March 2018 Archives by thread

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Starting: Thu Mar 1 08:25:30 CET 2018
Ending: Sat Mar 31 13:55:06 CEST 2018
Messages: 593

• [gmx-users] cpu/gpu utilization   Mahmood Naderan
  • [gmx-users] cpu/gpu utilization   Szilárd Páll
    • [gmx-users] cpu/gpu utilization   Mahmood Naderan
      • [gmx-users] cpu/gpu utilization   Szilárd Páll
      • [gmx-users] cpu/gpu utilization   Mahmood Naderan
      • [gmx-users] cpu/gpu utilization   Szilárd Páll
      • [gmx-users] cpu/gpu utilization   Mahmood Naderan
      • [gmx-users] cpu/gpu utilization   Magnus Lundborg
      • [gmx-users] cpu/gpu utilization   Mahmood Naderan
      • [gmx-users] cpu/gpu utilization   Szilárd Páll
      • [gmx-users] cpu/gpu utilization   Mahmood Naderan
      • [gmx-users] cpu/gpu utilization   Szilárd Páll
• [gmx-users] QM/MM optimization in gromacs/gaussian   nikolaev at spbau.ru
• [gmx-users] creating topology for ligand   neelam wafa
  • [gmx-users] creating topology for ligand   Justin Lemkul
    • [gmx-users] creating topology for ligand   neelam wafa
      • [gmx-users] creating topology for ligand   Justin Lemkul
      • [gmx-users] creating topology for ligand   neelam wafa
• [gmx-users] Pressure using solvation shell   Justin Lemkul
• [gmx-users] gmx, threads, pinoffset and stride   Michael Brunsteiner
• [gmx-users] atom naming needs to be considered.   neelam wafa
  • [gmx-users] atom naming needs to be considered.   Justin Lemkul
• [gmx-users] QM/MM optimization in gromacs/gaussian (nikolaev at spbau.ru)   Groenhof, Gerrit
  • [gmx-users] QM/MM optimization in gromacs/gaussian (nikolaev at spbau.ru)   nikolaev at spbau.ru
• [gmx-users] Creating Forcefield without ffbonded.itp   Momin Ahmad
  • [gmx-users] Creating Forcefield without ffbonded.itp   Smith, Micholas D.
• [gmx-users] GROMACS mpirun with extremely high load imbalance in output (vol 0.43! imb F 15- 53%)   Marc Hoemberger
  • [gmx-users] GROMACS mpirun with extremely high load imbalance in output (vol 0.43! imb F 15- 53%)   Mark Abraham
• [gmx-users] 2018: large performance variations   Michael Brunsteiner
  • [gmx-users] 2018: large performance variations   Szilárd Páll
    • [gmx-users] 2018: large performance variations   Szilárd Páll
• [gmx-users] Gromacs on CPU runs fine, same calculation crashes on GPU with nonbonded interaction larger than table limit   Marc Hoemberger
  • [gmx-users] Gromacs on CPU runs fine, same calculation crashes on GPU with nonbonded interaction larger than table limit   Mark Abraham
    • [gmx-users] Gromacs on CPU runs fine, same calculation crashes on GPU with nonbonded interaction larger than table limit   Marc Hoemberger
• [gmx-users] Parmbsc1 force-field   Dan Gil
  • [gmx-users] Parmbsc1 force-field   Dan Gil
    • [gmx-users] Parmbsc1 force-field   Mark Abraham
      • [gmx-users] Parmbsc1 force-field   Dan Gil
    • [gmx-users] Parmbsc1 force-field   Viveca Lindahl
      • [gmx-users] Parmbsc1 force-field   Dan Gil
      • [gmx-users] Parmbsc1 force-field   Viveca Lindahl
      • [gmx-users] Parmbsc1 force-field   Dan Gil
• [gmx-users] QM/MM optimization in gromacs/gaussian   Groenhof, Gerrit
  • [gmx-users] QM/MM optimization in gromacs/gaussian   nikolaev at spbau.ru
• [gmx-users] parallelization   Amin Rouy
  • [gmx-users] parallelization   Justin Lemkul
    • [gmx-users] parallelization   Amin Rouy
      • [gmx-users] parallelization   Mark Abraham
      • [gmx-users] parallelization   Amin Rouy
• [gmx-users] stride   Michael Brunsteiner
  • [gmx-users] stride   Szilárd Páll
• [gmx-users] CMAP entries for D-residues with GROMACS   ABEL Stephane
  • [gmx-users] CMAP entries for D-residues with GROMACS   Justin Lemkul
• [gmx-users] atom naming needs to be considered.   neelam wafa
  • [gmx-users] atom naming needs to be considered.   neelam wafa
    • [gmx-users] atom naming needs to be considered.   Mark Abraham
      • [gmx-users] atom naming needs to be considered.   neelam wafa
• [gmx-users] CMAP entries for D-residues with GROMACS (Justin Lemkul)   ABEL Stephane
• [gmx-users] Umbrella sampling   rose rahmani
  • [gmx-users] Umbrella sampling   Justin Lemkul
    • [gmx-users] Umbrella sampling   rose rahmani
      • [gmx-users] Umbrella sampling   Justin Lemkul
• [gmx-users] Cluster analysis on molecules   Pandya, Akash
• [gmx-users] Test particle insertion change in energy - group cut off scheme   Arun Srikanth
  • [gmx-users] Test particle insertion change in energy - group cut off scheme   Mark Abraham
