August 2013 Archives by thread

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Starting: Thu Aug 1 03:15:30 CEST 2013
Ending: Sat Aug 31 21:33:43 CEST 2013
Messages: 595

• [gmx-users] Re: inconsistent energy drops   Justin Lemkul
  • [gmx-users] Re: inconsistent energy drops   Brad Van Oosten
    • [gmx-users] Re: inconsistent energy drops   Justin Lemkul
      • [gmx-users] Re: inconsistent energy drops   Brad Van Oosten
      • [gmx-users] Re: inconsistent energy drops   Justin Lemkul
      • [gmx-users] Re: inconsistent energy drops   Brad Van Oosten
      • [gmx-users] Re: inconsistent energy drops   Justin Lemkul
      • [gmx-users] Re: inconsistent energy drops   Brad Van Oosten
      • [gmx-users] Re: inconsistent energy drops   Justin Lemkul
• [gmx-users] Potential Energy Scan   tarak karmakar
  • [gmx-users] Potential Energy Scan   Mark Abraham
    • [gmx-users] Potential Energy Scan   tarak karmakar
      • [gmx-users] Potential Energy Scan   Mark Abraham
• [gmx-users] concatenating 2 xtc files   Kavyashree M
  • [gmx-users] concatenating 2 xtc files   Tsjerk Wassenaar
    • [gmx-users] concatenating 2 xtc files   Kavyashree M
      • [gmx-users] concatenating 2 xtc files   Justin Lemkul
      • [gmx-users] concatenating 2 xtc files   Kavyashree M
      • [gmx-users] concatenating 2 xtc files   Justin Lemkul
      • [gmx-users] concatenating 2 xtc files   Kavyashree M
• [gmx-users] Energies in MM scanning using gmx   fantasticqhl
  • [gmx-users] Re: Energies in MM scanning using gmx   fantasticqhl
• [gmx-users] Re: fftw   Andrish Reddy
• [gmx-users] QM/MM with gromacs 4.5.5-gaussian03   azeif
• [gmx-users] Re: Conserved energy ("Conserved En.") in NVT simulation   Mark Abraham
• [gmx-users] fatal error with charmm/amber forcefield   Mark Abraham
• [gmx-users] Box dimension size errors in MARTINI soft core simulation   Scott Pendley
  • [gmx-users] Box dimension size errors in MARTINI soft core simulation   Justin Lemkul
• [gmx-users] Regarding g_order   Venkat Reddy
  • [gmx-users] Regarding g_order   Justin Lemkul
    • [gmx-users] Regarding g_order   Venkat Reddy
      • [gmx-users] Regarding g_order   Justin Lemkul
• [gmx-users] Re: CUDA with QUADRO GPUs   Szilárd Páll
• [gmx-users] GPU-based workstation   Szilárd Páll
• [gmx-users] Intel vs gcc compilers   Szilárd Páll
• [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher   akk5r
  • [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher   francesco oteri
  • [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher   Justin Lemkul
  • [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher   Mark Abraham
• [gmx-users] 1. Re: Interaction energy between specific residue in a set of residues (Justin Lemkul)   Collins Nganou
  • [gmx-users] 1. Re: Interaction energy between specific residue in a set of residues (Justin Lemkul)   Justin Lemkul
• [gmx-users] g_potential and trjconv: problems with bilayer simulation analysis   wood irene
  • [gmx-users] g_potential and trjconv: problems with bilayer simulation analysis   Justin Lemkul
    • [gmx-users] g_potential and trjconv: problems with bilayer simulation analysis   wood irene
      • [gmx-users] g_potential and trjconv: problems with bilayer simulation analysis   Justin Lemkul
• [gmx-users] COM of a molecule   Sikandar Mashayak
  • [gmx-users] Re: COM of a molecule   Brad Van Oosten
• [gmx-users] Trying to explain differences in behaviour between 2fs and 5fs timesteps   Trayder
  • [gmx-users] Trying to explain differences in behaviour between 2fs and 5fs timesteps   Mark Abraham
• [gmx-users] remd   Shine A
  • [gmx-users] remd   Mark Abraham
• [gmx-users] Gromacs: GPU detection   Jernej Zidar
  • [gmx-users] Gromacs: GPU detection   Szilárd Páll
    • [gmx-users] Re: Gromacs: GPU detection   Brad Van Oosten
• [gmx-users] Re: topology and coordinate file not matching after grompp   chinnu657
  • [gmx-users] Re: topology and coordinate file not matching after grompp   Justin Lemkul
    • [gmx-users] Re: topology and coordinate file not matching after grompp   chinnu657
    • [gmx-users] Re: topology and coordinate file not matching after grompp   chinnu657
    • [gmx-users] Re: topology and coordinate file not matching after grompp   chinnu657
      • [gmx-users] Re: topology and coordinate file not matching after grompp   Justin Lemkul
• [gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1   Guillaume Chevrot
  • [gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1   Mark Abraham
  • [gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1   rajat desikan
    • [gmx-users] Re: Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1   Guillaume Chevrot
      • [gmx-users] Re: Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1   Guillaume Chevrot
• [gmx-users] Re: energy conservation / frozen atoms   S. Alireza Bagherzadeh
  • [gmx-users] Re: energy conservation / frozen atoms   Justin Lemkul
• [gmx-users] restraint-lambdas for position restraints in hamiltonian exchange   Dejun Lin
