February 2015 Archives by thread

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Starting: Sun Feb 1 00:05:04 CET 2015
Ending: Sat Feb 28 21:16:11 CET 2015
Messages: 561

• [gmx-users] insert-molecules module   Mark Abraham
• [gmx-users] Finding Surface tension between two interface   Bishnu Acharya
  • [gmx-users] Finding Surface tension between two interface   David van der Spoel
    • [gmx-users] Finding Surface tension between two interface   Bishnu Acharya
• [gmx-users] residues in force fields   Mark Abraham
• [gmx-users] DNA-protein complex - which force field to use?   Jernej Zidar
  • [gmx-users] DNA-protein complex - which force field to use?   Paulo Netz
  • [gmx-users] DNA-protein complex - which force field to use?   Erik Marklund
    • [gmx-users] DNA-protein complex - which force field to use?   Felipe Merino
• [gmx-users] Force field For Protein-Ligand Complex   neha bharti
  • [gmx-users] Force field For Protein-Ligand Complex   rajendra kumar
  • [gmx-users] Force field For Protein-Ligand Complex   Justin Lemkul
• [gmx-users] Compilation errors (5.0.4)   Satyabrata Das
  • [gmx-users] Compilation errors (5.0.4)   Mark Abraham
• [gmx-users] template.cpp compilation problem with Gromacs 5.0.4   Milton Sonoda
• [gmx-users] template.cpp compilation problem with Gromacs 5.0.4   Milton Sonoda
• [gmx-users] topology and parameter set up   Jennifer Vo
  • [gmx-users] topology and parameter set up   Justin Lemkul
    • [gmx-users] topology and parameter set up   Jennifer Vo
      • [gmx-users] topology and parameter set up   Justin Lemkul
• [gmx-users] Umbrella Samling Alteration   Alexander Law
  • [gmx-users] Umbrella Samling Alteration   Justin Lemkul
    • [gmx-users] Umbrella Samling Alteration   Alexander Law
      • [gmx-users] Umbrella Samling Alteration   Justin Lemkul
      • [gmx-users] Umbrella Samling Alteration   Alexander Law
      • [gmx-users] Umbrella Samling Alteration   Justin Lemkul
• [gmx-users] Covalent bond/crosslink formation with calcium   Turgay Cakmak
  • [gmx-users] Covalent bond/crosslink formation with calcium   Justin Lemkul
    • [gmx-users] Covalent bond/crosslink formation with calcium   Turgay Cakmak
      • [gmx-users] Covalent bond/crosslink formation with calcium   Justin Lemkul
  • [gmx-users] single strand DNA in hairpin conformation   Urszula Uciechowska
    • [gmx-users] single strand DNA in hairpin conformation   Erik Marklund
• [gmx-users] ngmx tools   asasa qsqs
  • [gmx-users] ngmx tools   Justin Lemkul
• [gmx-users] Cluster recommendations   Carsten Kutzner
  • [gmx-users] Cluster recommendations   Szilárd Páll
  • [gmx-users] Cluster recommendations   David McGiven
• [gmx-users] Significant differences in Ewald Vs PME for clay sheet   Gaurav Goel
• [gmx-users] combine two solvent box to one large box.   BIRD
  • [gmx-users] combine two solvent box to one large box.   Mark Abraham
• [gmx-users] Problem with Lysozyme in Water Tutorial   Stephen P. Molnar
  • [gmx-users] Problem with Lysozyme in Water Tutorial   HANNIBAL LECTER
    • [gmx-users] Problem with Lysozyme in Water Tutorial   Stephen P. Molnar
      • [gmx-users] Problem with Lysozyme in Water Tutorial   Justin Lemkul
      • [gmx-users] Problem with Lysozyme in Water Tutorial   Stephen P. Molnar
  • [gmx-users] Problem with Lysozyme in Water Tutorial   Justin Lemkul
• [gmx-users] Hope this can help someone using REMD in Gromacs   jia jia
• [gmx-users] pressure simulation along the z-axis   felipe zapata
  • [gmx-users] pressure simulation along the z-axis   Justin Lemkul
• [gmx-users] q-bio Summer School 2015   Christoph Junghans
• [gmx-users] Using g_mindist for calculating hydrophobic interaction between protein and ligand   Agnivo Gosai
  • [gmx-users] Using g_mindist for calculating hydrophobic interaction between protein and ligand   Justin Lemkul
• [gmx-users] Virtual sites and diffusion coefficients.   sujithkakkat .
  • [gmx-users] Virtual sites and diffusion coefficients.   Mark Abraham
    • [gmx-users] Virtual sites and diffusion coefficients.   sujithkakkat .
