May 2008 Archives by thread

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Starting: Thu May 1 00:01:36 CEST 2008
Ending: Sat May 31 15:25:58 CEST 2008
Messages: 567

• [gmx-users] All tests failed   Ramadas Sunil Pophale
  • [gmx-users] All tests failed   Florian Dommert
• [gmx-users] Re: upgrade version - "make distclean"?   David van der Spoel
• [gmx-users] oxaloacetate and atp   E.M.
  • [gmx-users] oxaloacetate and atp   Justin A. Lemkul
• [gmx-users] adding missing hydrogen in PDB files   Arijit Maitra
  • [gmx-users] adding missing hydrogen in PDB files   Justin A. Lemkul
    • [gmx-users] adding missing hydrogen in PDB files   Vigneshwar Ramakrishnan
      • [gmx-users] adding missing hydrogen in PDB files   Mark Abraham
      • [gmx-users] adding missing hydrogen in PDB files   Justin A. Lemkul
      • [gmx-users] adding missing hydrogen in PDB files   Arijit Maitra
• [gmx-users] Building simple alcohol topologies   Jussi Lehtola
  • [gmx-users] Building simple alcohol topologies   Mark Abraham
    • [gmx-users] Building simple alcohol topologies   David van der Spoel
• [gmx-users] DCCM   tuhin at iitk.ac.in
  • [gmx-users] DCCM   Mark Abraham
• [gmx-users] combining differently-generated force-fields   chris.neale at utoronto.ca
  • [gmx-users] combining differently-generated force-fields   Mark Abraham
• [gmx-users] GROMACS parallel set up Questions.   Subhrangshu Supakar
  • [gmx-users] GROMACS parallel set up Questions.   Mark Abraham
    • [gmx-users] GROMACS parallel set up Questions.   David van der Spoel
• [gmx-users] Plotting B-factor   Alif M Latif
  • [gmx-users] Plotting B-factor   Kukol, Andreas
    • [gmx-users] Plotting B-factor   David van der Spoel
  • [gmx-users] Plotting B-factor   Ran Friedman
• [gmx-users] timesteps don't match error   maria goranovic
  • [gmx-users] timesteps don't match error   Mark Abraham
    • [gmx-users] timesteps don't match error   maria goranovic
      • [gmx-users] timesteps don't match error   Xavier Periole
      • [gmx-users] timesteps don't match error   maria goranovic
      • [gmx-users] timesteps don't match error   Xavier Periole
      • [gmx-users] timesteps don't match error   maria goranovic
      • [gmx-users] timesteps don't match error   Xavier Periole
      • [gmx-users] timesteps don't match error   maria goranovic
      • [gmx-users] timesteps don't match error   Xavier Periole
• [gmx-users] Building simple alcohol topologies   Jussi Lehtola
  • [gmx-users] Building simple alcohol topologies   David van der Spoel
• [gmx-users] Solvent insertion analysis 2   cfgauna at lab.cricyt.edu.ar
  • [gmx-users] Solvent insertion analysis 2   David van der Spoel
• [gmx-users] constraint pulling code   Brian Novak
• [gmx-users] Re: combining differently-generated force-fields   Low Soo Mei
  • [gmx-users] lipid paraemeters   Syma Khalid
    • [gmx-users] lipid paraemeters   Ángel Piñeiro
• [gmx-users] simple and complex test failure   Ramadas Sunil Pophale
  • [gmx-users] simple and complex test failure   David van der Spoel
• [gmx-users] using xmp file   pragya chohan
  • [gmx-users] using xmp file   Mark Abraham
    • [gmx-users] using xmp file   Florian Dommert
      • [gmx-users] using xmp file   pragya chohan
      • [gmx-users] using xmp file   Justin A. Lemkul
      • [gmx-users] using xmp file   Mark Abraham
      • [gmx-users] benchmark: buying a new cluster   andrea spitaleri
      • [gmx-users] benchmark: buying a new cluster   Yang Ye
      • [gmx-users] benchmark: buying a new cluster   Berk Hess
• [gmx-users] LJ SIMULATION   Arnab Senapati
  • [gmx-users] LJ SIMULATION   David van der Spoel
• [gmx-users] Calculating average of B-factor   Alif M Latif
  • [gmx-users] Calculating average of B-factor   Mark Abraham
    • [gmx-users] Calculating average of B-factor   David van der Spoel
• [gmx-users] I am now on Refriendz!   sunita gupta
• [gmx-users] Error of g_rms   s lal badshah
  • [gmx-users] Error of g_rms   Mark Abraham
• [gmx-users] Can not open file:md323.xtc   s lal badshah
  • [gmx-users] Can not open file:md323.xtc   Mark Abraham
• [gmx-users] Re: combining differently-generated force-fields   chris.neale at utoronto.ca
  • [gmx-users] Re: combining differently-generated force-fields   Kukol, Andreas
  • [gmx-users] Re: combining differently-generated force-fields   Maik Goette
• [gmx-users] Wrong potential energies in stochastic dynamics   reich at mpikg.mpg.de
• [gmx-users] Re: gmx-users Digest, Vol 49, Issue 11   Ramadas Sunil Pophale
  • [gmx-users] Re: gmx-users Digest, Vol 49, Issue 11   David van der Spoel
• [gmx-users] A question about DNA and normal mode analysis in gromacs   silvester.thu
  • [gmx-users] A question about DNA and normal mode analysis in gromacs   Mark Abraham