  • [gmx-users] restraint-lambdas for position restraints in hamiltonian exchange   Michael Shirts
    • [gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange   Dejun Lin
      • [gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange   Michael Shirts
      • [gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange   Dejun Lin
      • [gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange   Dejun Lin
• [gmx-users] Gromacs 4.6.3 installation Issue with Intel & CUDA   Jim Strong
  • [gmx-users] Re: Gromacs 4.6.3 installation Issue with Intel & CUDA   Brad Van Oosten
• [gmx-users] mixing of PCs for generating reduced free energy profile using g_sham   R.S.K.Vijayan
• [gmx-users] Invalid order for directive atomtypes   Jonathan Saboury
  • [gmx-users] Invalid order for directive atomtypes   Tsjerk Wassenaar
• [gmx-users] Re: energy conservation / frozen atoms   S. Alireza Bagherzadeh
  • [gmx-users] Re: energy conservation / frozen atoms   Justin Lemkul
• [gmx-users] REMD run on higher nodes.   suhani nagpal
  • [gmx-users] REMD run on higher nodes.   Mark Abraham
    • [gmx-users] REMD run on higher nodes.   suhani nagpal
      • [gmx-users] REMD run on higher nodes.   Justin Lemkul
• [gmx-users] g_wham error analysis hangs   Magnus Andersson
  • [gmx-users] g_wham error analysis hangs   Justin Lemkul
    • [gmx-users] g_wham error analysis hangs   Magnus Andersson
      • [gmx-users] g_wham error analysis hangs   Justin Lemkul
      • [gmx-users] g_wham error analysis hangs   Magnus Andersson
      • [gmx-users] g_wham error analysis hangs   Justin Lemkul
  • [gmx-users] g_wham error analysis hangs   Jochen Hub
    • [gmx-users] g_wham error analysis hangs   Magnus Andersson
• [gmx-users] Unphysical conformations in decoupled free energy simulation   Joerg Sauter
  • [gmx-users] Unphysical conformations in decoupled free energy simulation   Justin Lemkul
    • [gmx-users] Unphysical conformations in decoupled free energy simulation   Joerg Sauter
      • [gmx-users] Unphysical conformations in decoupled free energy simulation   Justin Lemkul
      • [gmx-users] Unphysical conformations in decoupled free energy simulation   Joerg Sauter
      • [gmx-users] Unphysical conformations in decoupled free energy simulation   Justin Lemkul
      • [gmx-users] Unphysical conformations in decoupled free energy simulation   Michael Shirts
• [gmx-users] analysis tool of 407 to 46x   Chandan Choudhury
• [gmx-users] Adding charges to a protein to observe interaction   chinnu657
  • [gmx-users] Adding charges to a protein to observe interaction   Justin Lemkul
• [gmx-users] The sum of the two largest charge group radii ..is larger than rlist   Kavyashree M
  • [gmx-users] The sum of the two largest charge group radii ..is larger than rlist   Justin Lemkul
    • [gmx-users] The sum of the two largest charge group radii ..is larger than rlist   Kavyashree M
• [gmx-users] Free Energy Ion Pair Decoupling   Quintin Sheridan
• [gmx-users] starting temperature equilibration phase   ypca
  • [gmx-users] starting temperature equilibration phase   Justin Lemkul
    • [gmx-users] Re: starting temperature equilibration phase   ypca
      • [gmx-users] Re: starting temperature equilibration phase   Justin Lemkul
      • [gmx-users] Re: starting temperature equilibration phase   ypca
      • [gmx-users] Re: starting temperature equilibration phase   Justin Lemkul
      • [gmx-users] Re: starting temperature equilibration phase   ypca
• [gmx-users] g_angle bin centers   Brandon Wiebe
  • [gmx-users] g_angle bin centers   Justin Lemkul
• [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   Prentice Bisbal
  • [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   Mark Abraham
    • [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   Prentice Bisbal
  • [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   Bogdan Costescu
    • [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   Prentice Bisbal
      • [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   Bogdan Costescu
• [gmx-users] Hamiltonian replica exchange not working in 4.6   Sanku M
  • [gmx-users] Hamiltonian replica exchange not working in 4.6   Michael Shirts
• [gmx-users] set charge as 0 in gromacs code   Shi, Yu (shiy4)
  • [gmx-users] set charge as 0 in gromacs code   Mark Abraham
    • [gmx-users] set charge as 0 in gromacs code   Shi, Yu (shiy4)
      • [gmx-users] set charge as 0 in gromacs code   Mark Abraham
• [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   Prentice Bisbal
• [gmx-users] Restrain lipid in a bilayer   Li, Hualin
• [gmx-users] Bond energy doesn't appear in gromacs rerun   Golshan Hejazi
  • [gmx-users] Bond energy doesn't appear in gromacs rerun   Justin Lemkul
• [gmx-users] Bond energy doesn't appear in gromacs rerun   Justin Lemkul
• [gmx-users] Re: how is the pulling force measured   zhuswf
• [gmx-users] Lipid Bilayer on the Graphene or GO substrate   朱文鹏
  • [gmx-users] Lipid Bilayer on the Graphene or GO substrate   David van der Spoel
• [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k   Golshan Hejazi