    • [gmx-users] Test particle insertion change in energy - group cut off scheme   Arun Srikanth
      • [gmx-users] Test particle insertion change in energy - group cut off scheme   Mark Abraham
      • [gmx-users] Test particle insertion change in energy - group cut off scheme   Arun Srikanth
• [gmx-users] DPPG/Slipid   m g
• [gmx-users] how to use fastpca?   Seera Suryanarayana
• [gmx-users] Tabulated potential between atoms and virtual sites   Thomas Tarenzi
• [gmx-users] 2018: large performance variations   Szilárd Páll
• [gmx-users] problem with inflategro   kordzadeh at aut.ac.ir
• [gmx-users] problems with the output of pullx   Alfredo E. Cardenas
• [gmx-users] Additional Ph.D. and Post-doc positions in MD simulations of enzymes   Jan Brezovsky
• [gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?   Daniel Bauer
  • [gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?   Simon Kit Sang Chu
    • [gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?   Mark Abraham
      • [gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?   Szilárd Páll
      • [gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?   Szilárd Páll
• [gmx-users] Gibbs free energy   dina dusti
• [gmx-users] Gibbs free energy   dina dusti
  • [gmx-users] Gibbs free energy   David van der Spoel
• [gmx-users] error in implicit MD   Vishwambhar Bhandare
  • [gmx-users] error in implicit MD   Justin Lemkul
• [gmx-users] problem with inflategro   kordzadeh at aut.ac.ir
  • [gmx-users] problem with inflategro   Justin Lemkul
    • [gmx-users] bond sequence and improper angles   Andrea Spitaleri
      • [gmx-users] bond sequence and improper angles   Justin Lemkul
• [gmx-users] problem with inflategro   kordzadeh at aut.ac.ir
  • [gmx-users] problem with inflategro   Justin Lemkul
• [gmx-users] segmentation fault   spss4 at iacs.res.in
• [gmx-users] Geometry Optimization for Metal organic Frame works   Nagasree Garapati
  • [gmx-users] Geometry Optimization for Metal organic Frame works   Smith, Micholas D.
    • [gmx-users] Geometry Optimization for Metal organic Frame works   Smith, Micholas D.
• [gmx-users] Gibbs free energy   dina dusti
• [gmx-users] segmentation fault   spss4 at iacs.res.in
  • [gmx-users] segmentation fault   Justin Lemkul
• [gmx-users] Gromacs Tutorial by Justin   Faezeh Pousaneh
  • [gmx-users] Gromacs Tutorial by Justin   Justin Lemkul
    • [gmx-users] Gromacs Tutorial by Justin   Faezeh Pousaneh
      • [gmx-users] Gromacs Tutorial by Justin   Faezeh Pousaneh
      • [gmx-users] Gromacs Tutorial by Justin   Justin Lemkul
• [gmx-users] Fw: Geometry Optimization for Metal organic Frame works   Nagasree Garapati
  • [gmx-users] Geometry Optimization for Metal organic Frame works   Smith, Micholas D.
  • [gmx-users] Fw: Geometry Optimization for Metal organic Frame works   Momin Ahmad
• [gmx-users] thermostat and barostat   Faezeh Pousaneh
  • [gmx-users] thermostat and barostat   Mark Abraham
• [gmx-users] X2top error, Could only find a forcefield type for 0 out of 66 atoms   John Adams
• [gmx-users] viscosity calculation using g_energy   Jo
• [gmx-users] viscosity calculation using Green-Kubo   Jo
• [gmx-users] Normal-mode analysis in Gromacs   Kevin C Chan
  • [gmx-users] Normal-mode analysis in Gromacs   David van der Spoel
• [gmx-users] OPLS-AA parameters for dimethylsiloxane   Alex
• [gmx-users] Hamiltonian replica exchange in gromacs 4.6.7   Carlo Martinotti
  • [gmx-users] Hamiltonian replica exchange in gromacs 4.6.7   Mark Abraham
• [gmx-users] Calculation of potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling in gromacs   Mayank Dixit
  • [gmx-users] Calculation of potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling in gromacs   Viveca Lindahl
  • [gmx-users] Calculation of potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling in gromacs   Marc Hoemberger
    • [gmx-users] Calculation of potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling in gromacs   Erik Marklund
• [gmx-users] Normal-mode analysis in Gromacs   Kevin C Chan
• [gmx-users] dipole moment for one residue of the whole protein   Neda Rafiee
  • [gmx-users] dipole moment for one residue of the whole protein   Justin Lemkul
• [gmx-users] asking guidance   Mansoureh Shahbazi
• [gmx-users] Missing dihedral parameter (CTD1 C NH1 CT1) for D-AA bonded to L-AA   ABEL Stephane
  • [gmx-users] Missing dihedral parameter (CTD1 C NH1 CT1) for D-AA bonded to L-AA   Justin Lemkul
• [gmx-users] Fw: asking guidance   Mansoureh Shahbazi
  • [gmx-users] Fw: asking guidance   Smith, Micholas D.
