March 2014 Archives by thread

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Starting: Sat Mar 1 04:25:00 CET 2014
Ending: Mon Mar 31 23:49:54 CEST 2014
Messages: 633

• [gmx-users] Two-body Bonded Distance   Justin Lemkul
  • [gmx-users] Two-body Bonded Distance   jolayfield
    • [gmx-users] Two-body Bonded Distance   Justin Lemkul
      • [gmx-users] Two-body Bonded Distance   jolayfield
      • [gmx-users] Two-body Bonded Distance   Justin Lemkul
• [gmx-users] A question about "blowing up"   sujithkakkat .
  • [gmx-users] A question about "blowing up"   Justin Lemkul
    • [gmx-users] A question about "blowing up"   sujith ks
      • [gmx-users] A question about "blowing up"   Justin Lemkul
      • [gmx-users] A question about "blowing up"   sujithkakkat .
      • [gmx-users] A question about "blowing up"   Justin Lemkul
• [gmx-users] g_bar crash   David van der Spoel
• [gmx-users] dihedral doubt   Andres Ortega
  • [gmx-users] dihedral doubt   Justin Lemkul
    • [gmx-users] dihedral doubt   Andres Ortega Guerrero
      • [gmx-users] dihedral doubt   Justin Lemkul
      • [gmx-users] dihedral doubt   Andres Ortega Guerrero
      • [gmx-users] dihedral doubt   Andres Ortega Guerrero
      • [gmx-users] dihedral doubt   Mark Abraham
• [gmx-users] .top file after using amber2gromacs   Chetan Mahajan
  • [gmx-users] .top file after using amber2gromacs   Chetan Mahajan
  • [gmx-users] .top file after using amber2gromacs   Justin Lemkul
    • [gmx-users] .top file after using amber2gromacs   Chetan Mahajan
      • [gmx-users] .top file after using amber2gromacs   Justin Lemkul
• [gmx-users] Two-body Bonded Distance   Mark Abraham
• [gmx-users] Fwd: Regarding trjorder   Venkat Reddy
  • [gmx-users] Fwd: Regarding trjorder   Mark Abraham
    • [gmx-users] Fwd: Regarding trjorder   Venkat Reddy
      • [gmx-users] Fwd: Regarding trjorder   Mark Abraham
• [gmx-users] Question about Improper Dihedral of Charmm in gmx & ParamChem   Tom
  • [gmx-users] Question about Improper Dihedral of Charmm in gmx & ParamChem   Mark Abraham
  • [gmx-users] Question about Improper Dihedral of Charmm in gmx & ParamChem   Justin Lemkul
• [gmx-users] md_pull code in umbrella sampling   Arunima Shilpi
  • [gmx-users] md_pull code in umbrella sampling   Justin Lemkul
• [gmx-users] Regarding structure analysis of DNA   Sathish Kumar
  • [gmx-users] Regarding structure analysis of DNA   Justin Lemkul
• [gmx-users] Set the environment variables of "FFTW3_INCLUDE_DIR" and "FFTW3_LIBRARIES"   Hassan Aaryapour
  • [gmx-users] Set the environment variables of "FFTW3_INCLUDE_DIR" and "FFTW3_LIBRARIES"   Justin Lemkul
    • [gmx-users] Set the environment variables of "FFTW3_INCLUDE_DIR" and "FFTW3_LIBRARIES"   Hassan Aaryapour
• [gmx-users] gromacs.org_gmx-users Digest, Vol 119, Issue 8   sauravsaha
• [gmx-users] md_pull code in umbrella sampling   Arunima Shilpi
  • [gmx-users] md_pull code in umbrella sampling   Christopher Neale
• [gmx-users] No default U-B types charmm   gromacs query
  • [gmx-users] No default U-B types charmm   Justin Lemkul
    • [gmx-users] No default U-B types charmm   gromacs query
      • [gmx-users] No default U-B types charmm   Justin Lemkul
      • [gmx-users] No default U-B types charmm   Justin Lemkul
      • [gmx-users] No default U-B types charmm   Mark Abraham
      • [gmx-users] No default U-B types charmm   gromacs query
      • [gmx-users] No default U-B types charmm   Justin Lemkul
      • [gmx-users] No default U-B types charmm   gromacs query
• [gmx-users] Problems with periodic syatems   susanta haldar
  • [gmx-users] Problems with periodic syatems   Mark Abraham
• [gmx-users] Error Mdrun   Andres Ortega
  • [gmx-users] Error Mdrun   Justin Lemkul
• [gmx-users] Apple cluster   Steve
  • [gmx-users] Apple cluster   Mark Abraham
• [gmx-users] Option:Coupled to heme   Gmail2
  • [gmx-users] Option:Coupled to heme   Justin Lemkul
    • [gmx-users] Option:Coupled to heme   Gmail2
      • [gmx-users] Option:Coupled to heme   Justin Lemkul
• [gmx-users] antiparallel beta sheet   Nidhi Katyal
  • [gmx-users] antiparallel beta sheet   Justin Lemkul
• [gmx-users] REMD Melting Curve   atanu_das
  • [gmx-users] REMD Melting Curve   David van der Spoel
    • [gmx-users] REMD Melting Curve   atanu das
      • [gmx-users] REMD Melting Curve   Justin Lemkul
      • [gmx-users] REMD Melting Curve   atanu das
      • [gmx-users] REMD Melting Curve   Justin Lemkul
• [gmx-users] tip5p and charmm   Rafael I. Silverman y de la Vega
  • [gmx-users] tip5p and charmm   Justin Lemkul
• [gmx-users] dna with charmm36   gromacs query
  • [gmx-users] dna with charmm36   Justin Lemkul
    • [gmx-users] dna with charmm36   gromacs query
      • [gmx-users] dna with charmm36   Justin Lemkul
• [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)   João M. Damas
