May 2009 Archives by thread

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Starting: Fri May 1 02:04:04 CEST 2009
Ending: Sun May 31 21:51:49 CEST 2009
Messages: 731

• [gmx-users] Error by pdb2gmx   Justin A. Lemkul
  • [gmx-users] Error by pdb2gmx   Yanmei Song
  • [gmx-users] Error by pdb2gmx   Yanmei Song
    • [gmx-users] Error by pdb2gmx   Justin A. Lemkul
      • [gmx-users] Error by pdb2gmx   Mark Abraham
      • [gmx-users] Error by pdb2gmx   Yanmei Song
      • [gmx-users] Error by pdb2gmx   Mark Abraham
• [gmx-users] configuration does not change in minimization trajectory   heiko252 at web.de
  • [gmx-users] configuration does not change in minimization trajectory   Justin A. Lemkul
• [gmx-users] energy xvg file shows a large energy change from time step 0 to time step 0.2 ps   Pawan Kumar
• [gmx-users] Coarse graining for Benzene and related molecules   Xavier Periole
• [gmx-users] energy xvg file shows a large energy change from time step 0 to time step 0.2 ps   Justin A. Lemkul
• [gmx-users] buckingham and LJ   Matthew Watkins
• [gmx-users] position restrain Software inconsistency error: Some interactions seem to be assigned multiple times   Creighton Buie
  • [gmx-users] position restrain Software inconsistency error: Some interactions seem to be assigned multiple times   Mark Abraham
• Re: [gmx-users] configuration does not change in minimization trajectory   heiko252 at web.de
  • [gmx-users] configuration does not change in minimization trajectory   Justin A. Lemkul
• [gmx-users] Conjugate Gradient - Equations   Tsjerk Wassenaar
• [gmx-users] How to build a lipid bilayer in GROMACS?   Anirban Ghosh
  • [gmx-users] How to build a lipid bilayer in GROMACS?   Justin A. Lemkul
  • [gmx-users] How to build a lipid bilayer in GROMACS?   Jack Shultz
• [gmx-users] Reducing Size of Data   Jack Shultz
  • [gmx-users] Reducing Size of Data   Justin A. Lemkul
• [gmx-users] Replacement for G43b1 force field?   Anirban Ghosh
  • [gmx-users] Replacement for G43b1 force field?   Justin A. Lemkul
• [gmx-users] No targets specified and no makefile found   Stefano Meliga
  • [gmx-users] No targets specified and no makefile found   Justin A. Lemkul
• [gmx-users] Problem with energy min. in membrane tutorial   Ragnarok sdf
  • [gmx-users] Problem with energy min. in membrane tutorial   Justin A. Lemkul
• [gmx-users] Problems with tabulated potentials   Harry Saavedra
• Re: [gmx-users] configuration does not change in minimization trajectory   heiko252 at web.de
• [gmx-users] Re: Error by pdb2gmx   wuxiao
• [gmx-users] Re: Replacement for G43b1 force field?   Anirban Ghosh
  • [gmx-users] Re: Replacement for G43b1 force field?   Justin A. Lemkul
• [gmx-users] Hi .. Gr8 offer   chandrabhanseniya at gmail.com
• [gmx-users] error during solvation of system   nitu sharma
  • [gmx-users] error during solvation of system   Mark Abraham
• [gmx-users] gmx4.0.3: simulations do not run on 16 processors but do run on 10   Ángel Piñeiro
  • [gmx-users] gmx4.0.3: simulations do not run on 16 processors but do run on 10   Mark Abraham
    • [gmx-users] segmentation fault - extending trajectory uwing gmx4.0.4 on 16 processors with PME   Ángel Piñeiro
      • [gmx-users] segmentation fault - extending trajectory uwing gmx4.0.4 on 16 processors with PME   Mark Abraham
      • [gmx-users] How to compile C++ propgram with xdrfile library?   Semen Esilevsky
      • [gmx-users] How to compile C++ propgram with xdrfile library?   David van der Spoel
      • [gmx-users] How to compile C++ propgram with xdrfile library?   Semen Esilevsky
      • [gmx-users] How to compile C++ propgram with xdrfile library?   David van der Spoel
      • [gmx-users] How to compile C++ propgram with xdrfile library?   Semen Esilevsky
      • [gmx-users] How to compile C++ propgram with xdrfile library?   Semen Esilevsky
      • [gmx-users] How to compile C++ propgram with xdrfile library?   Jussi Lehtola
• [gmx-users] find with which mpi library /environment gromacs was compiled   Claus Valka
  • [gmx-users] find with which mpi library /environment gromacs was compiled   Mark Abraham
• [gmx-users] help: z-direction component of box vector becomes 0.00000 when using pdc = xy after   Yinhe Zhang
  • [gmx-users] help: z-direction component of box vector becomes 0.00000 when using pdc = xy after   Berk Hess
    • [gmx-users] help: z-direction component of box vector becomes 0.00000 when using pdc = xy after   Yinhe Zhang
• [gmx-users] g_angle - Order of Legendre polynomial for ACF - BUG ?   Dennis Glass
  • [gmx-users] g_angle - Order of Legendre polynomial for ACF - BUG ?   David van der Spoel
  • [gmx-users] g_angle - Order of Legendre polynomial for ACF - BUG ?   XAvier Periole
  • [gmx-users] g_angle - Order of Legendre polynomial for ACF - BUG ?   David van der Spoel
• [gmx-users] Can we abstract any frame from the trajectory file(trr) and save it as a gro file?   wuxiao
  • [gmx-users] Can we abstract any frame from the trajectory file(trr) and save it as a gro file?   Justin A. Lemkul
  • [gmx-users] Can we abstract any frame from the trajectory file(trr) and save it as a gro file?   Cheong Wee Loong, Daniel
• [gmx-users] problem with mpi   jagannath mondal
  • [gmx-users] problem with mpi   Mark Abraham
• [gmx-users] How to concatenate several input trajectory files in sorted order in GMX4.01   zhang
  • Re: [gmx-users] How to concatenate several input trajectory files in sorted order in GMX4.01   Justin A. Lemkul
