re: Heating in NAMD Babban Mia (Sun Aug 21 2011 - 06:06:25 CDT)
• Relationship between High temperature and the boiling point of water albus hawking (Wed Aug 17 2011 - 13:29:56 CDT)
  • Re: Relationship between High temperature and the boiling point of water Jeffrey Potoff (Thu Aug 18 2011 - 09:22:36 CDT)
• (no subject) Andrea Holfelder (Thu Aug 18 2011 - 04:59:05 CDT)
  • (no subject) David Rogers (Mon Aug 22 2011 - 20:25:04 CDT)
  • (no subject) Axel Kohlmeyer (Tue Aug 23 2011 - 09:37:15 CDT)
• RHDO lattice as a PBC unit Cell in NAMD Andrea Holfelder (Thu Aug 18 2011 - 04:59:59 CDT)
• Multinode NAMD CUDA GPU Selection Norman Geist (Thu Aug 18 2011 - 01:25:00 CDT)
• differences in multiprocessor energy minimization results Markus Metz (Wed Aug 17 2011 - 11:44:19 CDT)
• Relative RMSD constraint jiyong (Wed Aug 17 2011 - 02:00:57 CDT)
  • Re: Relative RMSD constraint Alexander Predeus (Wed Aug 17 2011 - 02:31:56 CDT)
• Truncated octahedron - unwrapping the trajectory etc Alexander Predeus (Tue Aug 16 2011 - 21:46:22 CDT)
• MMTools Chathurika Abeyrathne (Tue Aug 16 2011 - 20:03:45 CDT)
  • Re: MMTools Axel Kohlmeyer (Wed Aug 17 2011 - 10:15:50 CDT)
    • Re: vmd-l: Re: MMTools Chathurika Abeyrathne (Wed Aug 17 2011 - 19:02:46 CDT)
      • Re: vmd-l: Re: MMTools Axel Kohlmeyer (Wed Aug 17 2011 - 20:28:28 CDT)
      • Re: vmd-l: Re: MMTools Chathurika Abeyrathne (Wed Aug 17 2011 - 21:07:21 CDT)
      • Re: vmd-l: Re: MMTools Boyang Wang (Thu Aug 18 2011 - 00:15:02 CDT)
• low dielectric constants in GBIS Branko (Tue Aug 16 2011 - 15:41:04 CDT)
• Generalized Born calcs Thomas Bishop (Tue Aug 16 2011 - 14:53:17 CDT)
• PME Grid Settings and its significance relative to a cutoff value Andrea Holfelder (Tue Aug 16 2011 - 15:07:14 CDT)
  • Re: PME Grid Settings and its significance relative to a cutoff value Erik Nordgren (Fri Aug 19 2011 - 12:38:34 CDT)
    • Re: PME Grid Settings and its significance relative to a cutoff value Axel Kohlmeyer (Fri Aug 19 2011 - 13:05:26 CDT)
• Namd / gromacs Sara baretller (Tue Aug 16 2011 - 09:17:41 CDT)
• (no subject) Anna James (Tue Aug 16 2011 - 08:38:14 CDT)
  • Re: Axel Kohlmeyer (Tue Aug 16 2011 - 08:43:00 CDT)
    • RE: Anna James (Tue Aug 16 2011 - 08:48:51 CDT)
    • RE: Anna James (Tue Aug 16 2011 - 09:20:49 CDT)
      • Re: Jeffrey J. Potoff (Tue Aug 16 2011 - 09:35:20 CDT)
      • Re: Babban Mia (Tue Aug 16 2011 - 09:41:58 CDT)
      • Re: Jeffrey Potoff (Tue Aug 16 2011 - 09:45:33 CDT)
      • RE: Anna James (Tue Aug 16 2011 - 12:23:05 CDT)
• Re: AW: Letzte Hilfe Bjoern Olausson (Tue Aug 16 2011 - 06:17:36 CDT)
• convergence and stability of simulation Jorgen Simonsen (Mon Aug 15 2011 - 14:08:29 CDT)
• AW: Letzte Hilfe Norman Geist (Mon Aug 15 2011 - 07:16:39 CDT)
• AW: Batch Mode MD simulation Script for NAMD Norman Geist (Mon Aug 15 2011 - 00:29:43 CDT)
• Denaturation via increased temperature Bjoern Olausson (Mon Aug 15 2011 - 04:11:06 CDT)
  • Re: Denaturation via increased temperature Bjoern Olausson (Mon Aug 15 2011 - 04:31:25 CDT)
  • Re: Denaturation via increased temperature Jernej Zidar (Mon Aug 15 2011 - 04:38:55 CDT)
    • Re: Denaturation via increased temperature Bjoern Olausson (Mon Aug 15 2011 - 06:11:17 CDT)
• Lingand Unbinding using SMD Jacopo Sgrignani (Mon Aug 15 2011 - 02:19:17 CDT)
  • Re: Lingand Unbinding using SMD Jian Liu (Mon Aug 15 2011 - 03:28:37 CDT)
• Re: Moving an atom 1A0 in one timestep then running MD for 10,000 timesteps while holding that one atom fixed Ehsan Ban (Mon Aug 15 2011 - 00:01:22 CDT)
• Periodic Boundary Condition for a 630 Amino Acid Protein Babban Mia (Sun Aug 14 2011 - 08:15:28 CDT)
  • Re: Periodic Boundary Condition for a 630 Amino Acid Protein Joshua Adelman (Sun Aug 14 2011 - 08:46:11 CDT)
    • Re: Periodic Boundary Condition for a 630 Amino Acid Protein Babban Mia (Sun Aug 14 2011 - 09:19:18 CDT)
• MD condition hamze rahimi (Sun Aug 14 2011 - 05:02:36 CDT)
• .COOR TO PDB FILE Babban Mia (Sat Aug 13 2011 - 01:11:48 CDT)
  • Re: .COOR TO PDB FILE JC Gumbart (Sat Aug 13 2011 - 01:29:04 CDT)
  • Re: .COOR TO PDB FILE Ehsan Ban (Sat Aug 13 2011 - 02:47:27 CDT)
  • AW: .COOR TO PDB FILE Norman Geist (Mon Aug 15 2011 - 00:34:58 CDT)
• Re: Batch Mode MD simulation Script for NAMD Babban Mia (Fri Aug 12 2011 - 05:46:32 CDT)
  • Re: Batch Mode MD simulation Script for NAMD Jeffrey Potoff (Fri Aug 12 2011 - 06:45:12 CDT)
    • Re: Batch Mode MD simulation Script for NAMD Axel Kohlmeyer (Fri Aug 12 2011 - 07:53:13 CDT)
      • Re: Batch Mode MD simulation Script for NAMD Jernej Zidar (Fri Aug 12 2011 - 08:03:21 CDT)
  • AW: Batch Mode MD simulation Script for NAMD Norman Geist (Fri Aug 12 2011 - 07:02:29 CDT)
  • Re: Batch Mode MD simulation Script for NAMD Babban Mia (Fri Aug 12 2011 - 12:06:28 CDT)
    • Re: Batch Mode MD simulation Script for NAMD Babban Mia (Fri Aug 12 2011 - 12:59:45 CDT)
    • RE: Batch Mode MD simulation Script for NAMD Ismail, Mohd F. (Fri Aug 12 2011 - 13:07:59 CDT)
      • Re: Batch Mode MD simulation Script for NAMD Babban Mia (Fri Aug 12 2011 - 13:55:03 CDT)
      • RE: Batch Mode MD simulation Script for NAMD Ismail, Mohd F. (Fri Aug 12 2011 - 14:40:31 CDT)
      • Re: Batch Mode MD simulation Script for NAMD Babban Mia (Sat Aug 13 2011 - 07:36:56 CDT)
      • Re: Batch Mode MD simulation Script for NAMD JC Gumbart (Sat Aug 13 2011 - 08:45:56 CDT)
      • AW: Batch Mode MD simulation Script for NAMD Norman Geist (Mon Aug 15 2011 - 00:34:15 CDT)
• Batch Mode MD simulation Script for NAMD Babban Mia (Thu Aug 11 2011 - 18:56:19 CDT)
  • AW: Batch Mode MD simulation Script for NAMD Norman Geist (Fri Aug 12 2011 - 00:47:19 CDT)
• Mixed TIP3/TIP4 Waters Keith Battle (Thu Aug 11 2011 - 06:29:18 CDT)
  • Re: Mixed TIP3/TIP4 Waters Jernej Zidar (Thu Aug 11 2011 - 07:28:29 CDT)
• image centering problem ipsita basu (Thu Aug 11 2011 - 00:41:20 CDT)
• sodium ion in water divya nayar (Thu Aug 11 2011 - 00:17:27 CDT)
  • Re: sodium ion in water Axel Kohlmeyer (Thu Aug 11 2011 - 00:36:08 CDT)
• Re: Topology file for ethanol Babban Mia (Wed Aug 10 2011 - 23:35:37 CDT)
• Topology file for ethanol Babban Mia (Wed Aug 10 2011 - 22:58:19 CDT)
• Solvation in VMD using Non Standard Solvent System Babban Mia (Wed Aug 10 2011 - 07:35:32 CDT)
  • Re: Solvation in VMD using Non Standard Solvent System Axel Kohlmeyer (Wed Aug 10 2011 - 07:47:35 CDT)
• Compiling Namd on MAC with Cuda Stan Skafidas (Wed Aug 10 2011 - 07:16:49 CDT)
• Custom CHARMM forcefield usage problem Jernej Zidar (Tue Aug 09 2011 - 23:12:04 CDT)
  • Re: Custom CHARMM forcefield usage problem Jernej Zidar (Tue Aug 09 2011 - 23:47:30 CDT)
    • RE: Custom CHARMM forcefield usage problem JC Gumbart (Wed Aug 10 2011 - 00:00:55 CDT)
• Fwd: Re: Explicit Solvent Sytem (40% Ethanol + 60% Water) Branko (Tue Aug 09 2011 - 13:29:52 CDT)
• Blue Waters Andy Somogyi (Tue Aug 09 2011 - 10:18:49 CDT)
• Re: Explicit Solvent Sytem (40% Ethanol + 60% Water) Babban Mia (Tue Aug 09 2011 - 09:42:26 CDT)
  • RE: Explicit Solvent Sytem (40% Ethanol + 60% Water) Ismail, Mohd F. (Tue Aug 09 2011 - 13:02:19 CDT)
    • Re: Explicit Solvent Sytem (40% Ethanol + 60% Water) Babban Mia (Wed Aug 10 2011 - 04:49:20 CDT)
• minimization problem Narasimhan LOGANATHAN (Tue Aug 09 2011 - 07:00:28 CDT)
  • Re: minimization problem Jeffrey Potoff (Tue Aug 09 2011 - 07:16:08 CDT)
    • Re: minimization problem Narasimhan LOGANATHAN (Tue Aug 09 2011 - 08:21:37 CDT)
• Explicit Solvent Sytem (40% Ethanol + 60% Water) Babban Mia (Tue Aug 09 2011 - 01:20:20 CDT)
• patch becoming too small Jorgen Simonsen (Tue Aug 09 2011 - 01:14:33 CDT)
  • AW: patch becoming too small Norman Geist (Tue Aug 09 2011 - 02:41:19 CDT)
• Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Andres Morales N (Sun Aug 07 2011 - 21:00:38 CDT)
  • Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Bjoern Olausson (Mon Aug 08 2011 - 02:57:08 CDT)
    • RE: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Andres Morales N (Mon Aug 08 2011 - 17:20:56 CDT)
      • Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Bjoern Olausson (Wed Aug 10 2011 - 02:49:01 CDT)
  • Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! flavio seixas (Mon Aug 08 2011 - 21:12:24 CDT)
  • Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Jeffrey Potoff (Mon Aug 08 2011 - 21:12:39 CDT)
• NAMD on PS3 Ali Khanlarkhani (Sat Aug 06 2011 - 11:02:22 CDT)
  • Re: NAMD on PS3 Andy Somogyi (Sat Aug 06 2011 - 13:16:20 CDT)
• nvidia cuda driver version Francesco Pietra (Fri Aug 05 2011 - 08:44:44 CDT)
  • AW: nvidia cuda driver version Norman Geist (Mon Aug 08 2011 - 00:04:40 CDT)
• Minimization is taking a lot of computing time. Kartheek (Fri Aug 05 2011 - 04:53:42 CDT)
  • AW: Minimization is taking a lot of computing time. Norman Geist (Fri Aug 05 2011 - 05:54:49 CDT)
  • Minimization is taking a lot of computing time. Kartheek (Tue Aug 09 2011 - 06:06:57 CDT)
    • Re: Minimization is taking a lot of computing time. Branko (Tue Aug 09 2011 - 12:42:17 CDT)
    • AW: Minimization is taking a lot of computing time. Norman Geist (Wed Aug 10 2011 - 00:44:55 CDT)
      • RE: Minimization is taking a lot of computing time. JC Gumbart (Wed Aug 10 2011 - 00:52:16 CDT)
      • AW: Minimization is taking a lot of computing time. Norman Geist (Wed Aug 10 2011 - 01:21:10 CDT)
• GBIS on GPU? Danny Xu (Thu Aug 04 2011 - 11:51:57 CDT)
• error: expected floating-point number but got Shen, Han (Thu Aug 04 2011 - 10:21:32 CDT)
  • Re: error: expected floating-point number but got Axel Kohlmeyer (Thu Aug 04 2011 - 10:29:08 CDT)
• online guide for using amber ff in NAMD George Madalin Giambasu (Wed Aug 03 2011 - 11:18:10 CDT)
• Re: [ppl] Regarding Compiling in Redhat linux. Phil Miller (Wed Aug 03 2011 - 09:30:01 CDT)
• Re: Namd-I: namd compiling problem Ye Yang (Wed Aug 03 2011 - 10:46:13 CDT)
  • AW: Namd-I: namd compiling problem Norman Geist (Thu Aug 04 2011 - 00:33:59 CDT)
• Namd-I: namd compiling problem Ye Yang (Tue Aug 02 2011 - 22:28:05 CDT)
  • AW: Namd-I: namd compiling problem Norman Geist (Wed Aug 03 2011 - 00:23:52 CDT)
• RE: System net charge Andres Morales N (Tue Aug 02 2011 - 19:20:38 CDT)
  • Re: System net charge Cruz-Chu Eduardo Roberto (Thu Aug 04 2011 - 03:28:45 CDT)
    • RE: System net charge Andres Morales N (Thu Aug 04 2011 - 23:43:11 CDT)
• Re: [ppl] Compliling NAMD in RedHat Phil Miller (Tue Aug 02 2011 - 10:10:18 CDT)
• Pair interaction and thermo integration Courtney Taylor (Mon Aug 01 2011 - 09:32:38 CDT)
• Temperature bath Chathurika Abeyrathne (Mon Aug 01 2011 - 02:20:15 CDT)
• 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 17-21, 2011, Bremen, Germany David Brandon (Fri Jul 29 2011 - 14:13:05 CDT)
• Moving an atom 1A0 in one timestep then running MD for 10,000 timesteps while holding that one atom fixed Ehsan Ban (Fri Jul 29 2011 - 12:40:27 CDT)
• namd-I: cionize problem in vmd Ye Yang (Fri Jul 29 2011 - 11:17:10 CDT)
  • Re: namd-I: cionize problem in vmd Axel Kohlmeyer (Fri Jul 29 2011 - 11:23:56 CDT)
    • Re: namd-I: cionize problem in vmd Ye Yang (Mon Aug 01 2011 - 11:36:26 CDT)
• Dividing a 2D ABF simulations into regions (on nodes with different speeds) Ajasja LjubetiÄ� (Fri Jul 29 2011 - 04:44:38 CDT)
  • Re: Dividing a 2D ABF simulations into regions (on nodes with different speeds) Axel Kohlmeyer (Fri Jul 29 2011 - 08:34:33 CDT)
    • Re: Dividing a 2D ABF simulations into regions (on nodes with different speeds) Ajasja LjubetiÄ� (Fri Jul 29 2011 - 11:56:17 CDT)
• About fastest CUDA cards Francesco Pietra (Fri Jul 29 2011 - 04:09:37 CDT)
• about D amino acid AB (Fri Jul 29 2011 - 03:50:16 CDT)
  • Re: about D amino acid Eduard Schreiner (Fri Jul 29 2011 - 04:27:39 CDT)
• System net charge Andres Morales N (Fri Jul 29 2011 - 03:25:11 CDT)
• RE: DPPC membrane Andres Morales N (Fri Jul 29 2011 - 03:16:50 CDT)
• "Constraint failure in RATTLE algorithm" when restart FEP Dong Luo (Thu Jul 28 2011 - 12:21:28 CDT)
  • Re: "Constraint failure in RATTLE algorithm" when restart FEP Dong Luo (Fri Jul 29 2011 - 14:36:44 CDT)
    • Re: "Constraint failure in RATTLE algorithm" when restart FEP Dong Luo (Mon Aug 01 2011 - 10:50:27 CDT)
• NAMD energy plugin politr_at_fh.huji.ac.il (Thu Jul 28 2011 - 04:22:42 CDT)
• DPPC membrane Andres Morales N (Thu Jul 28 2011 - 01:29:36 CDT)
  • Re: DPPC membrane Ajasja LjubetiÄ� (Thu Jul 28 2011 - 05:21:10 CDT)
• Quartz modelling Nikita Vakula (Thu Jul 28 2011 - 00:46:05 CDT)
  • Re: Quartz modelling Cruz-Chu Eduardo Roberto (Thu Jul 28 2011 - 03:20:53 CDT)
• Trp-cage folding simulation divya nayar (Thu Jul 28 2011 - 00:09:07 CDT)
• colvars, discontinuous rotation JC Gumbart (Wed Jul 27 2011 - 20:41:30 CDT)
  • Re: colvars, discontinuous rotation Giacomo Fiorin (Wed Jul 27 2011 - 21:20:41 CDT)
    • Re: colvars, discontinuous rotation JC Gumbart (Wed Jul 27 2011 - 23:27:23 CDT)
• Setting integrator parameters for ABF Ajasja LjubetiÄ� (Wed Jul 27 2011 - 12:49:24 CDT)
  • Re: Setting integrator parameters for ABF Giacomo Fiorin (Wed Jul 27 2011 - 13:12:46 CDT)
    • Re: Setting integrator parameters for ABF Ajasja LjubetiÄ� (Wed Jul 27 2011 - 14:01:31 CDT)
      • Re: Setting integrator parameters for ABF Giacomo Fiorin (Wed Jul 27 2011 - 14:10:17 CDT)
      • water sphere plus dielectric esmael (Wed Jul 27 2011 - 14:11:20 CDT)
• nitrogen in namd Marco Sant (Wed Jul 27 2011 - 04:47:15 CDT)
  • Re: nitrogen in namd Jim Phillips (Wed Jul 27 2011 - 15:07:25 CDT)
    • Re: nitrogen in namd Marco Sant (Sun Jul 31 2011 - 05:47:18 CDT)
  • Re: nitrogen in namd Erik Nordgren (Wed Jul 27 2011 - 14:49:04 CDT)
    • Re: nitrogen in namd Jeffrey Potoff (Wed Jul 27 2011 - 15:51:57 CDT)
      • Re: nitrogen in namd Jim Phillips (Thu Jul 28 2011 - 11:57:05 CDT)
• using colvars for bending modulus? JC Gumbart (Tue Jul 26 2011 - 15:43:50 CDT)
  • Re: using colvars for bending modulus? Jérôme Hénin (Wed Jul 27 2011 - 01:29:59 CDT)
    • RE: using colvars for bending modulus? JC Gumbart (Wed Jul 27 2011 - 01:40:24 CDT)
      • Re: using colvars for bending modulus? Jérôme Hénin (Wed Jul 27 2011 - 03:12:33 CDT)
• NAMD 2.8 on Cray XE6 segfaulting Tim Robinson (Tue Jul 26 2011 - 05:46:01 CDT)
  • Re: NAMD 2.8 on Cray XE6 segfaulting Jim Phillips (Tue Jul 26 2011 - 11:05:30 CDT)
    • Re: NAMD 2.8 on Cray XE6 segfaulting Jim Phillips (Tue Jul 26 2011 - 11:58:34 CDT)
      • Re: NAMD 2.8 on Cray XE6 segfaulting Jim Phillips (Tue Jul 26 2011 - 16:14:34 CDT)
• NAMD 2.8 job submission script for queenbee cnu gromacs (Mon Jul 25 2011 - 18:29:51 CDT)
  • Re: NAMD 2.8 job submission script for queenbee Jim Phillips (Tue Jul 26 2011 - 11:13:57 CDT)
  • Re: NAMD 2.8 job submission script for queenbee: ManyJobs Thomas Bishop (Tue Jul 26 2011 - 08:46:29 CDT)
• Segmentation Faults on Mac OS X Lion Arvind Kannan (Mon Jul 25 2011 - 16:48:21 CDT)
  • RE: Segmentation Faults on Mac OS X Lion Jesper Sørensen (Tue Jul 26 2011 - 03:40:33 CDT)
  • Re: Segmentation Faults on Mac OS X Lion Jim Phillips (Tue Jul 26 2011 - 15:46:30 CDT)
• Segmentation Faults on Mac OS X Lion Arvind Kannan (Mon Jul 25 2011 - 16:39:31 CDT)
• is there any difference between non-constrained equilibrium and normal MD production? AB (Mon Jul 25 2011 - 13:04:35 CDT)
• combining thermodynamic integration with replica exchange in NAMD Hugh Heldenbrand (Mon Jul 25 2011 - 10:05:50 CDT)
• how to generate transparent figures? AB (Sat Jul 23 2011 - 09:59:07 CDT)
  • Re: how to generate transparent figures? Nicholas M Glykos (Sat Jul 23 2011 - 10:47:54 CDT)
  • Re: how to generate transparent figures? Bjoern Olausson (Mon Jul 25 2011 - 04:04:58 CDT)
• SOLVED: Failure to run namd-cuda with gtx-470 Francesco Pietra (Fri Jul 22 2011 - 09:56:34 CDT)
• Controlling fans on a GTX 560 ti Ajasja LjubetiÄ� (Fri Jul 22 2011 - 05:24:26 CDT)
  • Re: Controlling fans on a GTX 560 ti Axel Kohlmeyer (Fri Jul 22 2011 - 08:56:17 CDT)
    • Re: Controlling fans on a GTX 560 ti Ajasja LjubetiÄ� (Fri Jul 22 2011 - 09:12:29 CDT)
      • Re: Controlling fans on a GTX 560 ti Axel Kohlmeyer (Fri Jul 22 2011 - 09:19:59 CDT)
• Re: Yan: analysis question Bjoern Olausson (Fri Jul 22 2011 - 03:01:05 CDT)
• how to calculate partial charge for ligand based on CHARMM principle? AB (Thu Jul 21 2011 - 11:49:39 CDT)
  • Re: how to calculate partial charge for ligand based on CHARMM principle? Jeffrey Potoff (Thu Jul 21 2011 - 12:02:49 CDT)
• Molecule2.C Andy Somogyi (Thu Jul 21 2011 - 11:45:11 CDT)
  • Re: Molecule2.C Jim Phillips (Tue Jul 26 2011 - 11:36:33 CDT)
• Suspend NAMD (to RAM) Ajasja LjubetiÄ� (Wed Jul 20 2011 - 17:10:06 CDT)
  • Re: Suspend NAMD (to RAM) Giacomo Fiorin (Wed Jul 20 2011 - 20:41:27 CDT)
  • Re: Suspend NAMD (to RAM) Nicholas M Glykos (Thu Jul 21 2011 - 01:20:14 CDT)
    • Re: Suspend NAMD (to RAM) Ajasja LjubetiÄ� (Sat Jul 30 2011 - 09:44:23 CDT)
• namd files Hasan haska (Wed Jul 20 2011 - 08:17:34 CDT)
  • Re: namd files Axel Kohlmeyer (Wed Jul 20 2011 - 08:48:08 CDT)
• TIP4P water model Molecular Dynamics (Wed Jul 20 2011 - 07:34:47 CDT)
  • Re: TIP4P water model Chris Harrison (Thu Jul 21 2011 - 16:54:33 CDT)
• Equilibration Andres Morales N (Tue Jul 19 2011 - 13:39:37 CDT)
  • Re: Equilibration bharat gupta (Wed Jun 29 2011 - 01:06:10 CDT)
    • AW: Re: Equilibration Norman Geist (Wed Jun 29 2011 - 01:39:13 CDT)
    • Re: Re: Equilibration johan strumpfer (Wed Jun 29 2011 - 01:25:35 CDT)
      • Re: Re: Equilibration saman amiri (Thu Jun 30 2011 - 02:53:42 CDT)
    • Re: Re: Equilibration saman amiri (Wed Jun 29 2011 - 16:05:11 CDT)
      • Re: Re: Equilibration snoze pa (Wed Jun 29 2011 - 18:00:48 CDT)
    • Re: Re: Equilibration Jim Phillips (Mon Jul 18 2011 - 16:01:26 CDT)
  • Re: Equilibration Chris Harrison (Tue Jul 19 2011 - 14:42:06 CDT)
    • Re: Equilibration Erik Nordgren (Thu Jul 21 2011 - 20:44:38 CDT)
  • Membranes Andres Morales N (Tue Jul 19 2011 - 15:46:54 CDT)
    • Re: Membranes Erik Nordgren (Thu Jul 21 2011 - 20:54:46 CDT)
• expect NAMD survey emails this week Jim Phillips (Tue Jul 19 2011 - 11:51:22 CDT)
• Query about switch function using AMBER ff99SB forcefield and NAMD simulation code Madhurima Jana (Tue Jul 19 2011 - 06:41:25 CDT)
• analysis question Namd Namd (Tue Jul 19 2011 - 04:32:06 CDT)
  • Re: analysis question Bjoern Olausson (Tue Jul 19 2011 - 05:43:34 CDT)
• vmd-l: No APBS output: 'cannot access output file' error Christian Jorgensen (Mon Jul 18 2011 - 18:44:07 CDT)
• zinc-finger protein simulation hamze rahimi (Mon Jul 18 2011 - 06:55:08 CDT)
• PME or not PME? What happens if PME is turned off? Bjoern Olausson (Mon Jul 18 2011 - 04:10:08 CDT)
  • Re: PME or not PME? What happens if PME is turned off? Jérôme Hénin (Mon Jul 18 2011 - 15:27:09 CDT)
    • Re: PME or not PME? What happens if PME is turned off? Bjoern Olausson (Tue Jul 19 2011 - 01:48:50 CDT)
    • Re: PME or not PME? What happens if PME is turned off? Chris Harrison (Tue Jul 19 2011 - 14:45:48 CDT)
      • Re: PME or not PME? What happens if PME is turned off? Bjoern Olausson (Wed Jul 20 2011 - 03:03:10 CDT)
      • alchDecouple esmael (Fri Jul 22 2011 - 19:10:59 CDT)
      • Re: alchDecouple Jérôme Hénin (Sat Jul 23 2011 - 02:44:36 CDT)
      • Re: alchDecouple Jérôme Hénin (Mon Jul 25 2011 - 15:19:14 CDT)
      • Re: PME or not PME? What happens if PME is turned off? esmael (Tue Aug 02 2011 - 18:54:03 CDT)
      • Re: PME or not PME? What happens if PME is turned off? Chris Harrison (Wed Aug 03 2011 - 14:48:12 CDT)
• Pico scale to nanoscale simulation....alteration if .conf files required amit banerjee (Sun Jul 17 2011 - 21:28:43 CDT)
  • Re: Pico scale to nanoscale simulation....alteration if .conf files required Erik Nordgren (Thu Jul 21 2011 - 20:22:25 CDT)
    • Re: Pico scale to nanoscale simulation....alteration if .conf files required amit banerjee (Mon Jul 25 2011 - 07:42:35 CDT)
      • Re: Pico scale to nanoscale simulation....alteration if .conf files required Erik Nordgren (Tue Jul 26 2011 - 20:54:30 CDT)
• control distance between solvent and solute Kang Hee Cho (Fri Jul 15 2011 - 20:07:56 CDT)
  • Re: control distance between solvent and solute Jim Phillips (Wed Jul 20 2011 - 11:57:16 CDT)
• FATAL ERROR: Setting parameter fixedAtomsFile from script failed! Jorgen Simonsen (Fri Jul 15 2011 - 15:55:26 CDT)
  • Re: FATAL ERROR: Setting parameter fixedAtomsFile from script failed! Rajan Vatassery (Fri Jul 15 2011 - 16:43:04 CDT)
• how to define the numsteps in ABF or metadynamics simulation? ÕÅÓÂ (Thu Jul 14 2011 - 19:48:32 CDT)
  • Re: how to define the numsteps in ABF or metadynamics simulation? Jérôme Hénin (Sat Jul 16 2011 - 10:57:21 CDT)
• TIP5P-model Maria Kamm (Thu Jul 14 2011 - 19:07:48 CDT)
  • Re: TIP5P-model Rajan Vatassery (Thu Jul 14 2011 - 20:30:00 CDT)
• hi kanchi subbarao rao (Thu Jul 14 2011 - 12:31:06 CDT)
  • Re: hi Sándor Kovács (Thu Jul 14 2011 - 14:19:52 CDT)
• FATAL ERROR: Unable to open binary file sibel.cakan (Thu Jul 14 2011 - 05:34:57 CDT)
• Colvars "tilt" component force constant units for WHAM Robert Elder (Tue Jul 12 2011 - 16:36:55 CDT)
  • Colvars "tilt" component force constant units for WHAM Robert Elder (Tue Jul 12 2011 - 16:48:48 CDT)
    • Re: Colvars "tilt" component force constant units for WHAM Giacomo Fiorin (Tue Jul 12 2011 - 23:19:31 CDT)
      • Re: Colvars "tilt" component force constant units for WHAM Robert Elder (Fri Jul 22 2011 - 11:06:16 CDT)
• hi kanchi subbarao rao (Wed Jul 13 2011 - 13:47:30 CDT)
• Low global exclusion count errors Austin B. Yongye (Wed Jul 13 2011 - 13:10:10 CDT)
  • Re: Low global exclusion count errors Jim Phillips (Mon Jul 18 2011 - 17:00:02 CDT)
• protein moving out during npt equilibration bharat gupta (Wed Jul 13 2011 - 10:48:48 CDT)
  • Re: protein moving out during npt equilibration Giacomo Fiorin (Wed Jul 13 2011 - 10:54:10 CDT)
• Help required for nanoscale simulation amit banerjee (Wed Jul 13 2011 - 03:03:45 CDT)
• unsubscribe Tibbitt, Jeffrey A. (Tue Jul 12 2011 - 19:32:21 CDT)
• Low global exclusion count Austin B. Yongye (Tue Jul 12 2011 - 15:08:51 CDT)
• Problem while using MARTINI force field with NAMD 2.8 rohan uttarwar (Tue Jul 12 2011 - 11:42:14 CDT)
• how to define the numsteps in ABF or metadynamics simulation? Clark Zhang (Wed Jul 06 2011 - 23:08:50 CDT)
  • Re: how to define the numsteps in ABF or metadynamics simulation? Giacomo Fiorin (Tue Jul 12 2011 - 15:06:17 CDT)
• tesla 2050 benchmark Burgess, Don E (Tue Jul 12 2011 - 13:56:45 CDT)
  • Re: tesla 2050 benchmark Axel Kohlmeyer (Tue Jul 12 2011 - 14:04:00 CDT)
• where can I find parameters for t-BuO(C=O)NH-? AlbertAlbert (Tue Jul 12 2011 - 12:33:39 CDT)
• Filtered mail? Austin B. Yongye (Tue Jul 12 2011 - 09:04:32 CDT)
  • Re: Filtered mail? Jérôme Hénin (Tue Jul 12 2011 - 10:19:41 CDT)
• Using VMD paratool æ�Žä½³é”® (Mon Jul 11 2011 - 16:24:12 CDT)
• Fixed COM Ali Khanlarkhani (Mon Jul 11 2011 - 13:30:32 CDT)
  • RE: Fixed COM Parisa Akhski (Mon Jul 11 2011 - 13:52:21 CDT)
    • Re: Fixed COM Ajasja LjubetiÄ� (Mon Jul 11 2011 - 14:37:43 CDT)
      • Re: Fixed COM Ajasja LjubetiÄ� (Tue Jul 12 2011 - 08:11:04 CDT)
• NAMD chares Andy Somogyi (Mon Jul 11 2011 - 10:35:17 CDT)
  • Re: NAMD chares Jim Phillips (Mon Jul 18 2011 - 16:47:44 CDT)
• Possibility of modifying the non-bonded terms of the potential Ali Emileh (Fri Jul 08 2011 - 16:58:44 CDT)
  • Re: Possibility of modifying the non-bonded terms of the potential Jérôme Hénin (Sat Jul 09 2011 - 03:34:36 CDT)
• Patch link flavio seixas (Fri Jul 08 2011 - 14:11:38 CDT)
  • Re: Patch link Erik Nordgren (Sun Jul 10 2011 - 03:27:51 CDT)
    • Re: Patch link flavio seixas (Mon Jul 11 2011 - 10:16:54 CDT)
• temperature-TS with NAMDplot Molecular Dynamics (Fri Jul 08 2011 - 05:44:50 CDT)
  • AW: temperature-TS with NAMDplot Norman Geist (Fri Jul 08 2011 - 06:02:14 CDT)
  • Re: temperature-TS with NAMDplot Bjoern Olausson (Fri Jul 08 2011 - 06:30:09 CDT)
    • Re: temperature-TS with NAMDplot Axel Kohlmeyer (Fri Jul 08 2011 - 08:09:57 CDT)
      • Re: temperature-TS with NAMDplot Bjoern Olausson (Fri Jul 08 2011 - 09:07:43 CDT)
    • Re: temperature-TS with NAMDplot johan strumpfer (Fri Jul 08 2011 - 07:23:44 CDT)
• Implicit solvent simulation jaya c.jose (Fri Jul 08 2011 - 05:35:40 CDT)
  • Re: Implicit solvent simulation Bjoern Olausson (Fri Jul 08 2011 - 05:57:03 CDT)
• does any body have the parameter file for aldehyde group? AlbertAlbert (Fri Jul 08 2011 - 01:34:22 CDT)
  • Re: does any body have the parameter file for aldehyde group? felmerino_at_uchile.cl (Fri Jul 08 2011 - 01:44:15 CDT)
• free energy of binding Francesco Pietra (Thu Jul 07 2011 - 04:52:38 CDT)
  • AW: free energy of binding Norman Geist (Thu Jul 07 2011 - 05:35:07 CDT)
  • Re: free energy of binding Dong Luo (Thu Jul 07 2011 - 10:50:07 CDT)
    • Re: free energy of binding Francesco Pietra (Thu Jul 07 2011 - 16:50:12 CDT)
      • Re: free energy of binding Gianluca Interlandi (Thu Jul 07 2011 - 17:08:55 CDT)
      • Re: free energy of binding Jeffrey Potoff (Thu Jul 07 2011 - 17:16:02 CDT)
      • Re: free energy of binding Gianluca Interlandi (Thu Jul 07 2011 - 17:29:18 CDT)
      • Re: free energy of binding Jeff Wereszczynski (Thu Jul 07 2011 - 18:27:55 CDT)
      • Re: free energy of binding Richard Wood (Thu Jul 07 2011 - 18:56:48 CDT)
      • Re: free energy of binding Chris Harrison (Thu Jul 07 2011 - 17:12:34 CDT)
• Failure to run namd-cuda with gtx-470 Francesco Pietra (Wed Jul 06 2011 - 10:44:38 CDT)
  • Re: Failure to run namd-cuda with gtx-470 Francesco Pietra (Wed Jul 06 2011 - 16:18:53 CDT)
    • Re: Failure to run namd-cuda with gtx-470 Francesco Pietra (Thu Jul 07 2011 - 01:57:25 CDT)
• Transferring environment variables when using charmrun Ajasja LjubetiÄ� (Wed Jul 06 2011 - 05:08:54 CDT)
  • Re: Transferring environment variables when using charmrun Axel Kohlmeyer (Wed Jul 06 2011 - 07:47:46 CDT)
• Difference between cwd and cd Ajasja LjubetiÄ� (Wed Jul 06 2011 - 04:43:43 CDT)
  • Re: Difference between cwd and cd Axel Kohlmeyer (Wed Jul 06 2011 - 07:49:18 CDT)
    • Re: Difference between cwd and cd Ajasja LjubetiÄ� (Wed Jul 06 2011 - 08:59:30 CDT)
• membrane simulation ERROR rattle algorithm Jorgen Simonsen (Tue Jul 05 2011 - 10:13:57 CDT)
  • Re: membrane simulation ERROR rattle algorithm sajad falsafi (Tue Jul 05 2011 - 11:44:10 CDT)
    • Re: membrane simulation ERROR rattle algorithm Ajasja LjubetiÄ� (Tue Jul 05 2011 - 12:01:53 CDT)
      • Re: membrane simulation ERROR rattle algorithm Jorgen Simonsen (Tue Jul 05 2011 - 12:41:49 CDT)
      • Re: membrane simulation ERROR rattle algorithm Ajasja LjubetiÄ� (Tue Jul 05 2011 - 12:54:40 CDT)
      • Re: membrane simulation ERROR rattle algorithm Axel Kohlmeyer (Tue Jul 05 2011 - 13:05:18 CDT)
      • Re: membrane simulation ERROR rattle algorithm Ajasja LjubetiÄ� (Tue Jul 05 2011 - 13:40:44 CDT)
      • Re: membrane simulation ERROR rattle algorithm Jorgen Simonsen (Wed Jul 06 2011 - 03:36:22 CDT)
      • Re: membrane simulation ERROR rattle algorithm Salvatore Mario Cosseddu (Wed Jul 06 2011 - 06:15:46 CDT)
      • Re: membrane simulation ERROR rattle algorithm Ajasja LjubetiÄ� (Wed Jul 06 2011 - 06:37:10 CDT)
      • Re: membrane simulation ERROR rattle algorithm snoze pa (Wed Jul 06 2011 - 10:06:03 CDT)
• clustering of trajectory Bala subramanian (Tue Jul 05 2011 - 09:46:24 CDT)
  • Re: clustering of trajectory Nicholas M Glykos (Tue Jul 05 2011 - 09:57:50 CDT)
  • Re: clustering of trajectory Jun Zhang (Tue Jul 05 2011 - 20:18:16 CDT)
• Re: Re: Protein moving out of box during npt simulation bharat gupta (Tue Jul 05 2011 - 03:40:59 CDT)
  • Re: Re: Protein moving out of box during npt simulation Bjoern Olausson (Tue Jul 05 2011 - 04:22:50 CDT)
    • Re: Re: Protein moving out of box during npt simulation snoze pa (Tue Jul 05 2011 - 10:00:23 CDT)
  • Re: Re: Protein moving out of box during npt simulation bharat gupta (Tue Jul 05 2011 - 21:25:04 CDT)
    • Re: Re: Protein moving out of box during npt simulation snoze pa (Thu Jul 07 2011 - 10:02:09 CDT)
  • Re: Re: Protein moving out of box during npt simulation Bjoern Olausson (Fri Jul 08 2011 - 02:50:29 CDT)
• DNA terminal Patch / How could I retain the primes in DNA raghav singh (Tue Jul 05 2011 - 03:23:21 CDT)
• Win64-MPI Patriche Simona (Tue Jul 05 2011 - 02:04:17 CDT)
  • Re: Win64-MPI Ajasja LjubetiÄ� (Tue Jul 05 2011 - 02:11:25 CDT)
    • Re: Win64-MPI Patriche Simona (Tue Jul 12 2011 - 08:08:14 CDT)
      • AW: Win64-MPI Norman Geist (Tue Jul 12 2011 - 08:20:11 CDT)
      • Re: Win64-MPI Ajasja LjubetiÄ� (Tue Jul 12 2011 - 08:24:28 CDT)
• Re: Protein moving out of box during npt simulation bharat gupta (Tue Jul 05 2011 - 00:33:30 CDT)
  • AW: Re: Protein moving out of box during npt simulation Norman Geist (Tue Jul 05 2011 - 01:15:20 CDT)
• Re: distortion of some bonds during structure preparation bharat gupta (Mon Jul 04 2011 - 03:36:39 CDT)
• bigdcd file help snoze pa (Mon Jul 04 2011 - 01:29:23 CDT)
  • RE: bigdcd file help Cosseddu, Salvatore (Mon Jul 04 2011 - 04:11:55 CDT)
    • Re: bigdcd file help sajad falsafi (Mon Jul 04 2011 - 08:52:36 CDT)
      • Re: bigdcd file help snoze pa (Tue Jul 05 2011 - 09:56:15 CDT)
      • Re: bigdcd file help snoze pa (Tue Jul 05 2011 - 13:19:06 CDT)
      • Re: bigdcd file help Nicholas M Glykos (Tue Jul 05 2011 - 13:35:43 CDT)
• Hi: some doubt about nvt and npt equilibration bharat gupta (Sun Jul 03 2011 - 20:36:19 CDT)
  • Re: Hi: some doubt about nvt and npt equilibration johan strumpfer (Sun Jul 03 2011 - 20:53:47 CDT)
• a bundle of coor files Massimiliano Porrini (Sat Jul 02 2011 - 13:21:56 CDT)
  • Re: a bundle of coor files Rajan Vatassery (Sat Jul 02 2011 - 16:26:32 CDT)
    • Re: a bundle of coor files Massimiliano Porrini (Sat Jul 02 2011 - 20:16:05 CDT)
    • Re: a bundle of coor files Massimiliano Porrini (Tue Jul 05 2011 - 10:34:16 CDT)
• restart simulation writing in the same .dcd file. Ranyere Deyler (Sat Jul 02 2011 - 02:25:51 CDT)
  • SV: restart simulation writing in the same .dcd file. Maria Musgaard (Sat Jul 02 2011 - 03:03:26 CDT)
  • Re: restart simulation writing in the same .dcd file. saman amiri (Sat Jul 02 2011 - 10:00:29 CDT)
• Re: NPT equilibration bharat gupta (Fri Jul 01 2011 - 04:04:56 CDT)
  • AW: Re: NPT equilibration Norman Geist (Fri Jul 01 2011 - 05:49:38 CDT)
  • AW: Re: NPT equilibration Norman Geist (Fri Jul 01 2011 - 05:50:23 CDT)
• Re: Fatal Error Periodic cell has become too small for original patch grid bharat gupta (Fri Jul 01 2011 - 00:59:56 CDT)
• Re: Final production run in MD bharat gupta (Thu Jun 30 2011 - 18:42:23 CDT)
  • Re: Re: Final production run in MD Jérôme Hénin (Fri Jul 01 2011 - 02:31:04 CDT)
• Fwd: nvidia 275.09.07 driver. SOLVED, NO DRIVER PROBLEM Francesco Pietra (Thu Jun 30 2011 - 14:49:56 CDT)
• can RHDO crystal shape works in NAMD pxq_at_dicp.ac.cn (Fri Jul 01 2011 - 01:33:14 CDT)
• Accessing Colvars Within NAMD TCL David Rogers (Thu Jun 30 2011 - 10:28:33 CDT)
  • Re: Accessing Colvars Within NAMD TCL Jérôme Hénin (Thu Jun 30 2011 - 12:05:01 CDT)
• nvidia 275.09.07 driver Francesco Pietra (Thu Jun 30 2011 - 03:24:48 CDT)
• Re: Equilibration - NVT & NPT bharat gupta (Thu Jun 30 2011 - 01:36:56 CDT)
• Namd-I: Implicit solvent problem Ye Yang (Wed Jun 29 2011 - 16:07:55 CDT)
  • Re: Namd-I: Implicit solvent problem Francesco Oteri (Wed Jun 29 2011 - 16:17:21 CDT)
    • Re: Namd-I: Implicit solvent problem Gianluca Interlandi (Wed Jun 29 2011 - 16:31:49 CDT)
      • Re: Namd-I: Implicit solvent problem Ye Yang (Wed Jun 29 2011 - 17:38:54 CDT)
      • Re: Namd-I: Implicit solvent problem Ye Yang (Wed Jun 29 2011 - 17:44:55 CDT)
      • Re: Namd-I: Implicit solvent problem Giovanni Settanni (Thu Jun 30 2011 - 01:56:13 CDT)
      • Re: Namd-I: Implicit solvent problem Matteo Rotter (Wed Jul 20 2011 - 11:04:03 CDT)
      • Re: Re: Namd-I: Implicit solvent problem Enrico Guarnera (Wed Jul 20 2011 - 11:22:46 CDT)
      • Re: Re: Namd-I: Implicit solvent problem Matteo Rotter (Wed Jul 20 2011 - 16:06:29 CDT)
      • Re: Namd-I: Implicit solvent problem Gianluca Interlandi (Wed Jun 29 2011 - 17:49:51 CDT)
• How to simulate a charged surface Yingzhe Liu (Wed Jun 22 2011 - 02:53:56 CDT)
• Charmm parameter for H2 gas Zhao Lina (Wed Jun 29 2011 - 04:41:15 CDT)
  • Re: Charmm parameter for H2 gas Mikhail Suyetin (Wed Jun 29 2011 - 05:00:05 CDT)
• AW: Re: Equilibration Norman Geist (Wed Jun 29 2011 - 04:08:26 CDT)
• AW: Re: Equilibration Norman Geist (Wed Jun 29 2011 - 04:04:42 CDT)
• Re: Energy minimization bharat gupta (Tue Jun 28 2011 - 18:49:01 CDT)
• Cannot find bond parameters Gayatri Rathod (Tue Jun 28 2011 - 11:03:45 CDT)
  • Re: Cannot find bond parameters Axel Kohlmeyer (Tue Jun 28 2011 - 11:09:12 CDT)
• SWM4 water model simulation saman amiri (Mon Jun 27 2011 - 12:27:34 CDT)
• Restarting an alchemic FEP calculation Giovanni Bellesia (Mon Jun 27 2011 - 09:32:25 CDT)
  • Re: Restarting an alchemic FEP calculation Jérôme Hénin (Mon Jun 27 2011 - 11:03:55 CDT)
• Implicit solvent Massimiliano Porrini (Mon Jun 27 2011 - 06:35:00 CDT)
  • Re: Implicit solvent David Tanner (Mon Jun 27 2011 - 09:04:24 CDT)
• Re: vmd-l: protein-water RDF Ajasja LjubetiÄ� (Mon Jun 27 2011 - 03:29:44 CDT)
  • Re: vmd-l: protein-water RDF Ajasja LjubetiÄ� (Mon Jun 27 2011 - 03:33:13 CDT)
• Methanol - Autocorrelation of total dipole moment Chathurika Abeyrathne (Sat Jun 25 2011 - 03:36:06 CDT)
• Memory leak and crash before first step Pedro Gonnet (Fri Jun 24 2011 - 14:28:08 CDT)
  • Re: Memory leak and crash before first step Pedro Gonnet (Tue Jul 05 2011 - 08:25:34 CDT)
  • Re: Memory leak and crash before first step Erik Nordgren (Sun Jul 10 2011 - 04:02:05 CDT)
    • Re: Memory leak and crash before first step Pedro Gonnet (Tue Jul 12 2011 - 15:00:45 CDT)
  • Re: Memory leak and crash before first step Jim Phillips (Mon Jul 18 2011 - 16:26:38 CDT)
• interpretation of timing data in output Hannes Loeffler (Fri Jun 24 2011 - 04:29:42 CDT)
  • Re: interpretation of timing data in output Jim Phillips (Wed Jul 20 2011 - 11:47:04 CDT)
• CG-MD high electrostatic energy values sibel.cakan (Fri Jun 24 2011 - 03:40:32 CDT)
• Re: formyl and ethanolamide parameters and topology flavio seixas (Thu Jun 23 2011 - 12:08:58 CDT)
  • Re: formyl and ethanolamide parameters and topology flavio seixas (Thu Jun 23 2011 - 21:58:27 CDT)
  • Re: formyl and ethanolamide parameters and topology Branko (Fri Jun 24 2011 - 03:52:32 CDT)
• formyl and ethanolamide parameters and topology Jorgen Simonsen (Thu Jun 23 2011 - 09:52:18 CDT)
  • Re: formyl and ethanolamide parameters and topology poker_at_physics.usyd.edu.au (Thu Jun 23 2011 - 19:11:57 CDT)
• FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1) Jorgen Simonsen (Thu Jun 23 2011 - 08:51:52 CDT)
  • Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1) JC Gumbart (Thu Jun 23 2011 - 16:17:59 CDT)
    • Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1) Ajasja LjubetiÄ� (Fri Jun 24 2011 - 03:46:18 CDT)
• slow heating md Hasan haska (Thu Jun 23 2011 - 06:11:51 CDT)
  • Re: slow heating md Ajasja LjubetiÄ� (Thu Jun 23 2011 - 06:32:24 CDT)
    • Re: slow heating md Richard Wood (Thu Jun 23 2011 - 08:13:25 CDT)
      • Re: slow heating md Grazia Cottone (Thu Jun 23 2011 - 08:33:37 CDT)
      • Re: slow heating md Axel Kohlmeyer (Thu Jun 23 2011 - 09:06:01 CDT)
    • Re: slow heating md poker_at_physics.usyd.edu.au (Thu Jun 23 2011 - 20:00:54 CDT)
• How to simulate a charged surface Yingzhe Liu (Thu Jun 23 2011 - 05:43:49 CDT)
• finding water around protein divya nayar (Thu Jun 23 2011 - 00:59:56 CDT)
• how to get the energy in vacuum of a molecule in NAMD jnsong (Wed Jun 22 2011 - 08:36:40 CDT)
  • Re: how to get the energy in vacuum of a molecule in NAMD Jim Phillips (Wed Jul 20 2011 - 11:25:59 CDT)
• Re: patch for phosphotyrosine residue bharat gupta (Tue Jun 21 2011 - 20:53:38 CDT)
  • Re: Re: patch for phosphotyrosine residue Jim Phillips (Wed Jun 22 2011 - 10:46:17 CDT)
• NAMD with TIP5P water David Huggins (Tue Jun 21 2011 - 13:24:49 CDT)
• hello murffyp_at_gmail.com (Tue Jun 21 2011 - 07:54:59 CDT)
• simulated annealing protocol Massimiliano Porrini (Tue Jun 21 2011 - 07:41:00 CDT)
  • Re: simulated annealing protocol Jim Phillips (Wed Jul 20 2011 - 11:31:19 CDT)
    • Re: simulated annealing protocol Massimiliano Porrini (Wed Jul 20 2011 - 12:25:18 CDT)
• Re: aligning two molecules by principal axes of inertia using measure.c Ajasja LjubetiÄ� (Mon Jun 20 2011 - 09:40:20 CDT)
• aligning two molecules by principal axes of inertia using measure.c Ada Sedova (Mon Jun 20 2011 - 08:18:41 CDT)
  • AW: aligning two molecules by principal axes of inertia using measure.c Norman Geist (Mon Jun 20 2011 - 09:30:02 CDT)
• restraining groups of atoms Massimiliano Porrini (Mon Jun 20 2011 - 07:03:09 CDT)
  • Re: restraining groups of atoms Jérôme Hénin (Mon Jun 20 2011 - 07:56:06 CDT)
  • Re: restraining groups of atoms Wang Yi (Mon Jun 20 2011 - 08:54:13 CDT)
• Periodic Boundary conditions ishiikai08_at_yahoo.co.jp (Mon Jun 20 2011 - 06:11:49 CDT)
• vdw value in parameter file ÅÓ´ºÀö (Mon Jun 20 2011 - 02:26:06 CDT)
• Re: phosphotyrosine bharat gupta (Sun Jun 19 2011 - 19:26:37 CDT)
  • Fwd: phosphotyrosine bharat gupta (Mon Jun 20 2011 - 00:29:04 CDT)
    • Re: Fwd: phosphotyrosine poker_at_physics.usyd.edu.au (Mon Jun 20 2011 - 01:42:49 CDT)
  • Re: Re: phosphotyrosine johan strumpfer (Mon Jun 20 2011 - 06:30:03 CDT)
• patch needed for tuple is missing JC Gumbart (Sat Jun 18 2011 - 23:49:47 CDT)
  • Re: patch needed for tuple is missing Jim Phillips (Mon Jul 18 2011 - 15:35:28 CDT)
• How to calculate Binding Free energy in NAMD jnsong (Sat Jun 18 2011 - 01:00:49 CDT)
  • Re: How to calculate Binding Free energy in NAMD Chris Chipot (Sat Jun 18 2011 - 07:51:20 CDT)
• SWM4 water model simulation saman amiri (Fri Jun 17 2011 - 16:07:14 CDT)
• REMD exchange ratios Massimiliano Porrini (Fri Jun 17 2011 - 08:47:48 CDT)
  • Re: REMD exchange ratios Jim Phillips (Fri Jun 17 2011 - 12:43:19 CDT)
• Re: Fwd: "cuda error cudastreamcreate", Francesco Pietra (Fri Jun 17 2011 - 00:50:05 CDT)
  • Re: vmd-l: Re: Fwd: "cuda error cudastreamcreate", John Stone (Fri Jun 17 2011 - 01:22:50 CDT)
    • Re: vmd-l: Re: Fwd: "cuda error cudastreamcreate", Francesco Pietra (Fri Jun 17 2011 - 02:36:49 CDT)
• Tcl issue with config script opronkri_at_msu.edu (Fri Jun 17 2011 - 00:06:53 CDT)
  • Re: Tcl issue with config script Cristhian Boetsch (Fri Jun 17 2011 - 10:13:25 CDT)
    • RE: Tcl issue with config script Kristopher Opron (Fri Jun 17 2011 - 15:40:31 CDT)
• rescaling velocity esmael (Wed Jun 15 2011 - 18:17:58 CDT)
  • Re: rescaling velocity Jim Phillips (Fri Jun 17 2011 - 12:45:44 CDT)
    • Re: rescaling velocity esmael (Fri Jun 17 2011 - 13:04:10 CDT)
      • Re: rescaling velocity Ajasja LjubetiÄ� (Fri Jun 17 2011 - 13:14:32 CDT)
      • Re: rescaling velocity Jim Phillips (Fri Jun 17 2011 - 13:16:44 CDT)
• namd-I: Problems with Namd coarsegrain and Gromacs top file Ye Yang (Wed Jun 15 2011 - 14:50:23 CDT)
• Channel flow equilibration Mao Mao (Wed Jun 15 2011 - 11:46:26 CDT)
  • Re: Channel flow equilibration Jim Phillips (Wed Jun 15 2011 - 17:02:10 CDT)
• NAMD-l: Get the PDB file from Steered Molecular Dynamics output files albus hawking (Tue Jun 14 2011 - 22:56:55 CDT)
  • Re: NAMD-l: Get the PDB file from Steered Molecular Dynamics output files Jim Phillips (Fri Jun 17 2011 - 13:14:11 CDT)
• Question about equilibration snoze pa (Wed Jun 15 2011 - 11:02:53 CDT)
  • Re: Question about equilibration snoze pa (Wed Jun 15 2011 - 11:07:51 CDT)
    • Re: Question about equilibration snoze pa (Wed Jun 15 2011 - 11:20:04 CDT)
      • Re: Question about equilibration johan strumpfer (Wed Jun 15 2011 - 11:27:45 CDT)
      • Re: Question about equilibration snoze pa (Wed Jun 15 2011 - 11:38:17 CDT)
      • Re: Question about equilibration johan strumpfer (Wed Jun 15 2011 - 11:48:06 CDT)
      • Re: Question about equilibration Richard Wood (Wed Jun 15 2011 - 12:35:44 CDT)
      • Re: Question about equilibration johan strumpfer (Wed Jun 15 2011 - 13:10:10 CDT)
      • Re: Question about equilibration Richard Wood (Wed Jun 15 2011 - 13:16:00 CDT)
      • Re: Question about equilibration johan strumpfer (Wed Jun 15 2011 - 13:22:56 CDT)
      • Re: Question about equilibration Richard Wood (Wed Jun 15 2011 - 13:47:59 CDT)
      • Re: Question about equilibration Gianluca Interlandi (Wed Jun 15 2011 - 14:03:57 CDT)
      • Re: Question about equilibration Richard Wood (Wed Jun 15 2011 - 14:12:14 CDT)
      • Re: Question about equilibration Gianluca Interlandi (Wed Jun 15 2011 - 14:18:43 CDT)
      • RE: Question about equilibration Reichert, David (Wed Jun 15 2011 - 14:21:33 CDT)
      • Re: Question about equilibration snoze pa (Thu Jun 16 2011 - 17:33:37 CDT)
    • Re: Question about equilibration johan strumpfer (Wed Jun 15 2011 - 11:19:17 CDT)
    • Re: Question about equilibration snoze pa (Wed Jun 15 2011 - 12:06:57 CDT)
• Re: AW: NAMD crashes with OpenMPI/OpenMX Thomas Albers (Wed Jun 15 2011 - 09:10:28 CDT)
  • AW: AW: NAMD crashes with OpenMPI/OpenMX Norman Geist (Wed Jun 15 2011 - 09:37:40 CDT)
    • Re: AW: AW: NAMD crashes with OpenMPI/OpenMX Thomas Albers (Wed Jun 15 2011 - 10:01:00 CDT)
      • AW: AW: AW: NAMD crashes with OpenMPI/OpenMX Norman Geist (Wed Jun 15 2011 - 10:37:47 CDT)
      • Re: AW: AW: AW: NAMD crashes with OpenMPI/OpenMX Jim Phillips (Wed Jun 15 2011 - 11:17:47 CDT)
• hi all kanchi subbarao rao (Wed Jun 15 2011 - 04:14:04 CDT)
  • Fwd: hi all kanchi subbarao rao (Wed Jun 15 2011 - 11:46:09 CDT)
  • Fwd: hi all kanchi subbarao rao (Thu Jun 16 2011 - 07:16:22 CDT)