• [gmx-users] Missing dihedral parameter (CTD1 C NH1 CT1) for D-AA bonded to L-AA   ABEL Stephane
• [gmx-users] computation/memory modifications   Mahmood Naderan
  • [gmx-users] computation/memory modifications   Justin Lemkul
  • [gmx-users] computation/memory modifications   Mahmood Naderan
    • [gmx-users] computation/memory modifications   Justin Lemkul
      • [gmx-users] computation/memory modifications   Mahmood Naderan
      • [gmx-users] computation/memory modifications   Justin Lemkul
• [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?   Debdas Dhabal
  • [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?   Mark Abraham
    • [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?   Debdas Dhabal
      • [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?   Debdas Dhabal
      • [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?   Mark Abraham
      • [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?   Debdas Dhabal
      • [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?   Debdas Dhabal
      • [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?   Mark Abraham
      • [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?   Shaun Tung
      • [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?   Debdas Dhabal
• [gmx-users] -sep option   Mansoureh Shahbazi
  • [gmx-users] -sep option   Justin Lemkul
    • [gmx-users] -sep option   Mansoureh Shahbazi
      • [gmx-users] Fw: -sep option   Mansoureh Shahbazi
      • [gmx-users] -sep option   Justin Lemkul
• [gmx-users] Comm-mode   Amin Rouy
  • [gmx-users] Comm-mode   Justin Lemkul
    • [gmx-users] Comm-mode   Amin Rouy
      • [gmx-users] Comm-mode   Justin Lemkul
      • [gmx-users] Comm-mode   Amin Rouy
      • [gmx-users] Comm-mode   Amin Rouy
      • [gmx-users] Comm-mode   Mark Abraham
      • [gmx-users] Comm-mode   Amin Rouy
      • [gmx-users] Comm-mode   Mark Abraham
      • [gmx-users] Comm-mode   Justin Lemkul
      • [gmx-users] Comm-mode   Amin Rouy
      • [gmx-users] Comm-mode   Justin Lemkul
      • [gmx-users] Comm-mode   Amin Rouy
• [gmx-users] Cavity analysis of Protein   Bhupendra Dandekar
• [gmx-users] Help with interpreting message for fatal error   Viveca Lindahl
  • [gmx-users] Help with interpreting message for fatal error   Gregory Poon
    • [gmx-users] Help with interpreting message for fatal error   Viveca Lindahl
      • [gmx-users] Help with interpreting message for fatal error   Justin Lemkul
      • [gmx-users] Help with interpreting message for fatal error   Viveca Lindahl
      • [gmx-users] Help with interpreting message for fatal error   Justin Lemkul
      • [gmx-users] Help with interpreting message for fatal error   Viveca Lindahl
      • [gmx-users] Help with interpreting message for fatal error   Gregory Poon
      • [gmx-users] Help with interpreting message for fatal error   Viveca Lindahl
• [gmx-users] RESTARTING THE CALCULATION   Neha Gupta
  • [gmx-users] RESTARTING THE CALCULATION   Mark Abraham
    • [gmx-users] RESTARTING THE CALCULATION   Neha Gupta
      • [gmx-users] RESTARTING THE CALCULATION   Mark Abraham
• [gmx-users] rvdw and rcoulomb   Ahmed Mashaly
  • [gmx-users] rvdw and rcoulomb   Justin Lemkul
    • [gmx-users] rvdw and rcoulomb   Szilárd Páll
• [gmx-users] seeming paradox with gmx wham   Alex
  • [gmx-users] seeming paradox with gmx wham   Alex
    • [gmx-users] seeming paradox with gmx wham   Justin Lemkul
      • [gmx-users] seeming paradox with gmx wham   Alex
      • [gmx-users] seeming paradox with gmx wham   Justin Lemkul
      • [gmx-users] seeming paradox with gmx wham   Alex
      • [gmx-users] seeming paradox with gmx wham   Alex
      • [gmx-users] seeming paradox with gmx wham   Justin Lemkul
      • [gmx-users] seeming paradox with gmx wham   Alex
      • [gmx-users] seeming paradox with gmx wham   Justin Lemkul
      • [gmx-users] seeming paradox with gmx wham   Alex
      • [gmx-users] seeming paradox with gmx wham   Justin Lemkul
      • [gmx-users] seeming paradox with gmx wham   Alex
      • [gmx-users] GMX 2018 and 'distance' pull   Alex
      • [gmx-users] GMX 2018 and 'distance' pull   Viveca Lindahl
      • [gmx-users] GMX 2018 and 'distance' pull   Justin Lemkul
      • [gmx-users] GMX 2018 and 'distance' pull   Justin Lemkul
      • [gmx-users] GMX 2018 and 'distance' pull   Alex
      • [gmx-users] GMX 2018 and 'distance' pull   Justin Lemkul
      • [gmx-users] GMX 2018 and 'distance' pull   Alex
      • [gmx-users] GMX 2018 and 'distance' pull   Justin Lemkul
      • [gmx-users] GMX 2018 and 'distance' pull   Alex
      • [gmx-users] GMX 2018 and 'distance' pull   Justin Lemkul
      • [gmx-users] GMX 2018 and 'distance' pull   Alex
• [gmx-users] NPT equilibration failing at high temperature   brataraj ghosh
  • [gmx-users] NPT equilibration failing at high temperature   Joe Jordan
    • [gmx-users] NPT equilibration failing at high temperature   Justin Lemkul
• [gmx-users] How to define ligand / metal atoms in gbsa.itp file of a force field for implicit MD??   Vishwambhar Bhandare
  • [gmx-users] How to define ligand / metal atoms in gbsa.itp file of a force field for implicit MD??   Mark Abraham
• [gmx-users] gmx potential calculation with one sodium ion at the center of box   이연경