• [gmx-users] Questions to pullx.xvg   Thomas Schlesier
  • [gmx-users] Questions to pullx.xvg   Berk Hess
• [gmx-users] extending simulations   Anna Marabotti
  • [gmx-users] extending simulations   Justin A. Lemkul
  • [gmx-users] extending simulations   zhang
  • [gmx-users] extending simulations   kyungchan chae
• [gmx-users] mpi problem   jagannath mondal
• [gmx-users] Questions to pullx.xvg   Thomas Schlesier
• [gmx-users] extending simulations   vidhya sankar
  • [gmx-users] extending simulations   Justin A. Lemkul
• [gmx-users] problem with particle decomposition in gromacs 4.0.4   Suman Chakrabarty
  • [gmx-users] problem with particle decomposition in gromacs 4.0.4   Berk Hess
    • [gmx-users] problem with particle decomposition in gromacs 4.0.4   Suman Chakrabarty
• [gmx-users] Martini+elastic network   Enrico Spiga
  • [gmx-users] Martini+elastic network   Justin A. Lemkul
• [gmx-users] P-coupling in vacuum, inflexibility   Pavel Semenyuk
  • [gmx-users] P-coupling in vacuum, inflexibility   Tsjerk Wassenaar
    • [gmx-users] P-coupling in vacuum, inflexibility   Pavel Semenyuk
    • [gmx-users] P-coupling in vacuum, inflexibility   Pavel Semenyuk
• [gmx-users] Energy minimization error by GMX 4.0.4   Yanmei Song
  • [gmx-users] Re: Energy minimization error by GMX 4.0.4   Yanmei Song
  • [gmx-users] Energy minimization error by GMX 4.0.4   Justin A. Lemkul
    • [gmx-users] Energy minimization error by GMX 4.0.4   Justin A. Lemkul
  • [gmx-users] Energy minimization error by GMX 4.0.4   Mark Abraham
    • [gmx-users] Energy minimization error by GMX 4.0.4   Yanmei Song
• [gmx-users] itp and gro files   Payman Pirzadeh
  • [gmx-users] itp and gro files   Justin A. Lemkul
    • [gmx-users] itp and gro files   Payman Pirzadeh
• [gmx-users] modify lennard jones parameters to time-dependent   Xinghua Shi
  • [gmx-users] modify lennard jones parameters to time-dependent   Mark Abraham
    • [gmx-users] modify lennard jones parameters to time-dependent   David van der Spoel
• [gmx-users] v-rescale - harmonic oscillator   servaas
  • [gmx-users] v-rescale - harmonic oscillator   Berk Hess
• [gmx-users] Atom -C not found in residue MET1 while adding hydrogens   Anirban Ghosh
  • [gmx-users] Atom -C not found in residue MET1 while adding hydrogens   Justin A. Lemkul
• [gmx-users] help-Test set   Zhanglin Ni
  • [gmx-users] help-Test set   Justin A. Lemkul
• [gmx-users] atom name O3PB not found in residue ATP 340 while generating exclusions when running pdb2gmx   Una Bjarnadottir
  • [gmx-users] atom name O3PB not found in residue ATP 340 while generating exclusions when running pdb2gmx   Justin A. Lemkul
    • [gmx-users] atom name O3PB not found in residue ATP 340 while generating exclusions when running pdb2gmx   TJ Piggot
• [gmx-users] Re: v-rescale - harmonic oscillator   servaas
  • [gmx-users] Re: v-rescale - harmonic oscillator   Berk Hess
• [gmx-users] Recentering box after simulation of self-assembly of a bilayer   maria goranovic
  • [gmx-users] Recentering box after simulation of self-assembly of a bilayer   Justin A. Lemkul
  • [gmx-users] Recentering box after simulation of self-assembly of a bilayer   machuque
• [gmx-users] v-rescale - harmonic oscillator   servaas
  • [gmx-users] v-rescale - harmonic oscillator   Berk Hess
• [gmx-users] Re: gmx-users Digest, Vol 61, Issue 22   Jacek Czub
• [gmx-users] Re: v-rescale - harmonic oscillator   servaas
  • [gmx-users] Re: v-rescale - harmonic oscillator   Berk Hess
• [gmx-users] Re:Re: Recentering box after simulation of self-assembly of a bilayer (Justin A. Lemkul)   maria goranovic
• [gmx-users] Test-set   Zhanglin Ni
  • [gmx-users] Test-set   Justin A. Lemkul
• [gmx-users] about coorelation fluctuation calculation   mircial at sjtu.edu.cn
• [gmx-users] How to set up the cut-off radius   Yanmei Song
  • [gmx-users] How to set up the cut-off radius   Yinhe Zhang
• [gmx-users] Some molecules disconnected into many parts after EM   Yanmei Song
  • [gmx-users] Some molecules disconnected into many parts after EM   Justin A. Lemkul
    • [gmx-users] Some molecules disconnected into many parts after EM   Yanmei Song
      • [gmx-users] Some molecules disconnected into many parts after EM   Justin A. Lemkul
      • [gmx-users] Some molecules disconnected into many parts after EM   Yanmei Song
  • [gmx-users] Some molecules disconnected into many parts after EM   Payman Pirzadeh
• [gmx-users] Test-set   Zhanglin Ni
  • [gmx-users] Test-set   Justin A. Lemkul
    • [gmx-users] Test-set   Dallas B. Warren
• [gmx-users] How are bond parameters linked to atoms when using #include?   darrellk at ece.ubc.ca
  • [gmx-users] How are bond parameters linked to atoms when using #include?   Justin A. Lemkul
• [gmx-users] Hi .. Gr8 offer   chandrabhanseniya at gmail.com
• [gmx-users] how to use atom2cg.awk   xi zhao
  • [gmx-users] how to use atom2cg.awk   Justin A. Lemkul
• [gmx-users] updated OPLS/AA   Alan
  • [gmx-users] updated OPLS/AA   Andreas Kring
• [gmx-users] (no subject)   Antonia V.
  • [gmx-users] (no subject)   Mark Abraham
    • FW: [gmx-users] (no subject)   Antonia V.
• [gmx-users] x2top and OPLS-AA vs. fudged 1-4 interactions   Vasilii Artyukhov
• [gmx-users] Re: v-rescale - harmonic oscillator   servaas
  • [gmx-users] Re: v-rescale - harmonic oscillator   Berk Hess
• [gmx-users] (no subject)   Antonia V.
  • [gmx-users] (no subject)   Mark Abraham
• [gmx-users] Re: gmx-users Digest, Vol 61, Issue 29   Jacek Czub
• [gmx-users] (no subject)   Antonia V.