    • Re: hi all Ajasja LjubetiÄ� (Thu Jun 16 2011 - 07:29:53 CDT)
• Fwd: cuda error cudastreamcreate. SOLVED (probably) Francesco Pietra (Wed Jun 15 2011 - 02:45:26 CDT)
  • Fwd: cuda error cudastreamcreate. SOLVED (probably) Francesco Pietra (Wed Jun 15 2011 - 09:43:28 CDT)
    • Re: cuda error cudastreamcreate. SOLVED (probably) Axel Kohlmeyer (Wed Jun 15 2011 - 09:51:33 CDT)
      • Re: cuda error cudastreamcreate. SOLVED (probably) Francesco Pietra (Thu Jun 16 2011 - 00:57:15 CDT)
      • Re: cuda error cudastreamcreate. SOLVED (probably) Axel Kohlmeyer (Thu Jun 16 2011 - 04:40:03 CDT)
• AW: AW: NAMD crashes with OpenMPI/OpenMX Norman Geist (Wed Jun 15 2011 - 01:01:25 CDT)
  • Re: AW: AW: NAMD crashes with OpenMPI/OpenMX Jim Phillips (Wed Jun 15 2011 - 11:25:34 CDT)
• water is forming bonds between oxigens PAUL NEWMAN (Tue Jun 14 2011 - 16:36:33 CDT)
  • AW: water is forming bonds between oxigens Norman Geist (Wed Jun 15 2011 - 01:05:35 CDT)
• Impropers in Charmm and OPLS Henriette Elisabeth Autzen (Tue Jun 14 2011 - 08:33:58 CDT)
  • Re: Impropers in Charmm and OPLS johan strumpfer (Tue Jun 14 2011 - 10:01:13 CDT)
• umbrella sampling by NAMD jafar azamat (Tue Jun 14 2011 - 06:27:45 CDT)
  • Re: umbrella sampling by NAMD Jérôme Hénin (Tue Jun 14 2011 - 07:31:53 CDT)
• cuda error cudastreamcreate Francesco Pietra (Tue Jun 14 2011 - 00:45:37 CDT)
  • Re: cuda error cudastreamcreate Ajasja LjubetiÄ� (Tue Jun 14 2011 - 08:23:23 CDT)
  • Re: cuda error cudastreamcreate Jim Phillips (Tue Jun 14 2011 - 11:02:33 CDT)
• A question on Jarkynski equation Jun Zhang (Mon Jun 13 2011 - 22:01:59 CDT)
  • Re: A question on Jarkynski equation Jérôme Hénin (Tue Jun 14 2011 - 03:43:55 CDT)
    • Re: A question on Jarkynski equation Wang Yi (Tue Jun 14 2011 - 08:11:46 CDT)
      • Re: A question on Jarkynski equation Jérôme Hénin (Tue Jun 14 2011 - 09:09:13 CDT)
      • Re: A question on Jarkynski equation johan strumpfer (Tue Jun 14 2011 - 09:51:22 CDT)
      • Re: A question on Jarkynski equation Jun Zhang (Wed Jun 15 2011 - 00:25:17 CDT)
    • Re: A question on Jarkynski equation Jun Zhang (Tue Jun 14 2011 - 23:03:53 CDT)
• namd ( please help me!!! ) Namd Namd (Mon Jun 13 2011 - 14:29:40 CDT)
  • Re: namd ( please help me!!! ) Axel Kohlmeyer (Mon Jun 13 2011 - 14:36:24 CDT)
  • Re: namd ( please help me!!! ) snoze pa (Mon Jun 13 2011 - 15:12:19 CDT)
• NAMD crashes with OpenMPI/OpenMX Thomas Albers (Mon Jun 13 2011 - 11:50:35 CDT)
  • Re: NAMD crashes with OpenMPI/OpenMX Jim Phillips (Tue Jun 14 2011 - 11:33:35 CDT)
    • Re: NAMD crashes with OpenMPI/OpenMX Thomas Albers (Tue Jun 14 2011 - 13:04:29 CDT)
      • Re: NAMD crashes with OpenMPI/OpenMX Axel Kohlmeyer (Tue Jun 14 2011 - 13:25:23 CDT)
      • Re: NAMD crashes with OpenMPI/OpenMX Ajasja LjubetiÄ� (Thu Jun 16 2011 - 06:23:36 CDT)
      • Re: NAMD crashes with OpenMPI/OpenMX Bjoern Olausson (Thu Jun 16 2011 - 07:40:07 CDT)
    • Re: NAMD crashes with OpenMPI/OpenMX Ajasja LjubetiÄ� (Fri Jun 17 2011 - 05:10:06 CDT)
    • Re: NAMD crashes with OpenMPI/OpenMX Thomas Albers (Sun Jun 19 2011 - 21:32:42 CDT)
      • AW: NAMD crashes with OpenMPI/OpenMX Norman Geist (Mon Jun 20 2011 - 00:36:54 CDT)
• Protein distort during equilibration snoze pa (Mon Jun 13 2011 - 10:22:10 CDT)
• changing solventDielectric in GBIS Andres Colubri (Mon Jun 13 2011 - 07:36:41 CDT)
  • Re: changing solventDielectric in GBIS Ajasja LjubetiÄ� (Mon Jun 13 2011 - 07:50:42 CDT)
    • Re: changing solventDielectric in GBIS Andres Colubri (Mon Jun 13 2011 - 08:17:36 CDT)
• force field Namd Namd (Mon Jun 13 2011 - 03:36:04 CDT)
• Iron Oxide and Arsenic Salvador H-V (Sat Jun 11 2011 - 17:09:20 CDT)
  • Re: Iron Oxide and Arsenic Axel Kohlmeyer (Sat Jun 11 2011 - 17:16:06 CDT)
    • Re: Iron Oxide and Arsenic Salvador H-V (Sat Jun 11 2011 - 17:25:25 CDT)
      • Re: Iron Oxide and Arsenic Axel Kohlmeyer (Sat Jun 11 2011 - 17:38:21 CDT)
      • Re: Iron Oxide and Arsenic felmerino_at_uchile.cl (Sat Jun 11 2011 - 17:48:57 CDT)
      • Re: Iron Oxide and Arsenic Axel Kohlmeyer (Sat Jun 11 2011 - 17:53:28 CDT)
• Compiling NAMD for CUDA Thomas Albers (Sat Jun 11 2011 - 16:23:01 CDT)
  • Re: Compiling NAMD for CUDA Axel Kohlmeyer (Sat Jun 11 2011 - 16:43:28 CDT)
    • Re: Compiling NAMD for CUDA Thomas Albers (Sat Jun 11 2011 - 21:53:56 CDT)
• about charmm force field oguz gurbulak (Fri Jun 10 2011 - 09:55:26 CDT)
• Re: max number of CPU PEs per GPU? Ajasja LjubetiÄ� (Fri Jun 10 2011 - 06:50:44 CDT)
  • Re: max number of CPU PEs per GPU? Danny Xu (Fri Jun 10 2011 - 11:20:13 CDT)
    • Re: max number of CPU PEs per GPU? Ajasja LjubetiÄ� (Fri Jun 10 2011 - 15:17:43 CDT)
      • Re: max number of CPU PEs per GPU? Danny Xu (Fri Jun 10 2011 - 22:34:34 CDT)
• AW: max number of CPU PEs per GPU? Norman Geist (Fri Jun 10 2011 - 06:25:45 CDT)
• max number of CPU PEs per GPU? Danny Xu (Fri Jun 10 2011 - 01:17:53 CDT)
  • AW: max number of CPU PEs per GPU? Norman Geist (Fri Jun 10 2011 - 02:56:30 CDT)
  • Re: max number of CPU PEs per GPU? Jim Phillips (Fri Jun 10 2011 - 15:15:19 CDT)
    • Re: max number of CPU PEs per GPU? Danny Xu (Sat Jun 11 2011 - 00:49:10 CDT)
      • Re: max number of CPU PEs per GPU? Jim Phillips (Sat Jun 11 2011 - 14:12:35 CDT)
• Re: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." Jim Phillips (Thu Jun 09 2011 - 10:53:46 CDT)
• about log file Molecular Dynamics (Thu Jun 09 2011 - 04:30:30 CDT)
  • Re: about log file Bjoern Olausson (Thu Jun 09 2011 - 05:02:36 CDT)
• Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." David McGiven (Wed Jun 08 2011 - 09:00:34 CDT)
  • AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." Norman Geist (Thu Jun 09 2011 - 00:26:13 CDT)
  • AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." Norman Geist (Thu Jun 09 2011 - 00:36:44 CDT)
  • AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." Norman Geist (Thu Jun 09 2011 - 00:44:01 CDT)
• Multiple Runs in a Single Conf File Rajan Vatassery (Wed Jun 08 2011 - 03:00:55 CDT)
  • AW: Multiple Runs in a Single Conf File Norman Geist (Wed Jun 08 2011 - 03:27:54 CDT)
    • Re: Multiple Runs in a Single Conf File Rajan Vatassery (Wed Jun 08 2011 - 09:53:55 CDT)
      • AW: Multiple Runs in a Single Conf File Norman Geist (Thu Jun 09 2011 - 00:40:18 CDT)
• Membrane simulation, Box X,Y enlarge, Z shrink and membrane thickness shrink juan du (Tue Jun 07 2011 - 18:27:25 CDT)
• Re: atom select within hbond analysis sajad falsafi (Tue Jun 07 2011 - 09:21:09 CDT)
• question about v2.8 sibel.cakan (Tue Jun 07 2011 - 09:01:58 CDT)
• atom select within hbond analysis Branko (Tue Jun 07 2011 - 07:40:09 CDT)
• Re: Gibbs potential sajad falsafi (Tue Jun 07 2011 - 02:14:40 CDT)
• Gibbs potential Patriche Simona (Mon Jun 06 2011 - 10:10:01 CDT)
• water equilibration Narasimhan LOGANATHAN (Mon Jun 06 2011 - 08:07:38 CDT)
  • Re: water equilibration Wang Yi (Mon Jun 06 2011 - 08:42:26 CDT)
    • Re: water equilibration Narasimhan LOGANATHAN (Mon Jun 06 2011 - 08:55:39 CDT)
      • Re: water equilibration Bjoern Olausson (Mon Jun 06 2011 - 09:12:33 CDT)
      • Re: water equilibration johan strumpfer (Mon Jun 06 2011 - 08:59:05 CDT)
      • Re: water equilibration Narasimhan LOGANATHAN (Tue Jun 07 2011 - 09:03:23 CDT)
      • Re: water equilibration johan strumpfer (Tue Jun 07 2011 - 09:44:33 CDT)
      • Re: water equilibration Narasimhan LOGANATHAN (Tue Jun 07 2011 - 11:15:10 CDT)
      • Re: water equilibration johan strumpfer (Tue Jun 07 2011 - 11:20:16 CDT)
      • Re: water equilibration Gurunath Katagi (Tue Jun 07 2011 - 15:14:51 CDT)
      • Re: water equilibration Jim Phillips (Wed Jun 08 2011 - 14:40:03 CDT)
      • Re: water equilibration Narasimhan LOGANATHAN (Tue Aug 02 2011 - 08:42:11 CDT)
      • water equilibration Narasimhan LOGANATHAN (Fri Aug 05 2011 - 05:41:27 CDT)
      • AW: water equilibration Norman Geist (Fri Aug 05 2011 - 05:56:04 CDT)
      • Re: AW: water equilibration Narasimhan LOGANATHAN (Fri Aug 05 2011 - 07:53:22 CDT)
      • Re: water equilibration Jeffrey Potoff (Fri Aug 05 2011 - 09:32:23 CDT)
      • Re: water equilibration Narasimhan LOGANATHAN (Wed Jun 08 2011 - 05:17:17 CDT)
      • Re: water equilibration Narasimhan LOGANATHAN (Thu Aug 04 2011 - 03:25:07 CDT)
• Re: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Axel Kohlmeyer (Mon Jun 06 2011 - 05:50:24 CDT)
  • AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Norman Geist (Mon Jun 06 2011 - 06:11:18 CDT)
  • Re: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Axel Kohlmeyer (Mon Jun 06 2011 - 06:29:38 CDT)
    • AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Norman Geist (Mon Jun 06 2011 - 06:49:06 CDT)
  • Re: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Axel Kohlmeyer (Mon Jun 06 2011 - 06:57:35 CDT)
    • AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Norman Geist (Mon Jun 06 2011 - 07:22:45 CDT)
• AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Francesco Pietra (Mon Jun 06 2011 - 02:54:52 CDT)
  • Fwd: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Francesco Pietra (Mon Jun 06 2011 - 04:15:44 CDT)
    • Fwd: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Francesco Pietra (Mon Jun 06 2011 - 04:30:46 CDT)
    • AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Norman Geist (Mon Jun 06 2011 - 04:51:31 CDT)
• MARTINI parameters and Bead definitions Edroaldo Lummertz da Rocha (Fri Jun 03 2011 - 18:56:49 CDT)
• I M wants to share "legis_2011" with you Dropbox (Fri Jun 03 2011 - 15:20:24 CDT)
• metadynamics combined with PCV Anurag Sethi (Fri Jun 03 2011 - 12:14:18 CDT)
  • Re: metadynamics combined with PCV Giacomo Fiorin (Fri Jun 03 2011 - 12:28:53 CDT)
    • Re: metadynamics combined with PCV Anurag Sethi (Fri Jun 03 2011 - 14:11:54 CDT)
• Ä°lt: Re: heat annealing conf file Molecular Dynamics (Fri Jun 03 2011 - 09:57:07 CDT)
• prm and top files for charmm19 force field oguz gurbulak (Fri Jun 03 2011 - 09:22:47 CDT)
• CthCreate failed to create fiber Patriche Simona (Fri Jun 03 2011 - 08:52:28 CDT)
  • Re: CthCreate failed to create fiber Jim Phillips (Fri Jun 03 2011 - 11:42:44 CDT)
    • Re: CthCreate failed to create fiber Ajasja LjubetiÄ� (Tue Jun 07 2011 - 13:57:00 CDT)
      • Re: CthCreate failed to create fiber Jim Phillips (Tue Jun 07 2011 - 18:02:21 CDT)
      • Re: CthCreate failed to create fiber Ajasja LjubetiÄ� (Thu Jun 09 2011 - 15:29:25 CDT)
• conf file script ( help needed ) Molecular Dynamics (Fri Jun 03 2011 - 08:37:57 CDT)
  • Re: conf file script ( help needed ) Axel Kohlmeyer (Fri Jun 03 2011 - 08:45:27 CDT)
    • Re: conf file script ( help needed ) flavio seixas (Mon Jun 06 2011 - 07:02:41 CDT)
  • Re: conf file script ( help needed ) flavio seixas (Sat Jun 04 2011 - 07:53:08 CDT)
• Alpha P.M.F. with NAMD 2.8 Prathit Chatterjee (Fri Jun 03 2011 - 06:21:46 CDT)
  • Re: Alpha P.M.F. with NAMD 2.8 Ajasja LjubetiÄ� (Fri Jun 03 2011 - 07:05:47 CDT)
  • Re: Alpha P.M.F. with NAMD 2.8 Giacomo Fiorin (Fri Jun 03 2011 - 07:16:05 CDT)
    • Re: Re: Alpha P.M.F. with NAMD 2.8 Prathit Chatterjee (Fri Jun 03 2011 - 07:55:52 CDT)
• Periodic Boundary Condition in NAMD Van Ngo (Thu Jun 02 2011 - 23:55:08 CDT)
  • Re: Periodic Boundary Condition in NAMD Jim Phillips (Fri Jun 03 2011 - 09:57:38 CDT)
• lengthening time-step with constraints causes RMSD "jump" P.-L. Chau (Thu Jun 02 2011 - 06:53:05 CDT)
  • Re: lengthening time-step with constraints causes RMSD "jump" Jim Phillips (Thu Jun 02 2011 - 11:11:28 CDT)
    • Re: lengthening time-step with constraints causes RMSD "jump" P.-L. Chau (Thu Jun 02 2011 - 11:23:34 CDT)
      • Re: lengthening time-step with constraints causes RMSD "jump" Jim Phillips (Thu Jun 02 2011 - 15:36:33 CDT)
      • Re: lengthening time-step with constraints causes RMSD "jump" P.-L. Chau (Thu Jun 02 2011 - 16:03:53 CDT)
• heat annealing conf file Molecular Dynamics (Thu Jun 02 2011 - 05:26:17 CDT)
  • RE: heat annealing conf file Ada Zhan (Thu Jun 02 2011 - 14:02:06 CDT)
• Re: Advice on buying GPUs Ajasja LjubetiÄ� (Thu Jun 02 2011 - 03:13:10 CDT)
  • Re: Advice on buying GPUs Axel Kohlmeyer (Thu Jun 02 2011 - 06:17:14 CDT)
    • Re: Advice on buying GPUs Ajasja Ljubetiè (Thu Jun 02 2011 - 08:27:47 CDT)
      • Re: Advice on buying GPUs Axel Kohlmeyer (Thu Jun 02 2011 - 09:06:08 CDT)
      • Re: Advice on buying GPUs Ajasja Ljubetiè (Thu Jun 02 2011 - 09:46:55 CDT)
      • Re: Advice on buying GPUs Ajasja LjubetiÄ� (Mon Jun 06 2011 - 06:39:31 CDT)
      • Re: Advice on buying GPUs Axel Kohlmeyer (Mon Jun 06 2011 - 06:50:16 CDT)
• regarding vmd kamal Kishor Thakur (Thu Jun 02 2011 - 01:28:36 CDT)
  • Re: regarding vmd scott stensland (Thu Jun 02 2011 - 08:59:15 CDT)
• question on residue rmsd.tcl amit banerjee (Wed Jun 01 2011 - 22:49:17 CDT)
  • RE: question on residue rmsd.tcl Ada Zhan (Thu Jun 02 2011 - 14:06:00 CDT)
    • Re: question on residue rmsd.tcl amit banerjee (Mon Jun 06 2011 - 00:18:48 CDT)
      • RE: question on residue rmsd.tcl Ada Zhan (Mon Jun 06 2011 - 14:25:36 CDT)
• problem in distance.tcl amit banerjee (Wed Jun 01 2011 - 22:37:42 CDT)
• Fwd: Fwd: hi kanchi subbarao rao (Wed Jun 01 2011 - 13:32:41 CDT)
  • Fwd: Fwd: hi kanchi subbarao rao (Thu Jun 02 2011 - 12:44:27 CDT)
    • Re: Fwd: Fwd: hi Axel Kohlmeyer (Thu Jun 02 2011 - 12:52:25 CDT)
• Advice on buying GPUs Ajasja LjubetiÄ� (Wed Jun 01 2011 - 09:43:24 CDT)
• PBC Werner Crous (Wed Jun 01 2011 - 05:09:27 CDT)
  • Re: PBC johan strumpfer (Wed Jun 01 2011 - 11:03:04 CDT)
    • Re: PBC johan strumpfer (Wed Jun 01 2011 - 12:19:04 CDT)
      • Re: PBC Werner Crous (Thu Jun 02 2011 - 04:05:41 CDT)
      • Re: PBC Werner Crous (Thu Jun 02 2011 - 04:18:38 CDT)
      • Re: PBC johan strumpfer (Fri Jun 03 2011 - 12:09:55 CDT)
• Periodic Boundary conditions ishiikai08_at_yahoo.co.jp (Tue May 31 2011 - 21:57:03 CDT)
  • Re: Periodic Boundary conditions Jim Phillips (Wed Jun 01 2011 - 13:08:55 CDT)
    • Re:Re: Periodic Boundary conditions ishiikai08_at_yahoo.co.jp (Thu Jun 02 2011 - 03:14:12 CDT)
      • Re: Re: Periodic Boundary conditions Axel Kohlmeyer (Thu Jun 02 2011 - 06:19:54 CDT)
• NAMD 2.8 released Jim Phillips (Tue May 31 2011 - 14:55:34 CDT)
• restart a simulation Mao Mao (Tue May 31 2011 - 14:50:22 CDT)
  • Re: restart a simulation Jim Phillips (Tue May 31 2011 - 15:00:23 CDT)
• Fail to Run VMD Àî¼Ñ¼ü (Tue May 31 2011 - 13:53:07 CDT)
  • Re: Fail to Run VMD Axel Kohlmeyer (Tue May 31 2011 - 13:57:24 CDT)
• Fwd: hi kanchi subbarao rao (Tue May 31 2011 - 05:10:32 CDT)
• vdw parameter of metal ion ÅÓ´ºÀö (Tue May 31 2011 - 04:49:55 CDT)
  • Re: vdw parameter of metal ion yandong Huang (Thu Jun 02 2011 - 07:32:41 CDT)
    • Re:Re: vdw parameter of metal ion yandong Huang (Thu Jun 02 2011 - 07:34:20 CDT)
• Script Help flavio seixas (Sun May 29 2011 - 18:16:51 CDT)
  • Re: Script Help Axel Kohlmeyer (Sun May 29 2011 - 18:58:44 CDT)
• Question about end of log file Rajan Vatassery (Sun May 29 2011 - 14:14:34 CDT)
  • Re: Question about end of log file Jim Phillips (Sun May 29 2011 - 22:37:30 CDT)
    • Re: Question about end of log file Azat Mukhametov (Mon May 30 2011 - 21:53:50 CDT)
• Re PMF Branko (Sat May 28 2011 - 12:18:22 CDT)
• RBCG water simulation Cristhian Boetsch (Fri May 27 2011 - 12:17:38 CDT)
  • Re: RBCG water simulation Chris Harrison (Fri May 27 2011 - 12:49:08 CDT)
    • Re: RBCG water simulation Cristhian Boetsch (Fri Jun 03 2011 - 07:22:38 CDT)
• NADPH topology flavio seixas (Fri May 27 2011 - 08:58:17 CDT)
• NAMD with GPU error : "Number of VDW types exceeds CUDA LJ_TABLE_SIZE" David McGiven (Fri May 27 2011 - 06:12:42 CDT)
• TIP5P water simulation David Huggins (Thu May 26 2011 - 15:57:25 CDT)
• Re: vmd-l: measure fit - wrong alignment Jérôme Hénin (Thu May 26 2011 - 13:09:29 CDT)
• about conf file oguz gurbulak (Thu May 26 2011 - 09:11:29 CDT)
  • Re: about conf file Jim Phillips (Thu May 26 2011 - 09:55:14 CDT)
• PSF and PDB file for SWM4 water models saman amiri (Thu May 26 2011 - 07:37:04 CDT)
  • Re: PSF and PDB file for SWM4 water models Jim Phillips (Thu May 26 2011 - 09:39:22 CDT)
• Truncated octahedron box issues (?) Massimiliano Porrini (Wed May 25 2011 - 10:38:03 CDT)
  • Re: Truncated octahedron box issues Q=3F=29?= Nikolaos Glykos (Wed May 25 2011 - 12:15:44 CDT)
  • Re: Truncated octahedron box issues Q=3F=29?= Nikolaos Glykos (Wed May 25 2011 - 12:19:03 CDT)
  • Re: Truncated octahedron box issues (?) Jim Phillips (Wed May 25 2011 - 13:57:05 CDT)
    • Re: Truncated octahedron box issues (?) Massimiliano Porrini (Thu May 26 2011 - 14:00:49 CDT)
      • Re: Truncated octahedron box issues (?) Jim Phillips (Thu May 26 2011 - 22:59:06 CDT)
• restart with constraints causes RMSD "jump" P.-L. Chau (Wed May 25 2011 - 07:24:11 CDT)
  • Re: restart with constraints causes RMSD "jump" Jim Phillips (Wed May 25 2011 - 11:31:29 CDT)
    • Re: restart with constraints causes RMSD "jump" P.-L. Chau (Wed May 25 2011 - 12:56:41 CDT)
      • Re: restart with constraints causes RMSD "jump" Jim Phillips (Wed May 25 2011 - 13:40:21 CDT)
• The Nudged Elastic Band Approach to Find the Lowest Energy Pathway Between two States Buddhadev Maiti (Tue May 24 2011 - 22:14:14 CDT)
• Joining PSF Files PAUL NEWMAN (Tue May 24 2011 - 08:58:24 CDT)
  • Re: Joining PSF Files Axel Kohlmeyer (Tue May 24 2011 - 09:00:57 CDT)
    • Re: Joining PSF Files PAUL NEWMAN (Tue May 24 2011 - 09:04:24 CDT)
      • Re: Joining PSF Files Axel Kohlmeyer (Tue May 24 2011 - 09:08:32 CDT)
  • Re: Joining PSF Files Jeffrey Potoff (Tue May 24 2011 - 09:04:53 CDT)
• the meaning of " 5-ZEROS" " 9-ZEROS" in the DCD file jnsong (Tue May 24 2011 - 03:12:57 CDT)
  • Re: the meaning of " 5-ZEROS" " 9-ZEROS" in the DCD file Bjoern Olausson (Tue May 24 2011 - 03:44:23 CDT)
• Coulombic component of configurational energy divya nayar (Tue May 24 2011 - 03:12:24 CDT)
• Development plan of NAMD? Norman Geist (Tue May 24 2011 - 02:03:37 CDT)
  • Re: Development plan of NAMD? Jim Phillips (Tue May 24 2011 - 13:54:09 CDT)
• PMF jafar azamat (Tue May 24 2011 - 00:47:30 CDT)
• AW: AW: AW: question about wrap atoms to its original coordinates Norman Geist (Mon May 23 2011 - 01:03:53 CDT)
• PMF calculation jafar azamat (Mon May 23 2011 - 07:31:13 CDT)
• Problem building NAMD (multiple definitions) Miroslav Hodak (Mon May 23 2011 - 05:47:08 CDT)
  • Re: Problem building NAMD (multiple definitions) Jim Phillips (Mon May 23 2011 - 17:08:21 CDT)
    • Re: Problem building NAMD (multiple definitions) Axel Kohlmeyer (Mon May 23 2011 - 17:12:21 CDT)
      • Re: Problem building NAMD (multiple definitions) Miroslav Hodak (Mon May 23 2011 - 17:38:47 CDT)
      • Re: Problem building NAMD (multiple definitions) Axel Kohlmeyer (Mon May 23 2011 - 17:41:37 CDT)
      • Re: Problem building NAMD (multiple definitions) Miroslav Hodak (Mon May 23 2011 - 17:49:59 CDT)
      • Re: Problem building NAMD (multiple definitions) Jim Phillips (Mon May 23 2011 - 17:57:27 CDT)
      • Re: Problem building NAMD (multiple definitions) Miroslav Hodak (Mon May 23 2011 - 18:14:35 CDT)
• hi murffyp_at_gmail.com (Sun May 22 2011 - 23:14:11 CDT)
• Dear friend Niraj kumar (Sun May 22 2011 - 20:29:53 CDT)
• questions about the heat diffusion calculation in the tutorial charlie (Sun May 22 2011 - 11:57:56 CDT)
• dcd files Molecular Dynamics (Sun May 22 2011 - 08:02:48 CDT)
  • Re: dcd files PAUL NEWMAN (Sun May 22 2011 - 08:24:15 CDT)
    • Re: dcd files Axel Kohlmeyer (Sun May 22 2011 - 09:15:48 CDT)
    • Re: dcd files Jim Phillips (Sun May 22 2011 - 14:38:55 CDT)
      • Re: dcd files PAUL NEWMAN (Sun May 22 2011 - 14:46:57 CDT)
      • Re: dcd files Jim Phillips (Sun May 22 2011 - 14:53:45 CDT)
      • Re: dcd files grazia cottone (Sun May 22 2011 - 15:14:41 CDT)
      • Re: dcd files Artem Zhmurov (Sun May 22 2011 - 16:52:19 CDT)
  • Re: dcd files Axel Kohlmeyer (Sun May 22 2011 - 09:10:29 CDT)
• error in the orientationAngle Prathit Chatterjee (Sat May 21 2011 - 03:51:10 CDT)
  • Re: error in the orientationAngle Giacomo Fiorin (Sat May 21 2011 - 09:47:49 CDT)
    • Re: error in the orientationAngle Prathit Chatterjee (Sun May 22 2011 - 05:01:55 CDT)
      • Re: error in the orientationAngle Ajasja LjubetiÄ� (Sun May 22 2011 - 05:48:29 CDT)
• SMD of three atom at a time snoze pa (Fri May 20 2011 - 11:32:03 CDT)
  • Re: SMD of three atom at a time Chris Harrison (Fri May 20 2011 - 12:22:09 CDT)
    • Re: SMD of three atom at a time snoze pa (Wed Jun 01 2011 - 08:14:39 CDT)
• Re: simulation box PAUL NEWMAN (Fri May 20 2011 - 11:11:52 CDT)
  • Re: simulation box Axel Kohlmeyer (Fri May 20 2011 - 11:25:36 CDT)
    • Re: simulation box PAUL NEWMAN (Fri May 20 2011 - 11:30:43 CDT)
      • Re: simulation box Axel Kohlmeyer (Fri May 20 2011 - 11:33:20 CDT)
      • Re: simulation box Jeffrey Potoff (Fri May 20 2011 - 11:36:57 CDT)
• simulation box PAUL NEWMAN (Fri May 20 2011 - 10:39:48 CDT)
• NAMD crashes when writing restart file and dcdfreq is 1 Ajasja LjubetiÄ� (Fri May 20 2011 - 05:16:30 CDT)
  • Re: NAMD crashes when writing restart file and dcdfreq is 1 Ajasja LjubetiÄ� (Fri May 20 2011 - 05:25:31 CDT)
    • Re: NAMD crashes when writing restart file and dcdfreq is 1 Jim Phillips (Fri May 20 2011 - 08:45:46 CDT)
    • Re: NAMD crashes when writing restart file and dcdfreq is 1 Ajasja LjubetiÄ� (Tue May 24 2011 - 07:25:25 CDT)
      • Re: NAMD crashes when writing restart file and dcdfreq is 1 Jim Phillips (Tue May 24 2011 - 13:39:51 CDT)
    • Re: NAMD crashes when writing restart file and dcdfreq is 1 Jim Phillips (Thu May 26 2011 - 09:12:02 CDT)
  • Re: NAMD crashes when writing restart file and dcdfreq is 1 Jim Phillips (Fri May 20 2011 - 17:06:32 CDT)
• My benchmark results with TeslaC2050 Norman Geist (Fri May 20 2011 - 01:02:36 CDT)
• Minimisation algorithm Christian Jorgensen (Thu May 19 2011 - 18:31:03 CDT)
  • Re: Minimisation algorithm Jim Phillips (Sun May 22 2011 - 14:49:16 CDT)
• NAMD 2.8b3 released Jim Phillips (Thu May 19 2011 - 16:28:04 CDT)
• Build .pdb and .psf after coarse graining results in errors Edroaldo Lummertz da Rocha (Thu May 19 2011 - 13:37:15 CDT)
• last frame and restart are different Francesco Oteri (Thu May 19 2011 - 11:12:22 CDT)
  • Re: last frame and restart are different Jim Phillips (Thu May 19 2011 - 14:02:25 CDT)
    • Re: last frame and restart are different Francesco Oteri (Thu May 19 2011 - 15:50:06 CDT)
• unsubscribe Cole Gleason (Thu May 19 2011 - 09:37:36 CDT)
• Typo in NAMD 2.8b2 output for Accelerated MD Bjoern Olausson (Thu May 19 2011 - 07:25:51 CDT)
  • Re: Typo in NAMD 2.8b2 output for Accelerated MD Chris Harrison (Thu May 19 2011 - 09:32:11 CDT)
• AW: AW: Automatic GPU selection in NAMD ? Norman Geist (Thu May 19 2011 - 01:41:37 CDT)
• Is there any difference between SMD and tclForces? Jun Zhang (Wed May 18 2011 - 20:29:07 CDT)
  • Re: Is there any difference between SMD and tclForces? Axel Kohlmeyer (Wed May 18 2011 - 20:34:13 CDT)
• RE: CUDA simulation memory usage Jesper Sørensen (Wed May 18 2011 - 05:55:59 CDT)
  • RE: CUDA simulation memory usage Jesper Sørensen (Wed May 18 2011 - 06:14:51 CDT)
    • AW: CUDA simulation memory usage Norman Geist (Wed May 18 2011 - 07:10:58 CDT)
      • RE: CUDA simulation memory usage Jesper Sørensen (Wed May 18 2011 - 07:23:28 CDT)
      • Re: CUDA simulation memory usage Axel Kohlmeyer (Wed May 18 2011 - 08:29:18 CDT)
      • RE: CUDA simulation memory usage Jesper Sørensen (Wed May 18 2011 - 08:41:34 CDT)
• CUDA simulation memory usage Jesper Sørensen (Wed May 18 2011 - 05:03:17 CDT)
  • Re: CUDA simulation memory usage Jim Phillips (Wed May 18 2011 - 17:37:45 CDT)
    • RE: CUDA simulation memory usage Jesper Sørensen (Thu May 19 2011 - 03:11:41 CDT)
• hi kanchi subbarao rao (Wed May 18 2011 - 03:43:25 CDT)
  • Re: hi Giacomo Fiorin (Wed May 18 2011 - 10:28:48 CDT)
    • Re: hi Jim Phillips (Wed May 18 2011 - 17:52:49 CDT)
  • Re: hi Bjoern Olausson (Thu May 19 2011 - 04:29:14 CDT)
• question about wrap atoms to its original coordinates jnsong (Wed May 18 2011 - 00:06:20 CDT)
  • AW: question about wrap atoms to its original coordinates Norman Geist (Wed May 18 2011 - 00:34:33 CDT)
    • Re: AW: question about wrap atoms to its original coordinates jnsong (Thu May 19 2011 - 21:31:54 CDT)
      • AW: AW: question about wrap atoms to its original coordinates Norman Geist (Fri May 20 2011 - 00:04:48 CDT)
• Umbrella Sampling Buddhadev Maiti (Tue May 17 2011 - 21:52:38 CDT)
  • Re: Umbrella Sampling Jérôme Hénin (Wed May 18 2011 - 09:40:25 CDT)
• trajectory_path.tcl Jacopo Sgrignani (Tue May 17 2011 - 09:16:47 CDT)
  • Re: trajectory_path.tcl Axel Kohlmeyer (Tue May 17 2011 - 09:38:19 CDT)
• Automatic GPU selection in NAMD ? Jesper Sørensen (Tue May 17 2011 - 06:17:43 CDT)
• Automatic GPU selection in NAMD ? David McGiven (Tue May 17 2011 - 04:58:56 CDT)
  • RE: Automatic GPU selection in NAMD ? Jesper Sørensen (Tue May 17 2011 - 05:05:27 CDT)
    • Re: Automatic GPU selection in NAMD ? David McGiven (Tue May 17 2011 - 05:34:21 CDT)
      • RE: Automatic GPU selection in NAMD ? Jesper Sørensen (Tue May 17 2011 - 05:41:03 CDT)
      • Re: Automatic GPU selection in NAMD ? David McGiven (Tue May 17 2011 - 06:02:29 CDT)
      • Re: Automatic GPU selection in NAMD ? Axel Kohlmeyer (Tue May 17 2011 - 07:19:44 CDT)
      • Re: Automatic GPU selection in NAMD ? David McGiven (Tue May 17 2011 - 09:35:57 CDT)
      • AW: Automatic GPU selection in NAMD ? Norman Geist (Wed May 18 2011 - 00:24:45 CDT)
      • Re: Automatic GPU selection in NAMD ? Jim Phillips (Wed May 18 2011 - 13:22:57 CDT)
      • Re: Automatic GPU selection in NAMD ? David McGiven (Thu May 19 2011 - 04:42:39 CDT)
• GPU-CPU small-scale machine for NAMD Francesco Pietra (Mon May 16 2011 - 03:45:37 CDT)
  • Re: GPU-CPU small-scale machine for NAMD Darko Stefanovski (Tue May 17 2011 - 12:10:31 CDT)
    • Re: GPU-CPU small-scale machine for NAMD Jim Phillips (Wed May 18 2011 - 12:48:52 CDT)
• deca-Ala simulations with different cutoff produce different results Jun Zhang (Mon May 16 2011 - 00:48:36 CDT)
  • RE: deca-Ala simulations with different cutoff produce different results Norman Geist (Mon May 16 2011 - 02:12:40 CDT)
    • RE: deca-Ala simulations with different cutoff produce different results Jun Zhang (Mon May 16 2011 - 03:47:44 CDT)
      • AW: deca-Ala simulations with different cutoff produce different results Norman Geist (Mon May 16 2011 - 04:20:58 CDT)
• (no subject) Chandra Ramananjara (Sun May 15 2011 - 12:32:07 CDT)
• NAMD question snoze pa (Fri May 13 2011 - 16:34:16 CDT)
• Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Fri May 13 2011 - 13:10:46 CDT)
  • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Jim Phillips (Fri May 13 2011 - 14:52:53 CDT)
    • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Sat May 14 2011 - 01:12:57 CDT)
  • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Mon May 16 2011 - 04:02:51 CDT)
  • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Mon May 16 2011 - 13:45:14 CDT)
    • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Jim Phillips (Tue May 17 2011 - 13:21:49 CDT)
      • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Wed May 18 2011 - 08:44:48 CDT)
      • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Jim Phillips (Wed May 18 2011 - 17:58:16 CDT)
      • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Thu May 19 2011 - 04:00:33 CDT)
• REMD segmentation fault Massimiliano Porrini (Fri May 13 2011 - 07:58:45 CDT)
  • Re: REMD segmentation fault Jim Phillips (Fri May 13 2011 - 08:30:08 CDT)
    • Re: REMD segmentation fault Massimiliano Porrini (Fri May 13 2011 - 08:41:09 CDT)
      • Re: REMD segmentation fault Jim Phillips (Fri May 13 2011 - 08:52:47 CDT)
• PhD position in Computational Structural Biology at MPI Muenster Vlad Cojocaru (Fri May 13 2011 - 04:47:24 CDT)
• parameter for TFA (trifluoroacetic acid) liupeng012_at_mail.nankai.edu.cn (Fri May 13 2011 - 03:36:55 CDT)
• (no subject) Chandra Ramananjara (Thu May 12 2011 - 19:58:21 CDT)
• NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Thu May 12 2011 - 17:20:09 CDT)
• Error when run Replica Exchange Method on Ranger Guoxiong Su (Thu May 12 2011 - 14:13:59 CDT)
• FATAL error when run Replica Exchange Method on Franklin Guoxiong Su (Thu May 12 2011 - 14:03:58 CDT)
• CUDA limitations Ajasja LjubetiÄ� (Thu May 12 2011 - 03:07:02 CDT)
  • Re: CUDA limitations Jim Phillips (Thu May 12 2011 - 12:45:44 CDT)
    • Re: CUDA limitations Ajasja LjubetiÄ� (Fri May 13 2011 - 07:00:49 CDT)
      • Re: CUDA limitations Jim Phillips (Fri May 13 2011 - 09:02:36 CDT)
      • Re: CUDA limitations Ajasja LjubetiÄ� (Thu Jun 09 2011 - 15:32:09 CDT)
    • Re: CUDA limitations Ajasja LjubetiÄ� (Fri Jun 24 2011 - 07:37:13 CDT)
• NAMD 2.8b2 released Jim Phillips (Wed May 11 2011 - 17:15:43 CDT)
• Re: NAMDEnergy Plugin - setting PMEGridSize / mesh density Michael S. Sellers (Cont, ARL/WMRD) (Wed May 11 2011 - 15:29:25 CDT)
• NAMDEnergy Plugin - setting PMEGridSize / mesh density Lela Vukovic (Wed May 11 2011 - 14:48:51 CDT)
• Corrupt dcd files Marc Baaden (Wed May 11 2011 - 11:15:55 CDT)
  • AW: Corrupt dcd files Norman Geist (Thu May 12 2011 - 01:46:51 CDT)
    • Re: AW: Corrupt dcd files Marc Baaden (Sat May 14 2011 - 16:23:30 CDT)
  • AW: Corrupt dcd files Norman Geist (Thu May 12 2011 - 01:51:56 CDT)
  • AW: Corrupt dcd files Norman Geist (Thu May 12 2011 - 01:53:23 CDT)
    • Re: AW: Corrupt dcd files Jim Phillips (Thu May 12 2011 - 17:20:36 CDT)
      • Re: AW: Corrupt dcd files Marc Baaden (Sun May 15 2011 - 06:28:38 CDT)
• what will be the best way to simulate substrate interaction only within a binding pocket of a large protein. Arun Kumar Subramanian (Sat May 07 2011 - 21:20:29 CDT)
  • Re: what will be the best way to simulate substrate interaction only within a binding pocket of a large protein. Giacomo Fiorin (Tue May 10 2011 - 15:20:18 CDT)
    • Re: what will be the best way to simulate substrate interaction only within a binding pocket of a large protein. Ajasja LjubetiÄ� (Tue May 10 2011 - 15:57:58 CDT)
• Namdstats.tcl flavio seixas (Tue May 10 2011 - 14:51:13 CDT)
• print center of mass Jacopo Sgrignani (Tue May 10 2011 - 10:54:09 CDT)
  • Re: print center of mass Axel Kohlmeyer (Tue May 10 2011 - 11:01:35 CDT)
    • Re: print center of mass Ajasja LjubetiÄ� (Tue May 10 2011 - 11:10:48 CDT)
• force field for 2-methyl-2,4-pentanediol (MPD) Yang Gao (Tue May 10 2011 - 10:40:40 CDT)
• A newer version of win32 libraries Ajasja LjubetiÄ� (Mon May 09 2011 - 07:35:47 CDT)
  • Re: A newer version of win32 libraries Jim Phillips (Tue May 10 2011 - 14:39:25 CDT)
    • Re: A newer version of win32 libraries Ajasja LjubetiÄ� (Tue May 10 2011 - 15:55:06 CDT)
• large load rate using implicit solvent charlie (Sun May 08 2011 - 20:45:10 CDT)
• (no subject) Chandra Ramananjara (Sun May 08 2011 - 09:37:04 CDT)
• ABF atom selection Parisa Akhski (Sat May 07 2011 - 18:14:24 CDT)
  • Re: ABF atom selection Jérôme Hénin (Sun May 08 2011 - 11:41:09 CDT)
    • RE: ABF atom selection Parisa Akhski (Tue May 10 2011 - 09:16:29 CDT)
      • Re: ABF atom selection Jérôme Hénin (Tue May 10 2011 - 09:59:08 CDT)
• (no subject) Chandra Ramananjara (Sat May 07 2011 - 14:00:37 CDT)
• Re: compilation of namd johan strumpfer (Fri May 06 2011 - 09:09:35 CDT)
  • Q=AD=94=E5=A4=8D:__compilation_of_namd?= TAO WANG (Sun May 08 2011 - 19:34:03 CDT)
  • Q=AD=94=E5=A4=8D:__compilation_of_namd?= TAO WANG (Mon May 09 2011 - 01:27:12 CDT)
    • unsubscribe Gary M. Skinner (Mon May 09 2011 - 03:31:45 CDT)
    • Re: Q=AD=94=E5=A4=8D:__compilation_of_namd?= Jim Phillips (Tue May 10 2011 - 20:32:27 CDT)
      • Q=AD=94=E5=A4=8D:_=E7=AD=94=E5=A4=8D:__compilation_of_n?= amd TAO WANG (Tue May 10 2011 - 20:42:49 CDT)
      • Re: ç­”å¤�: compilation of namd Axel Kohlmeyer (Tue May 10 2011 - 22:14:26 CDT)
      • Re: Re: ç­”å¤�: compilation of namd Jim Phillips (Wed May 11 2011 - 10:53:59 CDT)
      • Re: Re: ç­”å¤�: compilation of namd Axel Kohlmeyer (Wed May 11 2011 - 11:16:29 CDT)
      • Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd Bjoern Olausson (Thu May 12 2011 - 02:45:49 CDT)
      • Re: Re: ç­”å¤�: compilation of namd Axel Kohlmeyer (Thu May 12 2011 - 04:53:58 CDT)
      • Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd Bjoern Olausson (Thu May 12 2011 - 08:11:57 CDT)
      • Re: Re: ç­”å¤�: compilation of namd Axel Kohlmeyer (Thu May 12 2011 - 08:34:14 CDT)
      • Re: Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd Bjoern Olausson (Thu May 12 2011 - 09:58:47 CDT)
      • Re: Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd Bjoern Olausson (Thu May 12 2011 - 11:13:21 CDT)
      • Re: Re: Re: ç­”å¤�: compilation of namd Jim Phillips (Thu May 12 2011 - 12:32:28 CDT)
• REMD across gpus Massimiliano Porrini (Fri May 06 2011 - 07:39:56 CDT)
  • REMD across gpus Massimiliano Porrini (Sun May 08 2011 - 06:02:19 CDT)
    • REMD across gpus Massimiliano Porrini (Mon May 09 2011 - 09:28:51 CDT)
      • Re: REMD across gpus Axel Kohlmeyer (Tue May 10 2011 - 15:05:06 CDT)
      • Re: REMD across gpus Massimiliano Porrini (Tue May 10 2011 - 15:29:36 CDT)
      • Re: REMD across gpus Axel Kohlmeyer (Tue May 10 2011 - 15:52:42 CDT)
• AW: AW: Running NAMD parallel on two machines with 3 CUDAs Norman Geist (Fri May 06 2011 - 01:36:20 CDT)
• ABF atom selection question Parisa Akhski (Thu May 05 2011 - 21:50:00 CDT)
• compilation of namd TAO WANG (Thu May 05 2011 - 21:08:37 CDT)
  • AW: compilation of namd Norman Geist (Fri May 06 2011 - 00:46:01 CDT)
    • ??: compilation of namd TAO WANG (Fri May 06 2011 - 00:56:41 CDT)
      • AW: compilation of namd Norman Geist (Fri May 06 2011 - 01:16:56 CDT)
• msd calculation for lipid bilayers cnu gromacs (Thu May 05 2011 - 14:22:24 CDT)
• Running NAMD parallel on two machines with 3 CUDAs Darko Stefanovski (Thu May 05 2011 - 11:53:40 CDT)
  • AW: Running NAMD parallel on two machines with 3 CUDAs Norman Geist (Fri May 06 2011 - 00:36:27 CDT)
  • AW: Running NAMD parallel on two machines with 3 CUDAs Norman Geist (Fri May 06 2011 - 00:41:11 CDT)
• AMD Multicore + CUDA Benchmarks, are them ok ? David McGiven (Thu May 05 2011 - 04:08:30 CDT)
  • Re: AMD Multicore + CUDA Benchmarks, are them ok ? Nicholas M Glykos (Thu May 05 2011 - 04:31:52 CDT)
    • Re: AMD Multicore + CUDA Benchmarks, are them ok ? Axel Kohlmeyer (Thu May 05 2011 - 08:47:56 CDT)
    • Re: AMD Multicore + CUDA Benchmarks, are them ok ? Axel Kohlmeyer (Thu May 05 2011 - 08:57:18 CDT)
• alpha pmf Prathit Chatterjee (Wed May 04 2011 - 00:55:40 CDT)
  • Re: alpha pmf felmerino_at_uchile.cl (Wed May 04 2011 - 02:37:06 CDT)
    • Re: alpha pmf Ajasja LjubetiÄ� (Wed May 04 2011 - 03:04:14 CDT)
      • Re: alpha pmf Jérôme Hénin (Wed May 04 2011 - 04:17:16 CDT)
      • Re: alpha pmf Prathit Chatterjee (Thu May 05 2011 - 01:21:02 CDT)
      • Re: alpha pmf Giacomo Fiorin (Thu May 05 2011 - 09:31:51 CDT)
      • Re: alpha pmf Prathit Chatterjee (Fri May 06 2011 - 05:54:55 CDT)
      • Re: alpha pmf Jérôme Hénin (Fri May 06 2011 - 07:58:37 CDT)
      • Re: alpha pmf Prathit Chatterjee (Sat May 07 2011 - 00:33:28 CDT)
      • Re: alpha pmf Giacomo Fiorin (Mon May 09 2011 - 16:05:19 CDT)
    • Re: alpha pmf Jérôme Hénin (Tue May 10 2011 - 03:37:24 CDT)
• (no subject) Nicolas Sapay (Tue May 03 2011 - 11:51:42 CDT)
• run tests with CUDA Massimiliano Porrini (Mon May 02 2011 - 16:25:17 CDT)
  • Re: run tests with CUDA Axel Kohlmeyer (Mon May 02 2011 - 16:55:18 CDT)
  • Re: run tests with CUDA Nicholas M Glykos (Tue May 03 2011 - 03:09:12 CDT)
    • Re: run tests with CUDA Massimiliano Porrini (Wed May 04 2011 - 11:45:09 CDT)
• implicit solvent and cuda Francesco Oteri (Mon May 02 2011 - 16:03:15 CDT)
  • Re: implicit solvent and cuda Jim Phillips (Tue May 10 2011 - 20:24:17 CDT)
• Forcefield for simulating peptide with heparin!!!! Aditya Ranganathan (Mon May 02 2011 - 07:24:56 CDT)
• WG: Abnormal EOF Error in Extra Bonds File Norman Geist (Mon May 02 2011 - 06:48:41 CDT)
• NAMD_2.7_AIX-POWER-MPI Buddhadev Maiti (Sun May 01 2011 - 21:28:41 CDT)
• Add bonds and topology file problem Edroaldo Lummertz da Rocha (Sun May 01 2011 - 16:57:16 CDT)
• Add bonds and topology file problem Edroaldo Lummertz da Rocha (Sun May 01 2011 - 15:20:01 CDT)
  • Re: Add bonds and topology file problem Axel Kohlmeyer (Sun May 01 2011 - 15:52:30 CDT)
• non-bonded potential in NAMD Molecular Dynamics (Sat Apr 30 2011 - 15:06:58 CDT)
  • Re: non-bonded potential in NAMD Jérôme Hénin (Sat Apr 30 2011 - 17:28:14 CDT)
• colvars orientation problem appears in 2.8 only? JC Gumbart (Thu Apr 28 2011 - 18:41:17 CDT)
  • Re: colvars orientation problem appears in 2.8 only? Jérôme Hénin (Fri Apr 29 2011 - 06:16:55 CDT)
• ERROR: CUDA-enabled NAMD requires at least one patch per process Arash Azari (Wed Apr 27 2011 - 23:49:56 CDT)
• question about rotation force in SMD jnsong (Wed Apr 27 2011 - 09:34:09 CDT)
  • Re: question about rotation force in SMD Giacomo Fiorin (Wed Apr 27 2011 - 10:00:33 CDT)
• freeEnergy parsing error Lada Biedermannová (Wed Apr 27 2011 - 09:08:46 CDT)
• how to apply different temperature simultaneously to different atoms in the same system charlie (Wed Apr 27 2011 - 02:41:08 CDT)
• A namd2.8b1 bug ? charlie (Wed Apr 27 2011 - 02:23:56 CDT)
  • Re: A namd2.8b1 bug ? Jim Phillips (Tue May 10 2011 - 21:02:49 CDT)
• modify NAMD code for Lee-Edwards boundary conditions and compute stress tensor Van Ngo (Tue Apr 26 2011 - 19:17:47 CDT)
• Abnormal EOF Error in Extra Bonds File Eli Fine (Tue Apr 26 2011 - 14:22:11 CDT)
  • Re: Abnormal EOF Error in Extra Bonds File Jim Phillips (Tue May 10 2011 - 20:15:18 CDT)
• Coarse Graining problem resolved Stefan Franzen (Tue Apr 26 2011 - 05:32:21 CDT)
• Coarse Graining setup question Stefan Franzen (Tue Apr 26 2011 - 05:13:23 CDT)
• CG parameterization problem Stefan Franzen (Tue Apr 26 2011 - 05:07:32 CDT)
• velocity error during steered MD Markus K. Dahlgren (Tue Apr 26 2011 - 09:08:32 CDT)
• ABF calculation using RMSD Buddhadev Maiti (Mon Apr 25 2011 - 22:14:39 CDT)
  • Re: ABF calculation using RMSD Giacomo Fiorin (Mon Apr 25 2011 - 22:26:54 CDT)
• Gold nanoparticle and 1-octanethiol Edroaldo Lummertz da Rocha (Mon Apr 25 2011 - 13:14:22 CDT)
  • Re: Gold nanoparticle and 1-octanethiol Edroaldo Lummertz da Rocha (Wed Apr 27 2011 - 07:01:52 CDT)
    • Re: Gold nanoparticle and 1-octanethiol Edroaldo Lummertz da Rocha (Thu Apr 28 2011 - 19:07:44 CDT)
• 'cutting' colvars.traj file Branko (Sat Apr 23 2011 - 12:28:58 CDT)
  • Re: 'cutting' colvars.traj file Wang Yi (Sat Apr 23 2011 - 12:54:15 CDT)
    • Re: 'cutting' colvars.traj file Branko (Sat Apr 23 2011 - 13:07:20 CDT)
      • Re: 'cutting' colvars.traj file Bjoern Olausson (Wed Apr 27 2011 - 05:53:41 CDT)
    • Re: 'cutting' colvars.traj file Bjoern Olausson (Tue May 03 2011 - 05:45:23 CDT)
      • Re: 'cutting' colvars.traj file Branko (Tue May 03 2011 - 05:55:42 CDT)
      • Re: 'cutting' colvars.traj file Branko (Tue May 03 2011 - 06:41:34 CDT)
      • Re: 'cutting' colvars.traj file Bjoern Olausson (Tue May 03 2011 - 08:34:21 CDT)
• FATAL ERROR: Bad global angle count! PAUL NEWMAN (Fri Apr 22 2011 - 19:42:02 CDT)
  • Re: FATAL ERROR: Bad global angle count! PAUL NEWMAN (Sat Apr 23 2011 - 22:04:37 CDT)
    • Re: FATAL ERROR: Bad global angle count! johan strumpfer (Sun Apr 24 2011 - 16:16:52 CDT)
• pbc wrap option for x,y,z lengths Zumot, Elia Nabil (Fri Apr 22 2011 - 14:03:29 CDT)
  • Re: pbc wrap option for x,y,z lengths Axel Kohlmeyer (Fri Apr 22 2011 - 22:21:56 CDT)
    • RE: pbc wrap option for x,y,z lengths Zumot, Elia Nabil (Fri Apr 22 2011 - 22:52:11 CDT)
      • Re: pbc wrap option for x,y,z lengths Axel Kohlmeyer (Sat Apr 23 2011 - 03:37:20 CDT)
      • RE: pbc wrap option for x,y,z lengths Zumot, Elia Nabil (Sun Apr 24 2011 - 12:51:16 CDT)
      • Re: pbc wrap option for x,y,z lengths Axel Kohlmeyer (Sun Apr 24 2011 - 13:00:10 CDT)
      • RE: pbc wrap option for x,y,z lengths Zumot, Elia Nabil (Sun Apr 24 2011 - 14:44:06 CDT)
      • Re: pbc wrap option for x,y,z lengths Axel Kohlmeyer (Sun Apr 24 2011 - 14:53:20 CDT)
      • RE: pbc wrap option for x,y,z lengths Zumot, Elia Nabil (Sun Apr 24 2011 - 19:38:43 CDT)
      • Re: pbc wrap option for x,y,z lengths Axel Kohlmeyer (Mon Apr 25 2011 - 09:22:29 CDT)
• question on modifyAppliedForces() Bennion, Brian (Fri Apr 22 2011 - 12:11:27 CDT)
  • Re: question on modifyAppliedForces() Jim Phillips (Tue May 10 2011 - 21:31:42 CDT)
• Can I set a range to limit the ABF Shen, Han (Wed Apr 20 2011 - 10:24:46 CDT)
  • Re: Can I set a range to limit the ABF Giacomo Fiorin (Wed Apr 20 2011 - 11:25:44 CDT)
• infrequent rattle failure with charmm36 Edward Lyman (Wed Apr 20 2011 - 08:47:59 CDT)
  • Re: infrequent rattle failure with charmm36 Markus K. Dahlgren (Wed Apr 20 2011 - 09:30:11 CDT)
    • Re: infrequent rattle failure with charmm36 Edward Lyman (Wed Apr 20 2011 - 09:50:37 CDT)
• new error in NAMD2.8b1 with fixedAtoms dklose_at_uni-osnabrueck.de (Tue Apr 19 2011 - 11:45:25 CDT)
  • Re: new error in NAMD2.8b1 with fixedAtoms Jim Phillips (Tue May 10 2011 - 20:01:25 CDT)
    • Re: new error in NAMD2.8b1 with fixedAtoms alex digenova bravo (Fri May 13 2011 - 23:19:54 CDT)
• ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Tue Apr 19 2011 - 10:55:57 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Tue Apr 19 2011 - 11:05:09 CDT)
