November 2010 Archives by thread

• Messages sorted by: [ subject ] [ author ] [ date ]
• More info on this list...

Starting: Mon Nov 1 00:13:27 CET 2010
Ending: Tue Nov 30 23:46:31 CET 2010
Messages: 858

• [gmx-users] LINCS vs SHAKE   thompsjj at purdue.edu
  • [gmx-users] LINCS vs SHAKE   Sai Pooja
    • [gmx-users] LINCS vs SHAKE   Mark Abraham
      • [gmx-users] LINCS vs SHAKE   thompsjj at purdue.edu
      • [gmx-users] LINCS vs SHAKE   Sai Pooja
      • [gmx-users] LINCS vs SHAKE   thompsjj at purdue.edu
• [gmx-users] Re: Charmm36 FF and membrane   Thomas Piggot
• [gmx-users] Preserving chain id/information when using editconf (gromacs 4.0.7)   Shay Teaching
  • [gmx-users] Re: Preserving chain id/information when using editconf (gromacs 4.0.7)   Shay Teaching
• [gmx-users] Modifying gromacs   Sai Pooja
• [gmx-users] questions about umbrella sampling   mircial at sjtu.edu.cn
• [gmx-users] Radius of Gyration   C. Batistakis
  • [gmx-users] Radius of Gyration   Dmitri Dubov
• [gmx-users] Modifying gromacs   Sai Pooja
• [gmx-users] COM removal in Non_Equilibrium MD   Sikandar Mashayak
• [gmx-users] Non Equilibrium MD   Apoorv Kalyankar
• [gmx-users] nonbond_params scaled for forcefield   Sai Pooja
  • [gmx-users] nonbond_params scaled for forcefield   Justin A. Lemkul
    • [gmx-users] nonbond_params scaled for forcefield   Sai Pooja
• [gmx-users] High Temperature 498 K, NVT or NTP ?   Chih-Ying Lin
  • [gmx-users] High Temperature 498 K, NVT or NTP ?   Tsjerk Wassenaar
• [gmx-users] Question about Wall Potential   Bert
• [gmx-users] multiple torsions for one dihedral   Amin Arabbagheri
  • [gmx-users] multiple torsions for one dihedral   Mark Abraham
• [gmx-users] Reg:walls and pbc xy   vinothkumar mohanakrishnan
  • [gmx-users] Reg:walls and pbc xy   Berk Hess
    • [gmx-users] Reg:walls and pbc xy   vinothkumar mohanakrishnan
      • [gmx-users] Reg:walls and pbc xy   Berk Hess
      • [gmx-users] Reg:walls and pbc xy   vinothkumar mohanakrishnan
      • [gmx-users] Reg:walls and pbc xy   Berk Hess
      • [gmx-users] Reg:walls and pbc xy   vinothkumar mohanakrishnan
      • [gmx-users] Reg:walls and pbc xy   vinothkumar mohanakrishnan
      • [gmx-users] Reg:walls and pbc xy   Sander Pronk
      • [gmx-users] Reg:walls and pbc xy   Berk Hess
• [gmx-users] questions about umbrella sampling   mircial at sjtu.edu.cn
• [gmx-users] g_energy problem with 4.5.1 and 4.5.2   Michael Brunsteiner
  • [gmx-users] g_energy problem with 4.5.1 and 4.5.2   Sander Pronk
• [gmx-users] Re: Charmm36 FF and membrane   Thomas Piggot
• [gmx-users] Re:Re: gmx-users Digest, Vol 79, Issue 8   Amin Arabbagheri
  • [gmx-users] Re:Re: gmx-users Digest, Vol 79, Issue 8   Mark Abraham
• [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2   Michael Brunsteiner
  • [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2   Berk Hess
  • [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2   Sander Pronk
    • [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2   Rossen Apostolov
• [gmx-users] (no subject)   Green
• [gmx-users] Update: (Problem Solved) -- Job crash: checkpoint file   Shi, Chuanyin
• [gmx-users] g_hbond   Carla Jamous
  • [gmx-users] g_hbond   Erik Marklund
    • [gmx-users] g_hbond   Erik Marklund
      • [gmx-users] g_hbond   Carla Jamous
      • [gmx-users] g_hbond   Erik Marklund
      • [gmx-users] g_hbond   Erik Marklund
• [gmx-users] Principal axis (g_principal)   chris.neale at utoronto.ca
• [gmx-users] pressure of the liquid in NPT and NVT   Vitaly Chaban
  • [gmx-users] pressure of the liquid in NPT and NVT   Mark Abraham
    • [gmx-users] Re: pressure of the liquid in NPT and NVT   Vitaly Chaban
• [gmx-users] Re: pressure of the liquid in NPT and NVT   Dallas Warren
  • [gmx-users] Re: pressure of the liquid in NPT and NVT   Tsjerk Wassenaar
• [gmx-users] Standard Procedures to perform MD under High Temperature 498 K, either NVT or NTP ?   Chih-Ying Lin
  • Res: [gmx-users] Standard Procedures to perform MD under High Temperature 498 K, either NVT or NTP ?   Ricardo O. S. Soares
• [gmx-users] rotate a .xtc file?   chris.neale at utoronto.ca
  • [gmx-users] rotate a .xtc file?   Roland Schulz
• [gmx-users] rotate a .xtc file?   chris.neale at utoronto.ca
• [gmx-users] Reg:Usage of Walls   vinothkumar mohanakrishnan
• [gmx-users] center peptide in simulation box   leila karami
  • [gmx-users] center peptide in simulation box   Mark Abraham
    • [gmx-users] center peptide in simulation box   #ZHAO LINA#
• [gmx-users] trjconv -pbc/ box/ solvent   shahab shariati
  • [gmx-users] trjconv -pbc/ box/ solvent   Justin A. Lemkul
• [gmx-users] trjconv -pbc/box /solvent   shahab shariati
  • [gmx-users] trjconv -pbc/box /solvent   Justin A. Lemkul
• [gmx-users] trjconv -pbc/box /solvent   shahab shariati
  • [gmx-users] trjconv -pbc/box /solvent   Justin A. Lemkul
• [gmx-users] continue Prod run from NPT eq   Justin A. Lemkul
• [gmx-users] unexpexted stop of simulation   Hong, Liang
  • [gmx-users] unexpexted stop of simulation   Florian Dommert
    • [gmx-users] unexpexted stop of simulation   Carsten Kutzner
      • [gmx-users] unexpexted stop of simulation   Roland Schulz
      • [gmx-developers] Re: [gmx-users] unexpexted stop of simulation   Bogdan Costescu
• [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2   Thomas Piggot
  • [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2   Berk Hess
    • [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2   Berk Hess
      • [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2   Thomas Piggot
• [gmx-users] Replica exchange with scaled topology files   Sai Pooja
  • [gmx-users] Replica exchange with scaled topology files   Mark Abraham
• [gmx-users] About simulating lipid bi-continuous cubic phase   George Khelashvili
• [gmx-users] About simulating lipid bi-continuous cubic phase   Dallas Warren
• [gmx-users] extending simulation without cpt file   Yongchul Chung
  • [gmx-users] extending simulation without cpt file   Justin A. Lemkul
  • [gmx-users] extending simulation without cpt file   Mark Abraham
• [gmx-users] extending simulation without cpt file   Mark Abraham
  • [gmx-users] extending simulation without cpt file   Yongchul Chung
• [gmx-users] editconf   mustafa bilsel
  • [gmx-users] editconf   Tsjerk Wassenaar
• [gmx-users] charmm27 force filed bug for MET residue with vsites in gromacs 4.5.2   BIN ZHANG
  • [gmx-users] charmm27 force filed bug for MET residue with vsites in gromacs 4.5.2   Berk Hess
• [gmx-users] regarding error in editconf   Anamika Awasthi
  • [gmx-users] regarding error in editconf   Justin A. Lemkul
• [gmx-users] GB-polarization   Christian Mücksch
  • [gmx-users] GB-polarization   Per Larsson
• [gmx-users] g_sas resarea.xvg   Carla Jamous
  • [gmx-users] g_sas resarea.xvg   Justin A. Lemkul
    • [gmx-users] g_sas resarea.xvg   Mark Abraham
• [gmx-users] tip3p itp file parameters   Sai Pooja
  • [gmx-users] tip3p itp file parameters   Justin A. Lemkul
    • [gmx-users] tip3p itp file parameters   Sai Pooja