  • [gmx-users] (no subject)   Mark Abraham
• [gmx-users] x2top taking too long   Alan
  • [gmx-users] x2top taking too long   Justin A. Lemkul
    • [gmx-users] x2top taking too long   David van der Spoel
• [gmx-users] Problem with protein in lipid bilayer simulation   Anirban Ghosh
  • [gmx-users] Problem with protein in lipid bilayer simulation   Justin A. Lemkul
• [gmx-users] Test-set   Zhanglin Ni
  • [gmx-users] Test-set   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 61, Issue 31   Alan
• [gmx-users] make install-mdrun   Payman Pirzadeh
  • [gmx-users] make install-mdrun   Diego Enry Gomes
    • [gmx-users] make install-mdrun   Payman Pirzadeh
      • [gmx-users] make install-mdrun   Justin A. Lemkul
      • [gmx-users] make install-mdrun   Payman Pirzadeh
• [gmx-users] Test-set   Zhanglin Ni
• [gmx-users] grompp in gromacs-4.0.4   S. Vaitheeswaran
  • [gmx-users] grompp in gromacs-4.0.4   Justin A. Lemkul
    • [gmx-users] grompp in gromacs-4.0.4   S. Vaitheeswaran
• [gmx-users] diff behaviour from same .tpr file under v3.3 /3.3.2   Paul Rowntree
  • [gmx-users] diff behaviour from same .tpr file under v3.3 /3.3.2   Mark Abraham
• [gmx-users] angular COM removal   XAvier Periole
  • [gmx-users] angular COM removal   David van der Spoel
    • [gmx-users] angular COM removal   David van der Spoel
      • [gmx-users] angular COM removal   XAvier Periole
      • [gmx-users] angular COM removal   XAvier Periole
    • [gmx-users] angular COM removal   XAvier Periole
• [gmx-users] problem with genion   nitu sharma
  • [gmx-users] problem with genion   Justin A. Lemkul
  • [gmx-users] problem with genion   Pawan Kumar
    • [gmx-users] problem with system neutralization   Stefano Meliga
      • [gmx-users] problem with system neutralization   Pawan Kumar
      • [gmx-users] problem with system neutralization   Stefano Meliga
      • [gmx-users] problem with system neutralization   Pawan Kumar
      • [gmx-users] problem with system neutralization   Justin A. Lemkul
      • [gmx-users] problem with system neutralization   Stefano Meliga
      • [gmx-users] problem with system neutralization   Justin A. Lemkul
• [gmx-users] tpr files give stable run under v3.3, blows-up under v3.3.2   Paul Rowntree
  • [gmx-users] tpr files give stable run under v3.3, blows-up under v3.3.2   Mark Abraham
• [gmx-users] Ryckaert-Bellemans type dihedral   Suman Chakrabarty
  • [gmx-users] Ryckaert-Bellemans type dihedral   Mark Abraham
• [gmx-users] reg MOPAC/gromacs installations   vidhya sankar
  • [gmx-users] reg MOPAC/gromacs installations   Mark Abraham
• [gmx-users] how to use atom2cg.awk   xi zhao
  • [gmx-users] how to use atom2cg.awk   Justin A. Lemkul
• [gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?   Chih-Ying Lin
  • [gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?   Mark Abraham
  • [gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?   XAvier Periole
• [gmx-users] introducing constrain   anirban polley
• [gmx-users] Warning: Pressure scaling more than 1%.   Zhanglin Ni
  • [gmx-users] Warning: Pressure scaling more than 1%.   Mark Abraham
  • [gmx-users] Warning: Pressure scaling more than 1%.   Pawan Kumar
    • [gmx-users] Warning: Pressure scaling more than 1%.   Mark Abraham
• [gmx-users] pull code problem   Andrei Neamtu
  • [gmx-users] pull code problem   Berk Hess
• [gmx-users] how to use atom2cg.awk   xi zhao
  • [gmx-users] how to use atom2cg.awk   Justin A. Lemkul
• [gmx-users] pull code problem   Andrei Neamtu
  • [gmx-users] pull code problem   Berk Hess
• [gmx-users] pull code problem solved..   Andrei Neamtu
• [gmx-users] Re: reg Mopac/gromacs installations reply please   Justin A. Lemkul
• [gmx-users] how to use atom2cg.awk   xi zhao
  • [gmx-users] how to use atom2cg.awk   Justin A. Lemkul
• [gmx-users] how to use atom2cg.awk   Justin A. Lemkul
• [gmx-users] Force groups?   Chze Ling Wee
  • [gmx-users] Force groups?   Berk Hess
    • [gmx-users] Force groups?   Chze Ling Wee
• [gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?   Chih-Ying Lin
  • [gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?   Tsjerk Wassenaar
• [gmx-users] where is the normalization direction in radial axial g_densmap plots?   maria goranovic
  • [gmx-users] where is the normalization direction in radial axial g_densmap plots?   Berk Hess
• [gmx-users] restraining ligand for position restraint simulation   Halie Shah
  • [gmx-users] restraining ligand for position restraint simulation   Justin A. Lemkul
• [gmx-users] RDF in GMX 4   Eudes Fileti
  • [gmx-users] RDF in GMX 4   Justin A. Lemkul
• [gmx-users] How to create .pdb files?   Joseph Johnson
  • [gmx-users] How to create .pdb files?   Justin A. Lemkul
    • [gmx-users] How to create .pdb files?   Justin A. Lemkul
• [gmx-users] Some molecules disconnected into many parts after EM   Yanmei Song
  • [gmx-users] Some molecules disconnected into many parts after EM   Justin A. Lemkul
• [gmx-users] RE: RE: RDF in GMX 4 (Justin)   Eudes Fileti
  • [gmx-users] RE: RE: RDF in GMX 4 (Justin)   Dallas B. Warren
  • [gmx-users] RE: RE: RDF in GMX 4 (Justin)   Justin A. Lemkul
• [gmx-users] Protein-Ligand Docking?   Chih-Ying Lin
  • [gmx-users] Protein-Ligand Docking?   Justin A. Lemkul
  • [gmx-users] Protein-Ligand Docking?   Dallas B. Warren
• [gmx-users] No default Angle types   darrellk at ece.ubc.ca
  • [gmx-users] No default Angle types   Justin A. Lemkul
• [gmx-users] TestBed in MPI not working   Jones de Andrade
  • [gmx-users] TestBed in MPI not working   Justin A. Lemkul
    • [gmx-users] TestBed in MPI not working   Jones de Andrade
      • [gmx-users] TestBed in MPI not working   Justin A. Lemkul
      • [gmx-users] TestBed in MPI not working   Jones de Andrade
• [gmx-users] TestBed in MPI not working   Justin A. Lemkul
  • [gmx-users] TestBed in MPI not working   Jones de Andrade
    • [gmx-users] TestBed in MPI not working   Mark Abraham
    • [gmx-users] TestBed in MPI not working   Jones de Andrade
      • [gmx-users] TestBed in MPI not working   Jones de Andrade
      • [gmx-users] TestBed in MPI not working   Justin A. Lemkul
      • [gmx-users] TestBed in MPI not working   Jones de Andrade
      • [gmx-users] TestBed in MPI not working   Mark Abraham
• [gmx-users] how to use atom2cg.awk   Justin A. Lemkul
• [gmx-users] protein falls apart in energy minimization   Zhong Zheng
  • [gmx-users] protein falls apart in energy minimization   Mark Abraham
  • [gmx-users] protein falls apart in energy minimization   Pawan Kumar
    • [gmx-users] protein falls apart in energy minimization   Zhong Zheng
      • [gmx-users] protein falls apart in energy minimization   Justin A. Lemkul
