October 2007 Archives by thread

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Starting: Mon Oct 1 00:08:33 CEST 2007
Ending: Wed Oct 31 22:50:50 CET 2007
Messages: 551

• Patchfile? Re: [gmx-users] gromacs 3.3.2   Allen Smith
  • Patchfile? Re: [gmx-users] gromacs 3.3.2   David van der Spoel
• [gmx-users] Reading XTC files from fortran90   Jones de Andrade
  • [gmx-users] Reading XTC files from fortran90   Tsjerk Wassenaar
  • [gmx-users] Reading XTC files from fortran90   Mark Abraham
    • [gmx-users] Reading XTC files from fortran90   Jones de Andrade
      • [gmx-users] Reading XTC files from fortran90   Mark Abraham
      • [gmx-users] Reading XTC files from fortran90   Jones de Andrade
      • [gmx-users] g_lie problem   Blaise Mathias-Costa
      • [gmx-users] g_lie problem   Mark Abraham
      • [gmx-users] mdrun error after 2.6nS   Blaise Mathias-Costa
      • [gmx-users] mdrun error after 2.6nS   Tsjerk Wassenaar
      • [gmx-users] mdrun error after 2.6nS   Mark Abraham
      • [gmx-users] mdrun error after 2.6nS   Blaise Mathias-Costa
      • [gmx-users] mdrun error after 2.6nS   Tsjerk Wassenaar
      • [gmx-users] mdrun error after 2.6nS   Mark Abraham
      • [gmx-users] Reading XTC files from fortran90   Tsjerk Wassenaar
• [gmx-users] Reading XTC files from fortran90   Mark Abraham
• [gmx-users] MPIRUN problem when switched to 8 np (searched the list)   Florian Haberl
  • [gmx-users] MPIRUN problem when switched to 8 np (searched the list)   liu xin
    • [gmx-users] MPIRUN problem when switched to 8 np (searched the list)   Florian Haberl
• [gmx-users] MPIRUN problem when switched to 8 np (searched the list)   Mark Abraham
  • [gmx-users] MPIRUN problem when switched to 8 np (searched the list)   liu xin
• [gmx-users] Help for simulating the metalcluster   Utpal Sarkar
  • [gmx-users] Help for simulating the metalcluster   Vasilii Artyukhov
  • [gmx-users] Help for simulating the metalcluster   Mark Abraham
• [gmx-users] g_cluster questions   andrea carotti
  • [gmx-users] g_cluster questions   Erik Marklund
• [gmx-users] Distance restraint   jacopo.sgrignani at unifi.it
• [gmx-users] Nucleic Acid Simulations with Gromacs   Monika Sharma
  • [gmx-users] Nucleic Acid Simulations with Gromacs   gigo at poczta.ibb.waw.pl
    • [gmx-users] Nucleic Acid Simulations with Gromacs   Yang Ye
      • [gmx-users] Nucleic Acid Simulations with Gromacs   Monika Sharma
  • [gmx-users] Nucleic Acid Simulations with Gromacs   Yang Ye
  • [gmx-users] Nucleic Acid Simulations with Gromacs   Anna Reymer
• [gmx-users] Re: ANTECHAMBER & GAFF   David Mobley
• [gmx-users] Is there a test set for GROMACS 3.3.1 ?   maria goranovic
  • [gmx-users] Is there a test set for GROMACS 3.3.1 ?   David van der Spoel
• [gmx-users] g_rms   andrea carotti
  • [gmx-users] g_rms   Mark Abraham
• [gmx-users] g_order in GROMACS 3.3.2 and 3.3.1   林揚善
  • [gmx-users] g_order in GROMACS 3.3.2 and 3.3.1   Justin A. Lemkul
• [gmx-users] Re: Re: Is there a test set for GROMACS 3.3.1 ? (David van der Spoel)   maria goranovic
  • [gmx-users] Re: Re: Is there a test set for GROMACS 3.3.1 ? (David van der Spoel)   David van der Spoel
• [gmx-users] g_rms   andrea carotti
  • [gmx-users] g_rms   Mark Abraham
• [gmx-users] g_rms   andrea carotti
  • [gmx-users] g_rms   Mark Abraham
• [gmx-users] g_rms   andrea carotti
  • [gmx-users] g_rms   Mark Abraham
• [gmx-users] Re: Is there a test set for GROMACS 3.3.1 ?   maria goranovic
  • [gmx-users] Re: Is there a test set for GROMACS 3.3.1 ?   David van der Spoel
• [gmx-users] getting a good .gro file from a pdb file while the topology is ready   maria goranovic
  • [gmx-users] getting a good .gro file from a pdb file while the topology is ready   Allen Smith
    • [gmx-users] getting a good .gro file from a pdb file while the topology is ready   Mark Abraham
      • [gmx-users] getting a good .gro file from a pdb file while the topology is ready   Allen Smith
      • [gmx-users] getting a good .gro file from a pdb file while the topology is ready   Allen Smith
      • [gmx-users] getting a good .gro file from a pdb file while the topology is ready   Mark Abraham
      • [gmx-users] getting a good .gro file from a pdb file while the topology is ready   Tsjerk Wassenaar
  • [gmx-users] getting a good .gro file from a pdb file while the topology is ready   Mark Abraham
  • [gmx-users] getting a good .gro file from a pdb file while the topology is ready   Xavier Periole
• [gmx-users] grompp not recognizing mdp file parameters   toma0052
  • [gmx-users] grompp not recognizing mdp file parameters   David van der Spoel
• [gmx-users] protein in membrane   mahbubeh zarrabi
  • [gmx-users] protein in membrane   Itamar Kass
• [gmx-users] Re: getting a good .gro file from a pdb file while the topology is ready   maria goranovic