      • [gmx-users] Virtual sites and diffusion coefficients.   Justin Lemkul
• [gmx-users] Using "pairs" type 2   Liel Sapir
• [gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)   Felipe Villanelo
  • [gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)   Mark Abraham
  • [gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)   Felipe Villanelo
    • [gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)   Justin Lemkul
• [gmx-users] Problem with 5.0.4 build   Jim Tuccillo
  • [gmx-users] Problem with 5.0.4 build   Mark Abraham
• [gmx-users] Creating box,   Bishnu Acharya
  • [gmx-users] Creating box,   Justin Lemkul
    • [gmx-users] Creating box,   Bishnu Acharya
• [gmx-users] Peptide-membrane simulation force field parameters   tarak karmakar
  • [gmx-users] Peptide-membrane simulation force field parameters   Justin Lemkul
    • [gmx-users] Peptide-membrane simulation force field parameters   tarak karmakar
• [gmx-users] adding polyatomic species in water   #SUKRITI GUPTA#
  • [gmx-users] adding polyatomic species in water   Justin Lemkul
  • [gmx-users] adding polyatomic species in water   Kester Wong
• [gmx-users] chiara_marcolin wants to share a link | Gromacs   rossen at kth.se
• [gmx-users] How to recover the .xtc from wrong operation 'dos2unix'   Xia, Xiaole
  • [gmx-users] How to recover the .xtc from wrong operation 'dos2unix'   Justin Lemkul
• [gmx-users] gromacs.org_gmx-users Digest, Vol 130, Issue 12   Xia, Xiaole
  • [gmx-users] gromacs.org_gmx-users Digest, Vol 130, Issue 12   Mark Abraham
• [gmx-users] Distance restraint between two chains' com   WT Ren
  • [gmx-users] Distance restraint between two chains' com   Justin Lemkul
    • [gmx-users] Distance restraint between two chains' com   WT Ren
      • [gmx-users] Distance restraint between two chains' com   WT Ren
      • [gmx-users] Distance restraint between two chains' com   Justin Lemkul
      • [gmx-users] Distance restraint between two chains' com   WT Ren
• [gmx-users] Distance restraint between two chains' com   WT Ren
• [gmx-users] Position restraints and free energy calculations   Kortzak, Daniel
  • [gmx-users] Position restraints and free energy calculations   Justin Lemkul
• [gmx-users] sampling techniques when calculating diffusion coefficients using Green-Kubo   Ying Chen
• [gmx-users] Build-Gromacs installation error   rahul dhakne
  • [gmx-users] Build-Gromacs installation error   Dan Sponseller
    • [gmx-users] Build-Gromacs installation error   Szilárd Páll
• [gmx-users] Unable to install gromacs   Seera Suryanarayana
  • [gmx-users] Unable to install gromacs   Mark Abraham
• [gmx-users] no residue type with Amber99SB-ILDN ff   Ahmet yıldırım
  • [gmx-users] no residue type with Amber99SB-ILDN ff   Mark Abraham
    • [gmx-users] no residue type with Amber99SB-ILDN ff   Ahmet yıldırım
      • [gmx-users] no residue type with Amber99SB-ILDN ff   Justin Lemkul
      • [gmx-users] no residue type with Amber99SB-ILDN ff   Ahmet yıldırım
      • [gmx-users] no residue type with Amber99SB-ILDN ff   Justin Lemkul
      • [gmx-users] no residue type with Amber99SB-ILDN ff   Ahmet yıldırım
      • [gmx-users] no residue type with Amber99SB-ILDN ff   Justin Lemkul
      • [gmx-users] no residue type with Amber99SB-ILDN ff   Ahmet yıldırım
      • [gmx-users] problem installing gromacs- libcurl   Marcello Cammarata
      • [gmx-users] problem installing gromacs- libcurl   Marcello Cammarata
• [gmx-users] Position restraints and free energy calculations   Kortzak, Daniel
• [gmx-users] Helicity   shivangi nangia
  • [gmx-users] Helicity   Diogo Vila Viçosa
    • [gmx-users] Helicity   shivangi nangia
      • [gmx-users] Helicity   Diogo Vila Viçosa
      • [gmx-users] Helicity   Justin Lemkul
      • [gmx-users] Helicity   shivangi nangia
• [gmx-users] A quick question regarding topology generation   Agnivo Gosai
  • [gmx-users] A quick question regarding topology generation   Justin Lemkul
• [gmx-users] pdb2gmx question - protonation   Agnivo Gosai
  • [gmx-users] pdb2gmx question - protonation   Justin Lemkul
• [gmx-users] Conversion of Harmonic potential parameters to Morse potential parameters   Jashimuddin Ashraf
• [gmx-users] Changing atom names from pdb to gro in editconf   Rebeca García Fandiño
  • [gmx-users] Changing atom names from pdb to gro in editconf   Justin Lemkul
• [gmx-users] Question on forcefields?   sujithkakkat .
  • [gmx-users] Question on forcefields?   Yuri Garmay
• [gmx-users] New web server for setup of membrane simulation systems   Jochen Hub
• [gmx-users] After solvation and before adding ions, number of molecules does not agree   Thomas Lipscomb
• [gmx-users] H-Bonding residues against specific frames   Agnivo Gosai
  • [gmx-users] H-Bonding residues against specific frames   Justin Lemkul
• [gmx-users] Salt bridge calculation using GROMACS analysis tools   Agnivo Gosai
• [gmx-users] Free energy calculations with pull code and umbrella sampling   Kortzak, Daniel
• [gmx-users] Query regarding generation of gaps between lipid molecules after minimisation even after using position restraints   Antara mazumdar
  • [gmx-users] Query regarding generation of gaps between lipid molecules after minimisation even after using position restraints   Justin Lemkul
• [gmx-users] A question regarding electrostatic and coulomb energies.   IÑIGO SAENZ
  • [gmx-users] A question regarding electrostatic and coulomb energies.   Mark Abraham
• [gmx-users] g_rms with two trajectories   Julian
  • [gmx-users] g_rms with two trajectories   Erik Marklund
• [gmx-users] ERROR OBTAINED FOR NVT OF DOPC AND PROTEIN SIMULATIONS   Antara mazumdar
  • [gmx-users] ERROR OBTAINED FOR NVT OF DOPC AND PROTEIN SIMULATIONS   Justin Lemkul
• [gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg   Antara mazumdar
  • [gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg   Justin Lemkul
• [gmx-users] pH during free energy calculation   vivek sharma
  • [gmx-users] pH during free energy calculation   Justin Lemkul
• [gmx-users] g_rms with two trajectories   Julian
  • [gmx-users] g_rms with two trajectories   Erik Marklund
  • [gmx-users] g_rms with two trajectories   Smith, Micholas D.