• [gmx-users] Re: Problem with protein in lipid bilayer simulation   Anirban Ghosh
  • [gmx-users] Re: Problem with protein in lipid bilayer simulation   Pawan Kumar
• [gmx-users] Coordinate covalent bond   Zhanglin Ni
  • [gmx-users] Coordinate covalent bond   Mark Abraham
• [gmx-users] No default Angle types   darrellk at ece.ubc.ca
  • [gmx-users] No default Angle types   Justin A. Lemkul
• [gmx-users] lipid_posre.itp file   nitu sharma
  • [gmx-users] lipid_posre.itp file   Mark Abraham
  • [gmx-users] lipid_posre.itp file   Nuno Azoia
• [gmx-users] Re: v-rescale - harmonic oscillator   Giovanni Bussi
• [gmx-users] problem with the creating of a top-file   Saskia Frenzel
  • [gmx-users] problem with the creating of a top-file   Mark Abraham
• [gmx-users] Re: Problem with protein in lipid bilayer simulation   Anirban Ghosh
  • [gmx-users] Re: Problem with protein in lipid bilayer simulation   Pawan Kumar
• [gmx-users] UA simulation of PEO melt   Zuzana Benkova
  • [gmx-users] UA simulation of PEO melt   patrick fuchs
    • [gmx-users] UA simulation of PEO melt   Zuzana Benkova
• [gmx-users] Re: v-rescale - harmonic oscillator   servaas
  • [gmx-users] Re: v-rescale - harmonic oscillator   Berk Hess
• [gmx-users] TIP5P - dummies sit on top of each other   ilona.baldus at bioquant.uni-heidelberg.de
  • [gmx-users] TIP5P - dummies sit on top of each other   Justin A. Lemkul
  • [gmx-users] TIP5P - dummies sit on top of each other   David van der Spoel
• [gmx-users] CG to Atomistic   Edson Fauth Vargas Filho
• [gmx-users] g_cluster matrix input   Luisa Pugliese
• [gmx-users] Re: Require help in GROMACS   Justin A. Lemkul
• [gmx-users] CG to Atomistic   Edson Fauth Vargas Filho
• [gmx-users] No default LJ-14 types   Zuzana Benkova
• [gmx-users] DNA-ligand simulation with AMBER FF   Paulo Netz
• [gmx-users] DNA-ligand interactions with AMBER   Paulo Netz
  • [gmx-users] DNA-ligand interactions with AMBER   Mark Abraham
• [gmx-users] virtual sites   zhang
  • [gmx-users] virtual sites   Mark Abraham
• [gmx-users] want to calculate pressure from virial   anirban polley
  • [gmx-users] want to calculate pressure from virial   David van der Spoel
• [gmx-users] lateral stress and surface tension   anirban polley
  • [gmx-users] lateral stress and surface tension   Dallas B. Warren
• [gmx-users] local pressure   anirban polley
  • [gmx-users] local pressure   Dallas B. Warren
• [gmx-users] local pressure calculation   anirban polley
• [gmx-users] simulation of DNA model   nitu sharma
  • [gmx-users] simulation of DNA model   Justin A. Lemkul
• [gmx-users] Re: DNA-ligand interactions with AMBER   Alan
  • [gmx-users] Re: DNA-ligand interactions with AMBER   Paulo Netz
• [gmx-users] Parallel installation core2 quad -mpi?   Peyman Yamin
  • [gmx-users] Parallel installation core2 quad -mpi?   Mark Abraham
    • [gmx-users] Parallel installation core2 quad -mpi?   Peyman Yamin
      • [gmx-users] Parallel installation core2 quad -mpi?   Mark Abraham
• [gmx-users] problem in simulation of DNA-protein complex   nitu sharma
  • [gmx-users] problem in simulation of DNA-protein complex   Mark Abraham
  • [gmx-users] problem in simulation of DNA-protein complex   Dallas B. Warren
• [gmx-users] reg MOPAC/gromacs installation   vidhya sankar
• [gmx-users] reg MOPAC/gromacs installation   vidhya sankar
  • [gmx-users] reg MOPAC/gromacs installation   Mark Abraham
• [gmx-users] ? particles communicated to PME node...   Pavel Semenyuk
  • [gmx-users] ? particles communicated to PME node...   Mark Abraham
    • [gmx-users] adding non-polar hydrogens   Stefano Meliga
      • [gmx-users] adding non-polar hydrogens   Justin A. Lemkul
      • [gmx-users] adding non-polar hydrogens - incompatibility of pdb2gmx and grompp   Stefano Meliga
      • [gmx-users] adding non-polar hydrogens - incompatibility of pdb2gmx and grompp   Justin A. Lemkul
      • [gmx-users] adding non-polar hydrogens - incompatibility of pdb2gmx and grompp   Mark Abraham
• [gmx-users] Problem in Martini simulation with gromacs version 4.0.4 works fine with gromacs 3.3.1 error G96Angle of 2395 missing   maria goranovic
  • [gmx-users] Problem in Martini simulation with gromacs version 4.0.4 works fine with gromacs 3.3.1 error G96Angle of 2395 missing   XAvier Periole
• [gmx-users] Condensation analysis   Jacob Spooner
• [gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P   Manik Mayur
  • [gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P   Justin A. Lemkul
    • [gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P   Manik Mayur
      • [gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P   Justin A. Lemkul
      • [gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P   Manik Mayur
• [gmx-users] What becomes of kinetic energy in local minima?   yutong.zhao at utoronto.ca
  • [gmx-users] What becomes of kinetic energy in local minima?   Mark Abraham
• [gmx-users] Where are the good tutorials?   Joseph Johnson
  • [gmx-users] Where are the good tutorials?   Justin A. Lemkul
  • [gmx-users] Where are the good tutorials?   Rodrigo faccioli
  • [gmx-users] Where are the good tutorials?   Tsjerk Wassenaar
• [gmx-users] ? particles communicated to PME node...   Pavel Semenyuk
  • [gmx-users] ? particles communicated to PME node...   Justin A. Lemkul
• [gmx-users] problem in DNA simulation   nitu sharma
  • [gmx-users] problem in DNA simulation   Dallas B. Warren
• [gmx-users] Regarding the broken compiler gcc 4.1.x   rashmi_chem at iitb.ac.in
  • [gmx-users] Regarding the broken compiler gcc 4.1.x   Jussi Lehtola
• [gmx-users] problem in simulation of dna-protein complex   nitu sharma
  • [gmx-users] problem in simulation of dna-protein complex   Mark Abraham
• [gmx-users] How to remove water from lipid bilayer core   Anirban Ghosh
  • [gmx-users] How to remove water from lipid bilayer core   Pawan Kumar
• [gmx-users] Protein is not at the centre of octahedron box   sukesh chandra gain
  • [gmx-users] Protein is not at the centre of octahedron box   Justin A. Lemkul
• [gmx-users] How to set up dihedrals   Thomas Schlesier
  • [gmx-users] How to set up dihedrals   Mark Abraham
• [gmx-users] problem regarding dna-protein simulation   nitu sharma
  • [gmx-users] problem regarding dna-protein simulation   Justin A. Lemkul
• [gmx-users] gromacs benchmark SGI ALTIX ICE with Intel Quad-Core E5472   intra\sa175950
  • [gmx-users] gromacs benchmark SGI ALTIX ICE with Intel Quad-Core E5472   Justin A. Lemkul
  • [gmx-users] gromacs benchmark SGI ALTIX ICE with Intel Quad-Core E5472   David van der Spoel
• [gmx-users] Constraints specified in .mdp as well as in .top files   Vishwanath Dalvi
  • [gmx-users] Constraints specified in .mdp as well as in .top files   Mark Abraham