• [gmx-users] Free energy - Hydrogen bond solute-solvent - Ethanol as an example.   Eudes Fileti
  • [gmx-users] Re: Free energy - Hydrogen bond solute-solvent - Ethanol as an example.   Eudes Fileti
  • [gmx-users] Free energy - Hydrogen bond solute-solvent - Ethanol as an example.   Maik Goette
• [gmx-users] help with lipids and pdb2gmx   fabracht sdf
  • [gmx-users] help with lipids and pdb2gmx   Justin A. Lemkul
  • [gmx-users] help with lipids and pdb2gmx   Mark Abraham
• [gmx-users] when I switch to ffG43a1, the problem occurs   xin liu
  • [gmx-users] when I switch to ffG43a1, the problem occurs   Mark Abraham
    • [gmx-users] when I switch to ffG43a1, the problem occurs   xin liu
• [gmx-users] Alternate to xmgrace   s lal badshah
  • [gmx-users] Alternate to xmgrace   Mark Abraham
• [gmx-users] (no subject)   Arnab Senapati
  • [gmx-users] (no subject)   Tsjerk Wassenaar
  • [gmx-users] (no subject)   Florian Haberl
• [gmx-users] Equilibration   Arnab Senapati
  • [gmx-users] Equilibration   Mark Abraham
• [gmx-users] problem with simulation of phosphatidic acid, possibly in my topology?   himanshu khandelia
  • [gmx-users] problem with simulation of phosphatidic acid, possibly in my topology?   Mark Abraham
    • [gmx-users] problem with simulation of phosphatidic acid, possibly in my topology?   maria goranovic
      • [gmx-users] problem with simulation of phosphatidic acid, possibly in my topology?   Yiannis
  • [gmx-users] Re: problem with simulation of phosphatidic acid, possibly in my topology?   himanshu khandelia
• [gmx-users] Parallel processing   mariognu-outside at yahoo.com.br
  • [gmx-users] Parallel processing   Mark Abraham
• [gmx-users] Is such hardware suitable for gromacs   之光 贾
  • [gmx-users] Is such hardware suitable for gromacs   Yang Ye
• [gmx-users] double sids error ? what ?!   BON Michael
  • [gmx-users] double sids error ? what ?!   David van der Spoel
• [gmx-users] benchmark: buying a new cluster   Chris Neale
• [gmx-users] Angle definition in g_hbond ...   sharada
  • [gmx-users] Angle definition in g_hbond ...   Mark Abraham
    • [gmx-users] Angle definition in g_hbond ...   David van der Spoel
      • [gmx-users] Angle definition in g_hbond ...   Anil Kumar
      • [gmx-users] Angle definition in g_hbond ...   sharada
      • [gmx-users] Angle definition in g_hbond ...   David van der Spoel
      • [gmx-users] Angle definition in g_hbond ...   sharada
• [gmx-users] LINCS and parallel simulation   Philip Shushkov
• [gmx-users] cannot determin precesion of .trn file   kinshuk at chem.iitb.ac.in
  • [gmx-users] cannot determin precesion of .trn file   David van der Spoel
  • [gmx-users] cannot determin precesion of .trn file   Justin A. Lemkul
• [gmx-users] stochastic dynamics and barostat in Gromacs   Argyrios Karatrantos
• [gmx-users] topolbuild 1.1.1, minor revisions to an all-atoms model gromacs topology generator   Bruce D. Ray
• [gmx-users] (no subject)   Arnab Senapati
• [Fwd: [gmx-users] (no subject)]   Arnab Senapati
• [gmx-users] Box size Increase   Arnab Senapati
  • [gmx-users] Box size Increase   Mark Abraham
• [gmx-users] Help needed urgently...!!!   namita at ncbs.res.in
  • [gmx-users] Help needed urgently...!!!   Mark Abraham
  • [gmx-users] Help needed urgently...!!!   Xavier Periole
• [gmx-users] (no subject)   Arnab Senapati
  • [gmx-users] (no subject)   Mark Abraham
• [gmx-users] NVT simulation   Arnab Senapati
  • [gmx-users] NVT simulation   Daniel Larsson
  • [gmx-users] NVT simulation   Yang Ye
• [gmx-users] RE : double sids error ? what ?!   BON Michael
• [gmx-users] Fatal error: No such moleculetype Cl   namita at ncbs.res.in
  • [gmx-users] Fatal error: No such moleculetype Cl   Anil Kumar
  • [gmx-users] Fatal error: No such moleculetype Cl   Xavier Periole
  • [gmx-users] Fatal error: No such moleculetype Cl   Kukol, Andreas
• [gmx-users] Help for GNUPlot   s lal badshah
  • [gmx-users] Help for GNUPlot   Per Larsson
  • [gmx-users] Help for GNUPlot   Florian Haberl
    • [gmx-users] Help for GNUPlot   Mark Abraham
  • [gmx-users] Help for GNUPlot   Zoltan Varga
    • [gmx-users] Help for GNUPlot   Mark Abraham
• [gmx-users] Heat Flux on CNT   Andy Shelley
  • [gmx-users] Heat Flux on CNT   David van der Spoel
• [gmx-users] REMD: average potential energy as a function of temperatue   pascal.baillod at epfl.ch
  • [gmx-users] REMD: average potential energy as a function of temperatue   Robert Johnson
    • [gmx-users] REMD: average potential energy as a function of temperatue   Mark Abraham
• [gmx-users] (no subject)   hhhh huan
• [gmx-users] how to obtain no. of aggregates vs time graph   hhhh huan
