June 2012 Archives by thread

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Starting: Fri Jun 1 11:16:45 CEST 2012
Ending: Sat Jun 30 23:31:13 CEST 2012
Messages: 901

• [gmx-users] Re: Possible bug: energy changes with the number of nodes for energy minimization   Szilárd Páll
• [gmx-users] umbrella windows...   rama david
  • [gmx-users] umbrella windows...   Justin A. Lemkul
• [gmx-users] Incomplete frame   Turgay Cakmak
  • [gmx-users] Incomplete frame   Justin A. Lemkul
    • [gmx-users] Incomplete frame   Turgay Cakmak
      • [gmx-users] Incomplete frame   Justin A. Lemkul
• [gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface   Klniu
• [gmx-users] unit conversion of a force constant   Lara Bunte
• [gmx-users] Re: boundaries in PMF   Thomas Schlesier
• [gmx-users] Results of the GROMACS user survey & NVIDIA board winners   Erik Lindahl
  • [gmx-users] Results of the GROMACS user survey & NVIDIA board winners   Dommert Florian
    • [gmx-users] Results of the GROMACS user survey & NVIDIA board winners   Emanuel Birru
• [gmx-users] Configurational bias Monte Carlo   Benjamin Haley
  • [gmx-users] Configurational bias Monte Carlo   Michael Shirts
    • [gmx-users] Configurational bias Monte Carlo   Lara Bunte
      • [gmx-users] Configurational bias Monte Carlo   Justin A. Lemkul
  • [gmx-users] how to rename oxygen oxt to be recognized by MOLMOL   Acoot Brett
    • [gmx-users] how to rename oxygen oxt to be recognized by MOLMOL   Mark Abraham
• [gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface   Christopher Neale
• [gmx-users] unit conversion of a force constant   Christopher Neale
• [gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface   Klniu
• [gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface   Christopher Neale
  • [gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface   Klniu
• [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?   Klniu
  • [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?   Mark Abraham
    • [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?   Klniu
• [gmx-users] Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for   xi zhao
  • [gmx-users] Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for   Mark Abraham
• [gmx-users] About extend the run,,   rama david
  • [gmx-users] About extend the run,,   Justin A. Lemkul
    • [gmx-users] About extend the run,,   rama david
      • [gmx-users] About extend the run,,   Justin A. Lemkul
      • [gmx-users] how to run production MD for only a fragment of protein   Acoot Brett
      • [gmx-users] how to run production MD for only a fragment of protein   Justin A. Lemkul
      • [gmx-users] About extend the run,,   rama david
• [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?   Christopher Neale
  • [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?   Klniu
• [gmx-users] Calculate surface tension   cuong nguyen
• [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond   Erik Marklund
  • [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond   Acoot Brett
    • [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond   Erik Marklund
      • [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond   Acoot Brett
• [gmx-users] MD Training   Erik Marklund
  • [gmx-users] MD Training   Dommert Florian
• [gmx-users] Atomtype 1   xi zhao
  • [gmx-users] Atomtype 1   Justin A. Lemkul
    • [gmx-users] Atomtype 1   xi zhao
    • [gmx-users] Atomtype 1   xi zhao
      • [gmx-users] Atomtype 1   Mark Abraham
    • [gmx-users] Atomtype 1   xi zhao
      • [gmx-users] Atomtype 1   Justin A. Lemkul
      • [gmx-users] Atomtype 1   xi zhao
      • [gmx-users] Atomtype 1   Justin A. Lemkul
      • [gmx-users] Atomtype 1   xi zhao
    • [gmx-users] Parallel MD performance   delara aghaie
      • [gmx-users] Parallel MD performance   Mark Abraham
• [gmx-users] Re: dangling bond at at one of the terminal ends   ramaraju801
  • [gmx-users] Re: dangling bond at at one of the terminal ends   Justin A. Lemkul
    • [gmx-users] Re: dangling bond at at one of the terminal ends   ramaraju801
    • [gmx-users] Re: dangling bond at at one of the terminal ends   Thomas Piggot
      • [gmx-users] Re: dangling bond at at one of the terminal ends   ramaraju801
      • [gmx-users] Re: dangling bond at at one of the terminal ends   Justin A. Lemkul
• [gmx-users] Tabulated potentials for dihedrals - regd   ramesh cheerla
  • [gmx-users] Tabulated potentials for dihedrals - regd   Mark Abraham
    • [gmx-users] Tabulated potentials for dihedrals - regd   ramesh cheerla
      • [gmx-users] Tabulated potentials for dihedrals - regd   Mark Abraham
      • [gmx-users] Tabulated potentials for dihedrals - regd   ramesh cheerla
• [gmx-users] Regarding error   Seera Suryanarayana
  • [gmx-users] Regarding error   Emanuel Birru
  • [gmx-users] Regarding error   Seera Suryanarayana
    • [gmx-users] Regarding error   Mark Abraham
    • [gmx-users] Regarding error   Seera Suryanarayana
• [gmx-users] How to maintain the same exact positions of the protein and ligand in the extracted frame/pdb file as they were in the trajectory form?   Wayne Chen
  • [gmx-users] How to maintain the same exact positions of the protein and ligand in the extracted frame/pdb file as they were in the trajectory form?   Mark Abraham
• [gmx-users] Regarding error.   Seera Suryanarayana
• [gmx-users] Steered MD   Mike M
  • [gmx-users] Steered MD   Miguel Ángel Mompeán García
    • [gmx-users] Steered MD   Mike M
• [gmx-users] Electrostatic interactions and atoms with nul charge   Laurence Leherte
  • [gmx-users] Electrostatic interactions and atoms with nul charge   Mark Abraham
    • [gmx-users] Electrostatic interactions and atoms with nul charge   Laurence Leherte
      • [gmx-users] Electrostatic interactions and atoms with nul charge   Mark Abraham
• [gmx-users] Writing and compiling new analyses for gromacs   Shay Teaching
  • [gmx-users] Writing and compiling new analyses for gromacs   Justin A. Lemkul
    • [gmx-users] Writing and compiling new analyses for gromacs   Shay Teaching
      • [gmx-users] Writing and compiling new analyses for gromacs   Justin A. Lemkul
      • [gmx-users] Writing and compiling new analyses for gromacs   Peter C. Lai
      • [gmx-users] Writing and compiling new analyses for gromacs   francesco oteri
      • [gmx-users] Writing and compiling new analyses for gromacs   Shay Teaching
      • [gmx-users] Writing and compiling new analyses for gromacs   Shay Teaching
      • [gmx-users] Writing and compiling new analyses for gromacs   Peter C. Lai
      • [gmx-users] Writing and compiling new analyses for gromacs   Mark Abraham
      • [gmx-users] Writing and compiling new analyses for gromacs   Shay Teaching
      • [gmx-users] Writing and compiling new analyses for gromacs   Erik Marklund
      • [gmx-users] Writing and compiling new analyses for gromacs   Shay Teaching
      • [gmx-users] Writing and compiling new analyses for gromacs   Shay Teaching
• [gmx-users] Water molecules cannot be settled, why?   John Ladasky
  • [gmx-users] Water molecules cannot be settled, why?   Justin A. Lemkul
• [gmx-users] Angle deformation of Triphosphate moiety with charge -4 ?..   Alberto Sergio Garay
• [gmx-users] selenomethionine OPLS ff   tarak karmakar
• [gmx-users] How could I know whether I should use epsilon-sigma or c6-c12?   Bao Kai
  • [gmx-users] How could I know whether I should use epsilon-sigma or c6-c12?   Mark Abraham
• [gmx-users] Dielectric Constants   Size Zheng
• [gmx-users] How could I know whether I should use epsilon-sigma or c6-c12?   Bao Kai
  • [gmx-users] How could I know whether I should use epsilon-sigma or c6-c12?   Mark Abraham