  • [gmx-users] g_rms with two trajectories   Julian
• [gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg   Agnivo Gosai
  • [gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg   Justin Lemkul
• [gmx-users] Umbrella Sampling and histograms smoothness   Agnivo Gosai
  • [gmx-users] Umbrella Sampling and histograms smoothness   Justin Lemkul
• [gmx-users] Umbrella Sampling and histograms smoothness   Agnivo Gosai
  • [gmx-users] Umbrella Sampling and histograms smoothness   Justin Lemkul
    • [gmx-users] Umbrella Sampling and histograms smoothness   lloyd riggs
• [gmx-users] Insufficient disk space error   salam pradeep
  • [gmx-users] Insufficient disk space error   Mark Abraham
• [gmx-users] counting dihedral transitions not working with gmx angle   Cristi Amariei
  • [gmx-users] counting dihedral transitions not working with gmx angle   Mark Abraham
• [gmx-users] Effect of time step size   Faezeh Pousaneh
  • [gmx-users] Effect of time step size   Mark Abraham
    • [gmx-users] Effect of time step size   Faezeh Pousaneh
      • [gmx-users] Effect of time step size   Justin Lemkul
      • [gmx-users] Effect of time step size   Faezeh Pousaneh
      • [gmx-users] Effect of time step size   Justin Lemkul
      • [gmx-users] Effect of time step size   Faezeh Pousaneh
      • [gmx-users] Effect of time step size   Justin Lemkul
      • [gmx-users] Effect of time step size   Faezeh Pousaneh
      • [gmx-users] Effect of time step size   Justin Lemkul
      • [gmx-users] Effect of time step size   Faezeh Pousaneh
• [gmx-users] What is wrong with enthalpy?   Igor Shchechkin
  • [gmx-users] What is wrong with enthalpy?   David van der Spoel
• [gmx-users] After solvation and before adding ions, number of molecules does not agree   Thomas Lipscomb
• [gmx-users] counting dihedral transitions not working with gmx angle (Mark Abraham)   Cristi Amariei
  • [gmx-users] counting dihedral transitions not working with gmx angle (Mark Abraham)   Cristi Amariei
    • [gmx-users] counting dihedral transitions not working with gmx angle (Mark Abraham)   Mark Abraham
• [gmx-users] trajectory tools don't work with large .xtc / .trr files   Wojciech Kopeć
  • [gmx-users] trajectory tools don't work with large .xtc / .trr files   Rafael R. Pappalardo
    • [gmx-users] trajectory tools don't work with large .xtc / .trr files   Mark Abraham
• [gmx-users] msd calculation   mah maz
• [gmx-users] How to reply a message?   Igor Shchechkin
  • [gmx-users] How to reply a message?   Justin Lemkul
• [gmx-users] special coulombic interaction in 1-3 atoms (bonded atoms)   Ting Zheng
  • [gmx-users] special coulombic interaction in 1-3 atoms (bonded atoms)   Mark Abraham
• [gmx-users] the issue of calculation of viscosity with NEMD   陈思言
  • [gmx-users] the issue of calculation of viscosity with NEMD   David van der Spoel
• [gmx-users] Insertion of a carbon nanotube in a system   soumadwip ghosh
  • [gmx-users] Insertion of a carbon nanotube in a system   Justin Lemkul
• [gmx-users] Gromacs's FTP site problems   Silvio a Beccara
  • [gmx-users] Gromacs's FTP site problems   Mark Abraham
• [gmx-users] GAFF and alkynes   Rebeca García Fandiño
  • [gmx-users] GAFF and alkynes   Justin Lemkul
• [gmx-users] What is wrong with enthalpy?   Igor Shchechkin
• [gmx-users] GAFF and alkynes   Rebeca García Fandiño
  • [gmx-users] GAFF and alkynes   Justin Lemkul
• [gmx-users] Can only find GPU'S on first node   Barnett, James W
  • [gmx-users] Can only find GPU'S on first node   Smith, Micholas D.
• [gmx-users] how to calculate angles (molecules directions)   Maryam Kowsar
  • [gmx-users] Fwd: how to calculate angles (molecules directions)   Maryam Kowsar
    • [gmx-users] Fwd: how to calculate angles (molecules directions)   Christopher Neale
      • [gmx-users] Fwd: how to calculate angles (molecules directions)   Maryam Kowsar
      • [gmx-users] Fwd: how to calculate angles (molecules directions)   Christopher Neale
      • [gmx-users] Fwd: how to calculate angles (molecules directions)   Maryam Kowsar
      • [gmx-users] Fwd: how to calculate angles (molecules directions)   Christopher Neale
      • [gmx-users] Fwd: how to calculate angles (molecules directions)   Maryam Kowsar
• [gmx-users] Semiisotropic pressure coupling   shivangi nangia
  • [gmx-users] Semiisotropic pressure coupling   Justin Lemkul
    • [gmx-users] Semiisotropic pressure coupling   Christopher Neale
      • [gmx-users] Semiisotropic pressure coupling   Justin Lemkul
      • [gmx-users] Semiisotropic pressure coupling   Thomas Piggot
      • [gmx-users] Semiisotropic pressure coupling   Piggot T.