• [gmx-users] Easiest way to calculate the POTENTIAL ENERGY of a single isolated chain in GROMACS   sanjeet kumar singh ch16d012
  • [gmx-users] Easiest way to calculate the POTENTIAL ENERGY of a single isolated chain in GROMACS   Justin Lemkul
• [gmx-users] Strange jumps in box dimensions   Igor Ariz
  • [gmx-users] Strange jumps in box dimensions   Justin Lemkul
• [gmx-users] Decrease position restraints force constant on the fly   Dawid das
  • [gmx-users] Decrease position restraints force constant on the fly   Justin Lemkul
    • [gmx-users] Decrease position restraints force constant on the fly   Zheng Ruan
      • [gmx-users] Decrease position restraints force constant on the fly   Dawid das
• [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?   Douwe Pollmann
  • [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?   Mark Abraham
    • [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?   Douwe Pollmann
      • [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?   Mark Abraham
      • [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?   Douwe Pollmann
• [gmx-users] Problems in putting restraints during free energy perturbation calculations   Searle Duay
  • [gmx-users] Problems in putting restraints during free energy perturbation calculations   Mark Abraham
    • [gmx-users] Problems in putting restraints during free energy perturbation calculations   Searle Duay
• [gmx-users] Free energy perturbation for larger molecule - big Coulomb solvation energies   Krzysztof Makuch
• [gmx-users] Regarding minimum size   Chhavi Yadav
  • [gmx-users] Regarding minimum size   Justin Lemkul
    • [gmx-users] Regarding minimum size   Chhavi Yadav
      • [gmx-users] Regarding minimum size   Srinivasa Ramisetti
      • [gmx-users] Regarding minimum size   Justin Lemkul
      • [gmx-users] Regarding minimum size   Chhavi Yadav
      • [gmx-users] Regarding minimum size   Justin Lemkul
      • [gmx-users] Regarding minimum size   Mark Abraham
      • [gmx-users] Regarding minimum size   Chhavi Yadav
      • [gmx-users] Regarding minimum size   Mark Abraham
      • [gmx-users] Regarding minimum size   Chhavi Yadav
      • [gmx-users] Regarding minimum size   Chhavi Yadav
      • [gmx-users] Regarding minimum size   Mark Abraham
      • [gmx-users] Regarding minimum size   Chhavi Yadav
      • [gmx-users] Regarding minimum size   Mark Abraham
      • [gmx-users] Regarding minimum size   Chhavi Yadav
      • [gmx-users] Regarding minimum size   Chhavi Yadav
      • [gmx-users] Regarding minimum size   Mark Abraham
      • [gmx-users] Regarding minimum size   Mark Abraham
• [gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex   SHYANTANI MAITI
  • [gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex   Justin Lemkul
• [gmx-users] nve simulation   Jo
  • [gmx-users] nve simulation   Mark Abraham
• [gmx-users] Error while Installing GROMACS 2018 on Dell EMC T640(Xeon Gold 6152) with Tesla K880 GPU (RHEL 7.3)   신동규
  • [gmx-users] Error while Installing GROMACS 2018 on Dell EMC T640(Xeon Gold 6152) with Tesla K880 GPU (RHEL 7.3)   Mark Abraham
    • [gmx-users] Error while Installing GROMACS 2018 on Dell EMC T640(Xeon Gold 6152) with Tesla K880 GPU (RHEL 7.3)   신동규
• [gmx-users] GROMACS 5.1.4 and dssp 2.2.1   Simon Kit Sang Chu
  • [gmx-users] GROMACS 5.1.4 and dssp 2.2.1   João Henriques
    • [gmx-users] GROMACS 5.1.4 and dssp 2.2.1   João Henriques
    • [gmx-users] GROMACS 5.1.4 and dssp 2.2.1   Simon Kit Sang Chu
      • [gmx-users] GROMACS 5.1.4 and dssp 2.2.1   João Henriques
      • [gmx-users] GROMACS 5.1.4 and dssp 2.2.1   Mark Abraham
      • [gmx-users] GROMACS 5.1.4 and dssp 2.2.1   Simon Kit Sang Chu
      • [gmx-users] GROMACS 5.1.4 and dssp 2.2.1   Joe Jordan
      • [gmx-users] GROMACS 5.1.4 and dssp 2.2.1   Simon Kit Sang Chu
      • [gmx-users] GROMACS 5.1.4 and dssp 2.2.1   João Henriques
      • [gmx-users] GROMACS 5.1.4 and dssp 2.2.1   Mateusz Bieniek
• [gmx-users] Error with CHARMM36 force field   laurenmr
  • [gmx-users] Error with CHARMM36 force field   Mark Abraham
    • [gmx-users] Error with CHARMM36 force field   laurenmr
      • [gmx-users] Error with CHARMM36 force field   Mark Abraham
      • [gmx-users] Error with CHARMM36 force field   laurenmr
      • [gmx-users] Error with CHARMM36 force field   Justin Lemkul
      • [gmx-users] Error with CHARMM36 force field   laurenmr
• [gmx-users] rvdw and rcoulomb   Ahmed Mashaly
  • [gmx-users] rvdw and rcoulomb   Justin Lemkul
    • [gmx-users] rvdw and rcoulomb   Ahmed Mashaly
      • [gmx-users] rvdw and rcoulomb   Justin Lemkul
• [gmx-users] Regarding calculation of Hydrogen-Bond   Dilip H N
  • [gmx-users] Regarding calculation of Hydrogen-Bond   Erik Marklund
    • [gmx-users] Regarding calculation of Hydrogen-Bond   Dilip H N
      • [gmx-users] Regarding calculation of Hydrogen-Bond   Erik Marklund
      • [gmx-users] Regarding calculation of Hydrogen-Bond   Jeremy T First
      • [gmx-users] Regarding calculation of Hydrogen-Bond   Erik Marklund
      • [gmx-users] Regarding calculation of Hydrogen-Bond   Dilip H N
      • [gmx-users] Regarding calculation of Hydrogen-Bond   Joe Jordan