  • [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)   David van der Spoel
    • [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)   João M. Damas
      • [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)   João M. Damas
      • [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)   João M. Damas
      • [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)   Mark Abraham
• [gmx-users] gromacs.org_gmx-users Digest, Vol 119, Issue 10   Tom
  • [gmx-users] Question about Improper Dihedral of Charmm in gmx &, ParamChem   Justin Lemkul
• [gmx-users] Adding TPO and SEP to G53a6 Forcefield   Pavan Kumar
• [gmx-users] Launching MPI/OpenMP hybrid run   Alexander Björling
  • [gmx-users] Launching MPI/OpenMP hybrid run   Carsten Kutzner
    • [gmx-users] Launching MPI/OpenMP hybrid run   alex.bjorling
      • [gmx-users] Launching MPI/OpenMP hybrid run   Carsten Kutzner
      • [gmx-users] Launching MPI/OpenMP hybrid run   alex.bjorling
  • [gmx-users] Launching MPI/OpenMP hybrid run   Mark Abraham
• [gmx-users] Out of Disk Space   Pavan Kumar
  • [gmx-users] Out of Disk Space   MUSYOKA THOMMAS
    • [gmx-users] Out of Disk Space   Pavan Kumar
      • [gmx-users] Out of Disk Space   Christopher Neale
      • [gmx-users] Out of Disk Space   Dr. Vitaly Chaban
  • [gmx-users] Out of Disk Space   vansh
• [gmx-users] Parsing g_rms binary rmsd comparison matrix   João Henriques
  • [gmx-users] Parsing g_rms binary rmsd comparison matrix   Mark Abraham
    • [gmx-users] Parsing g_rms binary rmsd comparison matrix   João Henriques
      • [gmx-users] Parsing g_rms binary rmsd comparison matrix   Mark Abraham
• [gmx-users] access to gmx   Mostafa Javaheri
  • [gmx-users] access to gmx   Justin Lemkul
• [gmx-users] SImulation with urea   bharat gupta
  • [gmx-users] SImulation with urea   Justin Lemkul
    • [gmx-users] SImulation with urea   Mark Abraham
• [gmx-users] gmx gangle in the development version of gromacs   Eric Smoll
  • [gmx-users] gmx gangle in the development version of gromacs   Teemu Murtola
• [gmx-users] SImulation with urea   bharat gupta
• [gmx-users] pbc problems   申昊
  • [gmx-users] pbc problems   Justin Lemkul
• [gmx-users] how to set pair list buffer when use cutoff scheme = group setup   zhonghe xu
• [gmx-users] pbc problems   申昊
  • [gmx-users] pbc problems   Justin Lemkul
• [gmx-users] inclusion of water in gromacs input files   Chetan Mahajan
  • [gmx-users] inclusion of water in gromacs input files   Justin Lemkul
    • [gmx-users] inclusion of water in gromacs input files   Chetan Mahajan
      • [gmx-users] inclusion of water in gromacs input files   Justin Lemkul
• [gmx-users] charge group number   Chetan Mahajan
  • [gmx-users] charge group number   Justin Lemkul
• [gmx-users] Adding Urea in simulation   bharat gupta
  • [gmx-users] Adding Urea in simulation   Justin Lemkul
    • [gmx-users] Question about the electric field?   Xianwei Wang
• [gmx-users] Fwd: Need Help in Gromacs   Balasubramani GL
  • [gmx-users] Fwd: Need Help in Gromacs   Justin Lemkul
• [gmx-users] Adding Urea in simulation   bharat gupta
• [gmx-users] entropy calculation   申昊
  • [gmx-users] entropy calculation   Justin Lemkul
• [gmx-users] Generate many random configurations   rankinb
  • [gmx-users] Generate many random configurations   Mark Abraham
  • [gmx-users] Generate many random configurations   rankinb
    • [gmx-users] Generate many random configurations   Justin Lemkul
      • [gmx-users] Generate many random configurations   Tsjerk Wassenaar
      • [gmx-users] Generate many random configurations   rankinb
      • [gmx-users] Generate many random configurations   Justin Lemkul
      • [gmx-users] Generate many random configurations   rankinb
      • [gmx-users] Generate many random configurations   Justin Lemkul
      • [gmx-users] Generate many random configurations   rankinb
      • [gmx-users] Generate many random configurations   Justin Lemkul
      • [gmx-users] Generate many random configurations   rankinb
      • [gmx-users] Generate many random configurations   Justin Lemkul
• [gmx-users] (no subject)   cesteban at unsl.edu.ar
• [gmx-users] help with g_puckering   cesteban at unsl.edu.ar
  • [gmx-users] help with g_puckering   Justin Lemkul
• [gmx-users] gromacs.org_gmx-users Digest, Vol 119, Issue 23   Eric Smoll
• [gmx-users] sigma unit conversion   Chetan Mahajan
• [gmx-users] gmx gangle in the development version of gromacs   Teemu Murtola
• [gmx-users] (no subject)   Prajisha Sujaya
  • [gmx-users] (no subject)   Justin Lemkul
• [gmx-users] REST2 with gromacs-4.5.5 plumed2.2.0 -hrex   Saravanan
• [gmx-users] how to split gromacs tpr file   sidra rafi
  • [gmx-users] how to split gromacs tpr file   Mark Abraham
    • [gmx-users] how to split gromacs tpr file   sidra rafi
• [gmx-users] Fwd: sigma unit conversion   Barnett, James W.