      • [gmx-users] Semiisotropic pressure coupling   Justin Lemkul
      • [gmx-users] Semiisotropic pressure coupling   Christopher Neale
      • [gmx-users] Semiisotropic pressure coupling   shivangi nangia
      • [gmx-users] Semiisotropic pressure coupling   Justin Lemkul
      • [gmx-users] Semiisotropic pressure coupling   shivangi nangia
      • [gmx-users] Semiisotropic pressure coupling   Justin Lemkul
      • [gmx-users] Semiisotropic pressure coupling   shivangi nangia
• [gmx-users] Semiisotropic pressure coupling   shivangi nangia
  • [gmx-users] Semiisotropic pressure coupling   shivangi nangia
    • [gmx-users] Semiisotropic pressure coupling   Justin Lemkul
      • [gmx-users] Semiisotropic pressure coupling   shivangi nangia
      • [gmx-users] Semiisotropic pressure coupling   Justin Lemkul
• [gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff to the cluster "middle"   Christopher Neale
  • [gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff to the cluster "middle"   Christopher Neale
• [gmx-users] Variable force constant in umbrella sampling   Kortzak, Daniel
  • [gmx-users] Variable force constant in umbrella sampling   Christopher Neale
• [gmx-users] ffnonbonded.itp and ffbonded.itp files are missing DPPC somehow   Thomas Lipscomb
  • [gmx-users] ffnonbonded.itp and ffbonded.itp files are missing DPPC somehow   Justin Lemkul
• [gmx-users] gromacs   Abid Channa
  • [gmx-users] gromacs   Christopher Neale
    • [gmx-users] gromacs   Abid Channa
  • [gmx-users] gromacs   Alexander Law
    • [gmx-users] gromacs   Abid Channa
• [gmx-users] make_ndx selection of backbone residues   라지브간디
  • [gmx-users] make_ndx selection of backbone residues   Christopher Neale
• [gmx-users] Variable force constant in umbrella sampling   Kortzak, Daniel
• [gmx-users] Difference between dihedral and torsional angles.   B P
  • [gmx-users] Difference between dihedral and torsional angles.   Justin Lemkul
• [gmx-users] Problem executing do_dssp in gromacs   Aarti rana
  • [gmx-users] Problem executing do_dssp in gromacs   Justin Lemkul
    • [gmx-users] Problem executing do_dssp in gromacs   Aarti rana
      • [gmx-users] Problem executing do_dssp in gromacs   Justin Lemkul
      • [gmx-users] Problem executing do_dssp in gromacs   Justin Lemkul
      • [gmx-users] Problem executing do_dssp in gromacs   Aarti rana
      • [gmx-users] Problem executing do_dssp in gromacs   Justin Lemkul
      • [gmx-users] Problem executing do_dssp in gromacs   Aarti rana
      • [gmx-users] Problem executing do_dssp in gromacs   Justin Lemkul
      • [gmx-users] Problem executing do_dssp in gromacs   Aarti rana
      • [gmx-users] Problem executing do_dssp in gromacs   Justin Lemkul
• [gmx-users] check for bad contacts and/or reduce the time step if appropriate   Daniele Veclani
  • [gmx-users] check for bad contacts and/or reduce the time step if appropriate   Mark Abraham
• [gmx-users] multiple ligands topology   Jennifer Vo
  • [gmx-users] multiple ligands topology   Justin Lemkul
    • [gmx-users] multiple ligands topology   Jennifer Vo
      • [gmx-users] multiple ligands topology   Justin Lemkul
      • [gmx-users] multiple ligands topology   Jennifer Vo
      • [gmx-users] multiple ligands topology   Justin Lemkul
      • [gmx-users] multiple ligands topology   Jennifer Vo
      • [gmx-users] multiple ligands topology   Justin Lemkul
      • [gmx-users] multiple ligands topology   Jennifer Vo
• [gmx-users] Flat bottom position restraints   Sabine Reisser
  • [gmx-users] Flat bottom position restraints   Sabine Reisser
    • [gmx-users] Flat bottom position restraints   Sabine Reisser
• [gmx-users] calculating interaction energies of dimers and ligand   RJ
  • [gmx-users] calculating interaction energies of dimers and ligand   Justin Lemkul
• [gmx-users] merge group   BIRD
  • [gmx-users] merge group   Justin Lemkul
• [gmx-users] [ constraints ] in .rtp database not recognized by pdb2gmx   Barnett, James W
  • [gmx-users] [ constraints ] in .rtp database not recognized by pdb2gmx   Justin Lemkul
• [gmx-users] electric fields   mah maz
  • [gmx-users] electric fields   mah maz
    • [gmx-users] electric fields   Justin Lemkul
      • [gmx-users] electric fields   David van der Spoel
      • [gmx-users] electric fields   Justin Lemkul
    • [gmx-users] electric fields   mah maz
      • [gmx-users] electric fields   David van der Spoel
      • [gmx-users] electric fields   mah maz
• [gmx-users] Comb. Rule 2 LJ Params. Being Stored in .tpr as Rule 1 and Vice Versa?   Barnett, James W
  • [gmx-users] Comb. Rule 2 LJ Params. Being Stored in .tpr as Rule 1 and Vice Versa?   Justin Lemkul
• [gmx-users] GAFF and alkynes (Justin Lemkul)   Rebeca García Fandiño
  • [gmx-users] GAFF and alkynes (Justin Lemkul)   Justin Lemkul
• [gmx-users] Larger simulation times because of many [ pairs ]?   Fernando Yrazu
  • [gmx-users] Larger simulation times because of many [ pairs ]?   Mark Abraham