      • [gmx-users] Regarding calculation of Hydrogen-Bond   Justin Lemkul
• [gmx-users] Mentioning LJ Cutoff in mdp file   Tushar Ranjan Moharana
  • [gmx-users] Mentioning LJ Cutoff in mdp file   Mark Abraham
• [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 53   Jo
  • [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 53   Mark Abraham
• [gmx-users] long simulation in batch   roli.singh at aol.com
• [gmx-users] Long Simulations in Batch GMX 2018   R
• [gmx-users] rdf calculation for wormlike micelles   Esra Kaçar
  • [gmx-users] rdf calculation for wormlike micelles   Joe Jordan
• [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 73   Esra kaçar
  • [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 73   Joe Jordan
• [gmx-users] Umbrella Sampling - good histogram but no result in profile   Ben Tam
  • [gmx-users] Umbrella Sampling - good histogram but no result in profile   Mark Abraham
    • [gmx-users] Umbrella Sampling - good histogram but no result in profile   Awasthi, Neha
      • [gmx-users] Umbrella Sampling - good histogram but no result in profile   Ben Tam
      • [gmx-users] Umbrella Sampling - good histogram but no result in profile   Jochen Hub
  • [gmx-users] Umbrella Sampling - good histogram but no result in profile   Rose
• [gmx-users] Volume of peripheral protein   Pallavi Banerjee
  • [gmx-users] Volume of peripheral protein   Justin Lemkul
• [gmx-users] Three Regression tests were failed while Installing GROMACS 2018 on Dell EMC T640(Xeon Gold 6152) with Tesla K880 GPU (RHEL 7.4)   신동규
  • [gmx-users] Three Regression tests were failed while Installing GROMACS 2018 on Dell EMC T640(Xeon Gold 6152) with Tesla K880 GPU (RHEL 7.4)   Mark Abraham
    • [gmx-users] Three Regression tests were failed while Installing GROMACS 2018 on Dell EMC T640(Xeon Gold 6152) with Tesla K880 GPU (RHEL 7.4)   신동규
• [gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex   SHYANTANI MAITI
  • [gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex   Joe Jordan
  • [gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex   Justin Lemkul
• [gmx-users] nve energy conservation   Jo
  • [gmx-users] nve energy conservation   Mark Abraham
    • [gmx-users] nve energy conservation   Jo
      • [gmx-users] nve energy conservation   Mark Abraham
      • [gmx-users] nve energy conservation   Jo
      • [gmx-users] nve energy conservation   Jo
      • [gmx-users] nve energy conservation   Justin Lemkul
      • [gmx-users] nve energy conservation   Stéphane Téletchéa
      • [gmx-users] nve energy conservation   Mark Abraham
      • [gmx-users] nve energy conservation   Jo
      • [gmx-users] nve energy conservation   Mark Abraham
• [gmx-users] question   s.ghasemlou
• [gmx-users] question   s.ghasemlou
  • [gmx-users] question   Dallas Warren
• [gmx-users] rdf calculation for wormlike micelles   Esra Kaçar
  • [gmx-users] rdf calculation for wormlike micelles   Joe Jordan
  • [gmx-users] rdf calculation for wormlike micelles   Esra kaçar
• [gmx-users] free energy calculator   asaffarhi at post.tau.ac.il
• [gmx-users] free energy calculator   asaffarhi at post.tau.ac.il
• [gmx-users] Replica Exchange Output control   Akshay
  • [gmx-users] Replica Exchange Output control   Viveca Lindahl
• [gmx-users] Position restraints do not work with steepest descent   Dawid das
  • [gmx-users] Position restraints do not work with steepest descent   Justin Lemkul
• [gmx-users] Problem when installing gromacs 5.1.4 on linux   fang yuan
  • [gmx-users] Problem when installing gromacs 5.1.4 on linux   Szilárd Páll
• [gmx-users] deformation in structure of carbon nanotube   kordzadeh at aut.ac.ir
• [gmx-users] Managing long simulations GMX 2018   R
• [gmx-users] Reg. mdrun error: not all ion group molecules consist of 3 atoms   "가디 장데부 고라크스나트"
• [gmx-users] Reg. mdrun error: not all ion group molecules consist of 3 atoms   "가디 장데부 고라크스나트"
  • [gmx-users] Reg. mdrun error: not all ion group molecules consist of 3 atoms   Kutzner, Carsten
• [gmx-users] deformation in carbon nanotube structure   kordzadeh at aut.ac.ir
  • [gmx-users] deformation in carbon nanotube structure   Alex
• [gmx-users] Simulation of D-Alanine   prasun kumar
• [gmx-users] Simulation of D-Alanine (prasun kumar)   ABEL Stephane
• [gmx-users] QM/MM optimization in gromacs/gaussian (nikolaev at spbau.ru)   Groenhof, Gerrit
• [gmx-users] mdp options for Amber99sb-ildn   Saleheh Heidari
• [gmx-users] Installing gmx_mpi   Alex
  • [gmx-users] Installing gmx_mpi   Mark Abraham
    • [gmx-users] Installing gmx_mpi   Alex
      • [gmx-users] Installing gmx_mpi   Mark Abraham
      • [gmx-users] Installing gmx_mpi   Alex
• [gmx-users] regarding adaptive molecular dynamics simulation   Huda Zaqir
• [gmx-users] Precision about the "-surf" option in rdf calculation (gromacs 5.1.4)   Ambroise De Izarra
• [gmx-users] 2018 installation make check errors, probably CUDA related   Tresadern, Gary [RNDBE]
  • [gmx-users] 2018 installation make check errors, probably CUDA related   Tresadern, Gary [RNDBE]
    • [gmx-users] 2018 installation make check errors, probably CUDA related   Tresadern, Gary [RNDBE]
• [gmx-users] Why are the bond and angle energy at the first step of energy minimization not equal 0?   Hoa Trinh