    • [gmx-users] Constraints specified in .mdp as well as in .top files   Vishwanath Dalvi
      • [gmx-users] Constraints specified in .mdp as well as in .top files   Mark Abraham
      • [gmx-users] Constraints specified in .mdp as well as in .top files   Berk Hess
• [gmx-users] Coulomb energies for a charge seperated species   Ali Hassanali
• [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3   Harry Saavedra
  • [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3   Mark Abraham
    • [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3   Berk Hess
      • [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3   Harry Saavedra
• [gmx-users] Pressure coupling and cut-off   Yanmei Song
  • [gmx-users] Pressure coupling and cut-off   Justin A. Lemkul
    • [gmx-users] Pressure coupling and cut-off   Yanmei Song
      • [gmx-users] Pressure coupling and cut-off   Justin A. Lemkul
      • [gmx-users] Pressure coupling and cut-off   Yanmei Song
      • [gmx-users] Pressure coupling and cut-off   Justin A. Lemkul
• [gmx-users] -np switch   Payman Pirzadeh
  • [gmx-users] -np switch   Mark Abraham
  • [gmx-users] -np switch   Justin A. Lemkul
• [gmx-users] Protein-Ligand Docking?   Chih-Ying Lin
  • [gmx-users] Protein-Ligand Docking?   Justin A. Lemkul
  • [gmx-users] Protein-Ligand Docking?   Mark Abraham
• [gmx-users] Protein-Ligand Docking?   Chih-Ying Lin
  • [gmx-users] Protein-Ligand Docking?   Dallas B. Warren
• [gmx-users] pdb2gmx does not recognize residues   Rolf Erwin Isele-Holder
  • [gmx-users] pdb2gmx does not recognize residues   Kukol, Andreas
  • [gmx-users] pdb2gmx does not recognize residues   Nuno Azoia
• [gmx-users] MD with RMSD restraint   Sam Moors
  • [gmx-users] MD with RMSD restraint   Mark Abraham
    • [gmx-users] MD with RMSD restraint   David van der Spoel
• [gmx-users] xdrfile license   Jussi Lehtola
  • [gmx-users] xdrfile license   David van der Spoel
• [gmx-users] how to perform Combined essential dynamics analysis and procedure!   xi zhao
• [gmx-users] topology file with grompp program   วันเวลา อมรนพ
  • [gmx-users] topology file with grompp program   Justin A. Lemkul
• [gmx-users] positions and velocities of COM of whole water molecules instead of those of individual atoms?   bohumir
  • [gmx-users] positions and velocities of COM of whole water molecules instead of those of individual atoms?   Jussi Lehtola
  • [gmx-users] positions and velocities of COM of whole water molecules instead of those of individual atoms?   Justin A. Lemkul
    • [gmx-users] positions and velocities of COM of whole water molecules instead of those of individual atoms?   bohumir
• [gmx-users] parameter of RB potential for OPLS force field   Yanmei Song
  • [gmx-users] Re: parameter of RB potential for OPLS force field   Justin A. Lemkul
    • [gmx-users] Re: parameter of RB potential for OPLS force field   Yanmei Song
      • [gmx-users] Re: parameter of RB potential for OPLS force field   Justin A. Lemkul
      • [gmx-users] Re: parameter of RB potential for OPLS force field   Yanmei Song
      • [gmx-users] Re: parameter of RB potential for OPLS force field   Justin A. Lemkul
      • [gmx-users] Re: parameter of RB potential for OPLS force field   Yanmei Song
      • [gmx-users] Re: parameter of RB potential for OPLS force field   Mark Abraham
• [gmx-users] how to make the different displacement of ligand around protein?   Chih-Ying Lin
  • [gmx-users] how to make the different displacement of ligand around protein?   Justin A. Lemkul
• [gmx-users] how can i know the center of the cleft of protein?   Chih-Ying Lin
  • [gmx-users] how can i know the center of the cleft of protein?   David van der Spoel
• [gmx-users] how to setup the pH value   Chih-Ying Lin
  • [gmx-users] how to setup the pH value   Justin A. Lemkul
    • [gmx-users] how to setup the pH value   David van der Spoel
• [gmx-users] Molecule Jumps   darrellk at ece.ubc.ca
  • [gmx-users] Molecule Jumps   Mark Abraham
• [gmx-users] Segmentation fault   Chih-Ying Lin
  • [gmx-users] Segmentation fault   Justin A. Lemkul
• [gmx-users] How can i know if the protein swell during the MD simulation?   Chih-Ying Lin
  • [gmx-users] How can i know if the protein swell during the MD simulation?   Justin A. Lemkul
    • [gmx-users] How can i know if the protein swell during the MD simulation?   Tsjerk Wassenaar
      • [gmx-users] How can i know if the protein swell during the MD simulation?   Bhanu
      • [gmx-users] How can i know if the protein swell during the MD simulation?   Tsjerk Wassenaar
      • [gmx-users] How can i know if the protein swell during the MD simulation?   Marius Retegan
      • [gmx-users] How can i know if the protein swell during the MD simulation?   Tsjerk Wassenaar
• [gmx-users] RMS deviation after position restraint dynamics   sukesh chandra gain
  • [gmx-users] RMS deviation after position restraint dynamics   Joshua Adelman
  • [gmx-users] RMS deviation after position restraint dynamics   Mark Abraham
• [gmx-users] g_rdf -xy   Hongyan Xiao
  • [gmx-users] g_rdf -xy   Berk Hess
• [gmx-users] g_rdf -xy   Hongyan Xiao
• [gmx-users] Input/Output error using grompp   Stefano Meliga
  • [gmx-users] Input/Output error using grompp   David van der Spoel
  • [gmx-users] Input/Output error using grompp   Martin Höfling
• [gmx-users] mdp file for local pressure   anirban polley
  • [gmx-users] mdp file for local pressure   Dallas B. Warren
  • [gmx-users] mdp file for local pressure   Cheong Wee Loong, Daniel
• [gmx-users] how to add shear force in gromacs   He, Yang
• [gmx-users] shift function for vdwtype and density   Yanmei Song
  • [gmx-users] shift function for vdwtype and density   Mark Abraham
    • [gmx-users] shift function for vdwtype and density   Yanmei Song
      • [gmx-users] shift function for vdwtype and density   Justin A. Lemkul
      • [gmx-users] shift function for vdwtype and density   Yanmei Song
      • [gmx-users] shift function for vdwtype and density   Justin A. Lemkul
      • [gmx-users] shift function for vdwtype and density   Yanmei Song
      • [gmx-users] shift function for vdwtype and density   Justin A. Lemkul
      • [gmx-users] shift function for vdwtype and density   Justin A. Lemkul
      • [gmx-users] shift function for vdwtype and density   Yanmei Song
      • [gmx-users] shift function for vdwtype and density   David van der Spoel
      • [gmx-users] shift function for vdwtype and density   Yanmei Song
      • [gmx-users] shift function for vdwtype and density   Yanmei Song
      • [gmx-users] shift function for vdwtype and density   Mark Abraham
• [gmx-users] Re: Molecule Jumps   darrellk at ece.ubc.ca