• [gmx-users] trajectory analysis   Turgay Cakmak
  • [gmx-users] trajectory analysis   Justin A. Lemkul
    • [gmx-users] trajectory analysis   Turgay Cakmak
• [gmx-users] Dispersion Corrections   Erica Schulz
• [gmx-users] What does this message mean?   Bao Kai
  • [gmx-users] What does this message mean?   Mark Abraham
  • [gmx-users] Re:What does this message mean?   Bao Kai
    • [gmx-users] Re:What does this message mean?   Mark Abraham
• [gmx-users] Trajectories   rankinb
  • [gmx-users] Trajectories   Justin A. Lemkul
    • [gmx-users] Trajectories   Erik Marklund
      • [gmx-users] Trajectories   Thomas Piggot
      • [gmx-users] Trajectories   Erik Marklund
    • [gmx-users] Trajectories   lloyd riggs
      • [gmx-users] Trajectories   Blake Rankin
    • [gmx-users] Trajectories   lloyd riggs
  • [gmx-users] Trajectories   Peter C. Lai
    • [gmx-users] Trajectories   Erik Marklund
• [gmx-users] tip5p tip, not good, energy can only get -39, not -45   MD
  • [gmx-users] tip5p tip, not good, energy can only get -39, not -45   Mark Abraham
• [gmx-users] Selecting atom indices of residues whose centers of mass match a position range   Andrew DeYoung
  • [gmx-users] Selecting atom indices of residues whose centers of mass match a position range   Justin A. Lemkul
    • [gmx-users] Selecting atom indices of residues whose centers of mass match a position range   Teemu Murtola
• [gmx-users] How to add DMSO as solvent?   Yun Shi
  • [gmx-users] How to add DMSO as solvent?   Justin A. Lemkul
  • [gmx-users] How to add DMSO as solvent?   Peter C. Lai
• [gmx-users] chirality changes during the simulation   mu xiaojia
  • [gmx-users] chirality changes during the simulation   Mark Abraham
• [gmx-users] "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" error during minimization with TPO residue   Alex Cumberworth
  • [gmx-users] "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" error during minimization with TPO residue   Justin A. Lemkul
    • [gmx-users] "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" error during minimization with TPO residue   Alex Cumberworth
  • [gmx-users] MD continuation   delara aghaie
    • [gmx-users] MD continuation   Kowsar Bagherzadeh
    • [gmx-users] MD continuation   Mark Abraham
• [gmx-users] TIP3P or TIP4P   Amir Abbasi
  • [gmx-users] TIP3P or TIP4P   Mark Abraham
• [gmx-users] comparing simulations with diffrent forcefields   Kowsar Bagherzadeh
• [gmx-users] Regarding error   Seera Suryanarayana
• [gmx-users] Regarding error.   Seera Suryanarayana
  • [gmx-users] Regarding error.   Javier Cerezo
    • [gmx-users] Regarding error.   Erik Marklund
• [gmx-users] change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system   Sangita Kachhap
  • [gmx-users] change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system   Justin A. Lemkul
• [gmx-users] Regarding error.   Seera Suryanarayana
  • [gmx-users] Regarding error.   Javier Cerezo
• [gmx-users] Question regarding genion   Matthias Ernst
  • [gmx-users] Question regarding genion   Justin A. Lemkul
• [gmx-users] Atomtype OW_tip4p not found   Amir Abbasi
  • [gmx-users] Atomtype OW_tip4p not found   Justin A. Lemkul
• [gmx-users] Scaling/performance on Gromacs 4   Manu Vajpai
• [gmx-users] Atomtype OW_tip4p not found   Justin A. Lemkul
  • [gmx-users] Atomtype OW_tip4p not found   Amir Abbasi
    • [gmx-users] Atomtype OW_tip4p not found   Justin A. Lemkul
• [gmx-users] Regarding Free energy (Energy barrier) calculation   neeru sharma
• [gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system   Sangita Kachhap
  • [gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system   Justin A. Lemkul
• [gmx-users] Segmentation fault - pdb2gmx specbond.dat   Steven Neumann
• [gmx-users] energy conservation: shift vs shifted user potential   Anja Kuhnhold
• [gmx-users] Cannot get correct pressure value with MTTK pressure coupling   Bao Kai
  • [gmx-users] Cannot get correct pressure value with MTTK pressure coupling   Justin A. Lemkul
• [gmx-users] hydrophobic contacts   Turgay Cakmak
• [gmx-users] g_sas   Meisam Rezaei
• [gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system   Sangita Kachhap
  • [gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system   Justin A. Lemkul
• [gmx-users] GPU crashes   Justin A. Lemkul
  • [gmx-users] GPU crashes   lloyd riggs
    • [gmx-users] GPU crashes   Justin A. Lemkul
• [gmx-users] Regarding g_sham   bipin singh
  • [gmx-users] Regarding g_sham   Justin A. Lemkul
• [gmx-users] cluster fomation in triolein simulation   mahnam karim
  • [gmx-users] cluster fomation in triolein simulation   Dallas Warren
• [gmx-users] Warnings related to Berendsen pressure coupling and use the refcoord_scaling option   PAVAN PAYGHAN
  • [gmx-users] Warnings related to Berendsen pressure coupling and use the refcoord_scaling option   Mark Abraham
• [gmx-users] How to set up constraint distcance pulling   xiaowu759
  • [gmx-users] How to set up constraint distcance pulling   Justin A. Lemkul
• [gmx-users] Regarding Free Energy calculation tutorial   neeru sharma
  • [gmx-users] Regarding Free Energy calculation tutorial   Justin A. Lemkul
• [gmx-users] gmx-users Digest, Vol 98, Issue 42   PAVAN PAYGHAN
  • [gmx-users] Re: gmx-users Digest, Vol 98, Issue 42   Mark Abraham
• [gmx-users] How to set up constraint distcance pulling   xiaowu759
  • [gmx-users] How to set up constraint distcance pulling   Justin A. Lemkul
• [gmx-users] dssp doubt   Turgay Cakmak
  • [gmx-users] dssp doubt   Justin A. Lemkul
    • [gmx-users] dssp doubt   Emine Deniz Tekin
• [gmx-users] Re: gmx-users Digest, Vol 98, Issue 44   neeru sharma
• [gmx-users] About Umbrella sampling   vidhya sankar
  • [gmx-users] About Umbrella sampling   Justin A. Lemkul
• [gmx-users] Re: Thermodynamic Integration Glu -> Ala Mutation   Sai Kumar Ramadugu
• [gmx-users] Re: Restarting mdrun   Cuiying
• [gmx-users] qmmm and "real-life" meaning of null lennard-jones parameters   Edward Deira
  • [gmx-users] qmmm and "real-life" meaning of null lennard-jones parameters   Justin A. Lemkul
    • [gmx-users] qmmm and "real-life" meaning of null lennard-jones parameters   Javier Cerezo
• [gmx-users] Trouble with packing lipids around a protein using InflateGRO   Erica Hicks
  • [gmx-users] Trouble with packing lipids around a protein using InflateGRO   Justin A. Lemkul
• [gmx-users] Error in grompp steps of position restrained   Malai
  • [gmx-users] Error in grompp steps of position restrained   Mark Abraham
    • [gmx-users] Error in grompp steps of position restrained   Malai
      • [gmx-users] Error in grompp steps of position restrained   Mark Abraham
      • [gmx-users] Error in grompp steps of position restrained   Malai
• [gmx-users] query on table potential   Sanku M
  • [gmx-users] query on table potential   Mark Abraham
• [gmx-users] Regarding error   Seera Suryanarayana
  • [gmx-users] Regarding error   Dallas Warren
• [gmx-users] Re: energy conservation: shift vs shifted user potential   Anja Kuhnhold
  • [gmx-users] Re: energy conservation: shift vs shifted user potential   Mark Abraham
  • [gmx-users] radius of gyration   delara aghaie
• [gmx-users] Pulling - ligand outside the box   Steven Neumann
  • [gmx-users] Pulling - ligand outside the box   Mark Abraham
• [gmx-users] eneconv with -dt flag   Turgay Cakmak
  • [gmx-users] eneconv with -dt flag   Mark Abraham
    • [gmx-users] eneconv with -dt flag   Turgay Cakmak
      • [gmx-users] eneconv with -dt flag   Mark Abraham
• [gmx-users] QM/MM Calculation with Orca   Minos Matsoukas
• [gmx-users] md.log i/o error in futil.c +459   Inon Sharony