  • [gmx-users] Re: getting a good .gro file from a pdb file while thetopology is ready   Justin A. Lemkul
    • [gmx-users] Re: getting a good .gro file from a pdb file while thetopology is ready   Allen Smith
• [gmx-users] (no) superlinear Scaling on Opterons   Jens Krueger
  • [gmx-users] (no) superlinear Scaling on Opterons   David van der Spoel
• [gmx-users] human readable input for g_covar   mdaf at sina.com
  • [gmx-users] human readable input for g_covar   Tsjerk Wassenaar
• [gmx-users] remove periodic boundary in tpr file   tangxuan
  • [gmx-users] remove periodic boundary in tpr file   Tsjerk Wassenaar
    • [gmx-users] remove periodic boundary in tpr file   tangxuan
      • [gmx-users] remove periodic boundary in tpr file   Tsjerk Wassenaar
• [gmx-users] water molecules suffer from very long bond lengths   sarbani chattopadhyay
• [gmx-users] GROMACS-3.3.2 on BG/L   Ivano Eberini
• [gmx-users] xpm to ascii   andrea carotti
• [gmx-users] fix for range checking errors in parallel double precision mdrun   Berk Hess
• [gmx-users] g_order atom distance warning   Stephen M. Dutz
• [gmx-users] lot of pdb files written during minimization without asking for them ?   maria goranovic
  • [gmx-users] lot of pdb files written during minimization withoutasking for them ?   Dallas B. Warren
  • [gmx-users] lot of pdb files written during minimization without asking for them ?   Mark Abraham
• [gmx-users] running gromacs in parallel, and with nice levels   maria goranovic
  • [gmx-users] running gromacs in parallel, and with nice levels   Carsten Kutzner
    • [gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory   Tanping Li
      • [gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory   Tsjerk Wassenaar
      • [gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory   Tanping Li
      • [gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory   David van der Spoel
  • [gmx-users] running gromacs in parallel, and with nice levels   Yang Ye
• [gmx-users] Surface Tension units   priyanka srivastava
  • [gmx-users] Surface Tension units   Pedro Alexandre de Araújo Gomes Lapido Loureiro
• [gmx-users] Development of .ITP or .TOP file for non-standard molecules   Michelle Hyers
  • [gmx-users] Development of .ITP or .TOP file for non-standard molecules   David van der Spoel
    • [gmx-users] gmx continuation run   vijaya subramanian
      • [gmx-users] gmx continuation run   Mark Abraham
      • [gmx-users] gmx continuation run   Tsjerk Wassenaar
    • [gmx-users] IO problem on Cray XT3 MPP   vijaya subramanian
      • [gmx-users] IO problem on Cray XT3 MPP   David van der Spoel
      • [gmx-users] IO problem on Cray XT3 MPP   Erik Lindahl
• [gmx-users] Re:Re: g_order in GROMACS 3.3.2 and 3.3.1   林揚善
  • [gmx-users] Re:Re: g_order in GROMACS 3.3.2 and 3.3.1   Justin A. Lemkul
• [gmx-users] How to calculate the average distance or energy between two residues?   MoJie Duan
• [gmx-users] How to calculate the average distance or energy between two residues?   Yang Ye
• [gmx-users] Re: g_order in GROMACS 3.3.2 and 3.3.1   Stephen M. Dutz
• [gmx-users] simulation popc   pragya chohan
  • [gmx-users] simulation popc   Itamar Kass
    • [gmx-users] simulation popc   Zoltan Varga
• [gmx-users] genbox using tip5p water results in too few number of water molecules   JW Feng
  • [gmx-users] genbox using tip5p water results in too few number of water molecules   David van der Spoel
    • [gmx-users] genbox using tip5p water results in too few number of water molecules   JW Feng
      • [gmx-users] genbox using tip5p water results in too few number of water molecules   David van der Spoel
• [gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory   van Bemmelen
  • [gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory   Tanping Li
• [gmx-users] getting a good .gro file from a pdb file while the topology is ready   van Bemmelen
• [gmx-users] 3.3.2 mdrun problems   Mitchell Stanton-Cook
• [gmx-users] itp files   mahbubeh zarrabi
• [gmx-users] restart md from the point it had stopped   sarbani chattopadhyay
  • [gmx-users] restart md from the point it had stopped   Tsjerk Wassenaar
    • [gmx-users] restart md from the point it had stopped   Diego Enry
      • [gmx-users] restart md from the point it had stopped   Tsjerk Wassenaar
  • [gmx-users] restart md from the point it had stopped   Mark Abraham
    • [gmx-users] restart md from the point it had stopped   Diego Enry
• [gmx-users] only one cpu "works" in my linux cluster   liu xin
• [gmx-users] only one cpu "works" in my linux cluster   Alan Dodd
  • [gmx-users] only one cpu "works" in my linux cluster   liu xin
• [gmx-users] restart md from the point it had stopped   Diego Enry
• [gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory   van Bemmelen
