July 2010 Archives by thread

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Starting: Thu Jul 1 01:57:11 CEST 2010
Ending: Sat Jul 31 22:17:42 CEST 2010
Messages: 640

• [gmx-users] Capping residues   Justin A. Lemkul
  • [gmx-users] Capping residues   Mark Abraham
    • [gmx-users] Capping residues   Sai Pooja
      • [gmx-users] Capping residues   Justin A. Lemkul
      • [gmx-users] Capping residues   Sai Pooja
      • [gmx-users] Capping residues   Mark Abraham
      • [gmx-users] Capping residues   Sai Pooja
      • [gmx-users] Capping residues   Justin A. Lemkul
      • [gmx-users] Capping residues   Sai Pooja
      • [gmx-users] Capping residues   Sai Pooja
      • [gmx-users] Capping residues   Justin A. Lemkul
      • [gmx-users] Capping residues   Sai Pooja
      • [gmx-users] Capping residues   Justin A. Lemkul
      • [gmx-users] Capping residues   Sai Pooja
• [gmx-users] Re: gmx-users Digest, Vol 74, Issue 189   Justin A. Lemkul
• [gmx-users] Gromacs to APBS   Mark Abraham
• [gmx-users] the job is not being distributed   Mark Abraham
• [gmx-users] amber/charmm force field and HB lifetime at low temperature   Ramachandran G
  • [gmx-users] amber/charmm force field and HB lifetime at low temperature   Mark Abraham
    • [gmx-users] amber/charmm force field and HB lifetime at low temperature   Ramachandran G
• [gmx-users] protein stability as a dimer   sonali dhindwal
  • [gmx-users] protein stability as a dimer   Justin A. Lemkul
    • [gmx-users] protein stability as a dimer   sonali dhindwal
      • [gmx-users] protein stability as a dimer   Justin A. Lemkul
• [gmx-users] Re: Re: Re:Chain Terminus   lloyd riggs
  • [gmx-users] Re: Re: Re:Chain Terminus   Mark Abraham
  • [gmx-users] Re: Re: Re:Chain Terminus   Tsjerk Wassenaar
• [gmx-users] amber parameters in gromacs   Rolf Erwin Isele-Holder
  • [gmx-users] amber parameters in gromacs   Justin A. Lemkul
• [gmx-users] the job is not being distributed   Syed Tarique Moin
• [gmx-users] Re: amber parameters in gromacs   Alan
• [gmx-users] Re: QMMM cpmd   Christoph Riplinger
• [gmx-users] Ewald summation   Thanasis Koukoulas
• [gmx-users] Re: amber parameters in gromacs   Rolf Erwin Isele-Holder
  • [gmx-users] Re: amber parameters in gromacs   David van der Spoel
• [gmx-users] Re: amber parameters in gromacs   Alan
• [gmx-users] Problem with Lennard Jones cross terms   xrysostomos sfhsdfghsdfhsdgh
  • [gmx-users] Problem with Lennard Jones cross terms   Gaurav Goel
    • [gmx-users] Problem with Lennard Jones cross terms   xrysostomos sfhsdfghsdfhsdgh
      • [gmx-users] Problem with Lennard Jones cross terms   Mark Abraham
      • [gmx-users] Problem with Lennard Jones cross terms   Gaurav Goel
      • [gmx-users] Problem with Lennard Jones cross terms   xrysostomos sfhsdfghsdfhsdgh
• [gmx-users] Pull code   Gavin Melaugh
• [gmx-users] Re: Pull code   Thomas Schlesier
  • [gmx-users] Re: Pull code   Gavin Melaugh
• [gmx-users] pull code   Gavin Melaugh
• [gmx-users] another pull-code question   Gavin Melaugh
  • [gmx-users] another pull-code question   Justin A. Lemkul
    • [gmx-users] g_wham   Gavin Melaugh
      • [gmx-users] Re: g_wham   Justin A. Lemkul
• [gmx-users] g_energy output   lists at jsx.dk
• [gmx-users] hdb file   Moeed
  • [gmx-users] hdb file   Justin A. Lemkul
• [gmx-users] B-factor   Tsjerk Wassenaar
  • [gmx-users] B-factor   Mark Abraham
• [gmx-users] GBSA calculations   Hassan Shallal
• [gmx-users] Ewald summation   Thanasis
• [gmx-users] Re: another pull-code question   Thomas Schlesier
  • [gmx-users] Re: another pull-code question   Gavin Melaugh
• [gmx-users] Re: another pull-code question   Thomas Schlesier
  • [gmx-users] Re: another pull-code question   Justin A. Lemkul
    • [gmx-users] Re: another pull-code question   Gavin Melaugh
• [gmx-users] another pull-code question   chris.neale at utoronto.ca
  • [gmx-users] another pull-code question   Justin A. Lemkul
• [gmx-users] another pull-code question   chris.neale at utoronto.ca
  • [gmx-users] another pull-code question   Gavin Melaugh
• [gmx-users] another pull-code question   chris.neale at utoronto.ca
• [gmx-users] Is there a way to protonate small molecules with gromacs without editing ffgmx2.hdb file?   Arthur Roberts
  • [gmx-users] Is there a way to protonate small molecules with gromacs without editing ffgmx2.hdb file?   David van der Spoel
    • [gmx-users] Is there a way to protonate small molecules with gromacs without editing ffgmx2.hdb file?   ms
      • [gmx-users] Is there a way to protonate small molecules with gromacs without editing ffgmx2.hdb file?   Justin A. Lemkul
• [gmx-users] g_principal: memory corruption   kulleperuma.kulleperuma at utoronto.ca
  • [gmx-users] g_principal: memory corruption   David van der Spoel
• [gmx-users] Fwd: missing atom   Carsten Kutzner
  • [gmx-users] Fwd: missing atom   Oliver Grant
• [gmx-users] how to strip velocities out of a .gro file   chris.neale at utoronto.ca
  • [gmx-users] how to strip velocities out of a .gro file   shayamra at post.tau.ac.il
    • [gmx-users] how to strip velocities out of a .gro file   Tsjerk Wassenaar