• [gmx-users] Fwd: Odd behavior in log files for two simulations with only different nstlog for Gromacs 5.0.4   Shuxiang Li
  • [gmx-users] Fwd: Odd behavior in log files for two simulations with only different nstlog for Gromacs 5.0.4   Christopher Neale
    • [gmx-users] Fwd: Odd behavior in log files for two simulations with only different nstlog for Gromacs 5.0.4   Justin Lemkul
      • [gmx-users] Fwd: Odd behavior in log files for two simulations with only different nstlog for Gromacs 5.0.4   Mark Abraham
• [gmx-users] How to examine our created topology   Faezeh Pousaneh
  • [gmx-users] How to examine our created topology   Justin Lemkul
    • [gmx-users] How to examine our created topology   Faezeh Pousaneh
      • [gmx-users] How to examine our created topology   Justin Lemkul
• [gmx-users] Umbrella sampling restraining potential   Agnivo Gosai
  • [gmx-users] Umbrella sampling restraining potential   Justin Lemkul
• [gmx-users] lower Area per lipid for DPPC with CHARMM36   tarak karmakar
  • [gmx-users] lower Area per lipid for DPPC with CHARMM36   Justin Lemkul
    • [gmx-users] lower Area per lipid for DPPC with CHARMM36   tarak karmakar
      • [gmx-users] lower Area per lipid for DPPC with CHARMM36   tarak karmakar
• [gmx-users] error: Atom 1 in multiple Energy Mon. groups   nazli kashani javid
  • [gmx-users] error: Atom 1 in multiple Energy Mon. groups   Justin Lemkul
    • [gmx-users] error: Atom 1 in multiple Energy Mon. groups   nazli kashani javid
      • [gmx-users] error: Atom 1 in multiple Energy Mon. groups   Justin Lemkul
      • [gmx-users] error: Atom 1 in multiple Energy Mon. groups   nazli kashani javid
      • [gmx-users] error: Atom 1 in multiple Energy Mon. groups   Justin Lemkul
      • [gmx-users] error: Atom 1 in multiple Energy Mon. groups   nazli kashani javid
• [gmx-users] Semiisotropic pressure coupling   Justin Lemkul
  • [gmx-users] Semiisotropic pressure coupling   Justin Lemkul
    • [gmx-users] Semiisotropic pressure coupling   shivangi nangia
      • [gmx-users] Semiisotropic pressure coupling   Justin Lemkul
      • [gmx-users] Semiisotropic pressure coupling   shivangi nangia
      • [gmx-users] Semiisotropic pressure coupling   shivangi nangia
      • [gmx-users] Semiisotropic pressure coupling   tarak karmakar
      • [gmx-users] Semiisotropic pressure coupling   Justin Lemkul
      • [gmx-users] Semiisotropic pressure coupling   tarak karmakar
      • [gmx-users] Semiisotropic pressure coupling   Justin Lemkul
• [gmx-users] NVT step   asasa qsqs
  • [gmx-users] NVT step   Justin Lemkul
• [gmx-users] Can only find GPU'S on first node   Barnett, James W
• [gmx-users] Re;calculating interaction energies of dimers and ligand   라지브간디
• [gmx-users] Re;calculating interaction energies of dimers and ligand   RJ
  • [gmx-users] Re; calculating interaction energies of dimers and ligand   Justin Lemkul
• [gmx-users] Regarding DSSP   HANNIBAL LECTER
  • [gmx-users] Regarding DSSP   Justin Lemkul
    • [gmx-users] Regarding DSSP   HANNIBAL LECTER
      • [gmx-users] Regarding DSSP   Justin Lemkul
      • [gmx-users] Regarding DSSP   HANNIBAL LECTER
      • [gmx-users] Regarding DSSP   Justin Lemkul
      • [gmx-users] Regarding DSSP   HANNIBAL LECTER
      • [gmx-users] Regarding DSSP   Justin Lemkul
      • [gmx-users] Regarding DSSP   HANNIBAL LECTER
      • [gmx-users] Regarding DSSP   Justin Lemkul
      • [gmx-users] Regarding DSSP   HANNIBAL LECTER
      • [gmx-users] Regarding DSSP   Justin Lemkul
      • [gmx-users] Regarding DSSP   HANNIBAL LECTER
      • [gmx-users] Regarding DSSP   Mark Abraham
• [gmx-users] Plz help File input/output error: Cannot write trajectory frame;   salam pradeep
• [gmx-users] breaking S-S bond using pdb2gmx   Sahithya S Iyer
  • [gmx-users] breaking S-S bond using pdb2gmx   Justin Lemkul
    • [gmx-users] breaking S-S bond using pdb2gmx   Sahithya S Iyer
• [gmx-users] GPU Installation   Carmen Di Giovanni
  • [gmx-users] GPU Installation   Mark Abraham
    • [gmx-users] GPU Installation   Carmen Di Giovanni
• [gmx-users] Problem in new version of Gromacs 5.0   Faezeh Pousaneh
  • [gmx-users] Problem in new version of Gromacs 5.0   Justin Lemkul
    • [gmx-users] Problem in new version of Gromacs 5.0   Faezeh Pousaneh
      • [gmx-users] Problem in new version of Gromacs 5.0   Mark Abraham
      • [gmx-users] Problem in new version of Gromacs 5.0   Faezeh Pousaneh
      • [gmx-users] Problem in new version of Gromacs 5.0   Mark Abraham
• [gmx-users] Double counting of h-bonds g_hbond:issue   Udaya Dahal
  • [gmx-users] Double counting of h-bonds g_hbond:issue   Justin Lemkul
    • [gmx-users] Double counting of h-bonds g_hbond:issue   Udaya Dahal
      • [gmx-users] Double counting of h-bonds g_hbond:issue   Justin Lemkul
      • [gmx-users] Double counting of h-bonds g_hbond:issue   Udaya Dahal
• [gmx-users] Heads up on Intel MPI 5.0.1.035 bug in mpigcc causing cmake problems   Åke Sandgren
  • [gmx-users] Heads up on Intel MPI 5.0.1.035 bug in mpigcc causing cmake problems   Åke Sandgren