    • Re: ABF simulation with extendedLagrangian on keeps crashing Giacomo Fiorin (Tue Apr 19 2011 - 11:41:55 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Tue Apr 19 2011 - 12:05:23 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja Ljubetiè (Tue Apr 19 2011 - 12:43:12 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja Ljubetiè (Wed Apr 20 2011 - 09:22:21 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Giacomo Fiorin (Wed Apr 20 2011 - 11:22:37 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Thu Apr 21 2011 - 06:30:47 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Jérôme Hénin (Thu Apr 21 2011 - 09:43:21 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Fri Apr 22 2011 - 03:34:29 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Fri Apr 22 2011 - 09:27:24 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Jérôme Hénin (Fri Apr 22 2011 - 15:38:07 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Tue May 03 2011 - 08:11:26 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Jérôme Hénin (Tue May 03 2011 - 10:23:17 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Tue May 03 2011 - 11:02:12 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Wed May 04 2011 - 06:31:58 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Thu May 05 2011 - 03:38:16 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Jérôme Hénin (Thu May 05 2011 - 10:23:23 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Thu May 05 2011 - 15:50:34 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Giacomo Fiorin (Thu May 05 2011 - 16:22:09 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Jérôme Hénin (Thu May 05 2011 - 17:02:56 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Thu May 12 2011 - 03:55:03 CDT)
      • Re: ABF simulation with extendedLagrangian on keeps crashing Jérôme Hénin (Thu May 12 2011 - 04:36:20 CDT)
• Reduce the frequency of load balancer output Ajasja LjubetiÄ� (Tue Apr 19 2011 - 09:23:04 CDT)
  • Re: Reduce the frequency of load balancer output Jim Phillips (Tue May 10 2011 - 19:12:30 CDT)
• Does GB Implicit Solvent handle explicit ions? David Tanner (Sun Apr 17 2011 - 06:39:19 CDT)
  • Re: Does GB Implicit Solvent handle explicit ions? Gianluca Interlandi (Sun Apr 17 2011 - 22:43:37 CDT)
• SMD for two steered directions 常姗燕 (Sun Apr 17 2011 - 09:51:12 CDT)
  • Re: SMD for two steered directions felmerino_at_uchile.cl (Sun Apr 17 2011 - 13:53:35 CDT)
    • Re: SMD for two steered directions Jérôme Hénin (Sun Apr 17 2011 - 14:31:36 CDT)
• question on the center of mass calculation in colvar Hyonseok Hwang (Sat Apr 16 2011 - 09:57:16 CDT)
  • Re: question on the center of mass calculation in colvar Giacomo Fiorin (Sat Apr 16 2011 - 10:33:23 CDT)
  • Re: question on the center of mass calculation in colvar Jérôme Hénin (Sat Apr 16 2011 - 10:55:11 CDT)
• topology and parameter files Molecular Dynamics (Sat Apr 16 2011 - 07:13:28 CDT)
• NAMDenergy calculations for nucleic acid systems mon_sharma_at_research.iiit.ac.in (Sat Apr 16 2011 - 03:22:37 CDT)
  • Re: NAMDenergy calculations for nucleic acid systems Peter Freddolino (Sat Apr 16 2011 - 05:48:31 CDT)
    • Re: NAMDenergy calculations for nucleic acid systems mon_sharma_at_research.iiit.ac.in (Sat Apr 16 2011 - 08:18:17 CDT)
• NAMD cell dimension increasing in Z direction, problem with periodic cell snoze pa (Fri Apr 15 2011 - 13:23:53 CDT)
• Oh dear, 'namd2 invoked oom-killer' ... Nicholas M Glykos (Fri Apr 15 2011 - 09:55:35 CDT)
  • Re: Oh dear, 'namd2 invoked oom-killer' ... Jim Phillips (Fri Apr 15 2011 - 11:34:14 CDT)
    • Re: Oh dear, 'namd2 invoked oom-killer' ... Nicholas M Glykos (Fri Apr 15 2011 - 12:16:06 CDT)
• Error: keyword "group1" is not supported, or not recognized in this context. Shen, Han (Fri Apr 15 2011 - 09:14:11 CDT)
  • Re: Error: keyword "group1" is not supported, or not recognized in this context. Giacomo Fiorin (Fri Apr 15 2011 - 11:02:03 CDT)
• Replica Exchange alamng_at_uci.edu (Fri Apr 15 2011 - 04:35:47 CDT)
  • Re: Replica Exchange Jim Phillips (Tue May 10 2011 - 18:59:03 CDT)
• GeForce vs Tesla GPUs for high performance computing Salvador H-V (Thu Apr 14 2011 - 13:58:30 CDT)
  • Re: GeForce vs Tesla GPUs for high performance computing Axel Kohlmeyer (Thu Apr 14 2011 - 14:23:50 CDT)
    • Re: GeForce vs Tesla GPUs for high performance computing Gianluca Interlandi (Thu Apr 14 2011 - 14:48:58 CDT)
      • Re: GeForce vs Tesla GPUs for high performance computing Axel Kohlmeyer (Thu Apr 14 2011 - 14:57:16 CDT)
• problem in restarting ipsita basu (Thu Apr 14 2011 - 02:11:24 CDT)
  • Re: problem in restarting Axel Kohlmeyer (Thu Apr 14 2011 - 08:29:24 CDT)
    • Re: problem in restarting Jérôme Hénin (Thu Apr 14 2011 - 09:52:59 CDT)
      • Re: problem in restarting Ajasja LjubetiÄ� (Thu Apr 14 2011 - 10:28:19 CDT)
      • Re: problem in restarting Axel Kohlmeyer (Thu Apr 14 2011 - 11:42:59 CDT)
  • Re: problem in restarting Jim Phillips (Fri Apr 15 2011 - 08:06:56 CDT)
• fixing group of atoms, Proper for manipualation M Mahjour (Wed Apr 13 2011 - 17:06:43 CDT)
• NAMD feture request Ajasja LjubetiÄ� (Wed Apr 13 2011 - 09:46:07 CDT)
  • Re: NAMD feture request Giacomo Fiorin (Wed Apr 13 2011 - 10:17:27 CDT)
    • Re: NAMD feture request Thomas Evangelidis (Wed Apr 13 2011 - 12:06:57 CDT)
• Recent Geforce Cuda GPU cards(GT 440, GTX 560ti) Burgess, Don E (Wed Apr 13 2011 - 08:21:15 CDT)
  • Re: Recent Geforce Cuda GPU cards(GT 440, GTX 560ti) Axel Kohlmeyer (Wed Apr 13 2011 - 09:25:58 CDT)
• about rigid bonds oguz gurbulak (Wed Apr 13 2011 - 03:39:34 CDT)
  • Re: about rigid bonds Jim Phillips (Wed Apr 13 2011 - 10:32:07 CDT)
  • Re: about rigid bonds Axel Kohlmeyer (Wed Apr 13 2011 - 10:38:19 CDT)
• problem for simulation of membrane protein system Buddhadev Maiti (Tue Apr 12 2011 - 11:06:30 CDT)
  • Re: problem for simulation of membrane protein system Jeffrey Potoff (Tue Apr 12 2011 - 11:29:25 CDT)
  • Re: problem for simulation of membrane protein system Giacomo Fiorin (Tue Apr 12 2011 - 11:30:39 CDT)
• Re: Replica Exchange Simulations on Blue Gene/P Dong Luo (Tue Apr 12 2011 - 09:54:31 CDT)
  • Re: Replica Exchange Simulations on Blue Gene/P Axel Kohlmeyer (Tue Apr 12 2011 - 10:03:16 CDT)
• Replica Exchange Simulations on Blue Gene/P Jan H. Meinke (Tue Apr 12 2011 - 07:09:32 CDT)
• QM/MM QFrank_X=2E_V=E1zquez=22?= (Mon Apr 11 2011 - 18:23:26 CDT)
• (no subject) Buddhadev Maiti (Mon Apr 11 2011 - 14:27:13 CDT)
  • (no subject) Erik Nordgren (Mon Apr 11 2011 - 21:38:33 CDT)
    • Re: Re: Jim Phillips (Wed Apr 13 2011 - 10:19:45 CDT)
  • (no subject) David Rogers (Mon Apr 11 2011 - 22:26:09 CDT)
• vmd-l: ParseFEP output errors Christian Jorgensen (Mon Apr 11 2011 - 11:27:08 CDT)
  • Re: vmd-l: ParseFEP output errors Chris Chipot (Mon Apr 11 2011 - 11:40:10 CDT)
• dihedral rotation with ABF kakali sen (Sun Apr 10 2011 - 12:48:17 CDT)
• Help building a desktop for namd Salvador H-V (Sun Apr 10 2011 - 12:40:05 CDT)
  • Re: Help building a desktop for namd Axel Kohlmeyer (Sun Apr 10 2011 - 12:52:59 CDT)
    • Re: Help building a desktop for namd Salvador H-V (Mon Apr 11 2011 - 12:22:01 CDT)
      • Re: Help building a desktop for namd Axel Kohlmeyer (Mon Apr 11 2011 - 12:55:34 CDT)
      • Re: Help building a desktop for namd Gianluca Interlandi (Mon Apr 11 2011 - 14:41:28 CDT)
      • Re: Help building a desktop for namd Axel Kohlmeyer (Mon Apr 11 2011 - 15:06:33 CDT)
      • Re: Help building a desktop for namd Gianluca Interlandi (Mon Apr 11 2011 - 16:21:27 CDT)
      • Re: Help building a desktop for namd Axel Kohlmeyer (Mon Apr 11 2011 - 16:34:22 CDT)
      • Re: Help building a desktop for namd Gianluca Interlandi (Mon Apr 11 2011 - 16:25:26 CDT)
      • Re: Help building a desktop for namd Jim Phillips (Wed Apr 13 2011 - 10:17:27 CDT)
      • Re: Help building a desktop for namd Salvador H-V (Wed Apr 13 2011 - 11:34:18 CDT)
      • Re: Help building a desktop for namd Gianluca Interlandi (Wed Apr 13 2011 - 17:06:53 CDT)
      • Re: Help building a desktop for namd Axel Kohlmeyer (Wed Apr 13 2011 - 17:22:03 CDT)
      • Re: Help building a desktop for namd Jeffrey Potoff (Thu Apr 14 2011 - 00:07:16 CDT)
      • Re: Help building a desktop for namd Axel Kohlmeyer (Thu Apr 14 2011 - 08:37:20 CDT)
• (no subject) Buddhadev Maiti (Fri Apr 08 2011 - 10:45:19 CDT)
• protein on solid surface Giovanni Bellesia (Fri Apr 08 2011 - 09:48:50 CDT)
  • Re: protein on solid surface Giacomo Fiorin (Fri Apr 08 2011 - 11:21:33 CDT)
    • Re: protein on solid surface Giovanni Bellesia (Fri Apr 08 2011 - 13:45:31 CDT)
• SMD simulation: stop applying force during simulation? THANH NGUYEN (Thu Apr 07 2011 - 22:05:35 CDT)
  • Re: SMD simulation: stop applying force during simulation? Axel Kohlmeyer (Fri Apr 08 2011 - 07:46:54 CDT)
• Abe versus Lincoln Gianluca Interlandi (Thu Apr 07 2011 - 13:22:37 CDT)
  • Re: Abe versus Lincoln johan strumpfer (Thu Apr 07 2011 - 13:40:13 CDT)
    • Re: Abe versus Lincoln Axel Kohlmeyer (Thu Apr 07 2011 - 13:46:34 CDT)
      • Re: Abe versus Lincoln Gianluca Interlandi (Thu Apr 07 2011 - 13:57:41 CDT)
      • Re: Abe versus Lincoln Axel Kohlmeyer (Thu Apr 07 2011 - 14:21:33 CDT)
      • Re: Abe versus Lincoln Gianluca Interlandi (Thu Apr 07 2011 - 15:40:11 CDT)
      • Re: Abe versus Lincoln Axel Kohlmeyer (Thu Apr 07 2011 - 16:18:09 CDT)
      • Re: Abe versus Lincoln johan strumpfer (Thu Apr 07 2011 - 16:23:16 CDT)
      • Re: Abe versus Lincoln Gianluca Interlandi (Thu Apr 07 2011 - 16:55:51 CDT)
    • Re: Abe versus Lincoln Gianluca Interlandi (Thu Apr 07 2011 - 13:50:45 CDT)
• Fwd: ramd seed Francesco Pietra (Thu Apr 07 2011 - 08:41:08 CDT)
• NVT setup for monolayer Bjoern Olausson (Thu Apr 07 2011 - 08:24:32 CDT)
  • Re: NVT setup for monolayer Jim Phillips (Wed Apr 13 2011 - 10:09:49 CDT)
    • Re: NVT setup for monolayer Bjoern Olausson (Thu Apr 14 2011 - 02:17:35 CDT)
• FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Gary M. Skinner (Thu Apr 07 2011 - 07:17:14 CDT)
  • Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT johan strumpfer (Thu Apr 07 2011 - 09:23:02 CDT)
• multilevel summation in NAMD Francesco Oteri (Wed Apr 06 2011 - 17:32:49 CDT)
  • Re: multilevel summation in NAMD Chris Harrison (Wed Apr 06 2011 - 21:56:19 CDT)
• FEP with flattened free energy surface? Ivan Vyalov (Wed Apr 06 2011 - 04:49:50 CDT)
  • Re: FEP with flattened free energy surface? Jérôme Hénin (Wed Apr 06 2011 - 11:45:29 CDT)
    • Re: FEP with flattened free energy surface? Ivan Vyalov (Fri Apr 08 2011 - 14:12:38 CDT)
      • Re: FEP with flattened free energy surface? Jérôme Hénin (Fri Apr 08 2011 - 15:05:30 CDT)
      • Re: FEP with flattened free energy surface? Ivan Vyalov (Fri Apr 08 2011 - 15:48:09 CDT)
      • Re: FEP with flattened free energy surface? Jérôme Hénin (Sat Apr 09 2011 - 01:18:19 CDT)
• topology for monophosphate Irene Newhouse (Tue Apr 05 2011 - 15:25:52 CDT)
  • RE: topology for monophosphate Irene Newhouse (Wed Apr 06 2011 - 14:02:30 CDT)
• NAMD speed on MPICH2 Ubuntu 64 bit Cluster Robert McCarrick (Tue Apr 05 2011 - 13:51:55 CDT)
  • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Robert McCarrick (Wed Apr 06 2011 - 11:19:16 CDT)
    • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Axel Kohlmeyer (Wed Apr 06 2011 - 12:06:41 CDT)
      • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Robert McCarrick (Wed Apr 06 2011 - 15:50:11 CDT)
      • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Axel Kohlmeyer (Wed Apr 06 2011 - 16:22:48 CDT)
      • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Jim Phillips (Wed Apr 06 2011 - 17:01:31 CDT)
      • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Robert McCarrick (Thu Apr 07 2011 - 09:06:03 CDT)
  • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Norman Geist (Fri Apr 15 2011 - 07:46:00 CDT)
• NPT simulations in NAMD Hasan haska (Tue Apr 05 2011 - 07:31:52 CDT)
  • Re: NPT simulations in NAMD Axel Kohlmeyer (Tue Apr 05 2011 - 08:09:26 CDT)
• NAMD for windows cannot run correctly according to namd tutorials sciencekey (Tue Apr 05 2011 - 04:00:11 CDT)
• Wrong exit from RAMD runs Francesco Pietra (Tue Apr 05 2011 - 03:11:29 CDT)
  • Fwd: Wrong exit from RAMD runs Francesco Pietra (Tue Apr 05 2011 - 15:34:19 CDT)
    • Re: Fwd: Wrong exit from RAMD runs Jim Phillips (Wed Apr 13 2011 - 09:59:25 CDT)
      • Re: Fwd: Wrong exit from RAMD runs Jim Phillips (Wed Apr 13 2011 - 10:02:18 CDT)
      • Re: Fwd: Wrong exit from RAMD runs Vlad Cojocaru (Thu Apr 14 2011 - 03:08:54 CDT)
• implicit solvent job error in NAMD2.8b1 harish vashisth (Mon Apr 04 2011 - 15:47:33 CDT)
  • Re: implicit solvent job error in NAMD2.8b1 David Tanner (Mon Apr 04 2011 - 16:34:11 CDT)
    • Re: implicit solvent job error in NAMD2.8b1 harish vashisth (Mon Apr 04 2011 - 17:14:20 CDT)
      • Re: implicit solvent job error in NAMD2.8b1 David Tanner (Tue Apr 05 2011 - 11:35:49 CDT)
• gromacs analysis tools Molecular Dynamics (Sun Apr 03 2011 - 04:33:14 CDT)
• gromacs analysis tools Molecular Dynamics (Sun Apr 03 2011 - 04:54:35 CDT)
  • Re: gromacs analysis tools Joshua Adelman (Sun Apr 03 2011 - 10:45:16 CDT)
    • Re: gromacs analysis tools Francesco Oteri (Sun Apr 03 2011 - 13:47:19 CDT)
      • Re: gromacs analysis tools Axel Kohlmeyer (Sun Apr 03 2011 - 14:28:04 CDT)
• Why NAMD writes colvars step by step Leonardo Herrera (Fri Apr 01 2011 - 19:04:21 CDT)
  • Re: Why NAMD writes colvars step by step Giacomo Fiorin (Fri Apr 01 2011 - 21:10:15 CDT)
    • Re: Why NAMD writes colvars step by step Leonardo Herrera (Sat Apr 02 2011 - 19:22:23 CDT)
      • Re: Why NAMD writes colvars step by step Giacomo Fiorin (Sat Apr 02 2011 - 19:38:26 CDT)
• Why NAMD writes colvars step by step Leonardo Herrera (Fri Apr 01 2011 - 17:06:03 CDT)
  • Re: Why NAMD writes colvars step by step Jérôme Hénin (Sat Apr 02 2011 - 02:34:02 CDT)
• Multi node run causes "CUDA error cudaStreamCreate" Michael S. Sellers (Cont, ARL/WMRD) (Fri Apr 01 2011 - 12:32:35 CDT)
  • Re: Multi node run causes "CUDA error cudaStreamCreate" Axel Kohlmeyer (Fri Apr 01 2011 - 15:02:18 CDT)
    • Re: Multi node run causes "CUDA error cudaStreamCreate" Michael S. Sellers (Cont, ARL/WMRD) (Fri Apr 01 2011 - 15:46:21 CDT)
      • Re: Multi node run causes "CUDA error cudaStreamCreate" Axel Kohlmeyer (Fri Apr 01 2011 - 16:10:00 CDT)
      • Re: Multi node run causes "CUDA error cudaStreamCreate" Michael S. Sellers (Cont, ARL/WMRD) (Fri Apr 01 2011 - 16:27:08 CDT)
      • Re: Multi node run causes "CUDA error cudaStreamCreate" Jim Phillips (Wed Apr 06 2011 - 16:17:02 CDT)
• set dummyAtom position changing christos.lamprakis_at_dcb.unibe.ch (Fri Apr 01 2011 - 09:44:39 CDT)
• Setting up aMD simulation of a membrane protein Raul Araya (Fri Apr 01 2011 - 09:05:32 CDT)
  • Re: Setting up aMD simulation of a membrane protein Jeff Wereszczynski (Fri Apr 01 2011 - 11:00:23 CDT)
  • Re: Setting up aMD simulation of a membrane protein Yi Wang (Fri Apr 01 2011 - 13:59:01 CDT)
• New collective variable: biolRel Jérôme Hénin (Fri Apr 01 2011 - 09:01:53 CDT)
• Re: vmd-l: No probability distribution plot in ParseFEP liupeng012_at_mail.nankai.edu.cn (Thu Mar 31 2011 - 21:08:46 CDT)
• angles flavio seixas (Thu Mar 31 2011 - 15:57:33 CDT)
  • Re: angles Giacomo Fiorin (Thu Mar 31 2011 - 18:05:28 CDT)
• Accelerated MD: question about dual boost mode patrick wintrode (Thu Mar 31 2011 - 15:01:49 CDT)
  • Re: Accelerated MD: question about dual boost mode Jeff Wereszczynski (Thu Mar 31 2011 - 17:07:07 CDT)
    • Re: Accelerated MD: question about dual boost mode Bjoern Olausson (Tue May 10 2011 - 07:32:13 CDT)
    • Re: Accelerated MD: question about dual boost mode Bjoern Olausson (Tue May 10 2011 - 10:17:59 CDT)
• vmd-l: No probability distribution plot in ParseFEP Christian Jorgensen (Thu Mar 31 2011 - 13:24:27 CDT)
  • RE: vmd-l: No probability distribution plot in ParseFEP Christian Jorgensen (Fri Apr 01 2011 - 04:09:12 CDT)
• unsubscribe Chen, Zhihong (chenz2) (Thu Mar 31 2011 - 13:02:05 CDT)
• reassignFreq expression and relation with SMD Kang Hee Cho (Thu Mar 31 2011 - 10:56:47 CDT)
  • external forces Matteo Rotter (Mon Apr 04 2011 - 08:13:24 CDT)
    • Re: external forces johan strumpfer (Mon Apr 04 2011 - 11:07:02 CDT)
    • Re: external forces Jim Phillips (Wed Apr 13 2011 - 09:47:03 CDT)
• Reverse Mapping of RBCG Model Sibel Cakan (Thu Mar 31 2011 - 06:20:08 CDT)
• Reverse Mapping of RBCG Model Sibel Cakan (Thu Mar 31 2011 - 03:51:57 CDT)
• NAMD_CVS_Source Leonardo Herrera (Wed Mar 30 2011 - 16:43:52 CDT)
  • Re: NAMD_CVS_Source Axel Kohlmeyer (Wed Mar 30 2011 - 17:27:04 CDT)
• The biggest system simulated on one TESLA C2050 ? Marek Maly (Wed Mar 30 2011 - 13:30:11 CDT)
  • Re: The biggest system simulated on one TESLA C2050 ? Axel Kohlmeyer (Wed Mar 30 2011 - 14:42:56 CDT)
  • Re: The biggest system simulated on one TESLA C2050 ? Jim Phillips (Wed Apr 13 2011 - 09:37:46 CDT)
• Generalized Born implicit solvent model in 2.8b1 Enrico Guarnera (Wed Mar 30 2011 - 09:40:45 CDT)
  • Re: Generalized Born implicit solvent model in 2.8b1 David Tanner (Wed Mar 30 2011 - 12:04:20 CDT)
• Switching function for cut-off method yandong Huang (Wed Mar 30 2011 - 08:54:09 CDT)
• Network version gives inconsistent wall clock timings yashodhan karandikar (Wed Mar 30 2011 - 08:39:15 CDT)
  • Re: Network version gives inconsistent wall clock timings Jim Phillips (Wed Apr 13 2011 - 09:04:46 CDT)
• Incompatibility between colvars and tclforces? Francesco Pietra (Wed Mar 30 2011 - 05:04:02 CDT)
  • Re: Incompatibility between colvars and tclforces? Ajasja LjubetiÄ� (Wed Mar 30 2011 - 06:21:23 CDT)
    • Re: Incompatibility between colvars and tclforces? Wang Yi (Wed Mar 30 2011 - 09:16:25 CDT)
  • Re: Incompatibility between colvars and tclforces? Jérôme Hénin (Wed Mar 30 2011 - 06:23:42 CDT)
    • Re: Incompatibility between colvars and tclforces? Francesco Pietra (Wed Mar 30 2011 - 09:06:13 CDT)
      • Re: Incompatibility between colvars and tclforces? Jérôme Hénin (Wed Mar 30 2011 - 10:23:45 CDT)
      • Re: Incompatibility between colvars and tclforces? Francesco Pietra (Wed Mar 30 2011 - 11:29:15 CDT)
      • Fwd: Incompatibility between colvars and tclforces? Francesco Pietra (Wed Mar 30 2011 - 12:32:53 CDT)
      • Re: Fwd: Incompatibility between colvars and tclforces? Vlad Cojocaru (Thu Mar 31 2011 - 02:27:40 CDT)
      • Re: Fwd: Incompatibility between colvars and tclforces? Francesco Pietra (Thu Mar 31 2011 - 02:45:10 CDT)
      • Re: Fwd: Incompatibility between colvars and tclforces? Jérôme Hénin (Thu Mar 31 2011 - 03:25:18 CDT)
      • Re: Fwd: Incompatibility between colvars and tclforces? Vlad Cojocaru (Thu Mar 31 2011 - 05:12:10 CDT)
      • Re: Incompatibility between colvars and tclforces? Giacomo Fiorin (Wed Mar 30 2011 - 11:20:08 CDT)
• Setting PME Grid Size da xue (Tue Mar 29 2011 - 20:28:26 CDT)
  • Re: Setting PME Grid Size Jim Phillips (Wed Apr 13 2011 - 08:55:23 CDT)
• NAMD 2.7/2.8b1 and BlueGeneL Dong Luo (Tue Mar 29 2011 - 11:00:22 CDT)
  • Re: NAMD 2.7/2.8b1 and BlueGeneL Jim Phillips (Wed Apr 13 2011 - 08:46:26 CDT)
    • Re: NAMD 2.7/2.8b1 and BlueGeneL Dong Luo (Wed Apr 13 2011 - 16:46:00 CDT)
• Velocity distribution Philip Peartree (Tue Mar 29 2011 - 05:45:30 CDT)
  • Re: Velocity distribution Jim Phillips (Wed Apr 13 2011 - 08:38:58 CDT)
• vmd: ParseFEP plot mistake Christian Jorgensen (Tue Mar 29 2011 - 04:45:07 CDT)
  • Re: vmd: ParseFEP plot mistake Chris Chipot (Tue Mar 29 2011 - 07:06:46 CDT)
    • RE: vmd: ParseFEP plot mistake Christian Jorgensen (Tue Mar 29 2011 - 10:08:35 CDT)
• Get restart file (restart.coor) from DCD Ismail, Mohd F. (Mon Mar 28 2011 - 17:41:56 CDT)
  • Re: Get restart file (restart.coor) from DCD Joshua D. Moore (Mon Mar 28 2011 - 20:18:11 CDT)
• Fwd: RAMD Setting parameter TclForces from script failed Francesco Pietra (Mon Mar 28 2011 - 15:19:57 CDT)
  • Fwd: RAMD Setting parameter TclForces from script failed Francesco Pietra (Mon Mar 28 2011 - 15:37:24 CDT)
    • Re: RAMD Setting parameter TclForces from script failed Francesco Pietra (Mon Mar 28 2011 - 16:09:55 CDT)
      • RE: RAMD Setting parameter TclForces from script failed Cojocaru, Vlad (Mon Mar 28 2011 - 16:55:14 CDT)
    • Re: Fwd: RAMD Setting parameter TclForces from script failed Jim Phillips (Mon Mar 28 2011 - 16:49:25 CDT)
      • RE: Fwd: RAMD Setting parameter TclForces from script failed Cojocaru, Vlad (Mon Mar 28 2011 - 16:55:44 CDT)
• Accelerated MD with membrane embedded proteins. Raul Araya (Mon Mar 28 2011 - 13:45:36 CDT)
• RAMD Setting parameter TclForces from script failed Francesco Pietra (Mon Mar 28 2011 - 05:26:21 CDT)
  • Re: RAMD Setting parameter TclForces from script failed Vlad Cojocaru (Mon Mar 28 2011 - 08:45:49 CDT)
    • Re: RAMD Setting parameter TclForces from script failed Francesco Pietra (Mon Mar 28 2011 - 09:50:31 CDT)
      • RE: RAMD Setting parameter TclForces from script failed Cojocaru, Vlad (Mon Mar 28 2011 - 14:20:56 CDT)
      • Re: RAMD Setting parameter TclForces from script failed Francesco Pietra (Mon Mar 28 2011 - 14:43:34 CDT)
    • Re: RAMD Setting parameter TclForces from script failed Francesco Pietra (Tue Mar 29 2011 - 02:51:19 CDT)
      • Re: RAMD Setting parameter TclForces from script failed Vlad Cojocaru (Tue Mar 29 2011 - 04:59:25 CDT)
      • Re: RAMD Setting parameter TclForces from script failed Francesco Pietra (Tue Mar 29 2011 - 06:09:40 CDT)
      • Re: RAMD Setting parameter TclForces from script failed Jim Phillips (Wed Apr 13 2011 - 08:33:57 CDT)
  • Re: RAMD Setting parameter TclForces from script failed Jim Phillips (Mon Mar 28 2011 - 14:33:32 CDT)
• Net forces on each atom can be written to PDB in NAMD 2.8b1 oguz gurbulak (Mon Mar 28 2011 - 04:53:55 CDT)
• output forces with tclBC Eduardo Cruz-Chu (Mon Mar 28 2011 - 04:33:15 CDT)
• Net forces on each atom can be written to PDB in NAMD 2.8b1 oguz gurbulak (Mon Mar 28 2011 - 04:06:05 CDT)
  • Re: Net forces on each atom can be written to PDB in NAMD 2.8b1 Jim Phillips (Mon Mar 28 2011 - 12:00:59 CDT)
• ramd firstRamdAtom Francesco Pietra (Mon Mar 28 2011 - 02:22:20 CDT)
  • Fwd: ramd firstRamdAtom Francesco Pietra (Mon Mar 28 2011 - 03:15:56 CDT)
• NAMD 2.8b1 released Jim Phillips (Sun Mar 27 2011 - 12:25:13 CDT)
• partial charges for organic ligands Francesco Pietra (Sat Mar 26 2011 - 11:45:26 CDT)
  • Re: partial charges for organic ligands johan strumpfer (Sat Mar 26 2011 - 12:40:48 CDT)
  • Re: partial charges for organic ligands Branko (Sat Mar 26 2011 - 12:42:32 CDT)
    • Re: partial charges for organic ligands Francesco Pietra (Sat Mar 26 2011 - 15:23:05 CDT)
      • Re: partial charges for organic ligands Branko (Sat Mar 26 2011 - 16:09:35 CDT)
      • Re: partial charges for organic ligands Richard Wood (Sat Mar 26 2011 - 22:18:50 CDT)
• how to convert X_PLOR to CHARMM? Lisa Brown (Fri Mar 25 2011 - 11:01:26 CDT)
• CHARMM parameters for Mn 2+ ion Lisa Brown (Fri Mar 25 2011 - 10:43:45 CDT)
  • Re: vmd-l: CHARMM parameters for Mn 2+ ion Jernej Zidar (Fri Mar 25 2011 - 12:57:00 CDT)
    • Re: Re: vmd-l: CHARMM parameters for Mn 2+ ion Daniel Aguayo (Fri Mar 25 2011 - 14:45:15 CDT)
• ewald method Hasan haska (Fri Mar 25 2011 - 09:49:57 CDT)
  • Re: ewald method David Hardy (Fri Mar 25 2011 - 10:27:11 CDT)
• charmm 19 parameters Hasan haska (Fri Mar 25 2011 - 09:49:24 CDT)
• ewald method Hasan haska (Fri Mar 25 2011 - 09:45:45 CDT)
• charmm 19 parameters Hasan haska (Fri Mar 25 2011 - 09:38:41 CDT)
• Domain error ParseFEP Christian Jorgensen (Fri Mar 25 2011 - 09:14:02 CDT)
  • Re: Domain error ParseFEP Chris Chipot (Fri Mar 25 2011 - 09:41:25 CDT)
    • RE: Domain error ParseFEP Christian Jorgensen (Fri Mar 25 2011 - 09:42:29 CDT)
      • Re: Domain error ParseFEP Chris Chipot (Fri Mar 25 2011 - 09:57:19 CDT)
• Re: vmd-l: How to maximize the VMD display window Ajasja LjubetiÄ� (Fri Mar 25 2011 - 07:48:24 CDT)
• Advisable limit on the number of quadrants a 2D ABF simulation can be split. Ajasja LjubetiÄ� (Fri Mar 25 2011 - 04:52:09 CDT)
  • Re: Advisable limit on the number of quadrants a 2D ABF simulation can be split. Jérôme Hénin (Fri Mar 25 2011 - 06:25:30 CDT)
    • Re: Advisable limit on the number of quadrants a 2D ABF simulation can be split. Ajasja LjubetiÄ� (Mon Mar 28 2011 - 09:06:40 CDT)
      • Re: Advisable limit on the number of quadrants a 2D ABF simulation can be split. Jérôme Hénin (Mon Mar 28 2011 - 09:42:33 CDT)
• how to write the bond across the cell boundary Íõ—² (Fri Mar 25 2011 - 01:52:15 CDT)
  • Re: how to write the bond across the cell boundary Ajasja LjubetiÄ� (Fri Mar 25 2011 - 03:44:41 CDT)
    • Re: how to write the bond across the cell boundary Axel Kohlmeyer (Fri Mar 25 2011 - 08:17:05 CDT)
• Why are the pressures in my box of water systematically off? Tom Sisan (Thu Mar 24 2011 - 18:33:39 CDT)
  • Re: Why are the pressures in my box of water systematically off? Jim Phillips (Sun Mar 27 2011 - 10:04:35 CDT)
    • Re: Why are the pressures in my box of water systematically off? Tom Sisan (Wed Mar 30 2011 - 12:40:58 CDT)
    • Re: Why are the pressures in my box of water systematically off? Tom Sisan (Thu Mar 31 2011 - 17:04:03 CDT)
• Re: Using RAMD for studiying conformational changes in proteins Vlad Cojocaru (Thu Mar 24 2011 - 17:59:22 CDT)
• Using RAMD for studiying conformational changes in proteins Raul Araya (Thu Mar 24 2011 - 15:23:39 CDT)
• Re: question about force information Osman Yogurtcu (Thu Mar 24 2011 - 09:56:25 CDT)
  • Re: question about force information Ajasja LjubetiÄ� (Thu Mar 24 2011 - 14:22:10 CDT)
• question about force information oguz gurbulak (Thu Mar 24 2011 - 06:02:14 CDT)
• question about force information oguz gurbulak (Thu Mar 24 2011 - 04:43:20 CDT)
• switching function yandong Huang (Wed Mar 23 2011 - 22:52:32 CDT)
• subscribe namd-l Michael Zimmermann (Wed Mar 23 2011 - 13:24:38 CDT)
• Re: how obtain .xst form .dcd file? wood irene (Wed Mar 23 2011 - 12:59:01 CDT)
  • Re: how obtain .xst form .dcd file? Ajasja LjubetiÄ� (Wed Mar 23 2011 - 14:11:27 CDT)
  • Re: how obtain .xst form .dcd file? Erik Santiso (Wed Mar 23 2011 - 17:24:16 CDT)
• GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 Bjoern Olausson (Tue Mar 22 2011 - 17:56:09 CDT)
  • Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 Giacomo Fiorin (Tue Mar 22 2011 - 21:07:53 CDT)
    • Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 Bjoern Olausson (Wed Mar 23 2011 - 03:18:22 CDT)
      • Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 Jérôme Hénin (Wed Mar 23 2011 - 05:39:51 CDT)
      • Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 Bjoern Olausson (Wed Mar 23 2011 - 07:06:21 CDT)
• Am I using the right version for accelerated MD? patrick wintrode (Tue Mar 22 2011 - 15:34:29 CDT)
  • Re: Am I using the right version for accelerated MD? Chris Harrison (Tue Mar 22 2011 - 16:11:35 CDT)
• implementing RBCG Michael Zimmermann (Tue Mar 22 2011 - 15:11:30 CDT)
  • Re: implementing RBCG Peter Freddolino (Tue Mar 22 2011 - 21:17:32 CDT)
    • Re: implementing RBCG Chris Harrison (Tue Mar 22 2011 - 21:25:54 CDT)
      • Re: implementing RBCG Peter Freddolino (Wed Mar 23 2011 - 20:19:09 CDT)
• GBIS not compatible with CUDA at this time Michael S. Sellers (Cont, ARL/WMRD) (Tue Mar 22 2011 - 13:27:48 CDT)
  • Re: GBIS not compatible with CUDA at this time David Tanner (Tue Mar 22 2011 - 14:21:09 CDT)
• "FATAL ERROR: Bad global improper count" revisited Markus K. Dahlgren (Tue Mar 22 2011 - 10:42:49 CDT)
  • Re: "FATAL ERROR: Bad global improper count" revisited johan strumpfer (Tue Mar 22 2011 - 12:41:42 CDT)
• Fw: topology file for nucleic acids including ammonium ion Alex Liu (Mon Mar 21 2011 - 16:40:55 CDT)
• A "strange" observation during ColVar calculations Wang Yi (Mon Mar 21 2011 - 13:49:45 CDT)
  • Re: A "strange" observation during ColVar calculations Giacomo Fiorin (Mon Mar 21 2011 - 15:46:27 CDT)
    • Re: A "strange" observation during ColVar calculations Wang Yi (Mon Mar 21 2011 - 15:58:17 CDT)
      • Re: A "strange" observation during ColVar calculations Jérôme Hénin (Tue Mar 22 2011 - 11:30:56 CDT)
      • Re: A "strange" observation during ColVar calculations Wang Yi (Tue Mar 22 2011 - 12:54:29 CDT)
      • Re: A "strange" observation during ColVar calculations Jérôme Hénin (Mon Mar 28 2011 - 08:33:42 CDT)
      • Re: A "strange" observation during ColVar calculations Wang Yi (Mon Mar 28 2011 - 08:40:51 CDT)
      • Re: A "strange" observation during ColVar calculations Jérôme Hénin (Mon Mar 28 2011 - 09:51:21 CDT)
• rule of thumb for dcd sampling frequency? Irene Newhouse (Mon Mar 21 2011 - 13:26:25 CDT)
  • Re: rule of thumb for dcd sampling frequency? Branko (Mon Mar 21 2011 - 14:13:51 CDT)
    • Re: rule of thumb for dcd sampling frequency? Richard Wood (Mon Mar 21 2011 - 18:43:30 CDT)
      • Re: rule of thumb for dcd sampling frequency? Branko (Tue Mar 22 2011 - 04:47:29 CDT)
      • RE: rule of thumb for dcd sampling frequency? Irene Newhouse (Tue Mar 22 2011 - 13:00:28 CDT)
      • Re: rule of thumb for dcd sampling frequency? Michael S. Sellers (Cont, ARL/WMRD) (Tue Mar 22 2011 - 15:56:17 CDT)
  • Re: rule of thumb for dcd sampling frequency? Axel Kohlmeyer (Mon Mar 21 2011 - 14:12:00 CDT)
  • Re: rule of thumb for dcd sampling frequency? Nikolaos Glykos (Mon Mar 21 2011 - 14:51:09 CDT)
    • namd and Fedora14 flavio seixas (Tue Mar 22 2011 - 07:28:27 CDT)
      • Re: namd and Fedora14 Chris Harrison (Tue Mar 22 2011 - 08:08:28 CDT)
      • Re: namd and Fedora14 Axel Kohlmeyer (Tue Mar 22 2011 - 08:44:21 CDT)
      • Re: namd and Fedora14 Michael S. Sellers (Cont, ARL/WMRD) (Tue Mar 22 2011 - 10:10:02 CDT)
      • Re: namd and Fedora14 flavio seixas (Mon Mar 28 2011 - 08:55:57 CDT)
      • Re: namd and Fedora14 Michael S. Sellers (Cont, ARL/WMRD) (Mon Mar 28 2011 - 09:12:47 CDT)
      • Re: namd and Fedora14 Michael S. Sellers (Cont, ARL/WMRD) (Mon Mar 28 2011 - 09:16:51 CDT)
      • Re: namd and Fedora14 Chris Harrison (Tue Mar 29 2011 - 04:36:36 CDT)
      • Re: namd and Fedora14 Chris Harrison (Tue Mar 29 2011 - 04:33:39 CDT)
• Re: [ppl] Help Regarding NAMD Application Testing Phil Miller (Mon Mar 21 2011 - 09:00:13 CDT)
• how obtain .xst form .dcd file? wood irene (Mon Mar 21 2011 - 09:25:47 CDT)
• dcd to trr using catdcd Neelanjana Sengupta (Mon Mar 21 2011 - 05:44:39 CDT)
  • Re: dcd to trr using catdcd Neelanjana Sengupta (Tue Mar 22 2011 - 00:11:33 CDT)
    • Re: dcd to trr using catdcd Anurag Sethi (Tue Mar 22 2011 - 02:03:56 CDT)
• NAMD on GPU Ismail, Mohd F. (Sun Mar 20 2011 - 21:24:09 CDT)
  • Re: NAMD on GPU Jun Zhang (Mon Mar 21 2011 - 19:45:10 CDT)
• html manual 2.8, ref 46 and some GBIS questions Branko (Sun Mar 20 2011 - 09:05:27 CDT)
• ABF colvar error-capped nanotube interaction sakthi kumaran (Sat Mar 19 2011 - 11:12:57 CDT)
  • Re: ABF colvar error-capped nanotube interaction Axel Kohlmeyer (Sat Mar 19 2011 - 12:02:53 CDT)
  • Re: ABF colvar error-capped nanotube interaction Giacomo Fiorin (Sat Mar 19 2011 - 13:54:37 CDT)
    • Re: ABF colvar error-capped nanotube interaction sakthi kumaran (Sun Mar 20 2011 - 01:55:30 CDT)
      • Re: ABF colvar error-capped nanotube interaction sakthi kumaran (Sun Mar 20 2011 - 11:26:04 CDT)
      • Re: ABF colvar error-capped nanotube interaction Axel Kohlmeyer (Sun Mar 20 2011 - 12:13:43 CDT)
• Unpredictable crash at runtime pellegrini (Fri Mar 18 2011 - 03:14:22 CDT)
• ABF Restart Buddhadev Maiti (Thu Mar 17 2011 - 21:46:37 CDT)
  • Re: ABF Restart Jérôme Hénin (Fri Mar 18 2011 - 04:08:34 CDT)
• GBIS and ABF Branko (Thu Mar 17 2011 - 15:50:40 CDT)
  • Re: GBIS and ABF Giacomo Fiorin (Thu Mar 17 2011 - 20:02:37 CDT)
    • Re: GBIS and ABF Branko (Fri Mar 18 2011 - 04:53:00 CDT)
    • Re: GBIS and ABF Branko (Tue Mar 22 2011 - 17:16:54 CDT)
      • Re: GBIS and ABF Bjoern Olausson (Tue Mar 22 2011 - 18:13:18 CDT)
    • Re: GBIS and ABF Bjoern Olausson (Wed Mar 23 2011 - 07:04:29 CDT)
    • Re: GBIS and ABF Bjoern Olausson (Wed Mar 23 2011 - 09:32:43 CDT)
      • Re: GBIS and ABF Jérôme Hénin (Wed Mar 23 2011 - 12:10:15 CDT)
      • Re: GBIS and ABF Ajasja LjubetiÄ� (Wed Mar 23 2011 - 14:17:48 CDT)
      • Re: GBIS and ABF Bjoern Olausson (Mon Mar 28 2011 - 02:45:46 CDT)
      • Re: GBIS and ABF Ajasja LjubetiÄ� (Mon Mar 28 2011 - 08:37:36 CDT)
      • Re: GBIS and ABF Giacomo Fiorin (Mon Mar 28 2011 - 10:08:00 CDT)
      • Re: GBIS and ABF Giacomo Fiorin (Mon Mar 28 2011 - 10:09:55 CDT)
    • Re: GBIS and ABF Bjoern Olausson (Wed Mar 23 2011 - 06:57:32 CDT)
    • Re: GBIS and ABF Jérôme Hénin (Thu Mar 24 2011 - 05:39:52 CDT)
      • Re: GBIS and ABF Jérôme Hénin (Thu Mar 24 2011 - 10:01:43 CDT)
    • Re: GBIS and ABF Bjoern Olausson (Mon Mar 28 2011 - 09:56:41 CDT)
      • Re: GBIS and ABF Ajasja LjubetiÄ� (Mon Mar 28 2011 - 11:34:07 CDT)
• VMD inorganic builder plugin dota alexiou (Thu Mar 17 2011 - 05:36:31 CDT)
  • Re: VMD inorganic builder plugin Robert Brunner (Thu Mar 17 2011 - 14:17:48 CDT)
• specify acceptance ratio in REMD Neelanjana Sengupta (Thu Mar 17 2011 - 01:47:32 CDT)
• targeted molecular dynamics sakthi kumaran (Thu Mar 17 2011 - 01:28:59 CDT)
  • Re: targeted molecular dynamics sakthi kumaran (Thu Mar 17 2011 - 09:08:25 CDT)
• Fwd: Re: Bactenecine Branko (Wed Mar 16 2011 - 16:35:57 CDT)
• RE: Bactenecine Andres Morales N (Wed Mar 16 2011 - 14:22:09 CDT)
  • Re: Bactenecine johan strumpfer (Wed Mar 16 2011 - 15:54:46 CDT)
• Multiple runs of NAMD highly take fluctuating times yashodhan karandikar (Tue Mar 15 2011 - 23:06:59 CDT)
  • Re: Multiple runs of NAMD highly take fluctuating times Axel Kohlmeyer (Wed Mar 16 2011 - 00:36:28 CDT)
    • Re: Multiple runs of NAMD highly take fluctuating times yashodhan karandikar (Wed Mar 16 2011 - 00:48:27 CDT)
• Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Tue Mar 15 2011 - 14:20:00 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile Ajasja LjubetiÄ� (Tue Mar 15 2011 - 16:56:39 CDT)
    • Re: Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Sun Mar 20 2011 - 11:03:32 CDT)
      • Re: Rotate two linked proteins against each other and calculate energy profile Ajasja LjubetiÄ� (Mon Mar 21 2011 - 03:43:55 CDT)
      • Re: Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Mon Mar 28 2011 - 07:49:23 CDT)
      • Re: Rotate two linked proteins against each other and calculate energy profile Ajasja LjubetiÄ� (Mon Mar 28 2011 - 09:30:28 CDT)
      • Re: Rotate two linked proteins against each other and calculate energy profile Jérôme Hénin (Mon Mar 28 2011 - 11:07:43 CDT)
      • Re: Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Mon Mar 28 2011 - 11:36:13 CDT)
      • Re: Rotate two linked proteins against each other and calculate energy profile Jérôme Hénin (Mon Mar 28 2011 - 15:50:44 CDT)
      • Re: Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Mon Mar 28 2011 - 16:00:25 CDT)
      • Re: Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Mon Mar 28 2011 - 11:18:09 CDT)
      • Re: Rotate two linked proteins against each other and calculate energy profile Jérôme Hénin (Mon Mar 28 2011 - 15:43:46 CDT)
      • Re: Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Mon Mar 28 2011 - 16:46:29 CDT)
      • Re: Rotate two linked proteins against each other and calculate energy profile Jérôme Hénin (Tue Mar 29 2011 - 07:03:14 CDT)
      • Re: Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Tue Mar 29 2011 - 10:16:12 CDT)
• New NAMD version 2011-03-03 uses Christian Jorgensen (Tue Mar 15 2011 - 09:52:27 CDT)
  • Re: New NAMD version 2011-03-03 uses Chris Chipot (Tue Mar 15 2011 - 10:00:17 CDT)
    • Re: New NAMD version 2011-03-03 uses Chris Harrison (Tue Mar 15 2011 - 10:48:04 CDT)
    • Re: New NAMD version 2011-03-03 uses Jeff Wereszczynski (Tue Mar 15 2011 - 11:49:28 CDT)
      • Re: New NAMD version 2011-03-03 uses Chris Harrison (Tue Mar 15 2011 - 13:18:56 CDT)
      • Re: New NAMD version 2011-03-03 uses Chris Chipot (Tue Mar 15 2011 - 17:37:15 CDT)
      • RE: New NAMD version 2011-03-03 uses Christian Jorgensen (Thu Mar 17 2011 - 12:58:03 CDT)
      • Re: New NAMD version 2011-03-03 uses Chris Chipot (Thu Mar 17 2011 - 13:09:30 CDT)
      • RE: New NAMD version 2011-03-03 uses Christian Jorgensen (Thu Mar 17 2011 - 13:34:44 CDT)
      • Re: New NAMD version 2011-03-03 uses Chris Chipot (Thu Mar 17 2011 - 13:43:44 CDT)
      • Re: New NAMD version 2011-03-03 uses Chris Harrison (Thu Mar 17 2011 - 13:53:08 CDT)
• Accelerated MD documentation? patrick wintrode (Tue Mar 15 2011 - 08:05:19 CDT)
  • Re: Accelerated MD documentation? Bjoern Olausson (Tue Mar 15 2011 - 08:59:48 CDT)
    • Re: Accelerated MD documentation? Chris Harrison (Tue Mar 15 2011 - 09:28:35 CDT)
      • Re: Accelerated MD documentation? Francesco Pietra (Tue Mar 15 2011 - 10:20:18 CDT)
      • Re: Accelerated MD documentation? Chris Harrison (Sat Mar 19 2011 - 00:15:15 CDT)
  • Re: Accelerated MD documentation? Chris Harrison (Tue Mar 15 2011 - 09:22:55 CDT)
    • Re: Accelerated MD documentation? Bjoern Olausson (Tue Mar 15 2011 - 10:47:21 CDT)
• moving inner wall of nanotube with outer wall fixed sakthi kumaran (Tue Mar 15 2011 - 04:29:02 CDT)
  • Re: moving inner wall of nanotube with outer wall fixed johan strumpfer (Tue Mar 15 2011 - 12:01:36 CDT)
• Bactenecine Andres Morales N (Mon Mar 14 2011 - 23:11:05 CDT)
• Setting up values in distance colvar Francesco Pietra (Sun Mar 13 2011 - 12:49:51 CDT)
  • Re: Setting up values in distance colvar Jérôme Hénin (Sun Mar 13 2011 - 14:45:43 CDT)
• Fwd: Keyword "lower" not supported...colvars Francesco Pietra (Sun Mar 13 2011 - 05:37:41 CDT)
• Keyword "lower" not supported...colvars Francesco Pietra (Sat Mar 12 2011 - 11:16:19 CST)
  • Re: Keyword "lower" not supported...colvars Axel Kohlmeyer (Sat Mar 12 2011 - 16:02:38 CST)
    • Re: Keyword "lower" not supported...colvars Chris Harrison (Sat Mar 12 2011 - 20:52:30 CST)
• psf problem ipsita basu (Sat Mar 12 2011 - 04:33:39 CST)
• Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) Francesco Pietra (Fri Mar 11 2011 - 11:46:30 CST)
• Automatic PSF Builder Problem Marc Charendoff (Fri Mar 11 2011 - 10:43:15 CST)
  • Re: Automatic PSF Builder Problem ehenriques_at_qui.uc.pt (Sat Mar 12 2011 - 10:49:05 CST)
• psf problem ipsita basu (Fri Mar 11 2011 - 08:24:10 CST)
• creating .psf file for a nanotube sakthi kumaran (Fri Mar 11 2011 - 02:36:02 CST)
  • Re: creating .psf file for a nanotube sakthi kumaran (Fri Mar 11 2011 - 05:13:34 CST)
  • Re: creating .psf file for a nanotube Axel Kohlmeyer (Fri Mar 11 2011 - 05:18:57 CST)
    • Re: creating .psf file for a nanotube sakthi kumaran (Fri Mar 11 2011 - 06:34:36 CST)
      • Re: creating .psf file for a nanotube Axel Kohlmeyer (Fri Mar 11 2011 - 08:26:58 CST)
• psfgen - ACE cap on PRO Marc Charendoff (Thu Mar 10 2011 - 19:07:33 CST)
  • Re: psfgen - ACE cap on PRO Peter Freddolino (Thu Mar 10 2011 - 19:59:14 CST)
• topology file for nanotube sakthi kumaran (Thu Mar 10 2011 - 00:57:44 CST)
  • Re: topology file for nanotube Ranyere Deyler (Thu Mar 10 2011 - 02:10:13 CST)
    • Re: topology file for nanotube Axel Kohlmeyer (Thu Mar 10 2011 - 04:43:37 CST)
    • Re: topology file for nanotube Axel Kohlmeyer (Thu Mar 10 2011 - 08:11:13 CST)
  • Re: topology file for nanotube Axel Kohlmeyer (Thu Mar 10 2011 - 04:38:27 CST)
• Re: pentacoordinate heme grazia cottone (Tue Mar 08 2011 - 16:58:27 CST)
• IBverbs charmrun problem Seren Soner (Tue Mar 08 2011 - 05:41:33 CST)
• Fwd: vmd-l: Re: hBond colvars and patching Francesco Pietra (Tue Mar 08 2011 - 00:34:36 CST)
  • Re: Fwd: vmd-l: Re: hBond colvars and patching Peter Freddolino (Tue Mar 08 2011 - 13:48:53 CST)
  • Re: Fwd: vmd-l: Re: hBond colvars and patching Francesco Pietra (Fri Mar 11 2011 - 09:07:20 CST)
    • Re: Fwd: vmd-l: Re: hBond colvars and patching Giacomo Fiorin (Fri Mar 11 2011 - 11:40:06 CST)
• CT1 terminal patch for THR GONZALEZ NOYA, EVA (Mon Mar 07 2011 - 14:47:57 CST)
• colvars PMF history problem Ajasja LjubetiÄ� (Mon Mar 07 2011 - 08:43:08 CST)
  • Re: colvars PMF history problem Axel Kohlmeyer (Mon Mar 07 2011 - 09:27:19 CST)
    • Re: colvars PMF history problem Ajasja Ljubetiè (Mon Mar 07 2011 - 09:43:02 CST)
      • Re: colvars PMF history problem Axel Kohlmeyer (Mon Mar 07 2011 - 10:03:24 CST)
      • Re: colvars PMF history problem Ajasja LjubetiÄ� (Mon Mar 07 2011 - 15:01:08 CST)
      • Re: colvars PMF history problem Axel Kohlmeyer (Mon Mar 07 2011 - 17:56:05 CST)
      • Re: colvars PMF history problem Jérôme Hénin (Tue Mar 08 2011 - 22:55:42 CST)
      • Re: colvars PMF history problem Ajasja LjubetiÄ� (Wed Mar 09 2011 - 03:40:18 CST)
      • Re: colvars PMF history problem Nicholas M Glykos (Mon Mar 07 2011 - 11:14:40 CST)
      • Re: colvars PMF history problem Ajasja LjubetiÄ� (Mon Mar 07 2011 - 14:50:06 CST)
      • Re: colvars PMF history problem Nikolaos Glykos (Mon Mar 07 2011 - 16:54:35 CST)
• Job scheduling (managing) software recommendation Ajasja LjubetiÄ� (Mon Mar 07 2011 - 05:36:42 CST)
  • Re: Job scheduling (managing) software recommendation Francesco Oteri (Mon Mar 07 2011 - 06:30:53 CST)
    • Re: Job scheduling (managing) software recommendation Nicholas M Glykos (Mon Mar 07 2011 - 07:50:07 CST)
  • Re: Job scheduling (managing) software recommendation Axel Kohlmeyer (Mon Mar 07 2011 - 09:16:38 CST)
    • Re: Job scheduling (managing) software recommendation Ajasja LjubetiÄ� (Mon Mar 07 2011 - 15:13:48 CST)
  • Re: Job scheduling (managing) software recommendation Ajasja LjubetiÄ� (Wed Mar 09 2011 - 03:15:41 CST)
• (NAMD2.7b1) loadtotalforces gives output even when there are no forces in system Aoife Fogarty (Mon Mar 07 2011 - 03:43:14 CST)