• [gmx-users] Fwd: project 4   Russell Green
• [gmx-users] Wall Potential   Huey Ling Tan
• [gmx-users] No scale up beyond 4 processors for 240000 atom system   maria goranovic
  • [gmx-users] No scale up beyond 4 processors for 240000 atom system   Berk Hess
    • [gmx-users] No scale up beyond 4 processors for 240000 atom system   Christian Burisch
      • [gmx-users] No scale up beyond 4 processors for 240000 atom system   Diego Enry
• [gmx-users] only one cpu "works" in my linux cluster   Alan Dodd
  • [gmx-users] only one cpu "works" in my linux cluster   liu xin
• [gmx-users] limit on energygrp_table   Adrien Leygue
  • [gmx-users] limit on energygrp_table   Berk Hess
    • [gmx-users] limit on energygrp_table   Adrien Leygue
• [gmx-users] solubility of PVME in TIP5P   JW Feng
• [gmx-users] 3.3.2 Error when using the mpi option   Triguero, Luciano O
  • [gmx-users] 3.3.2 Error when using the mpi option   Erik Lindahl
    • [gmx-users] 3.3.2 Error when using the mpi option   Triguero, Luciano O
• [gmx-users] simulating Hexadecane in water   Adam Fraser
• [gmx-users] grompp error   pragya chohan
  • [gmx-users] grompp error   Diego Enry
• [gmx-users] grompp error   chris.neale at utoronto.ca
• [gmx-users] grompp error   chris.neale at utoronto.ca
• [gmx-users] Criteria and Energy Conservation   gtroiano at if.usp.br
  • [gmx-users] Criteria and Energy Conservation   David van der Spoel
    • [gmx-users] Criteria and Energy Conservation   gtroiano at if.usp.br
      • [gmx-users] Criteria and Energy Conservation   David van der Spoel
      • [gmx-users] Criteria and Energy Conservation   gtroiano at if.usp.br
• [gmx-users] Re: 3.3.2 trjconv -ur compact -pbc whole problem   JW Feng
  • [gmx-users] Re: 3.3.2 trjconv -ur compact -pbc whole problem   JW Feng
• [gmx-users] How to change the box size during simuation   WU Yanbin
  • [gmx-users] How to change the box size during simuation   Berk Hess
• [gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens   Haining Liu
  • [gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens   Tsjerk Wassenaar
    • [gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens   Haining Liu
      • [gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens   Tsjerk Wassenaar
• [gmx-users] anisotropic pressure coupling for temperature annealing   Q733
  • [gmx-users] anisotropic pressure coupling for temperature annealing   Mark Abraham
• [gmx-users] How to change the box size during simuation   Alan Dodd
• [gmx-users] anisotropic pressure coupling for temperature annealing   Alan Dodd
• [gmx-users] What is this warning on running grompp ? WARNING 1 [file md-new.mdp, line unknown]   maria goranovic
• [gmx-users] xtc error   luciano.pgomes
  • [gmx-users] xtc error   David van der Spoel
• [gmx-users] simulating hydrocarbons in water   Adam Fraser
  • [gmx-users] simulating hydrocarbons in water   David van der Spoel
    • [gmx-users] simulating hydrocarbons in water   Adam Fraser
      • [gmx-users] simulating hydrocarbons in water   TJ Piggot
      • [gmx-users] simulating hydrocarbons in water   Adam Fraser
      • [gmx-users] simulating hydrocarbons in water   David van der Spoel
      • [gmx-users] simulating hydrocarbons in water   Adam Fraser
• [gmx-users] xtc error   luciano.pgomes
  • [gmx-users] xtc error   David van der Spoel
• [gmx-users] Problems prior to running lipid-protein simulation   adak Nasiripour
  • [gmx-users] Problems prior to running lipid-protein simulation   Dallas B. Warren
• [gmx-users] Re:gmx-users Digest, Vol 42, Issue 36   luciano.pgomes
• [gmx-users] Re: Problems prior to running lipid-protein simulation   Bruce Milne
  • [gmx-users] Re: Problems prior to running lipid-protein simulation   Mark Abraham
• [gmx-users] Dummies usage doubts   Jones de Andrade
  • [gmx-users] Dummies usage doubts   David van der Spoel
    • [gmx-users] Dummies usage doubts   Jones de Andrade
      • [gmx-users] Dummies usage doubts   David van der Spoel
      • [gmx-users] Dummies usage doubts   Jones de Andrade
      • [gmx-users] Dummies usage doubts   David van der Spoel
      • [gmx-users] 3.3.2 volume   Yin Jian
      • [gmx-users] 3.3.2 volume   Christian Burisch
      • [gmx-users] 3.3.2 volume   Yin Jian
      • [gmx-users] 3.3.2 volume   Mark Abraham
      • [gmx-users] 3.3.2 volume   Yin Jian
      • [gmx-users] 3.3.2 volume   Mark Abraham
      • [gmx-users] Dummies usage doubts   David van der Spoel
      • [gmx-users] Dummies usage doubts   Jones de Andrade
      • [gmx-users] Dummies usage doubts   David van der Spoel
      • [gmx-users] g_sas by 3.3.1 and 3.3.2 give different results   Yin Jian
      • [gmx-users] g_sas by 3.3.1 and 3.3.2 give different results   Mark Abraham
      • [gmx-users] g_sas by 3.3.1 and 3.3.2 give different results   Yin Jian