  • [gmx-users] md.log i/o error in futil.c +459   Mark Abraham
  • [gmx-users] Re: md.log i/o error in futil.c +459   Inon Sharony
    • [gmx-users] Re: md.log i/o error in futil.c +459   Mark Abraham
• [gmx-users] 4. QM/MM Calculation with Orca (Minos Matsoukas)   Gerrit Groenhof
  • [gmx-users] 4. QM/MM Calculation with Orca (Minos Matsoukas)   Minos Matsoukas
• [gmx-users] Furthest distance between 2 atoms   Catarina Santos
  • [gmx-users] Furthest distance between 2 atoms   Mark Abraham
• [gmx-users] qmmm and "real-life" meaning of null   Gerrit Groenhof
• [gmx-users] parameters for bond types for GROMOS force field.   James Starlight
  • [gmx-users] parameters for bond types for GROMOS force field.   Mark Abraham
    • [gmx-users] parameters for bond types for GROMOS force field.   James Starlight
      • [gmx-users] parameters for bond types for GROMOS force field.   Justin A. Lemkul
      • [gmx-users] parameters for bond types for GROMOS force field.   James Starlight
      • [gmx-users] parameters for bond types for GROMOS force field.   Justin A. Lemkul
      • [gmx-users] parameters for bond types for GROMOS force field.   James Starlight
      • [gmx-users] parameters for bond types for GROMOS force field.   James Starlight
      • [gmx-users] parameters for bond types for GROMOS force field.   Justin A. Lemkul
      • [gmx-users] parameters for bond types for GROMOS force field.   James Starlight
      • [gmx-users] parameters for bond types for GROMOS force field.   Justin A. Lemkul
      • [gmx-users] parameters for bond types for GROMOS force field.   James Starlight
      • [gmx-users] parameters for bond types for GROMOS force field.   Mark Abraham
• [gmx-users] Total energy of a group of atoms   Markus Kaukonen
• [gmx-users] Electrostatic interaction energy   Turgay Cakmak
  • [gmx-users] Electrostatic interaction energy   Justin A. Lemkul
• [gmx-users] Re: Re: energy conservation: shift vs shifted user potential   Anja Kuhnhold
  • [gmx-users] Re: Re: energy conservation: shift vs shifted user potential   Mark Abraham
• [gmx-users] vsite as interaction site for COM of benzene   Thomas Schlesier
  • [gmx-users] vsite as interaction site for COM of benzene   Broadbent, Richard
• [gmx-users] Energy Minimization - not getting correct lipid area   Hicks, Erica
  • [gmx-users] Energy Minimization - not getting correct lipid area   Justin A. Lemkul
    • [gmx-users] Re: Energy Minimization - not getting correct lipid area   Erica Hicks
      • [gmx-users] Re: Energy Minimization - not getting correct lipid area   Justin A. Lemkul
      • [gmx-users] RE: Energy Minimization - not getting correct lipid area   Erica Hicks
      • [gmx-users] RE: Energy Minimization - not getting correct lipid area   Justin A. Lemkul
      • [gmx-users] RE: Energy Minimization - not getting correct lipid area   Erica Hicks
      • [gmx-users] RE: Energy Minimization - not getting correct lipid area   Justin A. Lemkul
      • [gmx-users] RE: Energy Minimization - not getting correct lipid area   Erica Hicks
      • [gmx-users] RE: Energy Minimization - not getting correct lipid area   Justin A. Lemkul
      • [gmx-users] RE: Energy Minimization - not getting correct lipid area   Erica Hicks
      • [gmx-users] RE: Energy Minimization - not getting correct lipid area   Justin A. Lemkul
      • [gmx-users] RE: Energy Minimization - not getting correct lipid area   Erica Hicks
      • [gmx-users] RE: Energy Minimization - not getting correct lipid area   Justin A. Lemkul
• [gmx-users] CECAM ScalaLife Workshop, Oct 03 - Oct 05, 2012   Rossen Apostolov
• [gmx-users] floating point exception in .xtc file   Christopher Neale
  • [gmx-users] floating point exception in .xtc file   Mark Abraham
    • [gmx-users] floating point exception in .xtc file   francesco oteri
• [gmx-users] vsite as interaction site for COM of benzene   Thomas Schlesier
• [gmx-users] Fatal error: Atomtype O2 not found   ramaraju801
  • [gmx-users] Fatal error: Atomtype O2 not found   Justin A. Lemkul
    • [gmx-users] Re: Fatal error: Atomtype O2 not found   ramaraju801
      • [gmx-users] Re: Fatal error: Atomtype O2 not found   Justin A. Lemkul
      • [gmx-users] Re: Fatal error: Atomtype O2 not found   ramaraju801
      • [gmx-users] Re: Fatal error: Atomtype O2 not found   Justin A. Lemkul
      • [gmx-users] Re: Fatal error: Atomtype O2 not found   Mark Abraham
      • [gmx-users] Re: Fatal error: Atomtype O2 not found   ramaraju801
      • [gmx-users] Re: Fatal error: Atomtype O2 not found   Justin A. Lemkul
      • [gmx-users] Re: Fatal error: Atomtype O2 not found   ramaraju801
      • [gmx-users] Re: Fatal error: Atomtype O2 not found   Mark Abraham
      • [gmx-users] Re: Fatal error: Atomtype O2 not found   Gurunath Katagi
      • [gmx-users] Re: Fatal error: Atomtype O2 not found   ramaraju801
      • [gmx-users] Re: Fatal error: Atomtype O2 not found   Justin A. Lemkul
• [gmx-users] Re: Automated Topology Builder job partially completed   James Starlight
  • [gmx-users] Re: Automated Topology Builder job partially completed   Justin A. Lemkul
• [gmx-users] floating point exception in .xtc file   Christopher Neale
• [gmx-users] g_msd and MSD analysis   Mr Bernard Ramos
  • [gmx-users] g_msd and MSD analysis   Dommert Florian
• [gmx-users] Temperature in NVT file   Shima Arasteh
  • [gmx-users] Temperature in NVT file   Justin A. Lemkul
    • [gmx-users] Temperature in NVT file   Shima Arasteh
• [gmx-users] Capping error in pdb2gmx   siddhant jain
  • [gmx-users] Capping error in pdb2gmx   Justin A. Lemkul
• [gmx-users] Question about documentation of -a switch in g_hbond   Andrew DeYoung
  • [gmx-users] Question about documentation of -a switch in g_hbond   Justin A. Lemkul
    • [gmx-users] Question about documentation of -a switch in g_hbond   Mark Abraham
• [gmx-users] pdb to xyz file format   Lara Bunte
  • [gmx-users] pdb to xyz file format   Matthias Ernst
    • [gmx-users] pdb to xyz file format   Chandan Choudhury
• [gmx-users] GPU   ifat shub
  • [gmx-users] GPU   Mark Abraham
• [gmx-users] Re : Capping error in pdb2gmx   siddhant jain
  • [gmx-users] Re : Capping error in pdb2gmx   Justin A. Lemkul
• [gmx-users] Re: [gmx-developers] issue on benchmarking FEP calculations in Gromacs and NAMD   Roland Schulz
• [gmx-users] LINCS warnings   rama david
  • [gmx-users] LINCS warnings   Mark Abraham
    • [gmx-users] LINCS warnings   rama david
      • [gmx-users] LINCS warnings   Mark Abraham
      • [gmx-users] LINCS warnings   rama david
      • [gmx-users] LINCS warnings   Justin A. Lemkul
      • [gmx-users] LINCS warnings   rama david
• [gmx-users] Regarding minim.mdp file.   Seera Suryanarayana
  • [gmx-users] Regarding minim.mdp file.   Mark Abraham
• [gmx-users] Rhamnose on 53a6   Marc Gordon
  • [gmx-users] Rhamnose on 53a6   Mark Abraham
  • [gmx-users] Rhamnose on 53a6   Thales Kronenberger
    • [gmx-users] Rhamnose on 53a6   Justin A. Lemkul
• [gmx-users] Regarding .mdp files.   Seera Suryanarayana
  • [gmx-users] Regarding .mdp files.   Mark Abraham
• [gmx-users] Regarding error.   Seera Suryanarayana
  • [gmx-users] Regarding error.   Justin A. Lemkul
• [gmx-users] radius of gyration   delara aghaie
  • [gmx-users] radius of gyration   Justin A. Lemkul
    • [gmx-users] radius of gyration   delara aghaie
      • [gmx-users] radius of gyration   Justin A. Lemkul
      • [gmx-users] radius of gyration   delara aghaie
      • [gmx-users] radius of gyration   Justin A. Lemkul
      • [gmx-users] radius of gyration   delara aghaie
      • [gmx-users] radius of gyration   Justin A. Lemkul
      • [gmx-users] radius of gyration   delara aghaie
