August 2008 Archives by thread

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Starting: Fri Aug 1 00:56:59 CEST 2008
Ending: Sun Aug 31 23:37:47 CEST 2008
Messages: 620

• [gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X)   Roland Schulz
• [gmx-users] analysizing the sam.edo script?   xi zhao
  • [gmx-users] analysizing the sam.edo script?   Bert de Groot
• [gmx-users] Tyrosine problems again   chris.neale at utoronto.ca
• [gmx-users] Tyrosine problems again   chris.neale at utoronto.ca
  • [gmx-users] Testing (was: Tyrosine problems again)   David van der Spoel
    • [gmx-users] Testing   Justin A. Lemkul
    • [gmx-users] Testing (was: Tyrosine problems again)   Roland Schulz
      • [gmx-users] Testing   David van der Spoel
      • [gmx-users] Testing   Roland Schulz
• [gmx-users] how to fix a position in the single eigenvector in essential dynamics sampling?   xi zhao
  • [gmx-users] how to fix a position in the single eigenvector in essential dynamics sampling?   Bert de Groot
• [gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X)   Carsten Kutzner
• [gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X)   Alan
  • [gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X)   Steffen Wolf
• [gmx-users] Re: gmx-users Digest, Vol 51, Issue 116   Alan
• [gmx-users] amb2gmx for big systems   Alan
• [gmx-users] Re: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue   Bert de Groot
  • [gmx-users] Re: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue   Tsjerk Wassenaar
• [gmx-users] dimerization problem   Tsjerk Wassenaar
• [gmx-users] Creating a new topology using OPLSAA   Mike Wykes
• [gmx-users] Re: Putting more than one peptide   alkasrivastava at iitb.ac.in
  • [gmx-users] Re: Putting more than one peptide   Justin A. Lemkul
• [gmx-users] Order parameters of lipid   Justin A. Lemkul
• [gmx-users] query about essential dynamics   sangeeta kundu
• [gmx-users] Order parameters of lipid   Alan Dodd
  • [gmx-users] Order parameters of lipid   Justin A. Lemkul
• [gmx-users] Re: Putting more than one peptide   Vitaly Chaban
  • [gmx-users] Re: Putting more than one peptide   Sheyore Omovie
• [gmx-users] Testing   chris.neale at utoronto.ca
• [gmx-users] Re: gmx-users Digest, Vol 52, Issue 5   minnale
• [gmx-users] Testing   David Chan
  • [gmx-users] Testing   David van der Spoel
• [gmx-users] Testing   chris.neale at utoronto.ca
• [gmx-users] Fwd: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue   Tsjerk Wassenaar
• [gmx-users] Testing (was: Tyrosine problems again)   dichan at ucalgary.ca
  • [gmx-users] Testing (was: Tyrosine problems again)   David van der Spoel
• [gmx-users] dihedral potential OPLSAA force field   David Huang
• [gmx-users] dihedral potential OPLSAA force field (correction)   David Huang
• [gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed   Vitaly Chaban
  • [gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed   David van der Spoel
    • [gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed   Vitaly Chaban
• [gmx-users] Fwd: membrane simulations with gromacs   chris.neale at utoronto.ca
• [gmx-users] AMOEBA in gromacs   Grange Hermitage
• [gmx-users] Normal Mode Analysis in Double-Precision   Inon Sharony
  • [gmx-users] Normal Mode Analysis in Double-Precision   Ran Friedman
    • [gmx-users] Normal Mode Analysis in Double-Precision   Inon Sharony
      • [gmx-users] Normal Mode Analysis in Double-Precision   Ran Friedman
      • [gmx-users] Normal Mode Analysis in Double-Precision   Inon Sharony
      • [gmx-users] Normal Mode Analysis in Double-Precision   Ran Friedman
      • [gmx-users] Normal Mode Analysis in Double-Precision   Inon Sharony
      • [gmx-users] Normal Mode Analysis in Double-Precision   Ran Friedman
      • [gmx-users] Normal Mode Analysis in Double-Precision   Inon Sharony
      • [gmx-users] Normal Mode Analysis in Double-Precision   Ran Friedman
• [gmx-users] segmentation fault in g_anaeig   Inon Sharony
  • [gmx-users] segmentation fault in g_anaeig   Tsjerk Wassenaar
    • [gmx-users] segmentation fault in g_anaeig   Inon Sharony
• [gmx-users] how to extend 1ns Unfolding simulation to 6ns   ravi sharma
  • [gmx-users] how to extend 1ns Unfolding simulation to 6ns   Justin A. Lemkul
• [gmx-users] Umbrella Sampling   Alexandr Malafeev
• [gmx-users] RE: Umbrella Sampling   Vitaly Chaban
  • [gmx-users] Re: Umbrella Sampling   Alexandr Malafeev
• [gmx-users] RE: how to extend 1ns Unfolding simulation to 6ns   Vitaly Chaban
• [gmx-users] Please help: POPC membrane simulation   mahesh kulharia
  • [gmx-users] Please help: POPC membrane simulation   Justin A. Lemkul
  • [gmx-users] Please help: POPC membrane simulation   Florian Haberl
• [gmx-users] Force Distance Curve from .trr .xtc   VENKATESH HARIHARAN
• [gmx-users] Question about octahedral boxes   Justin A. Lemkul
