January 2017 Archives by thread

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Starting: Sun Jan 1 05:30:57 CET 2017
Ending: Tue Jan 31 19:27:32 CET 2017
Messages: 556

• [gmx-users] Deletion of Lipids During InflateGro?   Sanim Rahman
  • [gmx-users] Deletion of Lipids During InflateGro?   Justin Lemkul
• [gmx-users] Exploding temp/pressure.   Nash, Anthony
  • [gmx-users] Exploding temp/pressure.   Mark Abraham
• [gmx-users] forward and backward states for the binding free energy energy   Qasim Pars
  • [gmx-users] forward and backward states for the binding free energy energy   Hannes Loeffler
    • [gmx-users] forward and backward states for the binding free energy energy   qasimpars at gmail.com
• [gmx-users] How the default parameters for PME (particle mesh Ewald) are chosen?   Dawid das
  • [gmx-users] How the default parameters for PME (particle mesh Ewald) are chosen?   Mark Abraham
    • [gmx-users] How the default parameters for PME (particle mesh Ewald) are chosen?   Dawid das
      • [gmx-users] How the default parameters for PME (particle mesh Ewald) are chosen?   Mark Abraham
      • [gmx-users] How the default parameters for PME (particle mesh Ewald) are chosen?   Dawid das
• [gmx-users] About the number of step in Argon Molecular Dynamic -Phase transition   Romulo Leoncio Cruz Simbron
  • [gmx-users] About the number of step in Argon Molecular Dynamic -Phase transition   Romulo Leoncio Cruz Simbron
    • [gmx-users] About the number of step in Argon Molecular Dynamic -Phase transition   Mark Abraham
    • [gmx-users] About the number of step in Argon Molecular Dynamic -Phase transition   Romulo Leoncio Cruz Simbron
• [gmx-users] force calculations in PMF calculations   deepak bapat
• [gmx-users] relative reorientation calculation   Md. Imrul Reza Shishir
• [gmx-users] About GTX-Titan-X(Pascal)   양창원
  • [gmx-users] About GTX-Titan-X(Pascal)   Szilárd Páll
• [gmx-users] About GTX-Titan-X(Pascal)   양창원
• [gmx-users] Exploding temp/pressure.   Daniel Bauer
• [gmx-users] New inGromacs   Mark Abraham
• [gmx-users] Reading tpx file (md_0_1.tpr) version 110 with version 100 program   Mark Abraham
• [gmx-users] mdrun initialises, fails to run, no error message   Natalie Tatum
  • [gmx-users] mdrun initialises, fails to run, no error message   Justin Lemkul
    • [gmx-users] mdrun initialises, fails to run, no error message   Natalie Tatum
      • [gmx-users] mdrun initialises, fails to run, no error message   Mark Abraham
      • [gmx-users] mdrun initialises, fails to run, no error message   Natalie Tatum
      • [gmx-users] mdrun initialises, fails to run, no error message   Mark Abraham
      • [gmx-users] mdrun initialises, fails to run, no error message   Natalie Tatum
• [gmx-users] The Rg does not change at all during the umbrella sampling   faride badalkhani
• [gmx-users] couple-intramol   Qasim Pars
  • [gmx-users] couple-intramol   Justin Lemkul
    • [gmx-users] couple-intramol   Qasim Pars
      • [gmx-users] couple-intramol   Justin Lemkul
      • [gmx-users] couple-intramol   qasimpars at gmail.com
      • [gmx-users] couple-intramol   Justin Lemkul
• [gmx-users] force calculations in PMF   deepak bapat
  • [gmx-users] force calculations in PMF   Alex
    • [gmx-users] force calculations in PMF   deepak bapat
      • [gmx-users] force calculations in PMF   Alex
      • [gmx-users] force calculations in PMF   deepak bapat
      • [gmx-users] force calculations in PMF   Justin Lemkul
      • [gmx-users] force calculations in PMF   deepak bapat
• [gmx-users] Bond lengths   suniba shuaib
  • [gmx-users] Bond lengths   Justin Lemkul
• [gmx-users] The Rg does not change during the umbrella sampling   faride badalkhani
• [gmx-users] Free energy calculation of protein and ligand   tasneem kausar
• [gmx-users] Free energy calculation of protein and ligand   tasneem kausar
• [gmx-users] Regression test error in gromacs 5.1.4 installation   Abhisheak Sharma
• [gmx-users] Index file group selection and gmx covar error   Aditya Padhi
  • [gmx-users] Index file group selection and gmx covar error   Justin Lemkul
• [gmx-users] Regarding gromacs commands..   Dilip H N
  • [gmx-users] Regarding gromacs commands..   Dilip H N
    • [gmx-users] Regarding gromacs commands..   Alex
      • [gmx-users] Regarding gromacs commands..   Dilip H N
      • [gmx-users] Regarding gromacs commands..   Justin Lemkul
      • [gmx-users] Regarding gromacs commands..   Dilip H N
      • [gmx-users] Regarding gromacs commands..   Justin Lemkul
• [gmx-users] How can I calculate Potential Energy of the segment divided by index file?   大木啓輔
  • [gmx-users] How can I calculate Potential Energy of the segment divided by index file?   Amir Zeb
  • [gmx-users] How can I calculate Potential Energy of the segment divided by index file?   Justin Lemkul
• [gmx-users] LJ cut-offs   Mohsen Ramezanpour