      • [gmx-users] g_sas by 3.3.1 and 3.3.2 give different results   David van der Spoel
      • [gmx-users] g_sas by 3.3.1 and 3.3.2 give different results   Yin Jian
      • [gmx-users] g_sas by 3.3.1 and 3.3.2 give different results   Yin Jian
      • [gmx-users] Dummies usage doubts   Jones de Andrade
      • [gmx-users] cut-offs in j. kerrigans drug/enzyme tutorial   merc mertens
      • [gmx-users] cut-offs in j. kerrigans drug/enzyme tutorial   Mark Abraham
      • [gmx-users] Dummies usage doubts   Jones de Andrade
• [gmx-users] HC atomtype   mahbubeh zarrabi
  • [gmx-users] HC atomtype   Mark Abraham
    • [gmx-users] HC atomtype   mahbubeh zarrabi
      • [gmx-users] HC atomtype   Mark Abraham
• [gmx-users] Calculating the energy of one molecule in the multi-molecule system   shibalagu
  • [gmx-users] Calculating the energy of one molecule in the multi-molecule system   Xavier Periole
  • [gmx-users] Calculating the energy of one molecule in themulti-molecule system   Yin Jian
• [gmx-users] Re: Problems prior to running lipid-protein simulation   Bruce Milne
• [gmx-users] non-existent angles found from trajectory g_angle   Sampo Karkola
  • [gmx-users] non-existent angles found from trajectory g_angle   Mark Abraham
    • [gmx-users] non-existent angles found from trajectory g_angle   Sampo Karkola
      • [gmx-users] non-existent angles found from trajectory g_angle   Sampo Karkola
      • [gmx-users] non-existent angles found from trajectory g_angle   Mark Abraham
      • [gmx-users] non-existent angles found from trajectory g_angle   Sampo Karkola
• [gmx-users] t-couple warning   JW Feng
  • [gmx-users] t-couple warning   Justin A. Lemkul
    • [gmx-users] t-couple warning   Mark Abraham
    • [gmx-users] t-couple warning   JW Feng
• [gmx-users] Correcting for box jumps in pdo file   bmmothan at ucalgary.ca
• [gmx-users] Compiling GROMACS with FORTRAN?   Ivano Eberini
  • [gmx-users] Compiling GROMACS with FORTRAN?   David van der Spoel
    • [gmx-users] Compiling GROMACS with FORTRAN?   Ivano Eberini
• [gmx-users] Constraining to fixed position   "Martin Höfling"
  • *** GMX Spamverdacht *** [gmx-users] Constraining to fixed position   "Martin Höfling"
• [gmx-users] Calculating the energy of one molecule in the   Li Zhenhai
• [gmx-users] (no subject)   sarbani chattopadhyay
  • [gmx-users] (no subject)   Carsten Kutzner
• [gmx-users] Re: gmx-users Digest, Vol 42, Issue 47   Li Zhenhai
• [gmx-users] stuck   Adam Fraser
  • [gmx-users] stuck   Mark Abraham
• [gmx-users] Fatal error   Mauro Puppett
  • [gmx-users] Fatal error   Mark Abraham
• [gmx-users] tabulated potential - why table length is rc+1nm   Nickle Fan
  • [gmx-users] tabulated potential - why table length is rc+1nm   Erik Lindahl
• [gmx-users] Amber to Gromacs   Dechang Li
• [gmx-users] Energy of each composition   chiloo Laohpongspaisan
  • [gmx-users] Energy of each composition   Mark Abraham
• [gmx-users] Re: gmx-users Digest, Vol 42, Issue 50   Li Zhenhai
• [gmx-users] Re: gmx-users Digest, Vol 42, Issue 50   chiloo Laohpongspaisan
• [gmx-users] ngmx error messages   Sagittarius
  • [gmx-users] ngmx error messages   David van der Spoel
    • [gmx-users] ngmx error messages   Sagittarius
      • [gmx-users] ngmx error messages   David van der Spoel
      • [gmx-users] ngmx error messages   Justin A. Lemkul
      • [gmx-users] ngmx error messages   Sagittarius
      • [gmx-users] ngmx error messages   Erik Lindahl
• [gmx-users] Re: Amber to Gromacs   Vojtěch Spiwok
• [gmx-users] Designing a topology file: bonded/non-bonded mess   Frankie Montenegro
  • [gmx-users] Designing a topology file: bonded/non-bonded mess   David van der Spoel
    • [gmx-users] Designing a topology file: bonded/non-bonded mess   Frankie Montenegro
      • [gmx-users] Designing a topology file: bonded/non-bonded mess   David van der Spoel
• [gmx-users] the comm_mode   Dechang Li
  • [gmx-users] the comm_mode   David van der Spoel
• [gmx-users] the comm_mode   Yang Ye
• [gmx-users] the comm_mode   OZGE ENGIN
• [gmx-users] Tool for visualizing disulphide bonds   OZGE ENGIN
• [gmx-users] the comm_mode   Yang Ye
• [gmx-users] Tool for visualizing disulphide bonds   van Bemmelen
  • [gmx-users] Tool for visualizing disulphide bonds   Yang Ye
    • [gmx-users] Tool for visualizing disulphide bonds   Erik Lindahl
• [gmx-users] the comm_mode   OZGE ENGIN
  • [gmx-users] the comm_mode   Yang Ye
• [gmx-users] errores during compilation of GROMACS 3.3.2   Itamar Kass
  • [gmx-users] errores during compilation of GROMACS 3.3.2   Mark Abraham
  • [gmx-users] errores during compilation of GROMACS 3.3.2   Erik Lindahl
    • [gmx-users] errores during compilation of GROMACS 3.3.2   Itamar Kass
      • [gmx-users] errores during compilation of GROMACS 3.3.2   Erik Lindahl