  • [gmx-users] Why are the bond and angle energy at the first step of energy minimization not equal 0?   Justin Lemkul
    • [gmx-users] Why are the bond and angle energy at the first step of energy minimization not equal 0?   Hoa Trinh
• [gmx-users] Graphene sheet topology   Mostafa Fakhraee
  • [gmx-users] Graphene sheet topology   Alex
• [gmx-users] Input GRO file for a calcite crystal slab (meant for use in adsorption study)   Anuradha Bhat
• [gmx-users] Structure factor and scattering intensity in gromacs 5.1.4   Rakesh Pant
  • [gmx-users] Structure factor and scattering intensity in gromacs 5.1.4   Joe Jordan
• [gmx-users] Free Energy solvation generate multiple dhdl.xvg output files   Javier Luque Di Salvo
  • [gmx-users] Free Energy solvation generate multiple dhdl.xvg output files   Wes Barnett
• [gmx-users] error in grompp step   Upendra N
• [gmx-users] error in grompp step   Upendra N
  • [gmx-users] error in grompp step   Justin Lemkul
• [gmx-users] Error in grompp step   Upendra N
• [gmx-users] Topol file for a bigger system   Alex
  • [gmx-users] Topol file for a bigger system   Justin Lemkul
    • [gmx-users] Topol file for a bigger system   Alex
      • [gmx-users] Topol file for a bigger system   Justin Lemkul
• [gmx-users] error in grompp step   Upendra N
  • [gmx-users] error in grompp step   Mark Abraham
• [gmx-users] Separate structure from box   rose rahmani
  • [gmx-users] Separate structure from box   Wes Barnett
• [gmx-users] Free energy of VDW transformation from state A to State B   deepak bapat
• [gmx-users] error in grompp step   Upendra N
• [gmx-users] Free Energy solvation generate multiple dhdl.xvg output files   Javier Luque Di Salvo
• [gmx-users] Regarding combination rules in gromos53a6 ff   Apramita Chand
• [gmx-users] crystal lattice topology generation   Bala subramanian
  • [gmx-users] crystal lattice topology generation   Alex
• [gmx-users] Potential energy   Alex
  • [gmx-users] Potential energy   Justin Lemkul
    • [gmx-users] Potential energy   Alex
      • [gmx-users] Potential energy   Justin Lemkul
• [gmx-users] Regarding time steps for calculation of Hydrogen Bond Dynamics   Dilip H N
  • [gmx-users] Regarding time steps for calculation of Hydrogen Bond Dynamics   Joe Jordan
    • [gmx-users] Regarding time steps for calculation of Hydrogen Bond Dynamics   Mark Abraham
• [gmx-users] source code for velocity information   刘杰
  • [gmx-users] source code for velocity information   Viveca Lindahl
• [gmx-users] source code for velocity information   刘杰
  • [gmx-users] source code for velocity information   Joe Jordan
    • [gmx-users] source code for velocity information   刘杰
      • [gmx-users] source code for velocity information   Paul bauer
• [gmx-users] Regarding combination rules in gromos53a6 ff   Apramita Chand
• [gmx-users] Solid state barostat   dgfd dgdfg
• [gmx-users] metal surface   Amin Rouy
• [gmx-users] Topolbuild   Alex
• [gmx-users] Doubt in specifying combination rule   Apramita Chand
  • [gmx-users] Doubt in specifying combination rule   Mark Abraham
• [gmx-users] Topolbuild   Ray, Bruce D
• [gmx-users] GROMACS 2018.1 patch release available   Mark Abraham
• [gmx-users] installation error   ali akgün
  • [gmx-users] installation error   Mark Abraham
• [gmx-users] 2018 installation make check errors, probably CUDA related   Mark Abraham
  • [gmx-users] 2018 installation make check errors, probably CUDA related   Tresadern, Gary [RNDBE]
    • [gmx-users] 2018 installation make check errors, probably CUDA related   Szilárd Páll
      • [gmx-users] 2018 installation make check errors, probably CUDA related   Tresadern, Gary [RNDBE]
      • [gmx-users] 2018 installation make check errors, probably CUDA related   Szilárd Páll
• [gmx-users] gromacs 2018.1 installation   Jo
  • [gmx-users] gromacs 2018.1 installation   Mark Abraham
    • [gmx-users] gromacs 2018.1 installation   Jo
• [gmx-users] gmx potential   Shreyas Kaptan
  • [gmx-users] gmx potential   Alex
    • [gmx-users] gmx potential   Alex
      • [gmx-users] gmx potential   Shreyas Kaptan
      • [gmx-users] gmx potential   Alex
      • [gmx-users] gmx potential   Shreyas Kaptan
      • [gmx-users] gmx potential   Alex
      • [gmx-users] gmx potential   Shreyas Kaptan
      • [gmx-users] gmx potential   Alex
• [gmx-users] pdb2gmx with CHARMM-GUI output   Lewis J Martin
• [gmx-users] gmx wham   Alex
  • [gmx-users] gmx wham   Justin Lemkul
    • [gmx-users] gmx wham   Alex
      • [gmx-users] gmx wham   Justin Lemkul
      • [gmx-users] gmx wham   Alex
      • [gmx-users] gmx wham   Justin Lemkul
      • [gmx-users] gmx wham   Alex
• [gmx-users] Thermodynamic integration of VDW transformation   deepak bapat
• [gmx-users] Converting pdb from CHARMM-GUI with pdb2gmx   Lewis Martin
  • [gmx-users] Converting pdb from CHARMM-GUI with pdb2gmx   Justin Lemkul
• [gmx-users] PBC problems related to comm-grps in membrane simulation?   D. Meral
• [gmx-users] gibbs' free energy tutorial: help with write_mdp.pl   Raag Saluja
  • [gmx-users] gibbs' free energy tutorial: help with write_mdp.pl   Justin Lemkul
• [gmx-users] write the eigenvectors of a PCA analysis   edesantis
• [gmx-users] (no subject)   Kingsley Theras Primus Dass .