  • [gmx-users] Fwd: LJ cut-offs   Mohsen Ramezanpour
    • [gmx-users] Fwd: LJ cut-offs   Mark Abraham
      • [gmx-users] Fwd: LJ cut-offs   Dawid das
      • [gmx-users] Fwd: LJ cut-offs   Dawid das
      • [gmx-users] Fwd: LJ cut-offs   Dawid das
    • [gmx-users] Fwd: LJ cut-offs   Justin Lemkul
      • [gmx-users] Fwd: LJ cut-offs   Mohsen Ramezanpour
      • [gmx-users] Fwd: LJ cut-offs   Justin Lemkul
      • [gmx-users] Fwd: LJ cut-offs   Mohsen Ramezanpour
      • [gmx-users] Fwd: LJ cut-offs   Justin Lemkul
      • [gmx-users] Fwd: LJ cut-offs   Thomas Piggot
      • [gmx-users] Fwd: LJ cut-offs   Mohsen Ramezanpour
      • [gmx-users] Fwd: LJ cut-offs   Dawid das
      • [gmx-users] Fwd: LJ cut-offs   Justin Lemkul
      • [gmx-users] Fwd: LJ cut-offs   Justin Lemkul
• [gmx-users] gromacs.org_gmx-users Digest, Vol 153, Issue 12   Nivedita Rai
• [gmx-users] generation of ions additional to solvent molecules   Raag Saluja
  • [gmx-users] generation of ions additional to solvent molecules   Erik Marklund
• [gmx-users] Free energy calculation of protein and ligand   tasneem kausar
• [gmx-users] Free energy calculation of protein and drug   tasneem kausar
  • [gmx-users] Free energy calculation of protein and drug   Amir Zeb
• [gmx-users] Protein-complex simulation   Nivedita Rai
  • [gmx-users] Protein-complex simulation   Justin Lemkul
• [gmx-users] HOW TO RUN GROMACS IN WINDOWS 7   Subashini .K
  • [gmx-users] HOW TO RUN GROMACS IN WINDOWS 7   Szilárd Páll
• [gmx-users] Specs for GPU box   Szilárd Páll
  • [gmx-users] Specs for GPU box   Alex
    • [gmx-users] Specs for GPU box   Szilárd Páll
      • [gmx-users] Specs for GPU box   Alex
      • [gmx-users] Specs for GPU box   Szilárd Páll
      • [gmx-users] Specs for GPU box   Alex
      • [gmx-users] Specs for GPU box   Szilárd Páll
• [gmx-users] gmx 2016 vs 5 benchmark   CLARK NICOLAS Joan
• [gmx-users] Continuing a FEP alchemical   Alex
• [gmx-users] PMF simulation in Gromacs 2016.1   Li, Shi
• [gmx-users] Simulated Tempering Issues   Alexander Yang
• [gmx-users] Save the velocities a subset of atoms in a trr file during a simulation   ABEL Stephane 175950
  • [gmx-users] Save the velocities a subset of atoms in a trr file during a simulation   Justin Lemkul
• [gmx-users] Fix the residues   liming_52
  • [gmx-users] Fix the residues   Justin Lemkul
    • [gmx-users] Fix the residues   liming_52
      • [gmx-users] Fix the residues   Justin Lemkul
  • [gmx-users] Fix the residues   Amir Zeb
• [gmx-users] Farideh Khamseh shared "histo.xlsx" with you   Farideh Khamseh (via Dropbox)
• [gmx-users] window spacing in umbrella sampling   faride badalkhani
  • [gmx-users] window spacing in umbrella sampling   Justin Lemkul
• [gmx-users] Farideh Khamseh shared "histo.xlsx" with you   Farideh Khamseh (via Dropbox)
• [gmx-users] replica exchange: checkpoint file not getting generated   shivangi nangia
• [gmx-users] Gromacs Simulation Question   Academic Research
  • [gmx-users] Gromacs Simulation Question   Zheng Ruan
  • [gmx-users] Gromacs Simulation Question   Justin Lemkul
    • [gmx-users] Gromacs Simulation Question   Peter Kroon
• [gmx-users] Free energy calculation of protein and drug   tasneem kausar
  • [gmx-users] Free energy calculation of protein and drug   Amir Zeb
    • [gmx-users] Free energy calculation of protein and drug   tasneem kausar
      • [gmx-users] Free energy calculation of protein and drug   Amir Zeb
      • [gmx-users] Free energy calculation of protein and drug   tasneem kausar
      • [gmx-users] Free energy calculation of protein and drug   Amir Zeb
      • [gmx-users] Free energy calculation of protein and drug   tasneem kausar
• [gmx-users] REg MD results   Parul Raj Srivastava
  • [gmx-users] REg MD results   Justin Lemkul
    • [gmx-users] REg MD results   Parul Raj Srivastava
      • [gmx-users] REg MD results   Justin Lemkul
• [gmx-users] Topology parameters for ligand   tasneem kausar
  • [gmx-users] Topology parameters for ligand   Justin Lemkul
    • [gmx-users] Topology parameters for ligand   tasneem kausar
      • [gmx-users] Topology parameters for ligand   Justin Lemkul
      • [gmx-users] Topology parameters for ligand   tasneem kausar
      • [gmx-users] Topology parameters for ligand   Justin Lemkul
      • [gmx-users] Topology parameters for ligand   tasneem kausar
      • [gmx-users] Topology parameters for ligand   Justin Lemkul
• [gmx-users] pulling protein-ligand complex   abhisek Mondal
  • [gmx-users] pulling protein-ligand complex   Justin Lemkul
    • [gmx-users] pulling protein-ligand complex   abhisek Mondal
      • [gmx-users] pulling protein-ligand complex   Justin Lemkul
      • [gmx-users] pulling protein-ligand complex   abhisek Mondal
      • [gmx-users] pulling protein-ligand complex   Justin Lemkul
      • [gmx-users] pulling protein-ligand complex   abhisek Mondal