  • [gmx-users] Re: Question about octahedral boxes (solved)   Justin A. Lemkul
• [gmx-users] how long simulation takes to get stable when constrains is none in mdp file?   wang kelvin
  • [gmx-users] how long simulation takes to get stable when constrains is none in mdp file?   David van der Spoel
    • [gmx-users] how long simulation takes to get stable when constrains is none in mdp file?   Tsjerk Wassenaar
      • [gmx-users] how long simulation takes to get stable when constrains is none in mdp file?   wang kelvin
• [gmx-users] parameters for protonated nitrogen   Samuel Coulbourn Flores 花山
• [gmx-users] Define proper set of topology parameters for new molecule in different FF.   Andrey Frolov
• [gmx-users] table force-field   Alexandr Malafeev
  • [gmx-users] table force-field   Justin A. Lemkul
    • [gmx-users] table force-field   Alexandr Malafeev
      • [gmx-users] table force-field   Justin A. Lemkul
      • [gmx-users] table force-field   Alexandr Malafeev
      • [gmx-users] table force-field   Justin A. Lemkul
      • [gmx-users] table force-field   Alexandr Malafeev
• [gmx-users] membrane with OPLS force field   Rebeca García Fandiño
  • [gmx-users] membrane with OPLS force field   Justin A. Lemkul
• [gmx-users] some questions about gmx_density.c   beibei
  • [gmx-users] some questions about gmx_density.c   Yang Ye
• [gmx-users] RE: Define proper set of topology parameters for new molecule in different FF.   Vitaly Chaban
• [gmx-users] RE: how long simulation takes to get stable when constrains is none in mdp file?   Vitaly Chaban
• [gmx-users] membrane with OPLS force field   Chris Neale
  • [gmx-users] membrane with OPLS force field   Rebeca García Fandiño
• [gmx-users] membrane with OPLS force field   Chris Neale
  • [gmx-users] membrane with OPLS force field   Volker Wirth
    • [gmx-users] membrane with OPLS force field   Justin A. Lemkul
      • [gmx-users] membrane with OPLS force field   Volker Wirth
      • [gmx-users] membrane with OPLS force field   Justin A. Lemkul
• [gmx-users] force feield paremeters for magnesium   Mahnam
  • [gmx-users] force feield paremeters for magnesium   Justin A. Lemkul
• [gmx-users] charge density   Sunjoo Lee
• [gmx-users] RE: Define proper set of topology parameters for new molecule in different FF.   Andrey Frolov
  • [gmx-users] RE: Define proper set of topology parameters for new molecule in different FF.   Justin A. Lemkul
• [gmx-users] how to fix the COM of group in the pull.   xi zhao
• [gmx-users] A fix to eigio.c ?   eladp at elaine.tau.ac.il
• [gmx-users] RE: how to fix the COM of group in the pull.   Vitaly Chaban
• [gmx-users] how to fix the center of mass of the protein in the pull simulation   xi zhao
• [gmx-users] RE[4]: Define proper set of topology parameters for new molecule in different FF.   Vitaly Chaban
• [gmx-users] Some Issues on Substrates/PBC   Michael Hirtz
  • [gmx-users] Some Issues on Substrates/PBC   André Farias de Moura
    • [gmx-users] Some Issues on Substrates/PBC   Justin A. Lemkul
      • [gmx-users] Some Issues on Substrates/PBC   Michael Hirtz
      • [gmx-users] Some Issues on Substrates/PBC   Justin A. Lemkul
    • [gmx-users] Some Issues on Substrates/PBC   Michael Hirtz
• [gmx-users] peptide translation   priyanka srivastava
• [gmx-users] Determining temperature from velocities   Andy Shelley
• [gmx-users] remove center of mass motion   M. Emal Alekozai
  • [gmx-users] remove center of mass motion   Justin A. Lemkul
• [gmx-users] top file definitions_1   rosip at qb.ffyb.uba.ar
  • [gmx-users] top file definitions_1   Justin A. Lemkul
• [gmx-users] gromos function type assigned by grompp   Romelia Salomon
  • [gmx-users] gromos function type assigned by grompp   Justin A. Lemkul
    • [gmx-users] gromos function type assigned by grompp   Romelia Salomon
• [gmx-users] Run test in parallel   ikedaike
  • [gmx-users] Run test in parallel   Yang Ye
    • [gmx-users] Run test in parallel   ikedaike
      • [gmx-users] Run test in parallel   Yang Ye
      • [gmx-users] Run test in parallel   ikedaike
• [gmx-users] nature of gromacs / gcc-4.x problem   chris.neale at utoronto.ca
  • [gmx-users] nature of gromacs / gcc-4.x problem   David van der Spoel
• [gmx-users] single-precision *.tpr data after a double-precision run   Inon Sharony
  • [gmx-users] single-precision *.tpr data after a double-precision run   Ran Friedman
    • [gmx-users] single-precision *.tpr data after a double-precision run   Inon Sharony
      • [gmx-users] single-precision *.tpr data after a double-precision run   Ran Friedman
      • [gmx-users] single-precision *.tpr data after a double-precision run   Inon Sharony
      • [gmx-users] single-precision *.tpr data after a double-precision run   Ran Friedman
  • [gmx-users] single-precision *.tpr data after a double-precision run   David Osguthorpe
• [gmx-users] g_covar with correlation matrix   Ran Friedman