      • [gmx-users] errores during compilation of GROMACS 3.3.2   Itamar Kass
      • [gmx-users] errores during compilation of GROMACS 3.3.2   Erik Lindahl
      • [gmx-users] errores during compilation of GROMACS 3.3.2   Mark Abraham
• [gmx-users] is there any size limit for simulation in gromacs   Anupam Nath Jha
  • [gmx-users] is there any size limit for simulation in gromacs   Tsjerk Wassenaar
• [gmx-users] Visualizing non-rectangular boxes   Ignacio Fernández Galván
  • [gmx-users] Visualizing non-rectangular boxes   sebastien santini
    • [gmx-users] Visualizing non-rectangular boxes   Ignacio Fernández Galván
  • [gmx-users] Rerefence on Berendsen vs Nose-Hoover   Jochen Hub
• [gmx-users] Visualizing non-rectangular boxes   chris.neale at utoronto.ca
  • [gmx-users] Visualizing non-rectangular boxes   Ignacio Fernández Galván
• [gmx-users] Rerefence on Berendsen vs. Nose-Hoover   Jochen Hub
  • [gmx-users] Rerefence on Berendsen vs. Nose-Hoover   Vasilii Artyukhov
• [gmx-users] Visualizing non-rectangular boxes   chris.neale at utoronto.ca
  • [gmx-users] Visualizing non-rectangular boxes   Ignacio Fernández Galván
• [gmx-users] Umbrella Sampling on peptides   Huey Ling Tan
• [gmx-users] Visualizing non-rectangular boxes   chris.neale at utoronto.ca
  • [gmx-users] Visualizing non-rectangular boxes   Ignacio Fernández Galván
    • [gmx-users] Visualizing non-rectangular boxes   David van der Spoel
• [gmx-users] Re: FEP problem   David Mobley
• [gmx-users] pbc problem   tangxuan
  • [gmx-users] pbc problem   Yang Ye
• [gmx-users] Postdoc position available (docking, free energy, drug design)   Erik Lindahl
• [gmx-users] Fwd: FEP calculations problem and posible BUG on GROMACS-3.3.2   Daniel Adriano Silva M
  • [gmx-users] Fwd: FEP calculations problem and posible BUG onGROMACS-3.3.2   Dallas B. Warren
• [gmx-users] Rerefence on Berendsen vs Nose-Hoover   John D. Chodera
  • [gmx-users] Rerefence on Berendsen vs Nose-Hoover   Jochen Hub
• [gmx-users] Re: Viewing Dodecahedral Systems   Sean Drummond
• [gmx-users] forcefield validation   Qin Shanshan
  • [gmx-users] forcefield validation   David Mobley
• [gmx-users] forcefield validation   Alan Dodd
• [gmx-users] weird problem on small molecules with triple bonds   David Mobley
  • [gmx-users] weird problem on small molecules with triple bonds   David van der Spoel
    • [gmx-users] weird problem on small molecules with triple bonds   David Mobley
      • [gmx-users] weird problem on small molecules with triple bonds   David van der Spoel
      • [gmx-users] weird problem on small molecules with triple bonds   David Mobley
• [gmx-users] pdb2gmx error - version 3.3.1   Justin A. Lemkul
  • [gmx-users] pdb2gmx error - version 3.3.1   Yang Ye
• [gmx-users] problem with linear molecules and suggested fix   David Mobley
  • [gmx-users] problem with linear molecules and suggested fix   Mark Abraham
• [gmx-users] GROMACS/G03 QM/MM   Bryan Op't Holt
• [gmx-users] density profile of bilayers   priyanka srivastava
  • [gmx-users] density profile of bilayers   Zoltan Varga
• [gmx-users] frequence from PCA eigenvalue   pascal.baillod at epfl.ch
• [gmx-users] g_hbond   Dechang Li
  • [gmx-users] g_hbond   Mark Abraham
• [gmx-users] forcefield validation   Qin Shanshan
  • [gmx-users] forcefield validation   Mark Abraham
  • [gmx-users] forcefield validation   David Mobley
• [gmx-users] forcefield validation   Qin Shanshan
• [gmx-users] Large VCM error for a POPC bilayer simulation   himanshu khandelia
• [gmx-users] forcefield validation   Qin Shanshan
  • [gmx-users] forcefield validation   David van der Spoel
  • [gmx-users] forcefield validation   David Mobley
• [gmx-users] Large VCM error for a POPC bilayer simulation : 2nd attempt   himanshu khandelia
  • [gmx-users] Large VCM error for a POPC bilayer simulation : 2nd attempt   Rainer Böckmann
    • [gmx-users] Large VCM error for a POPC bilayer simulation : 2nd attempt   himanshu khandelia
      • [gmx-users] Large VCM error for a POPC bilayer simulation : 2ndattempt   Justin A. Lemkul
      • [gmx-users] Large VCM error for a POPC bilayer simulation : 2ndattempt   himanshu khandelia
• [gmx-users] Long range electrostatic potential   Georgios Patargias
• [gmx-users] Long range electrostatic potential   van Bemmelen
  • [gmx-users] Long range electrostatic potential   Mark Abraham
    • [gmx-users] Long range electrostatic potential   Georgios Patargias
• [gmx-users] install problem on IBM powerpc AIX 5.3   liu xin
  • [gmx-users] install problem on IBM powerpc AIX 5.3   David van der Spoel
    • [gmx-users] install problem on IBM powerpc AIX 5.3   liu xin
      • [gmx-users] install problem on IBM powerpc AIX 5.3   Erik Lindahl
      • [gmx-users] install problem on IBM powerpc AIX 5.3   liu xin
