December 2010 Archives by thread

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Starting: Wed Dec 1 00:06:14 CET 2010
Ending: Fri Dec 31 15:28:15 CET 2010
Messages: 891

• [gmx-users] Ions and charge groups   Guido Polles
  • [gmx-users] Ions and charge groups   Justin A. Lemkul
    • [gmx-users] Ions and charge groups   Guido Polles
• [gmx-users] changing the velocity in trajectory file   sreelakshmi ramesh
• [gmx-users] water-air interface   铁锋 彭
  • [gmx-users] water-air interface   Mark Abraham
• [gmx-users] add a new force field to the pdb2gmx list   Jia Haitao
  • [gmx-users] add a new force field to the pdb2gmx list   Yang Ye
    • [gmx-users] add a new force field to the pdb2gmx list   Mark Abraham
  • [gmx-users] add a new force field to the pdb2gmx list   Mark Abraham
    • [gmx-users] add a new force field to the pdb2gmx list   Jia Haitao
      • [gmx-users] add a new force field to the pdb2gmx list   Mark Abraham
      • [gmx-users] add a new force field to the pdb2gmx list   Jia Haitao
• [gmx-users] Reg:Uncertainty in the average value   vinothkumar mohanakrishnan
• [gmx-users] how to specify a location of a molecule in the system   Adva Suez
  • [gmx-users] how to specify a location of a molecule in the system   Erik Marklund
  • [gmx-users] how to specify a location of a molecule in the system   Justin A. Lemkul
• [gmx-users] Reg: Standard error   vinothkumar mohanakrishnan
  • [gmx-users] Reg: Standard error   Mark Abraham
    • [gmx-users] Reg: Standard error   vinothkumar mohanakrishnan
      • [gmx-users] Reg: Standard error   Mark Abraham
• [gmx-users] Some tools not described any more in online manual   Emanuel Peter
  • [gmx-users] Some tools not described any more in online manual   Justin A. Lemkul
• [gmx-users] v-rescale and conserved energy   Mikhail Stukan
  • [gmx-users] v-rescale and conserved energy   Berk Hess
• [gmx-users] Re: gmx-users Digest, Vol 80, Issue 6   lloyd riggs
• [gmx-users] air-water interface   铁锋 彭
  • [gmx-users] air-water interface   Mark Abraham
• [gmx-users] Re:Re-installation(4.5.3) mdrun crashes?   lloyd riggs
  • [gmx-users] Re:Re-installation(4.5.3) mdrun crashes?   Justin A. Lemkul
• [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   Berk Hess
      • [gmx-users] C6 attractive term off OPLSAA   nishap.patel at utoronto.ca
      • [gmx-users] RE:C6 attractive term off OPLSAA   nishap.patel at utoronto.ca
      • [gmx-users] RE:C6 attractive term off OPLSAA   Mark Abraham
• [gmx-users] Re:Re: Re:RE:Re-installation(4.5.3) mdrun crashes? (Justin A. Lemkul)   lloyd riggs
• [gmx-users] Cut-offs using CHARMM27 ff   Hassan Shallal
  • [gmx-users] Cut-offs using CHARMM27 ff   Roland Schulz
    • [gmx-users] virtual sites and heavy atoms for longer time steps   Hassan Shallal
• [gmx-users] printing a trajectory file in readable format starting from a specific frame other than zero   Silvia Crivelli
  • [gmx-users] printing a trajectory file in readable format starting from a specific frame other than zero   Roland Schulz
• [gmx-users] virtual sites and heavy atoms for longer time steps   Mark Abraham
• [gmx-users] Restraining water   Guido Polles
  • [gmx-users] Restraining water   Mark Abraham
    • [gmx-users] Restraining water   David Rodríguez
      • [gmx-users] Restraining water   Oliver Grant
• [gmx-users] Re: air-water interface   Vitaly Chaban
• [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group"   WU Yanbin
  • [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group"   Mark Abraham
  • [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group"   Carsten Kutzner
• Antw: [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group"   Emanuel Peter
• [gmx-users] Fwd: lateral diffusion coefficients on a spherical surface   Thomas Piggot