  • [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k   David van der Spoel
    • [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k   Golshan Hejazi
      • [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k   Justin Lemkul
• [gmx-users] Lipid Bilayer on the Graphene or GO substrate   朱文鹏
  • [gmx-users] Lipid Bilayer on the Graphene or GO substrate   David van der Spoel
  • [gmx-users] Lipid Bilayer on the Graphene or GO substrate   朱文鹏
    • [gmx-users] Lipid Bilayer on the Graphene or GO substrate   David van der Spoel
• [gmx-users] GPU + surface   Ondrej Kroutil
  • [gmx-users] GPU + surface   Berk Hess
  • [gmx-users] GPU + surface   Lucio Montero
• [gmx-users] g_WHAM   Shima Arasteh
  • [gmx-users] g_WHAM   Justin Lemkul
    • [gmx-users] g_WHAM   Shima Arasteh
      • [gmx-users] g_WHAM   Justin Lemkul
• [gmx-users] Umbrella sampling - position restraints   rookie417
  • [gmx-users] Umbrella sampling - position restraints   Justin Lemkul
  • Aw: [gmx-users] Umbrella sampling - position restraints   lloyd riggs
    • Aw: [gmx-users] Umbrella sampling - position restraints   suram417
• [gmx-users] Trying to replicate Aqvist's results (solvation free energy).   Francis de Lasalle
  • [gmx-users] Trying to replicate Aqvist's results (solvation free energy).   André Farias de Moura
    • [gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy).   Heymman
      • [gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy).   André Farias de Moura
  • [gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy).   sumanc
• [gmx-users] Use pull code to restrain the COM   Bin Liu
  • [gmx-users] Use pull code to restrain the COM   Justin Lemkul
• [gmx-users] g_wham -sym   Shima Arasteh
  • [gmx-users] g_wham -sym   Justin Lemkul
    • [gmx-users] g_wham -sym   Shima Arasteh
      • [gmx-users] g_wham -sym   Jochen Hub
• [gmx-users] gromacs-4.5.5 CPMD QM/MM   tarak karmakar
• [gmx-users] Re: Use pull code to restrain the COM   Bin Liu
  • [gmx-users] Re: Use pull code to restrain the COM   Justin Lemkul
• [gmx-users] segmentation fault on g_protonate   Pedro Lacerda
  • [gmx-users] segmentation fault on g_protonate   Justin Lemkul
• [gmx-users] About running gromacs in GPU   vidhya sankar
  • [gmx-users] About running gromacs in GPU   Justin Lemkul
• [gmx-users] About running Production simulation in GPU with twinrange cut-off   vidhya sankar
  • [gmx-users] About running Production simulation in GPU with twinrange cut-off   Justin Lemkul
• [gmx-users] About Running production simualtion in GPU   vidhya sankar
  • [gmx-users] About Running production simualtion in GPU   Justin Lemkul
• [gmx-users] Cleaning up trajectory files after crash   Joshua Adelman
  • [gmx-users] Cleaning up trajectory files after crash   Justin Lemkul
    • [gmx-users] Cleaning up trajectory files after crash   Joshua Adelman
      • [gmx-users] Cleaning up trajectory files after crash   Justin Lemkul
• [gmx-users] hessian calculation with periodic boundary condition   John Travers
  • [gmx-users] hessian calculation with periodic boundary condition   David van der Spoel
    • [gmx-users] hessian calculation with periodic boundary condition   John Travers
    • [gmx-users] hessian calculation with periodic boundary condition   John Travers
• [gmx-users] Lateral Diffusion of Lipids   Kieu Thu Nguyen
  • [gmx-users] Lateral Diffusion of Lipids   Dr. Vitaly Chaban
  • [gmx-users] Lateral Diffusion of Lipids   Justin Lemkul
    • [gmx-users] Lateral Diffusion of Lipids   Kieu Thu Nguyen
  • [gmx-users] Lateral Diffusion of Lipids   Jochen Hub
• [gmx-users] script to add water in protein   pooja_gupta at nccs.res.in
  • [gmx-users] script to add water in protein   bharat gupta
    • [gmx-users] script to add water in protein   pooja_gupta at nccs.res.in
      • [gmx-users] script to add water in protein   Tsjerk Wassenaar
• Fwd: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   Mark Abraham
• [gmx-users] Force Field for peptides and proteins   Maria Astón Serrano
  • [gmx-users] Force Field for peptides and proteins   Kieu Thu Nguyen
  • [gmx-users] Force Field for peptides and proteins   Dr. Vitaly Chaban
  • [gmx-users] Force Field for peptides and proteins   Justin Lemkul
    • [gmx-users] Force Field for peptides and proteins   rajat desikan
  • Aw: [gmx-users] Force Field for peptides and proteins   lloyd riggs
• [gmx-users] Implement a modified pull module to mdrun   Li, Hualin
  • [gmx-users] Implement a modified pull module to mdrun   Justin Lemkul
    • [gmx-users] Implement a modified pull module to mdrun   Li, Hualin
      • [gmx-users] Implement a modified pull module to mdrun   Justin Lemkul
      • [gmx-users] Implement a modified pull module to mdrun   Li, Hualin
      • [gmx-users] Implement a modified pull module to mdrun   Justin Lemkul
• [gmx-users] charmm2gromacs.py error   Revthi Sanker
• [gmx-users] converting Charmm36 lipidds to gromacs   Revthi Sanker
• [gmx-users] perl scripts to convert CHARMM ff in GROMACS   Revthi Sanker