• [gmx-users] Coordinate file for lipid bilayer   James Starlight
  • [gmx-users] Coordinate file for lipid bilayer   Justin A. Lemkul
• [gmx-users] Total energy of a group of atoms   Markus Kaukonen
  • [gmx-users] Total energy of a group of atoms   Mark Abraham
• [gmx-users] Positive Potential Energy after equilibration   Satish Kamath
  • [gmx-users] Positive Potential Energy after equilibration   Justin A. Lemkul
    • [gmx-users] Re: Positive Potential Energy after equilibration   Satish Kamath
      • [gmx-users] Re: Positive Potential Energy after equilibration   Satish Kamath
      • [gmx-users] Re: Positive Potential Energy after equilibration   Justin A. Lemkul
      • [gmx-users] Re: Positive Potential Energy after equilibration   Satish Kamath
      • [gmx-users] Re: Positive Potential Energy after equilibration   Justin A. Lemkul
      • [gmx-users] Re: Positive Potential Energy after equilibration   Satish Kamath
      • [gmx-users] Re: Positive Potential Energy after equilibration   Satish Kamath
      • [gmx-users] Re: Positive Potential Energy after equilibration   Justin A. Lemkul
      • [gmx-users] Re: Positive Potential Energy after equilibration   Satish Kamath
      • [gmx-users] Re: Positive Potential Energy after equilibration   Justin A. Lemkul
• [gmx-users] Re: Question about documentation of -a switch in g_hbond   Andrew DeYoung
• [gmx-users] Bonds and atom-pairs in g_hbond   Andrew DeYoung
  • [gmx-users] Bonds and atom-pairs in g_hbond   Erik Marklund
• [gmx-users] RE: Bonds and atom-pairs in g_hbond   Andrew DeYoung
  • [gmx-users] RE: Bonds and atom-pairs in g_hbond   Justin A. Lemkul
• [gmx-users] (no subject)   tarak karmakar
  • [gmx-users] (no subject)   Klniu
  • [gmx-users] (no subject)   Mark Abraham
• [gmx-users] analysing of the long trajectories   James Starlight
  • [gmx-users] analysing of the long trajectories   Mark Abraham
    • [gmx-users] analysing of the long trajectories   James Starlight
      • [gmx-users] analysing of the long trajectories   Tsjerk Wassenaar
      • [gmx-users] analysing of the long trajectories   James Starlight
      • [gmx-users] analysing of the long trajectories   James Starlight
      • [gmx-users] analysing of the long trajectories   a a
      • [gmx-users] analysing of the long trajectories   Chandan Choudhury
      • [gmx-users] analysing of the long trajectories   Mark Abraham
• [gmx-users] simulated annealing mdp   rama david
  • [gmx-users] simulated annealing mdp   Justin A. Lemkul
    • [gmx-users] simulated annealing mdp   rama david
      • [gmx-users] simulated annealing mdp   Lord RaviRaj ..
      • [gmx-users] simulated annealing mdp   Justin A. Lemkul
      • [gmx-users] simulated annealing mdp   rama david
      • [gmx-users] simulated annealing mdp   Justin A. Lemkul
      • [gmx-users] simulated annealing mdp   rama david
• [gmx-users] g_rdf (lyzozyme tutorial)   delara aghaie
  • [gmx-users] g_rdf (lyzozyme tutorial)   Justin A. Lemkul
    • [gmx-users] g_rdf (lyzozyme tutorial)   delara aghaie
      • [gmx-users] g_rdf (lyzozyme tutorial)   Justin A. Lemkul
• [gmx-users] mdrun_mpi segmentation fault for run in vacuum   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] mdrun_mpi segmentation fault for run in vacuum   Justin A. Lemkul
    • [gmx-users] mdrun_mpi segmentation fault for run in vacuum   reisingere at rostlab.informatik.tu-muenchen.de
      • [gmx-users] mdrun_mpi segmentation fault for run in vacuum   Justin A. Lemkul
      • [gmx-users] mdrun_mpi segmentation fault for run in vacuum   reisingere at rostlab.informatik.tu-muenchen.de
      • [gmx-users] mdrun_mpi segmentation fault for run in vacuum   Justin A. Lemkul
      • [gmx-users] mdrun_mpi segmentation fault for run in vacuum   reisingere at rostlab.informatik.tu-muenchen.de
      • [gmx-users] mdrun_mpi segmentation fault for run in vacuum   Justin A. Lemkul
      • [gmx-users] mdrun_mpi segmentation fault for run in vacuum   reisingere at rostlab.informatik.tu-muenchen.de
      • [gmx-users] mdrun_mpi segmentation fault for run in vacuum   Justin A. Lemkul
      • [gmx-users] mdrun_mpi segmentation fault for run in vacuum   reisingere at rostlab.informatik.tu-muenchen.de
      • [gmx-users] mdrun_mpi segmentation fault for run in vacuum   Justin A. Lemkul
• [gmx-users] Re: energy conservation: shift vs shifted user potential   Anja Kuhnhold
  • [gmx-users] Re: energy conservation: shift vs shifted user potential   Mark Abraham
• [gmx-users] Press Equilibration   rama david
  • [gmx-users] Press Equilibration   Justin A. Lemkul
    • [gmx-users] Press Equilibration   rama david
  • [gmx-users] Re: Press Equilibration   rama david
    • [gmx-users] Re: Press Equilibration   Mark Abraham
• [gmx-users] question about pdb file   delara aghaie
  • [gmx-users] question about pdb file   Mark Abraham
    • [gmx-users] question about pdb file   Mike M
• [gmx-users] pdb2gmx error   delara aghaie
  • [gmx-users] pdb2gmx error   Justin A. Lemkul
  • [gmx-users] pdb2gmx error   tarak karmakar
• [gmx-users] GPU   Ehud Schreiber
  • [gmx-users] GPU   Mark Abraham
    • [gmx-users] GPU   Szilárd Páll
• [gmx-users] Hbonds and PBC   Steven Neumann
  • [gmx-users] Hbonds and PBC   Justin A. Lemkul
    • [gmx-users] Hbonds and PBC   Steven Neumann
  • [gmx-users] Re: Hbonds and PBC   Steven Neumann
• [gmx-users] bond autocorrelation function   Tom
• [gmx-users] dihedral restraint MD   Lin Huang
  • [gmx-users] dihedral restraint MD   Mark Abraham
• [gmx-users] user specified non bonded potentials - regd   ramesh cheerla
• [gmx-users] Can Gromacs functions be called by some other codes?   Bao Kai
  • [gmx-users] Can Gromacs functions be called by some other codes?   Da-Wei Li
• [gmx-users] Re: bond autocorrelation function   Dr. Vitaly V. G. Chaban
  • [gmx-users] Re: bond autocorrelation function   Justin A. Lemkul
• [gmx-users] Re: Can Gromacs functions be called by some other codes?   Bao Kai
  • [gmx-users] Re: Can Gromacs functions be called by some other codes?   Da-Wei Li
    • [gmx-users] Re: Can Gromacs functions be called by some other codes?   Tsjerk Wassenaar
      • [gmx-users] Re: Can Gromacs functions be called by some other codes?   Mark Abraham
• [gmx-users] problems occur during simulation   abhidon89
  • [gmx-users] problems occur during simulation   Justin A. Lemkul
• [gmx-users] What does the -don switch calculate in g_hbond?   Andrew DeYoung
• [gmx-users] Re: bond autocorrelation function   Dr. Vitaly V. G. Chaban
• [gmx-users] error in grompp run   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] error in grompp run   Mark Abraham
    • [gmx-users] error in grompp run   reisingere at rostlab.informatik.tu-muenchen.de
• [gmx-users] Errors in Minimization using grompp   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] Errors in Minimization using grompp   Mark Abraham
    • [gmx-users] Errors in Minimization using grompp   reisingere at rostlab.informatik.tu-muenchen.de
      • [gmx-users] Errors in Minimization using grompp   Justin A. Lemkul
      • [gmx-users] Errors in Minimization using grompp   reisingere at rostlab.informatik.tu-muenchen.de
      • [gmx-users] Errors in Minimization using grompp   reisingere at rostlab.informatik.tu-muenchen.de
      • [gmx-users] Errors in Minimization using grompp   Justin A. Lemkul
• [gmx-users] (no subject)   Seera Suryanarayana
  • [gmx-users] (no subject)   Justin A. Lemkul
• [gmx-users] unknown residue (BGC)   delara aghaie
  • [gmx-users] unknown residue (BGC)   Justin A. Lemkul
• [gmx-users] input/output error in production grompp   Malai
  • [gmx-users] input/output error in production grompp   Justin A. Lemkul