  • [gmx-users] how to obtain no. of aggregates vs time graph   David van der Spoel
• [gmx-users] position and distance restraining   jayant james
  • [gmx-users] position and distance restraining   Mark Abraham
• [gmx-users] box vectors entry in "gro" file   Makoto Yoneya
  • [gmx-users] box vectors entry in "gro" file   David van der Spoel
    • [gmx-users] box vectors entry in "gro" file   Tsjerk Wassenaar
  • [gmx-users] box vectors entry in "gro" file   Makoto Yoneya
• [gmx-users] Tabulated potential   Arnab Senapati
• [gmx-users] make_ndx problem   minnale
  • [gmx-users] make_ndx problem   Xavier Periole
• [gmx-users] GroMeta v.2.0   Carlo Camilloni
• [gmx-users] modify the distance constraints force constant during the simulation   Andrea Bortolato
  • [gmx-users] modify the distance constraints force constant during the simulation   Mitchell Stanton-Cook
• [gmx-users] Free energy of discharging and then recharging not zero   Robert Johnson
  • [gmx-users] Free energy of discharging and then recharging not zero   David Mobley
    • [gmx-users] Free energy of discharging and then recharging not zero   Robert Johnson
      • [gmx-users] Free energy of discharging and then recharging not zero   David Mobley
  • [gmx-users] Free energy of discharging and then recharging not zero   Maik Goette
    • [gmx-users] Free energy of discharging and then recharging not zero   Robert Johnson
      • [gmx-users] Free energy of discharging and then recharging not zero   Justin A. Lemkul
      • [gmx-users] Free energy of discharging and then recharging not zero   Robert Johnson
      • [gmx-users] Free energy of discharging and then recharging not zero   Maik Goette
• [gmx-users] ngmx crash   jayant james
  • [gmx-users] ngmx crash   Daniel Larsson
  • [gmx-users] ngmx crash   David van der Spoel
• [gmx-users] g_rms: Too many iterations in routine JACOBI   minnale
  • [gmx-users] g_rms: Too many iterations in routine JACOBI   Tsjerk Wassenaar
• [gmx-users] acetyl   Bernhard Knapp
  • [gmx-users] acetyl   Mark Abraham
• [gmx-users] Re: g_rms: Too many iterations in routine JACOBI   minnale
  • [gmx-users] Re: g_rms: Too many iterations in routine JACOBI   Tsjerk Wassenaar
• [gmx-users] g_rdf: normalization issues?   Vasilii Artyukhov
  • [gmx-users] Re: g_rdf: normalization issues?   Vasilii Artyukhov
    • [gmx-users] Re: g_rdf: normalization issues?   Berk Hess
      • [gmx-users] Re: g_rdf: normalization issues?   Vasilii Artyukhov
      • [gmx-users] Re: g_rdf: normalization issues?   Berk Hess
• [gmx-users] Re: modify the distance constraints force constant during the simulation   chaban at univer.kharkov.ua
• [gmx-users] Unable to neutralize my system   namita at ncbs.res.in
  • [gmx-users] Unable to neutralize my system   Justin A. Lemkul
  • [gmx-users] Unable to neutralize my system   Berk Hess
• [gmx-users] How to create S-S bond   kinshuk at chem.iitb.ac.in
• [gmx-users] How to create S-S bond   kinshuk at chem.iitb.ac.in
  • [gmx-users] How to create S-S bond   Justin A. Lemkul
• [gmx-users] Unable to neutralize my system   namita at ncbs.res.in
  • [gmx-users] Unable to neutralize my system   Justin A. Lemkul
• [gmx-users] Non integer charge for ARG and CYX?   Georgios Patargias
  • [gmx-users] Non integer charge for ARG and CYX?   Eric J. Sorin
    • [gmx-users] Non integer charge for ARG and CYX?   Georgios Patargias
• [gmx-users] Unable to neutralize my system   Alan Dodd
• [gmx-users] crash nsgrid.c   Fabio Affinito
  • [gmx-users] crash nsgrid.c   Berk Hess
• [gmx-users] Question about x2top   Jussi Lehtola
  • [gmx-users] Question about x2top   Justin A. Lemkul
• [gmx-users] SWCNT Topology   Mayank Verma
  • [gmx-users] SWCNT Topology   Justin A. Lemkul
• [gmx-users] High pressure   Arnab Senapati
  • [gmx-users] High pressure   Mark Abraham
  • [gmx-users] High pressure   David van der Spoel
• [gmx-users] msd and diffusion coefficient and getting unfolded trajectory   Ananya Debnath
  • [gmx-users] msd and diffusion coefficient and getting unfolded trajectory   Mark Abraham
• [gmx-users] gromacs 4.0 release   Bernhard Knapp
  • [gmx-users] gromacs 4.0 release   David van der Spoel
• [gmx-users] crash nsgrid.c   Fabio Affinito
• [gmx-users] gromos96 forcefield   Thomas Schlesier
  • [gmx-users] gromos96 forcefield   Justin A. Lemkul
  • [gmx-users] gromos96 forcefield   Kukol, Andreas
• [gmx-users] pdb2gmx   RAJAVARMAN.K
  • [gmx-users] pdb2gmx   Kukol, Andreas
  • [gmx-users] pdb2gmx   Mark Abraham
• [gmx-users] Fw: Electron Density Across the Lipid Bilayer   ANINDITA GAYEN
  • [gmx-users] Fw: Electron Density Across the Lipid Bilayer   Mark Abraham
• [gmx-users] Capped CNT   Christopher Stiles
  • [gmx-users] Capped CNT   Robert Johnson