      • [gmx-users] pulling protein-ligand complex   Justin Lemkul
      • [gmx-users] pulling protein-ligand complex   abhisek Mondal
      • [gmx-users] pulling protein-ligand complex   Justin Lemkul
      • [gmx-users] pulling protein-ligand complex   abhisek Mondal
      • [gmx-users] pulling protein-ligand complex   Justin Lemkul
      • [gmx-users] pulling protein-ligand complex   abhisek Mondal
      • [gmx-users] pulling protein-ligand complex   Justin Lemkul
      • [gmx-users] pulling protein-ligand complex   abhisek Mondal
      • [gmx-users] pulling protein-ligand complex   Justin Lemkul
      • [gmx-users] pulling protein-ligand complex   abhisek Mondal
      • [gmx-users] pulling protein-ligand complex   Justin Lemkul
• [gmx-users] LJ Interaction between 2 groups looks unusual   Mijiddorj Batsaikhan
  • [gmx-users] LJ Interaction between 2 groups looks unusual   Mark Abraham
• [gmx-users] Protein-ligand complex simulation   Nivedita Rai
  • [gmx-users] Protein-ligand complex simulation   Justin Lemkul
• [gmx-users] Mycobacterium cell wall protein   Shanmuga Priya V.G
  • [gmx-users] Mycobacterium cell wall protein   Justin Lemkul
• [gmx-users] Regarding calculation of diffusion constant (through MSD) of solvent molecules near protein surface   Apramita Chand
• [gmx-users] How to choose z component of two groups   Mijiddorj Batsaikhan
  • [gmx-users] How to choose z component of two groups   Peter Kroon
  • [gmx-users] How to choose z component of two groups   Justin Lemkul
• [gmx-users] Regarding gromacs commands..   Dilip H N
  • [gmx-users] Regarding gromacs commands..   Mark Abraham
    • [gmx-users] Regarding gromacs commands..   Thomas Allen
      • [gmx-users] Regarding gromacs commands..   Mark Abraham
• [gmx-users] Explicit Topology Question   Thomas Allen
  • [gmx-users] Explicit Topology Question   Mark Abraham
    • [gmx-users] Explicit Topology Question   Thomas Allen
      • [gmx-users] Explicit Topology Question   Mark Abraham
• [gmx-users] Error in leaprc.ff14SB (Amber14)   Subashini .K
  • [gmx-users] Error in leaprc.ff14SB (Amber14)   Justin Lemkul
• [gmx-users] Regarding calculation of diffusion constant of solvent molecules near protein surface   Apramita Chand
• [gmx-users] Regarding g_energy of heterogenous systems   Apramita Chand
  • [gmx-users] Regarding g_energy of heterogenous systems   Peter Stern
• [gmx-users] Adding a new(modefied) fatty acid to charm 36 force field.   Tushar Ranjan Moharana
  • [gmx-users] Adding a new(modefied) fatty acid to charm 36 force field.   Justin Lemkul
• [gmx-users] Adding detergent to simulation box   Yasser Almeida Hernández
  • [gmx-users] Adding detergent to simulation box - SOLVED   Yasser Almeida Hernández
• [gmx-users] Creating a temperature gradient in water   ibrahim khalil
  • [gmx-users] Creating a temperature gradient in water   Erik Marklund
    • [gmx-users] Creating a temperature gradient in water   Alex
      • [gmx-users] Creating a temperature gradient in water   Mark Abraham
      • [gmx-users] Creating a temperature gradient in water   Alex
      • [gmx-users] Creating a temperature gradient in water   Mark Abraham
      • [gmx-users] Creating a temperature gradient in water   Alex
• [gmx-users] Adding FE2+ or FE3+ into the system   liming_52
  • [gmx-users] Adding FE2+ or FE3+ into the system   CROUZY Serge 119222
    • [gmx-users] Adding FE2+ or FE3+ into the system   Hannes Loeffler
      • [gmx-users] Adding FE2+ or FE3+ into the system   liming_52
      • [gmx-users] Adding FE2+ or FE3+ into the system   Justin Lemkul
    • [gmx-users] Adding FE2+ or FE3+ into the system   liming_52
• [gmx-users] Adding FE2+ parameters   CROUZY Serge 119222
  • [gmx-users] Adding FE2+ parameters   Justin Lemkul
    • [gmx-users] Adding FE2+ parameters   Mark Abraham
    • [gmx-users] Adding FE2+ parameters   Hannes Loeffler
• [gmx-users] MMPBSA - with water molecules in the binding site   Gabriela Aucar
• [gmx-users] ENERGY MINIMIZATION   Subashini .K
  • [gmx-users] ENERGY MINIMIZATION   Mark Abraham
    • [gmx-users] GROMACS IN CGYWIN   Subashini .K
• [gmx-users] rlist, rcolumb, and rvdw   Mohsen Ramezanpour
  • [gmx-users] rlist, rcolumb, and rvdw   Mark Abraham
    • [gmx-users] rlist, rcolumb, and rvdw   Justin Lemkul
      • [gmx-users] rlist, rcolumb, and rvdw   Thomas Piggot
      • [gmx-users] rlist, rcolumb, and rvdw   Justin Lemkul
      • [gmx-users] rlist, rcolumb, and rvdw   Mohsen Ramezanpour
      • [gmx-users] rlist, rcolumb, and rvdw   Mark Abraham
      • [gmx-users] rlist, rcolumb, and rvdw   #SUKRITI GUPTA#
      • [gmx-users] rlist, rcolumb, and rvdw   Mark Abraham
• [gmx-users] protein XYZ dimension function of time   atanu das
• [gmx-users] domain decomposition error in the energy minimization step   Qasim Pars
  • [gmx-users] domain decomposition error in the energy minimization step   Kutzner, Carsten