• [gmx-users] GBSA calculations   Mark Abraham
• [gmx-users] mk_angndx   Andrei Neamtu
• [gmx-users] contact map   atila petrosian
  • [gmx-users] contact map   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 75, Issue 18   kulleperuma.kulleperuma at utoronto.ca
• [gmx-users] residue names in rtp file and their parameters   chiba.s.ac
• [gmx-users] Re: Re: Fwd: missing atom   lloyd riggs
  • [gmx-users] Re: Re: Fwd: missing atom   Mark Abraham
• [gmx-users] pressure coupling   Shuangxing Dai
  • [gmx-users] pressure coupling   Justin A. Lemkul
• [gmx-users] Free Energy calculations of peptide-protein binding   Ehud Schreiber
  • [gmx-users] Free Energy calculations of peptide-protein binding   Daniel Seeliger
• [gmx-users] Free Energy calculations of peptide-protein binding   chris.neale at utoronto.ca
• [gmx-users] Implicit solvent   ithu
  • [gmx-users] Implicit solvent   Justin A. Lemkul
    • [gmx-users] Implicit solvent   ms
• [gmx-users] pressure coupling   Shuangxing Dai
  • [gmx-users] pressure coupling   Justin A. Lemkul
• [gmx-users] how to strip velocities out of a .gro file   Chris Neale
• [gmx-users] problem in cluster determination : g_clustsize and trjconv -pbc cluster problem   Sanku M
• [gmx-users] how to strip velocities out of a .gro file   Tsjerk Wassenaar
• [gmx-users] Units of the Amber99 parameters   Amir Marcovitz
  • [gmx-users] Units of the Amber99 parameters   Mark Abraham
• [gmx-users] RE: gmx-users Digest, Vol 75, Issue 23   abdul wadood
  • [gmx-users] RE: gmx-users Digest, Vol 75, Issue 23   Justin A. Lemkul
  • [gmx-users] RE: gmx-users Digest, Vol 75, Issue 23   Oliver Grant
• [gmx-users] Problems with installing mpi-version of Gromacs   Pinchas Aped
• [gmx-users] visual program   leila karami
  • [gmx-users] visual program   Justin A. Lemkul
• [gmx-users] COM distances   Gavin Melaugh
  • [gmx-users] COM distances   Gavin Melaugh
• [gmx-users] sulfate in topology file with oplsaa forcefield   you zou
  • [gmx-users] sulfate in topology file with oplsaa forcefield   Justin A. Lemkul
• [gmx-users] problem while simulating metal ions   Kwee Hong
  • [gmx-users] problem while simulating metal ions   Mark Abraham
• [gmx-users] problem with trjconv -pbc cluster   jagannath mondal
  • [gmx-users] problem with trjconv -pbc cluster   Mark Abraham
    • [gmx-users] problem with trjconv -pbc cluster   jagannath mondal
• [gmx-users] Release of the R.E.D.-III.4 tools   FyD
• [gmx-users] No such moleculetype SOL   nanogroup
  • [gmx-users] No such moleculetype SOL   Mark Abraham
• [gmx-users] g_anaeig & pymol   Carla Jamous
  • [gmx-users] g_anaeig & pymol   Daniel Seeliger
• [gmx-users] No such moleculetype SOL   nanogroup
  • [gmx-users] No such moleculetype SOL   Justin A. Lemkul
  • [gmx-users] No such moleculetype SOL   Mark Abraham
• [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96   C. Batistakis
  • [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96   Mark Abraham
    • [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96   C. Batistakis
• [gmx-users] how gromacs calculate center of mass for broken molecules?   Kun Huang
• [gmx-users] problem with trjconv -pbc cluster   chris.neale at utoronto.ca
• [gmx-users] problem with trjconv -pbc cluster   chris.neale at utoronto.ca
  • [gmx-users] problem with trjconv -pbc cluster   jagannath mondal
• [gmx-users] Fatal error:   Nilesh Dhumal
  • [gmx-users] Fatal error:   Justin A. Lemkul
• [gmx-users] help: gromacs mistake   shuai shuai
• [gmx-users] Frozen N2 in a very long tube; was "help: gromacs mistake"   chris.neale at utoronto.ca
• [gmx-users] wrong charge assignment(?) on ATP in rtp file   chiba.s.ac
• [gmx-users] wrong charge assignment(?) on ATP in rtp file   chris.neale at utoronto.ca
  • [gmx-users] wrong charge assignment(?) on ATP in rtp file   chiba.s.ac
• [gmx-users] how gromacs calculate center of mass for broken molecules?   chris.neale at utoronto.ca
• [gmx-users] problem with trjconv -pbc cluster   chris.neale at utoronto.ca
  • [gmx-users] problem with g_clustsize   jagannath mondal
• [gmx-users] COM distances   chris.neale at utoronto.ca
  • [gmx-users] COM distances   Gavin Melaugh
• [gmx-users] problems with g_wham   Gavin Melaugh
• [gmx-users] problem with g_clustsize   chris.neale at utoronto.ca
• [gmx-users] problems with g_wham   chris.neale at utoronto.ca
  • [gmx-users] problems with g_wham   Gavin Melaugh
    • [gmx-users] problems with g_wham   Justin A. Lemkul
• [gmx-users] problems with g_wham   chris.neale at utoronto.ca
• [gmx-users] wrong charge assignment(?) on ATP in rtp file   chris.neale at utoronto.ca
  • [gmx-users] wrong charge assignment(?) on ATP in rtp file   Tsjerk Wassenaar
• [gmx-users] (no subject)   munubas at yahoo.com
  • [gmx-users] (no subject)   Justin A. Lemkul
• [gmx-users] problems with g_wham   chris.neale at utoronto.ca
  • [gmx-users] problems with g_wham   Gavin Melaugh
    • [gmx-users] problems with g_wham   Justin A. Lemkul
      • [gmx-users] problems with g_wham   Gavin Melaugh
      • [gmx-users] problems with g_wham   Justin A. Lemkul
      • [gmx-users] problems with g_wham   Gavin Melaugh