• [gmx-users] gcc 4.2.x   baloilgiullare
  • [gmx-users] mpi.h is missing...   Dmitri Dubov
    • [gmx-users] mpi.h is missing...   Jussi Lehtola
      • [gmx-users] mpi.h is missing...   Mark Abraham
      • [gmx-users] mpi.h is missing...   Jussi Lehtola
• [gmx-users] msd and diffusion coefficient and getting unfolded trajectory   Ananya Debnath
• [gmx-users] RDF values lower than 1   Argyrios Karatrantos
  • [gmx-users] Melting temperature of the potato, a bug in grompp?   Xavier Periole
    • [gmx-users] Melting temperature of the potato, a bug in grompp?   Tsjerk Wassenaar
  • [gmx-users] RDF values lower than 1   David van der Spoel
• [gmx-users] confusion regarding tpbconv   Anamika Awasthi
  • [gmx-users] confusion regarding tpbconv   Xavier Periole
• [gmx-users] problem with energy minimization   sanjay23 at iitb.ac.in
  • [gmx-users] problem with energy minimization   Justin A. Lemkul
• [gmx-users] User Contributions   Vitaly Chaban
  • [gmx-users] User Contributions   David van der Spoel
• [gmx-users] grompp -np -shuffle with position restraints   Low Soo Mei
• [gmx-users] confusion regarding tpbconv   Anamika Awasthi
  • [gmx-users] confusion regarding tpbconv   Mark Abraham
    • [gmx-users] cutting the trajectory in small subtrajectories   serdar durdagi
      • [gmx-users] cutting the trajectory in small subtrajectories   Florian Dommert
      • [gmx-users] cutting the trajectory in small subtrajectories   serdar durdagi
      • [gmx-users] cutting the trajectory in small subtrajectories   Florian Dommert
      • [gmx-users] cutting the trajectory in small subtrajectories   Kukol, Andreas
• [gmx-users] tabulated potential   Arnab Senapati
• [gmx-users] Re:confusion regarding tpbconv   sudheer babu
  • [gmx-users] Re:confusion regarding tpbconv   Xavier Periole
• [gmx-users] cutting the trajectory in small subtrajectories   Alan Dodd
• [gmx-users] a problem about adding organic solvent with genbox   zhuliang at tju.edu.cn
• [gmx-users] multiple time step algorithm   Cristina GRECO
  • [gmx-users] multiple time step algorithm   David van der Spoel
    • [gmx-users] multiple time step algorithm   Cristina GRECO
      • [gmx-users] multiple time step algorithm   Berk Hess
      • [gmx-users] multiple time step algorithm   Erik Marklund
      • [gmx-users] multiple time step algorithm   Ran Friedman
      • [gmx-users] multiple time step algorithm   David van der Spoel
      • [gmx-users] multiple time step algorithm   Ran Friedman
      • [gmx-users] multiple time step algorithm   Berk Hess
      • [gmx-users] multiple time step algorithm   Cristina GRECO
    • [gmx-users] hybrid or Hamiltonian REMD in gromacs   Mu Yuguang (Dr)
• [gmx-users] Simulation of ordered molecular structures   Peyman Yamin
  • [gmx-users] Simulation of ordered molecular structures   Justin A. Lemkul
• [gmx-users] Energy minimisation problem   Jussi Lehtola
  • [gmx-users] Energy minimisation problem   Kukol, Andreas
    • [gmx-users] Energy minimisation problem   Jussi Lehtola
      • [gmx-users] Energy minimisation problem   Jussi Lehtola
      • [gmx-users] Energy minimisation problem   silvester.thu
      • [gmx-users] Energy minimisation problem   Kukol, Andreas
• [gmx-users] dssp or xpm2ps?   andrea_guarnera at libero.it
• [gmx-users] gromos96 forcefield   Thomas Schlesier
  • [gmx-users] gromos96 forcefield   Justin A. Lemkul
• [gmx-users] .itp file for polymer   David Huang
  • [gmx-users] .itp file for polymer   Mark Abraham
• [gmx-users] bilayer DMPC   ANINDITA GAYEN
  • [gmx-users] bilayer DMPC   Mark Abraham
  • [gmx-users] bilayer DMPC   Yiannis
• [gmx-users] Re:confusion regarding tpbconv   Anamika Awasthi
  • [gmx-users] Re:confusion regarding tpbconv   Mark Abraham
• [gmx-users] bilayer DMPC   chris.neale at utoronto.ca
• [gmx-users] Re: gmx-users Digest, Vol 49, Issue 53 bilayer area problem   ANINDITA GAYEN
• [gmx-users] problem with energy minimization   sanjay23 at iitb.ac.in
  • [gmx-users] problem with energy minimization   Mark Abraham
• [gmx-users] Ramachandran plots in GRACE   Petr Sklenovsky
  • [gmx-users] Ramachandran plots in GRACE   Justin A. Lemkul
• [gmx-users] Semi-isotropic pressure coupling   Sumanth Jamadagni
  • [gmx-users] Semi-isotropic pressure coupling   Berk Hess
• [gmx-users] Re: gmx-users Digest, Vol 49, Issue 53 bilayer area problem   chris.neale at utoronto.ca
• [gmx-users] Pressure and All-bonds   Dimitris Dellis
  • [gmx-users] Re: Pressure and All-bonds   Dimitris Dellis
• [gmx-users] distance restrained energy minimisation   jayant james
  • [gmx-users] distance restrained energy minimisation   Mark Abraham
• [gmx-users] how to build the input files of an infinite system   silvester.thu