  • [gmx-users] Heads up on Intel MPI 5.0.1.035 bug in mpigcc causing cmake problems   Szilárd Páll
• [gmx-users] mdrun -nsteps   Sabine Reisser
  • [gmx-users] mdrun -nsteps   Tsjerk Wassenaar
  • [gmx-users] mdrun -nsteps   Mark Abraham
    • [gmx-users] mdrun -nsteps   Sabine Reisser
• [gmx-users] ffbond.itp   marzieh dehghan
  • [gmx-users] ffbond.itp   Justin Lemkul
• [gmx-users] [MGMS-DS]: Molecular Modelling Workshop March 9-11, 2015 in Erlangen, Germany   Harald Lanig
• [gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT   Jin Zhang
  • [gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT   Justin Lemkul
• [gmx-users] simulation of heme along with h2o2   Sanchaita Rajkhowa
  • [gmx-users] simulation of heme along with h2o2   Justin Lemkul
    • [gmx-users] simulation of heme along with h2o2   Sanchaita Rajkhowa
      • [gmx-users] simulation of heme along with h2o2   Sanchaita Rajkhowa
      • [gmx-users] simulation of heme along with h2o2   Justin Lemkul
      • [gmx-users] simulation of heme along with h2o2   Justin Lemkul
• [gmx-users] GPU low performance   Carmen Di Giovanni
  • [gmx-users] GPU low performance   Justin Lemkul
    • [gmx-users] GPU low performance   Carmen Di Giovanni
      • [gmx-users] GPU low performance   Barnett, James W
      • [gmx-users] GPU low performance   Justin Lemkul
      • [gmx-users] GPU low performance   Carmen Di Giovanni
      • [gmx-users] GPU low performance   Justin Lemkul
      • [gmx-users] GPU low performance   Szilárd Páll
      • [gmx-users] GPU low performance   Carmen Di Giovanni
      • [gmx-users] GPU low performance   Szilárd Páll
      • [gmx-users] GPU low performance   Szilárd Páll
      • [gmx-users] GPU low performance   Carmen Di Giovanni
      • [gmx-users] GPU low performance   Carmen Di Giovanni
• [gmx-users] Problems Running Gromacs v-5.0.4   Stephen P. Molnar
• [gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT (Justin Lemkul)   Jin Zhang
• [gmx-users] GPU low performance   Szilárd Páll
  • [gmx-users] GPU low performance   Carmen Di Giovanni
    • [gmx-users] GPU low performance   Szilárd Páll
      • [gmx-users] GPU low performance   Carmen Di Giovanni
      • [gmx-users] GPU low performance   Szilárd Páll
      • [gmx-users] GPU low performance   Carmen Di Giovanni
  • [gmx-users] GPU low performance   Carmen Di Giovanni
• [gmx-users] Need of mdp files   Antara mazumdar
  • [gmx-users] Need of mdp files   Justin Lemkul
• [gmx-users] Imidazolium ring opening during energy minimization   Meena Singh
  • [gmx-users] Imidazolium ring opening during energy minimization   Justin Lemkul
• [gmx-users] topolbuild error   Zahra Ghanbari
• [gmx-users] check_bonds_timestep() only reports the first suspicious bond   Mario Fernández Pendás
  • [gmx-users] check_bonds_timestep() only reports the first suspicious bond   Mark Abraham
    • [gmx-users] check_bonds_timestep() only reports the first suspicious bond   Mario Fernández Pendás
• [gmx-users] topolbuild error   Ray, Bruce D
  • [gmx-users] topolbuild error   Zahra Ghanbari
• [gmx-users] DNA-Protein complex MD failing   virginia miguel
  • [gmx-users] DNA-Protein complex MD failing   Justin Lemkul
• [gmx-users] topolbuild error   Ray, Bruce D
• [gmx-users] Umbrella Sampling and Histogram   Agnivo Gosai
  • [gmx-users] Umbrella Sampling and Histogram   Justin Lemkul
• [gmx-users] Heating a wall adjacent to the fluid   Rahul Chatterjee
  • [gmx-users] Heating a wall adjacent to the fluid   Justin Lemkul
• [gmx-users] MD run failed..   Kalyanashis Jana
  • [gmx-users] MD run failed..   Justin Lemkul
    • [gmx-users] MD run failed..   HANNIBAL LECTER
      • [gmx-users] MD run failed..   Justin Lemkul
      • [gmx-users] MD run failed..   HANNIBAL LECTER
• [gmx-users] DNA-Protein complex MD failing   virginia miguel
  • [gmx-users] DNA-Protein complex MD failing   Justin Lemkul
• [gmx-users] hello every one   rajan kumar
• [gmx-users] How to examine our created topology   Faezeh Pousaneh
  • [gmx-users] How to examine our created topology   Justin Lemkul
    • [gmx-users] How to examine our created topology   Faezeh Pousaneh
• [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   David McGiven
  • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   Szilárd Páll
    • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   David McGiven
      • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   Harry Mark Greenblatt
      • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   David McGiven
      • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   Harry Mark Greenblatt
      • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   Justin Lemkul
      • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   Szilárd Páll
      • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   David McGiven
      • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   Téletchéa Stéphane
      • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   Szilárd Páll
      • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   Téletchéa Stéphane
      • [gmx-users] modified residues and residual charge   Harry Mark Greenblatt
      • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   Szilárd Páll
      • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   Harry Mark Greenblatt
      • [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?   Szilárd Páll
• [gmx-users] Various errors in pulling simulations   Tim Stauch
  • [gmx-users] Various errors in pulling simulations   Justin Lemkul
• [gmx-users] HOW TO CONVERT .XTC FILE TO DCD FORMAT   rajan kumar
  • [gmx-users] HOW TO CONVERT .XTC FILE TO DCD FORMAT   Guillaume Chevrot
  • [gmx-users] HOW TO CONVERT .XTC FILE TO DCD FORMAT   Justin Lemkul
    • [gmx-users] HOW TO CONVERT .XTC FILE TO DCD FORMAT   rajan kumar
  • [gmx-users] HOW TO CONVERT .XTC FILE TO DCD FORMAT   Spyridon Vicatos
• [gmx-users] Simulation of polarizable Carbon nanotubes   Jashimuddin Ashraf
  • [gmx-users] Simulation of polarizable Carbon nanotubes   Justin Lemkul
    • [gmx-users] Simulation of polarizable Carbon nanotubes   Jashimuddin Ashraf
      • [gmx-users] Simulation of polarizable Carbon nanotubes   Peter Kroon
      • [gmx-users] Simulation of polarizable Carbon nanotubes   Justin Lemkul
• [gmx-users] Umbrella Sampling and Histogram   Agnivo Gosai
• [gmx-users] building topology by ATB server   Saman Shahriyari
• [gmx-users] Umbrella Sampling and Histogram   Agnivo Gosai
• [gmx-users] analysis of the secondary structure diagram   nazli kashani javid
  • [gmx-users] analysis of the secondary structure diagram   Justin Lemkul
    • [gmx-users] analysis of the secondary structure diagram   Nazli
• [gmx-users] help to select a faster system for gromacs MD runs   SAKO MIRZAIE
• [gmx-users] mdrun crash   rahul dhakne
  • [gmx-users] mdrun crash   Justin Lemkul
• [gmx-users] ffbond.itp   marzieh dehghan
  • [gmx-users] ffbond.itp   Justin Lemkul
• [gmx-users] g_rdf   leila salimi
  • [gmx-users] g_rdf   Justin Lemkul
    • [gmx-users] g_rdf   leila salimi
• [gmx-users] Error during mdrun   soumadwip ghosh
  • [gmx-users] Error during mdrun   Rohit Farmer
  • [gmx-users] Error during mdrun   Justin Lemkul
• [gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS   Thomas Lipscomb
  • [gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS   Justin Lemkul
    • [gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS   Thomas Lipscomb
      • [gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS   Justin Lemkul
      • [gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS   Thomas Lipscomb
      • [gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS   Justin Lemkul
• [gmx-users] How I extend command   Abid Channa
  • [gmx-users] How I extend command   Rohit Farmer
• [gmx-users] Gromacs in windows 7 with GPU   라지브간디
  • [gmx-users] Gromacs in windows 7 with GPU   Mirco Wahab
• [gmx-users] How I extend command?   Abid Channa
  • [gmx-users] How I extend command?   Chandan Choudhury
• [gmx-users] Application of electric field on membrane   petrishia petrishia
  • [gmx-users] Application of electric field on membrane   David van der Spoel
• [gmx-users] On the collective dynamics in terms of NMA and PCA   James Starlight
  • [gmx-users] On the collective dynamics in terms of NMA and PCA   Tsjerk Wassenaar
    • [gmx-users] On the collective dynamics in terms of NMA and PCA   Tsjerk Wassenaar
      • [gmx-users] On the collective dynamics in terms of NMA and PCA   James Starlight
      • [gmx-users] On the collective dynamics in terms of NMA and PCA   Tsjerk Wassenaar
• [gmx-users] How to perform simulation between initial and final structures   ananyachatterjee
• [gmx-users] Announcement: release of FESetup 1.1   Hannes Loeffler
• [gmx-users] Doubt about energies in a very simple system   IÑIGO SAENZ
  • [gmx-users] Doubt about energies in a very simple system   Justin Lemkul
    • [gmx-users] Doubt about energies in a very simple system   Mark Abraham
    • [gmx-users] Doubt about energies in a very simple system   IÑIGO SAENZ
      • [gmx-users] Doubt about energies in a very simple system   Justin Lemkul
      • [gmx-users] Doubt about energies in a very simple system   IÑIGO SAENZ
      • [gmx-users] Doubt about energies in a very simple system   Mark Abraham
• [gmx-users] several runs   mah maz
  • [gmx-users] several runs   mah maz
    • [gmx-users] several runs   Justin Lemkul
    • [gmx-users] several runs   mah maz
      • [gmx-users] several runs   Mark Abraham
      • [gmx-users] several runs   Victor Rosas Garcia
      • [gmx-users] several runs   Szilárd Páll
      • [gmx-users] several runs   Szilárd Páll
      • [gmx-users] several runs   mah maz
• [gmx-users] Computing Resource - Laptop   Douglas Grahame
  • [gmx-users] Computing Resource - Laptop   Szilárd Páll
    • [gmx-users] Computing Resource - Laptop   Douglas Grahame
      • [gmx-users] Computing Resource - Laptop   Szilárd Páll