• [gmx-users] ACE patch in FFG43a1   priyanka srivastava
  • [gmx-users] ACE patch in FFG43a1   David van der Spoel
• [gmx-users] nature of gromacs / gcc-4.x problem   chris.neale at utoronto.ca
• [gmx-users] error comm-grps=Protein SOL   M. Emal Alekozai
  • [gmx-users] error comm-grps=Protein SOL   Justin A. Lemkul
    • [gmx-users] error comm-grps=Protein SOL   M. Emal Alekozai
      • [gmx-users] error comm-grps=Protein SOL   Justin A. Lemkul
• [gmx-users] simulating with air   Andy Shelley
  • [gmx-users] simulating with air   Justin A. Lemkul
• [gmx-users] gromos function type assigned by grompp   Justin A. Lemkul
  • [gmx-users] gromos function type assigned by grompp   Romelia Salomon
    • [gmx-users] gromos function type assigned by grompp   Justin A. Lemkul
      • [gmx-users] gromos function type assigned by grompp   Romelia Salomon
• [gmx-users] regarding grompp warning   prasun kumar
  • [gmx-users] regarding grompp warning   Justin A. Lemkul
• [gmx-users] grompp and box size   prasun kumar
  • [gmx-users] grompp and box size   Justin A. Lemkul
• [gmx-users] RE: simulating with air   Vitaly Chaban
• [gmx-users] RE: grompp and box size   Vitaly Chaban
  • [gmx-users] RE: grompp and box size   Tsjerk Wassenaar
    • [gmx-users] RE: grompp and box size   Vitaly Chaban
• [gmx-users] Re: CHARMM FF   Roland Schulz
• [gmx-users] RMSD between   jayant james
  • [gmx-users] RMSD between   David van der Spoel
• [gmx-users] AMBER and gromacs atoms renaming   Ragnarok sdf
  • [gmx-users] AMBER and gromacs atoms renaming   Shay Amram
    • [gmx-users] AMBER and gromacs atoms renaming   Tsjerk Wassenaar
  • [gmx-users] AMBER and gromacs atoms renaming   Justin A. Lemkul
• [gmx-users] PROBLEM : rdf O-H of water from tutorial   niharendu choudhury
  • [gmx-users] PROBLEM : rdf O-H of water from tutorial   David van der Spoel
• [gmx-users] rdf O-H of water from tutorial   Vitaly Chaban
• [gmx-users] Residue specific secondary structure analysis   Biswaranjan Meher
  • [gmx-users] Residue specific secondary structure analysis   Justin A. Lemkul
• [gmx-users] Pressure coupling   Matteus Lindgren
• [gmx-users] AFM pulling: after bond-breakage force does not drop to zero   Thomas Schlesier
• [gmx-users] AFM pulling: after bond-breakage force does not drop to zero   Thomas Schlesier
• [gmx-users] pdb2gmx -inter automatised ?   Christian Fufezan
  • [gmx-users] pdb2gmx -inter automatised ?   Justin A. Lemkul
    • [gmx-users] pdb2gmx -inter automatised ?   Christian Fufezan
      • [gmx-users] pdb2gmx -inter automatised ?   Tsjerk Wassenaar
• [gmx-users] translation   priyanka srivastava
  • [gmx-users] translation   Justin A. Lemkul
• [gmx-users] translation   priyanka srivastava
  • [gmx-users] translation   Justin A. Lemkul
• [gmx-users] translation   priyanka srivastava
• [gmx-users] ensuring that compilation used gcc 3.x   Chris Neale
• [gmx-users] re: ensuring that compilation used gcc 3.x   David Chan
• [gmx-users] ensuring that compilation used gcc 3.x   Chris Neale
• [gmx-users] Error in pdb2gmx   vivek sharma
  • [gmx-users] Error in pdb2gmx   David van der Spoel
    • [gmx-users] Error in pdb2gmx   vivek sharma
      • [gmx-users] Error in pdb2gmx   David van der Spoel
      • [gmx-users] Error in pdb2gmx   vivek sharma
      • [gmx-users] Error in pdb2gmx   Justin A. Lemkul
      • [gmx-users] Error in pdb2gmx   Tsjerk Wassenaar
      • [gmx-users] Error in pdb2gmx   vivek sharma
      • [gmx-users] Error in pdb2gmx   Tsjerk Wassenaar
      • [gmx-users] Error in pdb2gmx   Tsjerk Wassenaar
• [gmx-users] requested for GROMACS package   shiny chandy
  • [gmx-users] requested for GROMACS package   Justin A. Lemkul
• [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens   vivek sharma
  • [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens   David van der Spoel
    • [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens   vivek sharma
      • [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens   Per Larsson
      • [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens   nahren manuel
      • [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens   vivek sharma
      • [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens   vivek sharma
      • [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens   Justin A. Lemkul
      • [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens   vivek sharma
      • [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens   Justin A. Lemkul
  • [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens   Justin A. Lemkul
• [gmx-users] ASP-LIG Interaction Energy : MDRUN   nahren manuel
  • [gmx-users] ASP-LIG Interaction Energy : MDRUN   Justin A. Lemkul
• [gmx-users] Re: requested for GROMACS package   Vitaly Chaban
  • [gmx-users] Re: requested for GROMACS package   Justin A. Lemkul