  • [gmx-users] how to build the input files of an infinite system   Mark Abraham
    • [gmx-users] how to build the input files of an infinite system   silvester.thu
• [gmx-users] Range checking error   namita at ncbs.res.in
  • [gmx-users] Range checking error   Mark Abraham
    • [gmx-users] Range checking error   namita at ncbs.res.in
      • [gmx-users] Range checking error   Mark Abraham
• [gmx-users] atomname -> atomic number   Daniel Baum
  • [gmx-users] atomname -> atomic number   Mark Abraham
    • [gmx-users] atomname -> atomic number   David van der Spoel
    • [gmx-users] atomname -> atomic number   Daniel Baum
• [gmx-users] Making PDB file   User Gromacs
  • [gmx-users] Making PDB file   Mark Abraham
  • [gmx-users] Making PDB file   Florian Haberl
• [gmx-users] how to neutralise: Non-integer charges   namita at ncbs.res.in
  • [gmx-users] how to neutralise: Non-integer charges   Daniel Larsson
  • [gmx-users] how to neutralise: Non-integer charges   Erik Marklund
• [gmx-users] atomname -> atomic number   Gerrit Groenhof
• [gmx-users] atomname -> atomic number   Mark Abraham
• [gmx-users] tip3p.gro   sarbani chattopadhyay
  • [gmx-users] tip3p.gro   Xavier Periole
  • [gmx-users] tip3p.gro   Nicolas Sapay
• [gmx-users] tip3p.gro   sarbani chattopadhyay
  • [gmx-users] tip3p.gro   Xavier Periole
• [gmx-users] (no subject)   minnale
  • [gmx-users] (no subject)   Justin A. Lemkul
• [gmx-users] RMSD plot   Justin A. Lemkul
  • [gmx-users] RMSD plot   Florian Haberl
• [gmx-users] RMSD plot   minnale
  • [gmx-users] RMSD plot   Mark Abraham
• [gmx-users] Ordering with trjorder   Dmitri Dubov
  • [gmx-users] Ordering with trjorder   Berk Hess
• [gmx-users] trjorder problems   cfgauna at lab.cricyt.edu.ar
  • [gmx-users] trjorder problems   Mark Abraham
• [gmx-users] How to build a custom protein (PDB file)   Ricardo Soares
  • [gmx-users] How to build a custom protein (PDB file)   Justin A. Lemkul
  • [gmx-users] How to build a custom protein (PDB file)   Erik Marklund
    • [gmx-users] How to build a custom protein (PDB file)   Ricardo Soares
• [gmx-users] [ angle_restraints_z ]   Terry Nelson
  • [gmx-users] [ angle_restraints_z ]   Berk Hess
    • [gmx-users] [ angle_restraints_z ]   Terry Nelson
      • [gmx-users] [ angle_restraints_z ]   Berk Hess
• [gmx-users] dipole momentum calculation in Gromacs/CPMD   yayan at chemie.fu-berlin.de
  • [gmx-users] dipole momentum calculation in Gromacs/CPMD   Berk Hess
• [gmx-users] g_hbond distance distribution problem   Dechang Li
  • [gmx-users] g_hbond distance distribution problem   David van der Spoel
    • [gmx-users] g_hbond distance distribution problem   Xavier Periole
• [gmx-users] g_hbond distance distribution problem   Dechang Li
  • [gmx-users] g_hbond distance distribution problem   David van der Spoel
• [gmx-users] problem regarding energy minimization   sangeeta kundu
  • [gmx-users] problem regarding energy minimization   Mark Abraham
• [gmx-users] water distortion above bilayer   ANINDITA GAYEN
  • [gmx-users] water distortion above bilayer   Mark Abraham
• [gmx-users] Re: Re: water distortion above bilayer   ANINDITA GAYEN
• [gmx-users] Combining LJ & Buckingham?   ttrudeau
• [gmx-users] Free energy calculations and speed problems   Justin A. Lemkul
• [gmx-users] 3rd Annual CMM 'Users Meet Developers' Workshop on QM/MM Simulations   Robert Johnson
• [gmx-users] Free energy calculations and speed problems   van Bemmelen
  • [gmx-users] Free energy calculations and speed problems   David Mobley
• [gmx-users] Re: Re: water distortion above bilayer   Alan Dodd
• [gmx-users] Free energy calculations and speed problems   Michael Shirts
  • [gmx-users] Free energy calculations and speed problems   Justin A. Lemkul
    • [gmx-users] Free energy calculations and speed problems   Justin A. Lemkul
      • [gmx-users] Free energy calculations and speed problems   David Mobley
      • [gmx-users] Free energy calculations and speed problems   Berk Hess
• [gmx-users] QM/MM compilation   Ramon Crehuet
• [gmx-users] chirality check   sanjay23 at iitb.ac.in
  • [gmx-users] chirality check   Daniel Larsson
• [gmx-users] QM/MM compilation   ggroenh
  • [gmx-users] QM/MM compilation   Ran Friedman
• [gmx-users] QM/MM compilation   Gerrit Groenhof
• [gmx-users] Invitation to connect on LinkedIn   Chandu_Cts Welcomes...All....Biotechies
• [gmx-users] Water molecule can not be settled   Robert Fenwick
  • [gmx-users] Water molecule can not be settled   Mark Abraham
• [gmx-users] how to edit pdb file   Wei, Xiupeng
  • [gmx-users] how to edit pdb file   andrea spitaleri
    • [gmx-users] how to edit pdb file   Yang Ye
  • [gmx-users] how to edit pdb file   Justin A. Lemkul
    • [gmx-users] how to edit pdb file   Wei, Xiupeng