      • [gmx-users] install problem on IBM powerpc AIX 5.3   Mark Abraham
      • [gmx-users] install problem on IBM powerpc AIX 5.3   Erik Lindahl
      • [gmx-users] install problem on IBM powerpc AIX 5.3   liu xin
      • [gmx-users] install problem on IBM powerpc AIX 5.3   Mark Abraham
      • [gmx-users] install problem on IBM powerpc AIX 5.3   liu xin
      • [gmx-users] install problem on IBM powerpc AIX 5.3   Mark Abraham
      • [gmx-users] install problem on IBM powerpc AIX 5.3   Mark Abraham
• [gmx-users] H- bond   emra Heshmati
  • [gmx-users] H- bond   Mark Abraham
• [gmx-users] Addition of ions in vacuum simulations   OZGE ENGIN
  • [gmx-users] Addition of ions in vacuum simulations   Mark Abraham
• [gmx-users] Addition of ions in vacuum simulations   OZGE ENGIN
  • [gmx-users] Addition of ions in vacuum simulations   Mark Abraham
    • [gmx-users] Addition of ions in vacuum simulations   Xavier Periole
  • [gmx-users] Addition of ions in vacuum simulations   David van der Spoel
• [gmx-users] qasi-harmonic entropy calculation   Naser, Md Abu
  • [gmx-users] qasi-harmonic entropy calculation   Pedro Alexandre de Araújo Gomes Lapido Loureiro
    • [gmx-users] qasi-harmonic entropy calculation   David van der Spoel
      • [gmx-users] qasi-harmonic entropy calculation   Naser, Md Abu
    • [gmx-users] qasi-harmonic entropy calculation   Naser, Md Abu
      • [gmx-users] qasi-harmonic entropy calculation   Pedro Alexandre de Araújo Gomes Lapido Loureiro
      • [gmx-users] qasi-harmonic entropy calculation   Naser, Md Abu
• [gmx-users] GROMETA - Gromacs with Metadynamics, and more   Carlo Camilloni
• [gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel   himanshu khandelia
  • [gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel   Mark Abraham
    • [gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel   himanshu khandelia
      • [gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel   Mark Abraham
  • [gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel   Xavier Periole
• [gmx-users] uneven distribution of water across the bilayer   Alok
  • [gmx-users] uneven distribution of water across the bilayer   Mark Abraham
    • [gmx-users] uneven distribution of water across the bilayer   Alok
• [gmx-users] 1-4 table size of 0 nm   Adrien Leygue
  • [gmx-users] 1-4 table size of 0 nm   Berk Hess
• [gmx-users] applying force and fixing atoms in gromacs   Adam Fraser
  • [gmx-users] applying force and fixing atoms in gromacs   Mark Abraham
    • [gmx-users] applying force and fixing atoms in gromacs   Adam Fraser
• [gmx-users] Pull code with runtype start   dtmirij
  • [gmx-users] Pull code with runtype start   Mark Abraham
    • [gmx-users] Pull code with runtype start   dtmirij
      • [gmx-users] Pull code with runtype start   Mark Abraham
      • [gmx-users] Pull code with runtype start   dtmirij
• [gmx-users] Using h-angles taking to much time   harpreet singh
  • [gmx-users] Using h-angles taking to much time   David van der Spoel
    • [gmx-users] Using h-angles taking to much time   harpreet singh
• [gmx-users] 1 out of 14 complex tests FAILED in GROMACS 3.3.1 installation dec+water   himanshu khandelia
  • [gmx-users] 1 out of 14 complex tests FAILED in GROMACS 3.3.1 installation dec+water   David van der Spoel
• [gmx-users] Postdoc position available (virtual reality, interactive simulations)   Marc Baaden
• [gmx-users] Concatenate .edr file   Qi Yan
  • [gmx-users] Concatenate .edr file   Marcelo Fabricio Masman
  • [gmx-users] Concatenate .edr file   Mark Abraham
• [gmx-users] solvate using genbox results in water in the center of the bilayer. How to edit pdb file contents in gromacs ?   maria goranovic
  • [gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ?   Alok
• [gmx-users] time constants for the Parrinello-Rahman/nose-hoover coupling   Hwankyu Lee
  • [gmx-users] time constants for the Parrinello-Rahman/nose-hoover coupling   Erik Lindahl
• [gmx-users] Qeury on freezing an atom with negatice co-ordinates   avinash kumar
  • [gmx-users] Qeury on freezing an atom with negatice co-ordinates   Mark Abraham
• [gmx-users] b-factor   tangxuan
  • [gmx-users] b-factor   Daniel Larsson
  • [gmx-users] b-factor   Steffen Wolf
  • [gmx-users] b-factor   Mark Abraham
• [gmx-users] gmxtest results: improper call in complex/acetonitrileRF   Bruce Ray
• [gmx-users] topolbuild: attempt at a Gromacs topology builder added to Gromacs user contributed software   Bruce Ray
• [gmx-users] frequence from PCA eigenvalue   pascal.baillod at epfl.ch
  • [gmx-users] frequence from PCA eigenvalue   Berk Hess
• [gmx-users] Problem in downloading source code   raja
  • [gmx-users] Problem in downloading source code   Mark Abraham
    • [gmx-users] Problem in downloading source code   raja