  • Re: (NAMD2.7b1) loadtotalforces gives output even when there are no forces in system Hugh Heldenbrand (Mon Mar 07 2011 - 07:10:09 CST)
    • Re: (NAMD2.7b1) loadtotalforces gives output even when there are no forces in system Aoife Fogarty (Tue Mar 15 2011 - 13:15:04 CDT)
• hBond colvars and patching Francesco Pietra (Sun Mar 06 2011 - 14:05:47 CST)
  • Re: hBond colvars and patching Giacomo Fiorin (Sun Mar 06 2011 - 22:57:04 CST)
    • Re: hBond colvars and patching Francesco Pietra (Mon Mar 07 2011 - 00:12:54 CST)
      • Re: vmd-l: Re: hBond colvars and patching Peter Freddolino (Mon Mar 07 2011 - 09:19:20 CST)
      • Re: vmd-l: Re: hBond colvars and patching Francesco Pietra (Mon Mar 07 2011 - 10:04:37 CST)
      • Re: vmd-l: Re: hBond colvars and patching Peter Freddolino (Mon Mar 07 2011 - 17:08:23 CST)
• pentacoordinate heme grazia cottone (Sun Mar 06 2011 - 09:43:02 CST)
• hBond component in colvars and patching Francesco Pietra (Sat Mar 05 2011 - 14:38:45 CST)
  • Fwd: hBond component in colvars and patching Francesco Pietra (Sun Mar 06 2011 - 02:36:10 CST)
• Error while using larger timesteps in Coarse grained Simulation of Polymer rohan uttarwar (Fri Mar 04 2011 - 15:53:56 CST)
• Problem with SPC/E water simulation Davide Vanzo/FS/VCU (Fri Mar 04 2011 - 15:07:42 CST)
  • Re: Problem with SPC/E water simulation Axel Kohlmeyer (Fri Mar 04 2011 - 15:50:13 CST)
  • Re: Problem with SPC/E water simulation Joshua D. Moore (Fri Mar 04 2011 - 17:54:20 CST)
• Model system spherical sieve Francesco Pietra (Fri Mar 04 2011 - 14:28:32 CST)
• membrane equilibration jeremy adler (Thu Mar 03 2011 - 13:02:57 CST)
  • Re: membrane equilibration Axel Kohlmeyer (Thu Mar 03 2011 - 13:43:48 CST)
    • Re: membrane equilibration jeremy adler (Thu Mar 03 2011 - 17:03:18 CST)
      • Re: membrane equilibration Chris Harrison (Thu Mar 03 2011 - 18:10:06 CST)
      • Re: membrane equilibration jeremy adler (Thu Mar 03 2011 - 18:30:46 CST)
      • Re: membrane equilibration Jeffrey Potoff (Thu Mar 03 2011 - 19:58:11 CST)
      • Re: membrane equilibration Axel Kohlmeyer (Thu Mar 03 2011 - 20:42:59 CST)
      • Re: membrane equilibration Ajasja LjubetiÄ� (Fri Mar 04 2011 - 05:09:19 CST)
• Uma wants to chat Uma (Thu Mar 03 2011 - 07:33:27 CST)
• NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Dong Luo (Wed Mar 02 2011 - 21:42:57 CST)
  • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Axel Kohlmeyer (Wed Mar 02 2011 - 22:32:28 CST)
    • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Dong Luo (Tue Apr 12 2011 - 09:44:09 CDT)
      • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Jim Phillips (Wed Apr 13 2011 - 10:39:41 CDT)
      • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Bjoern Olausson (Fri May 13 2011 - 02:47:16 CDT)
      • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Jim Phillips (Fri May 13 2011 - 08:18:37 CDT)
  • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Chris Harrison (Thu Mar 03 2011 - 00:41:50 CST)
    • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Dong Luo (Thu Mar 03 2011 - 19:59:10 CST)
      • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Chris Harrison (Thu Mar 03 2011 - 20:08:20 CST)
      • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Dong Luo (Fri Mar 04 2011 - 08:08:38 CST)
      • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Dong Luo (Fri Mar 04 2011 - 10:40:54 CST)
• example psf and pdb files for simulations with tip4p Ana Celia Vila Verde (Wed Mar 02 2011 - 12:21:44 CST)
  • Re: example psf and pdb files for simulations with tip4p Peter Freddolino (Wed Mar 02 2011 - 13:28:48 CST)
• Positional restraints - Dielectric constant Francesco Pietra (Wed Mar 02 2011 - 10:56:18 CST)
  • Re: Positional restraints - Dielectric constant Axel Kohlmeyer (Wed Mar 02 2011 - 11:39:39 CST)
  • Re: Positional restraints - Dielectric constant Giacomo Fiorin (Wed Mar 02 2011 - 13:42:33 CST)
• GBIS synamics Francesco Oteri (Wed Mar 02 2011 - 05:02:29 CST)
  • Re: GBIS synamics David Tanner (Wed Mar 02 2011 - 07:56:59 CST)
• Re: Psfgen Errors for C-type Heme Thomas Freeman (Tue Mar 01 2011 - 14:15:56 CST)
• Technique issue with free energy calculation on GPU Jun Zhang (Tue Mar 01 2011 - 08:24:59 CST)
• binaryrestart/binaryoutput problem Francesco Pietra (Tue Mar 01 2011 - 02:54:26 CST)
  • Fwd: binaryrestart/binaryoutput problem Francesco Pietra (Tue Mar 01 2011 - 02:56:29 CST)
    • help needed Richard Wood (Tue Mar 01 2011 - 09:25:51 CST)
      • Re: help needed harish vashisth (Tue Mar 01 2011 - 10:00:46 CST)
• Psfgen Errors for C-type Heme Thomas Freeman (Mon Feb 28 2011 - 13:46:04 CST)
• Compiling NAMD on Cray XE6 Jeff Wereszczynski (Mon Feb 28 2011 - 11:38:48 CST)
• Can paratools really parametrize a structure? Is it really finished? Ranyere Deyler (Mon Feb 28 2011 - 10:56:35 CST)
  • RE: Can paratools really parametrize a structure? Is it really finished? JC Gumbart (Mon Feb 28 2011 - 11:23:54 CST)
    • Re: Can paratools really parametrize a structure? Is it really finished? Ranyere Deyler (Mon Feb 28 2011 - 13:28:30 CST)
      • Re: Can paratools really parametrize a structure? Is it really finished? JC Gumbart (Mon Feb 28 2011 - 13:31:16 CST)
• NAMDenergy electrostatic energies Sebastian Maximilian Wilhelm (Mon Feb 28 2011 - 10:41:03 CST)
• Namd-1: problems using increment of temperature during simulation Ye Yang (Sun Feb 27 2011 - 14:27:16 CST)
• CG parameters from dcd file for protein CG modelling Nicolás Pérez (Sun Feb 27 2011 - 13:32:18 CST)
• maximum number of atoms per patch Branko (Sun Feb 27 2011 - 12:21:56 CST)
  • RE: maximum number of atoms per patch JC Gumbart (Sun Feb 27 2011 - 12:34:36 CST)
• Paratool`s error reading single point calculation. Ranyere Deyler (Sat Feb 26 2011 - 00:50:59 CST)
• Replica exchange MD with NAMD with SGE.... Raul Araya (Fri Feb 25 2011 - 15:14:19 CST)
  • Re: Replica exchange MD with NAMD with SGE.... Guoxiong Su (Wed Jul 13 2011 - 17:50:57 CDT)
• Hi, I am a new user of Namd, and I met some problems using increment of temperature during simulation Ye Yang (Fri Feb 25 2011 - 13:40:43 CST)
• NAMD + Plumed on Abe Gianluca Interlandi (Fri Feb 25 2011 - 00:03:17 CST)
• Turning off Electrostatics Completely gaborekt_at_duq.edu (Thu Feb 24 2011 - 16:05:41 CST)
  • Re: Turning off Electrostatics Completely David Tanner (Thu Feb 24 2011 - 18:50:56 CST)
  • Re: Turning off Electrostatics Completely Daniel Aguayo (Mon Mar 07 2011 - 11:53:55 CST)
• namd at ranger(tacc) Lei Shi (Thu Feb 24 2011 - 12:56:29 CST)
  • Re: namd at ranger(tacc) Axel Kohlmeyer (Thu Feb 24 2011 - 15:20:02 CST)
  • Re: namd at ranger(tacc) Jim Phillips (Thu Feb 24 2011 - 15:36:18 CST)
  • Re: namd at ranger(tacc) Sándor Kovács (Thu Feb 24 2011 - 16:46:41 CST)
    • Re: namd at ranger(tacc) Peter Freddolino (Thu Feb 24 2011 - 17:02:27 CST)
• using TIP4P 2005 in namd Ana Celia Vila Verde (Wed Feb 23 2011 - 11:57:03 CST)
  • Re: using TIP4P 2005 in namd V.Ovchinnikov (Wed Feb 23 2011 - 15:54:26 CST)
• Computing interaction energies in namd Samy Hamdouche (Tue Feb 22 2011 - 14:40:31 CST)
  • Re: Computing interaction energies in namd JC Gumbart (Tue Feb 22 2011 - 14:48:51 CST)
    • Re: Computing interaction energies in namd Samy Hamdouche (Tue Feb 22 2011 - 18:21:46 CST)
      • Re: Computing interaction energies in namd Axel Kohlmeyer (Tue Feb 22 2011 - 19:07:11 CST)
      • Re: Computing interaction energies in namd Jérôme Hénin (Wed Feb 23 2011 - 03:42:14 CST)
• accuracy of measurement Pletezhov Alexandr (Mon Feb 21 2011 - 17:14:16 CST)
  • Re: accuracy of measurement Gianluca Interlandi (Mon Feb 21 2011 - 22:11:43 CST)
• Simulating more than 20 Million atom system Harshad Joshi (Mon Feb 21 2011 - 16:01:47 CST)
• how to write out the dcd file by vmd python command? mjyang (Mon Feb 21 2011 - 08:53:58 CST)
• Calculation of IR spectra using VMD IRspec Plug-in Mikhail Suyetin (Thu Feb 17 2011 - 01:22:00 CST)
  • Re: Calculation of IR spectra using VMD IRspec Plug-in Branko (Sat Feb 19 2011 - 11:54:48 CST)
  • Re: Calculation of IR spectra using VMD IRspec Plug-in Axel Kohlmeyer (Sun Feb 20 2011 - 12:40:41 CST)
• ABF calculation using RMSD Buddhadev Maiti (Wed Feb 16 2011 - 21:04:11 CST)
  • RE: ABF calculation using RMSD JC Gumbart (Wed Feb 16 2011 - 21:24:01 CST)
• CHARMM General Force Field (CGENFF) Gianluca Interlandi (Wed Feb 16 2011 - 18:56:33 CST)
• forces on fixed atoms Bennion, Brian (Wed Feb 16 2011 - 16:01:44 CST)
  • Re: forces on fixed atoms Jérôme Hénin (Wed Feb 16 2011 - 17:58:28 CST)
    • RE: forces on fixed atoms Bennion, Brian (Wed Feb 16 2011 - 18:04:30 CST)
      • Re: forces on fixed atoms Jérôme Hénin (Thu Feb 17 2011 - 03:31:32 CST)
      • timing variation during 256core run on abe.ncsa.uiuc.edu Thomas C. Bishop (Mon Feb 21 2011 - 13:52:56 CST)
      • Re: timing variation during 256core run on abe.ncsa.uiuc.edu Axel Kohlmeyer (Mon Feb 21 2011 - 15:07:50 CST)
      • RE: timing variation during 256core run on abe.ncsa.uiuc.edu Bishop, Thomas C (Tue Feb 22 2011 - 10:14:30 CST)
      • Re: timing variation during 256core run on abe.ncsa.uiuc.edu Axel Kohlmeyer (Tue Feb 22 2011 - 11:06:26 CST)
• Re: membrane simulation Constraint failure in RATTLE algorithm snoze pa (Wed Feb 16 2011 - 14:43:06 CST)
• membrane simulation Constraint failure in RATTLE algorithm snoze pa (Wed Feb 16 2011 - 12:15:11 CST)
  • Re: membrane simulation Constraint failure in RATTLE algorithm Jeffrey Potoff (Wed Feb 16 2011 - 14:58:38 CST)
    • Re: membrane simulation Constraint failure in RATTLE algorithm snoze pa (Wed Feb 16 2011 - 17:51:32 CST)
      • Re: membrane simulation Constraint failure in RATTLE algorithm Jeffrey Potoff (Wed Feb 16 2011 - 22:18:57 CST)
      • Re: membrane simulation Constraint failure in RATTLE algorithm snoze pa (Thu Feb 17 2011 - 10:00:44 CST)
• Langevin Buffer Region David Huggins (Wed Feb 16 2011 - 04:19:51 CST)
• initial structures for md simulations oguz gurbulak (Wed Feb 16 2011 - 07:52:26 CST)
  • Re: initial structures for md simulations Jeffrey J. Potoff (Wed Feb 16 2011 - 09:02:13 CST)
• initial structures for md simulations oguz gurbulak (Wed Feb 16 2011 - 06:22:11 CST)
• Current status of polarizable force fields in NAMD lucie delemotte (Wed Feb 16 2011 - 04:37:03 CST)
• Setting Up A Langevin Buffer Region David Huggins (Wed Feb 16 2011 - 04:30:44 CST)
  • Re: Setting Up A Langevin Buffer Region Jérôme Hénin (Wed Feb 16 2011 - 06:34:58 CST)
• Can I do protein-ligand docking using NAMD? Àî¼Ñ¼ü (Tue Feb 15 2011 - 23:32:03 CST)
  • Re: Can I do protein-ligand docking using NAMD? Bo Liu (Wed Feb 16 2011 - 00:30:54 CST)
    • RE: Can I do protein-ligand docking using NAMD? JC Gumbart (Wed Feb 16 2011 - 01:08:36 CST)
• Computing several pair interactions Samy Hamdouche (Tue Feb 15 2011 - 18:11:25 CST)
• energy jump between minimization and simulation Eva Gonzalez Noya (Tue Feb 15 2011 - 18:06:25 CST)
  • Re: energy jump between minimization and simulation Ajasja LjubetiÄ� (Wed Feb 16 2011 - 03:27:53 CST)
    • Re: energy jump between minimization and simulation Eva Gonzalez Noya (Wed Feb 16 2011 - 10:14:45 CST)
      • RE: energy jump between minimization and simulation Bennion, Brian (Wed Feb 16 2011 - 10:58:33 CST)
      • Re: energy jump between minimization and simulation Eva Gonzalez Noya (Wed Feb 16 2011 - 13:15:01 CST)
      • RE: NAMD-l: energy jump between minimization and simulation Bennion, Brian (Wed Feb 16 2011 - 13:48:34 CST)
      • Re: RE: NAMD-l: energy jump between minimization and simulation Eva Gonzalez Noya (Wed Feb 16 2011 - 16:37:09 CST)
• energy jump running a simulation after minimization Eva Gonzalez Noya (Tue Feb 15 2011 - 17:23:07 CST)
• energy jump running a simulation after minimization Eva Gonzalez Noya (Tue Feb 15 2011 - 16:37:59 CST)
• Parameter in configuration NVE or NPT snoze pa (Tue Feb 15 2011 - 11:17:03 CST)
  • Re: Parameter in configuration NVE or NPT David Tanner (Wed Feb 16 2011 - 08:37:31 CST)
• problem with MD hamze rahimi (Tue Feb 15 2011 - 00:25:25 CST)
• Force constant for Umbrella Sampling Buddhadev Maiti (Mon Feb 14 2011 - 19:19:02 CST)
• ABF calculation using RMSD Buddhadev Maiti (Mon Feb 14 2011 - 19:08:32 CST)
  • Re: ABF calculation using RMSD Jérôme Hénin (Tue Feb 15 2011 - 04:46:25 CST)
• How to write gradual heating config files Cristina Rodríguez (Mon Feb 14 2011 - 19:08:07 CST)
• Re: Tetramer protein complex snoze pa (Mon Feb 14 2011 - 15:01:31 CST)
• NCS flavio seixas (Mon Feb 14 2011 - 14:09:35 CST)
  • Re: NCS snoze pa (Mon Feb 14 2011 - 15:09:33 CST)
    • Re: NCS flavio seixas (Tue Feb 15 2011 - 05:04:33 CST)
      • Re: NCS Jérôme Hénin (Tue Feb 15 2011 - 12:27:12 CST)
      • Re: NCS Joshua Adelman (Tue Feb 15 2011 - 11:51:46 CST)
      • Re: NCS Nikolaos Glykos (Tue Feb 15 2011 - 13:59:45 CST)
      • Another PSF question... Richard Wood (Tue Feb 15 2011 - 16:13:13 CST)
    • Re: NCS flavio seixas (Tue Feb 15 2011 - 17:20:49 CST)
      • Re: NCS felmerino_at_uchile.cl (Tue Feb 15 2011 - 20:22:38 CST)
      • Re: NCS Joshua Adelman (Tue Feb 15 2011 - 20:28:36 CST)
      • Re: NCS flavio seixas (Wed Feb 16 2011 - 18:42:38 CST)
      • Re: NCS Nicholas M Glykos (Wed Feb 16 2011 - 03:18:29 CST)
• New colvar feature request -- angleXY Ajasja LjubetiÄ� (Mon Feb 14 2011 - 07:19:46 CST)
  • Re: New colvar feature request -- angleXY Giacomo Fiorin (Mon Feb 14 2011 - 09:43:33 CST)
  • Re: New colvar feature request -- angleXY Jérôme Hénin (Mon Feb 14 2011 - 10:06:45 CST)
    • Re: New colvar feature request -- angleXY Ajasja Ljubetiè (Mon Feb 14 2011 - 10:13:28 CST)
      • Re: New colvar feature request -- angleXY Ajasja Ljubetiè (Mon Feb 14 2011 - 16:04:27 CST)
      • Re: New colvar feature request -- angleXY Giacomo Fiorin (Mon Feb 14 2011 - 17:07:05 CST)
• ABF reproducibility Parisa Akhski (Sun Feb 13 2011 - 15:08:26 CST)
  • Re: ABF reproducibility Jérôme Hénin (Mon Feb 14 2011 - 06:29:40 CST)
• Tetramer protein complex snoze pa (Sun Feb 13 2011 - 00:54:34 CST)
• psfgen - any version capable of reading extended PSF files? Bjoern Olausson (Fri Feb 11 2011 - 05:47:05 CST)
• coarse-grained MD Demet Akten (Fri Feb 11 2011 - 03:34:56 CST)
• job termination ipsita basu (Fri Feb 11 2011 - 00:46:17 CST)
  • Re: job termination Chris Harrison (Fri Feb 11 2011 - 11:50:20 CST)
• PME for electrostatics and cutoff for vdW? Christian Jorgensen (Thu Feb 10 2011 - 11:07:53 CST)
• FEP - Protein binding to Membrane surface Bjoern Olausson (Thu Feb 10 2011 - 03:50:37 CST)
• Mirror Image Energy Discrepency Keith Battle (Wed Feb 09 2011 - 13:23:28 CST)
  • Re: Mirror Image Energy Discrepency Jérôme Hénin (Wed Feb 09 2011 - 14:40:06 CST)
    • Re: Mirror Image Energy Discrepency Jérôme Hénin (Thu Feb 10 2011 - 13:01:33 CST)
  • Re: Mirror Image Energy Discrepency Richard Wood (Wed Feb 09 2011 - 16:42:18 CST)
• I need help with this Richard Wood (Wed Feb 09 2011 - 13:01:25 CST)
  • Re: I need help with this Cruz-Chu Eduardo Roberto (Thu Feb 10 2011 - 02:51:43 CST)
    • Re: I need help with this Richard Wood (Fri Feb 11 2011 - 06:07:23 CST)
      • Re: I need help with this felmerino_at_uchile.cl (Fri Feb 11 2011 - 10:35:52 CST)
      • Re: I need help with this Richard Wood (Fri Feb 11 2011 - 11:07:42 CST)
  • Re: I need help with this Chris Harrison (Fri Feb 11 2011 - 11:42:41 CST)
    • Re: I need help with this Richard Wood (Fri Feb 11 2011 - 12:00:11 CST)
      • Re: I need help with this Chris Harrison (Fri Feb 11 2011 - 12:08:56 CST)
      • Re: I need help with this Richard Wood (Fri Feb 11 2011 - 12:39:57 CST)
      • Re: I need help with this Chris Harrison (Fri Feb 11 2011 - 12:44:42 CST)
• water box deformation ais_at_fh.huji.ac.il (Wed Feb 09 2011 - 09:47:27 CST)
  • Re: water box deformation Jeffrey Potoff (Wed Feb 09 2011 - 10:51:41 CST)
  • Re: water box deformation felmerino_at_uchile.cl (Wed Feb 09 2011 - 12:57:23 CST)
• Abf force output stefhoor (Tue Feb 08 2011 - 20:58:39 CST)
  • Re: Abf force output Jérôme Hénin (Wed Feb 09 2011 - 03:25:59 CST)
    • Re: Abf force output stefhoor (Wed Feb 09 2011 - 04:12:50 CST)
      • Re: Abf force output Jérôme Hénin (Wed Feb 09 2011 - 07:30:16 CST)
• calculating energy term from extrabonds Segun Jung (Mon Feb 07 2011 - 23:50:43 CST)
• rescaling and reassignment parameter Kang Hee Cho (Mon Feb 07 2011 - 22:35:44 CST)
• calculating energy term from extrabonds Segun Jung (Mon Feb 07 2011 - 20:08:33 CST)
• Get number of timesteps from DCD via script Bjoern Olausson (Mon Feb 07 2011 - 06:52:39 CST)
  • Re: Get number of timesteps from DCD via script Chris Harrison (Mon Feb 07 2011 - 12:34:25 CST)
    • Re: Get number of timesteps from DCD via script Bjoern Olausson (Tue Feb 08 2011 - 05:24:29 CST)
      • Re: Get number of timesteps from DCD via script Andrew Emerson (Tue Feb 08 2011 - 08:00:07 CST)
      • Re: Get number of timesteps from DCD via script Joshua D. Moore (Tue Feb 08 2011 - 17:01:32 CST)
      • Re: Get number of timesteps from DCD via script Joshua D. Moore (Tue Feb 08 2011 - 16:56:02 CST)
      • Re: Get number of timesteps from DCD via script Bjoern Olausson (Wed Feb 09 2011 - 06:37:20 CST)
      • Re: Get number of timesteps from DCD via script Axel Kohlmeyer (Wed Feb 09 2011 - 07:43:17 CST)
      • Re: Get number of timesteps from DCD via script Bjoern Olausson (Wed Feb 09 2011 - 08:32:13 CST)
      • Re: Get number of timesteps from DCD via script Axel Kohlmeyer (Wed Feb 09 2011 - 08:43:21 CST)
      • Re: Get number of timesteps from DCD via script Bjoern Olausson (Thu Feb 10 2011 - 03:52:44 CST)
      • Re: Get number of timesteps from DCD via script Joshua D. Moore (Wed Feb 09 2011 - 06:41:06 CST)
      • Re: Get number of timesteps from DCD via script Bjoern Olausson (Wed Feb 09 2011 - 08:05:42 CST)
      • Re: Get number of timesteps from DCD via script Joshua D. Moore (Wed Feb 09 2011 - 08:40:27 CST)
• Re: [ppl] NAMD at linux on sparc Phil Miller (Sun Feb 06 2011 - 21:18:32 CST)
• determining force constant in exterbonds (harmonic potential) Segun Jung (Sat Feb 05 2011 - 10:09:50 CST)
• SMD negative forces S Richmond (Fri Feb 04 2011 - 10:39:44 CST)
  • Re: SMD negative forces S Richmond (Mon Feb 07 2011 - 17:37:09 CST)
    • Re: SMD negative forces S Richmond (Thu Feb 10 2011 - 15:32:35 CST)
      • Re: SMD negative forces Jérôme Hénin (Fri Feb 11 2011 - 03:24:54 CST)
• charmm force field Swarna M Patra (Thu Feb 03 2011 - 21:55:22 CST)
• Strange (very large) atom motions Craig Jolley (Thu Feb 03 2011 - 17:14:42 CST)
  • Re: Strange (very large) atom motions Chris Harrison (Thu Feb 03 2011 - 18:18:24 CST)
• (no subject) Alexandra Nemkevich (Thu Feb 03 2011 - 04:30:50 CST)
  • Re: Giacomo Fiorin (Thu Feb 03 2011 - 10:49:22 CST)
  • Re: Jérôme Hénin (Thu Feb 03 2011 - 11:13:22 CST)
• Proposed Feature in Targeted MD Ryan McGreevy (Wed Feb 02 2011 - 12:48:58 CST)
• ABF question (sampling and colvars output file) Parisa Akhski (Tue Feb 01 2011 - 10:27:43 CST)
  • ABF question (sampling and colvars output file) Parisa Akhski (Sun Feb 06 2011 - 15:20:47 CST)
    • Re: ABF question (sampling and colvars output file) Jérôme Hénin (Mon Feb 07 2011 - 04:20:28 CST)
      • Re: ABF question (sampling and colvars output file) Jérôme Hénin (Mon Feb 07 2011 - 11:16:28 CST)
      • RE: ABF question (sampling and colvars output file) Parisa Akhski (Mon Feb 07 2011 - 14:27:03 CST)
• volume calculation Swarna M Patra (Tue Feb 01 2011 - 04:02:48 CST)
• unsubscribe Purushottam Dixit (Mon Jan 31 2011 - 20:59:01 CST)
• Proposed Feature in Targeted MD Minh, David D. (Mon Jan 31 2011 - 13:12:38 CST)
  • Re: Proposed Feature in Targeted MD V.Ovchinnikov (Mon Jan 31 2011 - 15:14:15 CST)
    • Re: Proposed Feature in Targeted MD Minh, David D. (Mon Jan 31 2011 - 15:33:42 CST)
      • Re: Proposed Feature in Targeted MD V.Ovchinnikov (Mon Jan 31 2011 - 15:53:38 CST)
      • Re: Proposed Feature in Targeted MD Jérôme Hénin (Mon Jan 31 2011 - 16:39:37 CST)
      • Re: Proposed Feature in Targeted MD felmerino_at_uchile.cl (Mon Jan 31 2011 - 20:20:04 CST)
    • Re: Proposed Feature in Targeted MD Minh, David D. (Mon Jan 31 2011 - 15:34:48 CST)
• Problems compiling NAMD on 8-core Mac Minh, David D. (Mon Jan 31 2011 - 12:25:40 CST)
  • Re: Problems compiling NAMD on 8-core Mac Jim Phillips (Mon Jan 31 2011 - 16:39:49 CST)
    • Re: Problems compiling NAMD on 8-core Mac Chris Harrison (Mon Jan 31 2011 - 22:49:39 CST)
      • Re: Problems compiling NAMD on 8-core Mac Minh, David D. (Tue Feb 01 2011 - 00:23:07 CST)
      • Re: Problems compiling NAMD on 8-core Mac Jim Phillips (Tue Feb 01 2011 - 09:26:54 CST)
      • Re: Problems compiling NAMD on 8-core Mac Minh, David D. (Tue Feb 01 2011 - 11:28:43 CST)
  • Re: Problems compiling NAMD on 8-core Mac Chris Harrison (Mon Jan 31 2011 - 16:44:23 CST)
    • Re: Problems compiling NAMD on 8-core Mac Minh, David D. (Mon Jan 31 2011 - 17:44:01 CST)
• Question regarding NAMD membrane tutorial snoze pa (Mon Jan 31 2011 - 10:49:07 CST)
  • Re: Question regarding NAMD membrane tutorial Chris Harrison (Mon Jan 31 2011 - 11:11:43 CST)
    • Re: Question regarding NAMD membrane tutorial snoze pa (Wed Feb 02 2011 - 13:03:38 CST)
      • Re: Question regarding NAMD membrane tutorial Chris Harrison (Thu Feb 03 2011 - 18:32:04 CST)
• Help With colvars/abf Please Angelo Rossi (Sun Jan 30 2011 - 07:09:41 CST)
  • Re: Help With colvars/abf Please Jérôme Hénin (Sun Jan 30 2011 - 09:10:50 CST)
    • Re: Help With colvars/abf Please Angelo Rossi (Sun Jan 30 2011 - 11:00:38 CST)
• Coarse_Graining tempetrature Sibel Cakan (Fri Jan 28 2011 - 09:12:43 CST)
• Coarse_Graining tempetrature Sibel Cakan (Fri Jan 28 2011 - 08:31:02 CST)
• CG_MD temperature Sibel Cakan (Fri Jan 28 2011 - 07:52:15 CST)
• topology for DNA Neelanjana Sengupta (Fri Jan 28 2011 - 06:28:03 CST)
  • Re: topology for DNA Chris Harrison (Fri Jan 28 2011 - 07:59:06 CST)
    • Re: topology for DNA Eduardo Cruz-Chu (Fri Jan 28 2011 - 08:23:33 CST)
• water content Kang Hee Cho (Thu Jan 27 2011 - 23:18:24 CST)
• bond lengths angles in namd oguz gurbulak (Thu Jan 27 2011 - 06:35:34 CST)
• Equilibration when splitting an ABF calculation Ajasja LjubetiÄ� (Thu Jan 27 2011 - 06:25:04 CST)
  • Re: Equilibration when splitting an ABF calculation Jérôme Hénin (Thu Jan 27 2011 - 08:08:12 CST)
    • Re: Equilibration when splitting an ABF calculation Ajasja LjubetiÄ� (Thu Jan 27 2011 - 08:48:48 CST)
      • Re: Equilibration when splitting an ABF calculation Ajasja LjubetiÄ� (Fri Jan 28 2011 - 06:26:58 CST)
      • Re: Equilibration when splitting an ABF calculation Jérôme Hénin (Fri Jan 28 2011 - 06:44:32 CST)
• bond lengths angles in namd oguz gurbulak (Thu Jan 27 2011 - 05:43:09 CST)
  • Re: bond lengths angles in namd Jérôme Hénin (Thu Jan 27 2011 - 06:55:28 CST)
  • Re: bond lengths angles in namd Ajasja LjubetiÄ� (Thu Jan 27 2011 - 07:14:26 CST)
• Cu+2 parameters jose correa (Wed Jan 26 2011 - 07:36:59 CST)
• the meaning and effect of reassignFreq and reassignTemp Kang Hee Cho (Tue Jan 25 2011 - 08:46:39 CST)
  • How to set the right PME parameters for amber's prmtop and inpcrd files? a a (Wed Jan 26 2011 - 04:17:32 CST)
    • How to set the right PME parameters for amber's prmtop and inpcrd files? a a (Wed Jan 26 2011 - 04:34:33 CST)
• mainboard-power source for GPU Francesco Pietra (Tue Jan 25 2011 - 01:47:42 CST)
  • Re: mainboard-power source for GPU Axel Kohlmeyer (Tue Jan 25 2011 - 06:36:57 CST)
• NBFIX support in CUDA NAMD Burgess, Don E (Mon Jan 24 2011 - 20:41:26 CST)
• REMD with IBM SP6 LoadLeveler Luca Bellucci (Sat Jan 22 2011 - 11:45:31 CST)
  • Re: REMD with IBM SP6 LoadLeveler Andrew Emerson (Mon Jan 24 2011 - 02:24:58 CST)
• distance calculation between atoms of two segments mjyang (Sat Jan 22 2011 - 10:51:00 CST)
  • Re: distance calculation between atoms of two segments Ajasja LjubetiÄ� (Sat Jan 22 2011 - 13:48:54 CST)
• the meaning of reassignFreq and reassignTemp Kang Hee Cho (Sat Jan 22 2011 - 04:28:22 CST)
  • Re: the meaning of reassignFreq and reassignTemp Chris Harrison (Sun Jan 23 2011 - 09:51:01 CST)
• Missing angle parameters NH1 CT1 NH1 Christian Jorgensen (Fri Jan 21 2011 - 04:39:07 CST)
  • Re: Missing angle parameters NH1 CT1 NH1 Jérôme Hénin (Fri Jan 21 2011 - 06:44:14 CST)
    • RE: Missing angle parameters NH1 CT1 NH1 Christian Jorgensen (Fri Jan 21 2011 - 12:01:09 CST)
    • Re: Missing angle parameters NH1 CT1 NH1 Jérôme Hénin (Fri Jan 21 2011 - 11:01:56 CST)
• discrete energy value after restart Kang Hee Cho (Thu Jan 20 2011 - 21:25:46 CST)
  • Re: discrete energy value after restart Chris Harrison (Sun Jan 23 2011 - 10:00:07 CST)
• question from a tutorial Lisa Brown (Thu Jan 20 2011 - 14:17:29 CST)
  • Re: question from a tutorial JC Gumbart (Thu Jan 20 2011 - 14:29:23 CST)
• 4 x Opteron 12-core or 4 x Xeon 8-core ? David McGiven (Thu Jan 20 2011 - 05:59:13 CST)
• increasing MAX_EXCLUSIONS Francesco Oteri (Wed Jan 19 2011 - 16:07:05 CST)
  • Re: increasing MAX_EXCLUSIONS Axel Kohlmeyer (Wed Jan 19 2011 - 16:42:29 CST)
  • Re: increasing MAX_EXCLUSIONS Francesco Oteri (Thu Jan 20 2011 - 09:56:35 CST)
• non-zero charge Kwee Hong (Wed Jan 19 2011 - 10:17:45 CST)
  • Re: non-zero charge Bo Liu (Wed Jan 19 2011 - 16:31:22 CST)
  • Re: non-zero charge Chris Harrison (Wed Jan 19 2011 - 21:08:22 CST)
• peptide structure ipsita basu (Tue Jan 18 2011 - 23:05:34 CST)
  • Re: peptide structure Chris Harrison (Sun Jan 23 2011 - 10:10:08 CST)
    • Re: peptide structure ipsita basu (Thu Jan 27 2011 - 02:29:21 CST)
• Various practical colvar module related questions Ajasja LjubetiÄ� (Tue Jan 18 2011 - 11:31:46 CST)
  • Re: Various practical colvar module related questions Jérôme Hénin (Wed Jan 19 2011 - 09:46:23 CST)
    • Re: Various practical colvar module related questions Ajasja LjubetiÄ� (Thu Jan 20 2011 - 09:12:30 CST)
• Protein-DNA simulations S.Archana (Mon Jan 17 2011 - 04:41:27 CST)
  • Re: Protein-DNA simulations Chris Harrison (Wed Jan 19 2011 - 21:24:43 CST)
• NBFIX for carbonyl atoms and potassium ions -- User Defined Force -- CUDA Burgess, Don E (Mon Jan 17 2011 - 15:35:28 CST)
• Feature request for the colvars module -- TCL syntax Ajasja LjubetiÄ� (Mon Jan 17 2011 - 09:26:47 CST)
  • Re: Feature request for the colvars module -- TCL syntax Jérôme Hénin (Mon Jan 17 2011 - 11:52:23 CST)
    • Re: Feature request for the colvars module -- TCL syntax Ajasja LjubetiÄ� (Tue Jan 18 2011 - 07:17:54 CST)
      • Re: Feature request for the colvars module -- TCL syntax Axel Kohlmeyer (Tue Jan 18 2011 - 09:09:54 CST)
      • Re: Feature request for the colvars module -- TCL syntax Ajasja LjubetiÄ� (Tue Jan 18 2011 - 11:44:54 CST)
      • Re: Feature request for the colvars module -- TCL syntax Ajasja LjubetiÄ� (Mon Jan 24 2011 - 08:16:01 CST)
  • Re: Feature request for the colvars module -- TCL syntax Chris Harrison (Mon Jan 17 2011 - 11:00:22 CST)
• temperature range for residue-based CG Demet Akten (Mon Jan 17 2011 - 08:02:59 CST)
• Membrane protein simulaton snoze pa (Fri Jan 14 2011 - 18:19:24 CST)
  • Re: Membrane protein simulaton Eduard Schreiner (Fri Jan 14 2011 - 19:08:43 CST)
• NAMD CUDA error message snoze pa (Fri Jan 14 2011 - 11:37:54 CST)
  • RE: NAMD CUDA error message JC Gumbart (Fri Jan 14 2011 - 11:46:39 CST)
• Can DCD trajectory files contain only protein but water surround yandong Huang (Thu Jan 13 2011 - 08:44:10 CST)
  • Re£º Can DCD trajectory files contain only protein but water surround Jun Zhang (Thu Jan 13 2011 - 19:22:10 CST)
  • Re: Can DCD trajectory files contain only protein but water surround Axel Kohlmeyer (Thu Jan 13 2011 - 19:57:05 CST)
• Error on closing binary file Seren Soner (Thu Jan 13 2011 - 06:42:50 CST)
• Constraint failure; simulation has become unstable Wendy González (Fri Jan 07 2011 - 14:42:46 CST)
  • Re: Constraint failure; simulation has become unstable Athanassios Stavrakoudis (Fri Jan 07 2011 - 15:04:08 CST)
    • Re: Constraint failure; simulation has become unstable Wendy González (Fri Jan 07 2011 - 15:18:20 CST)
      • Re: Constraint failure; simulation has become unstable Wendy González (Fri Jan 07 2011 - 15:25:23 CST)
      • Re: Constraint failure; simulation has become unstable Joshua Adelman (Fri Jan 07 2011 - 18:18:05 CST)
      • Re: Constraint failure; simulation has become unstable Wendy González (Sat Jan 08 2011 - 07:53:11 CST)
      • Re: Constraint failure; simulation has become unstable Athanassios Stavrakoudis (Sat Jan 08 2011 - 08:05:15 CST)
      • Re: Constraint failure; simulation has become unstable Wendy González (Sat Jan 08 2011 - 08:29:37 CST)
      • Re: Constraint failure; simulation has become unstable Axel Kohlmeyer (Mon Jan 10 2011 - 08:49:07 CST)
      • Re: Constraint failure; simulation has become unstable Joshua Adelman (Sat Jan 08 2011 - 09:49:18 CST)
• NAMD initial coordinate file Ismail, Mohd F. (Fri Jan 07 2011 - 00:10:47 CST)
  • Re: NAMD initial coordinate file Chris Harrison (Mon Jan 10 2011 - 06:27:07 CST)
    • Re: NAMD initial coordinate file Mohd Farid Ismail (Thu Jan 13 2011 - 12:40:03 CST)
• Compiling NAMD 2.7 with the PLUMED patch Gianluca Interlandi (Thu Jan 06 2011 - 16:55:03 CST)
  • Re: Compiling NAMD 2.7 with the PLUMED patch Gianluca Interlandi (Thu Jan 06 2011 - 17:41:23 CST)
  • Re: Compiling NAMD 2.7 with the PLUMED patch Davide Branduardi (Thu Jan 06 2011 - 17:42:56 CST)
• Fix atoms-Colvars Alex Liu (Thu Jan 06 2011 - 15:46:14 CST)
  • Re: Fix atoms-Colvars Jérôme Hénin (Fri Jan 07 2011 - 13:04:10 CST)
• NAMD Tutorial Problem Jane Ren (Thu Jan 06 2011 - 13:19:50 CST)
• water sphere sara (Thu Jan 06 2011 - 03:14:01 CST)
  • Re: water sphere Axel Kohlmeyer (Thu Jan 06 2011 - 08:18:57 CST)
• (no subject) Chen, Zhihong (chenz2) (Wed Jan 05 2011 - 18:43:15 CST)
• Benchmark for NAMD2.7 (curent version) Branko (Wed Jan 05 2011 - 14:19:19 CST)
• unsubcribe Charlie Forde (Wed Jan 05 2011 - 10:49:54 CST)
• Distance XY-colvars Alex Liu (Tue Jan 04 2011 - 15:56:56 CST)
  • Re: Distance XY-colvars Giacomo Fiorin (Wed Jan 05 2011 - 16:12:32 CST)
• NAG simulation problem with CPS Adrian Jasiñski (Wed Jan 05 2011 - 05:36:00 CST)
  • RE: NAG simulation problem with CPS JC Gumbart (Wed Jan 05 2011 - 08:04:24 CST)
• free energy perturbation BIN ZHANG (Wed Jan 05 2011 - 02:07:57 CST)
  • Re: free energy perturbation Jérôme Hénin (Wed Jan 05 2011 - 07:39:37 CST)
    • Re: free energy perturbation Jérôme Hénin (Wed Jan 05 2011 - 12:07:39 CST)
• restart problem charlie (Wed Jan 05 2011 - 02:07:48 CST)
  • Re: restart problem JC Gumbart (Wed Jan 05 2011 - 14:23:32 CST)
• parameter file for DMPC lipid and protein system but with CHARMM36 lipids Erica Smith (Mon Jan 03 2011 - 21:53:59 CST)
  • RE: parameter file for DMPC lipid and protein system but with CHARMM36 lipids JC Gumbart (Mon Jan 03 2011 - 23:34:18 CST)
  • Re: parameter file for DMPC lipid and protein system but with CHARMM36 lipids Prathit Chatterjee (Tue Jan 04 2011 - 01:14:10 CST)
• .colvars.state file in ABF Alex Liu (Mon Jan 03 2011 - 15:53:45 CST)
  • .colvars.state file in ABF Parisa Akhski (Tue Jan 04 2011 - 15:51:09 CST)
  • Re: .colvars.state file in ABF Jérôme Hénin (Wed Jan 05 2011 - 07:15:45 CST)
• concatenate pmf files in colvars Parisa Akhski (Sat Jan 01 2011 - 12:23:06 CST)
• Force field for PDMS Yingzhe Liu (Fri Dec 31 2010 - 20:32:20 CST)
• problem regarding rattle algorithm Prathit Chatterjee (Fri Dec 31 2010 - 02:29:43 CST)
  • Re: problem regarding rattle algorithm Francesco Oteri (Fri Dec 31 2010 - 03:57:29 CST)
• Running bias exchange metadynamics simulations with NAMD Ajasja LjubetiÄ� (Thu Dec 30 2010 - 16:13:13 CST)
  • Re: Running bias exchange metadynamics simulations with NAMD Jérôme Hénin (Sat Jan 01 2011 - 15:48:06 CST)
    • Re: Running bias exchange metadynamics simulations with NAMD Ajasja LjubetiÄ� (Sun Jan 02 2011 - 15:03:48 CST)
      • Re: Running bias exchange metadynamics simulations with NAMD Giacomo Fiorin (Mon Jan 03 2011 - 18:13:21 CST)
      • Re: Running bias exchange metadynamics simulations with NAMD Ajasja LjubetiÄ� (Fri Jan 14 2011 - 09:31:49 CST)
      • Re: Running bias exchange metadynamics simulations with NAMD Jérôme Hénin (Fri Jan 14 2011 - 10:37:17 CST)
      • Re: Running bias exchange metadynamics simulations with NAMD Ajasja LjubetiÄ� (Mon Jan 17 2011 - 08:40:11 CST)
      • Re: Running bias exchange metadynamics simulations with NAMD Jérôme Hénin (Mon Jan 17 2011 - 10:35:20 CST)
• colvars-history file Jérôme Hénin (Wed Dec 29 2010 - 02:24:17 CST)
• help with the equilibration script matziast_at_med.uth.gr (Tue Dec 28 2010 - 16:31:44 CST)
• Colvars-history file Alex Liu (Sat Dec 25 2010 - 18:39:21 CST)
• Unsubscribe Pri... (Mon Dec 27 2010 - 23:03:02 CST)
• About plumed installation problem in NAMD_2.6_AIX-POWER-MPI Buddhadev Maiti (Mon Dec 27 2010 - 21:30:38 CST)
  • Re: About plumed installation problem in NAMD_2.6_AIX-POWER-MPI Axel Kohlmeyer (Tue Dec 28 2010 - 03:35:00 CST)
• structure of an equilibration script matziast_at_med.uth.gr (Sun Dec 26 2010 - 07:23:53 CST)
• equilibration script from restart files matziast_at_med.uth.gr (Sun Dec 26 2010 - 06:24:16 CST)
• Adding special VdW parameters Luca Bellucci (Sat Dec 25 2010 - 10:04:55 CST)
  • Re: Adding special VdW parameters Axel Kohlmeyer (Sat Dec 25 2010 - 11:22:38 CST)
• Re: question about repeating output text Ng Yao Zong (Wed Dec 22 2010 - 21:37:13 CST)
  • Re: Re: question about repeating output text Axel Kohlmeyer (Thu Dec 23 2010 - 04:07:46 CST)
• NBFIX and cuda Jacopo Sgrignani (Wed Dec 22 2010 - 03:13:48 CST)
  • Re: NBFIX and cuda Axel Kohlmeyer (Wed Dec 22 2010 - 10:51:19 CST)
• "Hands-On" Workshop on Computational Biophysics, March 21-25, 2011, Atlanta, GA, USA David Brandon (Tue Dec 21 2010 - 14:34:17 CST)
• compiling namd gpu Jacopo Sgrignani (Tue Dec 21 2010 - 03:13:57 CST)
  • Re: compiling namd gpu Jun Zhang (Wed Dec 22 2010 - 18:17:01 CST)
• ABF on NAMD 2.7b3 Alex Liu (Mon Dec 20 2010 - 15:03:22 CST)
  • Re: ABF on NAMD 2.7b3 JC Gumbart (Mon Dec 20 2010 - 15:37:54 CST)
    • Re: ABF on NAMD 2.7b3 JC Gumbart (Mon Dec 20 2010 - 18:11:08 CST)
      • Re: ABF on NAMD 2.7b3 Chris Harrison (Tue Dec 21 2010 - 08:20:43 CST)
• Why do different versions of NAMD deserve different simulation results? ºÎع»Ô (Mon Dec 20 2010 - 06:03:03 CST)
  • Re: Why do different versions of NAMD deserve different simulation results? Axel Kohlmeyer (Mon Dec 20 2010 - 06:48:27 CST)
  • Re: Why do different versions of NAMD deserve different simulation results? Axel Kohlmeyer (Mon Dec 20 2010 - 06:54:53 CST)
• The outputs of REMD were suspended Yingzhe Liu (Sun Dec 19 2010 - 08:21:11 CST)
• Problem with topology file Christian Jorgensen (Sat Dec 18 2010 - 07:35:25 CST)
• counting h-bond in system with vmd sara (Fri Dec 17 2010 - 15:10:21 CST)
  • Re: counting h-bond in system with vmd Axel Kohlmeyer (Sat Dec 18 2010 - 04:51:30 CST)
• Zcoord for ABF Parisa Akhski (Fri Dec 17 2010 - 13:22:49 CST)
  • Re: Zcoord for ABF Jérôme Hénin (Wed Dec 22 2010 - 15:11:29 CST)
• Re: vmd-l: why atom positions are reset after readpsf, coordpdb commands? Jim Phillips (Fri Dec 17 2010 - 10:58:39 CST)
• FEP VdW and electrostatic decoupling parameters Christian Jorgensen (Fri Dec 17 2010 - 10:21:39 CST)
  • Langevin Damping = 0? Mohd Farid Ismail (Fri Dec 17 2010 - 13:19:03 CST)
    • Re: Langevin Damping = 0? Axel Kohlmeyer (Fri Dec 17 2010 - 14:40:03 CST)
    • Re: Langevin Damping = 0? Gianluca Interlandi (Fri Dec 17 2010 - 15:47:00 CST)
• jobs get stuck using NAMDv2.7 and stop producing output in the log-file harish vashisth (Fri Dec 17 2010 - 10:20:10 CST)
• par_all36_cgenff.prm with NAMD2.7 - problem of file reading Branko (Fri Dec 17 2010 - 09:19:44 CST)
• NAMD cal with AMBER forces: Polarizable parameters in AMBER Xiao Ju Zhang (Thu Dec 16 2010 - 13:21:01 CST)
• a cv-smd puzzle charlie (Thu Dec 16 2010 - 10:09:55 CST)
• a cv-smd puzzle Charlie (Thu Dec 16 2010 - 09:21:43 CST)
• unsubscribe namd-l sripad chandan (Thu Dec 16 2010 - 09:04:49 CST)
• how to get topology and parameter file for ligand jnsong (Thu Dec 16 2010 - 08:58:07 CST)
• how to generate the topology and parameter file for ligand jnsong (Thu Dec 16 2010 - 07:45:52 CST)
• how to generate topology and parameter file for ligand jnsong (Thu Dec 16 2010 - 07:40:38 CST)
• Which compiler is used for the official (windows) NAMD binaries Ajasja LjubetiÄ� (Thu Dec 16 2010 - 07:09:52 CST)
• questions about smd Charlie (Wed Dec 15 2010 - 22:37:33 CST)
• questions about smd Charlie (Wed Dec 15 2010 - 21:42:56 CST)
• some questions about smd Charlie (Wed Dec 15 2010 - 21:03:17 CST)
• some questions about smd Charlie (Wed Dec 15 2010 - 20:08:45 CST)
• problem with cuda version hamze rahimi (Wed Dec 08 2010 - 12:30:23 CST)
  • Re: problem with cuda version Axel Kohlmeyer (Thu Dec 16 2010 - 05:24:44 CST)
• Constraint failures and TI electrostatic calcs Courtney Taylor (Mon Dec 06 2010 - 13:26:52 CST)
  • Re: Constraint failures and TI electrostatic calcs Courtney Taylor (Mon Dec 06 2010 - 14:18:40 CST)
• Interaction potentials W-S Evgeniya Volkova (Wed Dec 15 2010 - 08:13:40 CST)
  • Re: Interaction potentials W-S Axel Kohlmeyer (Thu Dec 16 2010 - 05:31:58 CST)
• Asking for some sample PDB and PSF files of carbon nanotube ºÎع»Ô (Wed Dec 15 2010 - 04:19:22 CST)
  • Re: Asking for some sample PDB and PSF files of carbon nanotube Leandro Martínez (Wed Dec 15 2010 - 04:55:59 CST)
  • RE: Asking for some sample PDB and PSF files of carbon nanotube JC Gumbart (Wed Dec 15 2010 - 10:52:32 CST)
  • Re: Asking for some sample PDB and PSF files of carbon nanotube Axel Kohlmeyer (Wed Dec 15 2010 - 10:52:08 CST)
• memory allocation failed on processor 0 matziast_at_med.uth.gr (Wed Dec 15 2010 - 04:07:02 CST)
  • Re: memory allocation failed on processor 0 Axel Kohlmeyer (Wed Dec 15 2010 - 10:40:47 CST)
• Simultaneous FEP simulation of two distinct residues Christian Jorgensen (Tue Dec 14 2010 - 13:44:10 CST)
  • Re: Simultaneous FEP simulation of two distinct residues Jérôme Hénin (Wed Dec 15 2010 - 04:04:47 CST)
• GPU heavy models? Michael Di Domenico (Tue Dec 14 2010 - 08:03:52 CST)
• dissociated quartz SiO2 groups in surface christos.lamprakis_at_dcb.unibe.ch (Tue Dec 14 2010 - 05:39:59 CST)
  • Re: dissociated quartz SiO2 groups in surface Eduardo (Tue Dec 14 2010 - 11:01:13 CST)
• input file for memory optimised version Stefano Pieraccini (Tue Dec 14 2010 - 03:43:12 CST)
• questions about user defined potential in NAMD Chen, Zhihong (chenz2) (Mon Dec 13 2010 - 15:48:47 CST)
  • Re: questions about user defined potential in NAMD felmerino_at_uchile.cl (Mon Dec 13 2010 - 18:23:42 CST)
  • Re: questions about user defined potential in NAMD Axel Kohlmeyer (Tue Dec 14 2010 - 04:10:05 CST)
• How were the output files of the Replica Exchange Method sorted? Guoxiong Su (Sun Dec 12 2010 - 14:11:37 CST)
• Adding extra bond Francesco Oteri (Sun Dec 12 2010 - 04:22:05 CST)
  • Re: Adding extra bond Erik Nordgren (Thu Dec 16 2010 - 13:00:34 CST)
  • Re: Adding extra bond Axel Kohlmeyer (Fri Dec 17 2010 - 04:20:11 CST)
    • Re: Adding extra bond Francesco Oteri (Fri Dec 17 2010 - 05:52:46 CST)
• Problem when using psfgen Christian Jorgensen (Sat Dec 11 2010 - 14:56:06 CST)
  • Re: Problem when using psfgen JC Gumbart (Mon Dec 13 2010 - 13:14:40 CST)
• plotting potential energy Kwee Hong (Thu Dec 09 2010 - 03:37:04 CST)
• ABF questions (Concatenate output files/force constant) Parisa Akhski (Wed Dec 08 2010 - 17:57:40 CST)
  • Re: ABF questions (Concatenate output files/force constant) Jérôme Hénin (Thu Dec 09 2010 - 04:51:14 CST)
• Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ� (Wed Dec 08 2010 - 10:31:16 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Branko (Wed Dec 08 2010 - 11:09:53 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Jérôme Hénin (Wed Dec 08 2010 - 16:16:58 CST)
    • Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ� (Wed Dec 15 2010 - 07:21:54 CST)
      • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Jérôme Hénin (Wed Dec 15 2010 - 09:31:20 CST)
      • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ� (Wed Dec 15 2010 - 10:34:43 CST)
      • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Jérôme Hénin (Wed Dec 15 2010 - 11:07:20 CST)
      • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ� (Thu Dec 16 2010 - 07:04:19 CST)
      • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Jérôme Hénin (Thu Dec 16 2010 - 07:47:42 CST)
    • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ� (Mon Jan 17 2011 - 09:56:28 CST)
      • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Jérôme Hénin (Mon Jan 17 2011 - 11:44:24 CST)
      • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ� (Tue Jan 18 2011 - 08:40:56 CST)
      • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ� (Wed Jan 19 2011 - 06:53:41 CST)
      • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Jérôme Hénin (Wed Jan 19 2011 - 09:23:03 CST)
      • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ� (Wed Jan 19 2011 - 10:01:42 CST)
      • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Jérôme Hénin (Thu Jan 20 2011 - 08:07:36 CST)
• SHAKE convergence property for CUDA and nonCUDA NAMD Jun Zhang (Wed Dec 08 2010 - 06:54:10 CST)
• SHAKE convergence property for CUDA and nonCUDA NAMD Jun Zhang (Wed Dec 08 2010 - 05:59:53 CST)
• Problem of running NAMD Yingzhe Liu (Wed Dec 08 2010 - 04:37:45 CST)
• Free energy perturbation (FEP) hybrid pdb file Christian Jorgensen (Tue Dec 07 2010 - 21:36:31 CST)
  • RE: Free energy perturbation (FEP) hybrid pdb file JC Gumbart (Tue Dec 07 2010 - 23:04:18 CST)