    • [gmx-users] input/output error in production grompp   Malai
      • [gmx-users] input/output error in production grompp   Justin A. Lemkul
      • [gmx-users] input/output error in production grompp   Malai
      • [gmx-users] input/output error in production grompp   Justin A. Lemkul
      • [gmx-users] input/output error in production grompp   Malai
      • [gmx-users] input/output error in production grompp   Justin A. Lemkul
• [gmx-users] unknown residue (BGC)   Justin A. Lemkul
• [gmx-users] unknown residue (BGC)   Justin A. Lemkul
• [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation   ms
  • [gmx-users] Re: Strong egative energy drift (losing energy) in explicit water AMBER protein simulation   ms
  • [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation   Justin A. Lemkul
    • [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation   ms
      • [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation   Justin A. Lemkul
      • [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation   ms
      • [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation   Justin A. Lemkul
      • [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation   ms
      • [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation   Justin A. Lemkul
      • [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED]   ms
      • [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED]   Justin A. Lemkul
      • [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED]   ms
• [gmx-users] Error in production run   Malai
  • [gmx-users] Error in production run   Justin A. Lemkul
    • [gmx-users] Error in production run   Malai
• [gmx-users] Effect of vdwradii.dat   Anna Duncan
  • [gmx-users] Effect of vdwradii.dat   Mark Abraham
    • [gmx-users] Re: Effect of vdwradii.dat   anna.duncan
• [gmx-users] unable to access redmine   Christopher Neale
  • [gmx-users] unable to access redmine   Justin A. Lemkul
  • [gmx-users] unable to access redmine   Mark Abraham
• [gmx-users] Re: Dihedral Constraints   bharat gupta
  • [gmx-users] Re: Dihedral Constraints   Justin A. Lemkul
    • [gmx-users] Re: Dihedral Constraints   bharat gupta
      • [gmx-users] Re: Dihedral Constraints   Mark Abraham
      • [gmx-users] Re: Dihedral Constraints   bharat gupta
      • [gmx-users] Re: Dihedral Constraints   Mark Abraham
      • [gmx-users] Re: Dihedral Constraints   bharat gupta
      • [gmx-users] Re: Dihedral Constraints   Mark Abraham
      • [gmx-users] Re: Dihedral Constraints   bharat gupta
      • [gmx-users] Re: Dihedral Constraints   bharat gupta
• [gmx-users] g_lie reproducibility (g_lie is lying)   Tom Dupree
  • [gmx-users] g_lie reproducibility (g_lie is lying)   Mark Abraham
• [gmx-users] Insertion protein in the membrane via G_membed   James Starlight
  • [gmx-users] Insertion protein in the membrane via G_membed   Mark Abraham
    • [gmx-users] Insertion protein in the membrane via G_membed   James Starlight
      • [gmx-users] Insertion protein in the membrane via G_membed   James Starlight
      • [gmx-users] Insertion protein in the membrane via G_membed   James Starlight
      • [gmx-users] Insertion protein in the membrane via G_membed   Mark Abraham
      • [gmx-users] Insertion protein in the membrane via G_membed   James Starlight
      • [gmx-users] Insertion protein in the membrane via G_membed   Mark Abraham
      • [gmx-users] Insertion protein in the membrane via G_membed   James Starlight
      • [gmx-users] Insertion protein in the membrane via G_membed   Peter C. Lai
• [gmx-users] (3x3) Hessian matrix without minimization   Hyuntae Na
  • [gmx-users] (3x3) Hessian matrix without minimization   Mark Abraham
• [gmx-users] protein near the edges of simulation box   Shima Arasteh
  • [gmx-users] protein near the edges of simulation box   Mark Abraham
    • [gmx-users] protein near the edges of simulation box   Shima Arasteh
      • [gmx-users] protein near the edges of simulation box   Mark Abraham
      • [gmx-users] protein near the edges of simulation box   Erik Marklund
      • [gmx-users] protein near the edges of simulation box   Tsjerk Wassenaar
      • [gmx-users] protein near the edges of simulation box   Elton Carvalho
      • [gmx-users] protein near the edges of simulation box   Shima Arasteh
      • [gmx-users] protein near the edges of simulation box   Shima Arasteh
      • [gmx-users] protein near the edges of simulation box   Justin A. Lemkul
      • [gmx-users] protein near the edges of simulation box   Shima Arasteh
      • [gmx-users] protein near the edges of simulation box   Justin A. Lemkul
      • [gmx-users] protein near the edges of simulation box   Shima Arasteh
      • [gmx-users] protein near the edges of simulation box   Justin A. Lemkul
      • [gmx-users] protein near the edges of simulation box   Shima Arasteh
      • [gmx-users] protein near the edges of simulation box   Elton Carvalho
  • [gmx-users] Protein near the edges of simulation box   Shima Arasteh
    • [gmx-users] Protein near the edges of simulation box   Tsjerk Wassenaar
• [gmx-users] (3x3) Hessian matrix without minimization   Hyuntae Na
  • [gmx-users] (3x3) Hessian matrix without minimization   Mark Abraham
• [gmx-users] dodssp segmentation fault   Denis Kazakiewicz
  • [gmx-users] dodssp segmentation fault SOLVED for DEBIAN   Denis Kazakiewicz
    • [gmx-users] dodssp segmentation fault SOLVED for DEBIAN   Erik Marklund
      • [gmx-users] dodssp segmentation fault SOLVED for DEBIAN   raf ponsaerts
• [gmx-users] Diameter of the micelle   Angie Paola Macias Lozano
• [gmx-users] Diameter of the micelle   Christopher Neale
• [gmx-users] Force constant in g_wham   rainy908
  • [gmx-users] Force constant in g_wham   Jochen Hub
• [gmx-users] Bootstrapping using g_wham   rainy908
  • [gmx-users] Bootstrapping using g_wham   Justin A. Lemkul
    • [gmx-users] Bootstrapping using g_wham   Tsjerk Wassenaar
      • [gmx-users] Bootstrapping using g_wham   Jochen Hub
• [gmx-users] RE: Re: g_lie reproducibility   Tom Dupree
  • [gmx-users] RE: Re: g_lie reproducibility   Mark Abraham
• [gmx-users] FEP   Sai Kumar Ramadugu
• [gmx-users] simulating dimer proteins   delara aghaie
  • [gmx-users] simulating dimer proteins   Mark Abraham
    • [gmx-users] simulating dimer proteins   delara aghaie
      • [gmx-users] simulating dimer proteins   delara aghaie
      • [gmx-users] simulating dimer proteins   Mark Abraham
      • [gmx-users] simulating dimer proteins   delara aghaie
      • [gmx-users] simulating dimer proteins   delara aghaie
      • [gmx-users] simulating dimer proteins   Justin A. Lemkul
      • [gmx-users] simulating dimer proteins   delara aghaie
      • [gmx-users] simulating dimer proteins   Justin A. Lemkul
      • [gmx-users] simulating dimer proteins   Mark Abraham
• [gmx-users] current directory files   tarak karmakar
  • [gmx-users] current directory files   Mark Abraham
    • [gmx-users] current directory files   tarak karmakar
      • [gmx-users] current directory files   Mark Abraham
      • [gmx-users] current directory files   tarak karmakar
• [gmx-users] How to calculate chemical shift?   Xianwei Wang
• [gmx-users] multi-chain pdbs with mdrun?   Samuel Flores
  • [gmx-users] multi-chain pdbs with mdrun?   Mark Abraham
    • [gmx-users] multi-chain pdbs with mdrun?   Erik Marklund
• [gmx-users] Re: Preserving chain id/information when using editconf (gromacs 4.0.7)   Samuel Flores
• [gmx-users] Regarding error.   Seera Suryanarayana
  • [gmx-users] Regarding error.   Justin A. Lemkul
  • [gmx-users] Fwd: Regarding error.   Seera Suryanarayana
• [gmx-users] help!!   ankita oindrila
  • [gmx-users] help!!   Justin A. Lemkul