      • [gmx-users] tip3p itp file parameters   Mark Abraham
• [gmx-users] deform option   Green
• [gmx-users] box shape   mustafa bilsel
  • [gmx-users] box shape   Justin A. Lemkul
• [gmx-users] Targeted Energy Minimization   Yao Yao
  • [gmx-users] Targeted Energy Minimization   Mark Abraham
• [gmx-users] installation of gromacs on windows using cygwin   bharat gupta
  • [gmx-users] installation of gromacs on windows using cygwin   Szilárd Páll
  • [gmx-users] installation of gromacs on windows using cygwin   Mark Abraham
    • [gmx-users] installation of gromacs on windows using cygwin   bharat gupta
      • [gmx-users] installation of gromacs on windows using cygwin   bharat gupta
      • [gmx-users] installation of gromacs on windows using cygwin   Justin A. Lemkul
      • [gmx-users] installation of gromacs on windows using cygwin   Mark Abraham
• [gmx-users] which force file has parameters for creatine md simulations   Olga Ivchenko
  • [gmx-users] which force file has parameters for creatine md simulations   #ZHAO LINA#
    • [gmx-users] which force file has parameters for creatine md simulations   Justin A. Lemkul
• [gmx-users] which force file has parameters for creatine md simulations?   Olga Ivchenko
• [gmx-users] which force file has parameters for creatine md simulations?   Olga Ivchenko
  • [gmx-users] Re: which force file has parameters for creatine md simulations?   Olga Ivchenko
    • [gmx-users] Re: which force file has parameters for creatine md simulations?   Justin A. Lemkul
      • [gmx-users] Re: which force file has parameters for creatine md simulations?   Olga Ivchenko
      • [gmx-users] Re: which force file has parameters for creatine md simulations?   Justin A. Lemkul
• [gmx-users] g_cluster: optimal cutoff   Fabio Affinito
  • [gmx-users] g_cluster: optimal cutoff   Xiaohu Hu
• [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2   Pär Bjelkmar
• [gmx-users] dssp   #ZHAO LINA#
  • [gmx-users] dssp   Justin A. Lemkul
    • [gmx-users] dssp   #ZHAO LINA#
      • [gmx-users] dssp   Linus Östberg
      • [gmx-users] dssp   Justin A. Lemkul
      • [gmx-users] dssp   #ZHAO LINA#
      • [gmx-users] dssp   #ZHAO LINA#
      • [gmx-users] dssp   Justin A. Lemkul
      • [gmx-users] dssp   #ZHAO LINA#
      • [gmx-users] dssp   Mark Abraham
      • [gmx-users] dssp   #ZHAO LINA#
• [gmx-users] genbox generating acetonitrile box with holes   Diana Lousa
  • [gmx-users] genbox generating acetonitrile box with holes   Justin A. Lemkul
  • [gmx-users] genbox generating acetonitrile box with holes   Mark Abraham
• [gmx-users] continue Prod run from NPT eq   manu.mura
  • [gmx-users] continue Prod run from NPT eq   Justin A. Lemkul
• [gmx-users] Re: genbox generating acetonitrile box with holes   Vitaly Chaban
• [gmx-users] Re: genbox generating acetonitrile box with holes   Vitaly Chaban
• [gmx-users] Re: genbox generating acetonitrile box with holes   Vitaly Chaban
  • [gmx-users] Re: genbox generating acetonitrile box with holes   Tsjerk Wassenaar
    • [gmx-users] Re: genbox generating acetonitrile box with holes   Vitaly Chaban
    • [gmx-users] Re: genbox generating acetonitrile box with holes   Diana Lousa
      • [gmx-users] Re: genbox generating acetonitrile box with holes   Tsjerk Wassenaar
      • [gmx-users] Re: genbox generating acetonitrile box with holes   Diana Lousa
      • [gmx-users] Re: genbox generating acetonitrile box with holes   Tsjerk Wassenaar
• [gmx-users] elastin   mustafa bilsel
  • [gmx-users] elastin   Justin A. Lemkul
• [gmx-users] ./mdrun-gpu fatal error   lin hen
  • [gmx-users] ./mdrun-gpu fatal error   Justin A. Lemkul
• [gmx-users] ./mdrun-gpu fatal error   Justin A. Lemkul
  • [gmx-users] ./mdrun-gpu fatal error   lin hen
    • [gmx-users] ./mdrun-gpu fatal error   Justin A. Lemkul
    • [gmx-users] ./mdrun-gpu fatal error   Szilárd Páll
• [gmx-users] questions about umbrella sampling   chris.neale at utoronto.ca
• [gmx-users] Non Equilibrium MD   chris.neale at utoronto.ca
• [gmx-users] problem in executing genbox command   bharat gupta
  • [gmx-users] problem in executing genbox command   Mark Abraham
    • [gmx-users] problem in executing genbox command   bharat gupta
    • [gmx-users] problem in executing genbox command   ms
• [gmx-users] Using mdrun -rerun to get energy values   Martin Kamp Jensen
  • [gmx-users] Using mdrun -rerun to get energy values   Krzysztof Mlynarczyk
    • [gmx-users] Using mdrun -rerun to get energy values   Martin Kamp Jensen
      • [gmx-users] Using mdrun -rerun to get energy values   Krzysztof Mlynarczyk
      • [gmx-users] Using mdrun -rerun to get energy values   Mark Abraham
      • [gmx-users] Using mdrun -rerun to get energy values   Martin Kamp Jensen
• [gmx-users] Re: genbox generating acetonitrile box with holes   Vitaly Chaban
• [gmx-users] High Temprature MD with scaled params   Sai Pooja
• [gmx-users] High Temprature MD with scaled params   chris.neale at utoronto.ca
• [gmx-users] Re: High Temprature MD with scaled params   Vitaly Chaban
• [gmx-users] kind of contacts in protein-dna interaction during simulation   leila karami
  • [gmx-users] kind of contacts in protein-dna interaction during simulation   Mark Abraham
• [gmx-users] kind of contacts in protein-dna interaction during simulation   leila karami
  • [gmx-users] kind of contacts in protein-dna interaction during simulation   Mark Abraham
• [gmx-users] add a group to an amino acid   hengame fallah
  • [gmx-users] add a group to an amino acid   Justin A. Lemkul
    • [gmx-users] add a group to an amino acid   hengame fallah
      • [gmx-users] add a group to an amino acid   Mark Abraham
      • [gmx-users] add a group to an amino acid   hengame fallah
      • [gmx-users] add a group to an amino acid   Mark Abraham
      • [gmx-users] add a group to an amino acid   hengame fallah
      • [gmx-users] add a group to an amino acid   Mark Abraham
      • [gmx-users] add a group to an amino acid   hengame fallah
      • [gmx-users] add a group to an amino acid   Mark Abraham
      • [gmx-users] add a group to an amino acid   hengame fallah
      • [gmx-users] add a group to an amino acid   Mark Abraham
      • [gmx-users] add a group to an amino acid   hengame fallah
      • [gmx-users] add a group to an amino acid   Mark Abraham
      • [gmx-users] add a group to an amino acid   hengame fallah
• [gmx-users] gpu   Erik Wensink
  • [gmx-users] gpu   Rossen Apostolov
    • [gmx-users] gpu   Erik Wensink
• [gmx-users] (no subject)   mustafa bilsel
  • [gmx-users] (no subject)   Justin A. Lemkul
• [gmx-users] -b -e   atila petrosian
  • [gmx-users] -b -e   Mark Abraham
• [gmx-users] -b -e   Erik Wensink
• [gmx-users] trjconv   mohsen ramezanpour
• [gmx-users] Re: trjconv   Vitaly Chaban
  • [gmx-users] Re: trjconv   Justin A. Lemkul
    • [gmx-users] Re: trjconv   mohsen ramezanpour
      • [gmx-users] Re: trjconv   mohsen ramezanpour
      • [gmx-users] Re: trjconv   mohsen ramezanpour
      • [gmx-users] Re: trjconv   Justin A. Lemkul