  • [gmx-users] perl scripts to convert CHARMM ff in GROMACS   David van der Spoel
• [gmx-users] Problem running do_dssp   Dipankar Roy
  • [gmx-users] Problem running do_dssp   Justin Lemkul
• [gmx-users] VDW switched off in CHARMM tip3p model   Weilong Zhao
  • [gmx-users] VDW switched off in CHARMM tip3p model   Mark Abraham
• [gmx-users] Unkwown Keyword HILLS   Albert
  • [gmx-users] Re: Unkwown Keyword HILLS   Albert
    • [gmx-users] Re: Unkwown Keyword HILLS   Michael Shirts
    • [gmx-users] Re: Unkwown Keyword HILLS   Michael Shirts
      • [gmx-users] Re: Unkwown Keyword HILLS   Albert
• [gmx-users] Yet another question about what force field to use   Pedro Lacerda
  • [gmx-users] Yet another question about what force field to use   Justin Lemkul
• [gmx-users] gromacs-4.5.5 cpmd QM/MM versions   tarak karmakar
• [gmx-users] how can we control output ?   Albert
  • [gmx-users] how can we control output ?   Justin Lemkul
• [gmx-users] plans for mdrun features to deprecate in GROMACS 5.0   Mark Abraham
  • [gmx-users] plans for mdrun features to deprecate in GROMACS 5.0   rajat desikan
    • [gmx-users] plans for mdrun features to deprecate in GROMACS 5.0   Mark Abraham
• [gmx-users] charmm36 proteins   Dina Mirijanian
• [gmx-users] All molecules being coupled for free energy of self solvation simulation   Brittany Zimmerman
  • [gmx-users] Re: All molecules being coupled for free energy of self solvation simulation   Brittany Zimmerman
• [gmx-users] VDW switched off in CHARMM tip3p model   Christopher Neale
  • [gmx-users] Re: VDW switched off in CHARMM tip3p model   qiuxing
  • [gmx-users] VDW switched off in CHARMM tip3p model   Mark Abraham
• [gmx-users] charmm36 proteins   Christopher Neale
  • [gmx-users] charmm36 proteins   Justin Lemkul
    • [gmx-users] charmm36 proteins   Dina Mirijanian
• [gmx-users] "Sign convention" g_energy total energies   gg jj
  • [gmx-users] "Sign convention" g_energy total energies   Justin Lemkul
• [gmx-users] GPU metadynamics   Albert
  • [gmx-users] GPU metadynamics   Jacopo Sgrignani
    • [gmx-users] GPU metadynamics   Albert
• [gmx-users] Running g_tune_pme on a BlueGene/Q cluster   Jernej Zidar
  • [gmx-users] Running g_tune_pme on a BlueGene/Q cluster   Mark Abraham
• [gmx-users] what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?   grita
  • [gmx-users] what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?   Justin Lemkul
    • [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?   grita
      • [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?   Justin Lemkul
      • [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?   grita
      • [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?   massimo sandal
      • [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?   grita
      • [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?   Justin Lemkul
      • [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?   grita
      • [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?   Richard Broadbent
      • [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?   grita
      • [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?   massimo sandal
• [gmx-users] LINCS Constraints - all-bonds or h-bonds?   Barnett, James W.
  • [gmx-users] LINCS Constraints - all-bonds or h-bonds?   Michael Shirts
    • [gmx-users] LINCS Constraints - all-bonds or h-bonds?   Erik Marklund
• [gmx-users] Partial incompatibility of pdb2gmx with 4 character residue names?   Joerg Sauter
  • [gmx-users] Partial incompatibility of pdb2gmx with 4 character residue names?   Mark Abraham
    • [gmx-users] Partial incompatibility of pdb2gmx with 4 character residue names?   Joerg Sauter
• [gmx-users] for help about reading xtc file   Xu, Yechuan
  • [gmx-users] for help about reading xtc file   Mark Abraham
    • [gmx-users] for help about reading xtc file   Xu, Yechuan
      • [gmx-users] for help about reading xtc file   Mark Abraham
      • [gmx-users] for help about reading xtc file   Xu, Yechuan
      • [gmx-users] for help about reading xtc file   Mark Abraham
      • [gmx-users] for help about reading xtc file   Xu, Yechuan
      • [gmx-users] for help about reading xtc file   Mark Abraham
• [gmx-users] Molecule removal by g_membed   Bin Liu
  • [gmx-users] Molecule removal by g_membed   Justin Lemkul
• [gmx-users] Re: Running g_tune_pme on a BlueGene/Q cluster   Jernej Zidar
  • [gmx-users] Re: Running g_tune_pme on a BlueGene/Q cluster   Mark Abraham
• [gmx-users] psf to tpr   Venkat Reddy
  • [gmx-users] psf to tpr   Mark Abraham
    • [gmx-users] psf to tpr   Dr. Vitaly Chaban
• [gmx-users] Restart REMD   Min Wu
  • [gmx-users] Restart REMD   Mark Abraham
• [gmx-users] Restart REMD   minwuh081
• [gmx-users] Hai friends   balu
  • [gmx-users] Hai friends   massimo sandal
• [gmx-users] About Error in mdrun   vidhya sankar
  • [gmx-users] About Error in mdrun   Justin Lemkul
• [gmx-users] Re: Hai friends (balu)   Muhammad Naqvi
  • [gmx-users] Re: Hai friends (balu)   jkrieger at mrc-lmb.cam.ac.uk