• [gmx-users] Allocation memory failure with g_msd (version 4.5.X)   Javier Cerezo
• [gmx-users] individual lateral diffusion coefficients   Ángel Piñeiro
  • [gmx-users] individual lateral diffusion coefficients   Justin A. Lemkul
• [gmx-users] Re: individual lateral diffusion coefficients   Ángel Piñeiro
  • [gmx-users] Re: individual lateral diffusion coefficients   Javier Cerezo
    • [gmx-users] Re: individual lateral diffusion coefficients   Ángel Piñeiro
      • [gmx-users] Re: individual lateral diffusion coefficients   Javier Cerezo
      • [gmx-users] Re: individual lateral diffusion coefficients   Ángel Piñeiro
      • [gmx-users] Re: individual lateral diffusion coefficients   Justin A. Lemkul
      • [gmx-users] Re: individual lateral diffusion coefficients   Javier Cerezo
      • [gmx-users] Re: individual lateral diffusion coefficients   Javier Cerezo
      • [gmx-users] Re: individual lateral diffusion coefficients   Justin A. Lemkul
  • [gmx-users] Re: individual lateral diffusion coefficients   XAvier Periole
    • [gmx-users] Re: individual lateral diffusion coefficients   Ángel Piñeiro
• [gmx-users] proton proton transfer   Olga Ivchenko
  • [gmx-users] proton proton transfer   Justin A. Lemkul
    • [gmx-users] proton proton transfer   Olga Ivchenko
      • [gmx-users] proton proton transfer   Ran Friedman
      • [gmx-users] proton proton transfer   Ran Friedman
  • [gmx-users] proton proton transfer   Erik Marklund
    • [gmx-users] proton proton transfer   Olga Ivchenko
• [gmx-users] .pqr to .pdb   mohsen ramezanpour
  • [gmx-users] .pqr to .pdb   Justin A. Lemkul
    • [gmx-users] .pqr to .pdb   mohsen ramezanpour
  • [gmx-users] .pqr to .pdb   Maximiliano Figueroa
    • [gmx-users] .pqr to .pdb   mohsen ramezanpour
• [gmx-users] Note on oscillation period / time step   Robin C. Underwood
  • [gmx-users] Note on oscillation period / time step   Javier Cerezo
    • [gmx-users] Note on oscillation period / time step   Justin A. Lemkul
      • [gmx-users] Note on oscillation period / time step   Javier Cerezo
  • [gmx-users] Note on oscillation period / time step   Naga Rajesh Tummala
• [gmx-users] Re: Note on oscillation period / time step   Robin C. Underwood
  • [gmx-users] Re: Note on oscillation period / time step   Justin A. Lemkul
• [gmx-users] Re: individual lateral diffusion coefficients   Dallas Warren
  • [gmx-users] Re: individual lateral diffusion coefficients   Javier Cerezo
    • [gmx-users] Re: individual lateral diffusion coefficients   Ángel Piñeiro
• [gmx-users] creat .gro; select force field   gromacs
  • [gmx-users] creat .gro; select force field   Justin A. Lemkul
• [gmx-users] cumulative numbers or running coordination numbers ?   Vitaly Chaban
• [gmx-users] tpbconv -zeroq results all coulombic energies to zero   BIN ZHANG
  • [gmx-users] tpbconv -zeroq results all coulombic energies to zero   David van der Spoel
• [gmx-users] Protein jumping out of water box   גדעון לפידות
  • [gmx-users] Protein jumping out of water box   Kukol, Andreas
  • [gmx-users] Protein jumping out of water box   Justin A. Lemkul
• [gmx-users] Which .tpr file to use for g_rms?   Anirban Ghosh
  • [gmx-users] Which .tpr file to use for g_rms?   Justin A. Lemkul
    • [gmx-users] Which .tpr file to use for g_rms?   Anirban Ghosh
      • [gmx-users] Which .tpr file to use for g_rms?   Justin A. Lemkul
      • [gmx-users] Which .tpr file to use for g_rms?   Anirban Ghosh
      • [gmx-users] Which .tpr file to use for g_rms?   Mark Abraham
      • [gmx-users] Which .tpr file to use for g_rms?   Anirban Ghosh
      • [gmx-users] Which .tpr file to use for g_rms?   Mark Abraham
• [gmx-users] pdb2gmx and atomtype.atp   Sarath Chandra
  • [gmx-users] pdb2gmx and atomtype.atp   Justin A. Lemkul