• [gmx-users] one component plasma simulations (OCP)   Argyrios Karatrantos
  • [gmx-users] one component plasma simulations (OCP)   David van der Spoel
• [gmx-users] gmx does not recognize HIE as protein   Rebeca García Fandiño
  • [gmx-users] gmx does not recognize HIE as protein   Tsjerk Wassenaar
• [gmx-users] debian packages from CVS versions   Martin Höfling
• [gmx-users] error: 1 particles communicated to PME node 3 (...)   Rebeca García Fandiño
  • [gmx-users] error: 1 particles communicated to PME node 3 (...)   Justin A. Lemkul
  • [gmx-users] error: 1 particles communicated to PME node 3 (...)   Berk Hess
• [gmx-users] Force Field Parameters Nitrogen and Oxygen   Andy Shelley
  • [gmx-users] Force Field Parameters Nitrogen and Oxygen   Justin A. Lemkul
• [gmx-users] OCP simulations   Argyrios Karatrantos
• [gmx-users] A bug of trjconv for force output?   LuLanyuan
  • [gmx-users] A bug of trjconv for force output?   Berk Hess
• [gmx-users] colour of the molecules   hhhh huan
  • [gmx-users] colour of the molecules   Florian Haberl
    • [gmx-users] colour of the molecules   hhhh huan
      • [gmx-users] colour of the molecules   Justin A. Lemkul
  • [gmx-users] colour of the molecules   Justin A. Lemkul
• [gmx-users] Re: Force Field Parameters Nitrogen and Oxygen   Vitaly Chaban
• [gmx-users] Re: simulating with air   Vitaly Chaban
  • [gmx-users] Re: simulating with air   Andy Shelley
    • [gmx-users] Re: simulating with air   Vitaly Chaban
      • [gmx-users] Re: simulating with air   Andy Shelley
      • [gmx-users] Re: simulating with air   Vitaly Chaban
• [gmx-users] Re: colour of the molecules   Vitaly Chaban
• [gmx-users] mistake!!   sarbani chattopadhyay
  • [gmx-users] mistake!!   Justin A. Lemkul
• [gmx-users] Problems extending a calculation (in steps and Benchmark)   Rebeca García Fandiño
  • [gmx-users] Problems extending a calculation (in steps and Benchmark)   Justin A. Lemkul
• [gmx-users] Re: categorization   Vitaly Chaban
  • [gmx-users] Re: categorization   Justin A. Lemkul
• [gmx-users] Re: Energy minimization output   alkasrivastava at iitb.ac.in
  • [gmx-users] Re: Energy minimization output   Kukol, Andreas
  • [gmx-users] Re: Energy minimization output   Justin A. Lemkul
• [gmx-users] invalid number of nodes   Rebeca García Fandiño
  • [gmx-users] invalid number of nodes   Carsten Kutzner
  • [gmx-users] invalid number of nodes   Berk Hess
    • [gmx-users] invalid number of nodes   Rebeca García Fandiño
      • [gmx-users] invalid number of nodes   Berk Hess
      • [gmx-users] invalid number of nodes   Carsten Kutzner
      • [gmx-users] invalid number of nodes   Berk Hess
      • [gmx-users] more than one drug in lipid?   serdar durdagi
      • [gmx-users] more than one drug in lipid?   Justin A. Lemkul
• [gmx-users] CHARMM FF   Roland Schulz
  • [gmx-users] CHARMM FF   Nicolas Sapay
• [gmx-users] Dielectric constant   avinash kumar
  • [gmx-users] Dielectric constant   Berk Hess
• [gmx-users] about size of group of monomers vs time   Rogelio Hernández
  • [gmx-users] about size of group of monomers vs time   Ran Friedman
    • [gmx-users] about size of group of monomers vs time   Rogelio Hernández
• [gmx-users] Re: Re: colour of the molecules   Vitaly Chaban
• [gmx-users] Re: about size of group of monomers vs time   Vitaly Chaban
• [gmx-users] tfe   shahrbanoo karbalaee
  • [gmx-users] tfe   Justin A. Lemkul
• [gmx-users] AFM pulling rate   Malin Bergenstråhle
  • [gmx-users] AFM pulling rate   Berk Hess
    • [gmx-users] LINCS warning   serdar durdagi
      • [gmx-users] LINCS warning   Justin A. Lemkul
    • [gmx-users] all-bonds option   serdar durdagi
• [gmx-users] not running on higher no of nodes   Anupam Nath Jha
• [gmx-users] Cluster Size Distribution   Alif M Latif
  • [gmx-users] Cluster Size Distribution   Ran Friedman
• [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens   Justin A. Lemkul
• [gmx-users] tfe   shahrbanoo karbalaee
  • [gmx-users] tfe   Justin A. Lemkul
• [gmx-users] water tip3p   Alan
• [gmx-users] flexible organic solvents   Sascha Rehm
  • [gmx-users] flexible organic solvents   Kukol, Andreas
    • [gmx-users] flexible organic solvents   patrick fuchs
• [gmx-users] [ atomtypes ] are not case sensitive?   Alan
  • [gmx-users] [ atomtypes ] are not case sensitive?   Berk Hess
• [gmx-users] problems with PBC in editconf   Rebeca García Fandiño
  • [gmx-users] problems with PBC in editconf   Justin A. Lemkul
• [gmx-users] addition of all hydrogens in pdb2gmx   sridhar acharya
  • [gmx-users] addition of all hydrogens in pdb2gmx   Tsjerk Wassenaar
• [gmx-users] Dielectric constant   avinash kumar
  • [gmx-users] Dielectric constant   Berk Hess
• [gmx-users] Empty trr file !!??   ranqi zhu
  • [gmx-users] Empty trr file !!??   Justin A. Lemkul
• [gmx-users] Re: Empty trr file   Vitaly Chaban
• [gmx-users] Re: gmx-users Digest, Vol 52, Issue 61   Vitaly Chaban