• Problem of running NAMD Yingzhe Liu (Tue Dec 07 2010 - 05:16:35 CST)
• Fwd: Installing NAMD on windows bharat gupta (Sat Dec 04 2010 - 02:07:05 CST)
  • Re: Fwd: Installing NAMD on windows Gianluca Interlandi (Sat Dec 04 2010 - 10:43:34 CST)
    • Re: Fwd: Installing NAMD on windows Branko2 (Sat Dec 04 2010 - 11:25:29 CST)
  • Re: Fwd: Installing NAMD on windows Axel Kohlmeyer (Sat Dec 04 2010 - 13:51:41 CST)
• ABF question Parisa Akhski (Fri Dec 03 2010 - 09:16:07 CST)
  • Re: ABF question Jérôme Hénin (Fri Dec 03 2010 - 10:45:24 CST)
• nodelist file for concurrent execution of 2 nodes Thomas Evangelidis (Fri Dec 03 2010 - 05:08:28 CST)
• NAMD on Shared Memory (Altix UV 1000) Alessandro Cembran (Thu Dec 02 2010 - 18:11:45 CST)
  • Re: NAMD on Shared Memory (Altix UV 1000) Axel Kohlmeyer (Thu Dec 02 2010 - 21:24:44 CST)
• trajectory in temperature from Replica Exchange MD Guoxiong Su (Thu Dec 02 2010 - 13:45:04 CST)
• Lowe-Andersen thermostat Jérôme Hénin (Thu Dec 02 2010 - 09:12:12 CST)
• Output of forces Pletezhov Alexandr (Thu Dec 02 2010 - 06:04:46 CST)
• SMD constant velocity pulling B. Nandy (Thu Dec 02 2010 - 00:21:32 CST)
  • Re: SMD constant velocity pulling Gianluca Interlandi (Thu Dec 02 2010 - 11:30:02 CST)
• Restart, discontinuity of energy juan du (Wed Dec 01 2010 - 09:56:51 CST)
• SMD constant velocity pulling B. Nandy (Wed Dec 01 2010 - 03:51:45 CST)
  • Re: SMD constant velocity pulling Jérôme Hénin (Wed Dec 01 2010 - 05:35:29 CST)
    • Re: SMD constant velocity pulling Gianluca Interlandi (Wed Dec 01 2010 - 10:36:07 CST)
      • Re: SMD constant velocity pulling Jérôme Hénin (Wed Dec 01 2010 - 11:40:25 CST)
    • Re: SMD constant velocity pulling Gianluca Interlandi (Wed Dec 01 2010 - 12:49:50 CST)
      • Re: SMD constant velocity pulling Jérôme Hénin (Wed Dec 01 2010 - 16:55:20 CST)
      • Re: SMD constant velocity pulling Gianluca Interlandi (Wed Dec 01 2010 - 17:22:40 CST)
      • Re: SMD constant velocity pulling B. Nandy (Wed Dec 01 2010 - 23:17:37 CST)
      • Re: SMD constant velocity pulling Gianluca Interlandi (Thu Dec 02 2010 - 01:38:59 CST)
• SMD constant velocity pulling B. Nandy (Wed Dec 01 2010 - 02:51:41 CST)
  • Re: SMD constant velocity pulling Gianluca Interlandi (Wed Dec 01 2010 - 10:33:19 CST)
• Jarzinsky's equation Gianluca Interlandi (Wed Dec 01 2010 - 01:54:57 CST)
  • Re: Jarzinsky's equation Fatemeh Khalili (Thu Dec 02 2010 - 13:54:33 CST)
    • Re: Jarzinsky's equation Gianluca Interlandi (Thu Dec 02 2010 - 14:35:54 CST)
      • Re: Jarzinsky's equation Fatemeh Khalili (Fri Dec 03 2010 - 13:25:31 CST)
      • Re: Jarzinsky's equation Gianluca Interlandi (Fri Dec 03 2010 - 14:08:00 CST)
      • Re: Jarzinsky's equation Fatemeh Khalili (Tue Dec 07 2010 - 12:39:45 CST)
• problem in generating psf file Alex Liu (Tue Nov 30 2010 - 09:12:36 CST)
  • Re: problem in generating psf file Erik Nordgren (Tue Nov 30 2010 - 18:44:33 CST)
• switching function for electrostaic interaction divya nayar (Tue Nov 30 2010 - 10:13:58 CST)
• RBCG dota alexiou (Tue Nov 30 2010 - 02:44:51 CST)
• periodic boundary conditions in namd energy calculation Lan Hua (Mon Nov 29 2010 - 15:52:43 CST)
  • Re: periodic boundary conditions in namd energy calculation Michael S. Sellers (Cont, ARL/WMRD) (Tue Nov 30 2010 - 14:06:09 CST)
    • Re: periodic boundary conditions in namd energy calculation Lan Hua (Tue Nov 30 2010 - 16:04:52 CST)
• Creating a NAMD Shared Library -> Undefined Symbols in Charm libs Michael S. Sellers (Cont, ARL/WMRD) (Mon Nov 29 2010 - 15:22:40 CST)
• Creating a NAMD Shared Library -> Undefined Symbols in Charm libs Michael S. Sellers (Cont, ARL/WMRD) (Mon Nov 29 2010 - 15:07:21 CST)
• wrapping problem Buddhadev Maiti (Mon Nov 29 2010 - 13:41:38 CST)
• CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS Amodeo, Pietro (Fri Nov 26 2010 - 11:21:22 CST)
• Local elevation method in NAMD? Cristina Rodríguez (Thu Nov 25 2010 - 16:54:12 CST)
• crash jp2854_at_columbia.edu (Mon Nov 29 2010 - 11:18:24 CST)
• restart ABF Parisa Akhski (Mon Nov 29 2010 - 10:43:26 CST)
  • Re: restart ABF Jérôme Hénin (Mon Nov 29 2010 - 11:38:29 CST)
• How to set improper dihedral for trans-double bond. Boyang Wang (Mon Nov 29 2010 - 06:15:16 CST)
• pair interaction energy for 2 water molecules divya nayar (Mon Nov 29 2010 - 04:00:14 CST)
  • Re: pair interaction energy for 2 water molecules Axel Kohlmeyer (Mon Nov 29 2010 - 04:56:45 CST)
    • Re: pair interaction energy for 2 water molecules Hugh Heldenbrand (Thu Dec 02 2010 - 20:21:01 CST)
      • Re: pair interaction energy for 2 water molecules Axel Kohlmeyer (Thu Dec 02 2010 - 21:35:23 CST)
• RMSD Question snoze pa (Sun Nov 28 2010 - 11:08:25 CST)
  • Re: vmd-l: RMSD Question Germain Salvato Vallverdu (Mon Nov 29 2010 - 02:56:05 CST)
• Re: pair interaction of water molecules divya nayar (Sun Nov 28 2010 - 08:54:43 CST)
• system density Kwee Hong (Sat Nov 27 2010 - 05:18:19 CST)
  • Re: system density felmerino_at_uchile.cl (Sat Nov 27 2010 - 09:08:28 CST)
    • Re: system density Kwee Hong (Sun Nov 28 2010 - 00:31:17 CST)
      • Re: system density Jeffrey Potoff (Sun Nov 28 2010 - 20:55:33 CST)
• CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS Pietro Amodeo (Fri Nov 26 2010 - 18:07:46 CST)
  • Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly Pietro Amodeo (Mon Dec 27 2010 - 14:01:04 CST)
    • Errata to: Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly Pietro Amodeo (Mon Dec 27 2010 - 14:20:03 CST)
      • Re: Errata to: Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly Axel Kohlmeyer (Tue Dec 28 2010 - 03:46:37 CST)
      • Re: Errata to: Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly Pietro Amodeo (Tue Dec 28 2010 - 05:45:16 CST)
• Local elevation method in NAMD? Cristina Rodríguez (Fri Nov 26 2010 - 12:07:20 CST)
• "GroupPressure no" resulting in negative pressure outputs Sebastian Stolzenberg (Thu Nov 25 2010 - 13:51:13 CST)
  • Re: "GroupPressure no" resulting in negative pressure outputs Jérôme Hénin (Thu Nov 25 2010 - 14:56:08 CST)
    • Re: "GroupPressure no" resulting in negative pressure outputs Sebastian Stolzenberg (Fri Nov 26 2010 - 13:03:56 CST)
      • Re: "GroupPressure no" resulting in negative pressure outputs Jérôme Hénin (Mon Nov 29 2010 - 10:26:16 CST)
      • Re: "GroupPressure no" resulting in negative pressure outputs Sebastian Stolzenberg (Thu Dec 02 2010 - 10:46:45 CST)
• Constant pressure Kwee Hong (Thu Nov 25 2010 - 10:29:29 CST)
  • Re: Constant pressure Sebastian Stolzenberg (Thu Nov 25 2010 - 13:04:51 CST)
    • Re: Constant pressure Kwee Hong (Thu Nov 25 2010 - 13:16:52 CST)
• writing back coordinates of waters that cross the unit cell kakali sen (Thu Nov 25 2010 - 08:29:09 CST)
  • Re: writing back coordinates of waters that cross the unit cell Axel Kohlmeyer (Thu Nov 25 2010 - 09:07:55 CST)
  • Re: writing back coordinates of waters that cross the unit cell Nicholas M Glykos (Thu Nov 25 2010 - 09:53:19 CST)
    • Re: writing back coordinates of waters that cross the unit cell Thomas Evangelidis (Fri Nov 26 2010 - 08:19:19 CST)
      • Re: writing back coordinates of waters that cross the unit cell Axel Kohlmeyer (Fri Nov 26 2010 - 11:26:13 CST)
• subtlety with PSFGEN - angle/dihedral regeneration Erik Nordgren (Wed Nov 24 2010 - 20:55:06 CST)
• Zcoord-1atom for ABF Parisa Akhski (Wed Nov 24 2010 - 16:11:16 CST)
  • Re: Zcoord-1atom for ABF Jérôme Hénin (Thu Nov 25 2010 - 02:42:47 CST)
• Warning about PSF file Alexander Predeus (Wed Nov 24 2010 - 15:27:22 CST)
• reloadCharges command Wendy González (Wed Nov 24 2010 - 13:35:07 CST)
• morse potentials in NAMD revisited Thomas C. Bishop (Wed Nov 24 2010 - 11:29:05 CST)
  • Re: morse potentials in NAMD revisited Axel Kohlmeyer (Wed Nov 24 2010 - 13:05:31 CST)
• ERROR: Atoms moving too fast with RBCG model wenchangyu2006_at_gmail.com (Wed Nov 24 2010 - 10:00:57 CST)
  • Re: ERROR: Atoms moving too fast with RBCG model Jeffrey Potoff (Wed Nov 24 2010 - 15:21:48 CST)
• Restart, RMSD increase juan du (Wed Nov 24 2010 - 08:58:05 CST)
• Restart RMSD increase juan du (Wed Nov 24 2010 - 07:54:45 CST)
  • Restart RMSD increase juan du (Wed Nov 24 2010 - 08:00:49 CST)
• pair interaction of water molecules divya nayar (Wed Nov 24 2010 - 03:41:13 CST)
• Allowed CMAP dimensions Ajasja LjubetiÄ� (Tue Nov 23 2010 - 11:07:33 CST)
  • Re: Allowed CMAP dimensions Ajasja LjubetiÄ� (Fri Nov 26 2010 - 10:23:23 CST)
    • Re: Re: Allowed CMAP dimensions yandong Huang (Tue Dec 28 2010 - 03:39:33 CST)
• Distance Restraint Jacopo Sgrignani (Tue Nov 23 2010 - 10:23:27 CST)
  • Re: Distance Restraint Benjamin Bouvier (Tue Nov 23 2010 - 11:00:45 CST)
  • Re: Distance Restraint Bo Liu (Tue Nov 23 2010 - 11:16:42 CST)
  • Re: Distance Restraint Jérôme Hénin (Tue Nov 23 2010 - 11:27:03 CST)
  • Re: Distance Restraint felmerino_at_uchile.cl (Tue Nov 23 2010 - 13:12:23 CST)
• MOnte carlo simulation Ramya Narasimhan (Tue Nov 23 2010 - 01:04:10 CST)
  • Re: MOnte carlo simulation Jérôme Hénin (Tue Nov 23 2010 - 03:14:31 CST)
• Namd with Amber ff for RNA minimization Irina Tuszynska (Tue Nov 23 2010 - 00:43:56 CST)
  • Re: Namd with Amber ff for RNA minimization Jérôme Hénin (Tue Nov 23 2010 - 02:14:20 CST)
    • Re: Namd with Amber ff for RNA minimization Irina Tuszynska (Tue Nov 23 2010 - 05:29:33 CST)
      • Re: Namd with Amber ff for RNA minimization Hannes Loeffler (Tue Nov 23 2010 - 07:28:26 CST)
      • Re: Namd with Amber ff for RNA minimization Irina Tuszynska (Tue Nov 23 2010 - 09:37:59 CST)
      • namd 2.7 iverbs error 93620 attaching to node Thomas C. Bishop (Tue Nov 23 2010 - 12:11:38 CST)
      • RE: namd 2.7 iverbs error 93620 attaching to node David A. Horita (Fri Dec 03 2010 - 11:42:46 CST)
• Run-time system modification JC S (Mon Nov 22 2010 - 23:38:54 CST)
  • Re: Run-time system modification Jérôme Hénin (Tue Nov 23 2010 - 02:05:39 CST)
    • Re: Run-time system modification Jérôme Hénin (Mon Nov 29 2010 - 06:26:47 CST)
• Different Dielectric constant value for different segment Madhurima Jana (Mon Nov 22 2010 - 07:48:39 CST)
  • Re: Different Dielectric constant value for different segment Axel Kohlmeyer (Mon Nov 22 2010 - 09:07:06 CST)
    • Re: Different Dielectric constant value for different segment Madhurima Jana (Wed Nov 24 2010 - 05:25:06 CST)
• how best to build a GPU-accelerated desktop machine for NAMD? Erik Nordgren (Fri Nov 19 2010 - 20:08:48 CST)
  • Re: how best to build a GPU-accelerated desktop machine for NAMD? Axel Kohlmeyer (Fri Nov 19 2010 - 22:00:38 CST)
• Need help preventing hydration of the lipid-protein interface in my system Maggie Pruitt (Fri Nov 19 2010 - 09:46:45 CST)
• atom type matziast_at_med.uth.gr (Fri Nov 19 2010 - 06:21:47 CST)
  • Re: atom type Chris Harrison (Fri Nov 19 2010 - 06:41:57 CST)
• atom type matziast_at_med.uth.gr (Fri Nov 19 2010 - 05:03:28 CST)
  • Re: atom type Chris Harrison (Fri Nov 19 2010 - 09:39:56 CST)
• TIP4P with NPT Jeffery Klauda (Thu Nov 18 2010 - 12:44:56 CST)
  • Re: TIP4P with NPT Peter Freddolino (Thu Nov 18 2010 - 19:17:03 CST)
    • Re: TIP4P with NPT Peter Freddolino (Fri Nov 19 2010 - 21:50:10 CST)
• Format of namd restartfile *.coor, *.vel) (2nd try ;) ) henri mone (Thu Nov 18 2010 - 10:05:15 CST)
  • Re: Format of namd restartfile *.coor, *.vel) (2nd try ;) ) Joshua D. Moore (Thu Nov 18 2010 - 18:27:22 CST)
• psf of insulin sara (Wed Nov 17 2010 - 10:27:20 CST)
  • Re: psf of insulin ehenriques_at_qui.uc.pt (Thu Nov 18 2010 - 05:08:19 CST)
• Bad Global Exclusion Count Errors in (Relatively) Simple System Jason Richard Mick (Tue Nov 16 2010 - 18:32:49 CST)
  • Re: Bad Global Exclusion Count Errors in (Relatively) Simple System Axel Kohlmeyer (Tue Nov 16 2010 - 21:27:25 CST)
• MD simulations increasing electrostatic potential of a certain residue Wendy González (Tue Nov 16 2010 - 16:35:06 CST)
  • Re: MD simulations increasing electrostatic potential of a certain residue Ajasja LjubetiÄ� (Wed Nov 17 2010 - 02:32:28 CST)
• berendsen thermostat divya nayar (Mon Nov 15 2010 - 08:15:37 CST)
  • Re: berendsen thermostat Axel Kohlmeyer (Mon Nov 15 2010 - 08:56:01 CST)
  • Re: berendsen thermostat Jérôme Hénin (Mon Nov 15 2010 - 09:24:13 CST)
• simulating Acetylated lysine substrate complex SUBHA KALYAANAMOORTHY (Sun Nov 14 2010 - 23:12:11 CST)
• pair interaction calculations dhacademic (Sun Nov 14 2010 - 09:51:40 CST)
  • Re: pair interaction calculations Peter Freddolino (Sun Nov 14 2010 - 11:56:25 CST)
    • Re: pair interaction calculations dhacademic (Sun Nov 14 2010 - 17:42:59 CST)
  • Re: pair interaction calculations Axel Kohlmeyer (Sun Nov 14 2010 - 11:58:19 CST)
• the usage of ++nodelist and ++local jnsong (Sun Nov 14 2010 - 06:25:21 CST)
• VdW parameters for Zn and Fe in metalloproteins Erik Nordgren (Fri Nov 12 2010 - 22:05:33 CST)
  • Re: VdW parameters for Zn and Fe in metalloproteins flavio seixas (Sat Nov 13 2010 - 14:06:59 CST)
    • Re: VdW parameters for Zn and Fe in metalloproteins felmerino_at_uchile.cl (Sat Nov 13 2010 - 18:10:23 CST)
      • Re: VdW parameters for Zn and Fe in metalloproteins felmerino_at_uchile.cl (Sat Nov 13 2010 - 21:55:27 CST)
• Issue with NAMD Not understand avl211_at_lehigh.edu (Fri Nov 12 2010 - 12:29:32 CST)
  • Re: Issue with NAMD Not understand harish vashisth (Fri Nov 12 2010 - 13:57:14 CST)
• Interactive MD driver/controller software no longer in beta Axel Kohlmeyer (Fri Nov 12 2010 - 09:41:59 CST)
• Restart simulation Henri Mone (Thu Nov 11 2010 - 19:54:39 CST)
• Minimization does not converge Christian Jorgensen (Thu Nov 11 2010 - 17:42:42 CST)
  • Re: Minimization does not converge Jeffrey Potoff (Sat Nov 13 2010 - 19:37:37 CST)
• Ions conversion from atomic model to coarse grained model ÖÜÎIJý (Wed Nov 10 2010 - 11:41:41 CST)
• NAMD FEP and GPU TJ Mustard (Tue Nov 09 2010 - 13:26:26 CST)
  • Re: NAMD FEP and GPU JC Gumbart (Tue Nov 09 2010 - 19:01:26 CST)
• Using NAMD for Metropolis Monte Carlo conformational searches Ajasja LjubetiÄ� (Tue Nov 09 2010 - 09:12:29 CST)
  • Re: Using NAMD for Metropolis Monte Carlo conformational searches Axel Kohlmeyer (Tue Nov 09 2010 - 10:06:58 CST)
    • Re: Using NAMD for Metropolis Monte Carlo conformational searches Ajasja LjubetiÄ� (Wed Nov 10 2010 - 04:04:31 CST)
      • Re: Using NAMD for Metropolis Monte Carlo conformational searches Ajasja LjubetiÄ� (Wed Nov 10 2010 - 04:22:53 CST)
      • Re: Using NAMD for Metropolis Monte Carlo conformational searches Axel Kohlmeyer (Wed Nov 10 2010 - 09:10:02 CST)
      • Re: Using NAMD for Metropolis Monte Carlo conformational searches Marc Baaden (Thu Nov 25 2010 - 06:26:43 CST)
• NAMDv2.7 stops producing output in the log-file--any help? harish vashisth (Tue Nov 09 2010 - 08:24:22 CST)
• residue based coarse-grained simulation Demet Akten (Tue Nov 09 2010 - 07:03:05 CST)
  • Re: residue based coarse-grained simulation Hannes Loeffler (Tue Nov 09 2010 - 09:37:18 CST)
  • Re: residue based coarse-grained simulation Joshua Adelman (Tue Nov 09 2010 - 09:51:03 CST)
• Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms Christian Jorgensen (Mon Nov 08 2010 - 16:23:51 CST)
  • Re: Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms felmerino_at_uchile.cl (Tue Nov 09 2010 - 00:38:58 CST)
    • RE: Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms Christian Jorgensen (Tue Nov 09 2010 - 09:42:22 CST)
      • RE: Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms felmerino_at_uchile.cl (Tue Nov 09 2010 - 10:26:55 CST)
• FEP and GPU TJ Mustard (Mon Nov 08 2010 - 15:06:51 CST)
• salt bridge Swarna M Patra (Mon Nov 08 2010 - 02:09:21 CST)
• finding appropriate topology file for polymers masoumeh ozmaeian (Sun Nov 07 2010 - 08:45:23 CST)
  • Re: finding appropriate topology file for polymers Axel Kohlmeyer (Sun Nov 07 2010 - 12:29:28 CST)
• FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR CC NH1 CT1 C NH1 CT1 C NH1 Gurunath Katagi (Sat Nov 06 2010 - 02:41:31 CDT)
• Recover high precision coordinates from binary .coor file Rajan Vatassery (Fri Nov 05 2010 - 19:37:48 CDT)
  • Re: Recover high precision coordinates from binary .coor file Nicholas M Glykos (Sat Nov 06 2010 - 06:30:01 CDT)
    • Re: Recover high precision coordinates from binary .coor file Rajan Vatassery (Wed Dec 08 2010 - 15:15:56 CST)
• Issue with Load Balancing Al-Ali, Hassan (Fri Nov 05 2010 - 10:15:52 CDT)
• NAMD OPLS Parameters Soran (Thu Nov 04 2010 - 16:57:56 CDT)
• Question for Developers: NAMD 2.7 performance issues and Questions about Compiling harish vashisth (Thu Nov 04 2010 - 05:43:49 CDT)
• Release of R.E.D. Server 2.0 FyD (Thu Nov 04 2010 - 04:50:36 CDT)
• about Hydrogen Bond correlation function Jun Zhang (Thu Nov 04 2010 - 00:55:28 CDT)
  • Re: about Hydrogen Bond correlation function Chris Harrison (Thu Nov 04 2010 - 06:49:40 CDT)
    • Re: about Hydrogen Bond correlation function Hannes Loeffler (Thu Nov 04 2010 - 08:42:59 CDT)
    • Re: about Hydrogen Bond correlation function Jun Zhang (Sat Nov 06 2010 - 23:24:02 CDT)
  • Re: about Hydrogen Bond correlation function Hannes Loeffler (Thu Nov 04 2010 - 08:11:16 CDT)
    • Re: about Hydrogen Bond correlation function Axel Kohlmeyer (Thu Nov 04 2010 - 08:59:45 CDT)
• NAMD 2.7 performance issues and Questions about Compiling David Lee Braun (Wed Nov 03 2010 - 15:27:58 CDT)
• Re: vmd-l: Asymmetric water molecule Jérôme Hénin (Wed Nov 03 2010 - 05:03:40 CDT)
  • Re: Re: vmd-l: Asymmetric water molecule Chris Harrison (Wed Nov 03 2010 - 06:02:40 CDT)
• problems with temperature control Pegah Khalili (Wed Nov 03 2010 - 04:35:50 CDT)
• problems with temperature control Pegah Khalili (Wed Nov 03 2010 - 04:28:59 CDT)
  • Re: problems with temperature control Peter Freddolino (Wed Nov 03 2010 - 19:58:06 CDT)
• Error in configuration file Christian Jorgensen (Tue Nov 02 2010 - 11:33:12 CDT)
  • Re: Error in configuration file JC Gumbart (Tue Nov 02 2010 - 11:46:34 CDT)
• Missing angle parameters CT3 CT3 CT3 Christian Jorgensen (Mon Nov 01 2010 - 18:12:06 CDT)
  • Re: Missing angle parameters CT3 CT3 CT3 JC Gumbart (Mon Nov 01 2010 - 18:52:17 CDT)
  • Re: Missing angle parameters CT3 CT3 CT3 felmerino_at_uchile.cl (Mon Nov 01 2010 - 20:50:45 CDT)
  • Re: Missing angle parameters CT3 CT3 CT3 Markus K. Dahlgren (Tue Nov 02 2010 - 07:38:08 CDT)
• MINIMIZER SLOWLY MOVING 810 ATOMS WITH BAD CONTACTS DOWNHILL nishtha mishra (Sat Oct 30 2010 - 08:40:36 CDT)
  • Re: MINIMIZER SLOWLY MOVING 810 ATOMS WITH BAD CONTACTS DOWNHILL Chris Harrison (Mon Nov 01 2010 - 13:26:21 CDT)
• namd install ipsita basu (Mon Nov 01 2010 - 05:53:21 CDT)
  • Re: namd install Chris Harrison (Mon Nov 01 2010 - 13:20:56 CDT)
• rmsd divya nayar (Mon Nov 01 2010 - 03:30:11 CDT)
  • Re: rmsd Chris Harrison (Mon Nov 01 2010 - 13:23:36 CDT)
• MINIMIZER SLOWLY MOVING 810 ATOMS WITH BAD CONTACTS DOWNHILL nishtha.mishra (Mon Nov 01 2010 - 02:27:18 CDT)
• MINIMIZER SLOWLY MOVING 810 ATOMS WITH BAD CONTACTS DOWNHILL nishtha.mishra (Mon Nov 01 2010 - 02:18:06 CDT)
• Radius of gyration Dhanashree Khanale (Sat Oct 30 2010 - 08:43:22 CDT)
  • Re: Radius of gyration Ajasja LjubetiÄ� (Sat Oct 30 2010 - 15:57:33 CDT)
    • Re: Radius of gyration Jérôme Hénin (Sun Oct 31 2010 - 04:22:25 CDT)
• H-bond and salt bridge between protein dimer surendra jain (Sat Oct 30 2010 - 07:17:55 CDT)
  • Re: H-bond and salt bridge between protein dimer Eduard Schreiner (Sat Oct 30 2010 - 08:31:02 CDT)
• script for calculation of an rmsd matziast_at_med.uth.gr (Sat Oct 30 2010 - 03:41:41 CDT)
  • Re: script for calculation of an rmsd Branko (Sat Oct 30 2010 - 07:09:44 CDT)
  • Re: script for calculation of an rmsd Chris Harrison (Sun Oct 31 2010 - 08:28:58 CDT)
• How to generate the tcouple file for NAMD runs? a a (Fri Oct 29 2010 - 22:45:42 CDT)
  • Re: How to generate the tcouple file for NAMD runs? Chris Harrison (Sun Oct 31 2010 - 08:23:46 CDT)
• extending namd / shared library build (UNCLASSIFIED) Sellers, Michael S. (Cont, ARL/WMRD) (Fri Oct 29 2010 - 08:23:41 CDT)
  • Re: extending namd / shared library build (UNCLASSIFIED) Jim Phillips (Mon Nov 01 2010 - 15:05:07 CDT)
    • Re: extending namd / shared library build (UNCLASSIFIED) Ajasja LjubetiÄ� (Tue Nov 09 2010 - 08:39:47 CST)
• NANMA free energy surface vacuum map problems Carles Corbi Verge (Fri Oct 29 2010 - 08:03:54 CDT)
  • Re: NANMA free energy surface vacuum map problems Jérôme Hénin (Fri Oct 29 2010 - 09:33:37 CDT)
    • Re: NANMA free energy surface vacuum map problems Carles Corbi Verge (Mon Nov 01 2010 - 06:16:36 CDT)
      • Re: NANMA free energy surface vacuum map problems JC Gumbart (Mon Nov 01 2010 - 20:33:14 CDT)
      • Re: NANMA free energy surface vacuum map problems Jérôme Hénin (Tue Nov 02 2010 - 05:40:08 CDT)
      • RE: NANMA free energy surface vacuum map problems JC Gumbart (Tue Nov 02 2010 - 07:23:30 CDT)
      • Re: NANMA free energy surface vacuum map problems Jérôme Hénin (Tue Nov 02 2010 - 08:18:30 CDT)
      • Re: NANMA free energy surface vacuum map problems Carles Corbi Verge (Thu Nov 04 2010 - 09:37:34 CDT)
• Constraint failure in RATTLE algorithm for atom 268 Ajasja LjubetiÄ� (Fri Oct 29 2010 - 05:46:16 CDT)
• Constraint failure in RATTLE algorithm for atom 268 surendra jain (Fri Oct 29 2010 - 04:54:38 CDT)
• questions about ABF simulations mjyang (Thu Oct 28 2010 - 13:26:59 CDT)
  • Re: questions about ABF simulations Jérôme Hénin (Thu Oct 28 2010 - 14:37:29 CDT)
  • Re: questions about ABF simulations Giacomo Fiorin (Thu Oct 28 2010 - 15:33:19 CDT)
    • RE: questions about ABF simulations mjyang (Mon Nov 01 2010 - 09:49:17 CDT)
      • Re: questions about ABF simulations Jérôme Hénin (Wed Nov 03 2010 - 05:51:48 CDT)
• Force field for replica Xiang Yu (Thu Oct 28 2010 - 09:12:25 CDT)
  • Re: Force field for replica Chris Harrison (Sun Oct 31 2010 - 08:47:09 CDT)
• force field for replica exchange with NAMD Xiang Yu (Wed Oct 27 2010 - 23:06:32 CDT)
  • Re: force field for replica exchange with NAMD Jim Phillips (Thu Oct 28 2010 - 14:18:46 CDT)
    • RE: force field for replica exchange with NAMD ÓáÏè (Thu Oct 28 2010 - 15:40:52 CDT)
      • Re: force field for replica exchange with NAMD Alexander Predeus (Thu Oct 28 2010 - 16:15:05 CDT)
      • Re: force field for replica exchange with NAMD S¨¢ndor Kov¨¢cs (Thu Oct 28 2010 - 17:47:21 CDT)
      • Re: force field for replica exchange with NAMD ä¿žç¿” (Thu Oct 28 2010 - 17:56:58 CDT)
• Enthalpy calculation divya nayar (Thu Oct 28 2010 - 10:12:00 CDT)
  • Re: Enthalpy calculation Jérôme Hénin (Thu Oct 28 2010 - 11:58:00 CDT)
• Least squares fitting of frames of trajectory divya nayar (Wed Oct 27 2010 - 23:01:29 CDT)
  • Re: Least squares fitting of frames of trajectory Nicholas Musolino (Thu Oct 28 2010 - 08:14:39 CDT)
• Charmrun: error on request socket-- Kwee Hong (Wed Oct 27 2010 - 12:08:11 CDT)
  • Re: Charmrun: error on request socket-- Kwee Hong (Wed Oct 27 2010 - 21:01:33 CDT)
  • Re: Charmrun: error on request socket-- Jim Phillips (Thu Oct 28 2010 - 14:14:28 CDT)
    • Re: Charmrun: error on request socket-- Kwee Hong (Thu Oct 28 2010 - 22:05:27 CDT)
• build nanoparticle sara (Wed Oct 27 2010 - 11:10:58 CDT)
  • Re: build nanoparticle Nicholas Musolino (Wed Oct 27 2010 - 13:25:57 CDT)
• Symmetry in NAMD, how to achieve during a MD simulation? Wendy González (Wed Oct 27 2010 - 10:46:03 CDT)
  • Re: Symmetry in NAMD, how to achieve during a MD simulation? JC Gumbart (Wed Oct 27 2010 - 18:37:35 CDT)
• global and internal motion of protein divya nayar (Wed Oct 27 2010 - 02:39:04 CDT)
  • Re: global and internal motion of protein Ajasja LjubetiÄ� (Wed Oct 27 2010 - 03:12:08 CDT)
  • Re: global and internal motion of protein Nicholas M Glykos (Wed Oct 27 2010 - 04:43:08 CDT)
• minimization problem ipsita basu (Wed Oct 27 2010 - 01:00:23 CDT)
  • Fwd: minimization problem ipsita basu (Fri Oct 29 2010 - 00:25:58 CDT)
  • Re: minimization problem Chris Harrison (Sun Oct 31 2010 - 08:43:45 CDT)
• protein fixed in simulation divya nayar (Wed Oct 27 2010 - 00:53:56 CDT)
  • Re: protein fixed in simulation Ajasja LjubetiÄ� (Wed Oct 27 2010 - 02:31:11 CDT)
  • RE: protein fixed in simulation Ada Zhan (Wed Oct 27 2010 - 18:04:55 CDT)
• error compiling charm-6.2.2 for bluegenep-xlc hannes.loeffler_at_stfc.ac.uk (Tue Oct 26 2010 - 14:22:50 CDT)
  • Re: [ppl] error compiling charm-6.2.2 for bluegenep-xlc Phil Miller (Wed Oct 27 2010 - 23:14:34 CDT)
    • Re: [ppl] error compiling charm-6.2.2 for bluegenep-xlc Hannes Loeffler (Thu Oct 28 2010 - 04:18:33 CDT)
• coordinate not the same between the input and frame 0 Kwee Hong (Tue Oct 26 2010 - 03:27:25 CDT)
  • Re: coordinate not the same between the input and frame 0 Nicholas M Glykos (Tue Oct 26 2010 - 05:10:29 CDT)
  • Re: coordinate not the same between the input and frame 0 Kwee Hong (Tue Oct 26 2010 - 05:06:22 CDT)
• a question about modifying the NAMD input file ying yu (Mon Oct 25 2010 - 12:06:50 CDT)
  • Re: a question about modifying the NAMD input file Axel Kohlmeyer (Mon Oct 25 2010 - 12:56:36 CDT)
• Warning: Bad global exclusion count, possible error! Kwee Hong (Sun Oct 24 2010 - 22:07:39 CDT)
  • Re: Warning: Bad global exclusion count, possible error! Jim Phillips (Mon Oct 25 2010 - 13:21:03 CDT)
• getting desired angle Kwee Hong (Sat Oct 23 2010 - 03:49:23 CDT)
  • Re: getting desired angle Axel Kohlmeyer (Sun Oct 24 2010 - 18:06:00 CDT)
    • Re: getting desired angle Kwee Hong (Sun Oct 24 2010 - 22:06:33 CDT)
      • Re: getting desired angle Axel Kohlmeyer (Mon Oct 25 2010 - 08:08:30 CDT)
• NAMD with missing residues snoze pa (Fri Oct 22 2010 - 15:46:34 CDT)
  • Re: NAMD with missing residues Francesco Oteri (Fri Oct 22 2010 - 16:33:12 CDT)
  • Re: NAMD with missing residues Axel Kohlmeyer (Sun Oct 24 2010 - 18:10:13 CDT)
    • Re: NAMD with missing residues snoze pa (Wed Oct 27 2010 - 09:27:06 CDT)
• potential functions in NAMD oguz gurbulak (Fri Oct 22 2010 - 04:22:45 CDT)
  • Re: potential functions in NAMD Jim Phillips (Mon Oct 25 2010 - 13:24:38 CDT)
• Strange vdw_dU/dl values in thermodynamic integration Hugh Heldenbrand (Thu Oct 21 2010 - 19:37:25 CDT)
  • Re: Strange vdw_dU/dl values in thermodynamic integration Floris Buelens (Fri Oct 22 2010 - 01:36:45 CDT)
    • Re: Strange vdw_dU/dl values in thermodynamic integration Hugh Heldenbrand (Fri Oct 22 2010 - 07:28:05 CDT)
    • Re: Strange vdw_dU/dl values in thermodynamic integration Floris Buelens (Tue Oct 26 2010 - 01:23:47 CDT)
• Cube vs. Truncated Octahedron Performance Alexander Predeus (Thu Oct 21 2010 - 17:04:42 CDT)
  • Re: Cube vs. Truncated Octahedron Performance Axel Kohlmeyer (Thu Oct 21 2010 - 18:02:20 CDT)
  • Electrostatic Potential Problems, WRT Minimizations Rajan Vatassery (Thu Oct 21 2010 - 21:34:23 CDT)
• Relaxed dihedral scans (or how to constrain a dihedral angle to a changing value). Ajasja LjubetiÄ� (Thu Oct 21 2010 - 08:45:43 CDT)
  • Re: Relaxed dihedral scans (or how to constrain a dihedral angle to a changing value). Jim Phillips (Fri Oct 22 2010 - 10:30:59 CDT)
    • Re: Relaxed dihedral scans (or how to constrain a dihedral angle to a changing value). Ajasja LjubetiÄ� (Mon Oct 25 2010 - 02:18:07 CDT)
• Enhance electrostatic interactions? Wendy González (Thu Oct 21 2010 - 07:32:46 CDT)
  • Re: Enhance electrostatic interactions? daniel aguayo (Fri Oct 22 2010 - 16:34:19 CDT)
• Angle in parameter file Christian Jorgensen (Thu Oct 21 2010 - 06:08:03 CDT)
  • Re: Angle in parameter file Ajasja LjubetiÄ� (Thu Oct 21 2010 - 07:13:17 CDT)
• the storage format of the coordinate binary file in NAMD jnsong (Thu Oct 21 2010 - 03:55:27 CDT)
  • Re: the storage format of the coordinate binary file in NAMD Jérôme Hénin (Thu Oct 21 2010 - 05:06:36 CDT)
• how to cenvert NAMD binary coordinate file to text file jnsong (Thu Oct 21 2010 - 02:27:06 CDT)
  • Re: how to cenvert NAMD binary coordinate file to text file OiniL (Thu Oct 21 2010 - 03:15:16 CDT)
    • Re: how to cenvert NAMD binary coordinate file to text file jnsong (Thu Oct 21 2010 - 03:34:11 CDT)
  • Re: how to cenvert NAMD binary coordinate file to text file Ajasja LjubetiÄ� (Thu Oct 21 2010 - 03:24:19 CDT)
    • Re: how to cenvert NAMD binary coordinate file to text file jnsong (Thu Oct 21 2010 - 03:40:42 CDT)
  • Re: how to cenvert NAMD binary coordinate file to text file Hannes Loeffler (Thu Oct 21 2010 - 04:48:59 CDT)
• Re:Re: Incorrect Atom Count in binary file Ada Zhan (Wed Oct 20 2010 - 14:20:08 CDT)
• ligand parameters grazia cottone (Wed Oct 20 2010 - 06:43:23 CDT)
• psfgen gives wrong psf file Christian Jorgensen (Wed Oct 20 2010 - 04:32:56 CDT)
  • Re: psfgen gives wrong psf file ehenriques_at_qui.uc.pt (Wed Oct 20 2010 - 08:51:16 CDT)
• error codes: 255 hgrabner (Wed Oct 20 2010 - 03:57:07 CDT)
  • Re: error codes: 255 Jim Phillips (Wed Oct 20 2010 - 14:35:05 CDT)
• PME Kappa and Non-bonded Cutoff Alexander Predeus (Tue Oct 19 2010 - 18:20:12 CDT)
• NAMD 2.7 released Jim Phillips (Tue Oct 19 2010 - 14:57:57 CDT)
  • Re: NAMD 2.7 released Gianluca Interlandi (Tue Oct 19 2010 - 20:26:03 CDT)
    • Re: NAMD 2.7 released Jim Phillips (Wed Oct 20 2010 - 14:47:28 CDT)
      • Re: NAMD 2.7 released Gianluca Interlandi (Wed Oct 20 2010 - 15:33:33 CDT)
      • Re: NAMD 2.7 released Gianluca Interlandi (Thu Mar 17 2011 - 17:58:46 CDT)
• Tcl script in NAMD divya nayar (Tue Oct 19 2010 - 08:21:48 CDT)
  • Re: Tcl script in NAMD Jim Phillips (Tue Oct 19 2010 - 11:49:16 CDT)
• Amber topology in CUDA NAMD - can it be done? Benjamin Bouvier (Tue Oct 19 2010 - 07:27:48 CDT)
  • Re: Amber topology in CUDA NAMD - can it be done? Axel Kohlmeyer (Tue Oct 19 2010 - 08:32:45 CDT)
    • Re: Amber topology in CUDA NAMD - can it be done? Axel Kohlmeyer (Tue Oct 19 2010 - 08:42:15 CDT)
      • Re: Amber topology in CUDA NAMD - can it be done? Jim Phillips (Tue Oct 19 2010 - 11:43:10 CDT)
• Changing functions without recompiling Cole Gleason (Mon Oct 18 2010 - 16:53:32 CDT)
  • Re: Changing functions without recompiling Axel Kohlmeyer (Mon Oct 18 2010 - 17:39:28 CDT)
    • Re: Changing functions without recompiling Joshua Adelman (Mon Oct 18 2010 - 20:42:42 CDT)
      • Re: Changing functions without recompiling Cole Gleason (Mon Oct 18 2010 - 21:27:27 CDT)
    • Re: Changing functions without recompiling Cole Gleason (Tue Oct 19 2010 - 13:53:17 CDT)
  • Re: Changing functions without recompiling Nicholas Musolino (Mon Oct 18 2010 - 20:20:58 CDT)
    • Re: Changing functions without recompiling Cole Gleason (Mon Oct 18 2010 - 21:24:01 CDT)
      • Re: Changing functions without recompiling Axel Kohlmeyer (Mon Oct 18 2010 - 22:12:10 CDT)
  • Re: Changing functions without recompiling Jim Phillips (Tue Oct 19 2010 - 11:56:40 CDT)
• rotation question jp d (Mon Oct 18 2010 - 16:35:55 CDT)
• Denied permission on dcd file preventing simulation Christian Jorgensen (Mon Oct 18 2010 - 09:32:07 CDT)
  • Re: Denied permission on dcd file preventing simulation Axel Kohlmeyer (Mon Oct 18 2010 - 10:06:45 CDT)
  • Re: Denied permission on dcd file preventing simulation Jim Phillips (Mon Oct 18 2010 - 11:40:28 CDT)
• High RMSD of Coarse grain Protein sunita gupta (Mon Oct 18 2010 - 06:52:18 CDT)
  • Re: High RMSD of Coarse grain Protein Hannes Loeffler (Mon Oct 18 2010 - 09:01:20 CDT)
• CHARMM Lorentz-berthelot mixing rules divya nayar (Mon Oct 18 2010 - 05:21:52 CDT)
  • Re: CHARMM Lorentz-berthelot mixing rules Jim Phillips (Mon Oct 18 2010 - 11:38:12 CDT)
• expansion of solvation box at high temperature mjyang (Sun Oct 17 2010 - 04:41:25 CDT)
• top file for CNT sara (Sun Oct 17 2010 - 03:10:13 CDT)
  • Re: top file for CNT Axel Kohlmeyer (Sun Oct 17 2010 - 13:49:44 CDT)
• expansion of solvation box at high temperature mjyang (Sun Oct 17 2010 - 02:03:31 CDT)
  • Re: expansion of solvation box at high temperature Nicholas Musolino (Sun Oct 17 2010 - 08:29:06 CDT)
    • RE: expansion of solvation box at high temperature mjyang (Sun Oct 17 2010 - 10:18:26 CDT)
      • Re: expansion of solvation box at high temperature Nicholas Musolino (Sun Oct 17 2010 - 10:27:40 CDT)
      • RE: expansion of solvation box at high temperature mjyang (Sun Oct 17 2010 - 10:56:15 CDT)
      • Re: expansion of solvation box at high temperature Jeffrey Potoff (Sun Oct 17 2010 - 11:44:53 CDT)
      • Re: expansion of solvation box at high temperature Joshua Adelman (Sun Oct 17 2010 - 12:25:19 CDT)
      • RE: expansion of solvation box at high temperature Jim Phillips (Mon Oct 18 2010 - 11:32:18 CDT)
      • RE: expansion of solvation box at high temperature mjyang (Mon Oct 18 2010 - 22:31:13 CDT)
• Re: hexane Jian Liu (Sat Oct 16 2010 - 20:32:09 CDT)
  • Re: hexane lara lara (Sun Oct 17 2010 - 23:29:53 CDT)
    • Re: Re: hexane Jian Liu (Sun Oct 17 2010 - 23:10:34 CDT)
• hexane lara lara (Sat Oct 16 2010 - 04:00:09 CDT)
  • Importance of the Topology File, .rtf, and Other Files Rajan Vatassery (Sat Oct 16 2010 - 13:57:10 CDT)
    • Distribute Points Evenly on Surface of a Sphere Rajan Vatassery (Mon Oct 18 2010 - 13:57:53 CDT)
• Conjugate gradient reference Philip Peartree (Fri Oct 15 2010 - 10:33:16 CDT)
  • Re: Conjugate gradient reference Athanassios Stavrakoudis (Fri Oct 15 2010 - 11:24:58 CDT)
• change force field in NAMD Chen, Zhihong (chenz2) (Fri Oct 15 2010 - 09:51:04 CDT)
  • Re: change force field in NAMD Axel Kohlmeyer (Fri Oct 15 2010 - 10:58:33 CDT)
• change force field in NAMD Chen, Zhihong (chenz2) (Fri Oct 15 2010 - 09:50:14 CDT)
  • Re: change force field in NAMD Erik Santiso (Fri Oct 15 2010 - 15:30:04 CDT)
  • I can patch namd for amber ff on GPU Francesco Oteri (Sun Oct 17 2010 - 21:50:58 CDT)
• tmd log file matziast_at_med.uth.gr (Fri Oct 15 2010 - 06:35:37 CDT)
  • Re: tmd log file Ajasja LjubetiÄ� (Fri Oct 15 2010 - 07:24:59 CDT)
• script for targeted molecular dynamics matziast_at_med.uth.gr (Fri Oct 15 2010 - 03:15:20 CDT)
• targeted molecular dynamics matziast_at_med.uth.gr (Thu Oct 14 2010 - 17:22:30 CDT)
  • Re: targeted molecular dynamics Chris Harrison (Thu Oct 14 2010 - 17:28:22 CDT)
• Restraint on XY Plane Peixi Zhu (Thu Oct 14 2010 - 16:12:30 CDT)
  • Re: Restraint on XY Plane Peixi Zhu (Fri Oct 15 2010 - 00:33:38 CDT)
    • Re: Restraint on XY Plane Giacomo Fiorin (Fri Oct 15 2010 - 10:39:24 CDT)
      • Re: Restraint on XY Plane Peixi Zhu (Fri Oct 15 2010 - 11:24:26 CDT)
• Assigning partial charges in topology file Christian Jorgensen (Thu Oct 14 2010 - 13:57:30 CDT)
• Restart MD from a certain point? Wendy González (Thu Oct 14 2010 - 07:45:48 CDT)
  • Re: Restart MD from a certain point? Axel Kohlmeyer (Thu Oct 14 2010 - 09:04:49 CDT)
    • Re: Restart MD from a certain point? Andreas Förster (Thu Oct 14 2010 - 10:50:14 CDT)
      • Re: Restart MD from a certain point? Wendy González (Thu Oct 21 2010 - 07:22:24 CDT)
• simulation time instead of frames Kwee Hong (Thu Oct 14 2010 - 06:05:47 CDT)
  • Re: simulation time instead of frames Francesco Oteri (Thu Oct 14 2010 - 07:12:33 CDT)
• Namd using Charmm restart files Courtney Taylor (Wed Oct 13 2010 - 16:55:00 CDT)
  • Re: Namd using Charmm restart files Ajasja LjubetiÄ� (Thu Oct 14 2010 - 02:31:41 CDT)
    • Re: Namd using Charmm restart files Courtney Taylor (Thu Oct 14 2010 - 10:09:34 CDT)
      • Re: Namd using Charmm restart files Jim Phillips (Thu Oct 14 2010 - 14:28:09 CDT)
      • Re: Namd using Charmm restart files Werner Crous (Fri Oct 15 2010 - 08:55:56 CDT)
      • Re: Namd using Charmm restart files Courtney Taylor (Fri Oct 15 2010 - 11:55:53 CDT)
• High RMSD in Coarse Grain Simulation of Protein sunita gupta (Wed Oct 13 2010 - 03:06:22 CDT)
• unsubscribe Katherine Parra (Tue Oct 12 2010 - 16:58:06 CDT)
  • unsubscribe Ibrahim Abou Hamad (Tue Oct 12 2010 - 18:21:20 CDT)
• Modification of Colvar Module Components Alexander Predeus (Tue Oct 12 2010 - 15:44:20 CDT)
  • Re: Modification of Colvar Module Components Jérôme Hénin (Wed Oct 13 2010 - 02:24:55 CDT)
• Langevin process in NAMD tutorial yi jiang (Mon Oct 11 2010 - 11:14:22 CDT)
  • Re: Langevin process in NAMD tutorial Axel Kohlmeyer (Mon Oct 11 2010 - 12:21:04 CDT)
    • Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Basak Isin (Mon Oct 11 2010 - 14:56:17 CDT)
      • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Axel Kohlmeyer (Mon Oct 11 2010 - 15:16:21 CDT)
      • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Basak Isin (Mon Oct 11 2010 - 15:44:42 CDT)
      • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Gianluca Interlandi (Mon Oct 11 2010 - 16:56:03 CDT)
      • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Basak Isin (Mon Oct 11 2010 - 18:11:14 CDT)
      • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Axel Kohlmeyer (Mon Oct 11 2010 - 18:54:28 CDT)
      • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial yi jiang (Mon Oct 11 2010 - 20:42:05 CDT)
      • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Jim Phillips (Wed Oct 13 2010 - 09:46:57 CDT)
• 2 Stray PME grid charges detected possible bug 2.7b2 Branko (Sun Oct 10 2010 - 11:12:09 CDT)
  • Re: 2 Stray PME grid charges detected possible bug 2.7b2 Jim Phillips (Wed Oct 13 2010 - 09:33:24 CDT)
• Stray PME grid charges detected possible bug 2.7b2 Branko (Sun Oct 10 2010 - 10:54:11 CDT)
  • Re: Stray PME grid charges detected possible bug 2.7b2 Branko (Sun Oct 10 2010 - 11:23:41 CDT)
• Comparision of GPU and multi-CPUs version of NAMD Jianing Song (Sun Oct 10 2010 - 09:51:54 CDT)
• how to improve the occupation of GPU with NAMD-2.7b3-CUDA Jianing Song (Sun Oct 10 2010 - 09:43:58 CDT)
  • Re: how to improve the occupation of GPU with NAMD-2.7b3-CUDA Axel Kohlmeyer (Mon Oct 11 2010 - 08:55:41 CDT)
    • Re: how to improve the occupation of GPU with NAMD-2.7b3-CUDA Axel Kohlmeyer (Mon Oct 11 2010 - 22:09:15 CDT)
      • RE: how to improve the occupation of GPU with NAMD-2.7b3-CUDA Jianing Song (Wed Oct 13 2010 - 20:45:59 CDT)
• unsubscribe Asmita Gupta (Fri Oct 08 2010 - 10:56:18 CDT)
• Re: problem caused by cluster? Jim Phillips (Fri Oct 08 2010 - 08:34:23 CDT)
• (no subject) ipsita basu (Fri Oct 08 2010 - 06:00:41 CDT)
• Flushing memory into output file Parisa Akhski (Thu Oct 07 2010 - 11:58:46 CDT)
  • Re: Flushing memory into output file Axel Kohlmeyer (Thu Oct 07 2010 - 12:42:50 CDT)
  • Re: Flushing memory into output file Nicholas M Glykos (Thu Oct 07 2010 - 14:39:25 CDT)
    • Re: Flushing memory into output file Axel Kohlmeyer (Thu Oct 07 2010 - 16:30:44 CDT)
      • Re: Flushing memory into output file Jim Phillips (Thu Oct 07 2010 - 17:06:26 CDT)
      • RE: Flushing memory into output file Parisa Akhski (Fri Oct 08 2010 - 09:04:37 CDT)
• change force field in NAMD Chen, Zhihong (chenz2) (Thu Oct 07 2010 - 09:49:45 CDT)
• Alchemical FEP tutorial files Christian Jorgensen (Thu Oct 07 2010 - 06:55:09 CDT)
  • Re: Alchemical FEP tutorial files Chris Harrison (Thu Oct 07 2010 - 07:23:24 CDT)
    • RE: Alchemical FEP tutorial files JC Gumbart (Thu Oct 07 2010 - 07:36:13 CDT)
      • RE: Alchemical FEP tutorial files Christian Jorgensen (Thu Oct 07 2010 - 09:35:31 CDT)
• Carma v.1.0 released. Nicholas M Glykos (Wed Oct 06 2010 - 06:14:15 CDT)
• Is the DCD file size consistent for consecutive runs? Bjoern Olausson (Wed Oct 06 2010 - 03:36:04 CDT)
  • Re: Is the DCD file size consistent for consecutive runs? Bjoern Olausson (Thu Oct 07 2010 - 06:40:17 CDT)
    • Re: Is the DCD file size consistent for consecutive runs? Axel Kohlmeyer (Thu Oct 07 2010 - 10:07:53 CDT)
    • Re: Is the DCD file size consistent for consecutive runs? Bjoern Olausson (Fri Oct 08 2010 - 04:27:54 CDT)
      • Re: Is the DCD file size consistent for consecutive runs? Jim Phillips (Fri Oct 08 2010 - 09:21:52 CDT)
    • Re: Is the DCD file size consistent for consecutive runs? Bjoern Olausson (Fri Oct 08 2010 - 11:30:36 CDT)
• ADENOSINE-5-DIPHOSPHORIBOSE topology Raul Araya (Tue Oct 05 2010 - 20:56:42 CDT)
  • Re: ADENOSINE-5-DIPHOSPHORIBOSE topology Eduard Schreiner (Tue Oct 05 2010 - 22:11:50 CDT)
• problem caused by cluster? Kwee Hong (Tue Oct 05 2010 - 20:17:50 CDT)
• Minimization problem on cluster Swarna M Patra (Mon Oct 04 2010 - 23:09:07 CDT)
  • Minimization problem on cluster Swarna M Patra (Mon Oct 04 2010 - 23:11:41 CDT)
• change force field in NAMD Chen, Zhihong (chenz2) (Mon Oct 04 2010 - 14:11:11 CDT)
  • Re: change force field in NAMD Jérôme Hénin (Tue Oct 05 2010 - 03:38:27 CDT)
    • Re: change force field in NAMD Erik Santiso (Fri Oct 22 2010 - 11:05:50 CDT)
• unable to open binary file Kwee Hong (Mon Oct 04 2010 - 09:00:10 CDT)
  • Re: unable to open binary file Axel Kohlmeyer (Mon Oct 04 2010 - 10:03:32 CDT)
    • Re: unable to open binary file Kwee Hong (Mon Oct 04 2010 - 22:55:00 CDT)
      • Re: unable to open binary file Kwee Hong (Tue Oct 26 2010 - 01:26:10 CDT)
• NAMD installation Hasan haska (Mon Oct 04 2010 - 05:25:06 CDT)
  • Re: NAMD installation Axel Kohlmeyer (Mon Oct 04 2010 - 10:04:58 CDT)
• Check out my photos on Facebook Kalyan Pulipaka (Sat Oct 02 2010 - 21:57:26 CDT)
• How to restraint angle in NAMD George Khelashvili (Fri Oct 01 2010 - 21:32:29 CDT)
• Fermi NVidia jose correa (Thu Sep 30 2010 - 09:13:47 CDT)
  • Re: Fermi NVidia Jim Phillips (Thu Oct 07 2010 - 15:36:47 CDT)
• NAMD and Gromacs oguz gurbulak (Thu Sep 30 2010 - 06:36:51 CDT)
  • Re: NAMD and Gromacs Francesco Oteri (Thu Sep 30 2010 - 07:55:48 CDT)
    • Re: NAMD and Gromacs Hannes Loeffler (Thu Sep 30 2010 - 10:26:56 CDT)
      • Re: NAMD and Gromacs oguz gurbulak (Thu Sep 30 2010 - 16:06:46 CDT)
      • Re: NAMD and Gromacs BIN ZHANG (Thu Sep 30 2010 - 17:02:04 CDT)
• FFTW and NAMD problems during compiling on BluegeneL I. Vyalov (Wed Sep 29 2010 - 05:00:55 CDT)