• [gmx-users] parallel run with integrator=nm ?   J. Rui Rodrigues
• [gmx-users] Re: Parameters for selenium   Luis Paulo
• [gmx-users] Parameters for selenium   chris.neale at utoronto.ca
• [gmx-users] Compiling problems on MacOS X 10.6.4   Patargias, George
  • [gmx-users] Compiling problems on MacOS X 10.6.4   J. Rui Rodrigues
    • [gmx-users] Compiling problems on MacOS X 10.6.4   Patargias, George
    • [gmx-users] Compiling problems on MacOS X 10.6.4   Patargias, George
      • [gmx-users] Compiling problems on MacOS X 10.6.4   J. Rui Rodrigues
      • [gmx-users] Compiling problems on MacOS X 10.6.4   Patargias, George
• [gmx-users] Capping residues   Justin A. Lemkul
  • [gmx-users] Capping residues   Justin A. Lemkul
• [gmx-users] Capping residues   Justin A. Lemkul
• [gmx-users] energy contributions / question about solvating   jojo J
  • [gmx-users] energy contributions   Mark Abraham
  • [gmx-users] question about solvating   Mark Abraham
• [gmx-users] mpi run   nanogroup
  • [gmx-users] mpi run   Carsten Kutzner
    • [gmx-users] mpi run   #ZHAO LINA#
      • [gmx-users] mpi run   Mark Abraham
• [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory   zhongjin
  • [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory   Carsten Kutzner
  • [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory   Mark Abraham
• [gmx-users] question about non-bonded parameters for CHARMM in GROMACS   Michael Francis Hagan
• [gmx-users] problems with g_wham   chris.neale at utoronto.ca
  • [gmx-users] problems with g_wham   Gavin Melaugh
• [gmx-users] Location of a molecule in a dodecahedron   Birgit Hischenhuber
  • [gmx-users] Location of a molecule in a dodecahedron   Justin A. Lemkul
• [gmx-users] P4_error for extending coarse grained MD simulations   张春雷
  • [gmx-users] P4_error for extending coarse grained MD simulations   Carsten Kutzner
    • [gmx-users] P4_error for extending coarse grained MD simulations   张春雷
      • [gmx-users] P4_error for extending coarse grained MD simulations   Carsten Kutzner
      • [gmx-users] P4_error for extending coarse grained MD simulations   XAvier Periole
• [gmx-users] genbox and water model   Sai Pooja
  • [gmx-users] genbox and water model   Justin A. Lemkul
• [gmx-users] how to determine the box size   jojo J
  • [gmx-users] how to determine the box size   Justin A. Lemkul
  • [gmx-users] how to determine the box size   Mark Abraham
• [gmx-users] top file   jojo J
  • [gmx-users] top file   Justin A. Lemkul
    • [gmx-users] top file   jojo J
      • [gmx-users] top file   Justin A. Lemkul
• [gmx-users] energygrp_excl and PME   jasmine
  • [gmx-users] energygrp_excl and PME   Mark Abraham
• [gmx-users] Adding ions   Sai Pooja
• [gmx-users] Ewald setting for hydrocarbon system?   jojo J
• [gmx-users] Solvating protein   Sai Pooja
  • [gmx-users] Solvating protein   Mark Abraham
    • [gmx-users] Solvating protein   Sai Pooja
      • [gmx-users] Solvating protein   Justin A. Lemkul
      • [gmx-users] Solvating protein   Sai Pooja
      • [gmx-users] Solvating protein   Sai Pooja
      • [gmx-users] Solvating protein   Justin A. Lemkul
• [gmx-users] fast rerun in order to get an energy   Magdalena
  • [gmx-users] fast rerun in order to get an energy   Justin A. Lemkul
  • [gmx-users] fast rerun in order to get an energy   Jeffery Perkins
    • [gmx-users] fast rerun in order to get an energy   XAvier Periole
• [gmx-users] Frozen N2 in a very long tube   shuai shuai
  • [gmx-users] Frozen N2 in a very long tube   Mark Abraham
• [gmx-users] information regarding the bootstrap method implemented with the g_wham   Ozge Engin
• [gmx-users] Missing sugar atom in CHARMM dna.rtp   Patargias, George
  • [gmx-users] Missing sugar atom in CHARMM dna.rtp   Justin A. Lemkul
• [gmx-users] pdb2gmx with DNA   Patargias, George
  • [gmx-users] pdb2gmx with DNA   Justin A. Lemkul
    • [gmx-users] pdb2gmx with DNA   Patargias, George
      • [gmx-users] pdb2gmx with DNA   Justin A. Lemkul
• [gmx-users] mdp file settings for PME   jojo J
  • [gmx-users] mdp file settings for PME   Justin A. Lemkul
• [gmx-users] Installing gromacs from git   Sai Pooja
  • [gmx-users] Installing gromacs from git   Carsten Kutzner
• [gmx-users] the Pressure control in GROMACS 4.0.7   zhongjin
  • [gmx-users] the Pressure control in GROMACS 4.0.7   Justin A. Lemkul
• [gmx-users] problem with angle restraints   subarna thakur
• [gmx-users] Re: the Pressure control in GROMACS 4.0.7   Vitaly Chaban
  • [gmx-users] Re: the Pressure control in GROMACS 4.0.7   David van der Spoel
• [gmx-users] Re: Frozen N2 in a very long tube   Vitaly Chaban
  • [gmx-users] Re: Frozen N2 in a very long tube   shuai shuai
    • [gmx-users] Re: Frozen N2 in a very long tube   Justin A. Lemkul
• [gmx-users] Re: Pressure control in GROMACS 4.0.7   Vitaly Chaban
  • [gmx-users] Re: Pressure control in GROMACS 4.0.7   David van der Spoel
• [gmx-users] Re: the Pressure control in GROMACS 4.0.7   zhongjin
  • [gmx-users] Re: the Pressure control in GROMACS 4.0.7   David van der Spoel
• [gmx-users] Treating nonbondend interactions in GROMACS   jojo J