    • [gmx-users] pdb2gmx and atomtype.atp   Sarath Chandra
      • [gmx-users] pdb2gmx and atomtype.atp   Justin A. Lemkul
      • [gmx-users] pdb2gmx and atomtype.atp   Justin A. Lemkul
• [gmx-users] Re:Re: tpbconv -zeroq results all coulombic energies to zero   BIN ZHANG
• [gmx-users] sasa calculation with different gromacs versions   Rocco Caliandro
  • [gmx-users] sasa calculation with different gromacs versions   Justin A. Lemkul
• [gmx-users] writing the means of every 100 potential energies into an output file   mustafa bilsel
  • [gmx-users] writing the means of every 100 potential energies into an output file   Justin A. Lemkul
• [gmx-users] two graphene sheets are blowing up   zhongjin
  • [gmx-users] two graphene sheets are blowing up   Mark Abraham
• [gmx-users] MOPAC gromacs mdreun error   vidhya sankar
• [gmx-users] Ramachandran plot for non standar residues   Rebeca García Fandiño
  • [gmx-users] Ramachandran plot for non standar residues   Justin A. Lemkul
• [gmx-users] Desktop Freezes While Using mdrun-gpu   Solomon Berman
  • [gmx-users] Desktop Freezes While Using mdrun-gpu   Szilárd Páll
• [gmx-users] [OT] Generate random coil protein conformations?   ms
  • [gmx-users] [OT] Generate random coil protein conformations?   Mark Abraham
    • [gmx-users] [OT] Generate random coil protein conformations?   ms
• [gmx-users] dna, lipid simulation   Amit Choubey
  • [gmx-users] dna, lipid simulation   Itamar Kass (Med)
    • [gmx-users] dna, lipid simulation   Thomas Piggot
      • [gmx-users] dna, lipid simulation   Amit Choubey
  • [gmx-users] dna, lipid simulation   Justin A. Lemkul
• [gmx-users] Re: MOPAC gromacs mdreun error (vidhya sankar)   Gerrit Groenhof
  • [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)   vidhya sankar
• [gmx-users] Change in structure after solvation_Gromacs   swagata chakraborty
  • [gmx-users] Change in structure after solvation_Gromacs   ms
    • [gmx-users] Change in structure after solvation_Gromacs   Justin A. Lemkul
      • [gmx-users] Change in structure after solvation_Gromacs   ms
• [gmx-users] LINCS WARNING   Raymond.nuist
  • [gmx-users] LINCS WARNING   Justin A. Lemkul
• [gmx-users] Re: Re: Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?   sa
• [gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1   Robin C. Underwood
  • [gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1   Erik Marklund
• [gmx-users] Re: polymer simulations in gromacs   Justin A. Lemkul
  • [gmx-users] Re: polymer simulations in gromacs   ms
• [gmx-users] Crashed run   shiva birgani
  • [gmx-users] Crashed run   Shi Wenxiong (Dr)
    • [gmx-users] Crashed run   Mark Abraham
• Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)   Gerrit Groenhof
  • [gmx-users] MOPAC gromacs mdreun error (vidhya sankar)   vidhya sankar
• [gmx-users] questions about long-range electrostatic interaction in membrane systems   Jianguo Li
• [gmx-users] Constraining two virtual sites   Sebastian Fritsch
  • [gmx-users] Constraining two virtual sites   Mark Abraham
  • [gmx-users] Constraining two virtual sites   Berk Hess
• [gmx-users] Re: Help - LINCS WARNING: bonds that rotated more than 30 degrees   Justin A. Lemkul
• [gmx-users] Constraining two virtual sites   Sebastian Fritsch
• [gmx-users] Energy-groups?   nishap.patel at utoronto.ca
  • [gmx-users] Energy-groups?   Justin A. Lemkul
    • [gmx-users] Energy-groups?   nishap.patel at utoronto.ca
      • [gmx-users] Energy-groups?   Justin A. Lemkul
      • [gmx-users] Energy-groups?   nishap.patel at utoronto.ca
• [gmx-users] Re: gmx-users Digest, Vol 80, Issue 41   Gerrit Groenhof
  • [gmx-users] Re: gmx-users Digest, Vol 80, Issue 41   vidhya sankar
    • [gmx-users] reg compilation error in mopac gromacs   vidhya sankar