• [gmx-users] problem regarding installation of gromacs-4.5.5   Nidhi Jatana
  • [gmx-users] problem regarding installation of gromacs-4.5.5   Justin A. Lemkul
    • [gmx-users] problem regarding installation of gromacs-4.5.5   Nidhi Jatana
      • [gmx-users] problem regarding installation of gromacs-4.5.5   Justin A. Lemkul
      • [gmx-users] problem regarding installation of gromacs-4.5.5   Nidhi Jatana
      • [gmx-users] problem regarding installation of gromacs-4.5.5   Chandan Choudhury
      • [gmx-users] problem regarding installation of gromacs-4.5.5   Nidhi Jatana
      • [gmx-users] problem regarding installation of gromacs-4.5.5   Chandan Choudhury
      • [gmx-users] problem regarding installation of gromacs-4.5.5   Justin A. Lemkul
      • [gmx-users] problem regarding installation of gromacs-4.5.5   Mark Abraham
• [gmx-users] Numbering for pbc_atom0   Erik Marklund
  • [gmx-users] Numbering for pbc_atom0   Erik Marklund
• [gmx-users] simulation box shape and length   tarak karmakar
  • [gmx-users] simulation box shape and length   Justin A. Lemkul
• [gmx-users] Tutorial KALP-15 in DPPC   Shima Arasteh
  • [gmx-users] Tutorial KALP-15 in DPPC   Justin A. Lemkul
    • [gmx-users] Tutorial KALP-15 in DPPC   Shima Arasteh
      • [gmx-users] Tutorial KALP-15 in DPPC   Justin A. Lemkul
      • [gmx-users] Tutorial KALP-15 in DPPC   Shima Arasteh
• [gmx-users] Simple question (confout)   Dariush Mohammadyani
  • [gmx-users] Simple question (confout)   Justin A. Lemkul
• [gmx-users] (no subject)   Pathumwadee Intharathep
• [gmx-users] problem in making a trajectory   francesca vitalini
  • [gmx-users] problem in making a trajectory   Justin A. Lemkul
    • [gmx-users] problem in making a trajectory   francesca vitalini
      • [gmx-users] problem in making a trajectory   Justin A. Lemkul
      • [gmx-users] problem in making a trajectory   francesca vitalini
      • [gmx-users] problem in making a trajectory   Justin A. Lemkul
      • [gmx-users] problem in making a trajectory   francesca vitalini
• [gmx-users] How to compare two pdb files   delara aghaie
  • [gmx-users] How to compare two pdb files   Justin A. Lemkul
    • [gmx-users] How to compare two pdb files   delara aghaie
      • [gmx-users] How to compare two pdb files   Justin A. Lemkul
      • [gmx-users] How to compare two pdb files   delara aghaie
      • [gmx-users] How to compare two pdb files   Justin A. Lemkul
      • [gmx-users] How to compare two pdb files   delara aghaie
      • [gmx-users] How to compare two pdb files   Justin A. Lemkul
      • [gmx-users] How to compare two pdb files   delara aghaie
• [gmx-users] pressure-lyzozyme tutorial   delara aghaie
  • [gmx-users] pressure-lyzozyme tutorial   Justin A. Lemkul
    • [gmx-users] pressure-lyzozyme tutorial   delara aghaie
• [gmx-users] Dihedral restraints   bharat gupta
  • [gmx-users] Dihedral restraints   bharat gupta
• [gmx-users] About Mike Harms python script   vidhya sankar
  • [gmx-users] About Mike Harms python script   Justin A. Lemkul
  • [gmx-users] About Mike Harms python script   lloyd riggs
• [gmx-users] simulation time   delara aghaie
  • [gmx-users] simulation time   Mark Abraham
• [gmx-users] structural analysis   delara aghaie
• [gmx-users] questiones about dihedral restrain   mircial at sjtu.edu.cn
• [gmx-users] Distance of pull group is larger than half the box size   Eudes Fileti
  • [gmx-users] Distance of pull group is larger than half the box size   Justin A. Lemkul
• [gmx-users] spatial distribution function   delara aghaie
  • [gmx-users] spatial distribution function   Justin A. Lemkul
• [gmx-users] SDF-error   delara aghaie
  • [gmx-users] SDF-error   Justin A. Lemkul
• [gmx-users] Strange behaviour of bonds   Shima Arasteh
  • [gmx-users] Strange behaviour of bonds   Justin A. Lemkul
    • [gmx-users] Strange behaviour of bonds   Shima Arasteh
      • [gmx-users] Strange behaviour of bonds   Justin A. Lemkul
• [gmx-users] jalemkul at vt.edu   vidhya sankar
  • [gmx-users] jalemkul at vt.edu   Justin A. Lemkul
• [gmx-users] the error in "bondfree.c" when installing gromacs 4.5.4   Xingcheng Lin
  • [gmx-users] the error in "bondfree.c" when installing gromacs 4.5.4   Mark Abraham
    • [gmx-users] the error in "bondfree.c" when installing gromacs 4.5.4   Xingcheng Lin
• [gmx-users] Expanding existing biphastic Box   James Starlight
  • [gmx-users] Expanding existing biphastic Box   Mark Abraham
• [gmx-users] Code precision is double message   Allen Mao
  • [gmx-users] Code precision is double message   Mark Abraham
• [gmx-users] mdrun -v output   Chandan Choudhury
  • [gmx-users] mdrun -v output   Javier Cerezo
    • [gmx-users] mdrun -v output   Chandan Choudhury
      • [gmx-users] mdrun -v output   Peter C. Lai
      • [gmx-users] mdrun -v output   Chandan Choudhury
• [gmx-users] (no subject)   ankita oindrila
  • [gmx-users] (no subject)   Justin A. Lemkul
• [gmx-users] hello   Anik Sen
  • [gmx-users] hello   Justin A. Lemkul
  • [gmx-users] hello   Mark Abraham
• [gmx-users] Checking interaction energies - regd   ramesh cheerla
• [gmx-users] Solvation Free Energy calculation (g_bar)   Daniel
  • [gmx-users] Solvation Free Energy calculation (g_bar)   Justin A. Lemkul
    • [gmx-users] Re: Solvation Free Energy calculation (g_bar)   Daniel
      • [gmx-users] Re: Solvation Free Energy calculation (g_bar)   Justin A. Lemkul
• [gmx-users] Trjconv error   Shima Arasteh
  • [gmx-users] Trjconv error   Mark Abraham
    • [gmx-users] Trjconv error   Shima Arasteh
      • [gmx-users] Trjconv error   Mark Abraham
      • [gmx-users] Trjconv error   Shima Arasteh
• [gmx-users] Regarding error.   Seera Suryanarayana
  • [gmx-users] Regarding error.   Emanuel Birru
• [gmx-users] OPLS parameters for amine oxide   sulatha M. S
• [gmx-users] segmentation fault-g_spatial   delara aghaie
  • Fw: [gmx-users] segmentation fault-g_spatial   delara aghaie
    • Fw: [gmx-users] segmentation fault-g_spatial   Justin A. Lemkul
• [gmx-users] REMD in explicit solvent   Esben Jannik Bjerrum
  • [gmx-users] REMD in explicit solvent   Mark Abraham
• [gmx-users] pair interaction energy decomposition analysis   Ngo Son Tung
  • [gmx-users] Re: pair interaction energy decomposition analysis   shounakb
  • [gmx-users] pair interaction energy decomposition analysis   Justin A. Lemkul
    • [gmx-users] Re: pair interaction energy decomposition analysis   Son Tung Ngo
      • [gmx-users] Re: pair interaction energy decomposition analysis   Mark Abraham
      • [gmx-users] Re: pair interaction energy decomposition analysis   Son Tung Ngo
• [gmx-users] (no subject)   ankita oindrila
  • [gmx-users] (no subject)   Justin A. Lemkul
• [gmx-users] Analysis of the torsion Chi angles dynamics during simulation   James Starlight
  • [gmx-users] Analysis of the torsion Chi angles dynamics during simulation   Justin A. Lemkul
• [gmx-users] error in g_cluster "diagonalization" method   Isaure Chauvot de Beauchêne
  • [gmx-users] error in g_cluster "diagonalization" method   Mark Abraham
• [gmx-users] CMAP in Gromacs Vs. CHARMM   Andy Somogyi
  • [gmx-users] CMAP in Gromacs Vs. CHARMM   Mark Abraham
• [gmx-users] CMAP and Free Energy   francesco oteri
• [gmx-users] How do you properly use g_msd to calculate MSD of bilayer and account for monolayer motion?   David Ackerman
• [gmx-users] to know about constraints   Anik Sen
  • [gmx-users] to know about constraints   Justin A. Lemkul
    • [gmx-users] to know about constraints   Anik Sen
      • [gmx-users] to know about constraints   Anik Sen
      • [gmx-users] to know about constraints   Justin A. Lemkul
      • [gmx-users] to know about constraints   Anik Sen