• [gmx-users] Regarding TCoupling and position restraints   HANNIBAL LECTER
  • [gmx-users] Regarding TCoupling and position restraints   Justin Lemkul
    • [gmx-users] Regarding TCoupling and position restraints   HANNIBAL LECTER
      • [gmx-users] Regarding TCoupling and position restraints   Justin Lemkul
• [gmx-users] generation of gro file   Musharaf Ali
  • [gmx-users] generation of gro file   Justin Lemkul
    • [gmx-users] generation of gro file   Musharaf Ali
      • [gmx-users] generation of gro file   Justin Lemkul
      • [gmx-users] generation of gro file   Musharaf Ali
      • [gmx-users] generation of gro file   Justin Lemkul
      • [gmx-users] generation of gro file   Musharaf Ali
• [gmx-users] Problem in Gyrate analysis   Sainitin Donakonda
• [gmx-users] Lennard jones energy   chinnu657
  • [gmx-users] Lennard jones energy   Justin Lemkul
• [gmx-users] itp problem   Albert
  • [gmx-users] itp problem   Justin Lemkul
• [gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?   massimo sandal
  • [gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?   Justin Lemkul
    • [gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?   massimo sandal
      • [gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?   Justin Lemkul
      • [gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?   massimo sandal
      • [gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?   Justin Lemkul
      • [gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?   massimo sandal
• [gmx-users] want to apply electric field in membrane system   udels can
  • [gmx-users] want to apply electric field in membrane system   Justin Lemkul
    • [gmx-users] want to apply electric field in membrane system   sudipta
      • [gmx-users] want to apply electric field in membrane system   Justin Lemkul
      • [gmx-users] want to apply electric field in membrane system   sudipta
      • [gmx-users] want to apply electric field in membrane system   Justin Lemkul
      • [gmx-users] want to apply electric field in membrane system   sudipta
      • [gmx-users] want to apply electric field in membrane system   Justin Lemkul
• [gmx-users] Insertion Events   balu
• [gmx-users] GPU version of Gromacs   grita
  • [gmx-users] GPU version of Gromacs   Justin Lemkul
  • [gmx-users] Re: GPU version of Gromacs   Dwey Kauffman
    • [gmx-users] Re: GPU version of Gromacs   grita
      • [gmx-users] Re: GPU version of Gromacs   Justin Lemkul
      • [gmx-users] Re: GPU version of Gromacs   grita
      • [gmx-users] Re: GPU version of Gromacs   Mark Abraham
• [gmx-users] Coordination number   Venkat Reddy
  • [gmx-users] Coordination number   Dallas Warren
    • [gmx-users] Coordination number   Venkat Reddy
      • [gmx-users] Coordination number   Dallas Warren
• [gmx-users] Query regarding membrane-peptide simulation   Aditya Padhi
  • [gmx-users] Query regarding membrane-peptide simulation   Justin Lemkul
• [gmx-users] question   mjm136525 at yahoo.com
  • [gmx-users] question   Андрей Гончар
• [gmx-users] question   mjm136525 at yahoo.com
  • [gmx-users] question   Андрей Гончар
• [gmx-users] gromacs installation in mac osx 10.8   Sudip Roy
  • [gmx-users] gromacs installation in mac osx 10.8   Mark Abraham
• [gmx-users] NPT, freezegroups and Position Restraints.   HANNIBAL LECTER
  • [gmx-users] NPT, freezegroups and Position Restraints.   Justin Lemkul
    • [gmx-users] NPT, freezegroups and Position Restraints.   HANNIBAL LECTER
      • [gmx-users] NPT, freezegroups and Position Restraints.   HANNIBAL LECTER
      • [gmx-users] NPT, freezegroups and Position Restraints.   Justin Lemkul
      • [gmx-users] NPT, freezegroups and Position Restraints.   HANNIBAL LECTER
      • [gmx-users] NPT, freezegroups and Position Restraints.   Justin Lemkul
      • [gmx-users] NPT, freezegroups and Position Restraints.   HANNIBAL LECTER
      • [gmx-users] NPT, freezegroups and Position Restraints.   HANNIBAL LECTER
      • [gmx-users] NPT, freezegroups and Position Restraints.   Justin Lemkul
      • [gmx-users] NPT, freezegroups and Position Restraints.   Mark Abraham
      • [gmx-users] NPT, freezegroups and Position Restraints.   HANNIBAL LECTER
      • [gmx-users] NPT, freezegroups and Position Restraints.   Mark Abraham
      • [gmx-users] NPT, freezegroups and Position Restraints.   HANNIBAL LECTER
• [gmx-users] PMF calculation   Za Pour
  • [gmx-users] PMF calculation   Justin Lemkul
• [gmx-users] regarding US   Abed Askari
• [gmx-users] regarding umbrella sampling   Abed Askari
  • [gmx-users] regarding umbrella sampling   Justin Lemkul
    • [gmx-users] regarding umbrella sampling   Abed Askari
      • [gmx-users] regarding umbrella sampling   Justin Lemkul
• [gmx-users] Early registration period ending for 2013 GROMACS USA Workshop and Conference   Michael Shirts
  • [gmx-users] Early registration period ending for 2013 GROMACS USA Workshop and Conference   rajat desikan
    • [gmx-users] Early registration period ending for 2013 GROMACS USA Workshop and Conference   Michael Shirts