  • [gmx-users] Treating nonbondend interactions in GROMACS   Justin A. Lemkul
• [gmx-users] high repulsion in packed system   Moeed
  • [gmx-users] high repulsion in packed system   Justin A. Lemkul
• [gmx-users] Re: high repulsion in packed system   Vitaly Chaban
• [gmx-users] HA1/HA2 chirality of GLY   Ehud Schreiber
• [gmx-users] Re: Frozen N2 in a very long tube   Vitaly Chaban
  • Fwd: [gmx-users] Re: Frozen N2 in a very long tube   Vitaly Chaban
• [gmx-users] HA1/HA2 chirality of GLY   chris.neale at utoronto.ca
• [gmx-users] high repulsion in packed system   Moeed
• [gmx-users] high repulsion in packed system   chris.neale at utoronto.ca
• [gmx-users] g_cluster settings   Marc Charendoff
• [gmx-users] Re: high repulsion in packed system   Vitaly Chaban
• [gmx-users] Re: g_cluster settings   Vitaly Chaban
  • [gmx-users] Re: g_cluster settings   Ran Friedman
• [gmx-users] ffamber99sb error   Arik Cohen
• [gmx-users] MD run for octanol system   vivek sharma
  • [gmx-users] MD run for octanol system   Esteban Gabriel Vega Hissi
• [gmx-users] Where can I dowload DSSP program?   chandran karunakaran
  • [gmx-users] Where can I dowload DSSP program?   Ajeeta kaushiki
• [gmx-users] Re: MD run for octanol system   Vitaly Chaban
  • [gmx-users] Re: MD run for octanol system   vivek sharma
• [gmx-users] Re: ffamber99sb error   Vitaly Chaban
• [gmx-users] -tu flag in g_hbond   shahab shariati
  • [gmx-users] -tu flag in g_hbond   Justin A. Lemkul
• [gmx-users] -tu flag in g_hbond   shahab shariati
  • [gmx-users] -tu flag in g_hbond   Justin A. Lemkul
• [gmx-users] Re: selenium parameter   chris.neale at utoronto.ca
• [gmx-users] -tu flag in g_hbond   shahab shariati
  • [gmx-users] -tu flag in g_hbond   Justin A. Lemkul
• [gmx-users] -tu flag in g_hbond   shahab shariati
• [gmx-users] number of degrees of frredom   Moeed
  • [gmx-users] number of degrees of frredom   Justin A. Lemkul
• [gmx-users] Re: number of degrees of frredom   Vitaly Chaban
• [gmx-users] OPLS-2005 forcefield parameters for carbohydrates in Gromacs 4.0.7?   Steven R. Kirk
• [gmx-users] question about dynamics   Shuangxing Dai
  • [gmx-users] question about dynamics   Justin A. Lemkul
    • [gmx-users] question about dynamics   Shuangxing Dai
      • [gmx-users] question about dynamics   Justin A. Lemkul
• [gmx-users] dissolution of gases in liquid   Vitaly Chaban
  • [gmx-users] Fwd: dissolution of gases in liquid   Vitaly Chaban
• [gmx-users] g_msd   Ricardo Cuya Guizado
  • [gmx-users] g_msd   Gaurav Goel
  • [gmx-users] g_msd   Mark Abraham
• [gmx-users] Compile-time errors with MKL   Elton Carvalho
  • [gmx-users] Compile-time errors with MKL   Mark Abraham
    • [gmx-users] Compile-time errors with MKL   Elton Carvalho
      • [gmx-users] Compile-time errors with MKL   Mark Abraham
      • [gmx-users] Compile-time errors with MKL   Elton Carvalho
      • [gmx-users] Compile-time errors with MKL   Mark Abraham
• [gmx-users] grommp_md error   Moeed
  • [gmx-users] grommp_md error   Justin A. Lemkul
• [gmx-users] Re: grommp_md error   Vitaly Chaban
• [gmx-users] Stabilizing a heavy metal ion in solution   Francisco Garcia
  • [gmx-users] Stabilizing a heavy metal ion in solution   Mark Abraham
• [gmx-users] Re: Stabilizing a heavy metal ion in solution   Vitaly Chaban
• [gmx-users] 1. Re: g_msd (Gaurav Goel)   Ricardo Cuya Guizado
• [gmx-users] grompp errors   Amanda Watkins
  • [gmx-users] grompp errors   Justin A. Lemkul
  • [gmx-users] grompp errors   David van der Spoel
• [gmx-users] g_cluster Jarvis-Patrick   Marc Charendoff
  • [gmx-users] g_cluster Jarvis-Patrick   Ran Friedman
• [gmx-users] Effects of reducing timestep   braffert at purdue.edu
• [gmx-users] NPT for compression   Moeed
  • [gmx-users] NPT for compression   Justin A. Lemkul
  • [gmx-users] NPT for compression   Mark Abraham
• [gmx-users] NPT for compressing the system   Moeed
  • [gmx-users] NPT for compressing the system   Justin A. Lemkul
  • [gmx-users] NPT for compressing the system   Mark Abraham
• [gmx-users] Removing water from a trajectory   Anirban Ghosh
  • [gmx-users] Removing water from a trajectory   Mark Abraham
  • [gmx-users] Removing water from a trajectory   shayamra at post.tau.ac.il
• [gmx-users] version 4 pdb2gmx with ffamber broken on Mac?   Daniel Ensign
  • [gmx-users] version 4 pdb2gmx with ffamber broken on Mac?   Justin A. Lemkul
• [gmx-users] version 4 pdb2gmx with ffamber broken on Mac?   Daniel Ensign
• [gmx-users] NPT for compressing the system   Moeed
  • [gmx-users] NPT for compressing the system   Justin A. Lemkul
• [gmx-users] position restrain file   Ping
  • [gmx-users] position restrain file   Justin A. Lemkul
• [gmx-users] (no subject)   munubas at yahoo.com
  • [gmx-users] (no subject)   David van der Spoel
  • [gmx-users] (no subject)   Justin A. Lemkul
• [gmx-users] Phonon calculations in periodic crystals   Anne Kelley
  • [gmx-users] Phonon calculations in periodic crystals   David van der Spoel
    • [gmx-users] Phonon calculations in periodic crystals   Anne Kelley
• [gmx-users] DSSP and g_sas   Bhanu Prakash Sandaka