• [gmx-users] how to edit pdb file   Alan Dodd
• [gmx-users] problem with genion (gromacs 3.3.99)   Julie Bernauer
• [gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)   CIHAN NADIR KAPLAN
  • [gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)   Justin A. Lemkul
    • [gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)   Nadir Kaplan
  • [gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)   Mark Abraham
    • [gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)   Nadir Kaplan
      • [gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)   Mark Abraham
• [gmx-users] how to remd analysi?   xi zhao
  • [gmx-users] how to remd analysi?   Mark Abraham
    • 回复： Re: [gmx-users] how to remd analysi?   xi zhao
      • 回复： Re: [gmx-users] how to remd analysi?   David van der Spoel
      • 回复： Re: [gmx-users] how to remd analysi?   Mark Abraham
• [gmx-users] QM/MM between Gromacs and Gamess-US   Hanning Chen
• [gmx-users] about DMSO c-c bond and c-o bond in ffg53a6 force field   wang kelvin
  • [gmx-users] about DMSO c-c bond and c-o bond in ffg53a6 force field   Mark Abraham
    • [gmx-users] about DMSO c-c bond and c-o bond in ffg53a6 force field   wang kelvin
      • [gmx-users] about DMSO c-c bond and c-o bond in ffg53a6 force field   Mark Abraham
• [gmx-users] .trr file   Low Soo Mei
  • [gmx-users] .trr file   Mark Abraham
  • [gmx-users] .trr file   David van der Spoel
• [gmx-users] which code should I rewrite the function of "position restraints"?   Makoto Yoneya
  • [gmx-users] which code should I rewrite the function of "position restraints"?   David van der Spoel
• [gmx-users] generation of amorphous surface   h a
  • [gmx-users] generation of amorphous surface   Mark Abraham
• [gmx-users] Error while running starting grompp and mdrun   Ragothaman Yennamalli
  • [gmx-users] Error while running starting grompp and mdrun   Mark Abraham
    • [gmx-users] Error while running starting grompp and mdrun   Ragothaman Yennamalli
      • [gmx-users] Error while running starting grompp and mdrun   Mark Abraham
• [gmx-users] Implicit Solvent Simulations   Una Bjarnadottir
  • [gmx-users] Implicit Solvent Simulations   Per Larsson
• [gmx-users] Force field parameters in water or in vacuum?   Chih-Ying Lin
  • [gmx-users] Force field parameters in water or in vacuum?   Justin A. Lemkul
  • [gmx-users] Force field parameters in water or in vacuum?   Mark Abraham
  • [gmx-users] Re: Force field parameters in water or in vacuum?   Chih-Ying Lin
    • [gmx-users] Re: Force field parameters in water or in vacuum?   Mark Abraham
• [gmx-users] Unable to minimize energy   Paul Whitford
  • [gmx-users] Unable to minimize energy   Mark Abraham
• [gmx-users] Simulate the organic molecule => input / output error   Chih-Ying Lin
  • [gmx-users] Simulate the organic molecule => input / output error   Mark Abraham
• [gmx-users] Force field parameters in water or in vacuum?   chris.neale at utoronto.ca
  • [gmx-users] Force field parameters in water or in vacuum?   David van der Spoel
• [gmx-users] announcement: Advanced Gromacs workshop in Goettingen September 24-26   ggroenh
• [gmx-users] Energy minimization of a simple model without PBC   Ivan Fedyanin
• [gmx-users] small typo in ions.itp: LI+ atom is NA   Chris Neale
• [gmx-users] Force field parameters in water or in vacuum?   Chris Neale
• [gmx-users] Re: 1-4 scaling problem?   chris.neale at utoronto.ca
• [gmx-users] Hessian matrix calculation   Collins Nganou
  • [gmx-users] Hessian matrix calculation   David van der Spoel
• [gmx-users] 1-4 Scaling Problem?   ANINDITA GAYEN
  • [gmx-users] 1-4 Scaling Problem?   Xavier Periole
• [gmx-users] g_sas and PBC   Gurpreet Singh
  • [gmx-users] g_sas and PBC   David van der Spoel
• [gmx-users] mutation FE calculation with oplsaa   Qiang Li
  • [gmx-users] mutation FE calculation with oplsaa   David Mobley
• [gmx-users] Force constant defined in flexible TIP3P water model   Changsun Eun
• [gmx-users] g_sas and PBC   Gurpreet Singh
  • [gmx-users] g_sas and PBC   David van der Spoel
• [gmx-users] amber ports in gromas - bond length warning   N-J.M. Macaluso
  • [gmx-users] amber ports in gromas - bond length warning   David van der Spoel
    • [gmx-users] amber ports in gromas - bond length warning   Yang Ye
      • [gmx-users] amber ports in gromas - bond length warning   N-J.M. Macaluso
• [gmx-users] coordinates of the mass center   yren at home.ipe.ac.cn
  • [gmx-users] coordinates of the mass center   Mark Abraham
    • [gmx-users] coordinates of the mass center   Berk Hess
      • [gmx-users] coordinates of the mass center   Mark Abraham
• [gmx-users] can we regenerate *.trr by *.log??   Anamika Awasthi