      • [gmx-users] to know about constraints   Marzinek, Jan
      • [gmx-users] to know about constraints   Mark Abraham
      • [gmx-users] to know about constraints   Anik Sen
      • [gmx-users] to know about constraints   Anik Sen
      • [gmx-users] to know about constraints   Marzinek, Jan
      • [gmx-users] to know about constraints   Marzinek, Jan
• [gmx-users] email id for posting   sreeta gorripaty
• [gmx-users] Regarding pdb file of a polymer   sreeta.g
  • [gmx-users] Regarding pdb file of a polymer   Justin A. Lemkul
    • [gmx-users] Re: Regarding pdb file of a polymer   sreeta.g
      • [gmx-users] Re: Regarding pdb file of a polymer   Justin A. Lemkul
      • [gmx-users] Re: Regarding pdb file of a polymer   sreeta.g
• [gmx-users] OPLS parametrs for aminoxide   sulatha M. S
• [gmx-users] Analysis of buried water dynamics   James Starlight
• [gmx-users] only three options for genrestr   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] only three options for genrestr   Justin A. Lemkul
    • [gmx-users] only three options for genrestr   reisingere at rostlab.informatik.tu-muenchen.de
• [gmx-users] plzz help   ankita oindrila
  • [gmx-users] plzz help   Justin A. Lemkul
• [gmx-users] GPU-GROMACS and OPLS-AA   Igor1963
• [gmx-users] GPU-GROMACS and OPLS-AA   Igor1963
• [gmx-users] Residue 'DUM' not found in residue topology database   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] Residue 'DUM' not found in residue topology database   Justin A. Lemkul
    • [gmx-users] Residue 'DUM' not found in residue topology database   reisingere at rostlab.informatik.tu-muenchen.de
      • [gmx-users] Residue 'DUM' not found in residue topology database   Justin A. Lemkul
• [gmx-users] Residue 'DUM' not found in residue topology database   Thomas Schlesier
  • [gmx-users] Residue 'DUM' not found in residue topology database   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] Residue 'DUM' not found in residue topology database   reisingere at rostlab.informatik.tu-muenchen.de
    • [gmx-users] Residue 'DUM' not found in residue topology database   Justin A. Lemkul
• [gmx-users] Residue 'DUM' not found in residue topology database   Thomas Schlesier
• [gmx-users] How Coulomb energy terms are calculated?   vincenzo moreschini
  • [gmx-users] How Coulomb energy terms are calculated?   Mark Abraham
• [gmx-users] center an atomic group   Dr. Vitaly V. G. Chaban
  • [gmx-users] center an atomic group   Justin A. Lemkul
    • [gmx-users] center an atomic group   Dr. Vitaly V. G. Chaban
• [gmx-users] Calculation of dihedral force constants   Covington, Cody Lance
  • [gmx-users] Calculation of dihedral force constants   Mark Abraham
• [gmx-users] umbrella sampling with distances larger than half box size   anaome at fundp.ac.be
  • [gmx-users] umbrella sampling with distances larger than half box size   lloyd riggs
    • [gmx-users] Re: umbrella sampling with distances larger than half box size   anaome
      • [gmx-users] Re: umbrella sampling with distances larger than half box size   lloyd riggs
• [gmx-users] RMS fluctuations and error estimate from block averaging   Atila Petrosian
• [gmx-users] rare huge forces in constraint simulation with direction_periodic   Jochen Hub
  • [gmx-users] rare huge forces in constraint simulation with direction_periodic   Jochen Hub
• [gmx-users] Top file   Shima Arasteh
  • [gmx-users] Top file   Justin A. Lemkul
• [gmx-users] Rotation aroud the z axis   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] Rotation aroud the z axis   Justin A. Lemkul
• [gmx-users] ewald_geometry 3dc with wall gives high pressure   zifeng li
• [gmx-users] H-atoms in .hdb file   Shima Arasteh
  • [gmx-users] H-atoms in .hdb file   Justin A. Lemkul
    • [gmx-users] H-atoms in .hdb file   Shima Arasteh
• [gmx-users] PBC   Nilesh Dhumal
  • [gmx-users] PBC   Tsjerk Wassenaar
• [gmx-users] H-atoms in .hdb file   Justin A. Lemkul
  • [gmx-users] H-atoms in .hdb file   Shima Arasteh
  • [gmx-users] H-atoms in .hdb file   Shima Arasteh
    • [gmx-users] H-atoms in .hdb file   Justin A. Lemkul
      • [gmx-users] H-atoms in .hdb file   Shima Arasteh
      • [gmx-users] H-atoms in .hdb file   Justin A. Lemkul
      • [gmx-users] H-atoms in .hdb file   Shima Arasteh
      • [gmx-users] H-atoms in .hdb file   Shima Arasteh
• [gmx-users] Lipid-protein simulation....   rama david
  • [gmx-users] Re: Lipid-protein simulation....   rama david
  • [gmx-users] Lipid-protein simulation....   Justin A. Lemkul
• [gmx-users] number of gauche <-> trans transitions with CHARMM36 and AMBER force fields   ABEL Stephane 175950
• [gmx-users] What's the effect of non-neotron charge group?   zifeng li
• [gmx-users] What does --enable-fahcore mean?   Bao Kai
  • [gmx-users] What does --enable-fahcore mean?   Michael Shirts
• [gmx-users] wrong distances with g_dist   Dmytro Kovalskyy
  • [gmx-users] wrong distances with g_dist   lloyd riggs
• [gmx-users] Unusual g_order with CHARMM36   Ricardo O. S. Soares
• [gmx-users] Atoms get frozen with "Nose Hoover thermostat with Parrinello-Rahman barostat" for a system of an ion of charge +2 in flexible water molecules   Surya Prakash Tiwari
  • [gmx-users] Atoms get frozen with "Nose Hoover thermostat with Parrinello-Rahman barostat" for a system of an ion of charge +2 in flexible water molecules   ms
• [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial   rama david
  • [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial   Justin A. Lemkul
• [gmx-users] residuetype.dat   Shima Arasteh
• [gmx-users] H-atoms in .hdb file   Shima Arasteh
  • [gmx-users] H-atoms in .hdb file   Justin A. Lemkul
    • [gmx-users] H-atoms in .hdb file   Shima Arasteh
      • [gmx-users] H-atoms in .hdb file   Justin A. Lemkul
      • [gmx-users] H-atoms in .hdb file   Shima Arasteh
• [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology   Justin A. Lemkul
    • [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology   reisingere at rostlab.informatik.tu-muenchen.de
    • [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology   reisingere at rostlab.informatik.tu-muenchen.de
• [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial   Justin A. Lemkul
  • [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial   rama david
    • [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial   Justin A. Lemkul
• Fwd: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial   rama david
• [gmx-users] About Exclusion of bonded and non bonded parameters while running grompp   PAVAN PAYGHAN
  • [gmx-users] About Exclusion of bonded and non bonded parameters while running grompp   Justin A. Lemkul
• [gmx-users] Pulling ligand - Different Profiles (Force vs time)   Steven Neumann
  • [gmx-users] Pulling ligand - Different Profiles (Force vs time)   Justin A. Lemkul
    • [gmx-users] Pulling ligand - Different Profiles (Force vs time)   Steven Neumann
      • [gmx-users] Pulling ligand - Different Profiles (Force vs time)   Justin A. Lemkul
      • [gmx-users] Pulling ligand - Different Profiles (Force vs time)   Steven Neumann
• [gmx-users] make index   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] make index   Justin A. Lemkul
• [gmx-users] pdb2gmx error   Shima Arasteh
  • [gmx-users] Re: pdb2gmx error   shounakb
  • [gmx-users] Re: pdb2gmx error   shounakb
    • [gmx-users] Re: pdb2gmx error   Shima Arasteh
      • [gmx-users] Re: pdb2gmx error   Justin A. Lemkul
      • [gmx-users] Re: pdb2gmx error   Shima Arasteh
      • [gmx-users] Re: pdb2gmx error   Justin A. Lemkul
      • [gmx-users] Re: pdb2gmx error   Shima Arasteh
      • [gmx-users] Re: pdb2gmx error   shounakb