    • [gmx-users] domain decomposition error in the energy minimization step   Qasim Pars
      • [gmx-users] domain decomposition error in the energy minimization step   Kutzner, Carsten
      • [gmx-users] domain decomposition error in the energy minimization step   qasimpars at gmail.com
      • [gmx-users] domain decomposition error in the energy minimization step   Kutzner, Carsten
• [gmx-users] gromacs in cgywin   Subashini .K
  • [gmx-users] gromacs in cgywin   liming_52
    • [gmx-users] gromacs in cgywin   Subashini .K
• [gmx-users] protein XYZ dimension function of time   atanu das
  • [gmx-users] protein XYZ dimension function of time   Justin Lemkul
    • [gmx-users] protein XYZ dimension function of time   atanu das
• [gmx-users] Group vs Verlet cutoff scheme   #SUKRITI GUPTA#
• [gmx-users] [gmx-developers] executing mdp file--error   Justin Lemkul
• [gmx-users] Fwd: Regarding gromacs   Dilip H N
• [gmx-users] Gromacs   Dilip H N
• [gmx-users] Gromacs   Dilip H N
  • [gmx-users] Gromacs   David van der Spoel
• [gmx-users] Results analysis of gromacs by VMD.   maria khan
  • [gmx-users] Results analysis of gromacs by VMD.   Mark Abraham
• [gmx-users] choosing group of atoms in trjconv   Irem Altan
  • [gmx-users] choosing group of atoms in trjconv   Mark Abraham
• [gmx-users] Running GROMACS in cluster with SGE   Yasser Almeida Hernández
  • [gmx-users] Running GROMACS in cluster with SGE   Mark Abraham
• [gmx-users] ERROR IN GROMPP   Subashini .K
  • [gmx-users] ERROR IN GROMPP   Justin Lemkul
• [gmx-users] MM dihedral scanning   Mohsen Ramezanpour
  • [gmx-users] MM dihedral scanning   Justin Lemkul
    • [gmx-users] MM dihedral scanning   Mohsen Ramezanpour
      • [gmx-users] MM dihedral scanning   Justin Lemkul
      • [gmx-users] MM dihedral scanning   Mohsen Ramezanpour
      • [gmx-users] MM dihedral scanning   Mohsen Ramezanpour
      • [gmx-users] MM dihedral scanning   Justin Lemkul
      • [gmx-users] MM dihedral scanning   Justin Lemkul
      • [gmx-users] MM dihedral scanning   Mohsen Ramezanpour
      • [gmx-users] MM dihedral scanning   Justin Lemkul
      • [gmx-users] MM dihedral scanning   Mohsen Ramezanpour
      • [gmx-users] MM dihedral scanning   Justin Lemkul
      • [gmx-users] MM dihedral scanning   Mohsen Ramezanpour
      • [gmx-users] MM dihedral scanning   Mohsen Ramezanpour
      • [gmx-users] MM dihedral scanning   Mohsen Ramezanpour
      • [gmx-users] MM dihedral scanning   Justin Lemkul
      • [gmx-users] MM dihedral scanning   Justin Lemkul
      • [gmx-users] MM dihedral scanning   Mohsen Ramezanpour
• [gmx-users] REGARDING PROTEIN LIGAND SIMULATION   Subashini .K
  • [gmx-users] REGARDING PROTEIN LIGAND SIMULATION   Justin Lemkul
• [gmx-users] about potential energy calculation   Albert
  • [gmx-users] about potential energy calculation   Mark Abraham
    • [gmx-users] about potential energy calculation   Albert
      • [gmx-users] about potential energy calculation   Anders Støttrup Larsen
      • [gmx-users] about potential energy calculation   Albert
      • [gmx-users] about potential energy calculation   Mark Abraham
• [gmx-users] G_ENERGY COMMAND   Subashini .K
  • [gmx-users] G_ENERGY COMMAND   gozde ergin
    • [gmx-users] G_ENERGY COMMAND   asaffarhi at post.tau.ac.il
• [gmx-users] [MGMS-DS]: Molecular Modelling Workshop March 27-29, 2017 in Erlangen, Germany   Harald Lanig
• [gmx-users] Position restraints umbrella sampling   Emil Marklund
  • [gmx-users] Position restraints umbrella sampling   gozde ergin
• [gmx-users] Fwd: protein-ligand complex simulation   Nivedita Rai
  • [gmx-users] Fwd: protein-ligand complex simulation   Justin Lemkul
• [gmx-users] extracting a list of frames from a trajectory   Irem Altan
  • [gmx-users] extracting a list of frames from a trajectory   Mark Abraham
    • [gmx-users] extracting a list of frames from a trajectory   Irem Altan
      • [gmx-users] extracting a list of frames from a trajectory   David van der Spoel
      • [gmx-users] extracting a list of frames from a trajectory   Irem Altan
      • [gmx-users] extracting a list of frames from a trajectory   Justin Lemkul
      • [gmx-users] extracting a list of frames from a trajectory   Irem Altan
• [gmx-users] mail stuck for moderator approval   abhisek Mondal
  • [gmx-users] mail stuck for moderator approval   Mark Abraham
    • [gmx-users] mail stuck for moderator approval   abhisek Mondal
      • [gmx-users] mail stuck for moderator approval   Mark Abraham
• [gmx-users] Cannot obtain center-of-mass radial distribution using Gromacs 2016.1   Boning Wu
  • [gmx-users] Cannot obtain center-of-mass radial distribution using Gromacs 2016.1   Mark Abraham
• [gmx-users] Pulling Mechanics   Alexander Yang
  • [gmx-users] Pulling Mechanics   Justin Lemkul
• [gmx-users] Protein-Ligand Complex MD simulation ; Command for Number of Hydrogen bond plo   Adarsh V. K.