• [gmx-users] Poisson equation, Hydrodynamic interaction   Amin Rouy
  • [gmx-users] Poisson equation, Hydrodynamic interaction   Amin Rouy
    • [gmx-users] Poisson equation, Hydrodynamic interaction   Mark Abraham
      • [gmx-users] Poisson equation, Hydrodynamic interaction   Alex
    • [gmx-users] Poisson equation, Hydrodynamic interaction   David van der Spoel
      • [gmx-users] Poisson equation, Hydrodynamic interaction   Amin Rouy
      • [gmx-users] Poisson equation, Hydrodynamic interaction   Alex
      • [gmx-users] Poisson equation, Hydrodynamic interaction   David van der Spoel
      • [gmx-users] Poisson equation, Hydrodynamic interaction   Amin Rouy
• [gmx-users] pause a run?   MD
  • [gmx-users] pause a run?   Smith, Micholas D.
    • [gmx-users] pause a run?   MD
      • [gmx-users] pause a run?   MD
      • [gmx-users] pause a run?   Justin Lemkul
      • [gmx-users] pause a run?   Smith, Micholas D.
      • [gmx-users] pause a run?   MD
• [gmx-users] Force displacement curve in SMD simulation   Parthiban Marimuthu
  • [gmx-users] Force displacement curve in SMD simulation   Joe Jordan
• [gmx-users] Typo in dry_martini force field   Myunggi Yi
• [gmx-users] Energy minimization with Walls   John Adams
• [gmx-users] Force displacement curve in SMD simulation   Parthiban Marimuthu
  • [gmx-users] Force displacement curve in SMD simulation   Justin Lemkul
• [gmx-users] cudaMallocHost filed: unknown error   Christopher Neale
  • [gmx-users] cudaMallocHost filed: unknown error   Mark Abraham
  • [gmx-users] cudaMallocHost filed: unknown error   Szilárd Páll
• [gmx-users] -rtpo option for pdb2gmx   Robert König
  • [gmx-users] -rtpo option for pdb2gmx   Justin Lemkul
• [gmx-users] Installation error   ali akgün
  • [gmx-users] Installation error   Mark Abraham
    • [gmx-users] Installation error   ali akgün
      • [gmx-users] Installation error   Mark Abraham
• [gmx-users] Different results from gmx rms   Dawid das
  • [gmx-users] Different results from gmx rms   Mark Abraham
    • [gmx-users] Different results from gmx rms   Dawid das
      • [gmx-users] Different results from gmx rms   Justin Lemkul
      • [gmx-users] Different results from gmx rms   Dawid das
      • [gmx-users] Different results from gmx rms   Mark Abraham
      • [gmx-users] Different results from gmx rms   Dawid das
• [gmx-users] How to understand compressed-x-precision?   Dawid das
  • [gmx-users] How to understand compressed-x-precision?   Mark Abraham
    • [gmx-users] How to understand compressed-x-precision?   Dawid das
• [gmx-users] What's new in GROMACS 2018? - a BioExcel webinar   Rossen Apostolov
  • [gmx-users] What's new in GROMACS 2018? - a BioExcel webinar   Rossen Apostolov
    • [gmx-users] What's new in GROMACS 2018? - a BioExcel webinar   Mark Abraham
  • [gmx-users] What's new in GROMACS 2018? - a BioExcel webinar   Rossen Apostolov
• [gmx-users] Periodicity in umbrella sampling   Matteo Busato
• [gmx-users] Confusions about rlist>=rcoulomb and rlist>=rvdw in the mdp options in Gromacs 2016 (or 2018) user guide??   huolei peng
  • [gmx-users] Confusions about rlist>=rcoulomb and rlist>=rvdw in the mdp options in Gromacs 2016 (or 2018) user guide??   Szilárd Páll
    • [gmx-users] Confusions about rlist>=rcoulomb and rlist>=rvdw in the mdp options in Gromacs 2016 (or 2018) user guide??   Mark Abraham
• [gmx-users] why "gmx gyrate" could not be supplied with "-tu ns" option?   ZHANG Cheng
  • [gmx-users] why "gmx gyrate" could not be supplied with "-tu ns" option?   Justin Lemkul
• [gmx-users] QMMM with GROMACS and DFTB3   S M Bargeen Turzo
  • [gmx-users] QMMM with GROMACS and DFTB3   dgfd dgdfg
• [gmx-users] Umbrella sampling: window distance - harmonic force constant   Hermann, Johannes
  • [gmx-users] Umbrella sampling: window distance - harmonic force constant   Justin Lemkul
    • [gmx-users] Umbrella sampling: window distance - harmonic force constant   Hermann, Johannes
• [gmx-users] Box shape changing from rectangle to parallelogram at NVT   Marlon Sidore
• [gmx-users] gmx mindist error   João Henriques
  • [gmx-users] gmx mindist error   João Henriques
  • [gmx-users] gmx mindist error   Justin Lemkul
    • [gmx-users] gmx mindist error   João Henriques
      • [gmx-users] gmx mindist error   Mark Abraham