• [gmx-users] DSSP and g_sas   Bhanu Prakash Sandaka
  • [gmx-users] DSSP and g_sas   Justin A. Lemkul
• [gmx-users] Grompp error: No default g96angle type   shahid nayeem
  • [gmx-users] Grompp error: No default g96angle type   Justin A. Lemkul
    • [gmx-users] Grompp error: No default g96angle type   shahid nayeem
      • [gmx-users] Grompp error: No default g96angle type   Justin A. Lemkul
      • [gmx-users] Grompp error: No default g96angle type   shahid nayeem
      • [gmx-users] Grompp error: No default g96angle type   Justin A. Lemkul
• [gmx-users] RE: trjcat -cat skips frames   Mike Wykes
• [gmx-users] strain-stress, Young modulus, etc   Vitaly Chaban
• [gmx-users] Semiisotropic Pressure coupling with PR   Sai Pooja
  • [gmx-users] Semiisotropic Pressure coupling with PR   Justin A. Lemkul
    • [gmx-users] Semiisotropic Pressure coupling with PR   Sai Pooja
      • [gmx-users] Semiisotropic Pressure coupling with PR   Justin A. Lemkul
      • [gmx-users] Semiisotropic Pressure coupling with PR   Sai Pooja
      • [gmx-users] Semiisotropic Pressure coupling with PR   Justin A. Lemkul
      • [gmx-users] Semiisotropic Pressure coupling with PR   Sai Pooja
      • [gmx-users] Semiisotropic Pressure coupling with PR   Justin A. Lemkul
      • [gmx-users] Semiisotropic Pressure coupling with PR   Sai Pooja
• [gmx-users] Pressure coupling   Sai Pooja
  • [gmx-users] Pressure coupling   Justin A. Lemkul
    • [gmx-users] Pressure coupling   David van der Spoel
• [gmx-users] NPH Simulations   sapna sarupria
  • [gmx-users] NPH Simulations   Ran Friedman
• [gmx-users] cuda gmx template   Timothy Sirk
• [gmx-users] Rcut-off etc.   Sai Pooja
  • [gmx-users] Rcut-off etc.   Mark Abraham
• [gmx-users] why the pulling force between Graphite and CNT is repulsive force?   Cun Zhang
• [gmx-users] to visualise protein conformation after every 1ns   sonali dhindwal
  • [gmx-users] to visualise protein conformation after every 1ns   David van der Spoel
    • [gmx-users] to visualise protein conformation after every 1ns   sonali dhindwal
      • [gmx-users] to visualise protein conformation after every 1ns   Tsjerk Wassenaar
      • [gmx-users] to visualise protein conformation after every 1ns   sonali dhindwal
      • [gmx-users] to visualise protein conformation after every 1ns   Oliver Grant
      • [gmx-users] to visualise protein conformation after every 1ns   sonali dhindwal
      • [gmx-users] to visualise protein conformation after every 1ns   Justin A. Lemkul
• Subject: [gmx-users] to visualise protein conformation after every 1ns   Cun Zhang
• [gmx-users] how to write a frames.ndx for -fr option of trjconv   Hassan Shallal
  • [gmx-users] how to write a frames.ndx for -fr option of trjconv   Justin A. Lemkul
• [gmx-users] g_lie query   Anirban Ghosh
  • [gmx-users] g_lie query   Anirban Ghosh
  • [gmx-users] g_lie query   Anirban Ghosh
    • [gmx-users] g_lie query   Justin A. Lemkul
• [gmx-users] inversion of lipid bilayer with water in the centre   ram bio
  • [gmx-users] inversion of lipid bilayer with water in the centre   Justin A. Lemkul
• [gmx-users] scripting question   Hassan Shallal
  • [gmx-users] scripting question   J. Rui Rodrigues
    • [gmx-users] scripting question   Hassan Shallal
      • [gmx-users] scripting question   ms
• [gmx-users] Selecting a force field for dioxane   Saikat Banerjee
  • [gmx-users] Selecting a force field for dioxane   Justin A. Lemkul
• [gmx-users] Re: Selecting a force field for dioxane   Vitaly Chaban
• [gmx-users] Avoid generation of angles, pairs and dihedrals from pdb2gmx   C. Batistakis
  • [gmx-users] Avoid generation of angles, pairs and dihedrals from pdb2gmx   Da-Wei Li
• [gmx-users] Need For a Script   Samrat Pal
  • [gmx-users] Need For a Script   Justin A. Lemkul
    • [gmx-users] Need For a Script   Samrat Pal
    • [gmx-users] Need For a Script   Samrat Pal
      • [gmx-users] Need For a Script   ms
• [gmx-users] frezzing a bond   Nilesh Dhumal
  • [gmx-users] frezzing a bond   Justin A. Lemkul
    • [gmx-users] frezzing a bond   Elton Carvalho
• [gmx-users] Charge grps and cut-off   Sai Pooja
  • [gmx-users] Charge grps and cut-off   Justin A. Lemkul
    • [gmx-users] Charge grps and cut-off   Sai Pooja
      • [gmx-users] Charge grps and cut-off   Justin A. Lemkul
      • [gmx-users] Charge grps and cut-off   Sai Pooja
      • [gmx-users] Charge grps and cut-off   Justin A. Lemkul
      • [gmx-users] Charge grps and cut-off   Sai Pooja
      • [gmx-users] Charge grps and cut-off   Justin A. Lemkul
      • [gmx-users] Charge grps and cut-off   Sai Pooja
      • [gmx-users] Charge grps and cut-off   Justin A. Lemkul
• [gmx-users] no-pbc simulation in parallel   Vitaly Chaban
• [gmx-users] Charge grps and cut-off   Sai Pooja
  • [gmx-users] Charge grps and cut-off   Sai Pooja
  • [gmx-users] Charge grps and cut-off   Justin A. Lemkul
    • [gmx-users] Charge grps and cut-off   Sai Pooja
• [gmx-users] pull code example   Vitaly Chaban
• [gmx-users] g_rmsf   Sai Pooja
  • [gmx-users] g_rmsf   Tsjerk Wassenaar
• [gmx-users] (no subject)   munubas at yahoo.com
  • [gmx-users] (no subject)   Justin A. Lemkul