  • [gmx-users] Protein-Ligand Complex MD simulation ; Command for Number of Hydrogen bond plo   Justin Lemkul
• [gmx-users] converting pdb file to gromacs input file   Subashini .K
  • [gmx-users] converting pdb file to gromacs input file   Sotirios Dionysios I. Papadatos
    • [gmx-users] converting pdb file to gromacs input file   Subashini .K
      • [gmx-users] converting pdb file to gromacs input file   Mark Abraham
• [gmx-users] permeation events- ion channels in bilayer   Alex Mathew
  • [gmx-users] permeation events- ion channels in bilayer   Justin Lemkul
• [gmx-users] Adding new residue - modified LYS   Dan Si
  • [gmx-users] Adding new residue - modified LYS   Justin Lemkul
• [gmx-users] Topology for Ligand   RAHUL SURESH
  • [gmx-users] Topology for Ligand   Justin Lemkul
• [gmx-users] position restrains   RAHUL SURESH
  • [gmx-users] position restrains   Justin Lemkul
• [gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27   Mijiddorj Batsaikhan
  • [gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27   Justin Lemkul
• [gmx-users] PREPARING THE RESIDUE TOPOLOGY FILE   Subashini .K
  • [gmx-users] PREPARING THE RESIDUE TOPOLOGY FILE   Justin Lemkul
• [gmx-users] Regarding topology...   Dilip H N
  • [gmx-users] Regarding topology...   Justin Lemkul
    • [gmx-users] Regarding topology...   Dilip H N
      • [gmx-users] Regarding topology...   Dilip H N
      • [gmx-users] Regarding topology...   Justin Lemkul
• [gmx-users] Freezing the solute   Jernej Zidar
  • [gmx-users] Freezing the solute   Mark Abraham
• [gmx-users] gromacs.org_gmx-users Digest, Vol 153, Issue 73   Mijiddorj Batsaikhan
• [gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27   Mijiddorj Batsaikhan
  • [gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27   Justin Lemkul
    • [gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27   Mark Abraham
• [gmx-users] temperature coupling groups for homogeneous mixtures/ ionic liquids?   Boning Wu
  • [gmx-users] temperature coupling groups for homogeneous mixtures/ ionic liquids?   Kroon, P.C.
• [gmx-users] European Hardware Vendors   Sean Anderson
  • [gmx-users] European Hardware Vendors   Sotirios Dionysios I. Papadatos
• [gmx-users] Pulling Mechanics   Alexander Yang
  • [gmx-users] Pulling Mechanics   Justin Lemkul
• [gmx-users] CLARIFICATION IN RESIDUE TOPOLOGY FILE   Subashini .K
  • [gmx-users] CLARIFICATION IN RESIDUE TOPOLOGY FILE   Mark Abraham
• [gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27   Mijiddorj Batsaikhan
• [gmx-users] Manual refinement of ATB topologies ?   Sim gmx
• [gmx-users] GROMACS 4.6.4 vs GROMACS 5.1.2   amitbehra at chemeng.iisc.ernet.in
• [gmx-users] ACPYPE now works with GAFF2   Alan
  • [gmx-users] ACPYPE now works with GAFF2   Anders Støttrup Larsen
• [gmx-users] Gromacs in Xeon Phi?   Albert
• [gmx-users] Using newly defined residue to neutralize the system   Sajeewa Pemasinghe
  • [gmx-users] Using newly defined residue to neutralize the system   Justin Lemkul
    • [gmx-users] Using newly defined residue to neutralize the system   Sajeewa Pemasinghe
      • [gmx-users] Using newly defined residue to neutralize the system   Justin Lemkul
      • [gmx-users] Using newly defined residue to neutralize the system   Sajeewa Pemasinghe
• [gmx-users] Segmentation fault error during run   Yasser Almeida Hernández
  • [gmx-users] Segmentation fault error during run   Justin Lemkul
• [gmx-users] converting .gro trajectory to .pdb   Irem Altan
  • [gmx-users] converting .gro trajectory to .pdb   Chandan Choudhury
  • [gmx-users] converting .gro trajectory to .pdb   Dawid das
    • [gmx-users] converting .gro trajectory to .pdb   Irem Altan
      • [gmx-users] converting .gro trajectory to .pdb   Justin Lemkul
      • [gmx-users] converting .gro trajectory to .pdb   Irem Altan
      • [gmx-users] converting .gro trajectory to .pdb   Mark Abraham