  • [gmx-users] Re: trjconv   mohsen ramezanpour
• [gmx-users] a bug in GMXRC.bash   Ye MEI
  • [gmx-users] a bug in GMXRC.bash   Roland Schulz
    • [gmx-users] a bug in GMXRC.bash   Ye MEI
• [gmx-users] Too many parameters in itp-file   Mikkel Vestergaard
  • [gmx-users] Too many parameters in itp-file   Justin A. Lemkul
  • [gmx-users] Too many parameters in itp-file   Mark Abraham
• [gmx-users] g_hbond / lifetime   shahab shariati
• [gmx-users] Generalized Born in GROMACS manual   Ehud Schreiber
• [gmx-users] g_hbond modification   Robin C. Underwood
  • [gmx-users] g_hbond modification   Justin A. Lemkul
  • [gmx-users] Re: g_hbond modification   Robin C. Underwood
    • [gmx-users] Re: g_hbond modification   Erik Marklund
    • [gmx-users] Re: g_hbond modification   David van der Spoel
• [gmx-users] Parallel do_dssp analysis over mpi?   Ali Naqvi
  • [gmx-users] Parallel do_dssp analysis over mpi?   Justin A. Lemkul
    • [gmx-users] Parallel do_dssp analysis over mpi?   Erik Marklund
      • [gmx-users] Parallel do_dssp analysis over mpi?   Justin A. Lemkul
      • [gmx-users] Parallel do_dssp analysis over mpi?   Erik Marklund
      • [gmx-users] Parallel do_dssp analysis over mpi?   Erik Marklund
  • [gmx-users] Parallel do_dssp analysis over mpi?   Mark Abraham
• [gmx-users] CHARMM FF and cmap   Zuzana Benkova
  • [gmx-users] CHARMM FF and cmap   Justin A. Lemkul
• [gmx-users] g_hbond / lifetime   Dallas Warren
• [gmx-users] Parallel do_dssp analysis over mpi?   Ali Naqvi
• [gmx-users] problem with g_density   vinothkumar mohanakrishnan
  • [gmx-users] problem with g_density   Justin A. Lemkul
• [gmx-users] error in editconf step   priyam saxena
  • [gmx-users] error in editconf step   vinothkumar mohanakrishnan
    • [gmx-users] error in editconf step   Mark Abraham
  • [gmx-users] error in editconf step   Roland Schulz
• [gmx-users] problem of tabulated bonded potential   Z.Xiao
  • [gmx-users] problem of tabulated bonded potential   XAvier Periole
• [gmx-users] g_hbond / lifetime   shahab shariati
• [gmx-users] Reg:Density Profile   vinothkumar mohanakrishnan
• [gmx-users] Installing gromacs in Red hat E5   Kamalesh Roy
  • [gmx-users] Installing gromacs in Red hat E5   Mark Abraham
  • [gmx-users] Installing gromacs in Red hat E5   Krzysztof Mlynarczyk
• [gmx-users] Re: problem of tabulated bonded potential   Z.Xiao
  • [gmx-users] Re: problem of tabulated bonded potential   XAvier Periole
• [gmx-users] problem with g_density   chris.neale at utoronto.ca
  • [gmx-users] problem with g_density   Justin A. Lemkul
• [gmx-users] problem with g_density   chris.neale at utoronto.ca
• [gmx-users] g_hbond   Carla Jamous
  • [gmx-users] g_hbond   Oliver Grant
    • [gmx-users] g_hbond   Erik Marklund
  • [gmx-users] g_hbond   Erik Marklund
    • [gmx-users] g_hbond   Carla Jamous
• [gmx-users] mdrun in gmx 4.5.1: how to reprogram periodic boundary conditions?   Adam Herbst
  • [gmx-users] mdrun in gmx 4.5.1: how to reprogram periodic boundary conditions?   Mark Abraham
• [gmx-users] Exclude the 1-2 and 1-3 interactions   Nilesh Dhumal
  • [gmx-users] Exclude the 1-2 and 1-3 interactions   Justin A. Lemkul
    • [gmx-users] Exclude the 1-2 and 1-3 interactions   Nilesh Dhumal
      • [gmx-users] Exclude the 1-2 and 1-3 interactions   Justin A. Lemkul
• [gmx-users] RE: gro file and topology files   Nimesh Jain
  • [gmx-users] RE: gro file and topology files   Justin A. Lemkul
    • [gmx-users] RE: gro file and topology files   Nimesh Jain
• [gmx-users] Re: GB-polarization   Christian Mücksch
  • [gmx-users] Re: GB-polarization   Justin A. Lemkul
  • [gmx-users] Re: GB-polarization   Christian Mücksch
    • [gmx-users] Re: GB-polarization   Justin A. Lemkul
      • [gmx-users] Re: GB-polarization   Per Larsson
• [gmx-users] mpirun   fahimeh baftizadeh
• [gmx-users] Fw: mpirun   fahimeh baftizadeh
  • [gmx-users] Fw: mpirun   Justin A. Lemkul
• [gmx-users] trjconv, pbc and breaking of multiple peptides   ms
  • [gmx-users] trjconv, pbc and breaking of multiple peptides   Justin A. Lemkul
    • [gmx-users] trjconv, pbc and breaking of multiple peptides   ms
    • [gmx-users] trjconv, pbc and breaking of multiple peptides   ms
      • [gmx-users] trjconv, pbc and breaking of multiple peptides   Justin A. Lemkul
      • [gmx-users] trjconv, pbc and breaking of multiple peptides   ms
      • [gmx-users] trjconv, pbc and breaking of multiple peptides   Justin A. Lemkul
      • [gmx-users] trjconv, pbc and breaking of multiple peptides   ms
• [gmx-users] New release: 4.5.2   Rossen Apostolov
  • [gmx-users] Re: [gmx-developers] New release: 4.5.3   Rossen Apostolov
• [gmx-users] g_hbond / lifetime   Dallas Warren
• [gmx-users] GFP chromophore topology help   Ramachandran G
  • [gmx-users] GFP chromophore topology help   Justin A. Lemkul
    • [gmx-users] GFP chromophore topology help   Ramachandran G
      • [gmx-users] GFP chromophore topology help   Ramachandran G
      • [gmx-users] GFP chromophore topology help   Justin A. Lemkul
      • [gmx-users] GFP chromophore topology help   Ramachandran G
      • [gmx-users] GFP chromophore topology help   Justin A. Lemkul
• [gmx-users] ./mdrun   lin hen
  • [gmx-users] ./mdrun   Roland Schulz
    • [gmx-users] ./mdrun   lin hen
      • [gmx-users] ./mdrun   Justin A. Lemkul
      • [gmx-users] ./mdrun   lin hen
      • [gmx-users] ./mdrun   Justin A. Lemkul
      • [gmx-users] ./mdrun   lin hen
• [gmx-users] multiplicity for qmmm simulations   Pradip Biswas
• [gmx-users] g_hbond / hbmap.xpm file   shahab shariati
  • [gmx-users] g_hbond / hbmap.xpm file   Erik Marklund
• [gmx-users] -don (g-hbond)   atila petrosian
  • [gmx-users] -don (g-hbond)   Justin A. Lemkul
• [gmx-users] mdrun -rerun: bonded interactions of protein   NG HUI WEN
  • [gmx-users] mdrun -rerun: bonded interactions of protein   Justin A. Lemkul
  • [gmx-users] mdrun -rerun: bonded interactions of protein   Mark Abraham
    • [gmx-users] mdrun -rerun: bonded interactions of protein   NG HUI WEN
      • [gmx-users] mdrun -rerun: bonded interactions of protein   Mark Abraham
      • [gmx-users] mdrun -rerun: bonded interactions of protein   NG HUI WEN
      • [gmx-users] mdrun -rerun: bonded interactions of protein   Justin A. Lemkul
      • [gmx-users] mdrun -rerun: bonded interactions of protein   NG HUI WEN
• [gmx-users] -don (g-hbond)   atila petrosian
  • [gmx-users] -don (g-hbond)   Justin A. Lemkul
• [gmx-users] g_hbond / hbmap.xpm file   shahab shariati
  • [gmx-users] g_hbond / hbmap.xpm file   Justin A. Lemkul
• [gmx-users] Gromacs 4.5 build problems   Miah Wadud Dr (ITCS)
  • [gmx-users] Gromacs 4.5 build problems   Roland Schulz
• [gmx-users] on calculation of the atomic covariance   Vigneshwar Ramakrishnan
  • [gmx-users] on calculation of the atomic covariance   Justin A. Lemkul
    • [gmx-users] on calculation of the atomic covariance   Vigneshwar Ramakrishnan
      • [gmx-users] on calculation of the atomic covariance   Vigneshwar Ramakrishnan