• [gmx-users] Change in structure after solvation_Gromacs   swagata chakraborty
  • [gmx-users] Change in structure after solvation_Gromacs   Justin A. Lemkul
• [gmx-users] LJ Plot   nishap.patel at utoronto.ca
  • [gmx-users] LJ Plot   Justin A. Lemkul
    • [gmx-users] LJ Plot   nishap.patel at utoronto.ca
      • [gmx-users] LJ Plot   Justin A. Lemkul
      • [gmx-users] LJ Plot   nishap.patel at utoronto.ca
      • [gmx-users] LJ Plot   ms
      • [gmx-users] LJ Plot   nishap.patel at utoronto.ca
      • [gmx-users] LJ Plot   Justin A. Lemkul
      • [gmx-users] LJ Plot   ms
• [gmx-users] LJ Plot   Mark Abraham
• [gmx-users] Re: MOPAC gromacs mdreun error (vidhya sankar)   Vitaly Chaban
• [gmx-users] pressure fluctuations   Hassan Shallal
  • [gmx-users] pressure fluctuations   Justin A. Lemkul
    • [gmx-users] trouble parallelizing a simulation over a cluster   Hassan Shallal
      • [gmx-users] Re: trouble parallelizing a simulation over a cluster   Carsten Kutzner
      • [gmx-users] Re: trouble parallelizing a simulation over a cluster   Hassan Shallal
      • [gmx-users] generating new velocities and exploring more of the phase space   Hassan Shallal
      • [gmx-users] generating new velocities and exploring more of the phase space   Justin A. Lemkul
      • [gmx-users] generating new velocities and exploring more of thephase space   Hassan Shallal
      • [gmx-users] generating new velocities and exploring more of thephase space   Justin A. Lemkul
      • [gmx-users] using recolor.sh to color the xpm matrix files produced by r_rms and g_mdmat   Hassan Shallal
      • [gmx-users] using recolor.sh to color the xpm matrix files produced by r_rms and g_mdmat   Tsjerk Wassenaar
      • [gmx-users] strange xpm output of g_rmsdist!   Hassan Shallal
• [gmx-users] Inaccurate time frame   Hsin-Lin Chiang
• [gmx-users] Inaccurate time frame   Mark Abraham
• [gmx-users] gromacs-4.5.3 installation error   pawan raghav
• [gmx-users] Inaccurate time frame   Hsin-Lin Chiang
• [gmx-users] Inaccurate time frame   Mark Abraham
• [gmx-users] Inaccurate time frame   Hsin-Lin Chiang
  • [gmx-users] Inaccurate time frame   Mark Abraham
  • [gmx-users] Inaccurate time frame   Hsin-Lin Chiang
• [gmx-users] conversion of gromacs files to amber files   leila karami
  • [gmx-users] conversion of gromacs files to amber files   Oliver Grant
  • [gmx-users] conversion of gromacs files to amber files   Francesco Oteri
• [gmx-users] Calculate ion disasociation constant   גדעון לפידות
  • [gmx-users] Calculate ion disasociation constant   Mark Abraham
• [gmx-users] QMMM, Segmentation fault   Olga Ivchenko
  • [gmx-users] Re: QMMM, Segmentation fault   Olga Ivchenko
• [gmx-users] Reg: Surface tension of water   vinothkumar mohanakrishnan
  • [gmx-users] Reg: Surface tension of water   André Farias de Moura
    • [gmx-users] Reg: Surface tension of water   vinothkumar mohanakrishnan
      • [gmx-users] Reg: Surface tension of water   André Farias de Moura
• [gmx-users] conversion of gromacs files to amber files   leila karami
  • [gmx-users] conversion of gromacs files to amber files   Shozeb Haider
  • [gmx-users] conversion of gromacs files to amber files   Oliver Grant
• [gmx-users] conversion of gromacs files to amber files   leila karami
  • [gmx-users] conversion of gromacs files to amber files   Oliver Grant
• [gmx-users] Re:6. QMMM, Segmentation fault (Olga Ivchenko)   Gerrit Groenhof
  • [gmx-users] Re:6. QMMM, Segmentation fault (Olga Ivchenko)   Olga Ivchenko
• [gmx-users] How to construct user specified bond potential   Jia Haitao
  • [gmx-users] How to construct user specified bond potential   Justin A. Lemkul
    • [gmx-users] How to construct user specified bond potential   Jia Haitao
      • [gmx-users] How to construct user specified bond potential   Justin A. Lemkul