• [gmx-users] problem with parallelization on a dual quad-core machine   Hongxian He
• [gmx-users] Imposing distance restraints between two residues   plmallip at mail.uh.edu
  • [gmx-users] Imposing distance restraints between two residues   Justin A. Lemkul
• [gmx-users] Imposing distance restraints between two residues   plmallip at mail.uh.edu
• [gmx-users] New Gromacs-CPMD QMMM webpage   Pradip Biswas
  • [gmx-users] New Gromacs-CPMD QMMM webpage   vidhya sankar
    • [gmx-users] New Gromacs-CPMD QMMM webpage   Pradip Biswas
• [gmx-users] Imposing distance restraints between two   plmallip at mail.uh.edu
  • [gmx-users] Imposing distance restraints between two   Grange Hermitage
• [gmx-users] tfe   shahrbanoo karbalaee
  • [gmx-users] tfe   Justin A. Lemkul
• [gmx-users] Out of office AutoReply   charloteaux.b
• [gmx-users] Out of office AutoReply   charloteaux.b
• [gmx-users] do_dssp   minnale
  • [gmx-users] do_dssp   Justin A. Lemkul
    • [gmx-users] do_dssp   Justin A. Lemkul
• [gmx-users] do_dssp   minnale
  • [gmx-users] do_dssp   Justin A. Lemkul
    • [gmx-users] do_dssp   Nuno Azoia
• [gmx-users] Out of office AutoReply   charloteaux.b
• [gmx-users] Position restraints on a pentamer   plmallip at mail.uh.edu
  • [gmx-users] Position restraints on a pentamer   plmallip at mail.uh.edu
    • [gmx-users] Position restraints on a pentamer   Justin A. Lemkul
• [gmx-users] Out of office AutoReply   charloteaux.b
• [gmx-users] topology for Amyloid beta peptide   ffavela at fis.cinvestav.mx
  • [gmx-users] AW: all-bonds option   serdar durdagi
• [gmx-users] G_RMS for different simulations   Ricardo Soares
• [gmx-users] G_RMS for different simulations   Ricardo Soares
• [gmx-users] Out of office AutoReply   charloteaux.b
• [gmx-users] tfe   shahrbanoo karbalaee
  • [gmx-users] tfe   Justin A. Lemkul
• [gmx-users] problem with protein secondary structure analysis   minnale
  • [gmx-users] problem with protein secondary structure analysis   Justin A. Lemkul
• [gmx-users] about how to set the environment variable   beibei
  • [gmx-users] about how to set the environment variable   Tsjerk Wassenaar
• [gmx-users] problem with protein secondary structure analysis   minnale
  • [gmx-users] problem with protein secondary structure analysis   Tsjerk Wassenaar
  • [gmx-users] problem with protein secondary structure analysis   Shay Amram
• [gmx-users] Out of office AutoReply   charloteaux.b
• [gmx-users] problem with protein secondary structure analysis   minnale
  • [gmx-users] problem with protein secondary structure analysis   Justin A. Lemkul
• [gmx-users] problem with protein secondary structure analysis   minnale
• [gmx-users] Out of office AutoReply   charloteaux.b
• [gmx-users] tfe   shahrbanoo karbalaee
  • [gmx-users] tfe   Justin A. Lemkul
• [gmx-users] Out of office AutoReply   charloteaux.b
• [gmx-users] problem with protein secondary structure analysis   minnale
• [gmx-users] Out of office AutoReply   charloteaux.b
• [gmx-users] XTC error   hhhh huan
  • [gmx-users] XTC error   David van der Spoel
• [gmx-users] Error in trjconv   M.Parthiban
  • [gmx-users] Error in trjconv   Tsjerk Wassenaar
• [gmx-users] quantum chemistry to gromacs topology approaches   Grange Hermitage
• [gmx-users] generating conf.gro   Vitaly Chaban
  • [gmx-users] generating conf.gro   Tsjerk Wassenaar
    • [gmx-users] generating conf.gro   Vitaly Chaban
• [gmx-users] Out of office AutoReply   charloteaux.b
• [gmx-users] temperature coupling for complex+ligand+water+ions   Alan
  • [gmx-users] temperature coupling for complex+ligand+water+ions   Justin A. Lemkul
• [gmx-users] Out of office AutoReply   charloteaux.b
• [gmx-users] catastrophic error: "timer not defined"   DimitryASuplatov
  • [gmx-users] catastrophic error: "timer not defined"   Berk Hess
• [gmx-users] tfe   shahrbanoo karbalaee
  • [gmx-users] tfe   Justin A. Lemkul
• [gmx-users] Out of office AutoReply   charloteaux.b
• [gmx-users] Re: gmx-users Digest, Vol 52, Issue 66   minnale
  • [gmx-users] Re: gmx-users Digest, Vol 52, Issue 66   Justin A. Lemkul
    • [gmx-users] Re: gmx-users Digest, Vol 52, Issue 66   Tsjerk Wassenaar
• [gmx-users] protein/dmso simulation   prasun kumar
  • [gmx-users] protein/dmso simulation   Justin A. Lemkul
    • [gmx-users] protein/dmso simulation   Bhanu
• [gmx-users] charge density   Sunjoo Lee
• [gmx-users] Re:Error in trjconv   M.Parthiban
  • [gmx-users] Re:Error in trjconv   Tsjerk Wassenaar
• [gmx-users] dmso/peptide simulation   prasun kumar
• [gmx-users] Re: protein/dmso simulation   Vitaly Chaban
• [gmx-users] charmm and oplsaa simulation results don't match   sarbani chattopadhyay
  • FW: [gmx-users] charmm and oplsaa simulation results don't match   Berk Hess
• [gmx-users] Re: gmx-users Digest, Vol 52, Issue 77   M.Parthiban
  • [gmx-users] Error in trjconv   M.Parthiban