      • [gmx-users] on calculation of the atomic covariance   Tsjerk Wassenaar
      • [gmx-users] on calculation of the atomic covariance   Vigneshwar Ramakrishnan
• [gmx-users] -don (g-hbond)   atila petrosian
  • [gmx-users] -don (g-hbond)   Justin A. Lemkul
    • [gmx-users] -don (g-hbond)   Erik Marklund
• [gmx-users] g_hbond / hbmap.xpm file   shahab shariati
  • [gmx-users] g_hbond / hbmap.xpm file   Justin A. Lemkul
• [gmx-users] DSSP error   ahmet yıldırım
  • [gmx-users] DSSP error   #ZHAO LINA#
    • [gmx-users] DSSP error   ahmet yıldırım
      • [gmx-users] DSSP error   Justin A. Lemkul
• [gmx-users] g_hbond / hbmap.xpm file   shahab shariati
  • [gmx-users] g_hbond / hbmap.xpm file   Justin A. Lemkul
• [gmx-users] y-axis label in hbang and hbdist.xvg file   atila petrosian
  • [gmx-users] y-axis label in hbang and hbdist.xvg file   Justin A. Lemkul
• [gmx-users] Re: g_hbond / hbmap.xpm file   Thomas Schlesier
• [gmx-users] y-axis label in hbang and hbdist.xvg file   atila petrosian
  • [gmx-users] y-axis label in hbang and hbdist.xvg file   Justin A. Lemkul
• [gmx-users] Re: the charmm force field in gromacs   Pär Bjelkmar
• [gmx-users] Freeze Groups in Gromacs 4.5.x (bug?)!!!   Miguel Machuqueiro
  • [gmx-users] Freeze Groups in Gromacs 4.5.x (bug?)!!!   Mark Abraham
    • [gmx-users] Freeze Groups in Gromacs 4.5.x (bug?)!!!   Miguel Machuqueiro
• [gmx-users] DSSP error   Justin A. Lemkul
  • [gmx-users] DSSP error   ahmet yıldırım
    • [gmx-users] DSSP error   Justin A. Lemkul
      • [gmx-users] DSSP error   Justin A. Lemkul
• [gmx-users] DSSP error   Ali Naqvi
  • [gmx-users] DSSP error   ahmet yıldırım
    • [gmx-users] DSSP error   Justin A. Lemkul
      • [gmx-users] DSSP error   ahmet yıldırım
      • [gmx-users] DSSP error   Justin A. Lemkul
      • [gmx-users] DSSP error   ahmet yıldırım
• [gmx-users] ngmx in windows   bharat gupta
  • [gmx-users] ngmx in windows   Roland Schulz
  • [gmx-users] ngmx in windows   Mark Abraham
    • [gmx-users] ngmx in windows   bharat gupta
• [gmx-users] difference between p(t) and c(t)   shahab shariati
• [gmx-users] hblife.xvg and hbac.xvg files   shahab shariati
• [gmx-users] hydration maps   babu gokul
• [gmx-users] New release of Wordom, molecular analysis program   michele seeber
• [gmx-users] Translation motion during MD   nahren manuel
  • [gmx-users] Translation motion during MD   Justin A. Lemkul
    • [gmx-users] Translation motion during MD   nahren manuel
      • [gmx-users] Translation motion during MD   Justin A. Lemkul
• [gmx-users] When will FEP be on GPU?   TJ Mustard
• [gmx-users] virtual site error   Ting Zhou
  • [gmx-users] virtual site error   Mark Abraham
• [gmx-users] What can we do with gromacs?   mustafa bilsel
  • [gmx-users] What can we do with gromacs?   Justin A. Lemkul
• [gmx-users] Regarding masses in Martini force field   George Khelashvili
  • [gmx-users] Regarding masses in Martini force field   Lutz Maibaum
• [gmx-users] umbrella sampling with position restraint   Víctor Bahamonde
• [gmx-users] Converting between cartesian coordinates and torsion angles   Martin Kamp Jensen
  • [gmx-users] Converting between cartesian coordinates and torsion angles   Mark Abraham
    • [gmx-users] Converting between cartesian coordinates and torsion angles   Martin Kamp Jensen
      • [gmx-users] Converting between cartesian coordinates and torsion angles   Mark Abraham
• [gmx-users] water hydration map analysis help   babu gokul
  • [gmx-users] water hydration map analysis help   Mark Abraham
• [gmx-users] GridCount   babu gokul
• [gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so   Yudong Sun
  • [gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so   Mark Abraham
    • [gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so   Yudong Sun
      • [gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so   Roland Schulz
      • [gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so   Yudong Sun
      • [gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so   Roland Schulz
      • [gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so   Mark Abraham
      • [gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so   Yudong Sun
      • [gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so   Justin A. Lemkul
• [gmx-users] g_densmap options and use   sa
  • [gmx-users] g_densmap options and use   Mark Abraham
• [gmx-users] Re: gmx-users Digest, Vol 79, Issue 88   sa
  • [gmx-users] g_densmap options and use   Justin A. Lemkul
  • [gmx-users] g_densmap options and use   Mark Abraham
• [gmx-users] umbrella sampling with position restraint   chris.neale at utoronto.ca
• [gmx-users] Re: gmx-users Digest, Vol 79, Issue 89   sa
• [gmx-users] Probability contact map from g_mdmat   Ali Naqvi
  • [gmx-users] Probability contact map from g_mdmat   Mark Abraham
• [gmx-users] Molecular dynamics hydration site   babu gokul
  • [gmx-users] Molecular dynamics hydration site   Mark Abraham
• [gmx-users] hblife.xvg and hbac.xvg files   shahab shariati
• [gmx-users] Reg: Surface tension ref_p   vinothkumar mohanakrishnan
• [gmx-users] water molecules (interfacial)   atila petrosian
  • [gmx-users] water molecules (interfacial)   Mark Abraham
• [gmx-users] Area per atom   pawan raghav
  • [gmx-users] Area per atom   Mark Abraham
• [gmx-users] water molecules (interfacial)   atila petrosian
  • [gmx-users] water molecules (interfacial)   Justin A. Lemkul
  • [gmx-users] water molecules (interfacial)   Mark Abraham
• [gmx-users] water molecules (interfacial)   atila petrosian
  • [gmx-users] water molecules (interfacial)   Justin A. Lemkul
• [gmx-users] water molecules (interfacial)   atila petrosian
• [gmx-users] NEMD   Junqiao Lee
  • [gmx-users] Re: NEMD   Junqiao Lee
    • [gmx-users] Re: NEMD   Mark Abraham
    • [gmx-users] Re: NEMD   Junqiao Lee
      • [gmx-users] Re: NEMD   Junqiao Lee
      • [gmx-users] Re: NEMD   Junqiao Lee
      • [gmx-users] Re: NEMD   Junqiao Lee
      • [gmx-users] Re: NEMD   Junqiao Lee
• [gmx-users] checkpoint file and *.gro -- energy calculation   Yongchul Chung
• [gmx-users] checkpoint file and *.gro -- energy calculation   Yongchul Chung
  • [gmx-users] checkpoint file and *.gro -- energy calculation   Justin A. Lemkul
    • [gmx-users] checkpoint file and *.gro -- energy calculation   Yongchul Chung
      • [gmx-users] checkpoint file and *.gro -- energy calculation   Yongchul Chung
      • [gmx-users] checkpoint file and *.gro -- energy calculation   Mark Abraham
      • [gmx-users] checkpoint file and *.gro -- energy calculation   Yongchul Chung
• [gmx-users] how to calculate per-atom energies   Silvia Crivelli
  • [gmx-users] how to calculate per-atom energies   Mark Abraham
• Subject: Re: [gmx-users] GFP chromophore topology help   Gerrit Groenhof
  • Subject: Re: [gmx-users] GFP chromophore topology help   Justin A. Lemkul
    • Subject: Re: [gmx-users] GFP chromophore topology help   Ramachandran G
• [gmx-users] 1-4 interaction, a distance greater than table size   Amin Arabbagheri