      • [gmx-users] gmx mindist error   João Henriques
      • [gmx-users] gmx mindist error   Mark Abraham
      • [gmx-users] gmx mindist error   Mark Abraham
      • [gmx-users] gmx mindist error   João Henriques
      • [gmx-users] gmx mindist error   João M. Damas
• [gmx-users] Excessive and gradually increasing memory usage with OpenCL   Albert Mao
  • [gmx-users] Excessive and gradually increasing memory usage with OpenCL   Mark Abraham
  • [gmx-users] Excessive and gradually increasing memory usage with OpenCL   Szilárd Páll
    • [gmx-users] Excessive and gradually increasing memory usage with OpenCL   Albert Mao
      • [gmx-users] Excessive and gradually increasing memory usage with OpenCL   Mark Abraham
• [gmx-users] QMMM with GROMACS and DFTB3   S M Bargeen Turzo
  • [gmx-users] QMMM with GROMACS and DFTB3   dgfd dgdfg
• [gmx-users] Number of Xeon cores per GTX 1080Ti   Jochen Hub
  • [gmx-users] QMMM with GROMACS and DFTB3   dgfd dgdfg
  • [gmx-users] Number of Xeon cores per GTX 1080Ti   Mark Abraham
    • [gmx-users] Number of Xeon cores per GTX 1080Ti   Szilárd Páll
• [gmx-users] 'constraints' directive and water   Alex
  • [gmx-users] 'constraints' directive and water   Justin Lemkul
    • [gmx-users] 'constraints' directive and water   Alex
      • [gmx-users] 'constraints' directive and water   Justin Lemkul
      • [gmx-users] 'constraints' directive and water   Alex
      • [gmx-users] 'constraints' directive and water   Justin Lemkul
      • [gmx-users] 'constraints' directive and water   Alex
      • [gmx-users] 'constraints' directive and water   Justin Lemkul
      • [gmx-users] 'constraints' directive and water   Mark Abraham
      • [gmx-users] 'constraints' directive and water   Alex
• [gmx-users] mdrun on single node with GPU   Myunggi Yi
  • [gmx-users] mdrun on single node with GPU   Szilárd Páll
• [gmx-users] RMSD values consideration   SHYANTANI MAITI
  • [gmx-users] RMSD values consideration   Ahmed Mashaly
• [gmx-users] ss.xpm file: first residue showing first, or last residue showing first?   ZHANG Cheng
• [gmx-users] Performance   Myunggi Yi
  • [gmx-users] Performance   Szilárd Páll
    • [gmx-users] Performance   Myunggi Yi
      • [gmx-users] Performance   Mark Abraham
      • [gmx-users] Performance   Myunggi Yi
      • [gmx-users] Performance   Myunggi Yi
      • [gmx-users] Performance   Szilárd Páll
      • [gmx-users] Performance   Myunggi Yi
      • [gmx-users] Performance   Myunggi Yi
• [gmx-users] Problems in putting restraints during free energy perturbation calculations (cont)   Searle Duay
• [gmx-users] RDF brads   Alex
  • [gmx-users] RDF brads   Joe Jordan
• [gmx-users] Parameters in top   Dawid das
  • [gmx-users] Parameters in top   Joe Jordan
  • [gmx-users] Parameters in top   Mark Abraham
• [gmx-users] Atoms in radius of X nm (linking atoms in selection by AND not OR)   Marc Hoemberger
  • [gmx-users] Atoms in radius of X nm (linking atoms in selection by AND not OR)   Mark Abraham
    • [gmx-users] Atoms in radius of X nm (linking atoms in selection by AND not OR)   Marc Hoemberger
      • [gmx-users] Atoms in radius of X nm (linking atoms in selection by AND not OR)   Marc Hoemberger
    • [gmx-users] Atoms in radius of X nm (linking atoms in selection by AND not OR)   Marc Hoemberger
• [gmx-users] Generate unit cell   ali akgün
• [gmx-users] Possible to extract gro file from a tpr?   Viveca Lindahl
  • [gmx-users] Possible to extract gro file from a tpr?   Gregory Man Kai Poon
  • [gmx-users] Possible to extract gro file from a tpr?   Justin Lemkul
    • [gmx-users] Possible to extract gro file from a tpr?   Alex
      • [gmx-users] Possible to extract gro file from a tpr?   Mark Abraham
• [gmx-users] gmx check precision   jt555
  • [gmx-users] gmx check precision   Justin Lemkul
• [gmx-users] ss.xpm file: chain separator location? first residue showing first, or last residue showing first?   ZHANG Cheng
• [gmx-users] Stochastic dynamics (sd)   Alex
• [gmx-users] Dose gpu support on flatbottom restraint   Bhupendra Dandekar
  • [gmx-users] Dose gpu support on flatbottom restraint   Kevin Boyd

Last message date: Sat Mar 31 13:55:06 CEST 2018
Archived on: Sat Mar 31 13:55:07 CEST 2018

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