• [gmx-users] GROMACS 2016.1 install fails 21/27 tests from 'make check'   Matthew Barcus
  • [gmx-users] GROMACS 2016.1 install fails 21/27 tests from 'make check'   Mark Abraham
• [gmx-users] dihedral MM scan   Mohsen Ramezanpour
  • [gmx-users] dihedral MM scan   Justin Lemkul
    • [gmx-users] dihedral MM scan   Mohsen Ramezanpour
      • [gmx-users] dihedral MM scan   Justin Lemkul
      • [gmx-users] dihedral MM scan   Mohsen Ramezanpour
      • [gmx-users] dihedral MM scan   Mohsen Ramezanpour
      • [gmx-users] dihedral MM scan   Mohsen Ramezanpour
      • [gmx-users] dihedral MM scan   Justin Lemkul
• [gmx-users] REGARDING TOPOLOGY FILE   Subashini .K
  • [gmx-users] REGARDING TOPOLOGY FILE   tasneem kausar
    • [gmx-users] REGARDING TOPOLOGY FILE   Subashini .K
      • [gmx-users] REGARDING TOPOLOGY FILE   tasneem kausar
      • [gmx-users] REGARDING TOPOLOGY FILE   Amir Zeb
      • [gmx-users] REGARDING TOPOLOGY FILE   Subashini .K
      • [gmx-users] REGARDING TOPOLOGY FILE   Amir Zeb
      • [gmx-users] REGARDING TOPOLOGY FILE   Subashini .K
      • [gmx-users] REGARDING TOPOLOGY FILE   tasneem kausar
• [gmx-users] REGARDING TOPOLOGY FILE   Amir Zeb
  • [gmx-users] REGARDING TOPOLOGY FILE   liming_52
    • [gmx-users] REGARDING TOPOLOGY FILE   Alan
  • [gmx-users] Please send me the source of acpype script   liming_52
• [gmx-users] readline support for gromacs tools   Peter Kroon
• [gmx-users] Pulling ligand out of protein for umbrella sampling   Suhaib Shekfeh
• [gmx-users] fitting of the RMSD matrix   Mike Nemec
• [gmx-users] K+ ions in gromos53a6 FF ?   Sim gmx
• [gmx-users] Simulation in vacuum   Мижээ Батсайхан
  • [gmx-users] Simulation in vacuum   Erik Marklund
    • [gmx-users] introduction to research on free energies   asaffarhi at post.tau.ac.il
• [gmx-users] Pulling Mechanics   Alexander Yang
• [gmx-users] posre_water.itp creation   Karolina Jadwiga Janik
  • [gmx-users] posre_water.itp creation   Mark Abraham
• [gmx-users] PROTEIN FOLDING IN GROMACS   Subashini .K
• [gmx-users] VISUALIZING PROTEIN FOLDING   Subashini .K
  • [gmx-users] VISUALIZING PROTEIN FOLDING   Mark Abraham
• [gmx-users] Simulation in vacuum   Мижээ Батсайхан
• [gmx-users] Simulation in vacuum   Мижээ Батсайхан
  • [gmx-users] Simulation in vacuum   Alex
  • [gmx-users] Simulation in vacuum   Mark Abraham
• [gmx-users] gmx make_ndx: select last created group without knowing its number   CLARK NICOLAS Joan
  • [gmx-users] gmx make_ndx: select last created group without knowing its number   Mark Abraham
    • [gmx-users] gmx make_ndx: select last created group without knowing its number   Peter Kroon
• [gmx-users] simulations with wall potential   Beibei Wang
• [gmx-users] Using backward.py with Gromacs 5.x?   SRINIVAS MUSHNOORI
  • [gmx-users] Using backward.py with Gromacs 5.x?   Peter Kroon
    • [gmx-users] Using backward.py with Gromacs 5.x?   SRINIVAS MUSHNOORI
• [gmx-users] NOTE: Cannot set thread affinities on the current platform.   liming_52
  • [gmx-users] NOTE: Cannot set thread affinities on the current platform.   Mark Abraham
• [gmx-users] Problem with the autocorrelation of Rg   faride badalkhani
• [gmx-users] Transition metals topology   Matteo Busato
  • [gmx-users] Transition metals topology   Mark Abraham
    • [gmx-users] Transition metals topology   Matteo Busato
• [gmx-users] topology file   RAHUL SURESH
  • [gmx-users] topology file   Mark Abraham
    • [gmx-users] topology file   RAHUL SURESH
      • [gmx-users] topology file   Justin Lemkul
      • [gmx-users] topology file   RAHUL SURESH
      • [gmx-users] topology file   Justin Lemkul
• [gmx-users] Problem with the autocorrelation of Rg   faride badalkhani
  • [gmx-users] Problem with the autocorrelation of Rg   Erik Marklund
    • [gmx-users] Problem with the autocorrelation of Rg   faride badalkhani