  • [gmx-users] 1-4 interaction, a distance greater than table size   Justin A. Lemkul
• [gmx-users] water molecules (interfacial) - IIRC   leila karami
  • [gmx-users] water molecules (interfacial) - IIRC   Mark Abraham
• [gmx-users] water molecules (interfacial)   leila karami
  • [gmx-users] water molecules (interfacial)   Teemu Murtola
• [gmx-users] Spurious results with pdb2gmx -chargegrp "yes" option   sa
• [gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3   Solomon Berman
  • [gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3   Rossen Apostolov
• [gmx-users] Fwd: gmx-users Digest, Vol 79, Issue 102   Silvia Crivelli
  • [gmx-users] Fwd: gmx-users Digest, Vol 79, Issue 102   Mark Abraham
• [gmx-users] still can not run md for creatine   Olga Ivchenko
  • [gmx-users] still can not run md for creatine   Mark Abraham
• [gmx-users] bitinilated peptide   Gloria Saracino
  • [gmx-users] bitinilated peptide   Justin A. Lemkul
• [gmx-users] g_sas and g_rdf   Carla Jamous
• [gmx-users] Extracting protein plus a shell of water from a .xtc file   Paolo Conflitti
  • [gmx-users] Extracting protein plus a shell of water from a .xtc file   Mark Abraham
• [gmx-users] Re: still can not run md for creatine   Vitaly Chaban
  • [gmx-users] Re: still can not run md for creatine   Olga Ivchenko
    • [gmx-users] Re: still can not run md for creatine   Vitaly Chaban
      • [gmx-users] Re: still can not run md for creatine   Mark Abraham
    • [gmx-users] Re: still can not run md for creatine   Justin A. Lemkul
      • [gmx-users] Re: still can not run md for creatine   Esteban Gabriel Vega Hissi
      • [gmx-users] Re: still can not run md for creatine   Justin A. Lemkul
• [gmx-users] Re: Freeze Groups in Gromacs 4.5.x (bug?)!!!   Vitaly Chaban
• [gmx-users] electrostatic interaction   nishap.patel at utoronto.ca
  • [gmx-users] electrostatic interaction   Mark Abraham
    • [gmx-users] electrostatic interaction   Justin A. Lemkul
      • [gmx-users] electrostatic interaction   nishap.patel at utoronto.ca
      • [gmx-users] electrostatic interaction   Mark Abraham
• [gmx-users] Parameterization   YUVRAJ UBOVEJA
  • [gmx-users] Parameterization   Anthony Cruz Balberdi
    • [gmx-users] Parameterization   Oliver Grant
• [gmx-users] Tinker FF parameters vs. GROMACS   Timothy E Pegg
• [gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3   Solomon Berman
  • [gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3   Szilárd Páll
• [gmx-users] compressing two selections or just the reverse of pulling simulation   Samrat Pal
  • [gmx-users] compressing two selections or just the reverse of pulling simulation   Justin A. Lemkul
    • [gmx-users] compressing two selections or just the reverse of pulling simulation   Samrat Pal
• [gmx-users] Protein in Electric Field   S. Mohamadi
  • [gmx-users] Protein in Electric Field   Mark Abraham
• [gmx-users] Re: gmx-users Digest, Vol 79, Issue 114   ITHAYARAJA
  • [gmx-users] ligand parameters (was Re: gmx-users Digest, Vol 79, Issue 114)   Justin A. Lemkul
• [gmx-users] distance VS. direction option in Umbrella sampling, in Gromacs 4.0   DeChang Li
  • [gmx-users] distance VS. direction option in Umbrella sampling, in Gromacs 4.0   Justin A. Lemkul
• [gmx-users] Atomtype CMET not found   Mina Madah
  • [gmx-users] Atomtype CMET not found   Justin A. Lemkul
  • [gmx-users] Atomtype CMET not found   Lucio Montero
• [gmx-users] nve run of carbon nanotube   Adwait Mevada
• [gmx-users] problem linking fftw2 with gromacs 4.5.3   Fabio Affinito
  • [gmx-users] problem linking fftw2 with gromacs 4.5.3   Mark Abraham
    • [gmx-users] problem linking fftw2 with gromacs 4.5.3   Fabio Affinito
• [gmx-users] Re: distance VS. direction option in Umbrella sampling, in Gromacs 4.0 (Justin A. Lemkul)   DeChang Li
  • [gmx-users] Re: distance VS. direction option in Umbrella sampling, in Gromacs 4.0 (Justin A. Lemkul)   Justin A. Lemkul
• [gmx-users] Re: nve run of carbon nanotube   Vitaly Chaban
  • [gmx-users] Re: nve run of carbon nanotube   Justin A. Lemkul
    • [gmx-users] Re: nve run of carbon nanotube   Vitaly Chaban
      • [gmx-users] Re: nve run of carbon nanotube   Justin A. Lemkul
  • [gmx-users] Re: nve run of carbon nanotube   Adwait Mevada
• [gmx-users] Re: nve run of carbon nanotube   Vitaly Chaban
• [gmx-users] question   Raymond
  • [gmx-users] question   Mark Abraham
    • Re: Re: [gmx-users] question   Raymond
• [gmx-users] Reg: pcoupling and ref_p   vinothkumar mohanakrishnan
• [gmx-users] rdf wrong convergence   Raymond
  • [gmx-users] rdf wrong convergence   Mark Abraham
• [gmx-users] [Fwd: Use an altenative folder for itp files]   Stephane Abel
  • [gmx-users] [Fwd: Use an altenative folder for itp files]   Justin A. Lemkul
  • [gmx-users] [Fwd: Use an altenative folder for itp files]   Mark Abraham
• [gmx-users] Re: Can I have the mdp file?   Pär Bjelkmar
• [gmx-users] domain decomposition error   Fabio Affinito
  • [gmx-users] domain decomposition error   Mark Abraham
• [gmx-users] Use an altenative folder for itp files   Stephane Abel
  • [gmx-users] Use an altenative folder for itp files   Justin A. Lemkul
• [gmx-users] Re: nve run of carbon nanotube   Adwait Mevada
  • [gmx-users] Re: nve run of carbon nanotube   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 79, Issue 124   Stephane Abel
• [gmx-users] RE: Temperature Fluctuations   Nimesh Jain
  • [gmx-users] RE: Temperature Fluctuations   Mark Abraham
• [gmx-users] (no subject)   Daniel Adriano Silva M
  • [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)   X Rules
    • [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)   Justin A. Lemkul
• [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)   X Rules
• [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)   Justin A. Lemkul
  • [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)   X Rules
    • [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)   Justin A. Lemkul
      • [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)   X Rules
      • [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)   Justin A. Lemkul
• [gmx-users] Re: nve run of carbon nanotube   Vitaly Chaban
• [gmx-users] Re: nve run of carbon nanotube   Adwait Mevada
  • [gmx-users] Re: nve run of carbon nanotube   Justin A. Lemkul
• [gmx-users] clusters of conformations of a molecular structure using g_cluster   段宝根
• [gmx-users] number of coordinates in pdb file does not match number of coordinates in topology file   Taylor Kaplan
  • [gmx-users] number of coordinates in pdb file does not match number of coordinates in topology file   Justin A. Lemkul
• [gmx-users] Re: nve run of carbon nanotube   Adwait Mevada
• [gmx-users] Reg: Unit Of Surface Tension   vinothkumar mohanakrishnan
  • [gmx-users] Reg: Unit Of Surface Tension   Sven
• [gmx-users] detailed energies per interaction   Efrat Noy
  • [gmx-users] detailed energies per interaction   Mark Abraham
• [gmx-users] DNA didnot wrap around CNT   Siamkhanthang Neihsial