  • [gmx-users] can we regenerate *.trr by *.log??   Mark Abraham
• [gmx-users] Max #atoms in a charge group: 68 > 64   Samuel Coulbourn Flores 花山
  • [gmx-users] Max #atoms in a charge group: 68 > 64   Mark Abraham
    • [gmx-users] Max #atoms in a charge group: 68 > 64   Samuel Coulbourn Flores 花山
      • [gmx-users] Max #atoms in a charge group: 68 > 64   Justin A. Lemkul
      • [gmx-users] Max #atoms in a charge group: 68 > 64   Mark Abraham
      • [gmx-users] Max #atoms in a charge group: 68 > 64   Berk Hess
• [gmx-users] pdb file error   hhhh huan
  • [gmx-users] pdb file error   Justin A. Lemkul
  • [gmx-users] pdb file error   Mark Abraham
• [gmx-users] Fatal error receive by running Hessian matrix   Collins Nganou
  • [gmx-users] Fatal error receive by running Hessian matrix   David van der Spoel
• [gmx-users] How to use tabulated potentials to do coarse grained simulation?   Catfish SUN
  • [gmx-users] How to use tabulated potentials to do coarse grained simulation?   Berk Hess
• [gmx-users] a problem about the minimization   zhuliang at tju.edu.cn
  • [gmx-users] a problem about the minimization   Mark Abraham
• [gmx-users] 1-4 Scaling Problem?   Chris Neale
  • [gmx-users] 1-4 Scaling Problem?   Marc F. Lensink
• [gmx-users] Re:Re: 1-4 scaling problem?   ANINDITA GAYEN
• [gmx-users] 1-4 scaling problem?   Chris Neale
• [gmx-users] noe restraints and g_disre problems   N-J.M. Macaluso
• [gmx-users] 1-4 Scaling Problem?   Chris Neale
• [gmx-users] Question about binding free energy calculation   Ming
  • [gmx-users] Question about binding free energy calculation   Mark Abraham
• [gmx-users] dihedral parameters in oplsaa   friendli
  • [gmx-users] dihedral parameters in oplsaa   David van der Spoel
  • [gmx-users] dihedral parameters in oplsaa   Mark Abraham
• [gmx-users] dihedral parameters in oplsaa   friendli
  • [gmx-users] dihedral parameters in oplsaa   David van der Spoel
• [gmx-users] Spice up your mobile   chandrabhanseniya at gmail.com
• [gmx-users] dihedral parameters in oplsaa   friendli
  • [gmx-users] dihedral parameters in oplsaa   David van der Spoel
• [gmx-users] bootrstrap complains about serial nr   Erik Marklund
  • [gmx-users] bootrstrap complains about serial nr   David van der Spoel
• [gmx-users] How to use tabulated potentials to do coarse grained simulation?("Segmentation fault" when running mdrun.)   Catfish SUN
  • [gmx-users] How to use tabulated potentials to do coarse grained simulation?("Segmentation fault   Berk Hess
• [gmx-users] Re: tip3p.gro   servaas michielssens
• [gmx-users] creating a box from a single molecule   Peyman Yamin
  • [gmx-users] creating a box from a single molecule   Tsjerk Wassenaar
• [gmx-users] pressure problems   Marcelo Müller
• [gmx-users] the pdb file => input / output error   Chih-Ying Lin
  • [gmx-users] the pdb file => input / output error   Justin A. Lemkul
    • [gmx-users] Killing mdrun based on execution time   Samuel Coulbourn Flores 花山
      • [gmx-users] Killing mdrun based on execution time   Mark Abraham
      • [gmx-users] Killing mdrun based on execution time   David van der Spoel
    • [gmx-users] the pdb file => input / output error   Tsjerk Wassenaar
• [gmx-users] Re: gmx-users Digest, Vol 49, Issue 93   friendli
• [gmx-users] Fw: Re: 1-4 scaling problem?   ANINDITA GAYEN
• [gmx-users] Protein out of box   Alif M Latif
  • [gmx-users] Protein out of box   Mark Abraham
• [gmx-users] dihedral parameters in oplsaa   friendli
  • [gmx-users] dihedral parameters in oplsaa   David van der Spoel
• [gmx-users] Script: Loading .ndx files into PyMol   Martin Höfling
• [gmx-users] Calculating bond energy   Yulia Einav
• [gmx-users] no of interacting water molecules with solvated protein atoms   Anupam Nath Jha
  • [gmx-users] no of interacting water molecules with solvated protein atoms   Mark Abraham
    • [gmx-users] no of interacting water molecules with solvated protein atoms   Erik Marklund
• [gmx-users] Hessian matrix calculation   Collins Nganou
• [gmx-users] Crashing NPT run, 1.5 ns   JMandumpal
• [gmx-users] Calculating bond energy   Yulia Einav
  • [gmx-users] Calculating bond energy   Mark Abraham
    • [gmx-users] Calculating bond energy   Yulia Einav
      • [gmx-users] Calculating bond energy   Erik Marklund
      • [gmx-users] Calculating bond energy   Mark Abraham
      • [gmx-users] Calculating bond energy   Yulia Einav
• [gmx-users] input/output error when running Hessian matrix in double precision   Collins Nganou
  • [gmx-users] input/output error when running Hessian matrix in double precision   Justin A. Lemkul
• [gmx-users] Re: Problem of lipid-protein simulation   chris.neale at utoronto.ca
• [gmx-users] Problem of lipid-protein simulation   Chris Neale