      • [gmx-users] Problem in downloading source code   Florian Haberl
      • [gmx-users] Problem in downloading source code   raja
• [gmx-users] Position restricted md   sarbani chattopadhyay
  • [gmx-users] Position restricted md   Mark Abraham
• [gmx-users] Position restricted md   sarbani chattopadhyay
  • [gmx-users] Position restricted md   Mark Abraham
• [gmx-users] Position restricted md   sarbani chattopadhyay
• [gmx-users] alpha Carbon-Aromatic ring hydrogen bond   sarbani chattopadhyay
  • [gmx-users] alpha Carbon-Aromatic ring hydrogen bond   Mark Abraham
  • [gmx-users] alpha Carbon-Aromatic ring hydrogen bond   Alok
• [gmx-users] problem in g_confrms   harpreet singh
  • [gmx-users] problem in g_confrms   Mark Abraham
• [gmx-users] entropy calaculted script??   xi zhao
  • [gmx-users] entropy calaculted script??   David van der Spoel
• [gmx-users] Position restricted md   Yang Ye
• [gmx-users] entropy calaculted script??   Yang Ye
• [gmx-users] g_rmsf and pbc   tangxuan
  • [gmx-users] g_rmsf and pbc   Mark Abraham
    • [gmx-users] g_rmsf and pbc   tangxuan
      • [gmx-users] g_rmsf and pbc   David van der Spoel
      • [gmx-users] g_rmsf and pbc   tangxuan
• [gmx-users] missing Ryckaert-Bell in 3.3.2 is now considered as ERROR?   Martin Höfling
  • [gmx-users] missing Ryckaert-Bell in 3.3.2 is now considered asERROR?   Berk Hess
• [gmx-users] Source code through email   raja
  • [gmx-users] Source code through email   Mark Abraham
• [gmx-users] make_ndx   sarbani chattopadhyay
  • [gmx-users] make_ndx   Mark Abraham
• [gmx-users] make_ndx   sarbani chattopadhyay
• [gmx-users] surface tension calculation in g_energy   Bo Zhou
  • [gmx-users] surface tension calculation in g_energy   David van der Spoel
• [gmx-users] reference for urea.itp   rzangi at att.net
  • [gmx-users] reference for urea.itp   David van der Spoel
• [gmx-users] reference for urea.itp   rzangi at att.net
  • [gmx-users] reference for urea.itp   David van der Spoel
• [gmx-users] g_energy has no bond entry when MD analysis   xi zhao
  • [gmx-users] g_energy has no bond entry when MD analysis   Mark Abraham
    • 回复： Re: [gmx-users] g_energy has no bond entry when MD analysis   xi zhao
• [gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ?   chris.neale at utoronto.ca
  • [gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ?   Alok
    • [gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ?   Mark Abraham
• [gmx-users] solvate using genbox results in water in the > centerofthe bilayer. How to edit pdb file contents in gromacs ?   chris.neale at utoronto.ca
  • [gmx-users] solvate using genbox results in water in the >centerofthe bilayer. How to edit pdb file contents in gromacs ?   Alok
• [gmx-users] No improvement in scaling on introducing flow control   himanshu khandelia
  • [gmx-users] No improvement in scaling on introducing flow control   Carsten Kutzner
    • [gmx-users] No improvement in scaling on introducing flow control   himanshu khandelia
      • [gmx-users] No improvement in scaling on introducing flow control   Carsten Kutzner
      • [gmx-users] No improvement in scaling on introducing flow control   David van der Spoel
      • [gmx-users] No improvement in scaling on introducing flow control   himanshu khandelia
      • [gmx-users] No improvement in scaling on introducing flow control   Carsten Kutzner
• [gmx-users] g_wham   Jose Javier Lopez Cascales
• [gmx-users] problems with opls_   hhhh huan
  • [gmx-users] problems with opls_   David van der Spoel
    • [gmx-users] problems with opls_   hhhh huan
      • [gmx-users] problems with opls_   TJ Piggot
      • [gmx-users] problems with opls_   Mark Abraham
• [gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ?   chris.neale at utoronto.ca
  • [gmx-users] solvate using genbox results in water in thecenterofthe bilayer. How to edit pdb file contents in gromacs ?   Alok
• [gmx-users] MSD near specific molecules   Jian Dai
• [gmx-users] queue up simulations   sarbani chattopadhyay
  • [gmx-users] queue up simulations   David van der Spoel
  • [gmx-users] queue up simulations   Vasilii Artyukhov
  • [gmx-users] queue up simulations   Mark Abraham
• [gmx-users] Fwd: trjconv help   sarbani chattopadhyay
• [gmx-users] Re: trjconv help   Mark Abraham
• [gmx-users] constraining two diff molecules removes LJ interaction?   Guilherme Menegon Arantes
  • [gmx-users] constraining two diff molecules removes LJ interaction?   Mark Abraham
• [gmx-users] Problem putting 2 identical peptide chains in a simulation box   Huey Ling Tan
  • [gmx-users] Problem putting 2 identical peptide chains in a simulation box   Justin A. Lemkul
  • [gmx-users] Problem putting 2 identical peptide chains in a simulation box   alokjain at iitk.ac.in