  • [gmx-users] Re: Molecule Jumps   Mark Abraham
• [gmx-users] Has anyone adapted an Allinger force field for GROMACS? (MM,MM+,MM2,MM3...)   Inon Sharony
  • [gmx-users] Has anyone adapted an Allinger force field for GROMACS? (MM,MM+,MM2,MM3...)   David van der Spoel
• [gmx-users] Re: MD with RMSD restraint   Sam Moors
  • [gmx-users] Re: MD with RMSD restraint   David van der Spoel
    • [gmx-users] Re: MD with RMSD restraint   Massimiliano Bonomi
    • [gmx-users] Re: MD with RMSD restraint   Ran Friedman
    • [gmx-users] Re: MD with RMSD restraint   Marc Baaden
• [gmx-users] .trr forces into VMD   Matteus Lindgren
• [gmx-users] Re: MD with RMSD restraint   Sam Moors
  • [gmx-users] Re: MD with RMSD restraint   David van der Spoel
• [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex   Nehme El Hachem
  • [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex   Justin A. Lemkul
  • [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex   Tsjerk Wassenaar
• [gmx-users] removal of water from hydrophobic core of lipid   nitu sharma
  • [gmx-users] removal of water from hydrophobic core of lipid   Justin A. Lemkul
• [gmx-users] Selection of force field   ANINDITA GAYEN
  • [gmx-users] Selection of force field   Tsjerk Wassenaar
• [gmx-users] .trr forces into VMD   Mark Abraham
  • [gmx-users] .trr forces into VMD   Berk Hess
• [gmx-users] Test suit failures   Bert
  • [gmx-users] Test suit failures   Justin A. Lemkul
  • [gmx-users] Test suit failures   Mark Abraham
• [gmx-users] how to apply shear force   He, Yang
  • [gmx-users] how to apply shear force   Berk Hess
• [gmx-users] FudgeQQ parameter with TraPPE FF and OPLS-AA   Rasmus "Termo" Lundsgaard
• [gmx-users] gromacs on glacier.westgrid.ca   Payman Pirzadeh
  • [gmx-users] gromacs on glacier.westgrid.ca   Tsjerk Wassenaar
    • [gmx-users] gromacs on glacier.westgrid.ca   Payman Pirzadeh
      • [gmx-users] gromacs on glacier.westgrid.ca   Justin A. Lemkul
      • [gmx-users] gromacs on glacier.westgrid.ca   Payman Pirzadeh
      • [gmx-users] gromacs on glacier.westgrid.ca   Justin A. Lemkul
      • [gmx-users] gromacs on glacier.westgrid.ca   Nicolas Sapay
      • [gmx-users] gromacs on glacier.westgrid.ca   Payman Pirzadeh
      • [gmx-users] gromacs on glacier.westgrid.ca   J. Rui Rodrigues
• [gmx-users] dt > = 0.002   Chih-Ying Lin
  • [gmx-users] dt > = 0.002   Justin A. Lemkul
  • [gmx-users] dt > = 0.002   Joshua Adelman
• [gmx-users] g_clustsize method   Jacob Spooner
  • [gmx-users] g_clustsize method   David van der Spoel
    • [gmx-users] g_clustsize method   Jacob Spooner
      • [gmx-users] g_clustsize method   David van der Spoel
• [gmx-users] Selection of force fields   ANINDITA GAYEN
  • [gmx-users] Selection of force fields   Tsjerk Wassenaar
• Hi: Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex   Tsjerk Wassenaar
• [gmx-users] Failing installation with --enable-mpi option   Bhanu
  • [gmx-users] Failing installation with --enable-mpi option   Justin A. Lemkul
    • [gmx-users] Failing installation with --enable-mpi option   Bhanu
      • [gmx-users] Failing installation with --enable-mpi option   Bhanu
      • [gmx-users] Failing installation with --enable-mpi option   Mark Abraham
• [gmx-users] autocorrelation functions from several simulations d   giordano mancini
• [gmx-users] Dihedral definition   ANINDITA GAYEN
  • [gmx-users] Dihedral definition   David van der Spoel
• [gmx-users] pdb2gmx file error   yimnai forlemu
  • [gmx-users] Re: pdb2gmx file error   Justin A. Lemkul
• [gmx-users] Help with nitrile group in complx protein-ligand md   Jocley Araujo
  • [gmx-users] Help with nitrile group in complx protein-ligand md   Justin A. Lemkul
  • [gmx-users] Help with nitrile group in complx protein-ligand md   David van der Spoel
• [gmx-users] Lipids forming unsual bonds   Anirban Ghosh
  • [gmx-users] Lipids forming unsual bonds   Dallas B. Warren
  • [gmx-users] Lipids forming unsual bonds   Mark Abraham
• [gmx-users] Lipids forming unsual bonds   chris.neale at utoronto.ca
• [gmx-users] RE: Lipids forming unsual bonds   Anirban Ghosh
• [gmx-users] mdp file to calculate local pressure   anirban polley
  • [gmx-users] mdp file to calculate local pressure   Justin A. Lemkul
• [gmx-users] in vacuo minimization of a multimeric protein   Anna Marabotti
  • [gmx-users] in vacuo minimization of a multimeric protein   Justin A. Lemkul
• [gmx-users] grompp 4.0.5 hangs while 3.2.1 works   Kaihsu Tai
  • [gmx-users] grompp 4.0.5 hangs while 3.2.1 works   David van der Spoel
    • [gmx-users] grompp 4.0.5 hangs while 3.2.1 works   Berk Hess
  • [gmx-users] Re: grompp 4.0.5 hangs while 3.2.1 works   Kaihsu Tai
• [gmx-users] bond, angle and dihedral restraints in Gromacs   Rebeca García Fandiño
  • [gmx-users] bond, angle and dihedral restraints in Gromacs   Justin A. Lemkul
    • [gmx-users] bond, angle and dihedral restraints in Gromacs   Rebeca García Fandiño
      • [gmx-users] bond, angle and dihedral restraints in Gromacs   Mark Abraham
• [gmx-users] topology of HEO compound in .rtp for G96 ff   Egidijus Kuprusevicius
  • [gmx-users] topology of HEO compound in .rtp for G96 ff   Justin A. Lemkul
• [gmx-users] mdp file to calculate local pressure   anirban polley
  • [gmx-users] mdp file to calculate local pressure   Justin A. Lemkul
• [gmx-users] problem in removal of unwanted water from hydrophobic core of lipid bilayer   nitu sharma
  • [gmx-users] problem in removal of unwanted water from hydrophobic core of lipid bilayer   Justin A. Lemkul
• [gmx-users] multiple outputs in mdrun with gromacs-4.0.3   vivek sharma
  • [gmx-users] multiple outputs in mdrun with gromacs-4.0.3   Mark Abraham
• [gmx-users] wrong number of control atoms (3 iso 4) on line   nitu sharma
  • [gmx-users] wrong number of control atoms (3 iso 4) on line   Justin A. Lemkul
• [gmx-users] in vacuo minimization of a multimeric protein   Anna Marabotti
• [gmx-users] simulation of protein in popc box   Samik Bhattacharya
  • [gmx-users] simulation of protein in popc box   Pawan Kumar
  • [gmx-users] simulation of protein in popc box   Justin A. Lemkul
  • [gmx-users] question about positive potential   Baofu Qiao
    • [gmx-users] question about positive potential   Mark Abraham
      • [gmx-users] question about positive potential   Baofu Qiao
      • [gmx-users] question about positive potential   Mark Abraham
• [gmx-users] changelog for gmx 4.0.5?   Alan
  • [gmx-users] changelog for gmx 4.0.5?   David van der Spoel
• [gmx-users] simulation of protein in popc box   Samik Bhattacharya
  • [gmx-users] simulation of protein in popc box   Pawan Kumar
• [gmx-users] bond, angle and dihedral restraints in Gromacs   Justin A. Lemkul