  • Re: FFTW and NAMD problems during compiling on BluegeneL Axel Kohlmeyer (Wed Sep 29 2010 - 05:52:15 CDT)
• (âÅÚ ÔÅÍÙ) I. Vyalov (Wed Sep 29 2010 - 04:46:48 CDT)
• Re: How to analysis RAMD data? Vlad Cojocaru (Wed Sep 29 2010 - 02:26:28 CDT)
• How to analysis RAMD data? asknamd asknamd (Tue Sep 28 2010 - 13:43:33 CDT)
• Selection of alchElecLambdaStart Courtney Taylor (Tue Sep 28 2010 - 10:50:24 CDT)
  • Re: Selection of alchElecLambdaStart Jérôme Hénin (Tue Sep 28 2010 - 14:51:36 CDT)
    • Re: Selection of alchElecLambdaStart Courtney Taylor (Tue Sep 28 2010 - 15:02:34 CDT)
      • Re: Selection of alchElecLambdaStart Jérôme Hénin (Tue Sep 28 2010 - 15:53:26 CDT)
• metadynamics simulations slow down and down OiniL (Sat Sep 25 2010 - 23:06:17 CDT)
  • Re: metadynamics simulations slow down and down Jérôme Hénin (Sun Sep 26 2010 - 05:47:28 CDT)
  • Re: metadynamics simulations slow down and down Giacomo Fiorin (Sun Sep 26 2010 - 08:38:51 CDT)
  • Re: metadynamics simulations slow down and down OiniL (Mon Oct 11 2010 - 09:36:29 CDT)
    • Re: Re: metadynamics simulations slow down and down Giacomo Fiorin (Mon Oct 11 2010 - 11:47:44 CDT)
• reg_membrane_peptide_interaction lara lara (Sat Sep 25 2010 - 04:24:09 CDT)
• flexible-cell constant pressure not supported in CUDA Jianing Song (Fri Sep 24 2010 - 19:50:26 CDT)
  • Re: flexible-cell constant pressure not supported in CUDA JC Gumbart (Mon Sep 27 2010 - 18:45:26 CDT)
• NAMD error message snoze pa (Fri Sep 24 2010 - 17:04:45 CDT)
• change force field in NAMD Chen, Zhihong (chenz2) (Fri Sep 24 2010 - 14:36:09 CDT)
• Colvars: Using "Alpha" Component Alexander Predeus (Thu Sep 23 2010 - 19:26:31 CDT)
  • Re: Colvars: Using "Alpha" Component Jérôme Hénin (Fri Sep 24 2010 - 03:27:40 CDT)
    • Re: Colvars: Using "Alpha" Component Alexander Predeus (Fri Sep 24 2010 - 13:25:31 CDT)
      • Re: Colvars: Using "Alpha" Component Giacomo Fiorin (Fri Sep 24 2010 - 15:48:59 CDT)
      • Re: Colvars: Using "Alpha" Component Alexander Predeus (Fri Sep 24 2010 - 16:10:46 CDT)
      • Re: Colvars: Using "Alpha" Component Giacomo Fiorin (Fri Sep 24 2010 - 16:35:44 CDT)
      • Re: Colvars: Using "Alpha" Component Alexander Predeus (Fri Sep 24 2010 - 16:56:21 CDT)
      • Re: Colvars: Using "Alpha" Component Giacomo Fiorin (Fri Sep 24 2010 - 17:01:27 CDT)
• Accelerated MD? patrick wintrode (Thu Sep 23 2010 - 09:44:41 CDT)
  • Re: Accelerated MD? Chris Harrison (Thu Sep 23 2010 - 11:17:07 CDT)
• Colvars and COM restraints for protein+membrane; plus a minor bug Marc Baaden (Thu Sep 23 2010 - 09:24:59 CDT)
  • Re: Colvars and COM restraints for protein+membrane; plus a minor bug Jérôme Hénin (Thu Sep 23 2010 - 14:37:52 CDT)
    • Re: Colvars and COM restraints for protein+membrane; plus a minor bug Marc Baaden (Fri Sep 24 2010 - 03:44:41 CDT)
      • Re: Colvars and COM restraints for protein+membrane; plus a minor bug Jérôme Hénin (Fri Sep 24 2010 - 04:59:59 CDT)
• about protein phosphorylation Zhang, Jiong (MU-Student) (Wed Sep 22 2010 - 11:59:36 CDT)
• (no subject) fereshteh moradi (Wed Sep 22 2010 - 04:59:49 CDT)
• unsubscribe Asmita Gupta (Wed Sep 22 2010 - 03:17:24 CDT)
• configuration file Demet Akten (Wed Sep 22 2010 - 02:51:48 CDT)
• ion concentration in residue-based coarse-grained model Demet Akten (Wed Sep 22 2010 - 02:49:01 CDT)
  • Re: ion concentration in residue-based coarse-grained model Francesco Oteri (Wed Sep 22 2010 - 03:50:41 CDT)
• membrane tutorial. Swarna M Patra (Wed Sep 22 2010 - 01:44:23 CDT)
  • Re: membrane tutorial. Francesco Oteri (Wed Sep 22 2010 - 03:24:58 CDT)
    • Re: membrane tutorial. Francesco Oteri (Wed Sep 22 2010 - 15:49:38 CDT)
• NAMD 2.7b4 released Jim Phillips (Tue Sep 21 2010 - 21:38:22 CDT)
• (no subject) Zhang, Jiong (MU-Student) (Tue Sep 21 2010 - 20:01:38 CDT)
• RBCG-dcd files dota alexiou (Tue Sep 21 2010 - 16:40:00 CDT)
  • Re: RBCG-dcd files Peter Freddolino (Tue Sep 21 2010 - 23:42:18 CDT)
• Colvars in NAMD 2.7b4 Jérôme Hénin (Tue Sep 21 2010 - 07:06:29 CDT)
• total charge correction Chen, Zhihong (chenz2) (Fri Sep 17 2010 - 11:33:38 CDT)
• Why NAMD run Slow down Ramin Omidvar (Fri Sep 17 2010 - 11:32:07 CDT)
• ewald self energy Chen, Zhihong (chenz2) (Thu Sep 16 2010 - 15:12:07 CDT)
• Re: Low temperature Molecular Dynamics Mert Gür (Thu Sep 16 2010 - 14:49:01 CDT)
• tcl script for saving .coor of each frame from dcd file Madhurima Jana (Wed Sep 15 2010 - 23:51:41 CDT)
• unsubscribe Katherine Parra (Wed Sep 15 2010 - 09:42:24 CDT)
• Re: Problem facing during Solvation of Coarse Grain Model Peter Freddolino (Tue Sep 14 2010 - 18:59:54 CDT)
• Low temperature Molecular Dynamics Mert Gür (Tue Sep 14 2010 - 15:42:53 CDT)
• replica exchange trans cis isomerisme Jorgen Simonsen (Sat Sep 11 2010 - 03:02:30 CDT)
• degrees of freedom Jorgen Simonsen (Sat Sep 11 2010 - 00:26:10 CDT)
• psfgen problem, not generating angles/dihedrals Rajan Vatassery (Fri Sep 10 2010 - 23:33:42 CDT)
  • RE: psfgen problem, not generating angles/dihedrals JC Gumbart (Fri Sep 10 2010 - 23:43:20 CDT)
    • RE: psfgen problem, not generating angles/dihedrals Rajan Vatassery (Sat Sep 11 2010 - 01:24:48 CDT)
      • RE: psfgen problem, not generating angles/dihedrals JC Gumbart (Sat Sep 11 2010 - 07:10:02 CDT)
• AMBER force field in NAMD Patargias, George (Fri Sep 10 2010 - 09:48:01 CDT)
  • Re: AMBER force field in NAMD Wei Chen (Fri Sep 10 2010 - 12:48:15 CDT)
• beta column Swarna M Patra (Fri Sep 10 2010 - 00:57:04 CDT)
  • Re: beta column ehenriques_at_qui.uc.pt (Fri Sep 10 2010 - 04:25:10 CDT)
  • Re: beta column Nicholas Musolino (Fri Sep 10 2010 - 07:48:46 CDT)
• parameters for Glutathione and BSO Raul Araya (Thu Sep 09 2010 - 11:44:38 CDT)
  • Re: parameters for Glutathione and BSO felmerino_at_uchile.cl (Thu Sep 09 2010 - 22:32:29 CDT)
• NAMD Energy types Lada Biedermannová (Wed Sep 08 2010 - 04:16:30 CDT)
  • Re: NAMD Energy types Peter Freddolino (Wed Sep 08 2010 - 19:19:02 CDT)
    • Re: NAMD Energy types Lada Biedermannová (Thu Sep 09 2010 - 03:51:12 CDT)
      • Re: NAMD Energy types Peter Freddolino (Thu Sep 09 2010 - 07:04:49 CDT)
      • Re: NAMD Energy types Lada Biedermannová (Thu Sep 09 2010 - 08:16:44 CDT)
      • Re: NAMD Energy types Peter Freddolino (Thu Sep 09 2010 - 20:40:15 CDT)
      • Re: NAMD Energy types Jim Phillips (Fri Sep 17 2010 - 14:39:29 CDT)
      • Re: NAMD Energy types Peter Freddolino (Fri Sep 17 2010 - 18:20:55 CDT)
• Q=B4=D7=D4crazylyf@163.com=B5=C4=D3=CA=BC=FE?= crazylyf (Tue Sep 07 2010 - 22:17:50 CDT)
• problem on pair interaction Chen, Zhihong (chenz2) (Tue Sep 07 2010 - 15:49:04 CDT)
• Acceptance ratio of REMD simulation jaya c.jose (Tue Sep 07 2010 - 05:47:04 CDT)
• user-defined energy function Ramya Narasimhan (Mon Sep 06 2010 - 04:53:47 CDT)
• question on hydrogen bond Kwee Hong (Sun Sep 05 2010 - 22:40:40 CDT)
  • Re: question on hydrogen bond Axel Kohlmeyer (Mon Sep 06 2010 - 04:08:32 CDT)
  • Re: question on hydrogen bond ehenriques_at_qui.uc.pt (Mon Sep 06 2010 - 05:06:57 CDT)
• FATAL ERROR: Couldn't open DCD file equil0.dcd: No such file or directory henri mone (Sun Sep 05 2010 - 10:16:27 CDT)
• Bad atom ID in extra bond file Kwee Hong (Sat Sep 04 2010 - 03:10:25 CDT)
  • Re: Bad atom ID in extra bond file Leonardo Trabuco (Sat Sep 04 2010 - 04:41:00 CDT)
    • Re: Bad atom ID in extra bond file Kwee Hong (Sat Sep 04 2010 - 05:08:03 CDT)
      • Re: Bad atom ID in extra bond file Jim Phillips (Fri Sep 17 2010 - 14:22:59 CDT)
• problem in cgsolvate.tcl while adding CG water to the system sunita gupta (Sat Sep 04 2010 - 02:52:12 CDT)
• solute movement in periodic box Mark M Huntress (Fri Sep 03 2010 - 09:53:38 CDT)
  • Re: solute movement in periodic box Chris Harrison (Fri Sep 03 2010 - 10:57:44 CDT)
• script for energy minimization of a .dcd file sudipta (Fri Sep 03 2010 - 02:39:22 CDT)
• Bioinformatics Symposium at C-DAC, Pune Anirban Ghosh (Fri Sep 03 2010 - 00:41:23 CDT)
• simulation cell enlarging too much after restart Parisa Akhski (Thu Sep 02 2010 - 17:26:40 CDT)
  • Re: simulation cell enlarging too much after restart JC Gumbart (Thu Sep 02 2010 - 18:16:08 CDT)
• Minimization convergence Wendy González (Thu Sep 02 2010 - 15:55:19 CDT)
• Does "rigidbond off" work instead of "rigidbonds none" Mert Gür (Thu Sep 02 2010 - 15:03:21 CDT)
  • Re: Does "rigidbond off" work instead of "rigidbonds none" Leonardo Trabuco (Fri Sep 03 2010 - 01:21:01 CDT)
    • Re: Does "rigidbond off" work instead of "rigidbonds none" Mert Gür (Fri Sep 03 2010 - 04:25:40 CDT)
      • Re: Does "rigidbond off" work instead of "rigidbonds none" Jim Phillips (Fri Sep 17 2010 - 14:19:26 CDT)
      • Re: Does "rigidbond off" work instead of "rigidbonds none" Mert Gür (Fri Sep 17 2010 - 14:44:14 CDT)
• 1-4 pair generation Jianhui Tian (Thu Sep 02 2010 - 13:12:42 CDT)
  • Re: 1-4 pair generation David Hardy (Thu Sep 02 2010 - 13:30:57 CDT)
• g(r) calculation for CNT sara (Thu Sep 02 2010 - 04:34:48 CDT)
  • Re: g(r) calculation for CNT felmerino_at_uchile.cl (Thu Sep 02 2010 - 10:30:55 CDT)
• NAMD Cuda NBFIX Terms Jane Ren (Wed Sep 01 2010 - 20:21:20 CDT)
  • Re: NAMD Cuda NBFIX Terms felmerino_at_uchile.cl (Wed Sep 01 2010 - 22:54:45 CDT)
    • RE: NAMD Cuda NBFIX Terms Jane Ren (Thu Sep 02 2010 - 15:45:18 CDT)
      • Re: NAMD Cuda NBFIX Terms Axel Kohlmeyer (Thu Sep 02 2010 - 16:42:56 CDT)
• Building PSF file for protein with ions anas . (Wed Sep 01 2010 - 05:22:50 CDT)
  • Re: Building PSF file for protein with ions ehenriques_at_qui.uc.pt (Wed Sep 01 2010 - 09:02:17 CDT)
• Charmm carbohydrate force field Jianhui Tian (Tue Aug 31 2010 - 13:09:58 CDT)
  • Re: Charmm carbohydrate force field Chris Harrison (Tue Aug 31 2010 - 13:30:03 CDT)
  • Re: Charmm carbohydrate force field JC Gumbart (Tue Aug 31 2010 - 13:55:44 CDT)
• Force constant scaling guardiani_at_fi.infn.it (Tue Aug 31 2010 - 09:45:14 CDT)
  • Re: Force constant scaling Jérôme Hénin (Wed Sep 01 2010 - 06:11:58 CDT)
• FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Tue Aug 31 2010 - 08:25:35 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. Jérôme Hénin (Tue Aug 31 2010 - 10:22:06 CDT)
    • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Fri Sep 03 2010 - 12:30:57 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Fri Sep 03 2010 - 23:26:49 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. Jérôme Hénin (Sat Sep 04 2010 - 02:50:54 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Mon Sep 06 2010 - 03:29:31 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. Jérôme Hénin (Mon Sep 06 2010 - 10:14:25 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Mon Sep 06 2010 - 10:29:38 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. Giacomo Fiorin (Mon Sep 06 2010 - 14:10:06 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Mon Sep 06 2010 - 17:26:29 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. Giacomo Fiorin (Tue Sep 07 2010 - 11:23:35 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Tue Sep 07 2010 - 15:31:07 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. Giacomo Fiorin (Wed Sep 08 2010 - 16:28:50 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Wed Sep 08 2010 - 17:07:09 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Wed Sep 08 2010 - 16:46:37 CDT)
    • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. Jérôme Hénin (Thu Sep 09 2010 - 11:06:33 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Fri Sep 10 2010 - 14:11:23 CDT)
      • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. Jérôme Hénin (Sat Sep 11 2010 - 04:02:52 CDT)
• protein shifts out of water box Kwee Hong (Tue Aug 31 2010 - 05:20:53 CDT)
• CatDCD installation bkziervogel_at_uchicago.edu (Mon Aug 30 2010 - 11:24:04 CDT)
• cholestrerol Swarna M Patra (Mon Aug 30 2010 - 04:29:38 CDT)
  • Re: cholestrerol Ajasja LjubetiÄ� (Mon Aug 30 2010 - 06:15:38 CDT)
• claen water Swarna M Patra (Sun Aug 29 2010 - 22:28:22 CDT)
  • Re: claen water Nicholas M Glykos (Mon Aug 30 2010 - 04:22:31 CDT)
    • Re: claen water Axel Kohlmeyer (Mon Aug 30 2010 - 07:53:17 CDT)
      • Re: claen water Nicholas M Glykos (Mon Aug 30 2010 - 08:26:44 CDT)
• restarting simulation sara (Sun Aug 29 2010 - 03:18:07 CDT)
• Protonation Andres Morales N (Sat Aug 28 2010 - 21:11:49 CDT)
  • Re: Protonation Branko (Sun Aug 29 2010 - 06:20:03 CDT)
• Unsubscribe namd-l udbhav ojha (Sat Aug 28 2010 - 16:20:45 CDT)
• unsubscribe namd-l sathish kumar gurupatham (Sat Aug 28 2010 - 14:07:25 CDT)
  • Re: unsubscribe namd-l Gianluca Interlandi (Sat Aug 28 2010 - 19:13:24 CDT)
• problem at applying patch Kwee Hong (Sat Aug 28 2010 - 12:58:21 CDT)
  • RE: problem at applying patch JC Gumbart (Sat Aug 28 2010 - 13:21:14 CDT)
• charge calculation Kwee Hong (Sat Aug 28 2010 - 09:09:12 CDT)
• unsubscribe namd-l sripad chandan (Sat Aug 28 2010 - 09:08:12 CDT)
• (no subject) Aakash C R (Sat Aug 28 2010 - 04:35:48 CDT)
• unsubscribe namd-l udbhav ojha (Sat Aug 28 2010 - 02:23:20 CDT)
• VdW and fixatoms Ranyere Deyler (Sat Aug 28 2010 - 00:07:06 CDT)
• unsubscribe namd-l Myunggi Yi (Fri Aug 27 2010 - 21:01:19 CDT)
• FEP substrate transformation with common moiety Sebastian Stolzenberg (Fri Aug 27 2010 - 20:35:01 CDT)
  • Re: FEP substrate transformation with common moiety Chris Harrison (Fri Aug 27 2010 - 21:47:26 CDT)
  • Re: FEP substrate transformation with common moiety Jérôme Hénin (Sat Aug 28 2010 - 08:52:46 CDT)
• write out the snapshot from MD trajectory mjyang (Fri Aug 27 2010 - 04:59:32 CDT)
  • Re: write out the snapshot from MD trajectory Eduard Schreiner (Fri Aug 27 2010 - 05:55:00 CDT)
    • RE: write out the snapshot from MD trajectory mjyang (Fri Aug 27 2010 - 10:28:25 CDT)
• Version 2.7 problems! Wendy González (Thu Aug 26 2010 - 11:55:47 CDT)
• build a layer hamid mosaddeghi (Wed Aug 25 2010 - 07:58:46 CDT)
  • Re: build a layer Eduardo (Wed Aug 25 2010 - 12:29:27 CDT)
• build a wall sara (Wed Aug 25 2010 - 11:01:39 CDT)
• WorkDistrib: Recursive bisection fails,invoking least-load algorithm Swarna M Patra (Tue Aug 24 2010 - 11:42:45 CDT)
• problem with water Swarna M Patra (Tue Aug 24 2010 - 11:26:45 CDT)
  • Re: problem with water Jeffrey J. Potoff (Tue Aug 24 2010 - 11:55:44 CDT)
• water escape Swarna M Patra (Tue Aug 24 2010 - 10:38:31 CDT)
  • Re: water escape Ajasja LjubetiÄ� (Tue Aug 24 2010 - 12:02:25 CDT)
• TIP4P/Ice usage in NAMD Ravinder Abrol (Tue Aug 24 2010 - 03:22:17 CDT)
  • Re: TIP4P/Ice usage in NAMD Peter Freddolino (Tue Aug 24 2010 - 09:14:39 CDT)
• possible bug with NAMD Energy plugin Zumot, Elia Nabil (Mon Aug 23 2010 - 15:19:07 CDT)
  • Re: possible bug with NAMD Energy plugin Peter Freddolino (Mon Aug 23 2010 - 18:58:26 CDT)
    • RE: possible bug with NAMD Energy plugin Zumot, Elia Nabil (Tue Aug 24 2010 - 12:15:35 CDT)
    • RE: possible bug with NAMD Energy plugin Zumot, Elia Nabil (Tue Aug 31 2010 - 18:00:17 CDT)
      • Re: possible bug with NAMD Energy plugin Peter Freddolino (Tue Aug 31 2010 - 19:42:59 CDT)
• Proline hybrid topology file for FEP Payel Das (Fri Aug 20 2010 - 19:54:28 CDT)
  • Re: Proline hybrid topology file for FEP JC Gumbart (Tue Aug 24 2010 - 14:49:16 CDT)
• ABF calculations: Jacobian term describing geometry entropy chengh_at_ringo.chem.pitt.edu (Mon Aug 23 2010 - 08:13:37 CDT)
  • Re: ABF calculations: Jacobian term describing geometry entropy Giacomo Fiorin (Mon Aug 23 2010 - 11:00:43 CDT)
  • Re: ABF calculations: Jacobian term describing geometry entropy Jérôme Hénin (Mon Aug 23 2010 - 10:51:53 CDT)
• problem at maintaining geometry coordinate Kwee Hong (Mon Aug 23 2010 - 02:22:53 CDT)
  • Re: problem at maintaining geometry coordinate ehenriques_at_qui.uc.pt (Mon Aug 23 2010 - 05:11:45 CDT)
    • Re: problem at maintaining geometry coordinate Kwee Hong (Mon Aug 23 2010 - 23:02:54 CDT)
      • Re: problem at maintaining geometry coordinate ehenriques_at_qui.uc.pt (Tue Aug 24 2010 - 05:51:07 CDT)
• Does CHARMM stabilize alpha helices? Rabab Toubar (Sat Aug 21 2010 - 15:58:24 CDT)
  • Re: Does CHARMM stabilize alpha helices? Nikolaos Glykos (Sun Aug 22 2010 - 03:57:22 CDT)
• zeroMomentum for SMD Ihsan Omur Akdag (Fri Aug 20 2010 - 05:58:18 CDT)
• About the solvate package c00jsw00 (Thu Aug 19 2010 - 22:25:31 CDT)
  • Re: About the solvate package ehenriques_at_qui.uc.pt (Fri Aug 20 2010 - 03:47:28 CDT)
• specific site-ion LJ parameters and CHARMM general force field 林星雨 (Thu Aug 19 2010 - 05:53:55 CDT)
• my problem was solved zhangliqun (Wed Aug 18 2010 - 15:39:36 CDT)
• Resources for trying out NVIDIA GPUs for free with NAMD Roy Kim (Wed Aug 18 2010 - 12:22:09 CDT)
• change solvent Leandro Martínez (Wed Aug 18 2010 - 11:36:59 CDT)
• change solvent sara (Wed Aug 18 2010 - 10:26:20 CDT)
  • Re: change solvent Nicholas Musolino (Wed Aug 18 2010 - 12:00:57 CDT)
  • Re: change solvent Branko (Wed Aug 18 2010 - 10:54:18 CDT)
  • Re: change solvent ehenriques_at_qui.uc.pt (Thu Aug 19 2010 - 05:32:51 CDT)
• zeroMomentum for SMD Ýhsan Ömür Akdað (Wed Aug 18 2010 - 07:29:45 CDT)
• interaction-energy balaji nagarajan (Wed Aug 18 2010 - 05:15:03 CDT)
• problem at maintaining geometry coordinate Kwee Hong (Tue Aug 17 2010 - 22:48:35 CDT)
  • Re: problem at maintaining geometry coordinate Kwee Hong (Tue Aug 17 2010 - 23:43:25 CDT)
• about recentering of namd trajectory zhangliqun (Tue Aug 17 2010 - 10:50:54 CDT)
• Re: parameter file for carbon nanotube Jian Liu (Mon Aug 16 2010 - 23:53:56 CDT)
  • Re: parameter file for carbon nanotube Axel Kohlmeyer (Tue Aug 17 2010 - 04:12:56 CDT)
• Applying a positional restraint with colvars module bkziervogel_at_uchicago.edu (Mon Aug 16 2010 - 12:06:24 CDT)
  • Re: Applying a positional restraint with colvars module Giacomo Fiorin (Mon Aug 16 2010 - 16:26:23 CDT)
• Dowser with RESIDUE LYR Ale Gomez (Mon Aug 16 2010 - 12:02:18 CDT)
• Umbrella Sampling Methodology Charlie Forde (Mon Aug 16 2010 - 06:23:15 CDT)
  • Re: Umbrella Sampling Methodology Giacomo Fiorin (Tue Aug 17 2010 - 10:58:46 CDT)
    • Re: Umbrella Sampling Methodology Charlie Forde (Wed Aug 18 2010 - 11:39:17 CDT)
• parameter file for carbon nanotube sara (Mon Aug 16 2010 - 10:34:53 CDT)
• Re: psf creating for carbon nanotube Jian Liu (Sun Aug 15 2010 - 07:40:32 CDT)
  • RE: psf creating for carbon nanotube JC Gumbart (Sun Aug 15 2010 - 07:52:34 CDT)
  • Re: Re: psf creating for carbon nanotube Jian Liu (Mon Aug 16 2010 - 00:23:54 CDT)
• specific heat - instability Alex Curutiu (Sun Aug 15 2010 - 05:49:52 CDT)
• psf creating for carbon nanotube sara (Sun Aug 15 2010 - 02:48:36 CDT)
• Modifying a peptide and introducing residues Aditya Ranganathan (Sat Aug 14 2010 - 05:57:28 CDT)
  • Re: Modifying a peptide and introducing residues Jason Richard Mick (Sat Aug 14 2010 - 08:37:31 CDT)
    • Re: Modifying a peptide and introducing residues Aditya Ranganathan (Sat Aug 14 2010 - 12:02:19 CDT)
      • Re: Modifying a peptide and introducing residues felmerino_at_uchile.cl (Sat Aug 14 2010 - 19:09:37 CDT)
• Re: how to save a DCD file without water in NAMD ? Lisa Brown (Fri Aug 13 2010 - 08:06:36 CDT)
  • Re: how to save a DCD file without water in NAMD ? Mert Gür (Fri Aug 13 2010 - 08:56:44 CDT)
  • Re: how to save a DCD file without water in NAMD ? Axel Kohlmeyer (Fri Aug 13 2010 - 08:54:51 CDT)
  • Re: how to save a DCD file without water in NAMD ? Athanassios Stavrakoudis (Fri Aug 13 2010 - 10:23:01 CDT)
    • Re: how to save a DCD file without water in NAMD ? Lisa Brown (Fri Aug 13 2010 - 11:02:36 CDT)
• "Hands-On" Workshop on Computational Biophysics, November 1-5, 2010 & November 29-December 3, 2010 in Urbana, IL TCBG Workshops (Thu Aug 12 2010 - 17:04:39 CDT)
• how to save a DCD file without water in NAMD ? Lisa Brown (Thu Aug 12 2010 - 15:00:40 CDT)
  • RE: how to save a DCD file without water in NAMD ? Zumot, Elia Nabil (Thu Aug 12 2010 - 16:52:51 CDT)
    • Re: how to save a DCD file without water in NAMD: COMMAND LINE Thomas C Bishop (Fri Aug 13 2010 - 08:44:09 CDT)
• grid-based correction map yandong Huang (Thu Aug 12 2010 - 08:52:33 CDT)
  • namd2.7b3 vs namd2.7b2 Francesco Oteri (Thu Aug 12 2010 - 17:11:42 CDT)
• Enthalpy calculation from NPT simulation sudipta (Wed Aug 11 2010 - 13:54:16 CDT)
• ABF problem with gyration radius/Cl and Br Branko (Wed Aug 11 2010 - 07:25:41 CDT)
  • Re: ABF problem with gyration radius/Cl and Br Jérôme Hénin (Wed Aug 11 2010 - 08:31:44 CDT)
• Reading NAMD coor files in CHARMM -> Fail for 64Bit Bjoern Olausson (Wed Aug 11 2010 - 06:57:27 CDT)
• Mysterious Formation of Solvent Spheres Charles Zhao (Wed Aug 11 2010 - 01:32:52 CDT)
  • Re: Mysterious Formation of Solvent Spheres Axel Kohlmeyer (Wed Aug 11 2010 - 05:23:36 CDT)
    • Re: Mysterious Formation of Solvent Spheres Charles Zhao (Wed Aug 11 2010 - 11:42:16 CDT)
    • Re: Mysterious Formation of Solvent Spheres Thomas C. Bishop (Wed Aug 11 2010 - 13:48:10 CDT)
    • Re: Mysterious Formation of Solvent Spheres Charles Zhao (Wed Aug 11 2010 - 15:23:53 CDT)
    • Re: Mysterious Formation of Solvent Spheres Charles Zhao (Wed Aug 11 2010 - 18:19:07 CDT)
      • LJ correction in NAMD2.7b3 Thomas C. Bishop (Thu Aug 12 2010 - 14:05:04 CDT)
      • Re: LJ correction in NAMD2.7b3 Jim Phillips (Thu Aug 12 2010 - 15:14:41 CDT)
• FEP calculation is doing nothing sudipta (Tue Aug 10 2010 - 10:09:29 CDT)
  • Re: FEP calculation is doing nothing Chris Chipot (Tue Aug 10 2010 - 11:06:11 CDT)
• positive total energy C. Navarro (Tue Aug 10 2010 - 08:48:59 CDT)
  • Re: positive total energy Mert Gür (Wed Aug 11 2010 - 03:15:26 CDT)
    • Re: positive total energy Axel Kohlmeyer (Wed Aug 11 2010 - 04:35:43 CDT)
      • Re: positive total energy Mert Gür (Wed Aug 11 2010 - 07:48:29 CDT)
      • Re: positive total energy Axel Kohlmeyer (Wed Aug 11 2010 - 08:44:03 CDT)
• restart from different snap shots Jorgen Simonsen (Tue Aug 10 2010 - 06:05:25 CDT)
  • Re: restart from different snap shots Mert Gür (Tue Aug 10 2010 - 07:48:32 CDT)
• version of namd to install Jorgen Simonsen (Mon Aug 09 2010 - 04:47:43 CDT)
• question regarding warning. Kwee Hong (Mon Aug 09 2010 - 02:28:16 CDT)
  • Re: question regarding warning. Bjoern Olausson (Mon Aug 09 2010 - 03:13:58 CDT)
    • Re: question regarding warning. Kwee Hong (Mon Aug 09 2010 - 04:29:16 CDT)
      • Re: question regarding warning. Axel Kohlmeyer (Mon Aug 09 2010 - 05:07:39 CDT)
      • Re: question regarding warning. Kwee Hong (Mon Aug 09 2010 - 21:48:14 CDT)
• Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Mert Gür (Sat Aug 07 2010 - 10:20:19 CDT)
  • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Mert Gür (Sat Aug 07 2010 - 11:39:13 CDT)
    • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Axel Kohlmeyer (Sat Aug 07 2010 - 13:10:15 CDT)
      • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Mert Gür (Sat Aug 07 2010 - 15:12:15 CDT)
      • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Axel Kohlmeyer (Sat Aug 07 2010 - 15:28:29 CDT)
      • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Mert Gür (Mon Aug 09 2010 - 08:14:39 CDT)
  • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT felmerino_at_uchile.cl (Sat Aug 07 2010 - 19:13:59 CDT)
    • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Mert Gür (Sun Aug 08 2010 - 17:07:56 CDT)
• reinitvels vs restart.vel Dhiraj Srivastava (Fri Aug 06 2010 - 15:06:05 CDT)
• CHARMM FF parameters for O2 Gas m.raviprasad_at_ndsu.edu (Fri Aug 06 2010 - 14:39:11 CDT)
• last call for 2.7b3 bug reports! Jim Phillips (Fri Aug 06 2010 - 09:59:00 CDT)
• Constraints on the plane and on the atom positions (in the same simulation) Ajasja LjubetiÄ� (Fri Aug 06 2010 - 03:15:16 CDT)
  • Re: Constraints on the plane and on the atom positions (in the same simulation) Jim Phillips (Fri Aug 06 2010 - 09:40:30 CDT)
• Problems with AutoPSF flavio seixas (Wed Aug 04 2010 - 21:20:26 CDT)
  • Re: Problems with AutoPSF Jim Phillips (Fri Aug 06 2010 - 09:36:28 CDT)
• abf_integrate Sabyashachi Mishra (Wed Aug 04 2010 - 04:50:08 CDT)
  • Re: abf_integrate Jérôme Hénin (Fri Aug 06 2010 - 05:20:59 CDT)
• Interface analisis Leonardo Herrera (Tue Aug 03 2010 - 12:20:00 CDT)
• heating and binvelocities Dhiraj Srivastava (Tue Aug 03 2010 - 11:26:36 CDT)
  • Re: heating and binvelocities Jim Phillips (Fri Aug 06 2010 - 09:30:38 CDT)
• Specifying Values for Rotating Constraints Megan Scoppa (Tue Aug 03 2010 - 11:09:54 CDT)
  • Re: Specifying Values for Rotating Constraints Jim Phillips (Fri Aug 06 2010 - 09:27:38 CDT)
• flashmob namd Ramon Rocha (Tue Aug 03 2010 - 10:52:15 CDT)
• NAMD Pair Interactions Finite Box Size Correction Hok-Hei Tam (Tue Aug 03 2010 - 09:58:53 CDT)
• coarse graining ipsita basu (Tue Aug 03 2010 - 04:43:20 CDT)
  • Re: coarse graining Anton Arkhipov (Sat Aug 07 2010 - 20:41:23 CDT)
• RetinalTop Ale Gomez (Mon Aug 02 2010 - 00:47:44 CDT)
  • RetinalTop Ale Gomez (Mon Aug 02 2010 - 08:52:10 CDT)
    • Re: RetinalTop Bjoern Olausson (Mon Aug 02 2010 - 09:49:32 CDT)
      • Re: RetinalTop Ale Gomez (Mon Aug 02 2010 - 10:15:41 CDT)
      • Re: RetinalTop Ale Gomez (Mon Aug 02 2010 - 11:07:52 CDT)
      • Re: RetinalTop Ale Gomez (Mon Aug 02 2010 - 20:00:49 CDT)
      • Re: RetinalTop Ale Gomez (Mon Aug 02 2010 - 22:53:13 CDT)
      • Re: RetinalTop Bjoern Olausson (Tue Aug 03 2010 - 02:57:26 CDT)
      • Re: RetinalTop tillmann.utesch_at_mail.tu-berlin.de (Tue Aug 03 2010 - 03:23:22 CDT)
      • Re: RetinalTop Ale Gomez (Tue Aug 03 2010 - 11:22:19 CDT)
      • Re: RetinalTop Ale Gomez (Wed Aug 04 2010 - 11:47:09 CDT)
• (no subject) fereshteh moradi (Sun Aug 01 2010 - 23:25:34 CDT)
• Problems installing NAMD Bruno Rodrigues (Sat Jul 31 2010 - 01:12:12 CDT)
• monolayere riya david (Fri Jul 30 2010 - 14:29:48 CDT)
• Using CHARMM-GUI membrane builder with NAMD Ajasja LjubetiÄ� (Fri Jul 30 2010 - 09:17:36 CDT)
  • Re: Using CHARMM-GUI membrane builder with NAMD Bjoern Olausson (Mon Aug 02 2010 - 02:37:09 CDT)
    • Re: Using CHARMM-GUI membrane builder with NAMD Ajasja LjubetiÄ� (Mon Aug 02 2010 - 03:43:53 CDT)
      • Re: Using CHARMM-GUI membrane builder with NAMD Bjoern Olausson (Mon Aug 02 2010 - 06:56:14 CDT)
      • Re: Using CHARMM-GUI membrane builder with NAMD Axel Kohlmeyer (Mon Aug 02 2010 - 07:45:53 CDT)
      • Re: Using CHARMM-GUI membrane builder with NAMD Bjoern Olausson (Mon Aug 02 2010 - 08:21:07 CDT)
      • Re: Using CHARMM-GUI membrane builder with NAMD Ajasja LjubetiÄ� (Mon Aug 02 2010 - 07:59:54 CDT)
• Pressure is not constant in NPT ensemble Parisa Akhski (Thu Jul 29 2010 - 14:01:05 CDT)
  • Re: Pressure is not constant in NPT ensemble Ajasja LjubetiÄ� (Fri Jul 30 2010 - 02:11:59 CDT)
    • RE: Pressure is not constant in NPT ensemble Parisa Akhski (Sun Aug 01 2010 - 13:31:11 CDT)
      • RE: Pressure is not constant in NPT ensemble Nikolaos Glykos (Sun Aug 01 2010 - 15:37:17 CDT)
• Z-direction shrinking crazylyf (Thu Jul 29 2010 - 03:33:11 CDT)
  • Re: Z-direction shrinking Giacomo Fiorin (Thu Jul 29 2010 - 09:43:23 CDT)
• Interaction energy difference m.raviprasad_at_ndsu.edu (Wed Jul 28 2010 - 22:42:07 CDT)
  • Re: Interaction energy difference Axel Kohlmeyer (Thu Jul 29 2010 - 00:08:52 CDT)
    • Re: Interaction energy difference Nicholas J Musolino (Thu Jul 29 2010 - 10:42:35 CDT)
• Namd 2.6 on ubuntu 9.10 oguz gurbulak (Wed Jul 28 2010 - 14:22:09 CDT)
  • Re: Namd 2.6 on ubuntu 9.10 Nicholas Musolino (Wed Jul 28 2010 - 16:16:30 CDT)
• Running namd on multiple win32 nodes Ajasja LjubetiÄ� (Wed Jul 28 2010 - 04:42:20 CDT)
  • Re: Running namd on multiple win32 nodes Ajasja LjubetiÄ� (Wed Jul 28 2010 - 07:18:16 CDT)
• Pressure parameter in minimization Parisa Akhski (Tue Jul 27 2010 - 16:31:03 CDT)
• structure breaking ipsita basu (Tue Jul 27 2010 - 00:36:35 CDT)
  • Re: structure breaking ehenriques_at_qui.uc.pt (Tue Jul 27 2010 - 04:40:21 CDT)
• FEP for GLY and PRO Mutations Michael LeVine (Mon Jul 26 2010 - 10:10:28 CDT)
  • Re: FEP for GLY and PRO Mutations Jérôme Hénin (Tue Jul 27 2010 - 05:01:36 CDT)
• Re: how to submit job on a HPC equipped with infiniband Bjoern Olausson (Mon Jul 26 2010 - 04:31:55 CDT)
• how to submit job on a HPC equipped with infiniband liupeng012 (Mon Jul 26 2010 - 02:59:34 CDT)
• dihedral terms for a parameter file Basak Isin (Sun Jul 25 2010 - 17:09:09 CDT)
• Running namd on Apple's XGrid Ido Gan (Sun Jul 25 2010 - 02:16:44 CDT)
  • Re: Running namd on Apple's XGrid Axel Kohlmeyer (Sun Jul 25 2010 - 07:19:56 CDT)
• tclforces: measure distances in NAMD 2.6b2 ? Sebastian Stolzenberg (Sat Jul 24 2010 - 21:46:51 CDT)
  • Re: tclforces: measure distances in NAMD 2.6b2 ? Axel Kohlmeyer (Sun Jul 25 2010 - 18:43:59 CDT)
• NAMD time connect out on multi-computers Nicolas Floquet (Fri Jul 23 2010 - 07:00:12 CDT)
• RAMD patch in NAMD CVS Vlad Cojocaru (Fri Jul 23 2010 - 04:18:15 CDT)
• Deprotonated Lys Dhiraj Srivastava (Thu Jul 22 2010 - 21:13:50 CDT)
  • Re: Deprotonated Lys felmerino_at_uchile.cl (Thu Jul 22 2010 - 23:33:39 CDT)
• Running NAMD on SGI Altix system Ronald Salesky (Thu Jul 22 2010 - 15:13:31 CDT)
  • Re: Running NAMD on SGI Altix system Axel Kohlmeyer (Thu Jul 22 2010 - 16:08:22 CDT)
• "gradient tolerance" for minimization Parisa Akhski (Thu Jul 22 2010 - 11:29:19 CDT)
  • Re: "gradient tolerance" for minimization Jim Phillips (Thu Jul 22 2010 - 14:52:07 CDT)
• Timeout waiting for node-program to connect Nicolas Floquet (Wed Jul 21 2010 - 10:43:02 CDT)
  • Re: Timeout waiting for node-program to connect Jim Phillips (Thu Jul 22 2010 - 13:20:56 CDT)
• parallel scaling issues Hyonseok Hwang (Wed Jul 21 2010 - 09:11:18 CDT)
  • Re: parallel scaling issues Jim Phillips (Thu Jul 22 2010 - 13:15:04 CDT)
• dual all-atom/coarse grain simulation Keith Battle (Tue Jul 20 2010 - 15:52:30 CDT)
• constraintScaling to gradually release harmonic restraints during minimization Scott Boyken (Tue Jul 20 2010 - 15:22:08 CDT)
• Running namd on Mac OS Patargias, George (Tue Jul 20 2010 - 12:25:04 CDT)
  • Re: Running namd on Mac OS Ian Stokes-Rees (Tue Jul 20 2010 - 13:38:05 CDT)
  • Re: Running namd on Mac OS Eric H. Lee (Tue Jul 20 2010 - 13:06:51 CDT)
• namd development mailing list? Nicholas Musolino (Tue Jul 20 2010 - 12:09:38 CDT)
  • Re: namd development mailing list? Victor Ovchinnikov (Tue Jul 20 2010 - 15:00:52 CDT)
• pair interaction self in 2.7b3 Kimura, Roy (Tue Jul 20 2010 - 09:28:48 CDT)
• Debug NAMD with CharmDebug Jaime Gonzalez (Tue Jul 20 2010 - 03:41:45 CDT)
• running namd faster ipsita basu (Tue Jul 20 2010 - 00:55:34 CDT)
  • Re: running namd faster Axel Kohlmeyer (Tue Jul 20 2010 - 05:52:40 CDT)
  • Re: running namd faster Nikolaos Glykos (Tue Jul 20 2010 - 06:01:41 CDT)
• 1us simulation of 80k atom system -- how much gross structure movement is expected? Ian Stokes-Rees (Mon Jul 19 2010 - 12:18:55 CDT)
  • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Francesco Oteri (Mon Jul 19 2010 - 13:39:54 CDT)
  • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Peter Freddolino (Mon Jul 19 2010 - 18:52:20 CDT)
    • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Ian Stokes-Rees (Mon Jul 19 2010 - 20:06:05 CDT)
      • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Axel Kohlmeyer (Mon Jul 19 2010 - 21:03:22 CDT)
      • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Branko (Tue Jul 20 2010 - 07:58:01 CDT)
      • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Peter Freddolino (Mon Jul 19 2010 - 20:52:48 CDT)
  • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Andrew Emerson (Tue Jul 20 2010 - 05:09:05 CDT)
• Extract trajectory from replica exchange simulation Shi, Chuanyin (Mon Jul 19 2010 - 09:19:21 CDT)
• Re: CPU GPU comparison francesco oteri (Fri Jul 16 2010 - 03:13:17 CDT)
  • Re: CPU GPU comparison Axel Kohlmeyer (Fri Jul 16 2010 - 08:39:18 CDT)
• alchemy FEP query Madhurima Jana (Fri Jul 16 2010 - 01:05:44 CDT)
• pairinteractionself in 2.7b3 Kimura, Roy (Thu Jul 15 2010 - 14:33:04 CDT)
• Different types of constraints at the same time Chao Zhang (Thu Jul 15 2010 - 14:05:30 CDT)
• mutation of DNA sudipta (Thu Jul 15 2010 - 05:57:46 CDT)
  • Re: mutation of DNA Thomas C. Bishop (Thu Jul 15 2010 - 10:56:27 CDT)
• CPU GPU comparison francesco oteri (Tue Jul 13 2010 - 11:47:05 CDT)
• RBCG doty alexiou (Tue Jul 13 2010 - 02:42:53 CDT)
  • Re: RBCG felmerino_at_uchile.cl (Tue Jul 13 2010 - 23:08:57 CDT)
    • RE: RBCG doty alexiou (Wed Jul 14 2010 - 04:33:12 CDT)
• Running problem with NAMD2.7b lixb07_at_lzu.cn (Mon Jul 12 2010 - 21:01:40 CDT)
• Cartesian vs dihedral angle space PCA patrick wintrode (Mon Jul 12 2010 - 10:12:29 CDT)
  • Re: Cartesian vs dihedral angle space PCA Nicholas M Glykos (Tue Jul 13 2010 - 04:35:22 CDT)
• headgroup area calculation ipsita basu (Mon Jul 12 2010 - 07:33:47 CDT)
  • Re: headgroup area calculation Branko (Mon Jul 12 2010 - 08:14:19 CDT)
    • Re: headgroup area calculation ipsita basu (Wed Jul 14 2010 - 02:05:22 CDT)
• about DCD file format document Jun Zhang (Mon Jul 12 2010 - 06:43:02 CDT)
  • Re: about DCD file format document Axel Kohlmeyer (Mon Jul 12 2010 - 07:29:02 CDT)
    • Re: about DCD file format document Ajasja LjubetiÄ� (Mon Jul 12 2010 - 08:52:05 CDT)
  • Re: about DCD file format document Nicholas M Glykos (Mon Jul 12 2010 - 08:15:50 CDT)
• problem wuth solvate plugin Mikhail Suyetin (Mon Jul 12 2010 - 05:53:28 CDT)
• the problem with NAMD2.7b lixb07_at_lzu.cn (Mon Jul 12 2010 - 05:13:41 CDT)
• NAMD checkpoint mechanism. Michael Harney (Fri Jul 09 2010 - 15:38:46 CDT)
• Bin Coordinate file to pdb Philip Peartree (Thu Jul 08 2010 - 15:50:34 CDT)
  • Re: Bin Coordinate file to pdb Chris Harrison (Thu Jul 08 2010 - 18:26:51 CDT)
• FATAL ERROR: Asymmetric water molecule found??? This can't be right. Jorgen Simonsen (Wed Jul 07 2010 - 17:34:44 CDT)
• Release of the R.E.D.-III.4 tools FyD (Wed Jul 07 2010 - 02:04:36 CDT)
• (no subject) Melanie Santos Marrero (Tue Jul 06 2010 - 15:35:18 CDT)
  • Re: Eduard Schreiner (Tue Jul 06 2010 - 16:21:53 CDT)
• NAMD 2.7b3 released Jim Phillips (Tue Jul 06 2010 - 13:45:58 CDT)
• Helix tilt stefhoor (Tue Jul 06 2010 - 09:29:42 CDT)
  • Re: Helix tilt Bjoern Olausson (Tue Jul 06 2010 - 10:59:54 CDT)
  • Re: Helix tilt Nicholas M Glykos (Tue Jul 06 2010 - 11:48:22 CDT)
    • Re: Helix tilt Eduard Schreiner (Tue Jul 06 2010 - 12:27:50 CDT)
      • Re: Helix tilt Thomas C Bishop (Tue Jul 13 2010 - 01:08:45 CDT)
• save trajectory only for two residues wenchangyu2006_at_gmail.com (Tue Jul 06 2010 - 08:13:42 CDT)
  • Re: save trajectory only for two residues Chris Harrison (Tue Jul 06 2010 - 09:42:40 CDT)
    • Re: save trajectory only for two residues Eduardo (Tue Jul 06 2010 - 11:47:22 CDT)
• residue based CG method doty alexiou (Tue Jul 06 2010 - 06:22:30 CDT)
• How can I connect different structures between them using VMD and NAMD? Patriche Simona (Sun Jul 04 2010 - 19:45:15 CDT)
• O-PHOSPHOTYROSINE link to DNA base pair. q md (Sun Jul 04 2010 - 02:37:44 CDT)
• hydration in membrane-protein simulations dhacademic (Sat Jul 03 2010 - 10:20:23 CDT)
  • Re: hydration in membrane-protein simulations Chris Harrison (Tue Jul 06 2010 - 09:36:22 CDT)
• Loadleveler Script on Bluegene for NAMD Dan J Martingano (Fri Jul 02 2010 - 22:48:42 CDT)
  • RE: Loadleveler Script on Bluegene for NAMD hannes.loeffler_at_stfc.ac.uk (Sat Jul 03 2010 - 06:56:49 CDT)
• Help: NAMD on cluster; nodes reject multiple connections David Kelly (Thu Jul 01 2010 - 00:33:11 CDT)
• namd2 still works but without any new messages in log file lixb07_at_lzu.cn (Thu Jul 01 2010 - 07:21:18 CDT)
  • Re: namd2 still works but without any new messages in log file Bjoern Olausson (Thu Jul 01 2010 - 09:27:47 CDT)
  • Re: namd2 still works but without any new messages in log file Jim Phillips (Tue Jul 06 2010 - 14:22:38 CDT)
• Dihedral angle potential energy function Ajasja LjubetiÄ� (Thu Jul 01 2010 - 05:07:27 CDT)
  • Re: Dihedral angle potential energy function Jérôme Hénin (Fri Jul 02 2010 - 07:13:10 CDT)
    • Re: Dihedral angle potential energy function Ajasja LjubetiÄ� (Fri Jul 02 2010 - 08:09:44 CDT)
• NAMD with Replica Exchange Simulations on Teragrid Shi, Chuanyin (Thu Jul 01 2010 - 00:17:45 CDT)
• "didn't find VdW parameter for atom type NH3" error Emily Chen (Tue Jun 29 2010 - 07:06:33 CDT)
  • Re: "didn't find VdW parameter for atom type NH3" error Peter Freddolino (Tue Jun 29 2010 - 13:17:44 CDT)
    • Re: "didn't find VdW parameter for atom type NH3" error felmerino_at_uchile.cl (Tue Jun 29 2010 - 20:34:07 CDT)
      • Re: "didn't find VdW parameter for atom type NH3" error Peter Freddolino (Tue Jun 29 2010 - 22:02:21 CDT)
  • Re: "didn't find VdW parameter for atom type NH3" error felmerino_at_uchile.cl (Tue Jun 29 2010 - 21:20:47 CDT)
• parameters for graphene nanoribbons annealed by hydrogen ºÎع»Ô (Tue Jun 29 2010 - 03:09:15 CDT)
• OPENING EXTENDED SYSTEM TRAJECTORY FILE Parisa Akhski (Mon Jun 28 2010 - 13:47:39 CDT)
  • Re: OPENING EXTENDED SYSTEM TRAJECTORY FILE Chris Harrison (Mon Jun 28 2010 - 20:23:43 CDT)
• regarding parameter and topology files for a new molecule ajay singh (Mon Jun 28 2010 - 02:31:26 CDT)
• How do I connect the non-overlwindows of ABF's results? Aurum Bai (Sun Jun 27 2010 - 23:14:38 CDT)
• modification of CHARMM force field lixb07_at_lzu.cn (Fri Jun 25 2010 - 20:05:56 CDT)
  • Re: modification of CHARMM force field Philip Peartree (Sat Jun 26 2010 - 02:45:09 CDT)
• How to calculate binding free energy of a protein-DNA complex by using NAMD? sudipta (Fri Jun 25 2010 - 11:14:38 CDT)
• ABF question Parisa Akhski (Thu Jun 24 2010 - 16:03:15 CDT)
• Query regarding ABF Tutorial on Methane Hydration Navendu bhatnagar (Thu Jun 24 2010 - 12:38:42 CDT)
  • Re: Query regarding ABF Tutorial on Methane Hydration Chris Chipot (Thu Jun 24 2010 - 18:23:43 CDT)
• NAMD terminates prematurely without error. Ajasja LjubetiÄ� (Wed Jun 23 2010 - 02:41:24 CDT)
• Simulation configuration file not accesible listowel agyarko (Tue Jun 22 2010 - 15:30:59 CDT)
  • Re: Simulation configuration file not accesible Ajasja LjubetiÄ� (Wed Jun 23 2010 - 02:24:38 CDT)
• Query regarding ABF Tutorial on Methane Hydration Navendu bhatnagar (Tue Jun 22 2010 - 14:52:41 CDT)
  • Re: Query regarding ABF Tutorial on Methane Hydration Chris Chipot (Tue Jun 22 2010 - 15:18:10 CDT)
• ABF question Parisa Akhski (Tue Jun 22 2010 - 13:06:55 CDT)
• ABF question Parisa Akhski (Tue Jun 22 2010 - 11:43:06 CDT)
  • Re: ABF question Jérôme Hénin (Wed Jun 23 2010 - 05:17:56 CDT)
• standard state correction of delta G from a PMF Elio Cino (Tue Jun 22 2010 - 10:06:30 CDT)
• Multi-step MD in a single .conf file Jun Zhang (Mon Jun 21 2010 - 19:02:22 CDT)
• waterbox changes shape during steered molecular dynamics Mert Gür (Mon Jun 21 2010 - 14:50:58 CDT)
• waterbox changes shape during steered molecular dynamics Mert Gür (Mon Jun 21 2010 - 14:13:21 CDT)
  • Re: waterbox changes shape during steered molecular dynamics Mert Gür (Sat Jul 03 2010 - 05:58:39 CDT)
• error during charm-6.1.3 building Mikhail Suyetin (Mon Jun 21 2010 - 13:40:04 CDT)
• impose restraint on the internal coordinate of protein dhacademic (Mon Jun 21 2010 - 13:43:58 CDT)
  • Re: impose restraint on the internal coordinate of protein Eduard Schreiner (Mon Jun 21 2010 - 14:41:53 CDT)
  • Re: impose restraint on the internal coordinate of protein Giacomo Fiorin (Mon Jun 21 2010 - 16:09:20 CDT)
• (no subject) Jun Zhang (Mon Jun 21 2010 - 08:13:01 CDT)
• a question about NAMD TI 林星雨 (Sun Jun 20 2010 - 22:26:48 CDT)
  • Re: a question about NAMD TI 林星雨 (Mon Jun 21 2010 - 04:17:57 CDT)
• Hepl whit colvar subrutiene Leonardo Herrera (Fri Jun 18 2010 - 16:11:19 CDT)
  • Re: Hepl whit colvar subrutiene Giacomo Fiorin (Fri Jun 18 2010 - 20:11:10 CDT)
• phosphate parameters BIN ZHANG (Fri Jun 18 2010 - 12:42:18 CDT)
  • RE: phosphate parameters JC Gumbart (Sun Jun 20 2010 - 08:55:26 CDT)
• Reply: couldn´t find rsh program Jun Zhang (Thu Jun 17 2010 - 19:03:41 CDT)
  • Re: Reply: couldn´t find rsh program jose correa (Fri Jun 18 2010 - 10:00:21 CDT)
• couldn´t find rsh program jose correa (Thu Jun 17 2010 - 14:39:56 CDT)
  • Re: couldn´t find rsh program Axel Kohlmeyer (Thu Jun 17 2010 - 15:36:10 CDT)
  • Re: couldn´t find rsh program francesco oteri (Wed Jun 23 2010 - 14:22:43 CDT)
• NAMD parralel processor windows Ramin Omidvar (Thu Jun 17 2010 - 13:25:54 CDT)
• Distance constraint Nicolas Floquet (Thu Jun 17 2010 - 03:30:45 CDT)
  • Re: Distance constraint Jérôme Hénin (Thu Jun 17 2010 - 06:31:23 CDT)
• different values of "1-4scaling" in a system D70039 (Wed Jun 16 2010 - 06:00:06 CDT)
  • Re: different values of "1-4scaling" in a system Chris Harrison (Fri Jun 18 2010 - 11:49:49 CDT)
• Minimization messes up C terminal Pavan G (Wed Jun 16 2010 - 10:32:42 CDT)
  • Re: Minimization messes up C terminal Peter Freddolino (Wed Jun 16 2010 - 11:48:05 CDT)
    • Re: Minimization messes up C terminal Pavan G (Fri Jun 25 2010 - 09:19:42 CDT)
      • Re: Minimization messes up C terminal Peter Freddolino (Fri Jun 25 2010 - 20:02:41 CDT)
      • Re: Minimization messes up C terminal Victor Ovchinnikov (Sat Jun 26 2010 - 09:07:45 CDT)
• pairinteractions Thomas C. Bishop (Tue Jun 15 2010 - 17:34:27 CDT)
• usage of NAMD with AMBER commands Giovanni Nico (Tue Jun 15 2010 - 11:51:08 CDT)
  • Re: usage of NAMD with AMBER commands Thomas C. Bishop (Tue Jun 15 2010 - 14:25:13 CDT)
    • Re: usage of NAMD with AMBER commands francesco oteri (Tue Jun 15 2010 - 16:29:15 CDT)
• Regarding NAMD algorithm jani vinod (Tue Jun 15 2010 - 07:38:29 CDT)
• Re: Help with cys unprotonated ehenriques_at_qui.uc.pt (Tue Jun 15 2010 - 05:08:55 CDT)