• [gmx-users] ParamChem CHARMM to GROMACS conversion   Justin Lemkul
  • [gmx-users] ParamChem CHARMM to GROMACS conversion   Albert
• [gmx-users] impropers in Gromacs and acepype tool   Chetan Mahajan
  • [gmx-users] impropers in Gromacs and acepype tool   Justin Lemkul
    • [gmx-users] impropers in Gromacs and acepype tool   Chetan Mahajan
      • [gmx-users] impropers in Gromacs and acepype tool   Chetan Mahajan
      • [gmx-users] impropers in Gromacs and acepype tool   Justin Lemkul
      • [gmx-users] impropers in Gromacs and acepype tool   Justin Lemkul
• [gmx-users] angle between benzene rings   Sanku M
  • [gmx-users] angle between benzene rings   Justin Lemkul
• [gmx-users] Regarding the change in number of processors of simulation job   Sujit Sarkar
• [gmx-users] MM-GB/SA analysis in Gromacs   kannan
• [gmx-users] Assistance required for ligand parameterization   Balasubramani GL
  • [gmx-users] Assistance required for ligand parameterization   Justin Lemkul
• [gmx-users] Area of Mixed lipid Bilayer   Nikhil Agrawal
  • [gmx-users] Area of Mixed lipid Bilayer   Justin Lemkul
  • [gmx-users] Area of Mixed lipid Bilayer   César Ávila
• [gmx-users] Bug in gromacs-5.0-beta2 [Jan 29]   Pavan Ghatty
  • [gmx-users] Bug in gromacs-5.0-beta2 [Jan 29]   Mark Abraham
• [gmx-users] Using pull code to keep two monomers near each other   Michael Daily
  • [gmx-users] Using pull code to keep two monomers near each other   Justin Lemkul
    • [gmx-users] Using pull code to keep two monomers near each other   Sébastien Côté
• [gmx-users] Neutralize or add an Ions Concentration for a Membrane Simulation?   Andres Ortega
  • [gmx-users] Neutralize or add an Ions Concentration for a Membrane Simulation?   Justin Lemkul
• [gmx-users] Area of Mixed lipid Bilayer   ABEL Stephane 175950
• [gmx-users] Area of Mixed lipid Bilayer   Björn Sommer
• [gmx-users] SETTLE and LINCS   Andres Ortega
  • [gmx-users] SETTLE and LINCS   Justin Lemkul
• [gmx-users] Docking validation   Mostafa Javaheri
  • [gmx-users] Docking validation   Justin Lemkul
• [gmx-users] CHARMM36 force field available for GROMACS   jim
  • [gmx-users] CHARMM36 force field available for GROMACS   Justin Lemkul
    • [gmx-users] CHARMM36 force field available for GROMACS   Jim
      • [gmx-users] CHARMM36 force field available for GROMACS   Justin Lemkul
      • [gmx-users] CHARMM36 force field available for GROMACS   Jim
      • [gmx-users] CHARMM36 force field available for GROMACS   Justin Lemkul
      • [gmx-users] CHARMM36 force field available for GROMACS   Tsjerk Wassenaar
      • [gmx-users] CHARMM36 force field available for GROMACS   Mark Abraham
      • [gmx-users] CHARMM36 force field available for GROMACS   Justin Lemkul
      • [gmx-users] CHARMM36 force field available for GROMACS   Gmail2
      • [gmx-users] CHARMM36 force field available for GROMACS   Justin Lemkul
• [gmx-users] tip3p   Chetan Mahajan
  • [gmx-users] tip3p   Mark Abraham
    • [gmx-users] tip3p   Chetan Mahajan
      • [gmx-users] tip3p   Justin Lemkul
• [gmx-users] parameters problem   Nidhi Katyal
  • [gmx-users] parameters problem   Justin Lemkul
    • [gmx-users] parameters problem   Nidhi Katyal
      • [gmx-users] parameters problem   Justin Lemkul
      • [gmx-users] parameters problem   Nidhi Katyal
      • [gmx-users] parameters problem   Mark Abraham
      • [gmx-users] parameters problem   Nidhi Katyal
      • [gmx-users] parameters problem   Justin Lemkul
• [gmx-users] Performing protein-ligand GROMACS MD under pH 5 conditions   MUSYOKA THOMMAS
  • [gmx-users] Performing protein-ligand GROMACS MD under pH 5 conditions   Justin Lemkul
  • [gmx-users] Performing protein-ligand GROMACS MD under pH 5 conditions   Mark Abraham
• [gmx-users] Spatial distribution   Norbert GARNIER
  • [gmx-users] Spatial distribution   Justin Lemkul
• [gmx-users] Problem in extending simulation with state.cpt while changing number of cores   Bappa Ghosh
  • [gmx-users] Problem in extending simulation with state.cpt while changing number of cores   Mark Abraham
    • [gmx-users] Problem in extending simulation with state.cpt while changing number of cores   Bappa Ghosh
      • [gmx-users] Problem in extending simulation with state.cpt while changing number of cores   Mark Abraham
• [gmx-users] about insane.py script on martini website.   jhosamelly
  • [gmx-users] about insane.py script on martini website.   Tsjerk Wassenaar
• [gmx-users] Simulation with Ligand   Kavyashree M
  • [gmx-users] Simulation with Ligand   Mark Abraham
• [gmx-users] swm4-ndp water with anisotropic polarizibility   Peter Hamm
  • [gmx-users] swm4-ndp water with anisotropic polarizibility   Justin Lemkul
    • [gmx-users] swm4-ndp water with anisotropic polarizibility   Peter Hamm
• [gmx-users] choosing Ensemble for production MD run   Archana Sonawani-Jagtap
  • [gmx-users] choosing Ensemble for production MD run   Mark Abraham
• [gmx-users] g_energy (energygrps)   Atila Petrosian
  • [gmx-users] g_energy (energygrps)   Justin Lemkul
  • [gmx-users] g_energy (energygrps)   Mark Abraham
• [gmx-users] g_energy (energygrps)   Atila Petrosian
  • [gmx-users] g_energy (energygrps)   Mark Abraham
• [gmx-users] g_energy (energygrps)   Atila Petrosian
• [gmx-users] g_energy (energygrps)   Atila Petrosian
• [gmx-users] No default Angle types   Mayank Dixit
• [gmx-users] No default Angle types   Mayank Dixit
  • [gmx-users] No default Angle types   Justin Lemkul
• [gmx-users] Problem with small number of water molecules   ehs
  • [gmx-users] Problem with small number of water molecules   Justin Lemkul
    • [gmx-users] Problem with small number of water molecules   ehs
      • [gmx-users] Problem with small number of water molecules   Justin Lemkul
• [gmx-users] Thread affinity error when Running Gromacs 4.6.3 on Bluegene/P   arrow50311