• [gmx-users] g_sas for martini coarse-grained particles   Sanku M
  • [gmx-users] g_sas for martini coarse-grained particles   XAvier Periole
  • [gmx-users] g_sas for martini coarse-grained particles   XAvier Periole
• [gmx-users] pull code example   chris.neale at utoronto.ca
• [gmx-users] gromacs-localp-3.0.2 installation problem   kambiz yaghmaei
• [gmx-users] tip5p in ffcharmm   Ramachandran G
  • [gmx-users] tip5p in ffcharmm   Justin A. Lemkul
• [gmx-users] gromacs-localp-3.0.2 local pressure installation   kambiz yaghmaei
  • [gmx-users] gromacs-localp-3.0.2 local pressure installation   Justin A. Lemkul
• [gmx-users] water Mediated Hydrogen Bond   babu gokul
• [gmx-users] Replica exhange - no. of processors   Sai Pooja
  • [gmx-users] Replica exhange - no. of processors   Lanyuan Lu
    • [gmx-users] Replica exhange - no. of processors   Sai Pooja
      • [gmx-users] Replica exhange - no. of processors   ms
      • [gmx-users] Replica exhange - no. of processors   Sai Pooja
• [gmx-users] Tabulated potentials and performance   ms
  • [gmx-users] Tabulated potentials and performance   Da-Wei Li
    • [gmx-users] Tabulated potentials and performance   ms
      • [gmx-users] Tabulated potentials and performance   Da-Wei Li
      • [gmx-users] Tabulated potentials and performance   ms
      • [gmx-users] Tabulated potentials and performance   Lanyuan Lu
      • [gmx-users] Tabulated potentials and performance   ms
• [gmx-users] Need For a Script   Samrat Pal
• [gmx-users] bond potential selection   Vitaly Chaban
• [gmx-users] topology for a cyclic peptide   Rebeca García Fandiño
  • [gmx-users] topology for a cyclic peptide   Justin A. Lemkul
• [gmx-users] selenomethionine parameters for ffG53a6   Deniz KARASU
• [gmx-users] Heme_Grompp Error   shahid nayeem
• [gmx-users] Help needed with ACPYPI   sunita gupta
• [gmx-users] Potential of mean force   abdul wadood
  • [gmx-users] Potential of mean force   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 75, Issue 107   Thanasis Koukoulas
• [gmx-users] Re: gmx-users Digest, Vol 75, Issue 107   Thanasis Koukoulas
• [gmx-users] Re: Help needed with ACPYPI   Alan
• [gmx-users] LINC warning but reasonable potential energy and force   Moeed
• [gmx-users] translation   Shuangxing Dai
• [gmx-users] extracting coordinates   Vishal Agarwal
  • [gmx-users] extracting coordinates   Gaurav Goel
• [gmx-users] Heme_Grompp_error   shahid nayeem
• [gmx-users] Segmentation Fault with g_dielectric   Jennifer Casey
• [gmx-users] I wonder if anyone has a "gmx2lmp" tool   Li, Shuo (liso)
• [gmx-users] Free Energy Calculation Using Tabulated Potentials   Nimesh Jain
• [gmx-users] charmmff   Sai Pooja
  • [gmx-users] charmmff   Rodrigo Faccioli
    • [gmx-users] charmmff   Sai Pooja
      • [gmx-users] charmmff   Rodrigo Faccioli
      • [gmx-users] charmmff   Sai Pooja
      • [gmx-users] charmmff   Rodrigo Faccioli
• [gmx-users] Need For a Script   Samrat Pal
• [gmx-users] topology builiding   pankhuri arora
• [gmx-users] Averege structure   pawan raghav
  • [gmx-users] Averege structure   Justin A. Lemkul
• [gmx-users] genion   Neha Gandhi
• [gmx-users] installation: gromacs on Mac.10.5.8 leopard   KACHMAR Ali
  • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   Esztermann, Ansgar
• [gmx-users] Heme_Grompp_error   shahid nayeem
• [gmx-users] Phosphorylated serine and threonine   sumanth kumar
• [gmx-users] installation: gromacs on Mac.10.5.8 leopard   Esztermann, Ansgar
  • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   KACHMAR Ali
    • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   Florian Dommert
      • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   KACHMAR Ali
      • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   Florian Dommert
      • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   KACHMAR Ali
      • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   KACHMAR Ali
      • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   KACHMAR Ali
      • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   KACHMAR Ali
      • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   Florian Dommert
      • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   KACHMAR Ali
      • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   Florian Dommert
      • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   KACHMAR Ali
      • [gmx-users] installation: gromacs on Mac.10.5.8 leopard   Florian Dommert
• [gmx-users] Topology file for phosphoserine (SEP) for OPLS force field   sumanth kumar
• [gmx-users] The grompp problem!! (Urgently)   Yuranat Saikatikorn
  • [gmx-users] The grompp problem!! (Urgently)   Krzysztof Mlynarczyk
• [gmx-users] Backward compatibility of charmm-ff implementation   Sai Pooja
• [gmx-users] g_rdf   Sanku M
• [gmx-users] switching off electrostatics   Moeed
• [gmx-users] Re: gmx-users Digest, Vol 75, Issue 117   Yuranat Saikatikorn
  • [gmx-users] Re: gmx-users Digest, Vol 75, Issue 117 (was: The grompp problem!!)   Justin A. Lemkul
• [gmx-users] how to compile x2top separately?   pankhuri arora