      • [gmx-users] Problem with the autocorrelation of Rg   Erik Marklund
      • [gmx-users] Problem with the autocorrelation of Rg   faride badalkhani
      • [gmx-users] Problem with the autocorrelation of Rg   Erik Marklund
      • [gmx-users] Problem with the autocorrelation of Rg   faride badalkhani
      • [gmx-users] Problem with the autocorrelation of Rg   faride badalkhani
• [gmx-users] water sphere formation   Amir Zeb
  • [gmx-users] water sphere formation   Mark Abraham
• [gmx-users] Farideh Khamseh shared "Rg9-polymer+Ligand.xlsx" with you   Farideh Khamseh (via Dropbox)
• [gmx-users] How to concatenate tpr files?   leila karami
  • [gmx-users] How to concatenate tpr files?   Justin Lemkul
  • [gmx-users] How to concatenate tpr files?   Erik Marklund
• [gmx-users] Atomtype CG311 not found   Poncho Arvayo Zatarain
  • [gmx-users] Atomtype CG311 not found   Justin Lemkul
• [gmx-users] Dihedral Population Analysis -Index file   Mohsen Ramezanpour
  • [gmx-users] Dihedral Population Analysis -Index file   Mark Abraham
    • [gmx-users] Dihedral Population Analysis -Index file   Mohsen Ramezanpour
      • [gmx-users] Dihedral Population Analysis -Index file   Mark Abraham
      • [gmx-users] Dihedral Population Analysis -Index file   Mohsen Ramezanpour
• [gmx-users] Extent and append the out put with out presence of .trr file   Alex
  • [gmx-users] Extent and append the out put with out presence of .trr file   Mark Abraham
• [gmx-users] How to concatenate tpr files?   leila karami
• [gmx-users] GPU file   RAHUL SURESH
  • [gmx-users] GPU file   Mark Abraham
    • [gmx-users] GPU file   RAHUL SURESH
      • [gmx-users] GPU file   Mark Abraham
• [gmx-users] simulation of ternary complex   maria khan
  • [gmx-users] simulation of ternary complex   Amir Zeb
  • [gmx-users] simulation of ternary complex   Erik Marklund
• [gmx-users] Having WCA bonded interaction with FENE potential   ARNAB MUKHERJEE
  • [gmx-users] Having WCA bonded interaction with FENE potential   Mark Abraham
• [gmx-users] velocity generation in Gromacs 2016   Kukol, Andreas
  • [gmx-users] velocity generation in Gromacs 2016   Justin Lemkul
• [gmx-users] Excluded Volume Effect   atanu das
• [gmx-users] VMD   RAHUL SURESH
  • [gmx-users] VMD   jkrieger at mrc-lmb.cam.ac.uk
    • [gmx-users] VMD   RAHUL SURESH
      • [gmx-users] VMD   Mark Abraham
      • [gmx-users] VMD   RAHUL SURESH
      • [gmx-users] VMD   Mark Abraham
      • [gmx-users] VMD   Tasneem Kausar
• [gmx-users] Segmentation fault in MDRUN   Matteo Busato
  • [gmx-users] Segmentation fault in MDRUN   gozde ergin
• [gmx-users] How to concatenate tpr files?   leila karami
  • [gmx-users] How to concatenate tpr files?   Mark Abraham
• [gmx-users] Protein-Ligand Complex MD simulation : Number of Hydrogen bond ; Options to Choose   Adarsh V. K.
  • [gmx-users] Protein-Ligand Complex MD simulation : Number of Hydrogen bond ; Options to Choose   Mark Abraham
• [gmx-users] Dynamics   RAHUL SURESH
  • [gmx-users] Dynamics   Mark Abraham
    • [gmx-users] Dynamics   RAHUL SURESH
      • [gmx-users] Dynamics   jkrieger at mrc-lmb.cam.ac.uk
      • [gmx-users] Dynamics   RAHUL SURESH
      • [gmx-users] Dynamics   Erik Marklund
      • [gmx-users] Dynamics   jkrieger at mrc-lmb.cam.ac.uk
• [gmx-users] Dynamics   RAHUL SURESH
• [gmx-users] Farideh Khamseh shared "profileNH2.xlsx" with you   Farideh Khamseh (via Dropbox)
  • [gmx-users] Farideh Khamseh shared "profileNH2.xlsx" with you   Erik Marklund
• [gmx-users] precision of coordinates   Irem Altan
  • [gmx-users] precision of coordinates   Mark Abraham
• [gmx-users] Why should I update my Gromacs to v. 5.x?   Simone Bolognini
  • [gmx-users] Why should I update my Gromacs to v. 5.x?   Mark Abraham
• [gmx-users] It is protein and ligand...Fwd: Protein-Ligand Complex MD simulation : Number of Hydrogen bond ; Options to Choose   Adarsh V. K.