  • [gmx-users] DNA didnot wrap around CNT   Justin A. Lemkul
• [gmx-users] cutoff values for amber ff   Jarmila Husby
  • [gmx-users] cutoff values for amber ff   Justin A. Lemkul
• [gmx-users] Gromacs "Quotes"   Sikandar Mashayak
  • [gmx-users] Gromacs "Quotes"   David van der Spoel
• [gmx-users] genion writes a log file?   Justin A. Lemkul
  • [gmx-users] Cumulative coordination number?   teklebrh at ualberta.ca
• [gmx-users] Using Charmm FF with implicit solvent on gromacs   César Ávila
  • [gmx-users] Using Charmm FF with implicit solvent on gromacs   Mark Abraham
  • [gmx-users] Using Charmm FF with implicit solvent on gromacs   Per Larsson
    • [gmx-users] charge group radii   Gavin Melaugh
      • [gmx-users] charge group radii   Mark Abraham
      • [gmx-users] charge group radii   Gavin Melaugh
      • [gmx-users] charge group radii   Mark Abraham
• [gmx-users] Area per lipid calculation   NG HUI WEN
  • [gmx-users] Area per lipid calculation   Justin A. Lemkul
• [gmx-users] 4-site rigid body model   Sanku M
  • [gmx-users] 4-site rigid body model   Justin A. Lemkul
• [gmx-users] Pairwise forces   Reiner Ribarics
  • [gmx-users] Pairwise forces   Mark Abraham
  • [gmx-users] Pairwise forces   Bogdan Costescu
    • [gmx-users] Pairwise forces   Reiner Ribarics
• [gmx-users] Role of epsilon_rf in implicit solvation   Christian Mücksch
  • [gmx-users] Role of epsilon_rf in implicit solvation   Per Larsson
• [gmx-users] question about simualtion of CNT from a rookie   Ye MEI
• [gmx-users] noxvgr   #ZHAO LINA#
  • [gmx-users] noxvgr   Justin A. Lemkul
    • [gmx-users] noxvgr   #ZHAO LINA#
      • [gmx-users] noxvgr   Justin A. Lemkul
      • [gmx-users] noxvgr   #ZHAO LINA#
  • [gmx-users] noxvgr   Florian Dommert
• [gmx-users] mpdboot and mpirun hangs (not crashing)   X Rules
  • [gmx-users] mpdboot and mpirun hangs (not crashing)   Mark Abraham
    • [gmx-users] mpdboot and mpirun hangs (not crashing)   X Rules
• [gmx-users] mutiple dihedral terms   Sanku M
  • [gmx-users] mutiple dihedral terms   Justin A. Lemkul
    • [gmx-users] mutiple dihedral terms   Mark Abraham
• [gmx-users] question regarding to PMF calculation between 2 plates   Zhe Wu
• [gmx-users] disparity in RMSD calculation   Sunita Patel
  • [gmx-users] disparity in RMSD calculation   Yongchul Chung
    • [gmx-users] disparity in RMSD calculation   Sunita Patel
  • [gmx-users] disparity in RMSD calculation   Mark Abraham
    • [gmx-users] disparity in RMSD calculation   X Rules
      • [gmx-users] disparity in RMSD calculation   Sunita Patel
    • [gmx-users] disparity in RMSD calculation   Sunita Patel
• [gmx-users] g_hbond -ac -life   shahab shariati
• [gmx-users] xtc corrupted during REMD   Spitaleri Andrea
  • [gmx-users] xtc corrupted during REMD   Mark Abraham
    • R: [gmx-users] xtc corrupted during REMD   Spitaleri Andrea
      • [gmx-users] xtc corrupted during REMD   Roland Schulz
      • [gmx-users] xtc corrupted during REMD   andrea spitaleri
      • [gmx-users] xtc corrupted during REMD   Mark Abraham
• [gmx-users] Position restrained..   pawan raghav
  • [gmx-users] Position restrained..   Mark Abraham
• [gmx-users] request   leila separdar
  • [gmx-users] request   Amit Choubey
    • [gmx-users] request   leila separdar
      • [gmx-users] request   Mark Abraham
• [gmx-users] question on KALP-15 in DPPC tutorial   Amit Choubey
  • [gmx-users] question on KALP-15 in DPPC tutorial   Mark Abraham
    • [gmx-users] question on KALP-15 in DPPC tutorial   Justin A. Lemkul
      • [gmx-users] question on KALP-15 in DPPC tutorial   Amit Choubey
• [gmx-users] PR   pawan raghav
  • [gmx-users] PR   Florian Dommert
  • [gmx-users] PR   Mark Abraham
    • [gmx-users] PR   Zhe Wu
• [gmx-users] extending simulation without cpt file   Hsin-Lin Chiang
  • [gmx-users] extending simulation without cpt file   Mark Abraham
• [gmx-users] find the relevant structure out   #ZHAO LINA#
  • [gmx-users] find the relevant structure out   Mark Abraham
    • [gmx-users] find the relevant structure out   #ZHAO LINA#
    • [gmx-users] find the relevant structure out   #ZHAO LINA#
      • [gmx-users] find the relevant structure out   Justin A. Lemkul
      • [gmx-users] find the relevant structure out   Tsjerk Wassenaar
      • [gmx-users] find the relevant structure out   #ZHAO LINA#
      • [gmx-users] find the relevant structure out   Mark Abraham
• [gmx-users] question regarding to PMF calculation between 2 plates   chris.neale at utoronto.ca
  • [gmx-users] question regarding to PMF calculation between 2 plates   Zhe Wu
• [gmx-users] extending simulation without cpt file   Hsin-Lin Chiang
  • [gmx-users] extending simulation without cpt file   Mark Abraham
• [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield   Jignesh Patel
  • [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield   Erik Marklund
  • [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield   #ZHAO LINA#
    • [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield   #ZHAO LINA#
• [gmx-users] protein folding   mohsen ramezanpour
  • [gmx-users] protein folding   Mark Abraham
  • [gmx-users] protein folding   ms
    • [gmx-users] protein folding   Thomas Evangelidis
      • [gmx-users] protein folding   David van der Spoel
      • [gmx-users] protein folding   mohsen ramezanpour
  • [gmx-users] protein folding   Lutz Maibaum
    • [gmx-users] protein folding   mohsen ramezanpour
• [gmx-users] .pqr to .pdb   mohsen ramezanpour
  • [gmx-users] .pqr to .pdb   Mark Abraham
    • [gmx-users] .pqr to .pdb   Tsjerk Wassenaar
• [gmx-users] grompp error version 4.5.2   Adva Suez
  • [gmx-users] grompp error version 4.5.2   Mark Abraham
    • [gmx-users] grompp error version 4.5.2   Adva Suez
• [gmx-users] How to obtain the coordinates of atom 100 with number in the frame 100 using xdrfile in C code   英雄不再寂寞
  • [gmx-users] How to obtain the coordinates of atom 100 with number in the frame 100 using xdrfile in C code   David van der Spoel
• [gmx-users] two problems with gromacs 4.5.3   Sanku M
  • [gmx-users] two problems with gromacs 4.5.3   Roland Schulz
• [gmx-users] Implementation of Andersen Thermostat   sapna sarupria
• [gmx-users] Problem regarding Gromacs - GPU   kapil mathur
  • [gmx-users] Problem regarding Gromacs - GPU   Szilárd Páll
  • [gmx-users] Problem regarding Gromacs - GPU   Rossen Apostolov
• [gmx-users] deprotonation and DNA   luo jinghui
  • [gmx-users] deprotonation and DNA   Erik Marklund
• [gmx-users] water model purpose?   ahmet yıldırım
  • [gmx-users] water model purpose?   Mark Abraham
• [gmx-users] .itp for simple atom   leila separdar
  • [gmx-users] .itp for simple atom   ms
• [gmx-users] Problem with large number of frames only one frame can be read from trajectory bug ?   maria goranovic
  • [gmx-users] Problem with large number of frames only one frame can be read from trajectory bug ?   Mark Abraham
    • [gmx-users] Problem with large number of frames only one frame can be read from trajectory bug ?   maria goranovic