• [gmx-users] g_WHAM   Shima Arasteh
  • [gmx-users] g_WHAM   Justin Lemkul
• [gmx-users] Number of SOL/Water in gmx_moltype_t   Pradip Biswas
  • [gmx-users] Number of SOL/Water in gmx_moltype_t   Mark Abraham
    • [gmx-users] Number of SOL/Water in gmx_moltype_t   Pradip Biswas
      • [gmx-users] Number of SOL/Water in gmx_moltype_t   Mark Abraham
• [gmx-users] Conversion of nm to Å   Arunima Shilpi
  • RE: [gmx-users] Conversion of nm to Å   Dallas Warren
  • Re: [gmx-users] Conversion of nm to Å   João Henriques
• [gmx-users] g_select problem   Albert
  • [gmx-users] g_select problem   Mark Abraham
    • [gmx-users] g_select problem   Albert
      • [gmx-users] g_select problem   Mark Abraham
  • [gmx-users] g_select problem   Teemu Murtola
    • [gmx-users] g_select problem   Albert
      • [gmx-users] g_select problem   Justin Lemkul
      • [gmx-users] g_select problem   Albert
• [gmx-users] GROMACS-CYSTEINE PROTEASES   MUSYOKA THOMMAS
  • [gmx-users] GROMACS-CYSTEINE PROTEASES   Justin Lemkul
    • [gmx-users] GROMACS-CYSTEINE PROTEASES   MUSYOKA THOMMAS
  • [gmx-users] Re: GROMACS-CYSTEINE PROTEASES   MUSYOKA THOMMAS
    • [gmx-users] Re: GROMACS-CYSTEINE PROTEASES   Justin Lemkul
      • [gmx-users] Re: GROMACS-CYSTEINE PROTEASES   MUSYOKA THOMMAS
      • [gmx-users] Re: GROMACS-CYSTEINE PROTEASES   Justin Lemkul
      • [gmx-users] Re: GROMACS-CYSTEINE PROTEASES   MUSYOKA THOMMAS
• [gmx-users] position restraint   Shima Arasteh
  • [gmx-users] position restraint   Gaurav Goel
    • [gmx-users] position restraint   Shima Arasteh
      • [gmx-users] position restraint   Justin Lemkul
• [gmx-users] position restraint   Shima Arasteh
  • [gmx-users] position restraint   Mark Abraham
    • [gmx-users] position restraint   Shima Arasteh
      • [gmx-users] position restraint   Mark Abraham
      • [gmx-users] position restraint   Shima Arasteh
      • [gmx-users] position restraint   Mark Abraham
• [gmx-users] Interpreting dihedrals in topology file   rdwducl
  • [gmx-users] Interpreting dihedrals in topology file   Justin Lemkul
• [gmx-users] SR-coulomb energy   SANTU BISWAS
• [gmx-users] Issue in ligand gyration analysis   Sainitin Donakonda
  • [gmx-users] Issue in ligand gyration analysis   Justin Lemkul
    • [gmx-users] Issue in ligand gyration analysis   Sainitin Donakonda
      • [gmx-users] Issue in ligand gyration analysis   Justin Lemkul
      • [gmx-users] Issue in ligand gyration analysis   Chandan Choudhury
• [gmx-users] Invalid order for directive atomtypes   afsaneh maleki
  • [gmx-users] Invalid order for directive atomtypes   Justin Lemkul
• [gmx-users] DMPC Bilayer   Rama
  • [gmx-users] DMPC Bilayer   Justin Lemkul
• [gmx-users] Gromacs 4.6.3 Installation Issues,   No One
  • [gmx-users] Gromacs 4.6.3 Installation Issues,   HANNIBAL LECTER
• [gmx-users] 'Command not found' after installation   Nimmy McNimmerson
  • [gmx-users] 'Command not found' after installation   Barnett, James W.
• [gmx-users] VDW Cut-off vs Switch with CHARMM force field   Gianluca Interlandi
  • [gmx-users] VDW Cut-off vs Switch with CHARMM force field   James Krieger
    • [gmx-users] VDW Cut-off vs Switch with CHARMM force field   James Krieger
      • [gmx-users] VDW Cut-off vs Switch with CHARMM force field   Gianluca Interlandi
      • [gmx-users] VDW Cut-off vs Switch with CHARMM force field   Justin Lemkul
      • [gmx-users] VDW Cut-off vs Switch with CHARMM force field   Gianluca Interlandi
      • [gmx-users] VDW Cut-off vs Switch with CHARMM force field   Justin Lemkul
• [gmx-users] 'Command not found' after installation   Barnett, James W.
• [gmx-users] Help with Error Message   The One And Only
  • [gmx-users] Help with Error Message   Rafael I. Silverman y de la Vega
    • [gmx-users] Help with Error Message   The One And Only
      • [gmx-users] Help with Error Message   Justin Lemkul
      • [gmx-users] Help with Error Message   The One And Only
      • [gmx-users] Help with Error Message   The One And Only
      • [gmx-users] Help with Error Message   Tsjerk Wassenaar
      • [gmx-users] Help with Error Message   The One And Only
      • [gmx-users] Help with Error Message   Tsjerk Wassenaar
      • [gmx-users] Help with Error Message   The One And Only
      • [gmx-users] Help with Error Message   Rafael I. Silverman y de la Vega
      • [gmx-users] Help with Error Message   Tsjerk Wassenaar
• [gmx-users] Ok now what?   The One And Only
  • [gmx-users] Ok now what?   Emanuel Birru
• [gmx-users] rvdw, rlist and rcoulomb for Amber03   Rajat Desikan
  • [gmx-users] rvdw, rlist and rcoulomb for Amber03   Justin Lemkul
• [gmx-users] #coordinates do not match   The One And Only
  • [gmx-users] #coordinates do not match   rajat desikan
    • [gmx-users] #coordinates do not match   The One And Only
• [gmx-users] 'Command not found' after installation   Nimmy McNimmerson
  • [gmx-users] 'Command not found' after installation   Mark Abraham
    • [gmx-users] 'Command not found' after installation   Nimmy McNimmerson