      • [gmx-users] Re: pdb2gmx error   Shima Arasteh
      • [gmx-users] Re: pdb2gmx error   Justin A. Lemkul
      • [gmx-users] Re: pdb2gmx error   Shima Arasteh
      • [gmx-users] Re: pdb2gmx error   Justin A. Lemkul
      • [gmx-users] Re: pdb2gmx error   Shima Arasteh
      • [gmx-users] Re: pdb2gmx error   shounakb
      • [gmx-users] Re: pdb2gmx error   Justin A. Lemkul
      • [gmx-users] Re: pdb2gmx error   Shima Arasteh
      • [gmx-users] Re: pdb2gmx error   Justin A. Lemkul
      • [gmx-users] Re: pdb2gmx error   Shima Arasteh
      • [gmx-users] Re: pdb2gmx error   Justin A. Lemkul
      • [gmx-users] Re: pdb2gmx error   Shima Arasteh
      • [gmx-users] Re: pdb2gmx error   Justin A. Lemkul
      • [gmx-users] Re: pdb2gmx error   Shima Arasteh
      • [gmx-users] Re: pdb2gmx error   Shima Arasteh
      • [gmx-users] Re: pdb2gmx error   shounakb
      • [gmx-users] Re: pdb2gmx error   Justin A. Lemkul
      • [gmx-users] Re: pdb2gmx error   shounakb
      • [gmx-users] Re: pdb2gmx error   Shima Arasteh
      • [gmx-users] Re: pdb2gmx error   Justin A. Lemkul
• [gmx-users] tabulated potentials and soft core free energy - this should not work ....   Michael Brunsteiner
• [gmx-users] NVT, NPT and then pulling?   Steven Neumann
  • [gmx-users] NVT, NPT and then pulling?   Justin A. Lemkul
    • [gmx-users] NVT, NPT and then pulling?   Steven Neumann
• [gmx-users] Discontinuity in first time-step velocities for diatomic molecule locally coupled to thermal drain   Inon Sharony
• [gmx-users] Free energy between residues   Steven Neumann
  • [gmx-users] Free energy between residues   lloyd riggs
    • [gmx-users] Free energy between residues   Steven Neumann
      • [gmx-users] Free energy between residues   Justin A. Lemkul
      • [gmx-users] Free energy between residues   Steven Neumann
      • [gmx-users] Free energy between residues   Justin A. Lemkul
      • [gmx-users] Free energy between residues   lloyd riggs
• [gmx-users] chi1/chi2   Raj
• [gmx-users] Justin's Paper   Steven Neumann
  • [gmx-users] Justin's Paper   Justin A. Lemkul
• [gmx-users] Fwd: Determine sec structure by MD   rama david
• [gmx-users] Problems with Dihedral transition times for dodecane   ABEL Stephane 175950
• [gmx-users] editbox removes dummy atoms   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] editbox removes dummy atoms   Justin A. Lemkul
    • [gmx-users] editbox removes dummy atoms   reisingere at rostlab.informatik.tu-muenchen.de
      • [gmx-users] editbox removes dummy atoms   Justin A. Lemkul
• [gmx-users] g_bar ... the right answer for the wrong reason?   Michael Brunsteiner
  • [gmx-users] g_bar ... the right answer for the wrong reason?   Justin A. Lemkul
• [gmx-users] RIMSP calculation   R.S.K.Vijayan
  • [gmx-users] RIMSP calculation   Tsjerk Wassenaar
    • [gmx-users] RIMSP calculation   R.S.K.Vijayan
• [gmx-users] g_bar ... the right answer for the wrong reason?   Justin A. Lemkul
  • [gmx-users] BAR gives different result than TI   David van der Spoel
• [gmx-users] segmentation fault-g_spatial   Christopher Neale
• [gmx-users] Regarding umbrella sampling simulations along H-bonds   neeru sharma
  • [gmx-users] Regarding umbrella sampling simulations along H-bonds   lloyd riggs
• [gmx-users] Can I set the dielectric constant for polymer and water separately   zifeng li
• [gmx-users] Berger lipid   Shima Arasteh
  • [gmx-users] Berger lipid   Justin A. Lemkul
    • [gmx-users] Berger lipid   Shima Arasteh
      • [gmx-users] Berger lipid   Justin A. Lemkul
      • [gmx-users] Berger lipid   Shima Arasteh
      • [gmx-users] Berger lipid   Justin A. Lemkul
      • [gmx-users] Berger lipid   Shima Arasteh
      • [gmx-users] Berger lipid   Justin A. Lemkul
      • [gmx-users] Berger lipid   Peter Lai
      • [gmx-users] Berger lipid   Shima Arasteh
      • [gmx-users] Berger lipid   Peter C. Lai
      • [gmx-users] Berger lipid   Shima Arasteh
      • [gmx-users] Berger lipid   Shima Arasteh
      • [gmx-users] Berger lipid   Justin A. Lemkul
      • [gmx-users] Berger lipid   Shima Arasteh
      • [gmx-users] Berger lipid   Justin A. Lemkul
      • [gmx-users] Berger lipid   Shima Arasteh
      • [gmx-users] Berger lipid   Peter C. Lai
      • [gmx-users] Berger lipid   Shima Arasteh
      • [gmx-users] Berger lipid   Shima Arasteh
      • [gmx-users] Berger lipid   Thomas Piggot
      • [gmx-users] Berger lipid   Shima Arasteh
• [gmx-users] Regarding umbrella sampling simulations along H-bonds   Christopher Neale
• [gmx-users] Berger lipid   Christopher Neale
• [gmx-users] popc36 + paper   Shima Arasteh
• [gmx-users] Force constant - units   Steven Neumann
  • [gmx-users] Force constant - units   Oliver Stueker
• [gmx-users] editconf do not center protein   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] editconf do not center protein   Justin A. Lemkul
• [gmx-users] no SOL in topology file after genbox command   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] no SOL in topology file after genbox command   Peter C. Lai
• [gmx-users] Structure optimization failure   Lara Bunte
  • [gmx-users] Structure optimization failure   Justin A. Lemkul
    • [gmx-users] Structure optimization failure   Lara Bunte
      • [gmx-users] Structure optimization failure   Justin A. Lemkul
  • AW: [gmx-users] Structure optimization failure   Rausch, Felix
• [gmx-users] problem with git/4.6   Michael Brunsteiner
  • [gmx-users] problem with git/4.6   Justin A. Lemkul
    • [gmx-users] problem with git/4.6   Michael Brunsteiner
      • [gmx-users] problem with git/4.6   Justin A. Lemkul
• [gmx-users] error with grompp   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] error with grompp   Shima Arasteh
    • [gmx-users] error with grompp   Justin A. Lemkul
    • [gmx-users] error with grompp   reisingere at rostlab.informatik.tu-muenchen.de
  • [gmx-users] error with grompp   Justin A. Lemkul
    • [gmx-users] error with grompp   Shima Arasteh
      • [gmx-users] error with grompp   Justin A. Lemkul
    • [gmx-users] error with grompp   reisingere at rostlab.informatik.tu-muenchen.de
      • [gmx-users] error with grompp   Justin A. Lemkul
      • [gmx-users] error with grompp   reisingere at rostlab.informatik.tu-muenchen.de
      • [gmx-users] error with grompp   Justin A. Lemkul
• [gmx-users] COM Pulling   Raj
  • [gmx-users] COM Pulling   Justin A. Lemkul
    • [gmx-users] Re: COM Pulling   Raj
      • [gmx-users] Re: COM Pulling   Justin A. Lemkul
• [gmx-users] Structure optimization failure   Justin A. Lemkul
• [gmx-users] Structure optimization failure   Justin A. Lemkul
  • [gmx-users] Structure optimization failure   ms
• [gmx-users] pdb file of polymer   Parvez khan
  • [gmx-users] pdb file of polymer   Justin A. Lemkul
    • [gmx-users] pdb file of polymer   Parvez khan
• [gmx-users] .top file incoherent with the values in the ffbonded.itp file   sreeta.g
  • [gmx-users] .top file incoherent with the values in the ffbonded.itp file   Justin A. Lemkul
    • [gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file   sreeta.g
      • [gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file   Justin A. Lemkul
      • [gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file   sreeta.g
      • [gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file   Justin A. Lemkul
      • [gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file   sreeta.g
• [gmx-users] atom type   Shima Arasteh
  • [gmx-users] atom type   Shima Arasteh
• [gmx-users] DNA simulations   SatyaK

Last message date: Sat Jun 30 23:31:13 CEST 2012
Archived on: Thu Nov 14 12:13:02 CET 2013

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