  • Re: Help with cys unprotonated Leonardo Herrera (Tue Jun 15 2010 - 11:43:47 CDT)
• Help with cys unprotonated Leonardo Herrera (Mon Jun 14 2010 - 20:24:39 CDT)
• colvars don't run with minimization ... Leonardo Herrera (Mon Jun 14 2010 - 19:44:21 CDT)
  • Re: colvars don't run with minimization ... Giacomo Fiorin (Mon Jun 14 2010 - 23:06:03 CDT)
    • Re: colvars don't run with minimization ... Leonardo Herrera (Tue Jun 15 2010 - 11:45:02 CDT)
• Possible way of performing a temperature gradient?? Ranyere Deyler (Sun Jun 13 2010 - 23:19:10 CDT)
  • Re: Possible way of performing a temperature gradient?? Jérôme Hénin (Tue Jun 15 2010 - 04:57:21 CDT)
    • Re: Possible way of performing a temperature gradient?? Patrick Yee (Tue Jun 15 2010 - 07:26:45 CDT)
• Workshop on GPU Programming for Molecular Modeling, August 6-8, 2010, at the Beckman Institute in Urbana, Illinois TCBG Workshops (Fri Jun 11 2010 - 17:28:26 CDT)
• colvars: Error: in parsing "centers" Leonardo Herrera (Thu Jun 10 2010 - 19:25:16 CDT)
  • Re: colvars: Error: in parsing "centers" Giacomo Fiorin (Thu Jun 10 2010 - 21:10:55 CDT)
• NAMD on Ranger at Teragrid Zumot, Elia Nabil (Thu Jun 10 2010 - 15:08:16 CDT)
• Balancer and singularities ... Nicholas M Glykos (Thu Jun 10 2010 - 10:52:05 CDT)
• rough edges of energy landscape when running ABF crazylyf (Thu Jun 10 2010 - 09:34:56 CDT)
  • Re: rough edges of energy landscape when running ABF Giacomo Fiorin (Thu Jun 10 2010 - 12:04:14 CDT)
• Protein in a Lipid Membrane Ale Gomez (Thu Jun 10 2010 - 05:22:33 CDT)
  • Re: Protein in a Lipid Membrane Basak Isin (Thu Jun 10 2010 - 18:18:03 CDT)
    • Re: Protein in a Lipid Membrane Ale Gomez (Fri Jun 11 2010 - 08:40:33 CDT)
• Could namd use the method ONIOM of Gaussian? Aurum Bai (Thu Jun 10 2010 - 04:51:29 CDT)
  • Re: Could namd use the method ONIOM of Gaussian? Axel Kohlmeyer (Thu Jun 10 2010 - 05:36:00 CDT)
• Re: parameter format for REMD simulations Neelanjana Sengupta (Thu Jun 10 2010 - 04:00:41 CDT)
• Dreiding parameters fereshteh moradi (Wed Jun 09 2010 - 07:17:21 CDT)
• where do I find info about freeEnergy ? Leonardo Herrera (Tue Jun 08 2010 - 13:28:15 CDT)
  • Re: where do I find info about freeEnergy ? Jérôme Hénin (Tue Jun 08 2010 - 15:36:49 CDT)
• colvar atom syntax Michael Zimmermann (Tue Jun 08 2010 - 13:11:29 CDT)
  • Re: colvar atom syntax Giacomo Fiorin (Tue Jun 08 2010 - 15:01:41 CDT)
  • Re: colvar atom syntax Michael Zimmermann (Thu Jun 10 2010 - 15:15:41 CDT)
    • Re: colvar atom syntax Michael Zimmermann (Thu Jun 10 2010 - 15:40:53 CDT)
    • Re: Re: colvar atom syntax Giacomo Fiorin (Thu Jun 10 2010 - 17:20:18 CDT)
      • Re: Re: colvar atom syntax Michael Zimmermann (Tue Jun 15 2010 - 15:59:09 CDT)
      • Re: Re: colvar atom syntax Jérôme Hénin (Wed Jun 16 2010 - 07:24:51 CDT)
      • Re: Re: colvar atom syntax Michael Zimmermann (Wed Jun 16 2010 - 10:24:50 CDT)
      • Re: Re: colvar atom syntax Giacomo Fiorin (Wed Jun 16 2010 - 11:20:33 CDT)
      • Re: Re: colvar atom syntax Jérôme Hénin (Wed Jun 16 2010 - 11:42:09 CDT)
• TIP4P water in AMBER parm7 format fails with 2010-06-07 nightly build Hugh Heldenbrand (Tue Jun 08 2010 - 10:30:41 CDT)
  • Re: TIP4P water in AMBER parm7 format fails with 2010-06-07 nightly build Peter Freddolino (Tue Jun 08 2010 - 19:12:11 CDT)
    • Re: TIP4P water in AMBER parm7 format fails with 2010-06-07 nightly build Hugh Heldenbrand (Fri Jun 11 2010 - 15:55:24 CDT)
      • Re: TIP4P water in AMBER parm7 format fails with 2010-06-07 nightly build Peter Freddolino (Sat Jun 12 2010 - 08:41:24 CDT)
• gradient tolerance Ramya Narasimhan (Tue Jun 08 2010 - 05:48:11 CDT)
• Regarding temperature accelerated MD Ramya Narasimhan (Tue Jun 08 2010 - 05:32:34 CDT)
• Fatal error when running ABF simulation crazylyf (Tue Jun 08 2010 - 01:00:01 CDT)
  • Re: Fatal error when running ABF simulation Giacomo Fiorin (Tue Jun 08 2010 - 08:45:10 CDT)
• Fwd: error : atom moving too fast ipsita basu (Tue Jun 08 2010 - 00:20:24 CDT)
  • Re: error : atom moving too fast ipsita basu (Fri Jun 11 2010 - 00:19:15 CDT)
    • Re: error : atom moving too fast francesco oteri (Fri Jun 11 2010 - 01:26:57 CDT)
      • Re: error : atom moving too fast ipsita basu (Mon Jun 14 2010 - 01:52:37 CDT)
      • Re: error : atom moving too fast francesco oteri (Mon Jun 14 2010 - 02:32:07 CDT)
• Control DCD file TAEJIN KIM (Mon Jun 07 2010 - 17:09:20 CDT)
• RDF.tcl selections Rabab Toubar (Mon Jun 07 2010 - 13:40:56 CDT)
• distance colvar Neelanjana Sengupta (Mon Jun 07 2010 - 03:07:51 CDT)
  • Re: distance colvar Branko (Mon Jun 07 2010 - 06:17:34 CDT)
  • Re: distance colvar Jérôme Hénin (Mon Jun 07 2010 - 06:27:00 CDT)
• compiling NAMD w. infiniband Irene Newhouse (Fri Jun 04 2010 - 16:21:37 CDT)
• rotational restrains Ziemys, Arturas (Fri Jun 04 2010 - 13:34:18 CDT)
  • Re: rotational restrains Jérôme Hénin (Fri Jun 04 2010 - 16:03:13 CDT)
• Problem with extraBonds Leonardo Herrera (Thu Jun 03 2010 - 20:23:32 CDT)
• Appropriate dcdfreq Philip Peartree (Thu Jun 03 2010 - 15:33:53 CDT)
  • Re: Appropriate dcdfreq poker_at_physics.usyd.edu.au (Fri Jun 04 2010 - 01:22:07 CDT)
• Minimization at higher temperature Rabab Toubar (Thu Jun 03 2010 - 14:08:37 CDT)
  • Unsubscribe Siddharth Srinivasan (Thu Jun 03 2010 - 16:58:21 CDT)
  • Re: Minimization at higher temperature felmerino_at_uchile.cl (Thu Jun 03 2010 - 17:41:15 CDT)
• Wrong energies in CUDA version Jeff Wereszczynski (Thu Jun 03 2010 - 11:45:13 CDT)
  • Re: Wrong energies in CUDA version francesco oteri (Thu Jun 03 2010 - 15:10:00 CDT)
    • Re: Wrong energies in CUDA version Jeff Wereszczynski (Thu Jun 03 2010 - 21:25:45 CDT)
• help whit distance restraint Leonardo Herrera (Wed Jun 02 2010 - 17:37:57 CDT)
  • Re: help whit distance restraint Axel Kohlmeyer (Wed Jun 02 2010 - 18:11:00 CDT)
• charges in psf and in namd (or vmd) fett_at_vtr.net (Wed Jun 02 2010 - 11:12:07 CDT)
• Sudden crash - any clue about the cause? --> wc[0] status 12 wc[i].opcode 0 Bjoern Olausson (Wed Jun 02 2010 - 08:32:24 CDT)
  • Re: Sudden crash - any clue about the cause? --> wc[0] status 12 wc[i].opcode 0 Bjoern Olausson (Wed Jun 02 2010 - 10:13:32 CDT)
• Run simulation in NAMD using files generated by CHARMM-GUI Dai, Jian1 (Tue Jun 01 2010 - 00:09:27 CDT)
  • Re: Run simulation in NAMD using files generated by CHARMM-GUI Bjoern Olausson (Tue Jun 01 2010 - 03:22:25 CDT)
• Dowser Basak Isin (Sat May 29 2010 - 19:25:37 CDT)
  • Re: Dowser Axel Kohlmeyer (Sat May 29 2010 - 20:09:24 CDT)
    • Re: Dowser Basak Isin (Sat May 29 2010 - 20:21:38 CDT)
  • RE: Dowser Song, Hyundeok (songhk) (Sat May 29 2010 - 20:42:49 CDT)
    • Re: Dowser Basak Isin (Sat May 29 2010 - 21:48:12 CDT)
      • RE: Dowser Song, Hyundeok (songhk) (Sat May 29 2010 - 22:22:15 CDT)
  • Re: Dowser Felipe Merino (Sat May 29 2010 - 21:51:28 CDT)
• multistep minimization with different constraint Mengchen Pu (Fri May 28 2010 - 06:29:34 CDT)
• are tclForces included in minimization? Michael Zimmermann (Fri May 28 2010 - 00:41:26 CDT)
• new NAMD user ABF setup question Elio Cino (Thu May 27 2010 - 14:10:04 CDT)
  • Re: new NAMD user ABF setup question Giacomo Fiorin (Thu May 27 2010 - 16:27:02 CDT)
    • Re: new NAMD user ABF setup question Elio Cino (Fri May 28 2010 - 07:48:03 CDT)
      • Re: new NAMD user ABF setup question Giacomo Fiorin (Fri May 28 2010 - 09:03:59 CDT)
      • Re: new NAMD user ABF setup question Jérôme Hénin (Sat May 29 2010 - 05:06:50 CDT)
      • Re: new NAMD user ABF setup question Elio Cino (Mon May 31 2010 - 09:57:21 CDT)
      • Re: new NAMD user ABF setup question Chris Chipot (Mon May 31 2010 - 10:29:53 CDT)
      • Re: new NAMD user ABF setup question Felipe Merino (Tue Jun 01 2010 - 20:15:53 CDT)
      • Re: new NAMD user ABF setup question Jérôme Hénin (Wed Jun 02 2010 - 09:53:05 CDT)
• monitoring instantaneous kinetic energy of a subsystem Rocchia Walter (Thu May 27 2010 - 06:52:16 CDT)
• multiplicity of dihedrals matziast_at_med.uth.gr (Thu May 27 2010 - 03:02:16 CDT)
  • Re: multiplicity of dihedrals Ajasja LjubetiÄ� (Thu May 27 2010 - 03:45:45 CDT)
• Temperature gradient! Ranyere Deyler (Wed May 26 2010 - 22:35:35 CDT)
  • Re: Temperature gradient! Jérôme Hénin (Thu May 27 2010 - 07:39:32 CDT)
• K25 NIH award Gianluca Interlandi (Wed May 26 2010 - 19:45:33 CDT)
• backbone restraints Michael Zimmermann (Wed May 26 2010 - 10:46:09 CDT)
  • Re: backbone restraints Jérôme Hénin (Wed May 26 2010 - 14:47:13 CDT)
• NAMD 2.7b2 versy slow on multiple nodes Laurent Chaloin (Tue May 25 2010 - 16:30:51 CDT)
• parameter file for CHARMM matziast_at_med.uth.gr (Tue May 25 2010 - 16:05:09 CDT)
  • Re: parameter file for CHARMM ehenriques_at_qui.uc.pt (Wed May 26 2010 - 03:53:39 CDT)
    • Re: parameter file for CHARMM fett_at_vtr.net (Wed Jun 02 2010 - 09:57:09 CDT)
• namd cuda with geforce 470 (fermi) gpu fatal error at runtime Phil Greer (Tue May 25 2010 - 13:52:41 CDT)
  • FW: namd cuda with geforce 470 (fermi) gpu fatal error at runtime ÁõÏþ¹â (Sun Jun 06 2010 - 06:50:56 CDT)
• RE: ABF question Patrick Yee (Tue May 25 2010 - 13:38:33 CDT)
  • Re: ABF question Giacomo Fiorin (Tue May 25 2010 - 20:07:51 CDT)
• ABF (NAMD 2.7x) speed ? Ziemys, Arturas (Tue May 25 2010 - 09:51:33 CDT)
  • Re: ABF (NAMD 2.7x) speed ? Jérôme Hénin (Tue May 25 2010 - 10:47:32 CDT)
    • Re: ABF (NAMD 2.7x) speed ? Jérôme Hénin (Wed May 26 2010 - 04:52:22 CDT)
      • RE: ABF (NAMD 2.7x) speed ? Ziemys, Arturas (Wed May 26 2010 - 07:24:54 CDT)
• ABF question Ziemys, Arturas (Tue May 25 2010 - 08:51:39 CDT)
  • Re: ABF question Jérôme Hénin (Tue May 25 2010 - 10:35:52 CDT)
• Question about Tcl/customising the colvar module poker_at_physics.usyd.edu.au (Tue May 25 2010 - 04:25:34 CDT)
  • Re: Question about Tcl/customising the colvar module Giacomo Fiorin (Tue May 25 2010 - 08:54:17 CDT)
    • Re: Question about Tcl/customising the colvar module Patrick Yee (Tue May 25 2010 - 18:47:35 CDT)
    • Re: Question about Tcl/customising the colvar module poker_at_physics.usyd.edu.au (Tue May 25 2010 - 22:39:48 CDT)
• New NVIDIA GPU C2050 Richard Owczarzy (Tue May 25 2010 - 00:29:24 CDT)
• Drift of the center of mass of lipid bilayer Dai, Jian1 (Mon May 24 2010 - 13:26:39 CDT)
• Two questions about essential dynamics Jun Zhang (Mon May 24 2010 - 06:48:34 CDT)
  • Re: Two questions about essential dynamics Axel Kohlmeyer (Mon May 24 2010 - 07:41:35 CDT)
  • Slab Boundary Conditions. Amr Zeinalabideen Majul (Mon May 24 2010 - 14:48:47 CDT)
• Problems about FEP simulation Yang Gao (Fri May 21 2010 - 11:03:08 CDT)
  • Re: Problems about FEP simulation m.raviprasad_at_ndsu.edu (Fri May 21 2010 - 14:52:53 CDT)
• Re: Error in running minimization m.raviprasad_at_ndsu.edu (Fri May 21 2010 - 09:27:08 CDT)
• Difference between the two Dowsers Ning Zhang (Fri May 21 2010 - 05:26:37 CDT)
  • Re: Difference between the two Dowsers Leonardo Trabuco (Fri Jun 04 2010 - 02:47:21 CDT)
• Error in running minimization Prija Ponnan (Fri May 21 2010 - 05:24:58 CDT)
• selective rigidbonds Sabyashachi Mishra (Fri May 21 2010 - 04:29:57 CDT)
  • Re: selective rigidbonds Jérôme Hénin (Fri May 21 2010 - 05:47:29 CDT)
• requirements for running the precompiled Linux-x86_64-ibverbs Guanglei Cui (Thu May 20 2010 - 08:49:26 CDT)
• Phi MD Rabab Toubar (Thu May 20 2010 - 08:07:45 CDT)
• How to solve the out of cell box for long time in Periodic Boundary Conditions? Aurum Bai (Wed May 19 2010 - 21:06:38 CDT)
  • Re: How to solve the out of cell box for long time in Periodic Boundary Conditions? Jérôme Hénin (Thu May 20 2010 - 10:00:08 CDT)
• Constraint Failure in SMD simulation Ramin Omidvar (Wed May 19 2010 - 11:51:20 CDT)
  • Re: Constraint Failure in SMD simulation felmerino_at_uchile.cl (Wed May 19 2010 - 14:48:31 CDT)
    • Re: Constraint Failure in SMD simulation Ramin Omidvar (Tue Jul 13 2010 - 08:04:20 CDT)
      • Re: Constraint Failure in SMD simulation felmerino_at_uchile.cl (Tue Jul 13 2010 - 23:18:47 CDT)
• Analysis of Results of only Lipid Bilayer Simulations Saumya (Wed May 19 2010 - 05:22:06 CDT)
  • Re: Analysis of Results of only Lipid Bilayer Simulations jani vinod (Wed May 19 2010 - 06:36:09 CDT)
• PLUMED release 1.2.0 available Massimiliano Bonomi (Tue May 18 2010 - 06:47:05 CDT)
• Input/output error Íõ—² (Tue May 18 2010 - 01:55:20 CDT)
  • Re: Input/output error Axel Kohlmeyer (Tue May 18 2010 - 04:18:20 CDT)
• duplicate residue key ALA will be ignored Mert Gür (Mon May 17 2010 - 16:42:59 CDT)
  • Re: duplicate residue key ALA will be ignored ehenriques_at_qui.uc.pt (Tue May 18 2010 - 04:28:24 CDT)
  • Re: duplicate residue key ALA will be ignored flavio seixas (Tue May 18 2010 - 11:21:07 CDT)
    • Re: duplicate residue key ALA will be ignored Mert Gür (Tue May 18 2010 - 11:37:57 CDT)
• (no subject) Mert Gür (Mon May 17 2010 - 16:11:22 CDT)
• ABF in various simulations stefhoor (Mon May 17 2010 - 08:30:36 CDT)
  • Re: ABF in various simulations Patrick Yee (Mon May 17 2010 - 10:47:58 CDT)
    • Re: ABF in various simulations stefhoor (Mon May 17 2010 - 11:31:03 CDT)
      • Re: ABF in various simulations Robert Elder (Mon May 17 2010 - 14:42:30 CDT)
      • Re: ABF in various simulations stefhoor (Mon May 17 2010 - 15:18:57 CDT)
      • Re: ABF in various simulations Robert Elder (Mon May 17 2010 - 18:43:41 CDT)
      • Re: ABF in various simulations Giacomo Fiorin (Mon May 17 2010 - 21:17:32 CDT)
  • Re: ABF in various simulations Jérôme Hénin (Mon May 17 2010 - 11:08:28 CDT)
• trouble running metalloprotein simulation from literature Sibo Lin (Sat May 15 2010 - 14:44:40 CDT)
• Generate psf files from Scott Feller's lipid coordinates Dai, Jian1 (Sat May 15 2010 - 13:46:36 CDT)
  • Re: Generate psf files from Scott Feller's lipid coordinates Jeffrey Potoff (Sun May 16 2010 - 01:35:23 CDT)
    • Re: Generate psf files from Scott Feller's lipid coordinates Ranyere Deyler (Mon May 17 2010 - 16:57:10 CDT)
• Acetyl group patch for lysine residue Prija Ponnan (Sat May 15 2010 - 08:19:51 CDT)
  • Re: Acetyl group patch for lysine residue ehenriques_at_qui.uc.pt (Mon May 17 2010 - 03:56:01 CDT)
• About RMSD based PMF's Felipe Merino (Thu May 13 2010 - 23:03:44 CDT)
  • Re: About RMSD based PMF's Jérôme Hénin (Fri May 14 2010 - 06:05:28 CDT)
• TCBG "Hands-on" Workshop on Computational Biophysics, July 12-16, 2010, at San Diego TCBG Workshops (Thu May 13 2010 - 16:33:11 CDT)
• Compiling NAMD under SGE and OpenMPI Gabriel Jara (Thu May 13 2010 - 11:34:49 CDT)
• Waterbox used in minimization? Cem Meydan (Thu May 13 2010 - 07:25:30 CDT)
  • Re: Waterbox used in minimization? Giacomo Fiorin (Thu May 13 2010 - 16:08:13 CDT)
• FEP yields the same results for forward and backward computation! Jun Zhang (Wed May 12 2010 - 22:38:44 CDT)
  • Re: FEP yields the same results for forward and backward computation! Felipe Merino (Thu May 13 2010 - 01:24:37 CDT)
    • Re: FEP yields the same results for forward and backward computation! Jun Zhang (Thu May 13 2010 - 08:48:42 CDT)
      • Re: FEP yields the same results for forward and backward computation! Lela Vukovic (Tue May 18 2010 - 13:08:02 CDT)
• protein unfolding no increase in conf energy Odysseas Axillews (Wed May 12 2010 - 05:25:24 CDT)
• Atom movement within a range of Z value muniyamuthu.raviprasad_at_ndsu.edu (Tue May 11 2010 - 14:47:15 CDT)
  • Re: Atom movement within a range of Z value Axel Kohlmeyer (Tue May 11 2010 - 15:27:44 CDT)
  • Re: Atom movement within a range of Z value Eduardo Cruz-Chu (Tue May 11 2010 - 15:45:59 CDT)
    • Re: Atom movement within a range of Z value Jérôme Hénin (Wed May 12 2010 - 02:31:51 CDT)
• a gap in flowing water fereshteh moradi (Tue May 11 2010 - 06:45:31 CDT)
• psfgen creates too many bonds in a distorted Fe4S4 cluster Sibo Lin (Mon May 10 2010 - 22:50:00 CDT)
• mininization do not go on flavio seixas (Sun May 09 2010 - 08:58:19 CDT)
  • Re: mininization do not go on muniyamuthu.raviprasad_at_ndsu.edu (Mon May 10 2010 - 22:18:19 CDT)
• blank between nanotube and the bulk water fereshteh moradi (Fri May 07 2010 - 23:29:22 CDT)
• installation of namd without tcl and fftw ipsita basu (Mon May 10 2010 - 06:11:39 CDT)
  • Re: installation of namd without tcl and fftw Axel Kohlmeyer (Mon May 10 2010 - 06:58:59 CDT)
    • Re: installation of namd without tcl and fftw Jérôme Hénin (Tue May 11 2010 - 05:16:01 CDT)
      • Re: installation of namd without tcl and fftw Axel Kohlmeyer (Tue May 11 2010 - 06:55:33 CDT)
      • Re: installation of namd without tcl and fftw ipsita basu (Tue May 11 2010 - 08:02:11 CDT)
      • Re: installation of namd without tcl and fftw Axel Kohlmeyer (Tue May 11 2010 - 08:11:24 CDT)
  • Re: installation of namd without tcl and fftw Jérôme Hénin (Mon May 10 2010 - 07:51:53 CDT)
    • Re: installation of namd without tcl and fftw ipsita basu (Tue May 11 2010 - 00:40:59 CDT)
      • Re: installation of namd without tcl and fftw Jérôme Hénin (Tue May 11 2010 - 03:41:00 CDT)
• Timestep 594 flavio seixas (Sun May 09 2010 - 09:39:36 CDT)
  • Re: Timestep 594 Bo Liu (Sun May 09 2010 - 11:28:05 CDT)
    • Re: Timestep 594 flavio seixas (Tue May 11 2010 - 15:38:14 CDT)
      • Re: Timestep 594 Bo Liu (Tue May 11 2010 - 18:50:09 CDT)
• looking for topology and parameters of methamphetamine Liao Chen (Sun May 09 2010 - 08:47:46 CDT)
  • Re: looking for topology and parameters of methamphetamine harish vashisth (Sun May 09 2010 - 12:42:37 CDT)
• Free energy calculation yields strange results Jun Zhang (Sun May 09 2010 - 07:53:36 CDT)
  • Re: Free energy calculation yields strange results Jérôme Hénin (Mon May 10 2010 - 08:04:43 CDT)
    • Re: Free energy calculation yields strange results Jun Zhang (Tue May 11 2010 - 21:25:57 CDT)
• ReassignFreq script fail!! Ranyere Deyler (Sat May 08 2010 - 03:10:14 CDT)
• How I can insert de harmonic restraint? Leonardo Herrera (Fri May 07 2010 - 15:33:18 CDT)
• Nightly build version: Parallel IO can not be used with langevin On Yudong Sun (Fri May 07 2010 - 06:21:57 CDT)
  • Re: Nightly build version: Parallel IO can not be used with langevin On Yudong Sun (Wed May 19 2010 - 07:01:51 CDT)
    • Re: Nightly build version: Parallel IO can not be used with langevin On Gabriel Jara (Wed May 19 2010 - 07:46:18 CDT)
    • Re: Nightly build version: Parallel IO can not be used with langevin On Bryan Holland (Wed May 19 2010 - 09:21:25 CDT)
    • Re: Nightly build version: Parallel IO can not be used with langevin On Bryan Holland (Wed May 19 2010 - 10:21:59 CDT)
• Best tool to use to generate a custom (patched) polypeptide PDB? Jason Richard Mick (Thu May 06 2010 - 17:23:54 CDT)
• NAMD 2.7b1 distanceDir Guanglei Cui (Thu May 06 2010 - 13:03:34 CDT)
  • Re: NAMD 2.7b1 distanceDir Giacomo Fiorin (Thu May 06 2010 - 17:22:40 CDT)
    • Re: NAMD 2.7b1 distanceDir Guanglei Cui (Fri May 07 2010 - 12:02:15 CDT)
      • Re: NAMD 2.7b1 distanceDir Giacomo Fiorin (Fri May 07 2010 - 17:16:31 CDT)
      • Re: NAMD 2.7b1 distanceDir Guanglei Cui (Mon May 10 2010 - 11:04:25 CDT)
• Re: error : atom moving too fast muniyamuthu.raviprasad_at_ndsu.edu (Wed May 05 2010 - 09:58:50 CDT)
  • Re: error : atom moving too fast ipsita basu (Thu May 06 2010 - 05:32:13 CDT)
    • Re: error : atom moving too fast Bjoern Olausson (Thu May 06 2010 - 06:34:45 CDT)
    • Re: error : atom moving too fast muniyamuthu.raviprasad_at_ndsu.edu (Thu May 06 2010 - 09:35:02 CDT)
      • Re: error : atom moving too fast ipsita basu (Fri May 14 2010 - 00:14:30 CDT)
      • Re: error : atom moving too fast muniyamuthu.raviprasad_at_ndsu.edu (Fri May 14 2010 - 14:20:42 CDT)
  • Re: error : atom moving too fast muniyamuthu.raviprasad_at_ndsu.edu (Wed May 19 2010 - 09:40:00 CDT)
• error : atom moving too fast ipsita basu (Wed May 05 2010 - 01:10:33 CDT)
• high atom velocity Mark M Huntress (Tue May 04 2010 - 14:36:56 CDT)
  • Re: high atom velocity francesco oteri (Tue May 04 2010 - 16:33:43 CDT)
    • Re: high atom velocity francesco oteri (Wed May 05 2010 - 14:12:49 CDT)
• Using RMSD in colvar Stefan Franzen (Mon May 03 2010 - 17:42:18 CDT)
  • Re: Using RMSD in colvar Jérôme Hénin (Tue May 04 2010 - 15:07:38 CDT)
  • Re: Using RMSD in colvar Giacomo Fiorin (Tue May 04 2010 - 16:41:37 CDT)
    • unsubscribe Cojocaru,Vlad (Thu May 06 2010 - 03:12:48 CDT)
• Particle Mesh Ewald question (from the tutorial) Stefan Franzen (Mon May 03 2010 - 17:39:38 CDT)
• RE: TMD simulations Andres Morales N (Mon May 03 2010 - 21:25:29 CDT)
• TMD simulations Andres Morales N (Fri Apr 30 2010 - 02:52:52 CDT)
  • FW: TMD simulations Andres Morales N (Fri Apr 30 2010 - 19:42:08 CDT)
    • Re: FW: TMD simulations Joshua Adelman (Fri Apr 30 2010 - 21:21:15 CDT)
• langevinhydrogen on with rigidbonds water Mark M Huntress (Fri Apr 30 2010 - 11:29:55 CDT)
• colvar: coordnum output Neelanjana Sengupta (Fri Apr 30 2010 - 05:34:29 CDT)
  • Re: colvar: coordnum output Jérôme Hénin (Fri Apr 30 2010 - 07:16:44 CDT)
    • Re: colvar: coordnum output Neelanjana Sengupta (Fri Apr 30 2010 - 07:32:55 CDT)
      • Re: colvar: coordnum output Jérôme Hénin (Fri Apr 30 2010 - 07:44:20 CDT)
  • Re: colvar: coordnum output Giacomo Fiorin (Fri Apr 30 2010 - 09:25:14 CDT)
    • Re: colvar: coordnum output Jérôme Hénin (Sat May 01 2010 - 03:28:02 CDT)
      • Re: colvar: coordnum output Neelanjana Sengupta (Thu May 06 2010 - 05:17:19 CDT)
• software/algorithm to cluster protein conformations Basak Isin (Thu Apr 29 2010 - 17:51:59 CDT)
  • Re: software/algorithm to cluster protein conformations Joshua Adelman (Thu Apr 29 2010 - 18:06:38 CDT)
  • Re: software/algorithm to cluster protein conformations Nicholas M Glykos (Fri Apr 30 2010 - 04:40:02 CDT)
    • Re: software/algorithm to cluster protein conformations Ajasja LjubetiÄ� (Fri Apr 30 2010 - 12:08:48 CDT)
• NAMD complain about gromacs ff parameter ATOMTYPES definition Íõ—² (Wed Apr 28 2010 - 22:36:10 CDT)
• Charmm parameters for Joakim Swedberg (Wed Apr 28 2010 - 21:47:03 CDT)
• NVE crash pellegrini (Wed Apr 28 2010 - 10:30:09 CDT)
• Dielectric Constant ydhuang2727 (Tue Apr 27 2010 - 20:23:11 CDT)
  • Re: Dielectric Constant Axel Kohlmeyer (Wed Apr 28 2010 - 11:17:58 CDT)
    • Re:Re: Dielectric Constant ydhuang2727 (Wed Apr 28 2010 - 22:54:30 CDT)
      • Re: Re: Dielectric Constant Axel Kohlmeyer (Wed Apr 28 2010 - 23:44:20 CDT)
      • Re: Re: Dielectric Constant Axel Kohlmeyer (Thu Apr 29 2010 - 00:06:18 CDT)
      • Re:Re: Re: Dielectric Constant ydhuang2727 (Thu Apr 29 2010 - 01:19:46 CDT)
      • Re: Re: Dielectric Constant Jérôme Hénin (Thu Apr 29 2010 - 02:59:42 CDT)
      • Re:Re: Re: Dielectric Constant ydhuang2727 (Thu Apr 29 2010 - 07:39:49 CDT)
      • Re: Re: Re: Dielectric Constant Axel Kohlmeyer (Thu Apr 29 2010 - 08:34:36 CDT)
      • Re: Re: Re: Dielectric Constant Jérôme Hénin (Thu Apr 29 2010 - 10:06:57 CDT)
      • TMD SCRIPT Sebastian Stolzenberg (Thu Apr 29 2010 - 11:11:42 CDT)
      • Re:Re: Re: Re: Dielectric Constant ydhuang2727 (Thu Apr 29 2010 - 20:59:23 CDT)
      • Re: Re: Re: Re: Dielectric Constant Axel Kohlmeyer (Thu Apr 29 2010 - 21:34:42 CDT)
      • Re:Re: Re: Re: Re: Dielectric Constant ydhuang2727 (Sat May 01 2010 - 08:03:01 CDT)
      • Re: Re:Re: Re: Re: Re: Dielectric Constant Axel Kohlmeyer (Sat May 01 2010 - 13:22:10 CDT)
    • Re: Re: Re:Re: Re: Re: Re: Dielectric Constant Axel Kohlmeyer (Tue May 04 2010 - 08:03:08 CDT)
      • Re:Re: Re: Re:Re: Re: Re: Re: Dielectric Constant ydhuang2727 (Wed May 05 2010 - 09:45:20 CDT)
      • Re: Dielectric Constant David Hardy (Wed May 05 2010 - 21:16:06 CDT)
• evaluating energy in a trajectory of variable box size? Jose Borreguero (Tue Apr 27 2010 - 14:04:11 CDT)
• the unit of dipole moment in the calculation of dielectric constant. superdirac (Sun Apr 25 2010 - 21:58:11 CDT)
  • Pair interaction calculation - Direction of the force Priyan Amaras (Thu May 06 2010 - 10:25:44 CDT)
• something is wrong with my equilibration Ning Zhang (Sun Apr 25 2010 - 21:52:10 CDT)
  • Re: something is wrong with my equilibration francesco oteri (Mon Apr 26 2010 - 05:12:04 CDT)
• VRPN driver for Novint Falcon haptic device available - Looking for testers Axel Kohlmeyer (Fri Apr 23 2010 - 16:03:08 CDT)
• Dihedral parameters for side-chains? Igor Petrik (Fri Apr 23 2010 - 11:50:30 CDT)
  • Re: Dihedral parameters for side-chains? Jun Zhang (Sat Apr 24 2010 - 22:29:12 CDT)
    • Re: Dihedral parameters for side-chains? Igor Petrik (Sat Apr 24 2010 - 22:41:06 CDT)
      • Re: Dihedral parameters for side-chains? Jérôme Hénin (Mon Apr 26 2010 - 07:29:40 CDT)
      • Re: Dihedral parameters for side-chains? Igor Petrik (Mon Apr 26 2010 - 07:54:41 CDT)
• lipids moving crazylyf (Thu Apr 22 2010 - 21:05:33 CDT)
• Re: help Jérôme Hénin (Thu Apr 22 2010 - 16:44:58 CDT)
• error while running config file Asmita Gupta (Thu Apr 22 2010 - 13:41:29 CDT)
  • Re: error while running config file muniyamuthu.raviprasad_at_ndsu.edu (Thu Apr 22 2010 - 16:01:30 CDT)
• Running REMD with CHARMM f.f. jaya c.jose (Thu Apr 22 2010 - 06:37:05 CDT)
• Re: topology file for dissacharides with psfgen Milton Sonoda (Thu Apr 22 2010 - 00:11:03 CDT)
• topology file for dissacharides with psfgen Milton Sonoda (Wed Apr 21 2010 - 23:38:56 CDT)
• NAMD CONFIG FILE:: Asmita Gupta (Wed Apr 21 2010 - 12:50:51 CDT)
  • Re: NAMD CONFIG FILE:: Patrick Yee (Wed Apr 21 2010 - 14:34:49 CDT)
• building a MARTINI bilayer Edward Lyman (Wed Apr 21 2010 - 12:41:35 CDT)
  • Re: building a MARTINI bilayer Peter Freddolino (Wed Apr 21 2010 - 13:16:00 CDT)
• setting transfer rate in IMD protocol Magdalena Gruziel (Wed Apr 21 2010 - 09:22:22 CDT)
  • Re: setting transfer rate in IMD protocol Axel Kohlmeyer (Wed Apr 21 2010 - 10:57:30 CDT)
• the total energy of single H2O molecule uu zhu (Wed Apr 21 2010 - 09:11:45 CDT)
  • Re: the total energy of single H2O molecule Jérôme Hénin (Wed Apr 21 2010 - 11:50:13 CDT)
    • Re: the total energy of single H2O molecule uu zhu (Wed Apr 21 2010 - 21:04:24 CDT)
• colvar for PMF calculation Navendu bhatnagar (Tue Apr 20 2010 - 18:02:28 CDT)
  • Re: colvar for PMF calculation Jérôme Hénin (Wed Apr 21 2010 - 05:13:48 CDT)
• simulating dna Asmita Gupta (Tue Apr 20 2010 - 12:02:36 CDT)
  • Re: simulating dna Ronald Salesky (Tue Apr 20 2010 - 14:18:51 CDT)
• simulating DNA using namd:: Asmita Gupta (Tue Apr 20 2010 - 07:07:34 CDT)
  • Re: simulating DNA using namd:: Xueqing Zou (Tue Apr 20 2010 - 09:48:46 CDT)
• Running REMD with CHARMM f.f. jaya c.jose (Tue Apr 20 2010 - 06:52:58 CDT)
• unsubscribe sathish kumar gurupatham (Mon Apr 19 2010 - 09:25:06 CDT)
  • Re: unsubscribe Jérôme Hénin (Mon Apr 19 2010 - 11:10:47 CDT)
• ABF: moving system in Z direction sefer baday (Mon Apr 19 2010 - 08:49:09 CDT)
  • Re: ABF: moving system in Z direction Jérôme Hénin (Mon Apr 19 2010 - 11:20:35 CDT)
    • Re: ABF: moving system in Z direction sefer baday (Mon Apr 19 2010 - 11:59:03 CDT)
  • Re: ABF: moving system in Z direction Giacomo Fiorin (Mon Apr 19 2010 - 12:16:08 CDT)
    • Re: ABF: moving system in Z direction sefer baday (Tue Apr 20 2010 - 04:58:51 CDT)
      • Re: ABF: moving system in Z direction Giacomo Fiorin (Tue Apr 20 2010 - 09:06:52 CDT)
      • NAMD2.7/MEtadynamics simulation analysis disparity neville forlemu (Thu Apr 29 2010 - 13:30:42 CDT)
      • Re: NAMD2.7/MEtadynamics simulation analysis disparity felmerino_at_uchile.cl (Thu Apr 29 2010 - 20:49:34 CDT)
      • Re: NAMD2.7/MEtadynamics simulation analysis disparity neville forlemu (Fri Apr 30 2010 - 09:20:41 CDT)
      • Re: NAMD2.7/MEtadynamics simulation analysis disparity Giacomo Fiorin (Fri Apr 30 2010 - 09:16:17 CDT)
• Q=B4=D7=D4y=5Fja@163.com=B5=C4=D3=CA=BC=FE?= y_ja (Mon Apr 19 2010 - 02:09:29 CDT)
• unsubscribe Falgun Shah (Sun Apr 18 2010 - 22:53:44 CDT)
• modifying velocities within global master Nicholas Musolino (Sun Apr 18 2010 - 16:42:51 CDT)
  • RE: modifying velocities within global master Bennion, Brian (Tue Apr 20 2010 - 15:09:06 CDT)
• re a problem with "Charging a spherical ion" Jun Zhang (Sun Apr 18 2010 - 03:21:38 CDT)
• unsubscribe shivam ghosh (Sat Apr 17 2010 - 21:10:14 CDT)
• (no subject) 张鋆 (Fri Apr 16 2010 - 22:04:17 CDT)
  • Re: Chris Chipot (Sat Apr 17 2010 - 19:34:24 CDT)
• colvar: atom group defn. fails Neelanjana Sengupta (Fri Apr 16 2010 - 05:29:29 CDT)
  • Re: colvar: atom group defn. fails y_ja_at_163.com (Fri Apr 16 2010 - 05:35:46 CDT)
  • Re: colvar: atom group defn. fails Jérôme Hénin (Fri Apr 16 2010 - 07:17:38 CDT)
  • Problems with tcl scripts for REMD simulation Wei Huang (Fri Apr 16 2010 - 15:41:25 CDT)
• ABF non-uniform sampling Patrick Yee (Thu Apr 15 2010 - 22:19:45 CDT)
  • Re: ABF non-uniform sampling Branko (Fri Apr 16 2010 - 05:04:37 CDT)
    • Re: ABF non-uniform sampling Patrick Yee (Sat May 01 2010 - 11:14:52 CDT)
      • Re: ABF non-uniform sampling Giacomo Fiorin (Sat May 01 2010 - 14:37:22 CDT)
      • Re: ABF non-uniform sampling Branko (Sun May 02 2010 - 13:36:40 CDT)
  • Re: ABF non-uniform sampling Jérôme Hénin (Fri Apr 16 2010 - 04:48:17 CDT)
• FATAL ERROR: ABNORMAL EOF FOUND-buffer Jignesh Patel (Thu Apr 15 2010 - 15:11:55 CDT)
• How to use harmonic restraint parameter for 2 selection of atoms Íõ—² (Thu Apr 15 2010 - 02:00:06 CDT)
• which one is better to use - fixed atoms or constraints? Jignesh Patel (Wed Apr 14 2010 - 12:09:07 CDT)
  • Re: which one is better to use - fixed atoms or constraints? Giacomo Fiorin (Wed Apr 14 2010 - 14:21:35 CDT)
    • Re: which one is better to use - fixed atoms or constraints? Jérôme Hénin (Wed Apr 14 2010 - 16:41:09 CDT)
• Implementation of Martini CG FF in NAMD Liao Chuan (Wed Apr 14 2010 - 11:25:50 CDT)
• file writing stopped francesco oteri (Wed Apr 14 2010 - 03:34:59 CDT)
  • Re: file writing stopped Nicholas M Glykos (Wed Apr 14 2010 - 05:01:06 CDT)
  • Re: file writing stopped francesco oteri (Mon Apr 19 2010 - 10:47:30 CDT)
• colvars: free energy change with rmsd Neelanjana Sengupta (Wed Apr 14 2010 - 00:54:08 CDT)
  • Re: colvars: free energy change with rmsd Kyle Hong (Wed Apr 14 2010 - 04:05:03 CDT)
    • Re: colvars: free energy change with rmsd Jérôme Hénin (Tue May 04 2010 - 10:37:47 CDT)
      • Re: colvars: free energy change with rmsd Jérôme Hénin (Tue May 04 2010 - 10:41:19 CDT)
  • Re: colvars: free energy change with rmsd Jérôme Hénin (Wed Apr 14 2010 - 04:39:57 CDT)
• colvars error running ABF Patrick Yee (Tue Apr 13 2010 - 20:47:21 CDT)
  • Re: colvars error running ABF Axel Kohlmeyer (Tue Apr 13 2010 - 22:03:23 CDT)
• Performance peoblem about NAMD-CUDA benchmarks xiaoguang liu (Sun Apr 11 2010 - 06:53:16 CDT)
  • Re: Performance peoblem about NAMD-CUDA benchmarks Axel Kohlmeyer (Tue Apr 13 2010 - 13:44:21 CDT)
• Re: Performance peoblem about NAMD-CUDA benchmarks Biff Forbush (Mon Apr 12 2010 - 14:42:37 CDT)
• calculate side-chain dihedral/torsion angles Ajasja LjubetiÄ� (Mon Apr 12 2010 - 02:40:47 CDT)
  • in NAMD tutorials: why "HSE" instead of "HSD"? Sebastian Stolzenberg (Mon Apr 26 2010 - 18:57:04 CDT)
• Andres Morales sent you a little gift Andres Morales (Sun Apr 11 2010 - 20:33:49 CDT)
• get total force on a group of atoms within GlobalMasterSMD Liao Chen (Sun Apr 11 2010 - 19:02:16 CDT)
• How to get PMF from SMD with colvars Jian Liu (Sat Apr 10 2010 - 03:45:05 CDT)
• (no subject) #SHEPHERDSON IGNATIUS MARK# (Fri Apr 09 2010 - 20:24:37 CDT)
• REGARDING Topology file Aakash C R (Fri Apr 09 2010 - 16:57:31 CDT)
• Job restart neville forlemu (Fri Apr 09 2010 - 16:39:57 CDT)
• LES dcd file split Dong Luo (Fri Apr 09 2010 - 15:09:08 CDT)
• Can AMBER topology be used in NAMD-CUDA? Lela Vukovic (Fri Apr 09 2010 - 14:54:08 CDT)
• selecting potential binding cavities with MD Thomas Evangelidis (Fri Apr 09 2010 - 14:11:21 CDT)
• Regarding ligand forcefield Jignesh Patel (Thu Apr 08 2010 - 14:13:15 CDT)
  • Re: Regarding ligand forcefield ehenriques_at_qui.uc.pt (Fri Apr 09 2010 - 04:52:07 CDT)
• A problem of the forces-tutorial ÕÅÄþ (Thu Apr 08 2010 - 07:18:33 CDT)
• Ionize script Tommy Kahn (Wed Apr 07 2010 - 18:35:55 CDT)
  • Re: Ionize script Axel Kohlmeyer (Wed Apr 07 2010 - 19:15:28 CDT)
  • Re: Ionize script ehenriques_at_qui.uc.pt (Thu Apr 08 2010 - 10:55:44 CDT)
    • Re: Ionize script Axel Kohlmeyer (Thu Apr 08 2010 - 11:52:45 CDT)
• ammonia to methane Dale l. Schruben (Wed Apr 07 2010 - 11:37:10 CDT)
  • FW: ammonia to methane/DISREGARD this post-changes to files below make methane work now Dale l. Schruben (Wed Apr 07 2010 - 22:36:49 CDT)
  • FW: ammonia to methane/ c/o Jerome Henin Dale l. Schruben (Fri Apr 23 2010 - 10:19:19 CDT)
    • Re: FW: ammonia to methane/ c/o Jerome Henin Jérôme Hénin (Fri Apr 23 2010 - 10:57:05 CDT)
    • Re: FW: ammonia to methane/ c/o Jerome Henin ehenriques_at_qui.uc.pt (Mon Apr 26 2010 - 08:38:41 CDT)
    • FW: ammonia to methane/ c/o Jerome Henin Dale l. Schruben (Mon Apr 26 2010 - 21:18:01 CDT)
• for your suggestions on Pressure Control of transmembrane protein (GPCR) ÅÓÑ©ÇÛ Pang Xueqin (Wed Apr 07 2010 - 03:30:20 CDT)
• how to ensure molecules adopt their favor orientations in SMD simulation crazylyf (Tue Apr 06 2010 - 22:39:11 CDT)
• Postdoc Position available Angela Weiss (Tue Apr 06 2010 - 10:35:04 CDT)
• NAMD/VMD Research Programmer Position available Angela Weiss (Tue Apr 06 2010 - 08:41:21 CDT)
• NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance. Priyan Amaras (Tue Apr 06 2010 - 11:36:25 CDT)
  • Re: NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance. Axel Kohlmeyer (Tue Apr 06 2010 - 12:04:40 CDT)
• OPLS mixing rules fett_at_vtr.net (Tue Apr 06 2010 - 09:40:05 CDT)
• problem with NVT using TIP4P jampani srinivas (Tue Apr 06 2010 - 09:26:09 CDT)
  • Re: problem with NVT using TIP4P muniyamuthu.raviprasad_at_ndsu.edu (Tue Apr 06 2010 - 11:50:49 CDT)
  • Re: problem with NVT using TIP4P Peter Freddolino (Tue Apr 06 2010 - 13:59:27 CDT)
• coarse-grained model building Edward Lyman (Mon Apr 05 2010 - 13:12:50 CDT)
  • Re: coarse-grained model building Anton Arkhipov (Tue Apr 06 2010 - 10:31:57 CDT)
• Size of Timestep Aditya Ranganathan (Mon Apr 05 2010 - 06:33:48 CDT)
  • Re: Size of Timestep Axel Kohlmeyer (Mon Apr 05 2010 - 07:54:27 CDT)
    • Re: Size of Timestep Roman Petrenko (Mon Apr 05 2010 - 11:20:26 CDT)
• NAMD on GPU bahare bamdad (Sun Apr 04 2010 - 09:38:00 CDT)
  • Re: NAMD on GPU Axel Kohlmeyer (Sun Apr 04 2010 - 10:37:24 CDT)
  • Re: NAMD on GPU Biff Forbush (Sun Apr 04 2010 - 16:58:34 CDT)
• Generate missing atoms of a coarse grained structure Mert Gür (Sun Apr 04 2010 - 04:40:13 CDT)
  • Re: Generate missing atoms of a coarse grained structure Peter Freddolino (Sun Apr 04 2010 - 07:55:56 CDT)
    • Re:Re: Generate missing atoms of a coarse grained structure y_ja_at_163.com (Sun Apr 04 2010 - 08:25:06 CDT)
      • Re: Re: Generate missing atoms of a coarse grained structure Ajasja LjubetiÄ� (Tue Apr 06 2010 - 10:22:02 CDT)
      • Re: Re: Generate missing atoms of a coarse grained structure Mert Gür (Wed Apr 14 2010 - 03:34:41 CDT)
    • Re: Generate missing atoms of a coarse grained structure Mert Gür (Wed Apr 14 2010 - 03:35:13 CDT)
• About matdcd Gong Xiaojing (Sat Apr 03 2010 - 21:23:39 CDT)
  • Re: About matdcd Mert Gür (Sun Apr 04 2010 - 04:20:50 CDT)
• NPT simulation schemes Philip Peartree (Fri Apr 02 2010 - 18:04:55 CDT)
• CmiAbort+0x5f Demet Akten (Fri Apr 02 2010 - 05:25:54 CDT)
• Installation problem on Win64 Kwee Hong (Fri Apr 02 2010 - 04:46:28 CDT)
  • Re: Installation problem on Win64 Giacomo Fiorin (Fri Apr 02 2010 - 09:11:02 CDT)
  • RE: Installation problem on Win64 Richard Owczarzy (Fri Apr 02 2010 - 09:39:19 CDT)
  • Re: Installation problem on Win64 muniyamuthu.raviprasad_at_ndsu.edu (Fri Apr 02 2010 - 10:27:02 CDT)
• Periodic cell has become too small for original patch grid! Philip Peartree (Thu Apr 01 2010 - 09:27:16 CDT)
  • Re: Periodic cell has become too small for original patch grid! snoze pa (Fri Apr 02 2010 - 13:33:35 CDT)
    • Re: Periodic cell has become too small for original patch grid! Philip Peartree (Fri Apr 02 2010 - 15:36:54 CDT)
      • Re: Periodic cell has become too small for original patch grid! Jeff Wereszczynski (Fri Apr 02 2010 - 17:05:50 CDT)
      • Re: Periodic cell has become too small for original patch grid! Philip Peartree (Fri Apr 02 2010 - 18:06:43 CDT)
      • Re: Periodic cell has become too small for original patch grid! Philip Peartree (Tue Apr 06 2010 - 09:52:59 CDT)
      • Re: Periodic cell has become too small for original patch grid! snoze pa (Tue Apr 06 2010 - 10:26:09 CDT)
      • Re: Periodic cell has become too small for original patch grid! Jeffrey J. Potoff (Tue Apr 06 2010 - 11:18:24 CDT)
      • Re: Periodic cell has become too small for original patch grid! Philip Peartree (Tue Apr 06 2010 - 16:19:15 CDT)
      • Re: Periodic cell has become too small for original patch grid! Philip Peartree (Tue Apr 06 2010 - 17:56:17 CDT)
• questions about Constant Pressure Control (variable volume) 海清 æ¢� (Thu Apr 01 2010 - 02:18:11 CDT)
• how to set pH crazylyf (Wed Mar 31 2010 - 05:23:58 CDT)
  • Re: how to set pH Axel Kohlmeyer (Wed Mar 31 2010 - 05:54:15 CDT)
  • Re: how to set pH Jérôme Hénin (Wed Mar 31 2010 - 06:29:20 CDT)
    • Re: how to set pH Ajasja LjubetiÄ� (Wed Mar 31 2010 - 06:59:06 CDT)
      • Re: how to set pH felmerino_at_uchile.cl (Wed Mar 31 2010 - 15:01:01 CDT)
• ABF Simulation Crash from TCL script Patrick Yee (Tue Mar 30 2010 - 17:10:49 CDT)
  • Re: ABF Simulation Crash from TCL script Jérôme Hénin (Wed Mar 31 2010 - 04:55:00 CDT)
    • Re: ABF Simulation Crash from TCL script Patrick Yee (Sun Apr 11 2010 - 14:07:52 CDT)
• Parameter file problem udbhav ojha (Tue Mar 30 2010 - 14:54:23 CDT)
  • Re: Parameter file problem Axel Kohlmeyer (Tue Mar 30 2010 - 15:29:19 CDT)
  • Re: Parameter file problem jose correa (Tue Mar 30 2010 - 15:29:45 CDT)
• How to confirm water box is big enough? Jin Liu (Tue Mar 30 2010 - 14:29:15 CDT)
  • Re: How to confirm water box is big enough? snoze pa (Tue Mar 30 2010 - 15:11:44 CDT)
  • Re: How to confirm water box is big enough? Giacomo Fiorin (Tue Mar 30 2010 - 16:38:00 CDT)
    • Re: How to confirm water box is big enough? Jin Liu (Tue Mar 30 2010 - 17:09:06 CDT)
      • Re: How to confirm water box is big enough? Giacomo Fiorin (Tue Mar 30 2010 - 17:36:12 CDT)
      • Re: How to confirm water box is big enough? Jin Liu (Tue Mar 30 2010 - 17:48:37 CDT)
  • Re: How to confirm water box is big enough? David Tanner (Tue Mar 30 2010 - 15:13:10 CDT)
    • Re: How to confirm water box is big enough? Jin Liu (Tue Mar 30 2010 - 15:44:26 CDT)
      • Re: How to confirm water box is big enough? Dimitar V Pachov (Tue Mar 30 2010 - 15:53:46 CDT)
• Problem in energy minimization using Fixatoms or Constraints Ranyere Deyler (Tue Mar 30 2010 - 12:52:09 CDT)
• Re: altering residues in .pdb files muniyamuthu.raviprasad_at_ndsu.edu (Mon Mar 29 2010 - 11:20:08 CDT)
  • Re: altering residues in .pdb files Grace Brannigan (Mon Mar 29 2010 - 15:20:39 CDT)
• ABF Displacement Patrick Yee (Sat Mar 27 2010 - 14:42:18 CDT)
  • Re: ABF Displacement Jérôme Hénin (Mon Mar 29 2010 - 12:10:04 CDT)
• NAMD in TACC lonestar snoze pa (Mon Mar 29 2010 - 10:51:57 CDT)
  • RE: NAMD in TACC lonestar Song, Hyundeok (songhk) (Mon Mar 29 2010 - 11:42:32 CDT)
• psf file error udbhav ojha (Mon Mar 29 2010 - 08:47:36 CDT)
  • Re: psf file error Axel Kohlmeyer (Mon Mar 29 2010 - 09:23:17 CDT)
• rigid molecule Mark M Huntress (Sun Mar 28 2010 - 15:34:30 CDT)
  • Re: rigid molecule Felipe Merino (Sun Mar 28 2010 - 17:45:56 CDT)
  • Re: rigid molecule David Tanner (Sun Mar 28 2010 - 19:25:37 CDT)
    • Re: rigid molecule Grace Brannigan (Mon Mar 29 2010 - 14:10:40 CDT)
• Calculating interaction energy in NAMD DimitryASuplatov (Sun Mar 28 2010 - 04:28:52 CDT)
  • Re: Calculating interaction energy in NAMD BIN ZHANG (Sun Mar 28 2010 - 13:50:38 CDT)
• Installation of NAMD & charm - fatal errors DDR (Sat Mar 27 2010 - 18:23:25 CDT)
  • Re: Installation of NAMD & charm - fatal errors DimitryASuplatov (Sun Mar 28 2010 - 04:24:43 CDT)
• altering residues in .pdb files Thomas Kahn (Fri Mar 26 2010 - 18:34:53 CDT)
  • RE: altering residues in .pdb files Peter Jones (Fri Mar 26 2010 - 20:29:00 CDT)
• Atom type for protonated pyridine N Branko (Fri Mar 26 2010 - 02:24:16 CDT)
• NAMD regression test suite? Ronald Salesky (Fri Mar 26 2010 - 11:46:59 CDT)
• colvar error Ferenc Ötvös, PhD (Fri Mar 26 2010 - 04:45:27 CDT)
  • Re: colvar error Jérôme Hénin (Fri Mar 26 2010 - 06:34:11 CDT)
• Atom type for protonated pyridine N Branko (Fri Mar 26 2010 - 02:31:59 CDT)
• NAMD with two GPUs Priyan Amaras (Wed Mar 24 2010 - 21:35:46 CDT)
  • Re: NAMD with two GPUs Axel Kohlmeyer (Wed Mar 24 2010 - 22:41:50 CDT)
    • NAMD/metadynamics neville forlemu (Thu Mar 25 2010 - 21:16:08 CDT)
      • Re: NAMD/metadynamics Giacomo Fiorin (Fri Mar 26 2010 - 09:14:17 CDT)
• NAMD stalled at startup phase 0 when working on a large numbr of processors lucie delemotte (Wed Mar 24 2010 - 13:07:44 CDT)
• Pressure profile calculation problem wenchangyu2006_at_gmail.com (Tue Mar 23 2010 - 15:38:56 CDT)
• STRIDE Structure Assignment and Ramachandran Plot Beta Strand allowed regions Aditya Ranganathan (Tue Mar 23 2010 - 01:36:42 CDT)
• Fwd: STRIDE Question from article "Interpeptide interactions induce helix to strand structural transition in Abeta peptides" Aditya Ranganathan (Tue Mar 23 2010 - 01:34:47 CDT)
• No. of processors in the namd command. Priyan Amaras (Mon Mar 22 2010 - 21:13:55 CDT)
  • Re: No. of processors in the namd command. uu zhu (Tue Mar 23 2010 - 00:39:29 CDT)