      • [gmx-users] 'Command not found' after installation   Justin Lemkul
      • [gmx-users] 'Command not found' after installation   Nimmy McNimmerson
      • [gmx-users] 'Command not found' after installation   Mark Abraham
• [gmx-users] NPT-REMD   rahul seth
  • [gmx-users] NPT-REMD   Mark Abraham
    • [gmx-users] NPT-REMD   Michael Shirts
      • [gmx-users] Re: NPT-REMD   rahul.seth.gromacs
      • [gmx-users] Re: NPT-REMD   Michael Shirts
      • [gmx-users] Re: NPT-REMD   rahul seth
• [gmx-users] Regarding adding ions error   sanjay choubey
  • [gmx-users] Regarding adding ions error   Mark Abraham
• [gmx-users] Re: 'Command not found' after installation   Christoph Junghans
• [gmx-users] g_hydorder error   Nidhi Katyal
  • [gmx-users] g_hydorder error   Justin Lemkul
• [gmx-users] error with g_dist   chinnu657
  • [gmx-users] error with g_dist   Justin Lemkul
    • [gmx-users] Re: error with g_dist   chinnu657
      • [gmx-users] Re: error with g_dist   Justin Lemkul
      • [gmx-users] Re: error with g_dist   chinnu657
      • [gmx-users] Re: error with g_dist   Justin Lemkul
      • [gmx-users] Re: error with g_dist   chinnu657
      • [gmx-users] Re: error with g_dist   Justin Lemkul
      • [gmx-users] Re: error with g_dist   chinnu657
      • [gmx-users] Re: error with g_dist   Justin Lemkul
      • [gmx-users] Re: error with g_dist   chinnu657
      • [gmx-users] Re: error with g_dist   Justin Lemkul
      • [gmx-users] Re: error with g_dist   chinnu657
      • [gmx-users] Re: error with g_dist   Justin Lemkul
      • [gmx-users] Re: error with g_dist   chinnu657
      • [gmx-users] Re: error with g_dist   chinnu657
      • [gmx-users] Re: error with g_dist   chinnu657
• [gmx-users] LIGAND TOPOLOGY   MUSYOKA THOMMAS
  • [gmx-users] LIGAND TOPOLOGY   Justin Lemkul
• [gmx-users] Regarding coordinate mismatching.   sanjay choubey
  • [gmx-users] Regarding coordinate mismatching.   Justin Lemkul
• [gmx-users] general question about molecule.rtp and pdb2gmx   Valentina
  • [gmx-users] general question about molecule.rtp and pdb2gmx   Justin Lemkul
    • [gmx-users] general question about molecule.rtp and pdb2gmx   Mark Abraham
    • [gmx-users] Re: general question about molecule.rtp and pdb2gmx   Valentina
      • [gmx-users] Re: general question about molecule.rtp and pdb2gmx   Sergey
      • [gmx-users] Re: general question about molecule.rtp and pdb2gmx   Valentina
      • [gmx-users] Re: general question about molecule.rtp and pdb2gmx   Justin Lemkul
• [gmx-users] About script for free energy calculation   vidhya sankar
  • [gmx-users] About script for free energy calculation   Mark Abraham
• [gmx-users] Rescale: Cloud simulation platform research grants   Ilea Graedel
• [gmx-users] Wrapping of protein molecules during simulation   Gianluca Interlandi
  • [gmx-users] Wrapping of protein molecules during simulation   Justin Lemkul
• [gmx-users] Gentle heating with implicit solvent   Gianluca Interlandi
  • [gmx-users] Gentle heating with implicit solvent   Mark Abraham
• [gmx-users] Genion command not working   Deepak Ojha
  • [gmx-users] Genion command not working   Tsjerk Wassenaar
• [gmx-users] Long range Lennard Jones   Gianluca Interlandi
  • [gmx-users] Long range Lennard Jones   Dallas Warren
  • [gmx-users] Long range Lennard Jones   Mark Abraham
    • [gmx-users] Long range Lennard Jones   rajat desikan
      • [gmx-users] Long range Lennard Jones   David van der Spoel
      • [gmx-users] Long range Lennard Jones   Mark Abraham
      • [gmx-users] Long range Lennard Jones   Gianluca Interlandi
      • [gmx-users] Long range Lennard Jones   Justin Lemkul
      • [gmx-users] Long range Lennard Jones   Gianluca Interlandi
      • [gmx-users] Long range Lennard Jones   Justin Lemkul
      • [gmx-users] Long range Lennard Jones   Gianluca Interlandi
      • [gmx-users] Long range Lennard Jones   Justin Lemkul
      • [gmx-users] Long range Lennard Jones   Michael Shirts
      • [gmx-users] Long range Lennard Jones   Gianluca Interlandi
      • [gmx-users] Long range Lennard Jones   Justin Lemkul
      • [gmx-users] Long range Lennard Jones   Gianluca Interlandi
      • [gmx-users] Long range Lennard Jones   Justin Lemkul
      • [gmx-users] Long range Lennard Jones   Gianluca Interlandi
      • [gmx-users] Long range Lennard Jones   Gianluca Interlandi
      • [gmx-users] Long range Lennard Jones   Justin Lemkul
      • [gmx-users] Long range Lennard Jones   Gianluca Interlandi
      • [gmx-users] Long range Lennard Jones   Justin Lemkul
• [gmx-users] total charge   Group Gro
  • [gmx-users] total charge   Mark Abraham
• [gmx-users] DMPC Bilayer   Rama
  • [gmx-users] DMPC Bilayer   Justin Lemkul
• [gmx-users] work in 4.5.5 but failed in 4.6.1   Albert
  • [gmx-users] work in 4.5.5 but failed in 4.6.1   Justin Lemkul
    • [gmx-users] work in 4.5.5 but failed in 4.6.1   Albert
      • [gmx-users] work in 4.5.5 but failed in 4.6.1   Justin Lemkul
      • [gmx-users] work in 4.5.5 but failed in 4.6.1   Albert