  • [gmx-users] Thread affinity error when Running Gromacs 4.6.3 on Bluegene/P   Szilárd Páll
    • [gmx-users] Thread affinity error when Running Gromacs 4.6.3 on Bluegene/P   Mark Abraham
• [gmx-users] why not coordinates from cpt file   gromacs query
  • [gmx-users] why not coordinates from cpt file   Justin Lemkul
• [gmx-users] FW: error after 1ns of md run during production   Sucharita Dey
  • [gmx-users] FW: error after 1ns of md run during production   Mark Abraham
• [gmx-users] error after 1ns of md run during production   sucharita
• [gmx-users] surprising: what's the reason?   Chetan Mahajan
  • [gmx-users] surprising: what's the reason?   Tsjerk Wassenaar
    • [gmx-users] surprising: what's the reason?   Chetan Mahajan
      • [gmx-users] surprising: what's the reason?   Mark Abraham
      • [gmx-users] surprising: what's the reason?   Chetan Mahajan
      • [gmx-users] surprising: what's the reason?   Tsjerk Wassenaar
      • [gmx-users] surprising: what's the reason?   Mark Abraham
      • [gmx-users] surprising: what's the reason?   Chetan Mahajan
      • [gmx-users] surprising: what's the reason?   Chetan Mahajan
      • [gmx-users] surprising: what's the reason?   Mark Abraham
• [gmx-users] Regarding calculation of torsion angles in DNA   Sathish Kumar
  • [gmx-users] Regarding calculation of torsion angles in DNA   Justin Lemkul
• [gmx-users] Single or Double precision?   Dario Corrada
  • [gmx-users] Single or Double precision?   Szilárd Páll
    • [gmx-users] Single or Double precision?   Mark Abraham
• [gmx-users] Dubious results with NPT   sujithkakkat .
  • [gmx-users] Dubious results with NPT   Justin Lemkul
    • [gmx-users] Dubious results with NPT   sujithkakkat .
      • [gmx-users] Dubious results with NPT   Mark Abraham
      • [gmx-users] Dubious results with NPT   sujithkakkat .
• [gmx-users] GPU problem   pratibha kapoor
  • [gmx-users] GPU problem   Mark Abraham
• [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   arrow50311
  • [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   Mark Abraham
  • [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   Christopher Neale
    • [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   arrow50311
      • [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   Mark Abraham
      • [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   Christopher Neale
      • [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   arrow50311
      • [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P   Mark Abraham
• [gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI: version 1.7.4-2 for OpenMPI is compatibel   Christian Wagner
  • [gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI: version 1.7.4-2 for OpenMPI is compatibel   Szilárd Páll
    • [gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI: version 1.7.4-2 for OpenMPI is compatibel   Mirco Wahab
    • [gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI: version 1.7.4-2 for OpenMPI is compatibel   Christian Wagner
• [gmx-users] Cross-correlation analysis in multidomain proteins   James Starlight
• [gmx-users] g_tune_pme scalevdw option not working?   João Rodrigues
• [gmx-users] g_tune_pme scalevdw option not working?   Carsten Kutzner
  • [gmx-users] g_tune_pme scalevdw option not working?   João Rodrigues
    • [gmx-users] g_tune_pme scalevdw option not working?   Carsten Kutzner
    • [gmx-users] g_tune_pme scalevdw option not working?   Carsten Kutzner
      • [gmx-users] g_tune_pme scalevdw option not working?   João Rodrigues
      • [gmx-users] g_tune_pme scalevdw option not working?   João Rodrigues
      • [gmx-users] Position restraints   Nimmy McNimmerson
      • [gmx-users] Position restraints   Justin Lemkul
• [gmx-users] No equilibration, annealing   ehs
  • [gmx-users] No equilibration, annealing   Justin Lemkul
• [gmx-users] Golshan Hejazi   Golshan Hejazi
• [gmx-users] h_bonds   virk
  • [gmx-users] h_bonds   Justin Lemkul
    • [gmx-users] h_bonds   virk
      • [gmx-users] h_bonds   Justin Lemkul
      • [gmx-users] h_bonds   virk
      • [gmx-users] h_bonds   Mark Abraham
• [gmx-users] looping job: time not updating   gromacs query
  • [gmx-users] looping job: time not updating   Justin Lemkul
    • [gmx-users] looping job: time not updating   gromacs query
      • [gmx-users] looping job: time not updating   Mark Abraham
• [gmx-users] Bond length not finite error   gromacs query
  • [gmx-users] Bond length not finite error   Justin Lemkul
    • [gmx-users] Bond length not finite error   gromacs query
• [gmx-users] genion   Andrew Bostick
  • [gmx-users] genion   Kalyan Reddy
• [gmx-users] multi threading on rocks cluster   michael.b
  • [gmx-users] multi threading on rocks cluster   Mark Abraham
• [gmx-users] g_potential   Neha Gandhi
• [gmx-users] asking for N and C termini for DNA and giving error   Sucharita Dey
  • [gmx-users] asking for N and C termini for DNA and giving error   Justin Lemkul
    • [gmx-users] asking for N and C termini for DNA and giving error   Sucharita Dey
      • [gmx-users] asking for N and C termini for DNA and giving error   Justin Lemkul
      • [gmx-users] asking for N and C termini for DNA and giving error   Sucharita Dey
• [gmx-users] Free energy calculation of a charged system   Valentina
  • [gmx-users] Free energy calculation of a charged system   Dr. Vitaly Chaban
    • [gmx-users] Free energy calculation of a charged system   Valentina
• [gmx-users] Rigid water model   Michelle Aranha
  • [gmx-users] Rigid water model   Mark Abraham
    • [gmx-users] Rigid water model   Michael Shirts
      • [gmx-users] Rigid water model   Michelle Aranha
• [gmx-users] Interaction energy graph   Kannan S
  • [gmx-users] Interaction energy graph   Justin Lemkul