    • Re: No. of processors in the namd command. Priyan Amaras (Tue Mar 23 2010 - 10:04:52 CDT)
  • Re: No. of processors in the namd command. Roman Petrenko (Tue Mar 23 2010 - 10:45:50 CDT)
• CHARM parameter file needed for simple organic molecules like Methanol, Formamide, Chloroform, TCE, Toluene MD. ZILLUR RAHMAN (Sun Mar 21 2010 - 22:07:46 CDT)
• request help- namd error abortion stack error Odysseas Axillews (Sun Mar 21 2010 - 20:24:30 CDT)
• Cationic Dummy Atom models Hok-Hei Tam (Sun Mar 21 2010 - 16:31:39 CDT)
• Error: This application has requested the Runtime to terminate it in an unusual way: Please contact the application's support team for more information" after specifying the namd2.exe path Mary Newcomb (Fri Mar 19 2010 - 16:17:27 CDT)
  • RE: Error: This application has requested the Runtime to terminate it in an unusual way: Please contact the application's support team for more information" after specifying the namd2.exe path Richard Owczarzy (Fri Mar 19 2010 - 17:13:53 CDT)
• CMAP dimension limited to 24 dimensions alpertunga daðcan (Thu Mar 18 2010 - 21:42:03 CDT)
  • Re: CMAP dimension limited to 24 dimensions Grace Brannigan (Fri Mar 19 2010 - 14:29:13 CDT)
• request help- namd error abortion stack error Odysseas Axillews (Thu Mar 18 2010 - 21:21:44 CDT)
• water "flying out of the box" 林星雨 (Fri Mar 19 2010 - 06:06:30 CDT)
• Allowed CMAP dimensions in NAMD A D (Thu Mar 18 2010 - 20:11:24 CDT)
• CMAP dimensions in NAMD A D (Thu Mar 18 2010 - 19:07:43 CDT)
• Removing some water from a .dcd file or .coor file Rabab Toubar (Wed Mar 17 2010 - 15:36:14 CDT)
  • Re: Removing some water from a .dcd file or .coor file tillmann.utesch_at_mail.tu-berlin.de (Thu Mar 18 2010 - 07:29:55 CDT)
    • Re: Removing some water from a .dcd file or .coor file Brian Novak (Sat Mar 27 2010 - 10:27:27 CDT)
• Hello! Eric Perim (Wed Mar 17 2010 - 07:45:19 CDT)
• Could namd support the ATI-GPU Aurum Bai (Wed Mar 17 2010 - 07:35:34 CDT)
• free energy changes of one subunit Lixia Jin Day (Tue Mar 16 2010 - 13:39:55 CDT)
  • Re: free energy changes of one subunit felmerino_at_uchile.cl (Tue Mar 16 2010 - 15:29:17 CDT)
    • Namd. Small molecules Roberto Rivera (Fri Mar 19 2010 - 18:53:45 CDT)
      • Re: Namd. Small molecules jose correa (Fri Mar 19 2010 - 21:37:57 CDT)
  • Re: free energy changes of one subunit Giacomo Fiorin (Tue Mar 16 2010 - 15:43:52 CDT)
• Fixatoms minimization problem!! Ranyere Deyler (Tue Mar 16 2010 - 12:45:57 CDT)
  • Re: Fixatoms minimization problem!! Chris Harrison (Wed Mar 17 2010 - 00:27:37 CDT)
    • Re: Fixatoms minimization problem!! Ranyere Deyler (Mon Mar 29 2010 - 09:14:13 CDT)
    • Re: Fixatoms minimization problem!! Ranyere Deyler (Mon Mar 29 2010 - 18:41:29 CDT)
• NAMD CUDA bahare bamdad (Tue Mar 16 2010 - 03:23:04 CDT)
  • Re: NAMD CUDA Axel Kohlmeyer (Wed Mar 17 2010 - 08:51:52 CDT)
• simulating TIP4P with NAMD 2.7b2 Guillaume Stirnemann (Tue Mar 16 2010 - 08:33:48 CDT)
  • Re: simulating TIP4P with NAMD 2.7b2 Peter Freddolino (Tue Mar 16 2010 - 14:42:36 CDT)
• CUDA error memcpy to exclusions: invalid argument Priyan Amaras (Tue Mar 16 2010 - 09:37:28 CDT)
• (no subject) Daniel Hornburg (Tue Mar 16 2010 - 07:17:02 CDT)
  • Re: Chris Harrison (Tue Mar 16 2010 - 23:58:40 CDT)
• (no subject) Daniel Hornburg (Tue Mar 16 2010 - 06:19:40 CDT)
  • Re: Axel Kohlmeyer (Tue Mar 16 2010 - 06:59:05 CDT)
• What is the Potential Energy of a Protein in Namdenergy Mert Gür (Tue Mar 16 2010 - 05:51:39 CDT)
  • Re: What is the Potential Energy of a Protein in Namdenergy Jérôme Hénin (Tue Mar 16 2010 - 07:10:00 CDT)
    • Re: What is the Potential Energy of a Protein in Namdenergy Mert Gür (Tue Mar 16 2010 - 07:59:31 CDT)
  • Re: What is the Potential Energy of a Protein in Namdenergy Axel Kohlmeyer (Tue Mar 16 2010 - 06:55:55 CDT)
• benchmarking on Cray XT4 Hannes Loeffler (Tue Mar 16 2010 - 05:50:17 CDT)
  • Re: benchmarking on Cray XT4 Axel Kohlmeyer (Tue Mar 16 2010 - 06:49:58 CDT)
  • Re: benchmarking on Cray XT4 Philip Peartree (Tue Mar 16 2010 - 07:59:49 CDT)
    • Re: benchmarking on Cray XT4 Hannes Loeffler (Tue Mar 16 2010 - 09:32:38 CDT)
      • Re: benchmarking on Cray XT4 Axel Kohlmeyer (Tue Mar 16 2010 - 10:35:56 CDT)
• How to get information of computing time for LJ calculation and pair list generation Hideya Nakamura (Mon Mar 15 2010 - 12:08:20 CDT)
  • How to get information of computing time for LJ calculation and pair list generation Hideya Nakamura (Mon Mar 15 2010 - 12:15:18 CDT)
    • Re: How to get information of computing time for LJ calculation and pair list generation Chris Harrison (Wed Mar 17 2010 - 00:06:07 CDT)
      • Re: How to get information of computing time for LJ calculation and pair list generation Hideya Nakamura (Wed Mar 17 2010 - 03:32:31 CDT)
• patch missing residues BIN ZHANG (Mon Mar 15 2010 - 15:42:49 CDT)
  • Re: patch missing residues Chris Harrison (Wed Mar 17 2010 - 01:10:27 CDT)
• Problem in minimization, Energy "-1.#IND" and bad dcd file. Ranyere Deyler (Sun Mar 14 2010 - 17:36:19 CDT)
• Problem in minimization, Energy "-1.#IND" and bad dcd file. Ranyere Deyler (Sun Mar 14 2010 - 17:28:58 CDT)
• FATAL ERROR:BAD GLOBAL EXCLUSION COUNT:Please help Werner Crous (Sat Mar 13 2010 - 10:22:47 CST)
  • Re: FATAL ERROR:BAD GLOBAL EXCLUSION COUNT:Please help Chris Harrison (Wed Mar 17 2010 - 00:13:12 CDT)
    • Re: FATAL ERROR:BAD GLOBAL EXCLUSION COUNT:Please help Werner Crous (Thu Mar 18 2010 - 04:23:55 CDT)
      • Re: FATAL ERROR:BAD GLOBAL EXCLUSION COUNT:Please help Werner Crous (Thu Mar 18 2010 - 04:29:55 CDT)
• Fwd: help to improve the script to predict mean square displacement jampani srinivas (Fri Mar 12 2010 - 14:51:55 CST)
  • Re: Fwd: help to improve the script to predict mean square displacement Luca Muccioli (Fri Mar 12 2010 - 17:08:31 CST)
• segmentation faults with AMBER topology Ibrahim Abou Hamad (Fri Mar 12 2010 - 13:39:59 CST)
• Problem Compiling NAMD (version 2.7b2) Michael Homa (Fri Mar 12 2010 - 12:06:34 CST)
• question about NAMD Pengcheng Yin (Thu Mar 11 2010 - 19:20:21 CST)
  • Re: question about NAMD Axel Kohlmeyer (Thu Mar 11 2010 - 19:55:11 CST)
    • Re: question about NAMD Jérôme Hénin (Fri Mar 12 2010 - 02:49:24 CST)
      • Re: question about NAMD Axel Kohlmeyer (Fri Mar 12 2010 - 04:56:19 CST)
      • Re: question about NAMD Pengcheng Yin (Fri Mar 12 2010 - 09:03:09 CST)
• run multiple walkers Naiyin Yu (Thu Mar 11 2010 - 16:15:33 CST)
  • Re: run multiple walkers Giacomo Fiorin (Fri Mar 12 2010 - 16:03:18 CST)
• Parallel replicas? Jason Russler (Thu Mar 11 2010 - 14:40:41 CST)
  • Re: Parallel replicas? Segun Jung (Fri Mar 12 2010 - 10:51:05 CST)
• Re: vmd-l: water molecules around proteins Axel Kohlmeyer (Thu Mar 11 2010 - 11:49:50 CST)
• highthroughput NAMD Thomas C. Bishop (Thu Mar 11 2010 - 11:25:35 CST)
• high pressure tillmann.utesch_at_mail.tu-berlin.de (Thu Mar 11 2010 - 06:01:06 CST)
  • Re: high pressure Dimitar V Pachov (Thu Mar 11 2010 - 09:09:56 CST)
    • Re: high pressure Tillmann Utesch (Thu Mar 11 2010 - 10:29:22 CST)
      • Re: high pressure Giacomo Fiorin (Thu Mar 11 2010 - 13:00:56 CST)
      • Re: high pressure Tillmann Utesch (Thu Mar 11 2010 - 15:05:59 CST)
      • Re: high pressure tillmann.utesch_at_mail.tu-berlin.de (Tue Apr 20 2010 - 06:52:01 CDT)
• NAMD CUDA bahare bamdad (Thu Mar 11 2010 - 03:11:21 CST)
  • Re: NAMD CUDA Axel Kohlmeyer (Thu Mar 11 2010 - 03:50:25 CST)
• colvars fixes Giacomo Fiorin (Tue Mar 09 2010 - 19:36:08 CST)
• Regenerating a .dcd file Rabab Toubar (Mon Mar 08 2010 - 14:02:15 CST)
  • Re: Regenerating a .dcd file JC Gumbart (Mon Mar 08 2010 - 19:14:39 CST)
    • Re: Regenerating a .dcd file Rabab Toubar (Tue Mar 09 2010 - 07:27:35 CST)
      • RE: Regenerating a .dcd file JC Gumbart (Tue Mar 09 2010 - 07:31:51 CST)
      • Re: Regenerating a .dcd file Ajasja LjubetiÄ� (Tue Mar 09 2010 - 07:52:18 CST)
      • Re: Regenerating a .dcd file Axel Kohlmeyer (Tue Mar 09 2010 - 08:17:47 CST)
• script for lipid density Demet Akten (Mon Mar 08 2010 - 05:34:39 CST)
• Error: atom group "group1" is set, but has no definition Jagan Mohan (Mon Mar 08 2010 - 00:05:08 CST)
  • Re: Error: atom group "group1" is set, but has no definition Jagan Mohan (Mon Mar 08 2010 - 00:34:43 CST)
• Unstable atoms Ale Gomez (Sat Mar 06 2010 - 23:00:30 CST)
• Water Box Shape Changing during NVT Simulation! Aditya Ranganathan (Fri Mar 05 2010 - 21:59:26 CST)
  • Re: Water Box Shape Changing during NVT Simulation! Pablo Campomanes (Fri Mar 05 2010 - 22:50:53 CST)
    • Re: Water Box Shape Changing during NVT Simulation! Pablo Campomanes (Sat Mar 06 2010 - 11:50:45 CST)
      • Re: Water Box Shape Changing during NVT Simulation! Ronald Salesky (Mon Mar 08 2010 - 11:46:24 CST)
      • Re: Water Box Shape Changing during NVT Simulation! Axel Kohlmeyer (Mon Mar 08 2010 - 12:39:16 CST)
      • Re: Water Box Shape Changing during NVT Simulation! Jeffrey J. Potoff (Mon Mar 08 2010 - 15:05:10 CST)
    • Re: Water Box Shape Changing during NVT Simulation! Axel Kohlmeyer (Tue Mar 09 2010 - 03:38:09 CST)
      • Re: Water Box Shape Changing during NVT Simulation! Aditya Ranganathan (Tue Mar 09 2010 - 04:12:29 CST)
• RE: RAMD scripts version 4.1 Cojocaru,Vlad (Fri Mar 05 2010 - 13:56:20 CST)
• restarting a simulation ? Reichert, David (Fri Mar 05 2010 - 13:17:14 CST)
  • Re: restarting a simulation ? Chris Harrison (Wed Mar 17 2010 - 00:39:27 CDT)
• Distance Analysis for Constant Force Pulling for kinesin neck linker Patriche Simona (Fri Mar 05 2010 - 05:44:37 CST)
• tcl forces and tcl 8.5 Vlad Cojocaru (Fri Mar 05 2010 - 03:19:16 CST)
• RAMD scripts version 4.1 Vlad Cojocaru (Fri Mar 05 2010 - 03:08:51 CST)
  • Re: RAMD scripts version 4.1 Chris Harrison (Fri Mar 05 2010 - 06:57:34 CST)
    • Re: Re: RAMD scripts version 4.1 Shulin Zhuang (Fri Mar 05 2010 - 11:43:01 CST)
      • RE: Re: RAMD scripts version 4.1 Cojocaru,Vlad (Fri Mar 05 2010 - 13:54:14 CST)
• Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2 PREVIOUS VALUES Jignesh Patel (Thu Mar 04 2010 - 11:29:03 CST)
• isopropanol parameters? Jose Borreguero (Thu Mar 04 2010 - 09:24:58 CST)
  • restraint potential used in the ABF calculations chengh_at_ringo.chem.pitt.edu (Tue Mar 23 2010 - 13:36:22 CDT)
    • Re: restraint potential used in the ABF calculations Giacomo Fiorin (Tue Mar 23 2010 - 17:41:11 CDT)
• segmentation fault with AMBER topology (cvs code 03.03.2010) Cojocaru,Vlad (Thu Mar 04 2010 - 05:28:38 CST)
• update: segmentation faults with AMBER topology (cvscode 03 Mar 2010) Vlad Cojocaru (Thu Mar 04 2010 - 07:43:09 CST)
• Volume of the Solution used for MD simulation Aditya Ranganathan (Thu Mar 04 2010 - 06:32:57 CST)
• Alchemical calculations in CUDA version of NAMD? Lela Vukovic (Wed Mar 03 2010 - 11:33:36 CST)
  • Re: Alchemical calculations in CUDA version of NAMD? Lela Vukovic (Wed Mar 03 2010 - 12:01:03 CST)
    • Re: Alchemical calculations in CUDA version of NAMD? Lela Vukovic (Wed Mar 17 2010 - 01:28:50 CDT)
  • Re: Alchemical calculations in CUDA version of NAMD? Chris Harrison (Wed Mar 17 2010 - 02:37:21 CDT)
• job script for Kraken Zumot, Elia Nabil (Wed Mar 03 2010 - 09:14:15 CST)
  • Re: job script for Kraken Giacomo Fiorin (Wed Mar 03 2010 - 13:15:11 CST)
    • RE: job script for Kraken Zumot, Elia Nabil (Thu Mar 11 2010 - 16:04:56 CST)
      • Re: job script for Kraken Chris Harrison (Wed Mar 17 2010 - 00:54:50 CDT)
• error jbp087_at_gmail.com (Tue Mar 02 2010 - 23:48:53 CST)
  • RE: error Zumot, Elia Nabil (Wed Mar 03 2010 - 08:23:41 CST)
• creating an output file from a dcd file Rabab Toubar (Tue Mar 02 2010 - 10:34:15 CST)
  • Re: creating an output file from a dcd file Axel Kohlmeyer (Tue Mar 02 2010 - 11:27:20 CST)
    • Re: creating an output file from a dcd file Rabab Toubar (Thu Mar 04 2010 - 10:40:12 CST)
      • Re: creating an output file from a dcd file Axel Kohlmeyer (Thu Mar 04 2010 - 11:20:31 CST)
  • Re: creating an output file from a dcd file Nicholas M Glykos (Tue Mar 02 2010 - 12:30:49 CST)
    • Re: creating an output file from a dcd file Rabab Toubar (Tue Mar 02 2010 - 14:51:20 CST)
      • Re: creating an output file from a dcd file Nicholas M Glykos (Tue Mar 02 2010 - 15:11:54 CST)
  • RE: creating an output file from a dcd file Zumot, Elia Nabil (Tue Mar 02 2010 - 12:52:17 CST)
• RE: cell basis vector restart Mark M Huntress (Tue Mar 02 2010 - 09:51:21 CST)
  • RE: cell basis vector restart Mark M Huntress (Tue Mar 02 2010 - 12:09:07 CST)
    • Re: cell basis vector restart Jeffrey J. Potoff (Tue Mar 02 2010 - 13:09:37 CST)
• wrapping ions Bala subramanian (Tue Mar 02 2010 - 03:05:45 CST)
• cell basis vector restart Mark M Huntress (Mon Mar 01 2010 - 16:47:47 CST)
• electrostatic vs van der waals Mark M Huntress (Mon Mar 01 2010 - 09:57:35 CST)
  • Re: electrostatic vs van der waals David Tanner (Mon Mar 01 2010 - 11:49:07 CST)
    • Re: electrostatic vs van der waals Rabab Toubar (Tue Mar 02 2010 - 08:16:20 CST)
• NAMD starts AMBER calculation only from 3rd run Q=C1=D2=D8=D1_=FB=C1=CC=C1=C5=D7=C1?= (Mon Mar 01 2010 - 09:38:43 CST)
  • Re: NAMD starts AMBER calculation only from 3rd run Artem Zhmurov (Mon Mar 01 2010 - 14:47:14 CST)
• Dihedral angle energy in silica block Jindal Shah (Sun Feb 28 2010 - 21:51:15 CST)
  • Re: Dihedral angle energy in silica block Eduardo (Sun Feb 28 2010 - 22:41:09 CST)
    • Re: Dihedral angle energy in silica block Jindal Shah (Mon Mar 01 2010 - 09:11:47 CST)
      • Re: Dihedral angle energy in silica block Eduardo (Mon Mar 01 2010 - 15:46:54 CST)
• Problem with Targeted molecular dynamics Agostino Bruno (Sun Feb 28 2010 - 10:07:25 CST)
• multiple trajectories Bala subramanian (Fri Feb 26 2010 - 10:50:38 CST)
• Issue attaching to nodes Bryan Holland (Thu Feb 25 2010 - 10:24:13 CST)
• Consecutive Simulations Keith Battle (Thu Feb 25 2010 - 09:25:33 CST)
  • Re: Consecutive Simulations Lewyn Li (Thu Feb 25 2010 - 10:08:47 CST)
• Explicit Water System Condensing Keith Battle (Thu Feb 25 2010 - 09:17:53 CST)
  • Re: Explicit Water System Condensing Jeffrey J. Potoff (Thu Feb 25 2010 - 10:13:43 CST)
• anomalous behaviour of ASPP and GLUP during MD run Andreini Matteo (Thu Feb 25 2010 - 08:24:45 CST)
  • Re: anomalous behaviour of ASPP and GLUP during MD run La Fosca (Thu Feb 25 2010 - 09:04:29 CST)
    • Re: anomalous behaviour of ASPP and GLUP during MD run Michel Espinoza-Fonseca (Thu Feb 25 2010 - 10:51:36 CST)
      • RE: anomalous behaviour of ASPP and GLUP during MD run Andreini Matteo (Thu Feb 25 2010 - 10:57:23 CST)
• anomalous behaviour of ASPP and GLUP during MD run Andreini Matteo (Thu Feb 25 2010 - 02:31:45 CST)
• psfgen errors tpreeprem3_at_gatech.edu (Thu Feb 25 2010 - 00:37:46 CST)
• Problem on periodic boundary condition Indrajit Deb (Wed Feb 24 2010 - 07:25:28 CST)
  • Re: Problem on periodic boundary condition Axel Kohlmeyer (Wed Feb 24 2010 - 08:13:10 CST)
  • Re: Problem on periodic boundary condition Nicholas M Glykos (Wed Feb 24 2010 - 08:41:12 CST)
• Fwd: Coarse Graining Problem Aditya Ranganathan (Wed Feb 24 2010 - 05:59:51 CST)
  • Re: Fwd: Coarse Graining Problem Anton Arkhipov (Wed Feb 24 2010 - 11:20:08 CST)
• psfgen error Syed Kashif Zafar (Tue Feb 23 2010 - 22:44:21 CST)
  • Re: psfgen error Axel Kohlmeyer (Wed Feb 24 2010 - 00:19:44 CST)
    • Restarting A NAMD job with velocity file neville forlemu (Mon Mar 22 2010 - 15:50:07 CDT)
      • Re: Restarting A NAMD job with velocity file Wei Chen (Mon Mar 22 2010 - 16:25:50 CDT)
      • Re: Restarting A NAMD job with velocity file Giacomo Fiorin (Mon Mar 22 2010 - 17:30:00 CDT)
      • Re: Restarting A NAMD job with velocity file neville forlemu (Thu Mar 25 2010 - 21:59:01 CDT)
• update: segmentation faults with AMBER topology and RAMD tcl scripts Vlad Cojocaru (Tue Feb 23 2010 - 08:31:27 CST)
• running tcl scripting ipsita basu (Tue Feb 23 2010 - 04:26:05 CST)
• about NAMD nonbonded routines  (Tue Feb 23 2010 - 02:55:29 CST)
• atom charges for protonated carboxyl termini Zumot, Elia Nabil (Mon Feb 22 2010 - 14:48:59 CST)
  • RE: atom charges for protonated carboxyl termini Peter Jones (Mon Feb 22 2010 - 18:46:25 CST)
• sucrose top/par Ziemys, Arturas (Mon Feb 22 2010 - 13:41:14 CST)
• version of tcl in binary builds Francesco Pietra (Mon Feb 22 2010 - 10:53:08 CST)
  • Re: version of tcl in binary builds Francesco Pietra (Mon Feb 22 2010 - 11:38:22 CST)
    • Re: version of tcl in binary builds Giacomo Fiorin (Tue Feb 23 2010 - 01:52:23 CST)
      • RAMD scripts and tcl version Vlad Cojocaru (Tue Feb 23 2010 - 02:37:25 CST)
      • Re: RAMD scripts and tcl version Balazs Jojart (Tue Feb 23 2010 - 03:33:24 CST)
      • Re: RAMD scripts and tcl version Vlad Cojocaru (Tue Feb 23 2010 - 03:45:44 CST)
      • Re: RAMD scripts and tcl version Balazs Jojart (Tue Feb 23 2010 - 04:27:03 CST)
      • Re: RAMD scripts and tcl version George Madalin Giambasu (Tue Feb 23 2010 - 09:52:30 CST)
• NAMD running error bahare bamdad (Mon Feb 22 2010 - 09:38:37 CST)
• Re: About the err of "distanceZ"! Jian Liu (Mon Feb 22 2010 - 07:57:37 CST)
• About the err of "distanceZ"! Aurum Bai (Mon Feb 22 2010 - 03:28:31 CST)
• The problem of annihilating the solute in the aqueous Aurum Bai (Mon Feb 22 2010 - 00:47:45 CST)
• namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase George Madalin Giambasu (Sun Feb 21 2010 - 18:01:43 CST)
  • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase Vlad Cojocaru (Mon Feb 22 2010 - 01:31:07 CST)
    • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase George Madalin Giambasu (Mon Feb 22 2010 - 10:26:46 CST)
      • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase Vlad Cojocaru (Mon Feb 22 2010 - 10:30:25 CST)
      • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase George Madalin Giambasu (Mon Feb 22 2010 - 10:50:13 CST)
  • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase Philipp M. (Mon Feb 22 2010 - 05:23:20 CST)
  • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase Nicolas Sapay (Wed Feb 24 2010 - 06:49:47 CST)
    • Re: Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase Vlad Cojocaru (Wed Feb 24 2010 - 07:11:42 CST)
  • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase Vlad Cojocaru (Wed Mar 31 2010 - 07:02:07 CDT)
    • Re: Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase Marcello Sega (Sat Apr 03 2010 - 19:35:01 CDT)
      • Re: Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase George Madalin Giambasu (Tue Apr 06 2010 - 12:12:44 CDT)
• About the err of "Constraint failure" Aurum Bai (Sun Feb 21 2010 - 03:13:25 CST)
  • About viscosity calculation Armen H. Poghosyan (Sun Feb 21 2010 - 18:22:12 CST)
• About "equilibrate.conf' of FEP tutorial Aurum Bai (Sat Feb 20 2010 - 07:15:58 CST)
  • Re: About "equilibrate.conf' of FEP tutorial Jérôme Hénin (Sat Feb 20 2010 - 10:36:43 CST)
• Lipid and protein interactions Marie N (Fri Feb 19 2010 - 17:25:29 CST)
  • Re: Lipid and protein interactions Axel Kohlmeyer (Sat Feb 20 2010 - 09:49:08 CST)
    • Re: Lipid and protein interactions snoze pa (Mon Feb 22 2010 - 10:24:55 CST)
• Parameters/topology entries for non-standard nucleotides Thomas Kahn (Fri Feb 19 2010 - 16:14:33 CST)
  • Re: Parameters/topology entries for non-standard nucleotides Jérôme Hénin (Sat Feb 20 2010 - 10:40:04 CST)
• Is two colvars file output possible during single simulation (ABF/2.7b) Branko (Fri Feb 19 2010 - 10:51:10 CST)
  • Re: Is two colvars file output possible during single simulation (ABF/2.7b) Giacomo Fiorin (Fri Feb 19 2010 - 18:45:48 CST)
  • Re: Is two colvars file output possible during single simulation (ABF/2.7b) Giacomo Fiorin (Fri Feb 19 2010 - 18:44:21 CST)
    • Re: Is two colvars file output possible during single simulation (ABF/2.7b) Branko (Sat Feb 20 2010 - 08:58:04 CST)
      • Re: Is two colvars file output possible during single simulation (ABF/2.7b) Giacomo Fiorin (Sun Feb 21 2010 - 00:15:53 CST)
      • Re: Is two colvars file output possible during single simulation (ABF/2.7b) Jérôme Hénin (Wed Feb 24 2010 - 11:55:26 CST)
  • Re: Is two colvars file output possible during single simulation (ABF/2.7b) Jerome Henin (Sat Feb 20 2010 - 10:05:26 CST)
• Drude polarizability parameters Igor Petrik (Fri Feb 19 2010 - 06:09:57 CST)
  • Re: Drude polarizability parameters David Hardy (Sat Feb 20 2010 - 10:17:55 CST)
    • Re: Drude polarizability parameters Igor Petrik (Thu May 06 2010 - 17:35:20 CDT)
      • Re: Drude polarizability parameters David Hardy (Thu May 06 2010 - 18:12:58 CDT)
• reading prameter file ipsita basu (Fri Feb 19 2010 - 03:58:16 CST)
  • Fwd: reading prameter file ipsita basu (Mon Feb 22 2010 - 00:27:10 CST)
• Re: namd trouble Joshua Adelman (Thu Feb 18 2010 - 07:08:46 CST)
  • Re: Re: namd trouble snoze pa (Thu Feb 18 2010 - 14:08:42 CST)
• Re: tutorial-l: Nanotubes tutorial - coorList(577) no such element Jian Liu (Thu Feb 18 2010 - 04:09:25 CST)
  • Re: tutorial-l: Nanotubes tutorial - coorList(577) no such element Drew buschhorn (Thu Feb 18 2010 - 20:30:10 CST)
• tutorial-l: Nanotubes tutorial - coorList(577) no such element Drew buschhorn (Thu Feb 18 2010 - 00:45:24 CST)
• trouble in dynamics Sweta Ramachandran (Wed Feb 17 2010 - 23:18:48 CST)
  • Re: trouble in dynamics Mert Gür (Thu Feb 18 2010 - 04:32:18 CST)
  • Re: trouble in dynamics Andreas Förster (Thu Feb 18 2010 - 04:54:31 CST)
• calculation van der Waals force field parameters Mikhail Suyetin (Wed Feb 17 2010 - 13:27:50 CST)
• Fwd: electric field unit conversion Mikhail Suyetin (Wed Feb 17 2010 - 11:25:21 CST)
  • Re: electric field unit conversion Mikhail Suyetin (Wed Feb 17 2010 - 11:27:25 CST)
• coordinates and cells Andreas Förster (Wed Feb 17 2010 - 11:00:54 CST)
  • Re: coordinates and cells Rogan Carr (Wed Feb 17 2010 - 11:25:06 CST)
    • Re: coordinates and cells Andreas Förster (Thu Feb 18 2010 - 04:47:29 CST)
• Windows binaries of NAMD 2.72b supports CUDA? Mohd Farid Ismail (Wed Feb 17 2010 - 09:52:16 CST)
• electric field unit conversion Ziemys, Arturas (Wed Feb 17 2010 - 09:45:46 CST)
  • Re: electric field unit conversion Roman Petrenko (Wed Feb 17 2010 - 11:53:02 CST)
• Problem of compiling Version Nightly Build (2010-02-16) Shulin Zhuang (Tue Feb 16 2010 - 18:28:30 CST)
• bonded FAD topology file Demet Akten (Tue Feb 16 2010 - 07:23:13 CST)
• error in scripting ipsita basu (Tue Feb 16 2010 - 05:26:07 CST)
  • Re: error in scripting Axel Kohlmeyer (Tue Feb 16 2010 - 06:28:55 CST)
  • Re: error in scripting Jeffrey J. Potoff (Tue Feb 16 2010 - 11:51:03 CST)
    • Re: error in scripting ipsita basu (Wed Feb 17 2010 - 23:09:16 CST)
• installation of namd ipsita basu (Tue Feb 16 2010 - 04:00:23 CST)
  • Re: installation of namd Axel Kohlmeyer (Tue Feb 16 2010 - 06:40:06 CST)
• Large protein translation during minimization Rachel Ruskin (Mon Feb 15 2010 - 16:24:20 CST)
  • Re: Large protein translation during minimization Rachel Ruskin (Mon Feb 15 2010 - 23:48:00 CST)
• Can't find C-PDB bond parameters Francesco Pietra (Mon Feb 15 2010 - 03:46:29 CST)
  • RE: Can't find C-PDB bond parameters JC Gumbart (Mon Feb 15 2010 - 08:15:53 CST)
    • Re: Can't find C-PDB bond parameters Francesco Pietra (Mon Feb 15 2010 - 11:44:52 CST)
      • Re: Can't find C-PDB bond parameters JC Gumbart (Mon Feb 15 2010 - 12:06:41 CST)
• CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES Francesco Pietra (Sun Feb 14 2010 - 10:26:01 CST)
• Generating binvelocities, bincoordinates, and extendedSystem files (AMBER) Johann Morr (Sat Feb 13 2010 - 23:01:32 CST)
  • Re: Generating binvelocities, bincoordinates, and extendedSystem files (AMBER) Axel Kohlmeyer (Sun Feb 14 2010 - 04:54:11 CST)
• installation of namd in parallel mode ipsita basu (Sat Feb 13 2010 - 01:40:28 CST)
  • Re: installation of namd in parallel mode Mert Gür (Sun Feb 14 2010 - 05:51:55 CST)
  • Re: installation of namd in parallel mode Andreas Förster (Mon Feb 15 2010 - 03:46:03 CST)
• Job Offer Jim Phillips (Fri Feb 12 2010 - 20:21:33 CST)
• Topology files Thomas Kahn (Fri Feb 12 2010 - 17:13:48 CST)
• apologize for the typo Bennion, Brian (Fri Feb 12 2010 - 13:13:30 CST)
• RE: Questions about lattice information in NAMD2.7b2 Bennion, Brian (Fri Feb 12 2010 - 12:42:45 CST)
• Is it possible to run replica exchange simulation on BlueGeneL? Dong Luo (Fri Feb 12 2010 - 11:47:21 CST)
• water-molecules/coordenates jose correa (Thu Feb 11 2010 - 13:19:01 CST)
  • Re: water-molecules/coordenates JC Gumbart (Thu Feb 11 2010 - 15:16:28 CST)
    • Re: water-molecules/coordenates jose correa (Thu Feb 11 2010 - 16:10:09 CST)
      • Re: water-molecules/coordenates JC Gumbart (Fri Feb 12 2010 - 12:20:25 CST)
      • Re: water-molecules/coordenates jose correa (Fri Feb 12 2010 - 12:45:49 CST)
• The accuracy of FEP calculation chengh_at_ringo.chem.pitt.edu (Thu Feb 11 2010 - 09:58:20 CST)
  • Re: The accuracy of FEP calculation Chris Chipot (Thu Feb 11 2010 - 10:45:18 CST)
    • Re: The accuracy of FEP calculation chengh_at_ringo.chem.pitt.edu (Thu Feb 11 2010 - 11:51:54 CST)
• SMD normal vector snoze pa (Wed Feb 10 2010 - 17:48:00 CST)
• Crashing ibverbs binary of NAMD_2.7b2 Philipp M. (Wed Feb 10 2010 - 10:58:03 CST)
  • Re: Crashing ibverbs binary of NAMD_2.7b2 snoze pa (Wed Feb 10 2010 - 17:44:24 CST)
    • Re: Crashing ibverbs binary of NAMD_2.7b2 Philipp M. (Thu Feb 11 2010 - 05:30:32 CST)
    • Re: Crashing ibverbs binary of NAMD_2.7b2 Philipp M. (Thu Feb 11 2010 - 05:16:47 CST)
• Pressure Questions Rick Calloway (Wed Feb 10 2010 - 08:16:50 CST)
  • Re: Pressure Questions Jérôme Hénin (Wed Feb 10 2010 - 11:52:30 CST)
• Fatal Error by charmc - Compiling NAMD_2.7b2_Source philipp.coloc_at_gmx.de (Wed Feb 10 2010 - 04:59:30 CST)
• Re: Problem compiling namd philipp.coloc_at_gmx.de (Wed Feb 10 2010 - 03:53:21 CST)
• Bringing UMA-type mainboards to TESLA Francesco Pietra (Tue Feb 09 2010 - 15:59:16 CST)
  • Re: Bringing UMA-type mainboards to TESLA Axel Kohlmeyer (Tue Feb 09 2010 - 18:03:38 CST)
    • Re: Bringing UMA-type mainboards to TESLA Biff Forbush (Wed Feb 10 2010 - 12:34:57 CST)
• Re: Multiplicity of Parameters for dihedral bond exceeded Ajasja LjubetiÄ� (Tue Feb 09 2010 - 06:07:22 CST)
• SMD and langevin dynamics snoze pa (Sat Feb 06 2010 - 19:00:15 CST)
• FW: Parallel Simulations #SHEPHERDSON IGNATIUS MARK# (Sat Feb 06 2010 - 09:56:55 CST)
  • Re: FW: Parallel Simulations Axel Kohlmeyer (Sat Feb 06 2010 - 10:40:15 CST)
  • Re: FW: Parallel Simulations snoze pa (Sat Feb 06 2010 - 19:08:28 CST)
    • Re: FW: Parallel Simulations Axel Kohlmeyer (Sat Feb 06 2010 - 21:16:14 CST)
• Re: apoa1 bencmark for 2.7 MPI compiled Branko (Fri Feb 05 2010 - 16:02:29 CST)
• apoa1 bencmark for 2.7 MPI compiled Branko (Fri Feb 05 2010 - 13:00:21 CST)
• Simulations with NAMD Santanu Chatterjee (Fri Feb 05 2010 - 10:37:44 CST)
  • Re: Simulations with NAMD Axel Kohlmeyer (Fri Feb 05 2010 - 11:14:19 CST)
  • Re: Simulations with NAMD snoze pa (Sat Feb 06 2010 - 19:13:11 CST)
  • Re: Simulations with NAMD DimitryASuplatov (Sun Feb 07 2010 - 04:39:40 CST)
• Changing the Potential Energy Function Hok-Hei Tam (Thu Feb 04 2010 - 22:08:41 CST)
  • Re: Changing the Potential Energy Function Axel Kohlmeyer (Thu Feb 04 2010 - 22:50:30 CST)
• minimization gradient question Goutham (Thu Feb 04 2010 - 19:20:32 CST)
• NAMD on Ranger neville forlemu (Wed Feb 03 2010 - 17:57:14 CST)
• Definitions of certain routine names in source Bennion, Brian (Wed Feb 03 2010 - 17:01:52 CST)
• Plumed and NAMD neville forlemu (Wed Feb 03 2010 - 12:45:37 CST)
• StepsPerCycle Myunggi Yi (Wed Feb 03 2010 - 09:33:08 CST)
  • Re: StepsPerCycle David Hardy (Wed Feb 03 2010 - 10:07:36 CST)
    • Re: StepsPerCycle David Hardy (Wed Feb 03 2010 - 10:28:38 CST)
• psfgen error Anna Dejardin (Wed Feb 03 2010 - 07:35:54 CST)
  • Re: psfgen error snoze pa (Wed Feb 03 2010 - 10:25:43 CST)
• saving psf ipsita basu (Tue Feb 02 2010 - 00:53:38 CST)
  • Re: saving psf Benjamin Bouvier (Tue Feb 02 2010 - 02:18:51 CST)
• Questions about thermodynamic integration in NAMD 2.7b2 Jeffrey J. Potoff (Mon Feb 01 2010 - 14:27:22 CST)
  • RE: Questions about thermodynamic integration in NAMD 2.7b2 Courtney Taylor (Tue Sep 21 2010 - 15:14:22 CDT)
• IMD VMD NAMD adding frames Scooter Willis (Mon Feb 01 2010 - 13:35:37 CST)
• unsubscribe prasun kumar (Mon Feb 01 2010 - 12:00:49 CST)
  • Re: unsubscribe Axel Kohlmeyer (Mon Feb 01 2010 - 12:53:12 CST)
• firsttimestep in NAMD snoze pa (Mon Feb 01 2010 - 11:31:42 CST)
• namd job crashed Bala subramanian (Mon Feb 01 2010 - 10:55:23 CST)
  • Re: namd job crashed gbellesia_at_chem.ucsb.edu (Mon Feb 01 2010 - 11:29:33 CST)
  • Re: namd job crashed snoze pa (Mon Feb 01 2010 - 11:26:42 CST)
• Re: dcd] Branko (Mon Feb 01 2010 - 10:59:57 CST)
  • Re: dcd] snoze pa (Mon Feb 01 2010 - 11:33:56 CST)
• water structure ipsita basu (Mon Feb 01 2010 - 05:40:54 CST)
  • Re: water structure Axel Kohlmeyer (Mon Feb 01 2010 - 06:15:22 CST)
    • Re: water structure ipsita basu (Mon Feb 01 2010 - 23:52:03 CST)
      • Re: water structure Axel Kohlmeyer (Tue Feb 02 2010 - 04:56:41 CST)
• dcd ipsita basu (Mon Feb 01 2010 - 03:27:17 CST)
  • Re: dcd Ajasja LjubetiÄ� (Mon Feb 01 2010 - 04:25:25 CST)
    • Re: dcd Ajasja LjubetiÄ� (Mon Feb 01 2010 - 05:40:14 CST)
• Info: Attempting to read FFTW data from FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt Bala subramanian (Mon Feb 01 2010 - 03:12:04 CST)
  • Re: Info: Attempting to read FFTW data from FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt Ajasja LjubetiÄ� (Mon Feb 01 2010 - 04:09:24 CST)
  • RE: Info: Attempting to read FFTW data from FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt Richard Owczarzy (Mon Feb 01 2010 - 10:27:44 CST)
• analysis of dcd ipsita basu (Sun Jan 31 2010 - 22:58:41 CST)
  • Re: analysis of dcd Roman Petrenko (Sun Jan 31 2010 - 23:25:36 CST)
    • Re: analysis of dcd Gianluca Interlandi (Mon Feb 01 2010 - 01:13:45 CST)
• Parameter File Scooter Willis (Sun Jan 31 2010 - 21:19:32 CST)
  • Re: Parameter File JC Gumbart (Sun Jan 31 2010 - 21:34:21 CST)
• Tcl Forces error Brittany Morgan (Thu Jan 28 2010 - 19:39:16 CST)
• ERROR: Constraint failure in RATTLE algorithm for atom snoze pa (Sun Jan 31 2010 - 12:41:16 CST)
• langevinTemp and system temperature snoze pa (Fri Jan 29 2010 - 09:30:07 CST)
  • Re: langevinTemp and system temperature Axel Kohlmeyer (Fri Jan 29 2010 - 10:01:21 CST)
  • Re: langevinTemp and system temperature Joshua Adelman (Fri Jan 29 2010 - 09:42:19 CST)
    • Re: langevinTemp and system temperature snoze pa (Fri Jan 29 2010 - 11:19:28 CST)
• Tcl Forces error Brittany Morgan (Thu Jan 28 2010 - 20:00:10 CST)
  • Re: Tcl Forces error Axel Kohlmeyer (Sun Jan 31 2010 - 16:19:53 CST)
• implicit solvent with iapbs BIN ZHANG (Thu Jan 28 2010 - 01:33:38 CST)
  • Re: implicit solvent with iapbs Robert Konecny (Mon Feb 01 2010 - 17:30:09 CST)
• Magnesium Ions Placement Thomas Kahn (Wed Jan 27 2010 - 19:18:02 CST)
  • Re: Magnesium Ions Placement Axel Kohlmeyer (Wed Jan 27 2010 - 19:52:40 CST)
• how to get .coor .vel and .xsc for a .dcd file ÅÓÑ©ÇÛ Pang Xueqin (Wed Jan 27 2010 - 08:42:44 CST)
  • Re: how to get .coor .vel and .xsc for a .dcd file Axel Kohlmeyer (Wed Jan 27 2010 - 09:13:17 CST)
• velocities from a DCD file Raul Araya (Wed Jan 27 2010 - 08:01:00 CST)
  • Re: velocities from a DCD file Axel Kohlmeyer (Wed Jan 27 2010 - 08:46:28 CST)
  • Re: velocities from a DCD file francesco oteri (Wed Jan 27 2010 - 08:37:28 CST)
  • Re: velocities from a DCD file Jérôme Hénin (Wed Jan 27 2010 - 09:08:52 CST)
• the maximum numbers of atoms in NAMD? uu zhu (Wed Jan 27 2010 - 06:19:58 CST)
  • Re: the maximum numbers of atoms in NAMD? Axel Kohlmeyer (Wed Jan 27 2010 - 07:57:10 CST)
• problem whit comand "COM" Leonardo Herrera (Tue Jan 26 2010 - 20:21:19 CST)
  • Re: problem whit comand "COM" Axel Kohlmeyer (Tue Jan 26 2010 - 21:54:40 CST)
• Announcement: TCBG workshop at Pittsburgh Supercomputing Center May 10-14, 2010 TCBG Workshops (Tue Jan 26 2010 - 13:41:36 CST)
• PLUMED tutorial announcement Massimiliano Bonomi (Tue Jan 26 2010 - 02:38:12 CST)
• Re: colvar module question BIN ZHANG (Tue Jan 26 2010 - 01:32:50 CST)
  • Re: colvar module question Giacomo Fiorin (Tue Jan 26 2010 - 08:18:15 CST)
    • ABF question Austin B. Yongye (Tue Jan 26 2010 - 17:07:05 CST)
      • Re: ABF question Jérôme Hénin (Wed Jan 27 2010 - 04:18:13 CST)
      • Solute moves outside of solvent box Austin B. Yongye (Thu Jan 28 2010 - 12:28:37 CST)
      • Re: Solute moves outside of solvent box Jeffrey J. Potoff (Thu Jan 28 2010 - 12:55:08 CST)
      • Re: Solute moves outside of solvent box Jeffrey J. Potoff (Tue Feb 02 2010 - 10:26:09 CST)
      • Re: ABF question Jérôme Hénin (Wed Sep 21 2011 - 07:01:50 CDT)
    • Re: colvar module question BIN ZHANG (Tue Jan 26 2010 - 23:54:19 CST)
• colvar module question BIN ZHANG (Mon Jan 25 2010 - 15:09:24 CST)
• problems with NAMD plot and .DCD file parsons_at_umbi.umd.edu (Mon Jan 25 2010 - 11:35:13 CST)
• reading dcd file ipsita basu (Mon Jan 25 2010 - 03:20:39 CST)
  • Re: reading dcd file Axel Kohlmeyer (Mon Jan 25 2010 - 05:44:37 CST)
  • Re: reading dcd file Mert Gür (Tue Jan 26 2010 - 15:46:00 CST)
• scripting problem ipsita basu (Mon Jan 25 2010 - 00:15:51 CST)
  • Re: scripting problem Eduard Schreiner (Mon Jan 25 2010 - 01:04:06 CST)
• NAMD on AMD Istanbul versus intel Nehalem with infiniband Vlad Cojocaru (Fri Jan 22 2010 - 07:56:11 CST)
• Colvar on 2.7b2 win vs Linux MPI instalation Branko (Fri Jan 22 2010 - 14:28:30 CST)
  • Re: Colvar on 2.7b2 win vs Linux MPI instalation Jerome Henin (Fri Jan 22 2010 - 15:19:33 CST)
    • Re: Colvar on 2.7b2 win vs Linux MPI instalation Branko (Sat Jan 23 2010 - 05:32:48 CST)
    • Re: Re: Colvar on 2.7b2 win vs Linux MPI instalation Branko (Tue Feb 09 2010 - 15:15:46 CST)
      • Re: Re: Colvar on 2.7b2 win vs Linux MPI instalation Axel Kohlmeyer (Tue Feb 09 2010 - 16:01:44 CST)
• NAMD on AMD Istanbul versus intel Nehalem with infiniband Vlad Cojocaru (Fri Jan 22 2010 - 08:47:58 CST)
• scripting error ipsita basu (Thu Jan 21 2010 - 23:36:02 CST)
  • Re: scripting error Ajasja LjubetiÄ� (Fri Jan 22 2010 - 01:48:34 CST)
    • Re: scripting error Ajasja LjubetiÄ� (Mon Jan 25 2010 - 07:19:48 CST)
  • Re: scripting error Jérôme Hénin (Mon Jan 25 2010 - 09:10:19 CST)
• NAMD on linux Lixia Jin Day (Thu Jan 21 2010 - 10:55:57 CST)
  • Re: NAMD on linux Axel Kohlmeyer (Thu Jan 21 2010 - 11:25:00 CST)
• protein unfolding jose correa (Thu Jan 21 2010 - 08:57:06 CST)
  • Re: protein unfolding Andrew Emerson (Thu Jan 21 2010 - 09:45:55 CST)
    • Re: protein unfolding jose correa (Thu Jan 21 2010 - 09:55:14 CST)
• Erratic behavior of TclBC in parallel Jérôme Hénin (Thu Jan 21 2010 - 08:38:35 CST)
  • Re: Erratic behavior of TclBC in parallel Jérôme Hénin (Fri Jan 22 2010 - 11:08:02 CST)
• protein unfolding jose correa (Thu Jan 21 2010 - 07:29:13 CST)
  • Re: protein unfolding Axel Kohlmeyer (Thu Jan 21 2010 - 08:15:10 CST)
    • Re: protein unfolding jose correa (Thu Jan 21 2010 - 11:03:27 CST)
  • Re: protein unfolding Pu Tian (Thu Jan 21 2010 - 09:19:16 CST)
    • Re: protein unfolding jose correa (Thu Jan 21 2010 - 09:29:42 CST)
• simulation error ipsita basu (Thu Jan 21 2010 - 00:13:46 CST)
• Re: Fwd: suitable motherboards for both graphical visualization and NAMD-CUDA computation? Biff Forbush (Wed Jan 20 2010 - 20:32:06 CST)
• suitable motherboards for both graphical visualization and NAMD-CUDA computation? Lela Vukovic (Wed Jan 20 2010 - 14:56:45 CST)
  • Re: suitable motherboards for both graphical visualization and NAMD-CUDA computation? Biff Forbush (Wed Jan 20 2010 - 17:29:49 CST)
• Re: Reply:Re: How to convert the GROMOS parameter unit into charmm22 style Jérôme Hénin (Wed Jan 20 2010 - 07:05:37 CST)
  • Re: Reply:Re: How to convert the GROMOS parameter unit into charmm22 style Axel Kohlmeyer (Wed Jan 20 2010 - 07:50:29 CST)
• NAMD ibverbs not working on new cluster Jesper Soerensen (Wed Jan 20 2010 - 03:11:35 CST)
• How to convert the GROMOS parameter unit into charmm22 style Íõ—² (Wed Jan 20 2010 - 00:24:27 CST)
  • Re: How to convert the GROMOS parameter unit into charmm22 style Jérôme Hénin (Wed Jan 20 2010 - 03:27:42 CST)
• Regarding Periodic Boundary Jagan Mohan (Tue Jan 19 2010 - 23:45:44 CST)
• Simulation question snoze pa (Tue Jan 19 2010 - 11:26:06 CST)
  • Re: Simulation question Gianluca Interlandi (Tue Jan 19 2010 - 13:18:58 CST)
  • Re: Simulation question Paul Rigor (uci-ics) (Tue Jan 19 2010 - 18:29:03 CST)
• (Infiniband-related?) NAMD 2.7b2 (ibverbs x86_64) runtime error during a MD run Pietro Amodeo (Tue Jan 19 2010 - 05:03:21 CST)
• starting namd ipsita basu (Tue Jan 19 2010 - 04:50:41 CST)
  • Re: starting namd Santanu Chatterjee (Tue Jan 19 2010 - 10:35:30 CST)
    • Re: starting namd ipsita basu (Thu Jan 21 2010 - 00:14:49 CST)
• units of position coordinate velocity coordinate and timestep in .dcd and .veldcd file sudipta (Tue Jan 19 2010 - 04:57:58 CST)
• Center of Mass Harmonic Potentials Keith Battle (Mon Jan 18 2010 - 18:59:25 CST)
  • Re: Center of Mass Harmonic Potentials Axel Kohlmeyer (Mon Jan 18 2010 - 19:33:18 CST)
    • Re: Center of Mass Harmonic Potentials Jérôme Hénin (Tue Jan 19 2010 - 01:56:34 CST)
• convergence of ABF Jorgen Simonsen (Sun Jan 17 2010 - 20:42:30 CST)
• harmonic constraint when equilibrate the system Naiyin Yu (Sun Jan 17 2010 - 00:32:57 CST)
• error of the energy output when equilibration xyhu1127 (Thu Jan 14 2010 - 19:17:18 CST)
• Excluding interactions? Charles Zhao (Thu Jan 14 2010 - 19:46:57 CST)
  • Re: Excluding interactions? Jérôme Hénin (Fri Jan 15 2010 - 06:53:51 CST)
    • Re: Excluding interactions? Charles Zhao (Fri Jan 15 2010 - 21:12:23 CST)
      • Re: Excluding interactions? Jérôme Hénin (Sat Jan 16 2010 - 12:37:26 CST)
      • Re: Excluding interactions? Charles Zhao (Wed Jan 20 2010 - 13:44:47 CST)
      • Re: Excluding interactions? Jérôme Hénin (Thu Jan 21 2010 - 08:17:26 CST)
• Number of MC steps in ABF integrate gives entirely diferent surfaces Branko (Thu Jan 14 2010 - 04:42:14 CST)
  • Re: Number of MC steps in ABF integrate gives entirely diferent surfaces Jerome Henin (Thu Jan 14 2010 - 05:00:18 CST)
    • Re: Number of MC steps in ABF integrate gives entirely diferent surfaces Branko (Thu Jan 14 2010 - 05:30:42 CST)
• Strange behavior of NAMD 2.7b1 Alexandre Suman de Araujo (Wed Jan 13 2010 - 12:25:49 CST)
  • Re: Strange behavior of NAMD 2.7b1 Axel Kohlmeyer (Wed Jan 13 2010 - 13:22:13 CST)
    • Re: Strange behavior of NAMD 2.7b1 Alexandre Suman de Araujo (Thu Jan 14 2010 - 06:25:33 CST)
      • Re: Strange behavior of NAMD 2.7b1 Axel Kohlmeyer (Thu Jan 14 2010 - 08:53:43 CST)
• starting a job ipsita basu (Wed Jan 13 2010 - 04:39:34 CST)
  • Re: starting a job Jérôme Hénin (Wed Jan 13 2010 - 07:00:58 CST)
    • Re: starting a job Jian Liu (Wed Jan 13 2010 - 07:35:03 CST)
• Problem compiling namd Philipp M. (Mon Jan 11 2010 - 07:19:43 CST)
• NAMD-CUDA benchmarks, dual GTX295, dual Xeon Nehalem system Biff Forbush (Sat Jan 09 2010 - 22:16:41 CST)
• CPU usage when exec function is used daniel aguayo (Fri Jan 08 2010 - 14:48:42 CST)
  • Re: CPU usage when exec function is used Axel Kohlmeyer (Fri Jan 08 2010 - 15:31:16 CST)
    • Re: CPU usage when exec function is used daniel aguayo (Fri Jan 08 2010 - 17:46:30 CST)
• release of RAMD scripts for NAMD 2.6 and 2.7 Vlad Cojocaru (Fri Jan 08 2010 - 05:52:52 CST)
• colvarsInput filename problem BIN ZHANG (Wed Jan 06 2010 - 19:51:43 CST)
  • Re: colvarsInput filename problem Jérôme Hénin (Thu Jan 07 2010 - 04:28:09 CST)
• CUDA-NAMD hangs -- check the Northbridge temp! Biff Forbush (Tue Jan 05 2010 - 21:51:51 CST)
  • Re: CUDA-NAMD hangs -- check the Northbridge temp! Pu Tian (Wed Jan 06 2010 - 09:36:55 CST)
    • Re: CUDA-NAMD hangs -- check the Northbridge temp! Paul Rigor (uci-ics) (Wed Jan 06 2010 - 17:12:54 CST)
      • Re: CUDA-NAMD hangs -- check the Northbridge temp! Biff Forbush (Wed Jan 06 2010 - 18:12:08 CST)
• Re: ABF - sequence of MD runs Jérôme Hénin (Tue Jan 05 2010 - 11:26:22 CST)
• ABF questions Austin B. Yongye (Tue Jan 05 2010 - 10:27:47 CST)
  • Re: ABF questions Jérôme Hénin (Tue Jan 05 2010 - 11:44:58 CST)
    • Re: ABF questions Austin B. Yongye (Tue Jan 05 2010 - 12:10:04 CST)
    • Re: ABF questions Austin B. Yongye (Tue Jan 05 2010 - 16:19:57 CST)
      • Re: ABF questions Branko (Wed Jan 06 2010 - 07:17:02 CST)
      • Re: ABF questions Austin B. Yongye (Wed Jan 06 2010 - 09:56:28 CST)
  • Re: ABF questions Jérôme Hénin (Wed Jan 13 2010 - 10:40:49 CST)
    • Re: ABF questions Austin B. Yongye (Wed Jan 13 2010 - 11:45:51 CST)
• NAMD-FEP tutorial-alchemify problem Lisa Brown (Tue Jan 05 2010 - 09:21:41 CST)
  • Re: NAMD-FEP tutorial-alchemify problem Jérôme Hénin (Tue Jan 05 2010 - 10:54:38 CST)
    • Re: NAMD-FEP tutorial-alchemify problem Lisa Brown (Tue Jan 05 2010 - 12:38:43 CST)
• run NAMD_2.7B2 hamze rahimi (Sat Jan 02 2010 - 00:58:42 CST)
  • Re: run NAMD_2.7B2 Leonardo Trabuco (Mon Jan 04 2010 - 13:57:27 CST)
  • Re: run NAMD_2.7B2 Paul Rigor (uci-ics) (Mon Jan 04 2010 - 15:29:08 CST)
• CMAP in NAMD output Yang MIngjun (Mon Jan 04 2010 - 01:50:47 CST)
  • Re: CMAP in NAMD output Jérôme Hénin (Mon Jan 04 2010 - 17:07:38 CST)
• Re: Definition of two colvars for ABF Branko (Fri Jan 01 2010 - 09:58:30 CST)
  • Re: Definition of two colvars for ABF Jérôme Hénin (Mon Jan 04 2010 - 16:59:22 CST)
  • Re: Definition of two colvars for ABF Jérôme Hénin (Tue Jan 05 2010 - 08:12:47 CST)
    • Re: Definition of two colvars for ABF Branko (Tue Jan 05 2010 - 08:19:14 CST)