    • [gmx-users] Error in trjconv   Tsjerk Wassenaar
• [gmx-users] dmso/peptide simulation   prasun kumar
  • [gmx-users] dmso/peptide simulation   Justin A. Lemkul
    • [gmx-users] dmso/peptide simulation   Anil Kumar
• [gmx-users] Re: temperature coupling for complex+ligand+water+ions   Alan
  • [gmx-users] Re: temperature coupling for complex+ligand+water+ions   Justin A. Lemkul
• [Fwd: Re: [gmx-users]build topology file for a molecule define with new residues]   cilpa at users.csc.fi
  • [Fwd: Re: [gmx-users]build topology file for a molecule define with new residues]   Justin A. Lemkul
    • [Fwd: Re: [gmx-users]build topology file for a molecule define with new residues]   cilpa at users.csc.fi
• [gmx-users] Re: gmx-users Digest, Vol 52, Issue 78   Vitaly Chaban
• [gmx-users] RE: [ atomtypes ] are not case sensitive?   Alan
  • [gmx-users] RE: [ atomtypes ] are not case sensitive?   Berk Hess
  • [gmx-users] RE: [ atomtypes ] are not case sensitive?   Alan
• [gmx-users] charmm and oplsaa simulation results don't match   Chris Neale
• FW: [gmx-users] charmm and oplsaa simulation results don't match   sarbani chattopadhyay
• [gmx-users] Questions about brownian/langevin dynamics of bead-spring polymers   Suman Chakrabarty
• [gmx-users] Help with grompp with amber99 forcefield   Ragnarok sdf
  • [gmx-users] Help with grompp with amber99 forcefield   Justin A. Lemkul
• [gmx-users] charmm and oplsaa simulation results don't match   Chris Neale
• [gmx-users] Using Morse potentials with ENCAD force field   Andy Shelley
  • [gmx-users] Using Morse potentials with ENCAD force field   David van der Spoel
  • [gmx-users] Using Morse potentials with ENCAD force field   Andy Shelley
• [gmx-users] REMD trjcat -demux problem   Di Pan
  • [gmx-users] REMD trjcat -demux problem   David van der Spoel
• [gmx-users] tfe.itp   shahrbanoo karbalaee
  • [gmx-users] tfe.itp   Justin A. Lemkul
• [gmx-users] FFTW & Gromacs installation on AIX 5.3   Senthil Kumar M
  • [gmx-users] FFTW & Gromacs installation on AIX 5.3   Justin A. Lemkul
  • [gmx-users] FFTW & Gromacs installation on AIX 5.3   Dimitris Dellis
• [gmx-users] MDRUN with MPIRUN   vivek sharma
  • [gmx-users] MDRUN with MPIRUN   Kukol, Andreas
    • [gmx-users] MDRUN with MPIRUN   vivek sharma
• [gmx-users] FFTW & Gromacs installation on AIX 5.3   chris.neale at utoronto.ca
• [gmx-users] rb1 test failed after recompiling gromacs 3.3.2   Nicolas Sapay
  • [gmx-users] rb1 test failed after recompiling gromacs 3.3.2   Nicolas Sapay
    • [gmx-users] rb1 test failed after recompiling gromacs 3.3.2   Justin A. Lemkul
      • [gmx-users] rb1 test failed after recompiling gromacs 3.3.2   Nicolas Sapay
• [gmx-users] AFM and g_wham   xi zhao
• [gmx-users] Simulations backward in time.   Sumanth Jamadagni
  • [gmx-users] Simulations backward in time.   David van der Spoel
• [gmx-users] tfe.itp   shahrbanoo karbalaee
• [gmx-users] pdb file ???   Chih-Ying Lin
  • [gmx-users] pdb file ???   Tsjerk Wassenaar
• [gmx-users] The WARNING   Chih-Ying Lin
  • [gmx-users] The WARNING   David van der Spoel
• [gmx-users] call for help   曹臻
• [gmx-users] Re: tfe.itp   Vitaly Chaban
• [gmx-users] Re: The WARNING   Vitaly Chaban
  • [gmx-users] Re: The WARNING   Tsjerk Wassenaar
    • [gmx-users] Re: The WARNING   Vitaly Chaban
• [gmx-users] Re: Simulations backward in time   Vitaly Chaban
  • [gmx-users] Re: Simulations backward in time   David van der Spoel
  • [gmx-users] Re: Simulations backward in time   Jochen Hub
    • [gmx-users] Re: Simulations backward in time   Vitaly Chaban
      • FW: [gmx-users] Re: Simulations backward in time   Berk Hess
• [gmx-users] tfe   shahrbanoo karbalaee
  • [gmx-users] tfe   Justin A. Lemkul
• [gmx-users] simulation problems   baloilgiullare
• [gmx-users] HELP::Running Gromacs in parellel   vivek sharma
  • [gmx-users] HELP::Running Gromacs in parellel   Justin A. Lemkul
• [gmx-users] Re: Using Morse potentials with ENCAD force field   Vitaly Chaban
• [gmx-users] Re: New Gromacs-CPMD QMMM webpage   Vitaly Chaban
• [gmx-users] Visualizing gromacs result   vivek sharma
  • [gmx-users] Visualizing gromacs result   Jochen Hub
• [gmx-users] Re: gmx-users Digest, Vol 52, Issue 89   Vitaly Chaban
• [gmx-users] Re: Simulations backward in time   Vitaly Chaban
• [gmx-users] Re: Simulations backward in time   Vitaly Chaban
• [gmx-users] simulations backward in time   Sumanth Jamadagni
  • [gmx-users] simulations backward in time   Jussi Lehtola
• [gmx-users] [Fwd: WARNING: Found more than 12 triclinic correction vectors, ignoring some.]   Justin A. Lemkul
• [gmx-users] regarding 2002 post showing protein unfolding with long timesteps   chris.neale at utoronto.ca
  • [gmx-users] regarding 2002 post showing protein unfolding with long timesteps   David van der Spoel
• [gmx-users] Re: Using Morse potentials with ENCAD force field   Vitaly Chaban