    • [gmx-users] Interaction energy graph   kannan
    • [gmx-users] Interaction energy graph   kannan
      • [gmx-users] Interaction energy graph   Justin Lemkul
      • [gmx-users] Interaction energy graph   kannan
• [gmx-users] Interaction energy   Kannan S
• [gmx-users] Swiss pdb viewer   Nazanin
• [gmx-users] Swiss pdb viewer   Negar Parvizi
  • [gmx-users] Swiss pdb viewer   Justin Lemkul
• [gmx-users] NVT problem   Andres Ortega
  • [gmx-users] NVT problem   Justin Lemkul
    • [gmx-users] NVT problem   Andres Ortega Guerrero
      • [gmx-users] NVT problem   Justin Lemkul
      • [gmx-users] NVT problem   Andres Ortega Guerrero
      • [gmx-users] NVT problem   Justin Lemkul
      • [gmx-users] NVT problem   Andres Ortega Guerrero
      • [gmx-users] NVT problem   Justin Lemkul
      • [gmx-users] NVT problem   Andres Ortega Guerrero
      • [gmx-users] NVT problem   Justin Lemkul
• [gmx-users] problem of running multiple cores   Tom
  • [gmx-users] problem of running multiple cores   Justin Lemkul
• [gmx-users] NVT problem (Justin Lemkul)   Tom
  • [gmx-users] problem of running multiple cores (Tom)   Justin Lemkul
• [gmx-users] ligand binding sampling   Albert
  • [gmx-users] ligand binding sampling   Mark Abraham
• [gmx-users] genion   Andrew Bostick
  • [gmx-users] genion   Justin Lemkul
• [gmx-users] excuse me, I want to ask you some question about bond energy   David van der Spoel
• [gmx-users] enthalpy of ion + protein interaction   Andrew Bostick
  • [gmx-users] enthalpy of ion + protein interaction   Tsjerk Wassenaar
• [gmx-users] binding delta G, H and S for ion-protein   Andrew Bostick
  • [gmx-users] binding delta G, H and S for ion-protein   Justin Lemkul
  • [gmx-users] binding delta G, H and S for ion-protein   Andrew Bostick
    • [gmx-users] binding delta G, H and S for ion-protein   Justin Lemkul
    • [gmx-users] binding delta G, H and S for ion-protein   David van der Spoel
      • [gmx-users] binding delta G, H and S for ion-protein   lloyd riggs
• [gmx-users] binding delta G, H and S for ion-protein   Andrew Bostick
  • [gmx-users] binding delta G, H and S for ion-protein   David van der Spoel
• [gmx-users] How to calculate RMSD between residues   sidra rafi
• [gmx-users] Detection of Internal water along MD trajectory   James Starlight
  • [gmx-users] Detection of Internal water along MD trajectory   Trayder Thomas
• [gmx-users] Compilation issues with GROMACS 5 beta 2   jk
• [gmx-users] Compilation issues with GROMACS 5 beta 2   Roland Schulz
  • [gmx-users] Compilation issues with GROMACS 5 beta 2   jk
• [gmx-users] constraint pulling   leila karami
  • [gmx-users] constraint pulling   Justin Lemkul
• [gmx-users] free energy calculations   michael.b
• [gmx-users] CELLmicrocosmos 2.2.2_1 MembraneEditor Minor Release   Björn Sommer
• [gmx-users] How can I concatenate multiple g96 configurations into a single trajectory?   Andrew DeYoung
  • [gmx-users] How can I concatenate multiple g96 configurations into a single trajectory?   Tsjerk Wassenaar
• [gmx-users] How can I concatenate multiple g96 configurations into a single trajectory?   Andrew DeYoung
  • [gmx-users] How can I concatenate multiple g96 configurations into a single trajectory?   Justin Lemkul
    • [gmx-users] How can I concatenate multiple g96 configurations into a single trajectory?   Mark Abraham
• [gmx-users] PEG residue   dan42
  • [gmx-users] PEG residue   Justin Lemkul
  • [gmx-users] PEG residue   lloyd riggs
  • [gmx-users] PEG residue   Christopher Neale
• [gmx-users] segmentation fault in vanilla TI calculation, death without further noitice   michael.b
  • [gmx-users] segmentation fault in vanilla TI calculation, death without further noitice   michael.b
• [gmx-users] Is cholesterol model available in Charmm36 ff?   davhak
  • [gmx-users] Is cholesterol model available in Charmm36 ff?   davhak
  • [gmx-users] Is cholesterol model available in Charmm36 ff?   Justin Lemkul
    • [gmx-users] Is cholesterol model available in Charmm36 ff?   davhak
      • [gmx-users] Is cholesterol model available in Charmm36 ff?   davhak
      • [gmx-users] Is cholesterol model available in Charmm36 ff?   Justin Lemkul
      • [gmx-users] Is cholesterol model available in Charmm36 ff?   davhak
      • [gmx-users] Is cholesterol model available in Charmm36 ff?   Mark Abraham
• [gmx-users] Cavity size calculation   Praveen Kumar
  • [gmx-users] Cavity size calculation   David van der Spoel
• [gmx-users] binding delta G, H and S for ion-protein   Andrew Bostick
• [gmx-users] creation coordinate file with special distance between system components   Atila Petrosian
  • [gmx-users] creation coordinate file with special distance between system components   Mark Abraham
• [gmx-users] constraint pulling   leila karami
  • [gmx-users] constraint pulling   Justin Lemkul
• [gmx-users] constraint pulling   Thomas Schlesier
• [gmx-users] topology file   Michelle Aranha
  • [gmx-users] topology file   Justin Lemkul
• [gmx-users] missing residues in PDB file   Guo, Yanan
  • [gmx-users] missing residues in PDB file   Andres Ortega Guerrero
• [gmx-users] editconf -box a b c   ehs
  • [gmx-users] editconf -box a b c   Justin Lemkul
    • [gmx-users] editconf -box a b c   ehs
      • [gmx-users] editconf -box a b c   Justin Lemkul
• [gmx-users] Multi-GPU calculation   arrow50311
  • [gmx-users] Multi-GPU calculation   Szilárd Páll
    • [gmx-users] Multi-GPU calculation   arrow50311
      • [gmx-users] Multi-GPU calculation   Mark Abraham
• [gmx-users] plotting rmsf   vansh
  • [gmx-users] plotting rmsf   Mark Abraham
• [gmx-users] Running a single job using 2 different GROMACS version   MUSYOKA THOMMAS
  • [gmx-users] Running a single job using 2 different GROMACS version   Mark Abraham
• [gmx-users] Question about topology construction.   sujithkakkat .