    • [gmx-users] Problem putting 2 identical peptide chains in a simulation box   Huey Ling Tan
      • [gmx-users] Problem putting 2 identical peptide chains in a simulation box   Mark Abraham
  • [gmx-users] Problem putting 2 identical peptide chains in a simulation box   Mark Abraham
• [gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ????   himanshu khandelia
  • [gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ????   Mark Abraham
    • [gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ????   himanshu khandelia
      • [gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ????   Mark Abraham
• [gmx-users] solvate using genbox results in water in thecenterofthe bilayer. How to edit pdb file contents in gromacs ?   chris.neale at utoronto.ca
  • [gmx-users] Removal of unwanted water from lipid bilayer after solvating the structure from genbox: problem and solution   Alok
• [gmx-users] PBC, lincs and bonds breaking   Paul Whitford
  • [gmx-users] PBC, lincs and bonds breaking   Mark Abraham
  • [gmx-users] PBC, lincs and bonds breaking   David van der Spoel
• [gmx-users] PBC, lincs and bonds breaking   Paul Whitford
• [gmx-users] NVT to NPT. Works on a single processor, does VT to NPT. Works on a single processor, does not work on 4 ????   chris.neale at utoronto.ca
• [gmx-users] thermodynamic integration   Argyrios Karatrantos
  • [gmx-users] thermodynamic integration   David Mobley
• [gmx-users] ascii Covariance matrix   Russell Green
  • [gmx-users] ascii Covariance matrix   Arneh Babakhani
• [gmx-users] angle between helices   Anupam Nath Jha
  • [gmx-users] angle between helices   Mark Abraham
    • [gmx-users] angle between helices   Marc F. Lensink
      • [gmx-users] angle between helices   David van der Spoel
      • [gmx-users] angle between helices   Marc F. Lensink
      • [gmx-users] angle between helices   Anupam Nath Jha
      • [gmx-users] angle between helices   Berk Hess
• [gmx-users] angle between helices   Alan Dodd
• [gmx-users] x2top problem   Patricia Gómez
• [gmx-users] Running Gromacs on the Grid Workshop 14.-15.11.   Atte Sillanpää
• [gmx-users] what do negative eigenvalues imply?   Chris Neale
  • [gmx-users] what do negative eigenvalues imply?   David van der Spoel
• [gmx-users] what do negative eigenvalues imply?   Chris Neale
• [gmx-users] mopac gcc g77 and x86_64   Andrey V. Golovin
• [gmx-users] GLYCAM (sugars) with TIP5P in GROMACS   JMandumpal
• [gmx-users] potential energy of only the protein   sarbani chattopadhyay
  • [gmx-users] potential energy of only the protein   David Mobley
  • [gmx-users] potential energy of only the protein   Mark Abraham
• [gmx-users] g_sas problem   tangxuan
  • [gmx-users] g_sas problem   David van der Spoel
    • [gmx-users] g_sas problem   tangxuan
      • [gmx-users] g_sas problem   Mark Abraham
      • [gmx-users] g_sas problem   tangxuan
      • [gmx-users] g_sas problem   David van der Spoel
• [gmx-users] Re: mopac gcc g77 and x86_64   Gerrit Groenhof
  • [gmx-users] Re: mopac gcc g77 and x86_64   Andrey V. Golovin
• [gmx-users] Gromacs on IBM cluster   Marius Retegan
  • [gmx-users] Gromacs on IBM cluster   David van der Spoel
    • [gmx-users] Gromacs on IBM cluster   Marius Retegan
      • [gmx-users] Gromacs on IBM cluster   David van der Spoel
      • [gmx-users] Gromacs on IBM cluster   Marius Retegan
• [gmx-users] langevin dynamics   Syma Khalid
  • [gmx-users] langevin dynamics   Mark Abraham
    • [gmx-users] langevin dynamics   Syma Khalid
      • [gmx-users] langevin dynamics   Georgios Patargias
      • [gmx-users] langevin dynamics   Mark Abraham
  • [gmx-users] langevin dynamics   David Mobley
  • [gmx-users] langevin dynamics   Berk Hess
• [gmx-users] GNU compilers   giordano mancini
  • [gmx-users] GNU compilers   David van der Spoel
    • [gmx-users] GNU compilers   giordano mancini
• [gmx-users] Exploding box after 55.5ns of simulation   JW Feng
  • [gmx-users] Exploding box after 55.5ns of simulation   Justin A. Lemkul
• [gmx-users] (no) superlinear Scaling on Opterons   Jens Krueger
• [gmx-users] grompp error for alamethicin   pragya chohan
  • [gmx-users] grompp error for alamethicin   Mark Abraham
• [gmx-users] g_rmsf Segmentation fault   Tommy Carstensen
  • [gmx-users] g_rmsf Segmentation fault   David van der Spoel
• [gmx-users] editconf -mead   marcos
  • [gmx-users] editconf -mead   Ran Friedman
    • [gmx-users] editconf -mead   marcos
• [gmx-users] quasiharmonic eigenvalue units / Schlitter entropy   Marcin Krol
  • [gmx-users] quasiharmonic eigenvalue units / Schlitter entropy   Ran Friedman, Biochemisches Inst.
• [gmx-users] bug energy - continuity md   Ricardo Gobato

Last message date: Wed Oct 31 22:50:50 CET 2007
Archived on: Thu Nov 14 12:03:58 CET 2013

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