• [gmx-users] tfe and gromos9653a   shahrbanoo karbalaee
  • [gmx-users] tfe and gromos9653a   Justin A. Lemkul
• [gmx-users] cgnr   Chih-Ying Lin
  • [gmx-users] cgnr   LuLanyuan
• [gmx-users] Salt molecule - ion bond   Chih-Ying Lin
  • [gmx-users] Salt molecule - ion bond   Justin A. Lemkul
• [gmx-users] Re: Salt molecule - ion bond   Vitaly Chaban
• [gmx-users] The WARNING   Chih-Ying Lin
  • [gmx-users] Re: The WARNING   Tsjerk Wassenaar
• [gmx-users] How to display simulation box in VMD?   Suman Chakrabarty
  • [gmx-users] How to display simulation box in VMD?   Nicolas Sapay
• [gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"   M. Emal Alekozai
• [gmx-users] Re: The WARNING   Vitaly Chaban
• [gmx-users] g_rotacf   rams rams
• [gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"   Chris Neale
  • [gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"   M. Emal Alekozai
• [gmx-users] Help - No default Bond types dna   Ragnarok sdf
  • [gmx-users] Help - No default Bond types dna   Justin A. Lemkul
• [gmx-users] pull.pdo and AFM force   xi zhao
• [gmx-users] Vacuum Simulation of Alanine Dipeptide =>production run   M. Emal Alekozai
• [gmx-users] Error while running gromacs in parellel   vivek sharma
• [gmx-users] groups to write to trr   Vitaly Chaban
  • [gmx-users] groups to write to trr   Shay Amram
    • [gmx-users] groups to write to trr   Justin A. Lemkul
    • [gmx-users] groups to write to trr   Vitaly Chaban
• [gmx-users] Re: gmx-users Digest, Vol 52, Issue 96   Ragnarok sdf
  • [gmx-users] Re: gmx-users Digest, Vol 52, Issue 96   Justin A. Lemkul
• [gmx-users] g_sgangle   Chih-Ying Lin
  • [gmx-users] g_sgangle   Justin A. Lemkul
• [gmx-users] g_angle , g_bond distribution   Chih-Ying Lin
• [gmx-users] g_energy   Chih-Ying Lin
  • [gmx-users] g_energy   Justin A. Lemkul
• [gmx-users] Re: groups to write to trr   Vitaly Chaban
  • [gmx-users] Re: groups to write to trr   Justin A. Lemkul
    • [gmx-users] Re: groups to write to trr   Tsjerk Wassenaar
• [gmx-users] g_rotacf   rams rams
• [gmx-users] #include "ffG45a3.itp"   Chih-Ying Lin
  • [gmx-users] #include "ffG45a3.itp"   David van der Spoel
• [gmx-users] QMMM   ha salem
  • [gmx-users] QMMM   Pradip Biswas
• [gmx-users] #include "ffG45a3.itp"   Chih-Ying Lin
  • [gmx-users] #include "ffG45a3.itp"   Justin A. Lemkul
• [gmx-users] Mailman CGI error!!! The Mailman CGI wrapper encountered a fatal error. This entry is being stored in your syslog: Group mismatch error. Mailman expected the CGI wrapper script to be executed as group "nobody", but the system's web server executed the CGI script as group "apache". Try tweaking the web server to run the script as group "nobody", or re-run configure, providing the command line option `--with-cgi-gid=apache'.   Brian Wengerter
• [gmx-users] Re: Using Morse potentials with ENCAD force field   Andy Shelley
• [gmx-users] g_hbond output analysis   parthiban at ncbs.res.in
  • [gmx-users] g_hbond output analysis   Florian Haberl
• [gmx-users] Re: Using Morse potentials with ENCAD force field   Vitaly Chaban
• [gmx-users] heat_capacity_&_viscosity   Sang-Min Park
• [gmx-users] Genion failing in parallel runs.   Bhanu
  • [gmx-users] Genion failing in parallel runs.   Justin A. Lemkul
  • [gmx-users] Genion failing in parallel runs.   Florian Haberl
• [gmx-users] Choose groups for force output   Matteus Lindgren
• [gmx-users] Re:g_mindist option   alkasrivastava at iitb.ac.in
  • [gmx-users] Re:g_mindist option   Justin A. Lemkul
• [gmx-users] Re[2]: Using Morse potentials with ENCAD force field   Vitaly Chaban
  • [gmx-users] Re[2]: Using Morse potentials with ENCAD force field   Justin A. Lemkul
• [gmx-users] Corrupt TRR file -- skipping a bad frame?   Matt Wyczalkowski
  • [gmx-users] Corrupt TRR file -- skipping a bad frame?   Justin A. Lemkul
    • [gmx-users] Corrupt TRR file -- skipping a bad frame?   Tsjerk Wassenaar
• [gmx-users] The molecular structure   Chih-Ying Lin
  • [gmx-users] The molecular structure   Justin A. Lemkul
• [gmx-users] g_hbond output analysis   parthiban at ncbs.res.in
  • [gmx-users] g_hbond output analysis   David van der Spoel
• [gmx-users] How to use g_energy after parellal mdrun   vivek sharma
  • [gmx-users] How to use g_energy after parellal mdrun   Jochen Hub
    • [gmx-users] How to use g_energy after parellal mdrun   vivek sharma
      • [gmx-users] How to use g_energy after parellal mdrun   Jochen Hub
• [gmx-users] ffg53a5   shahrbanoo karbalaee
  • [gmx-users] ffg53a5   Tsjerk Wassenaar
  • [gmx-users] ffg53a5   Justin A. Lemkul
• [gmx-users] trjconv error   parthiban at ncbs.res.in
  • [gmx-users] trjconv error   Tsjerk Wassenaar
• [gmx-users] Re: Re:Re:g_mindist option   alkasrivastava at iitb.ac.in
  • [gmx-users] Re: Re:Re:g_mindist option   Tsjerk Wassenaar
• [gmx-users] G_SDF if reference atoms are in different residues   Hawtin R.