• [gmx-users] Re: switching off electrostatics   Vitaly Chaban
• [gmx-users] trjcat : Magic Number Error in XTC file (read 0, should be 1995)   ram bio
  • [gmx-users] trjcat : Magic Number Error in XTC file (read 0, should be 1995)   Justin A. Lemkul
• [gmx-users] Lincs warning but reasonable energy!   Moeed
• [gmx-users] Re: Lincs warning but reasonable energy   Vitaly Chaban
• [gmx-users] pdb2gmx doesn´t generate H   Pascal Baumann
  • Re: [gmx-users] pdb2gmx doesn´t generate H   Oliver Grant
    • [gmx-users] pdb2gmx doesn´t generate H   Justin A. Lemkul
• [gmx-users] Simulation stops   Jose Tusell
• [gmx-users] "simulated long enough" message from tpbconv   Krzysztof Kuczera
• [gmx-users] The iron-sulfur bond!!   Yuranat Saikatikorn
  • [gmx-users] The iron-sulfur bond!!   Justin A. Lemkul
• [gmx-users] implicit water model for protein folding simulation   Samrat Pal
  • [gmx-users] implicit water model for protein folding simulation   ms
• [gmx-users] Ryckaert Bellemanm-dihedral in OPLS-AA   sumanth kumar
  • [gmx-users] Ryckaert Bellemanm-dihedral in OPLS-AA   Justin A. Lemkul
• [gmx-users] Fwd: PE compressing - for reference only   Vitaly Chaban
• [gmx-users] frezzing a bond : NPT and NVT simulations   Nilesh Dhumal
• [gmx-users] PE compressing   Moeed
• [gmx-users] Cohesive energies of Polymer Materials   wuxiao
• [gmx-users] hydrogen-bonded complex   Hao Sun
  • [gmx-users] hydrogen-bonded complex   Dallas Warren
• [gmx-users] Re: PE compressing   Vitaly Chaban
• [gmx-users] Re: NPT and NVT simulations   Vitaly Chaban
  • [gmx-users] Re: NPT and NVT simulations   Nilesh Dhumal
    • [gmx-users] Re: NPT and NVT simulations   Justin A. Lemkul
      • [gmx-users] Re: NPT and NVT simulations   Nilesh Dhumal
    • [gmx-users] Re: NPT and NVT simulations   Vitaly Chaban
• [gmx-users] periodicity and correct output   Vitaly Chaban
  • [gmx-users] periodicity and correct output   Shuangxing Dai
    • [gmx-users] periodicity and correct output   Vitaly Chaban
      • [gmx-users] periodicity and correct output   Shuangxing Dai
• [gmx-users] Problem in setup energy minimization step(grompp)   bipin.singh at research.iiit.ac.in
• [gmx-users] Problem in setup energy minimization step(grompp)   bipin.singh at research.iiit.ac.in
  • [gmx-users] Problem in setup energy minimization step(grompp)   Justin A. Lemkul
    • [gmx-users] Problem in setup energy minimization step(grompp)   X Rules
      • [gmx-users] Problem in setup energy minimization step(grompp)   Justin A. Lemkul
      • [gmx-users] Problem in setup energy minimization step(grompp)   X Rules
      • [gmx-users] Problem in setup energy minimization step(grompp)   Justin A. Lemkul
• [gmx-users] Fatal error: No such moleculetype Cl   Abhinav Verma
  • [gmx-users] Fatal error: No such moleculetype Cl   X Rules
• [gmx-users] decomposition   Jacopo Sgrignani
  • [gmx-users] decomposition   Carsten Kutzner
• [gmx-users] nonbond_params   Amir Marcovitz
  • [gmx-users] nonbond_params   Justin A. Lemkul
    • [gmx-users] nonbond_params   Amir Marcovitz
      • [gmx-users] nonbond_params   Justin A. Lemkul
• [gmx-users] energies in amber, namd and gromacs   Alan
• [gmx-users] alchemical free energy changes upon change in sc_alpha and sc_power   Ilja Khavrutskii
  • [gmx-users] Re: alchemical free energy changes upon change in sc_alpha and sc_power   Ilja Khavrutskii
• [gmx-users] Errors with g_dielectric   Jennifer Casey
  • [gmx-users] Errors with g_dielectric   Florian Dommert
• [gmx-users] Re: Ryckaert Bellemanm-dihedral in OPLS-AA   sumanth kumar
• [gmx-users] gromacs energies very different from other MD engines for the very same system and conditions   Alan
• [gmx-users] Dear all Re: Topology file for phosphothreonine (TPO) for OPLS force field   sumanth kumar
  • [gmx-users] Dear all Re: Topology file for phosphothreonine (TPO) for OPLS force field   Justin A. Lemkul
• [gmx-users] gromacs energies very different from other MD engine for the very same system and conditions   chris.neale at utoronto.ca
  • [gmx-users] gromacs energies very different from other MD engine for the very same system and conditions   Berk Hess
    • [gmx-users] gromacs energies very different from other MD engine for the very same system and conditions   Ilja Khavrutskii
      • [gmx-users] gromacs energies very different from other MD engine for the very same system and conditions   Erik Lindahl
• [gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition   Alan
  • [gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition   Justin A. Lemkul
• [gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition   Alan
• [gmx-users] energygrps and simulation run time   Amir Marcovitz
  • [gmx-users] energygrps and simulation run time   Justin A. Lemkul
• [gmx-users] Re: NPT and NVT simulations   Justin A. Lemkul
• [gmx-users] Re: NPT and NVT simulations   Justin A. Lemkul
  • [gmx-users] Re: NPT and NVT simulations   Nilesh Dhumal
    • [gmx-users] Re: NPT and NVT simulations   Justin A. Lemkul
      • [gmx-users] Re: NPT and NVT simulations   Nilesh Dhumal
• [gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition   chris.neale at utoronto.ca