• [gmx-users] perl script for g_hbond   leila karami
  • [gmx-users] perl script for g_hbond   Carla Jamous
  • [gmx-users] perl script for g_hbond   Justin A. Lemkul
• [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?   ms
  • [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?   Florian Dommert
  • [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?   Mark Abraham
    • [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?   ms
      • [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?   Mark Abraham
      • [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?   ms
    • [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?   ms
    • [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?   ms
• [gmx-users] perl script for g_hbond   leila karami
• [gmx-users] The trouble with dihedral restraints: frozen peptide backbones   ms
• [gmx-users] AMOEBA/AMBER 11 in Gromacs?   J. Nathan Scott
  • [gmx-users] AMOEBA/AMBER 11 in Gromacs?   Erik Marklund
• [gmx-users] Re: Please help me solve this fatal error   Justin A. Lemkul
• [gmx-users] perl script for g_hbond   leila karami
  • [gmx-users] perl script for g_hbond   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 79, Issue 152   J. Nathan Scott
• [gmx-users] perl script for g_hbond   leila karami
  • [gmx-users] perl script for g_hbond   Justin A. Lemkul
• [gmx-users] Adding custom residue to Charmm FF in Gromacs   César Ávila
  • [gmx-users] Adding custom residue to Charmm FF in Gromacs   Justin A. Lemkul
• [gmx-users] perl script for g_hbond   leila karami
  • [gmx-users] perl script for g_hbond   Justin A. Lemkul
• [gmx-users] Run input file prepared by different gmx version   Deniz KARASU
  • [gmx-users] Run input file prepared by different gmx version   Mark Abraham
• [gmx-users] Residue Residue Contact   nahren manuel
  • [gmx-users] Residue Residue Contact   Erik Marklund
• [gmx-users] mdrun crashed with tables   Sai Pooja
  • [gmx-users] mdrun crashed with tables   ms
  • [gmx-users] mdrun crashed with tables   Mark Abraham
    • [gmx-users] mdrun crashed with tables   Sai Pooja
• [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?   Dallas Warren
• [gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU   lin hen
  • [gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU   lin hen
  • [gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU   Rossen Apostolov
• [gmx-users] error found in gmx   ITHAYARAJA
  • [gmx-users] error found in gmx   Mark Abraham
  • [gmx-users] error found in gmx   Tsjerk Wassenaar
• [gmx-users] LINCS Warnings in the middle of an MD run   Shi Wenxiong (Dr)
• [gmx-users] find the relevant structure out   #ZHAO LINA#
• [gmx-users] perl script for g_hbond / summary_HBmap.dat   leila karami
  • [gmx-users] perl script for g_hbond / summary_HBmap.dat   Justin A. Lemkul
• [gmx-users] Re: displacement of Drug molecule during position restrained MD   Justin A. Lemkul
• [gmx-users] perl script for g_hbond / summary_HBmap.dat   leila karami
  • [gmx-users] perl script for g_hbond / summary_HBmap.dat   Erik Marklund
• [gmx-users] Electric field: phosphate moves in the wrong direction   Susana Tomasio
  • [gmx-users] Electric field: phosphate moves in the wrong direction   Susana Tomasio
• [gmx-users] installation   Rossella Noschese
  • [gmx-users] installation   Carsten Kutzner
  • [gmx-users] installation   Justin A. Lemkul
    • [gmx-users] installation   Rossella Noschese
      • [gmx-users] installation   Rossella Noschese
• [gmx-users] perl script for g_hbond / summary_HBmap.dat   leila karami
  • [gmx-users] perl script for g_hbond / summary_HBmap.dat   Erik Marklund
• [gmx-users] g_hbond -ac -life   shahab shariati
  • [gmx-users] g_hbond -ac -life   Erik Marklund
• [gmx-users] g_hbond -ac -life   shahab shariati
  • [gmx-users] g_hbond -ac -life   Erik Marklund
• [gmx-users] Re: perl script for g_hbond / summary_HBmap.dat   Causgrove, Tim
• [gmx-users] perl script for g_hbond / summary_HBmap.dat   leila karami
  • [gmx-users] perl script for g_hbond / summary_HBmap.dat   Erik Marklund
• [gmx-users] (no subject)   Olga Ivchenko
  • [gmx-users] (no subject)   Justin A. Lemkul
• [gmx-users] heme   shahid nayeem
  • [gmx-users] heme   Erik Marklund
    • [gmx-users] heme   Justin A. Lemkul
      • [gmx-users] heme   shahid nayeem
    • [gmx-users] heme   shahid nayeem
• [gmx-users] Nose-Hoover Thermostat for Non Equilibrium Simulations   Apoorv Kalyankar
• [gmx-users] Martini parameters for formyl group   George Khelashvili
• [gmx-users] Reg: Interfacial tension   vinothkumar mohanakrishnan
• [gmx-users] Reg: Interfacial tension   vinothkumar mohanakrishnan
• [gmx-users] RMSD and Resolution   ahmet yıldırım
  • [gmx-users] RMSD and Resolution   Tsjerk Wassenaar
• [gmx-users] perl script for g_hbond / summary_HBmap.dat   leila karami
  • [gmx-users] perl script for g_hbond / summary_HBmap.dat   Erik Marklund
• [gmx-users] demo problems   Rossella Noschese
• [gmx-users] free energy perturbation   antonio
  • [gmx-users] free energy perturbation   Justin A. Lemkul
• [gmx-users] Failed to lock: pre.log (Gromacs 4.5.3)   Baofu Qiao
  • [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)   Baofu Qiao
    • [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)   Carsten Kutzner
      • [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)   Baofu Qiao
      • [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)   Roland Schulz
      • [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)   Baofu Qiao
      • [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)   Roland Schulz
      • [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)   Baofu Qiao
      • [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)   Florian Dommert
      • [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3): SOLVED   Baofu Qiao
      • [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3): SOLVED   Roland Schulz
      • [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3) Neither of 4.5.1, 4.5.2 and 4.5.3 works   Baofu Qiao
• [gmx-users] Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?   sa
  • [gmx-users] Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?   Thomas Piggot
  • [gmx-users] Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?   Francesco Oteri
    • [gmx-users] Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 79, Issue 167   sa
  • [gmx-users] Re: gmx-users Digest, Vol 79, Issue 167   Thomas Piggot
• [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero   Anirban Ghosh
  • [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero   Anirban Ghosh
    • [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero   Justin A. Lemkul
      • [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero   Anirban Ghosh
      • [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero   Justin A. Lemkul
• [gmx-users] Phosphorylated Serine in charmm   Yasmine Chebaro
  • [gmx-users] Phosphorylated Serine in charmm   Justin A. Lemkul