  • [gmx-users] Question about topology construction.   Justin Lemkul
    • [gmx-users] Question about topology construction.   sujith ks
      • [gmx-users] Question about topology construction.   Mark Abraham
• [gmx-users] Parameterisation of transition metal ions in gromacs   sukriti002
  • [gmx-users] Parameterisation of transition metal ions in gromacs   Mark Abraham
• [gmx-users] Error: illegal instruction (core dumped)   Ly Minh Nhat
  • [gmx-users] Error: illegal instruction (core dumped)   Mark Abraham
  • [gmx-users] Error: illegal instruction (core dumped)   ooker
    • [gmx-users] Error: illegal instruction (core dumped)   Mark Abraham
    • [gmx-users] Error: illegal instruction (core dumped)   Justin Lemkul
      • [gmx-users] Error: illegal instruction (core dumped)   ooker
      • [gmx-users] Error: illegal instruction (core dumped)   Justin Lemkul
      • [gmx-users] Error: illegal instruction (core dumped)   Mark Abraham
      • [gmx-users] Error: illegal instruction (core dumped)   Ly Minh Nhat
      • [gmx-users] Error: illegal instruction (core dumped)   Mark Abraham
• [gmx-users] Guidance on how to install Gromacs-5.0-beta2   ooker
• [gmx-users] User-defined potentials and meaning of table extension   Davide Mercadante
  • [gmx-users] User-defined potentials and meaning of table extension   Justin Lemkul
  • [gmx-users] User-defined potentials and meaning of table extension   Mark Abraham
• [gmx-users] Question for bdc = xy   ookami a
  • [gmx-users] Question for bdc = xy   Justin Lemkul
    • [gmx-users] Question for bdc = xy   ookami a
      • [gmx-users] Question for bdc = xy   Justin Lemkul
• [gmx-users] Double parameters   Josip Lovrić
  • [gmx-users] Double parameters   Mark Abraham
    • [gmx-users] Double parameters   Josip Lovrić
• [gmx-users] probability density map   pratibha
  • [gmx-users] probability density map   GtrAngus
  • [gmx-users] probability density map   Erik Marklund
    • [gmx-users] probability density map   Erik Marklund
• [gmx-users] False Atommass and charge?   GtrAngus
  • [gmx-users] False Atommass and charge?   Justin Lemkul
    • [gmx-users] False Atommass and charge?   GtrAngus
      • [gmx-users] False Atommass and charge?   GtrAngus
• [gmx-users] index file group names: Case sensitive   shivangi nangia
  • [gmx-users] index file group names: Case sensitive   Justin Lemkul
• [gmx-users] Unable to generate file.gro with gromacs.4.6.3-1   Collins Nganou
  • [gmx-users] Unable to generate file.gro with gromacs.4.6.3-1   Christopher Neale
  • [gmx-users] Unable to generate file.gro with gromacs.4.6.3-1   Justin Lemkul
    • [gmx-users] Unable to generate file.gro with gromacs.4.6.3-1   Christopher Neale
      • [gmx-users] Unable to generate file.gro with gromacs.4.6.3-1   Mark Abraham
• [gmx-users] Pulling code   Andres Ortega
• [gmx-users] berger lipid parameters in amber99sb-ildn ff   Monoj Mon Kalita
  • [gmx-users] berger lipid parameters in amber99sb-ildn ff   Christopher Neale
• [gmx-users] Velocity Verlet integrator   Mario Fernández Pendás
  • [gmx-users] Velocity Verlet integrator   Michael Shirts
• [gmx-users] free energy of removal of a molecule from the bulk   Valentina
  • [gmx-users] free energy of removal of a molecule from the bulk   Mark Abraham
  • [gmx-users] free energy of removal of a molecule from the bulk   Justin Lemkul
    • [gmx-users] free energy of removal of a molecule from the bulk   Valentina
• [gmx-users] PME on GPU4.6.2)   Albert Romano
  • [gmx-users] PME on GPU4.6.2)   Mark Abraham
• [gmx-users] refcoord-scaling   Chetan Mahajan
  • [gmx-users] refcoord-scaling   Chetan Mahajan
  • [gmx-users] refcoord-scaling   Mark Abraham
    • [gmx-users] refcoord-scaling   Chetan Mahajan
      • [gmx-users] refcoord-scaling   Mark Abraham
      • [gmx-users] refcoord-scaling   Chetan Mahajan
      • [gmx-users] refcoord-scaling   Justin Lemkul
      • [gmx-users] refcoord-scaling   Chetan Mahajan
      • [gmx-users] refcoord-scaling   Justin Lemkul
      • [gmx-users] refcoord-scaling   Chetan Mahajan
      • [gmx-users] refcoord-scaling   Christopher Neale
• [gmx-users] Add atom to .itp file   deep
  • [gmx-users] Add atom to .itp file   Mark Abraham
    • [gmx-users] Add atom to .itp file   Satyadeep Roat
      • [gmx-users] Add atom to .itp file   Justin Lemkul
• [gmx-users] amber ff gromacs   virk
  • [gmx-users] amber ff gromacs   Mark Abraham
• [gmx-users] MPI error in gromacs 4.6   Ankita Naithani
  • [gmx-users] MPI error in gromacs 4.6   Pavan Kumar
    • [gmx-users] MPI error in gromacs 4.6   Ankita Naithani
      • [gmx-users] MPI error in gromacs 4.6   Pavan Kumar
      • [gmx-users] MPI error in gromacs 4.6   Justin Lemkul
      • [gmx-users] MPI error in gromacs 4.6   Mark Abraham
      • [gmx-users] MPI error in gromacs 4.6   Mark Abraham
      • [gmx-users] MPI error in gromacs 4.6   Justin Lemkul
  • [gmx-users] MPI error in gromacs 4.6   Mark Abraham
• [gmx-users] MPI error in gromacs 4.6, more Errors   Ankita Naithani