• [gmx-users] when gen_vel should be "no"   sarbani chattopadhyay
  • [gmx-users] when gen_vel should be "no"   Justin A. Lemkul
  • [gmx-users] when gen_vel should be "no"   Florian Dommert
  • [gmx-users] when gen_vel should be "no"   Jochen Hub
• [gmx-users] Re: Help   Justin A. Lemkul
• [gmx-users] Error with LINC warning   vivek sharma
  • [gmx-users] Error with LINC warning   Justin A. Lemkul
• [gmx-users] trjconv error   parthiban at ncbs.res.in
  • [gmx-users] trjconv error   Tsjerk Wassenaar
• [gmx-users] Re: Help   Justin A. Lemkul
• [gmx-users] error ffg53a5   shahrbanoo karbalaee
  • [gmx-users] error ffg53a5   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97   Ragnarok sdf
  • [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97   Justin A. Lemkul
• [gmx-users] RE: g_mindist option   van Bemmelen
• [gmx-users] error ffg53a   shahrbanoo karbalaee
  • [gmx-users] error ffg53a   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97   Ragnarok sdf
  • [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97   Justin A. Lemkul
• [gmx-users] error ffg53a and thanks   shahrbanoo karbalaee
• [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97 (Justin A. Lemkul)   Ragnarok sdf
  • [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97 (Justin A. Lemkul)   Justin A. Lemkul
• [gmx-users] Keeping portions of a protein fixed during energy minimization and MD simulations   shyamala iyer
  • [gmx-users] Keeping portions of a protein fixed during energy minimization and MD simulations   Justin A. Lemkul
• [gmx-users] Re: trjconv error   parthiban at ncbs.res.in
  • [gmx-users] Re: trjconv error   Tsjerk Wassenaar
• [gmx-users] Differences in version 3.0 and 3.3   Cheong Wee Loong, Daniel
• [gmx-users] Warnings while grompp_d   vivek sharma
  • [gmx-users] Warnings while grompp_d   Jochen Hub
• [gmx-users] Corrupt TRR file -- skipping a bad frame?   Alan Dodd
• [gmx-users] problems creating mixed solvent systems   Ted Fischer
  • [gmx-users] problems creating mixed solvent systems   Justin A. Lemkul
• [gmx-users] M*tif installation   Ross KK Leung
  • [gmx-users] M*tif installation   Justin A. Lemkul
    • [gmx-users] M*tif installation   Ross KK Leung
      • [gmx-users] M*tif installation   Justin A. Lemkul
      • [gmx-users] M*tif installation   Florian Haberl
      • [gmx-users] M*tif installation   Tsjerk Wassenaar
      • [gmx-users] M*tif installation   Suman Chakrabarty
• [gmx-users] Re: M*tif installation   Vitaly Chaban
• [gmx-users] compare 3.3.3 vs 3.99.4 (bit long)   spitaleri.andrea at hsr.it
• [gmx-users] Disappear my solution   Morteza Khabiri
  • [gmx-users] Disappear my solution   Justin A. Lemkul
• [gmx-users] g_hbond + invalid command line argument -g   minnale
  • [gmx-users] g_hbond + invalid command line argument -g   Justin A. Lemkul
• [gmx-users] g_hbond + invalid command line argument -g   minnale
  • [gmx-users] g_hbond + invalid command line argument -g   Justin A. Lemkul
• [gmx-users] g_hbond + invalid command line argument -g   minnale
• [gmx-users] Disappear my solution   Morteza Khabiri
  • [gmx-users] Disappear my solution   Justin A. Lemkul
• [gmx-users] LJ question   Anthony Cruz
  • [gmx-users] LJ question   David van der Spoel
    • [gmx-users] LJ question   Anthony Cruz
      • [gmx-users] LJ question   David van der Spoel
• [gmx-users] Disappear my solution   Morteza Khabiri
  • [gmx-users] Disappear my solution   Justin A. Lemkul
• [gmx-users] (no subject)   Anjelika Gasilina
  • [gmx-users] (no subject)   Tsjerk Wassenaar
• [gmx-users] Re: gmx-users Digest, Vol 52, Issue 109   Ragnarok sdf
  • [gmx-users] Re: gmx-users Digest, Vol 52, Issue 109   Justin A. Lemkul
• [gmx-users] mdrun failing with error message "reading tpx file (em.tpr) version 40 with version 31 program"   Anjelika Gasilina
• [gmx-users] Disappear my solution   Morteza Khabiri
  • [gmx-users] Disappear my solution   Justin A. Lemkul
• [gmx-users] g_msd   ram ram
  • [gmx-users] g_msd   Xavier Periole
• [gmx-users] g_hbond + invalid command line argument -g   minnale
  • [gmx-users] g_hbond + invalid command line argument -g   David van der Spoel
• [gmx-users] a question about the content in atm-pair.out file   Cao, Yang
  • [gmx-users] a question about the content in atm-pair.out file   Shay Amram
• [gmx-users] about connections   ravi sharma
• [gmx-users] problems creating mixed solvent systems   Ted Fischer
• [gmx-users] FENE potential (Finitely extensible Nonlinear elastic model)   avinash kumar
  • [gmx-users] FENE potential (Finitely extensible Nonlinear elastic model)   David van der Spoel
  • [gmx-users] how to define small in RMSD   Ross KK Leung
• [gmx-users] Re: gmx-users Digest, Vol 52, Issue 118   minnale
  • [gmx-users] Re: gmx-users Digest, Vol 52, Issue 118   Justin A. Lemkul
• [gmx-users] NPT restarts without .edr, can the simulations be used anyway?   Matteus Lindgren
• [gmx-users] Re: g_msd   Vitaly Chaban
• [gmx-users] Different results with and without constraints for pr coupling.   A.Rzepiela
  • [gmx-users] Different results with and without constraints for pr coupling.   David van der Spoel
• [gmx-users] genbox and triclinic boxes. Problem an workaround.   Jochen Hub
• [gmx-users] G_SDF if reference atoms are in different residues   chris.neale at utoronto.ca
• [gmx-users] Differences in version 3.0 and 3.3   chris.neale at utoronto.ca
• [gmx-users] using gromacs for protein site-mutagenesis study   Ross KK Leung
  • [gmx-users] using gromacs for protein site-mutagenesis study   Justin A. Lemkul
• [gmx-users] NPT restarts without .edr, can the simulations be used anyway?   Justin A. Lemkul
• [gmx-users] g_velacc   rams rams
  • [gmx-users] g_velacc   David van der Spoel
  • [gmx-users] Re: g_velacc   rams rams
    • [gmx-users] Re: g_velacc   Florian Dommert
      • [gmx-users] Re: g_velacc   David van der Spoel
• [gmx-users] Re: g_velacc   Vitaly Chaban
• [gmx-users] Re: g_hbond in version 3.4.1 vs rest (Especially higher one)   Justin A. Lemkul
• [gmx-users] Re: g_velacc   Vitaly Chaban
  • [gmx-users] Re: g_velacc   rams rams
    • [gmx-users] Re: g_velacc   Vitaly Chaban
• [gmx-users] Multiple ppa files from a single parallel mdrun_mpi job   chris.neale at utoronto.ca
• [gmx-users] LINCS error   sarbani chattopadhyay
  • [gmx-users] LINCS error   Justin A. Lemkul
• [gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein?   Limei Zhang
  • [gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein?   Justin A. Lemkul

Last message date: Sun Aug 31 23:37:47 CEST 2008
Archived on: Thu Nov 14 12:05:01 CET 2013

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