  • [gmx-users] Problem of lipid-protein simulation   Mark Abraham
• [gmx-users] Fwd: Problem of lipid-protein Simulation   Xavier Periole
• [gmx-users] Understanding of production run with same parameters in md.mdp file   minnale
  • [gmx-users] Understanding of production run with same parameters in md.mdp file   Florian Haberl
• [gmx-users] Re: bilayer area now gradually increasing!!!!!!!!!!!!!!!!   chris.neale at utoronto.ca
• [gmx-users] Understanding of production run with same parameters in md.mdp file   minnale
  • [gmx-users] Understanding of production run with same parameters in md.mdp file   Mark Abraham
• [gmx-users] bilayer area gradually increasing!!!!!   ANINDITA GAYEN
  • [gmx-users] bilayer area gradually increasing!!!!!   Marc F. Lensink
• [gmx-users] Constraints only on Backbone   Bjoern Olausson
  • [gmx-users] Constraints only on Backbone   Justin A. Lemkul
• [gmx-users] calculation of eigenfrequency   Collins Nganou
• [gmx-users] Mdrun kills all other（single CPU）mdrun processes started by same father process?   Peter Mueller
  • [gmx-users] Mdrun kills all other(single CPU)mdrun processes started by same father process?   David van der Spoel
    • [gmx-users] Mdrun kills all other(single CPU)mdrun processes started by same father process?   Berk Hess
• Fwd: Re: [gmx-users] Constraints only on Backbone   Justin A. Lemkul
• [gmx-users] Generate velocity frame   Collins Nganou
  • [gmx-users] Generate velocity frame   Justin A. Lemkul
• [gmx-users] simulating chemical reactions   gfunch
  • [gmx-users] simulating chemical reactions   Mark Abraham
    • [gmx-users] Atom names mismatch   George Abadir
• [gmx-users] lipid gel phase simulation model building   Carsten Selle
  • [gmx-users] lipid gel phase simulation model building   Justin A. Lemkul
  • [gmx-users] lipid gel phase simulation model building   Marc F. Lensink
• [gmx-users] FEP doubts   Diego Nolasco
  • [gmx-users] FEP doubts   David Mobley
• [gmx-users] lipid gel phase simulation model building   chris.neale at utoronto.ca
• [gmx-users] Increase number of decimal places in force.xvg (g_traj)   Lee-Ping Wang
• [gmx-users] Grid statement in md.log   sapna sarupria
  • [gmx-users] Grid statement in md.log   David van der Spoel
  • [gmx-users] Re: Grid statement in md.log   sapna sarupria
    • [gmx-users] Re: Grid statement in md.log   David van der Spoel
• [gmx-users] inconsistency in .pdb files   h a
  • [gmx-users] inconsistency in .pdb files   Justin A. Lemkul
  • [gmx-users] inconsistency in .pdb files   Mark Abraham
• [gmx-users] Is Gay-Berne potential available in GROMACS?   zhenlong li
• [gmx-users] mutation FE calculation with oplsaa   friendli
• [gmx-users] Atom names mismatch   chris.neale at utoronto.ca
  • [gmx-users] Atom names mismatch   George Abadir
    • [gmx-users] Atom names mismatch   Mark Abraham
      • [gmx-users] Atom names mismatch   George Abadir
      • [gmx-users] Atom names mismatch   George Abadir
      • [gmx-users] Atom names mismatch   Mark Abraham
      • [gmx-users] Atom names mismatch   George Abadir
      • [gmx-users] Atom names mismatch - PyMol retain order   Martin Höfling
      • [gmx-users] Atom names mismatch - PyMol retain order   Erik Marklund
      • [gmx-users] Atom names mismatch - PyMol retain order   George Abadir
      • [gmx-users] Atom names mismatch - PyMol retain order   Martin Höfling
      • [gmx-users] Atom names mismatch - PyMol retain order   Mark Abraham
• [gmx-users] how to fill water molecules only in required place   Santan William
  • [gmx-users] how to fill water molecules only in required place   Santan William
  • [gmx-users] how to fill water molecules only in required place   David van der Spoel
• [gmx-users] Re: Atom names mismatch   Low Soo Mei
  • [gmx-users] Re: Atom names mismatch   George Abadir
• [gmx-users] problems to get gromacs running on cluster   Bernhard Knapp
  • [gmx-users] problems to get gromacs running on cluster   Florian Haberl
• [gmx-users] lipid gel phase simulation model building   Carsten Selle
• [gmx-users] Re: Thanks a lot / information   Justin A. Lemkul
• [gmx-users] Pdb2gmx and tip4p dummy atom position   TJ Piggot
  • [gmx-users] Pdb2gmx and tip4p dummy atom position   David van der Spoel
    • [gmx-users] Pdb2gmx and tip4p dummy atom position   TJ Piggot
• [gmx-users] lipid gel phase simulation model building   chris.neale at utoronto.ca
• [gmx-users] Local pressure profiles   Philip Shushkov
  • [gmx-users] Local pressure profiles   David van der Spoel
• [gmx-users] Green-Cubo relation   Vitaly Chaban

Last message date: Sat May 31 15:25:58 CEST 2008
Archived on: Thu Nov 14 12:04:34 CET 2013

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