• [gmx-users] What is the purpose that we make the bond constraints?   Chih-Ying Lin
  • [gmx-users] What is the purpose that we make the bond constraints?   David van der Spoel
  • [gmx-users] What is the purpose that we make the bond constraints?   Justin A. Lemkul
• [gmx-users] extending simulations   Alexander Itkin
• [gmx-users] Why does protein carry charges?   Chih-Ying Lin
  • [gmx-users] Why does protein carry charges?   jadelman at berkeley.edu
• [gmx-users] How to choose the counter ions for proteins?   Chih-Ying Lin
  • [gmx-users] How to choose the counter ions for proteins?   Mark Abraham
• [gmx-users] parameter for iron(HEME) and S-Cys   Zhanglin Ni
  • [gmx-users] parameter for iron(HEME) and S-Cys   Mark Abraham
• [gmx-users] (no subject)   chandrabhan seniya
  • [gmx-users] (no subject)   Mark Abraham
• [gmx-users] mdp file to calculate local pressure   anirban polley
  • [gmx-users] mdp file to calculate local pressure   Justin A. Lemkul
• [gmx-users] problem in neutralising my system   nitu sharma
  • [gmx-users] problem in neutralising my system   Justin A. Lemkul
• [gmx-users] Why NaCl and KCl solution?   Chih-Ying Lin
  • [gmx-users] Why NaCl and KCl solution?   David van der Spoel
  • [gmx-users] Why NaCl and KCl solution?   Justin A. Lemkul
    • [gmx-users] Why NaCl and KCl solution?   Lucio Ricardo Montero Valenzuela
• [gmx-users] The default pH =7.0 ???   Chih-Ying Lin
  • [gmx-users] The default pH =7.0 ???   Mark Abraham
• [gmx-users] The default pH =7.0 ??? and the protonation state after pdb2gmx   Chih-Ying Lin
  • [gmx-users] The default pH =7.0 ??? and the protonation state after pdb2gmx   Mark Abraham
• [gmx-users] Counter ions added   Chih-Ying Lin
  • [gmx-users] Counter ions added   Mark Abraham
• [gmx-users] question about force field parameter   Zhanglin Ni
  • [gmx-users] question about force field parameter   Mark Abraham
    • [gmx-users] question about force field parameter   Yan Chai
      • [gmx-users] question about force field parameter   Mark Abraham
      • [gmx-users] question about force field parameter   David van der Spoel
      • [gmx-users] question about force field parameter   Yan Chai
      • [gmx-users] question about force field parameter   David van der Spoel
• [gmx-users] Re: question about force field parameter   Zhanglin Ni
  • [gmx-users] Re: question about force field parameter   Tsjerk Wassenaar
• [gmx-users] how to solve the warning   Jinyao Wang
  • [gmx-users] how to solve the warning   Justin A. Lemkul
• [gmx-users] charge distribution   Cheong Wee Loong, Daniel
• [gmx-users] The default pH =7.0 ??? and the protonation state after pdb2gmx   Chih-Ying Lin
  • [gmx-users] The default pH =7.0 ??? and the protonation state after pdb2gmx   Joshua Adelman
  • [gmx-users] The default pH =7.0 ??? and the protonation state after pdb2gmx   Tsjerk Wassenaar
• [gmx-users] Installing topolbuild   vivek sharma
• [gmx-users] force field parameter for ligands   Zhanglin Ni
  • [gmx-users] force field parameter for ligands   Mark Abraham
• [gmx-users] oplsaa parametrization   R. A.
  • [gmx-users] oplsaa parametrization   Ran Friedman
• [gmx-users] Re: force field parameter for ligands   Dechang Li
• [gmx-users] oplsaa parametrization   R. A.
  • [gmx-users] oplsaa parametrization   Ran Friedman
• [gmx-users] some puzzled about the dihedral paramaters   Jinyao Wang
  • [gmx-users] some puzzled about the dihedral paramaters   Mark Abraham
• [gmx-users] Lingering problems with the test set   Justin A. Lemkul
  • [gmx-users] Lingering problems with the test set   Mark Abraham
• [gmx-users] maximum size for Freeze group?   ilona.baldus at bioquant.uni-heidelberg.de
  • [gmx-users] maximum size for Freeze group?   Mark Abraham
• [gmx-users] Viscosity using periodic perturbation method   Yanmei Song
  • [gmx-users] Viscosity using periodic perturbation method   Berk Hess
    • [gmx-users] Viscosity using periodic perturbation method   Yanmei Song
    • [gmx-users] Viscosity using periodic perturbation method   Yanmei Song
• [gmx-users] amber to gromos topology   baloilgiullare at interfree.it
  • [gmx-users] amber to gromos topology   Justin A. Lemkul
• [gmx-users] oplsaa parametrization   R. A.
• [gmx-users] Dynamics with DNA   tanos at ime.eb.br
  • [gmx-users] Dynamics with DNA   Mark Abraham
  • [gmx-users] Dynamics with DNA   Justin A. Lemkul
    • [gmx-users] Dynamics with DNA   Tsjerk Wassenaar
• [gmx-users] Lennard-Jones 9-6 potential problems   zhangjianguo2002
  • [gmx-users] Lennard-Jones 9-6 potential problems   David van der Spoel
    • [gmx-users] Lennard-Jones 9-6 potential problems   Berk Hess
• Hi: Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex   Tsjerk Wassenaar
• [gmx-users] Re: oplsaa parametrization   Alan
• [gmx-users] Re: Dynamics with DNA   Alan
• [gmx-users] constant term in dihedral potential function   Kukol, Andreas
  • [gmx-users] constant term in dihedral potential function   Berk Hess
    • [gmx-users] constant term in dihedral potential function   Kukol, Andreas
      • [gmx-users] constant term in dihedral potential function   Mark Abraham
      • [gmx-users] constant term in dihedral potential function   Berk Hess
      • [gmx-users] constant term in dihedral potential function   Kukol, Andreas
      • [gmx-users] constant term in dihedral potential function   Mark Abraham
      • [gmx-users] constant term in dihedral potential function   Berk Hess
      • [gmx-users] constant term in dihedral potential function   Mark Abraham
  • [gmx-users] constant term in dihedral potential function   Mark Abraham
• [gmx-users] Normal Mode Analysis   Franzi Hoffgaard
  • [gmx-users] Normal Mode Analysis   Berk Hess
    • [gmx-users] Normal Mode Analysis   Franzi Hoffgaard
      • [gmx-users] Normal Mode Analysis   Berk Hess
      • [gmx-users] Normal Mode Analysis   Franzi Hoffgaard
      • [gmx-users] Normal Mode Analysis   Berk Hess
      • [gmx-users] Normal Mode Analysis   Franzi Hoffgaard
• [gmx-users] solution molecules cannot be set by mdrun after neutralization   Stefano Meliga
  • [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization   Stefano Meliga
    • [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization   Justin A. Lemkul
    • [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization   Mark Abraham
      • [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization   Stefano Meliga
      • [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization   Justin A. Lemkul
• [gmx-users] Shared library version binary on CYGWIN   Makoto Yoneya
  • [gmx-users] Shared library version binary on CYGWIN   Mark Abraham
• [gmx-users] gmxtest   Simba Xiao
  • [gmx-users] gmxtest   Mark Abraham