• [gmx-users] mean square displacement frequency   Yongchul Chung
  • [gmx-users] mean square displacement frequency   Tsjerk Wassenaar
    • [gmx-users] mean square displacement frequency   Yongchul Chung
• [gmx-users] Coarse-Grain: GROMACS bond information to VMD   C. Batistakis
  • [gmx-users] Coarse-Grain: GROMACS bond information to VMD   Justin A. Lemkul
• [gmx-users] Re: g_saltbr   Ilya Chorny
  • [gmx-users] Re: g_saltbr   Justin A. Lemkul
    • [gmx-users] Re: g_saltbr   Ilya Chorny
      • [gmx-users] Re: g_saltbr   Justin A. Lemkul
      • [gmx-users] Re: g_saltbr   Ilya Chorny
  • [gmx-users] g_saltbr   Ilya Chorny
• [gmx-users] Jarzynski equality in pulling simulation   Samrat Pal
• [gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition   Alan
  • [gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition   Berk Hess
• [gmx-users] Entropy from NMA   nahren manuel
  • [gmx-users] Entropy from NMA   Ran Friedman
    • [gmx-users] Entropy from NMA   Ran Friedman
      • [gmx-users] Entropy from NMA   nahren manuel
      • [gmx-users] Entropy from NMA   Ran Friedman
      • [gmx-users] Entropy from NMA   J. Rui Rodrigues
      • [gmx-users] Entropy from NMA   Ran Friedman
• [gmx-users] [nonbond_params] section , choice of parameters   Amir Marcovitz
• [gmx-users] energy corresponding to H-bond   supti mukherjee
• [gmx-users] RE: [nonbond_params] section , choice of parameters   Ehud Schreiber
  • [gmx-users] RE: [nonbond_params] section , choice of parameters   Amir Marcovitz
    • [gmx-users] RE: [nonbond_params] section , choice of parameters   Florian Dommert
• [gmx-users] RE: RE: [nonbond_params] section , choice of parameters   Ehud Schreiber
  • [gmx-users] RE: RE: [nonbond_params] section , choice of parameters   Amir Marcovitz
• [gmx-users] Re: Jarzynski equality in pulling simulation   Samrat Pal
• [gmx-users] mpi installation problems   Ryan S Davis (rsdavis1)
  • [gmx-users] mpi installation problems   Carsten Kutzner
• [gmx-users] potential git server downtime   Rossen Apostolov
• [gmx-users] Maximum table size for tabulated non-bonded potential   Julie Bernauer
• [gmx-users] compressing the system   Moeed
• [gmx-users] Re: compressing the system   Vitaly Chaban
• [gmx-users] trjcat skipping frames   Jared James Thompson
  • [gmx-users] trjcat skipping frames   Justin A. Lemkul
    • [gmx-users] trjcat skipping frames   Jared James Thompson
      • [gmx-users] trjcat skipping frames   Justin A. Lemkul
• [gmx-users] (no subject)   Anitha
  • [gmx-users] (no subject)   Justin A. Lemkul
    • [gmx-users] (no subject)   Anitha
      • [gmx-users] (no subject)   Justin A. Lemkul
      • [gmx-users] (no subject)   Anitha
      • [gmx-users] (no subject)   Justin A. Lemkul
• [gmx-users] compressing the system   Moeed
• [gmx-users] parallel mdrun (mpimdrun) is slower than non-parallel mdrun?   wuxiao
• [gmx-users] Re: compressing the system   Vitaly Chaban
• [gmx-users] Re: parallel mdrun (mpimdrun) is slower than   Vitaly Chaban
• [gmx-users] does generating velocity keep centre of mass motion zero?   Gaurav Goel
• [gmx-users] Re: NPT and NVT simulations   Nilesh Dhumal
  • [gmx-users] Re: NPT and NVT simulations   Justin A. Lemkul
    • [gmx-users] Re: NPT and NVT simulations   Nilesh Dhumal
      • [gmx-users] Re: NPT and NVT simulations   Justin A. Lemkul
• [gmx-users] no non bonded parameters from PRODRG   Jennifer Williams
  • [gmx-users] no non bonded parameters from PRODRG   Justin A. Lemkul
• [gmx-users] hydrogen bonds   Vasilis Georgilas
  • [gmx-users] hydrogen bonds   Justin A. Lemkul
• [gmx-users] Re: hydrogen bonds   Vasilis Georgilas
  • [gmx-users] Re: hydrogen bonds   Justin A. Lemkul
    • [gmx-users] Re: hydrogen bonds   Vasilis Georgilas
      • [gmx-users] Re: hydrogen bonds   Justin A. Lemkul
      • [gmx-users] Re: hydrogen bonds   Vasilis Georgilas
      • [gmx-users] Re: hydrogen bonds   Justin A. Lemkul
• [gmx-users] Posting to list   Andrew Mauro
• [gmx-users] Using the Berendsen Barostat to Initialize and then switch to Parrinello-Rahman   Andrew Mauro
  • [gmx-users] Using the Berendsen Barostat to Initialize and then switch to Parrinello-Rahman   Justin A. Lemkul
• [gmx-users] GROMACS-4.5-beta1 is out!   Rossen Apostolov
  • [gmx-users] GROMACS-4.5-beta1 is out!   Amit Choubey
    • [gmx-users] GROMACS-4.5-beta1 is out!   David van der Spoel
  • [gmx-users] GROMACS-4.5-beta1 is out!   ms
• [gmx-users] Install error for gmx-4.5_beta1   Justin A. Lemkul
• [gmx-users] Another install error: gmx-4.5 beta1   Justin A. Lemkul
• [gmx-users] Pullx file   Aswathy
  • [gmx-users] Pullx file   Justin A. Lemkul
• [gmx-users] gmx 4.5 configure options confusing   Alan
• [gmx-users] error compiling gmx 4.5 on Mac 10.6.4   Alan
  • [gmx-users] Re: error compiling gmx 4.5 on Mac 10.6.4   Alan
• [gmx-users] Pullx file   chris.neale at utoronto.ca
• [gmx-users] tests for gmx 4.5   Alan
• [gmx-users] gmx 4.5 issue with grompp   Alan

Last message date: Sat Jul 31 22:17:42 CEST 2010
Archived on: Thu Nov 14 12:09:04 CET 2013

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