  • [gmx-users] MPI error in gromacs 4.6, more Errors   Justin Lemkul
    • [gmx-users] MPI error in gromacs 4.6, more Errors   Ankita Naithani
      • [gmx-users] MPI error in gromacs 4.6, more Errors   Mark Abraham
• [gmx-users] Protein-Ligand MS simulation   MUSYOKA THOMMAS
  • [gmx-users] Protein-Ligand MS simulation   Justin Lemkul
• [gmx-users] Umbrella pulling Drug + Ion channel   Andres Ortega
  • [gmx-users] Umbrella pulling Drug + Ion channel   Justin Lemkul
    • [gmx-users] Umbrella pulling Drug + Ion channel   Andres Ortega Guerrero
      • [gmx-users] Umbrella pulling Drug + Ion channel   Justin Lemkul
      • [gmx-users] Umbrella pulling Drug + Ion channel   Andres Ortega Guerrero
      • [gmx-users] Umbrella pulling Drug + Ion channel   Justin Lemkul
      • [gmx-users] Umbrella pulling Drug + Ion channel   Andres Ortega Guerrero
      • [gmx-users] Umbrella pulling Drug + Ion channel   Justin Lemkul
      • [gmx-users] Umbrella pulling Drug + Ion channel   Andres Ortega Guerrero
      • [gmx-users] Umbrella pulling Drug + Ion channel   Justin Lemkul
• [gmx-users] berger lipid parameters in amber99sb-ildn ff   Monoj Mon Kalita
  • [gmx-users] berger lipid parameters in amber99sb-ildn ff   Christopher Neale
• [gmx-users] Gromos DPPC bilayer: different results for 4.0.7 and 4.6.5   Patrick Fuchs
• [gmx-users] g_select   Josip Lovrić
  • [gmx-users] g_select   Justin Lemkul
    • [gmx-users] g_select   Josip Lovrić
      • [gmx-users] g_select   Justin Lemkul
      • [gmx-users] g_select   Josip Lovrić
      • [gmx-users] g_select   Justin Lemkul
      • [gmx-users] g_select   Josip Lovrić
• [gmx-users] Gromacs not writing checkpoint files with multidir/replex (v 4.6.4)   Michael Daily
  • [gmx-users] Gromacs not writing checkpoint files with multidir/replex (v 4.6.4)   Mark Abraham
• [gmx-users] [gmx-developers] Problem in compiling Gromacs 4.6.1 with GPU on MAC OS X   Mark Abraham
  • [gmx-users] [gmx-developers] Problem in compiling Gromacs 4.6.1 with GPU on MAC OS X   Mark Abraham
  • [gmx-users] [gmx-developers] Problem in compiling Gromacs 4.6.1 with GPU on MAC OS X   Szilárd Páll
    • [gmx-users] [gmx-developers] Problem in compiling Gromacs 4.6.1 with GPU on MAC OS X   Anders Gabrielsson
• [gmx-users] compilation error with gcc in non-standard location   michael.b
  • [gmx-users] compilation error with gcc in non-standard location   Carsten Kutzner
    • [gmx-users] compilation error with gcc in non-standard location   Christian Wagner
      • [gmx-users] compilation error with gcc in non-standard location   michael.b
• [gmx-users] Reg Gromacs in cluster problem   vidhya sankar
  • [gmx-users] Reg Gromacs in cluster problem   Justin Lemkul
• [gmx-users] Effect of a single mutation in a protein   Pappu Kumar
  • [gmx-users] Effect of a single mutation in a protein   Justin Lemkul
• [gmx-users] Problems when loading .trr and/or .trj GROMACS trajectory files in VMD?   Juan Munoz-Garcia
  • [gmx-users] Problems when loading .trr and/or .trj GROMACS trajectory files in VMD?   Mark Abraham
• [gmx-users] Ryckaert-Bellemans Dihedral with AMBER   tarak karmakar
  • [gmx-users] Ryckaert-Bellemans Dihedral with AMBER   Justin Lemkul
    • [gmx-users] Ryckaert-Bellemans Dihedral with AMBER   tarak karmakar
      • [gmx-users] Ryckaert-Bellemans Dihedral with AMBER   Justin Lemkul
      • [gmx-users] Difficulty preparing a polymer (PEG) for simulation.   Dan Sponseller
      • [gmx-users] Difficulty preparing a polymer (PEG) for simulation.   Justin Lemkul
      • [gmx-users] Ryckaert-Bellemans Dihedral with AMBER   tarak karmakar
• [gmx-users] Effect of a single mutation in a protein   Pappu Kumar
  • [gmx-users] Effect of a single mutation in a protein   Justin Lemkul
    • [gmx-users] Effect of a single mutation in a protein   Pappu Kumar
      • [gmx-users] Effect of a single mutation in a protein   Justin Lemkul
• [gmx-users] G_bundle for PN vector orientation   Wood Irene
• [gmx-users] Warning: pressure scaling more than 1%, mu: 58.1548 58.1548 58.1548 Received the TERM signal, stopping at the next NS step   Lakshmi
  • [gmx-users] Warning: pressure scaling more than 1%, mu: 58.1548 58.1548 58.1548 Received the TERM signal, stopping at the next NS step   Mark Abraham
• [gmx-users] Coulomb and Lennnard-Jones parameters   Maria Astón Serrano
  • [gmx-users] Coulomb and Lennnard-Jones parameters   Justin Lemkul
• [gmx-users] re-sort frames by RMSD   unitALX
  • [gmx-users] re-sort frames by RMSD   João Henriques
    • [gmx-users] re-sort frames by RMSD   João Henriques
      • [gmx-users] re-sort frames by RMSD   João Henriques
      • [gmx-users] re-sort frames by RMSD   unitALX
      • [gmx-users] re-sort frames by RMSD   Tsjerk Wassenaar
      • [gmx-users] re-sort frames by RMSD   andrea
      • [gmx-users] re-sort frames by RMSD   João Henriques
• [gmx-users] Difficulty preparing a polymer (PEG) for simulation   Dan Sponseller