  • [gmx-users] It is protein and ligand...Fwd: Protein-Ligand Complex MD simulation : Number of Hydrogen bond ; Options to Choose   Justin Lemkul
• [gmx-users] Version 5.1.4: cannot open source file "mkl_dfti.h"   Loris Bennett
  • [gmx-users] Version 5.1.4: cannot open source file "mkl_dfti.h"   Mark Abraham
    • [gmx-users] Version 5.1.4: cannot open source file "mkl_dfti.h"   Loris Bennett
      • [gmx-users] Version 5.1.4: cannot open source file "mkl_dfti.h"   Mark Abraham
      • [gmx-users] Version 5.1.4: cannot open source file "mkl_dfti.h"   Loris Bennett
• [gmx-users] gmx spatial   Hoda Alibiglou
• [gmx-users] Farideh Khamseh shared "profileNH2.xlsx" with you   faride badalkhani
• [gmx-users] Cyclic Peptide Construction using pdb2gmx issue   Sarah McCartan
  • [gmx-users] Cyclic Peptide Construction using pdb2gmx issue   Mark Abraham
• [gmx-users] Gro file does not match topology   Poncho Arvayo Zatarain
  • [gmx-users] Gro file does not match topology   Sotirios Dionysios I. Papadatos
• [gmx-users] CG run on GPU   Atila Petrosian
  • [gmx-users] CG run on GPU   Mark Abraham
• [gmx-users] Software inconsistency error with version 2016.1   Qasim Pars
  • [gmx-users] Software inconsistency error with version 2016.1   Mark Abraham
• [gmx-users] HB analysis at surfaces   Eudes Fileti
  • [gmx-users] HB analysis at surfaces   Salman Zarrini
• [gmx-users] Gro file does not match topology file... continue   Poncho Arvayo Zatarain
  • [gmx-users] Gro file does not match topology file... continue   Justin Lemkul
  • [gmx-users] Gro file does not match topology file... continue   Tasneem Kausar
    • [gmx-users] Gro file does not match topology file... continue   Justin Lemkul
      • [gmx-users] Gro file does not match topology file... continue   Tasneem Kausar
      • [gmx-users] Gro file does not match topology file... continue   Mark Abraham
      • [gmx-users] Gro file does not match topology file... continue   Tasneem Kausar
      • [gmx-users] Gro file does not match topology file... continue   Justin Lemkul
      • [gmx-users] Gro file does not match topology file... continue   Tasneem Kausar
• [gmx-users] MSD   Maryam Kowsar
• [gmx-users] HB analysis at surfaces   Eudes Fileti
• [gmx-users] setting tc-grps and gen-vel   qasimpars at gmail.com
  • [gmx-users] setting tc-grps and gen-vel   Justin Lemkul
• [gmx-users] having problem with topology file   Neda Rafiee
  • [gmx-users] having problem with topology file   Justin Lemkul
    • [gmx-users] having problem with topology file   Neda Rafiee
• [gmx-users] Pulling occurs in the smaller side of reaction coordinate   faride badalkhani
  • [gmx-users] Pulling occurs in the smaller side of reaction coordinate   Justin Lemkul
• [gmx-users] g_membed in 5.1.4?   Albert
  • [gmx-users] g_membed in 5.1.4?   Mark Abraham
    • [gmx-users] g_membed in 5.1.4?   Albert
      • [gmx-users] g_membed in 5.1.4?   David van der Spoel
      • [gmx-users] g_membed in 5.1.4?   Albert
      • [gmx-users] g_membed in 5.1.4?   David van der Spoel
      • [gmx-users] g_membed in 5.1.4?   Albert
      • [gmx-users] g_membed in 5.1.4?   Mark Abraham
      • [gmx-users] g_membed in 5.1.4?   Mark Abraham
      • [gmx-users] g_membed in 5.1.4?   Albert
• [gmx-users] domain decomposition problems   Albert
  • [gmx-users] domain decomposition problems   Justin Lemkul
• [gmx-users] Mixed Solvation - MEA and water   Chintan Bhagat
  • [gmx-users] Mixed Solvation - MEA and water   Mark Abraham
• [gmx-users] Linker error during GMX make   Clemens Grimm
  • [gmx-users] Linker error during GMX make   Szilárd Páll
• [gmx-users] Protein-surface interaction during flow   Kamps, M.
  • [gmx-users] Protein-surface interaction during flow   Smith, Micholas D.
• [gmx-users] Too many error at first step   Chintan Bhagat
  • [gmx-users] Too many error at first step   Justin Lemkul
    • [gmx-users] Too many error at first step   Chintan Bhagat
      • [gmx-users] Too many error at first step   Justin Lemkul
• [gmx-users] gmx spatial   Christopher Neale
• [gmx-users] g_spatial Problem   Badmos, Sakiru
• [gmx-users] g_spatial Problem   Christopher Neale
• [gmx-users] Side chain distance   Amir Zeb
• [gmx-users] (no subject)   Mahboobeh Eslami
  • [gmx-users] (no subject)   Erik Marklund
• [gmx-users] Metalloenzyme MD   Reza Esmaeili
  • [gmx-users] Metalloenzyme MD   Justin Lemkul
    • [gmx-users] Metalloenzyme MD   Reza Esmaeili
• [gmx-users] Protein-surface interaction during flow   Kamps, M.
  • [gmx-users] Protein-surface interaction during flow   Smith, Micholas D.
• [gmx-users] installation problems with gromacs-2016.1   sunyeping
• [gmx-users] Pulling ligand out of protein for umbrella sampling   Christopher Neale
• [gmx-users] Protein-surface interaction during flow   Christopher Neale
  • [gmx-users] Protein-surface interaction during flow   Smith, Micholas D.
• [gmx-users] Protein-surface interaction during flow   Christopher Neale
• [gmx-users] About gromacs density command   Poncho Arvayo Zatarain
  • [gmx-users] About gromacs density command   Justin Lemkul

Last message date: Tue Jan 31 19:27:32 CET 2017
Archived on: Tue Jan 31 19:27:33 CET 2017

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