• [gmx-users] system is exploding   Olga Ivchenko
  • [gmx-users] system is exploding   Baofu Qiao
    • [gmx-users] system is exploding   Olga Ivchenko
      • [gmx-users] system is exploding   Baofu Qiao
      • [gmx-users] system is exploding   T.M.D. Graen
      • [gmx-users] system is exploding   Justin A. Lemkul
• [gmx-users] [Fwd: charge group radii]   Gavin Melaugh
• [gmx-users] Error while using forcefield GROMOS 43a1p   Jignesh Patel
  • [gmx-users] Error while using forcefield GROMOS 43a1p   Justin A. Lemkul
• [gmx-users] Thermostat for REMD simulations in implicit solvent   César Ávila
  • [gmx-users] Thermostat for REMD simulations in implicit solvent   Per Larsson
    • [gmx-users] Thermostat for REMD simulations in implicit solvent   César Ávila
• [gmx-users] PR   pawan raghav
  • [gmx-users] PR   Justin A. Lemkul
• [gmx-users] Re: displacement of drug molecule   Justin A. Lemkul
• [gmx-users] Re: HEME Charmm Force field in Gromacs format   Pär Bjelkmar
• [gmx-users] How to save the coordinates of all atoms in the 2D-arrays using xdrfile?   英雄不再寂寞
  • [gmx-users] How to save the coordinates of all atoms in the 2D-arrays using xdrfile?   Mark Abraham
• [gmx-users] Replica exchange   Sai Pooja
  • [gmx-users] Replica exchange   ms
  • [gmx-users] Replica exchange   ms
  • [gmx-users] Replica exchange   Mark Abraham
• [gmx-users] Thermostating in NEMD   Apoorv Kalyankar
  • [gmx-users] Thermostating in NEMD   David van der Spoel
• [gmx-users] Problem with coulombtype=user and 1,4 interactions   Christian Mücksch
• [gmx-users] fix center of mass vs fix residues close to COM   哦哦
• [gmx-users] Re: Re: Error while using forcefield GROMOS 43a1p (Justin A. Lemkul)   Jignesh Patel
  • [gmx-users] Re: Re: Error while using forcefield GROMOS 43a1p (Justin A. Lemkul)   Jignesh Patel
• [gmx-users] changing the velocity in trajectory file   sreelakshmi ramesh
  • [gmx-users] changing the velocity in trajectory file   Baofu Qiao
    • [gmx-users] changing the velocity in trajectory file   sreelakshmi ramesh
      • [gmx-users] changing the velocity in trajectory file   Justin A. Lemkul
      • [gmx-users] changing the velocity in trajectory file   sreelakshmi ramesh
      • [gmx-users] changing the velocity in trajectory file   Justin A. Lemkul
      • [gmx-users] changing the velocity in trajectory file   sreelakshmi ramesh
      • [gmx-users] changing the velocity in trajectory file   Bogdan Costescu
      • [gmx-users] changing the velocity in trajectory file   Mark Abraham
      • [gmx-users] changing the velocity in trajectory file   sreelakshmi ramesh
      • [gmx-users] changing the velocity in trajectory file   sreelakshmi ramesh
      • [gmx-users] changing the velocity in trajectory file   Lutz Maibaum
      • [gmx-users] changing the velocity in trajectory file   sreelakshmi ramesh
      • [gmx-users] changing the velocity in trajectory file   Lutz Maibaum
• [gmx-users] Re: error in grompp command   Justin A. Lemkul
• [gmx-users] perl script for g_hbond   leila karami
  • [gmx-users] perl script for g_hbond   Olga Ivchenko
    • [gmx-users] perl script for g_hbond   Justin A. Lemkul
      • [gmx-users] perl script for g_hbond   Olga Ivchenko
  • [gmx-users] perl script for g_hbond   Erik Marklund
• [gmx-users] pdb file problem   benrezkallah djamila
  • [gmx-users] pdb file problem   Justin A. Lemkul
• [gmx-users] Attractive and repulsive components of Pot energy   Sai Pooja
  • [gmx-users] Attractive and repulsive components of Pot energy   Mark Abraham
• [gmx-users] g_rama problem about dihedrals   Rebeca García Fandiño
• [gmx-users] What does "Conserved-En." stands for   Jim (Rui) Qiao
  • [gmx-users] What does "Conserved-En." stands for   Michael Shirts
    • [gmx-users] What does "Conserved-En." stands for   Jim (Rui) Qiao
• [gmx-users] C6 attractive term off OPLSAA   nishap.patel at utoronto.ca
  • [gmx-users] C6 attractive term off OPLSAA   Justin A. Lemkul
    • [gmx-users] C6 attractive term off OPLSAA   nishap.patel at utoronto.ca
      • [gmx-users] C6 attractive term off OPLSAA   nishap.patel at utoronto.ca
      • [gmx-users] C6 attractive term off OPLSAA   Justin A. Lemkul
      • [gmx-users] C6 attractive term off OPLSAA   Mark Abraham
• 回复： [gmx-users] How to save the coordinates of all atoms in the 2D-arrays using xdrfile?   英雄不再寂寞
  • =?x-gbk?Q?=BB=D8=B8=B4=A3=BA_=5Bgmx-users=5D_How_to_?= =?x-gbk?Q?save_the_coordinates_of_all_atoms_in_the_2D-ar?= =?x-gbk?Q?rays_using_xdrfile=3F?=   Mark Abraham
• [gmx-users] changing the velocity in trajectory file   chris.neale at utoronto.ca
  • [gmx-users] changing the velocity in trajectory file   Justin A. Lemkul
• [gmx-users] tfe.gro   hengame fallah
• [gmx-users] Claculating Equilibrium constants   גדעון לפידות
  • [gmx-users] Claculating Equilibrium constants   Ran Friedman
• [gmx-users] Looking for Gromacs test users   Wibke Sudholt
• [gmx-users] g_select / Input error or input inconsistency   leila karami
  • [gmx-users] g_select / Input error or input inconsistency   Justin A. Lemkul
• [gmx-users] tfe.gro   ABEL Stephane 175950
  • [gmx-users] tfe.gro   hengame fallah
• [gmx-users] g_select / Input error or input inconsistency   leila karami
  • [gmx-users] g_select / Input error or input inconsistency   Justin A. Lemkul
• [gmx-users] intra-chain peptide bond   Semin Lee
  • [gmx-users] intra-chain peptide bond   Justin A. Lemkul
    • [gmx-users] intra-chain peptide bond   Justin A. Lemkul
• [gmx-users] g_select / Input error or input inconsistency   leila karami
  • [gmx-users] g_select / Input error or input inconsistency   Justin A. Lemkul
• [gmx-users] g_select / Input error or input inconsistency   leila karami
  • [gmx-users] g_select / Input error or input inconsistency   Justin A. Lemkul
  • [gmx-users] g_select / Input error or input inconsistency   Teemu Murtola
• [gmx-users] Temporary downtime for git.gromacs.org Wednesday   Erik Lindahl
• [gmx-users] Ions and charge groups   Guido Polles
  • [gmx-users] Ions and charge groups   Justin A. Lemkul
    • [gmx-users] Ions and charge groups   Justin A. Lemkul
• [gmx-users] A warning concerning file ffnonbonded.itp overriding atomtype OT   Hassan Shallal
  • [gmx-users] A warning concerning file ffnonbonded.itp overriding atomtype OT   Justin A. Lemkul
• [gmx-users] Large Periodic Molecule   Rogan Carr
• [gmx-users] VDW radious (Gideon)   גדעון לפידות
  • [gmx-users] VDW radious (Gideon)   Justin A. Lemkul
• [gmx-users] Trouble with Gromacs finding the files it needs   J. Nathan Scott
  • [gmx-users] Trouble with Gromacs finding the files it needs   Justin A. Lemkul
    • [gmx-users] Trouble with Gromacs finding the files it needs   J. Nathan Scott
      • [gmx-users] Trouble with Gromacs finding the files it needs   Justin A. Lemkul
      • [gmx-users] Trouble with Gromacs finding the files it needs   Rogan Carr

Last message date: Tue Nov 30 23:46:31 CET 2010
Archived on: Thu Nov 14 12:09:46 CET 2013

• Messages sorted by: [ subject ] [ author ] [ date ]
• More info on this list...