      • [gmx-users] work in 4.5.5 but failed in 4.6.1   Justin Lemkul
      • [gmx-users] work in 4.5.5 but failed in 4.6.1   Albert
• [gmx-users] problem of submitting job in HPC   Albert
  • [gmx-users] problem of submitting job in HPC   Justin Lemkul
    • [gmx-users] problem of submitting job in HPC   Mark Abraham
      • [gmx-users] problem of submitting job in HPC   Albert
• [gmx-users] CGennFF in gromacs   Golshan Hejazi
  • [gmx-users] CGennFF in gromacs   Justin Lemkul
• [gmx-users] ERROR : GROMACS finsihed with error 74   sri2201
  • [gmx-users] ERROR : GROMACS finsihed with error 74   Tsjerk Wassenaar
• [gmx-users] MD vs. free energy simulations   Jernej Zidar
  • [gmx-users] MD vs. free energy simulations   Justin Lemkul
• [gmx-users] Creating an infinite sheet of graphene   #TAN BENG HAU IAN#
  • [gmx-users] Re: Creating an infinite sheet of graphene   Valentina
    • [gmx-users] Re: Creating an infinite sheet of graphene   Justin Lemkul
  • [gmx-users] Creating an infinite sheet of graphene   Justin Lemkul
• [gmx-users] pdb2gmx breaking bonds   Ewa Brylska
  • [gmx-users] pdb2gmx breaking bonds   Justin Lemkul
• [gmx-users] Cyclodextrin_Ligand_Protein System   marawan hussain
• [gmx-users] periodic_molecule & missing interactions   Valentina
  • [gmx-users] periodic_molecule & missing interactions   Justin Lemkul
    • [gmx-users] Re: periodic_molecule & missing interactions   Valentina
      • [gmx-users] Re: periodic_molecule & missing interactions   Dr. Vitaly Chaban
• [gmx-users] A question about velocity rescaling thermostat and velocity verlet integrator   Ali Sinan Saglam
  • [gmx-users] A question about velocity rescaling thermostat and velocity verlet integrator   Michael Shirts
  • [gmx-users] A question about velocity rescaling thermostat and velocity verlet integrator   Mark Abraham
    • [gmx-users] A question about velocity rescaling thermostat and velocity verlet integrator   Ali Sinan Saglam
• [gmx-users] Regarding Position restraint and freezegroups   rahul seth
  • [gmx-users] Regarding Position restraint and freezegroups   Justin Lemkul
    • [gmx-users] Regarding Position restraint and freezegroups   rahul seth
      • [gmx-users] Regarding Position restraint and freezegroups   Justin Lemkul
• [gmx-users] efficiency in HPC   Albert
  • [gmx-users] efficiency in HPC   Prentice Bisbal
    • [gmx-users] efficiency in HPC   Albert
  • [gmx-users] efficiency in HPC   Mark Abraham
• [gmx-users] Question about HREMD in .log file   drew.w.ritchie
  • [gmx-users] Question about HREMD in .log file   andrew ritchie
• [gmx-users] Regarding g_densmap output   Venkat Reddy
  • [gmx-users] Regarding g_densmap output   Chandan Choudhury
    • [gmx-users] Regarding g_densmap output   Venkat Reddy
• [gmx-users] Distance restraints exploding system   Trayder
  • [gmx-users] Distance restraints exploding system   Mark Abraham
• [gmx-users] Creating an infinite sheet of grapheme   #TAN BENG HAU IAN#
• [gmx-users] Distribution of an atom along a trajectory   Shima Arasteh
  • [gmx-users] Distribution of an atom along a trajectory   Justin Lemkul
• [gmx-users] AVX libraries with GMX4.6.3   Ali Sinan Saglam
  • [gmx-users] AVX libraries with GMX4.6.3   Mark Abraham
    • [gmx-users] AVX libraries with GMX4.6.3   Ali Sinan Saglam
      • [gmx-users] AVX libraries with GMX4.6.3   Mark Abraham
• [gmx-users] TPIC and GMX_TPI_DUMP   Rafael I. Silverman y de la Vega
  • [gmx-users] TPIC and GMX_TPI_DUMP   João M. Damas
    • [gmx-users] TPIC and GMX_TPI_DUMP   Rafael I. Silverman y de la Vega
      • [gmx-users] TPIC and GMX_TPI_DUMP   João M. Damas
      • [gmx-users] TPIC and GMX_TPI_DUMP   Rafael I. Silverman y de la Vega
      • [gmx-users] TPIC and GMX_TPI_DUMP   João M. Damas
      • [gmx-users] TPIC and GMX_TPI_DUMP   João M. Damas
      • [gmx-users] TPIC and GMX_TPI_DUMP   Rafael I. Silverman y de la Vega
      • [gmx-users] TPIC and GMX_TPI_DUMP   Rafael I. Silverman y de la Vega
• [gmx-users] Reg Mpi run Error   vidhya sankar
  • [gmx-users] Reg Mpi run Error   Justin Lemkul
• [gmx-users] Reg mpirun error   vidhya sankar
  • [gmx-users] Reg mpirun error   Mark Abraham
• [gmx-users] grompy and how to call energy routine   Gianluca Interlandi
  • [gmx-users] grompy and how to call energy routine   Gianluca Interlandi
    • [gmx-users] grompy and how to call energy routine   Justin Lemkul
      • [gmx-users] grompy and how to call energy routine   Gianluca Interlandi
      • [gmx-users] grompy and how to call energy routine   Justin Lemkul
      • [gmx-users] grompy and how to call energy routine   Gianluca Interlandi
      • [gmx-users] grompy and how to call energy routine   Justin Lemkul
      • [gmx-users] grompy and how to call energy routine   Justin Lemkul
      • [gmx-users] grompy and how to call energy routine   Gianluca Interlandi
• [gmx-users] question about g_hydorder   Nidhi Katyal

Last message date: Sat Aug 31 21:33:43 CEST 2013
Archived on: Thu Nov 14 12:14:44 CET 2013

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