      • [gmx-users] Computing Resource - Laptop   VITALY VITALIEVICH CHABAN
• [gmx-users] GROMOS vs. CHARMM dihedrals   Bianca Villavicencio
  • [gmx-users] GROMOS vs. CHARMM dihedrals   Justin Lemkul
• [gmx-users] Umbrella Sampling Dissociation Constant   Alexander Law
  • [gmx-users] Umbrella Sampling Dissociation Constant   Alexander Law
• [gmx-users] Energy minimization for Inositol pyrophosphate   ashish bihani
  • [gmx-users] Energy minimization for Inositol pyrophosphate   Justin Lemkul
• [gmx-users] Application of electric field on membrane   petrishia petrishia
  • [gmx-users] Application of electric field on membrane   Justin Lemkul
• [gmx-users] GTX980 performance   Carmen Di Giovanni
  • [gmx-users] GTX980 performance   Szilárd Páll
    • [gmx-users] GTX980 performance   Carmen Di Giovanni
    • [gmx-users] GTX980 performance   Carmen Di Giovanni
• [gmx-users] g_MSD results for different sampling intervals   Carlos SOTO GARZA
  • [gmx-users] g_MSD results for different sampling intervals   Justin Lemkul
• [gmx-users] screen output and total drift   Ahmet yıldırım
• [gmx-users] Format for nonbonded interactions (pairs) in a residue definition   ashish bihani
• [gmx-users] GNM from .xtc file   rajan kumar
• [gmx-users] User Defined walls and Potential   Karnesh Jain
• [gmx-users] GROMACS 4.6.7 not running on more than 16 MPI threads   Agnivo Gosai
  • [gmx-users] GROMACS 4.6.7 not running on more than 16 MPI threads   Mark Abraham
    • [gmx-users] GROMACS 4.6.7 not running on more than 16 MPI threads   Szilárd Páll
• [gmx-users] GROMACS 4.6.7 not running on more than 16 MPI threads   Agnivo Gosai
• [gmx-users] GROMACS 4.6.7 not running on more than 16 MPI threads   Agnivo Gosai
• [gmx-users] How do we calculate free energy of simulated protein   Seera Suryanarayana
  • [gmx-users] How do we calculate free energy of simulated protein   ms
• [gmx-users] about source code of the old version of GROAMCS (1.0 to 2.0)   Man Hoang Viet
  • [gmx-users] about source code of the old version of GROAMCS (1.0 to 2.0)   Mark Abraham
• [gmx-users] Regarding RDF calculations   soumadwip ghosh
  • [gmx-users] Regarding RDF calculations   Justin Lemkul
• [gmx-users] gromacs_win32.zip CPU version: All MS_Windows version: XP/NT/95 Libraries: Static Size: 17633280 FFTW version: 2.1.3 MPI support: no Installation prefix: customizable Comments: This is an unsupported native port of Gromacs to MS Windows. Start setup.exe after you have extracted all files. Note that you will have to specify the location of cpp in your mdp files - I\'ve included a free cpp in the gromacs binary directory. Contributed by: Erik Lindahl (lindahl at gromacs.org)   Vasiliy Znamenskiy
  • [gmx-users] gromacs_win32.zip CPU version: All MS_Windows version: XP/NT/95 Libraries: Static Size: 17633280 FFTW version: 2.1.3 MPI support: no Installation prefix: customizable Comments: This is an unsupported native port of Gromacs to MS Windows. Start setup.exe after you have extracted all files. Note that you will have to specify the location of cpp in your mdp files - I\'ve included a free cpp in the gromacs binary directory. Contributed by: Erik Lindahl (lindahl at gromacs.org)   ms
• [gmx-users] Error in generated Replica Exchange statistics in log file   Abhi Acharya
  • [gmx-users] Error in generated Replica Exchange statistics in log file   Mark Abraham
• [gmx-users] GMX 5.0 compilation across different platforms   David McGiven
  • [gmx-users] GMX 5.0 compilation across different platforms   Szilárd Páll
    • [gmx-users] GMX 5.0 compilation across different platforms   David McGiven
• [gmx-users] Re : GROMACS 4.6.7 not running on more than 16 MPI threads   Agnivo Gosai
  • [gmx-users] Re : GROMACS 4.6.7 not running on more than 16 MPI threads   Szilárd Páll
• [gmx-users] Problems Running Gromacs v-5.0.4   Stephen P. Molnar
  • [gmx-users] Problems Running Gromacs v-5.0.4   Justin Lemkul
    • [gmx-users] Problems Running Gromacs v-5.0.4   Stephen P. Molnar
• [gmx-users] Re : Re : GROMACS 4.6.7 not running on more than 16 MPI threads   Agnivo Gosai
• [gmx-users] Umbrella sampling Tutorial Fatal Error   Nima Soltani
  • [gmx-users] Fwd: Umbrella sampling Tutorial Fatal Error   Nima Soltani
    • [gmx-users] Fwd: Umbrella sampling Tutorial Fatal Error   Mohsen Ramezanpour
    • [gmx-users] Fwd: Umbrella sampling Tutorial Fatal Error   Justin Lemkul
• [gmx-users] Creating POSRES option for MDP file   Agnivo Gosai
  • [gmx-users] Creating POSRES option for MDP file   Justin Lemkul
• [gmx-users] Questions regarding usage of the covariance analysis   James Starlight
  • [gmx-users] Questions regarding usage of the covariance analysis   James Starlight
  • [gmx-users] Questions regarding usage of the covariance analysis   Justin Lemkul
• [gmx-users] about source code of the old version of GROAMCS (1.0 to 2.0)   Man Hoang Viet

Last message date: Sat Feb 28 21:16:11 CET 2015
Archived on: Sat Feb 28 21:16:13 CET 2015

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