    • [gmx-users] gmxtest   Mark Abraham
      • [gmx-users] gmxtest   Simba Xiao
• [gmx-users] Shared library version binary on CYGWIN   Makoto Yoneya
  • [gmx-users] Shared library version binary on CYGWIN   Jussi Lehtola
• [gmx-users] Lennard-Jones 9-6 potential problems   zhangjianguo2002
  • [gmx-users] Lennard-Jones 9-6 potential problems   David van der Spoel
  • [gmx-users] Lennard-Jones 9-6 potential problems   Mark Abraham
• [gmx-users] Lennard-Jones 9-6 potential problems   zhangjianguo2002
  • [gmx-users] Lennard-Jones 9-6 potential problems   David van der Spoel
• [gmx-users] Strange assignment of atoms to processors with pd   Erik Marklund
  • [gmx-users] Strange assignment of atoms to processors with pd   Erik Marklund
    • [gmx-users] Strange assignment of atoms to processors with pd   David van der Spoel
      • [gmx-users] Strange assignment of atoms to processors with pd   Erik Marklund
      • [gmx-users] Strange assignment of atoms to processors with pd   David van der Spoel
      • [gmx-users] Strange assignment of atoms to processors with pd   Berk Hess
      • [gmx-users] Strange assignment of atoms to processors with pd   Erik Marklund
      • [gmx-users] Strange assignment of atoms to processors with pd   Erik Marklund
      • [gmx-users] Strange assignment of atoms to processors with pd   Berk Hess
• [gmx-users] Twin range cut-off's: rlist and rvdw   Yan Chai
  • [gmx-users] Twin range cut-off's: rlist and rvdw   Jussi Lehtola
    • [gmx-users] Twin range cut-off's: rlist and rvdw   Yan Chai
      • [gmx-users] Twin range cut-off's: rlist and rvdw   Jussi Lehtola
      • [gmx-users] Twin range cut-off's: rlist and rvdw   Berk Hess
      • [gmx-users] Twin range cut-off's: rlist and rvdw   Yan Chai
• [gmx-users] Packages for building topologies   vivek sharma
  • [gmx-users] Packages for building topologies   Justin A. Lemkul
• [gmx-users] structure factor using g_rdf: grid option does not work   Suman Chakrabarty
• [gmx-users] Ac-CoA topology problem   Thamu
  • [gmx-users] Ac-CoA topology problem   Justin A. Lemkul
• [gmx-users] mpi problem during installation   Itamar Kass
  • [gmx-users] mpi problem during installation   Mark Abraham
• [gmx-users] Question about g_cluster   Jacob Durrant
  • [gmx-users] Question about g_cluster   Mark Abraham
• [gmx-users] The system setup   Chih-Ying Lin
  • [gmx-users] The system setup   Mark Abraham
• [gmx-users] atomic stress distribution map   farzaneh fatahi
• [gmx-users] hardware recommendation   Bernhard Knapp
• [gmx-users] Shared library version binary on CYGWIN   Makoto Yoneya
  • [gmx-users] Shared library version binary on CYGWIN   Mark Abraham
• [gmx-users] removal of unwanted water from hydrphobic core of lipid   nitu sharma
  • [gmx-users] removal of unwanted water from hydrphobic core of lipid   Mark Abraham
• [gmx-users] Re: Unexplained crashes with Gromacs-4.0 & Neighbor Searching   Inon Sharony
  • [gmx-users] Re: Unexplained crashes with Gromacs-4.0 & Neighbor Searching   Justin A. Lemkul
    • [gmx-users] Re: Re: Unexplained crashes with Gromacs-4.0 & Neighbor Searching   Inon Sharony
      • [gmx-users] Re: Re: Unexplained crashes with Gromacs-4.0 & Neighbor Searching   Justin A. Lemkul
      • [gmx-users] Re: Re: Unexplained crashes with Gromacs-4.0 & Neighbor Searching   Mark Abraham
• [gmx-users] g_wham output   Schor, M.
• [gmx-users] GROMACS on glacier.westgrid.ca   Paymon Pirzadeh
  • [gmx-users] GROMACS on glacier.westgrid.ca   David van der Spoel
  • [gmx-users] GROMACS on glacier.westgrid.ca   Mark Abraham
• [gmx-users] LINCS warnings (6153)   Ernesto Andres Román
  • [gmx-users] LINCS warnings (6153)   David van der Spoel
  • [gmx-users] LINCS warnings (6153)   Vishwanath Dalvi
• [gmx-users] GROMACS on glacier.westgrid.ca   p.yamin at fz-juelich.de
  • [gmx-users] GROMACS on glacier.westgrid.ca   Paymon Pirzadeh
• [gmx-users] Nanoparticles does not interact   osmair oliveira
• [gmx-users] GROMACS on glacier.westgrid.ca   Chris Neale
• [gmx-users] Nanoparticles does not interact   p.yamin at fz-juelich.de
  • [gmx-users] Nanoparticles does not interact   osmair oliveira
    • [gmx-users] Nanoparticles does not interact   Mark Abraham
      • [gmx-users] Nanoparticles does not interact   osmair oliveira
      • [gmx-users] Nanoparticles does not interact   Mark Abraham
• [gmx-users] Shared library version binary on CYGWIN   Makoto Yoneya
  • [gmx-users] Shared library version binary on CYGWIN   Mark Abraham
• [gmx-users] grompp warning   sarbani chattopadhyay
  • [gmx-users] grompp warning   Mark Abraham
• [gmx-users] missing atoms   swatik at ncbs.res.in
  • [gmx-users] missing atoms   Kukol, Andreas
  • [gmx-users] missing atoms   Mark Abraham
• [gmx-users] how to do MD simulation of protein with Fe-S cluster   amri ta
  • [gmx-users] how to do MD simulation of protein with Fe-S cluster   Mark Abraham
• [gmx-users] membrane protein simulation   Samik Bhattacharya
  • [gmx-users] membrane protein simulation   Justin A. Lemkul
• [gmx-users] membrane protein simulation   Samik Bhattacharya
• [gmx-users] Non standard amino acids.   david.lisgarten at canterbury.ac.uk
  • [gmx-users] Non standard amino acids.   Mark Abraham
• [gmx-users] Installing topolbuild   Bruce D. Ray
• [gmx-users] protein molecular weight?   Chih-Ying Lin
  • [gmx-users] protein molecular weight?   Justin A. Lemkul
• [gmx-users] Re: Long-range (LR) energies in gromacs v3.3.3   Justin A. Lemkul
• [gmx-users] Re: Long-range (LR) energies in gromacs v3.3.3   Justin A. Lemkul
• [gmx-users] Installation Problem   farzaneh fatahi
  • [gmx-users] Installation Problem   Mark Abraham
• [gmx-users] protein molecular weight?   Chih-Ying Lin
  • [gmx-users] protein molecular weight?   Mark Abraham
• [gmx-users] How to print out .gro per 100 ps?   Chih-Ying Lin
  • [gmx-users] How to print out .gro per 100 ps?   Mark Abraham
• [gmx-users] Extend water layer along negative Z-direction   Anirban Ghosh
  • [gmx-users] Extend water layer along negative Z-direction   Justin A. Lemkul
• [gmx-users] Error for 1-4 interaction   Anirban Ghosh
  • [gmx-users] Error for 1-4 interaction   Justin A. Lemkul
• [gmx-users] Extend water layer along negative Z-direction   chris.neale at utoronto.ca
  • [gmx-users] Extend water layer along negative Z-direction   Tsjerk Wassenaar
• [gmx-users] Extend water layer along negative Z-direction   chris.neale at utoronto.ca
• [gmx-users] essential dynamics analysis   jayant james
  • [gmx-users] essential dynamics analysis   Tsjerk Wassenaar

Last message date: Sun May 31 21:51:49 CEST 2009
Archived on: Thu Nov 14 12:06:49 CET 2013

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