  • [gmx-users] Difficulty preparing a polymer (PEG) for simulation   Mark Abraham
• [gmx-users] Problem with trjconv to keep molecule whole for multi-chain protein   arrow50311
  • [gmx-users] Problem with trjconv to keep molecule whole for multi-chain protein   Justin Lemkul
• [gmx-users] g_covar warnings   João Henriques
  • [gmx-users] g_covar warnings   Justin Lemkul
    • [gmx-users] g_covar warnings   João Henriques
      • [gmx-users] g_covar warnings   Justin Lemkul
      • [gmx-users] g_covar warnings   João Henriques
• [gmx-users] Checking the possibility of one complex out of possible two   Pappu Kumar
  • [gmx-users] Checking the possibility of one complex out of possible two   Justin Lemkul
    • [gmx-users] Checking the possibility of one complex out of possible two   Pappu Kumar
• [gmx-users] Question for bdc = xy   ookami a
  • [gmx-users] Question for bdc = xy   Mark Abraham
    • [gmx-users] Question for bdc = xy   ookami a
      • [gmx-users] Question for bdc = xy   Justin Lemkul
• [gmx-users] question about free energy   pratibha
• [gmx-users] restarting run on GPU   pratibha
  • [gmx-users] restarting run on GPU   pratibha
    • [gmx-users] restarting run on GPU   Mark Abraham
• [gmx-users] A converter for lammps to gromacs   X Rules
  • [gmx-users] A converter for lammps to gromacs   David van der Spoel
    • [gmx-users] A converter for lammps to gromacs   X Rules
• [gmx-users] g_traj time unit   Tegar Nurwahyu Wijaya
  • [gmx-users] g_traj time unit   X Rules
    • [gmx-users] g_traj time unit   Tegar Nurwahyu Wijaya
      • [gmx-users] g_traj time unit   Chandan Choudhury
      • [gmx-users] g_traj time unit   Justin Lemkul
      • [gmx-users] g_traj time unit   Tegar Nurwahyu Wijaya
• [gmx-users] help regarding building topology of Lanitibiotics (small natural peptides)   Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU)
  • [gmx-users] help regarding building topology of Lanitibiotics (small natural peptides)   chetan kumar meena
    • [gmx-users] help regarding building topology of Lanitibiotics (small natural peptides)   Justin Lemkul
    • [gmx-users] help regarding building topology of Lanitibiotics (small natural peptides)   bipin singh
• [gmx-users] Dispersion correction for protein interfaces   Jason Grosch
  • [gmx-users] Dispersion correction for protein interfaces   CHEN Pan
• [gmx-users] umbrella sampling with force clamping unfolding of ubiquitin   gwonchan
  • [gmx-users] umbrella sampling with force clamping unfolding of ubiquitin   Justin Lemkul
• [gmx-users] charmm forcefield patches in gromacs   Gurunath Katagi
  • [gmx-users] charmm forcefield patches in gromacs   Justin Lemkul
  • [gmx-users] charmm forcefield patches in gromacs   Mark Abraham
• [gmx-users] simulation of a trimer   Pappu Kumar
• [gmx-users] interaction energy   pratibha
  • [gmx-users] interaction energy   Justin Lemkul
  • [gmx-users] interaction energy   pratibha
    • [gmx-users] interaction energy   Justin Lemkul
  • [gmx-users] interaction energy   pratibha
    • [gmx-users] interaction energy   Justin Lemkul
• [gmx-users] How to provide the FFTW3 install directory   Ly Minh Nhat
  • [gmx-users] How to provide the FFTW3 install directory   Justin Lemkul
    • [gmx-users] How to provide the FFTW3 install directory   Ly Minh Nhat
      • [gmx-users] How to provide the FFTW3 install directory   Justin Lemkul
      • [gmx-users] How to provide the FFTW3 install directory   Ly Minh Nhat
      • [gmx-users] How to provide the FFTW3 install directory   Justin Lemkul
      • [gmx-users] How to provide the FFTW3 install directory   Ly Minh Nhat
      • [gmx-users] How to provide the FFTW3 install directory   Justin Lemkul
      • [gmx-users] How to provide the FFTW3 install directory   Ly Minh Nhat
      • [gmx-users] How to provide the FFTW3 install directory   Justin Lemkul
• [gmx-users] Saving velocities of one atom at every timestep   Andrew DeYoung
  • [gmx-users] Saving velocities of one atom at every timestep   Justin Lemkul
    • [gmx-users] Saving velocities of one atom at every timestep   Mark Abraham
• [gmx-users] Function type Fourier Dih. not implemented in ip_pert   Dr. Vitaly Chaban
  • [gmx-users] Function type Fourier Dih. not implemented in ip_pert   Justin Lemkul
    • [gmx-users] Function type Fourier Dih. not implemented in ip_pert   Dr. Vitaly Chaban
      • [gmx-users] Function type Fourier Dih. not implemented in ip_pert   Justin Lemkul
      • [gmx-users] Function type Fourier Dih. not implemented in ip_pert   Mark Abraham
• [gmx-users] Function type Fourier Dih. not implemented in ip_pert   Dr. Vitaly Chaban
• [gmx-users] protein water contacts   pratibha
  • [gmx-users] protein water contacts   Justin Lemkul
• [gmx-users] Water out of box? Negative Z-Coordinates   GtrAngus
  • [gmx-users] Water out of box? Negative Z-Coordinates   Justin Lemkul

Last message date: Mon Mar 31 23:49:54 CEST 2014
Archived on: Mon Mar 31 23:49:55 CEST 2014

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