      • [gmx-users] How to construct user specified bond potential   Jia Haitao
      • [gmx-users] How to construct user specified bond potential   Justin A. Lemkul
• [gmx-users] profile   Gavin Melaugh
• [gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?   J. Nathan Scott
  • [gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?   Mark Abraham
    • [gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?   J. Nathan Scott
• [gmx-users] Entropy by total atoms   nahren manuel
• [gmx-users] neutral plasma   Igor Marques
  • [gmx-users] neutral plasma   Mark Abraham
• [gmx-users] what is the "nicelevel" ?   GZ Zhang
  • [gmx-users] what is the "nicelevel" ?   Justin A. Lemkul
  • [gmx-users] what is the "nicelevel" ?   Linus Östberg
• [gmx-users] NVE simulation and pressure scaling in one dimension and constant size simulation in another.   zhongjin
  • [gmx-users] NVE simulation and pressure scaling in one dimension and constant size simulation in another.   Justin A. Lemkul
  • [gmx-users] NVE simulation and pressure scaling in one dimension and constant size simulation in another.   Mark Abraham
• [gmx-users] group temperatures and kinetic energies   Dmitri Dubov
  • [gmx-users] group temperatures and kinetic energies   Dmitri Dubov
• [gmx-users] Hard Spheres   Sascha Hempel
  • [gmx-users] Hard Spheres   Amit Choubey
• [gmx-users] -symm option   Morteza Khabiri
  • [gmx-users] -symm option   Amit Choubey
• [gmx-users] g_energy: Energy names magic number mismatch   Mikhail Stukan
  • [gmx-users] g_energy: Energy names magic number mismatch   Berk Hess
  • [gmx-users] g_energy: Energy names magic number mismatch   Justin A. Lemkul
• [gmx-users] Umberella sampling   mohsen ramezanpour
  • [gmx-users] Umberella sampling   Justin A. Lemkul
• [gmx-users] Can't build gromacs-4.5.3 with cmake   Keith Callenberg
  • [gmx-users] Can't build gromacs-4.5.3 with cmake   Roland Schulz
• [gmx-users] COM   mohsen ramezanpour
  • [gmx-users] COM   Justin A. Lemkul
• [gmx-users] g_principal   Carla Jamous
• [gmx-users] Can't build gromacs-4.5.3 with cmake   Keith Callenberg
  • [gmx-users] Can't build gromacs-4.5.3 with cmake   Justin A. Lemkul
    • [gmx-users] Can't build gromacs-4.5.3 with cmake   Keith Callenberg
• [gmx-users] Re: correlation function   David van der Spoel
• [gmx-users] Regarding parameters of octane box in ffamber99sb - ildn   YUVRAJ UBOVEJA
  • [gmx-users] Regarding parameters of octane box in ffamber99sb - ildn   Justin A. Lemkul
• [gmx-users] anaeig   pawan raghav
• [gmx-users] Re: Re:6. QMMM, Segmentation fault (Olga Ivchenko) (Olga Ivchenko)   Gerrit Groenhof
• [gmx-users] Hard Spheres   Sascha Hempel
  • [gmx-users] Hard Spheres   Berk Hess
    • [gmx-users] Hard Spheres   Sascha Hempel
      • [gmx-users] Hard Spheres   devicerandom
• [gmx-users] water-air interface surface tension   gromacs
  • [gmx-users] water-air interface surface tension   David van der Spoel
    • [gmx-users] water-air interface surface tension   vinothkumar mohanakrishnan
• [gmx-users] Can the g_order calculate order parameters for two polymer backbone atoms?   英雄不再寂寞
• [gmx-users] Pull simulation odditites when viewed in VMD   Natalie Stephenson
  • [gmx-users] Pull simulation odditites when viewed in VMD   Justin A. Lemkul
    • [gmx-users] Pull simulation odditites when viewed in VMD   Natalie Stephenson
• [gmx-users] crashed run   shiva birgani
  • [gmx-users] crashed run   Justin A. Lemkul
• [gmx-users] g_wham   Nilesh Dhumal
  • [gmx-users] g_wham   Justin A. Lemkul
• [gmx-users] -sel option for g_hbond   Olga Ivchenko
  • [gmx-users] -sel option for g_hbond   Justin A. Lemkul
• [gmx-users] How to force gromacs to fix all bad bonds and angles in a homology model?   Arthur Roberts
  • [gmx-users] How to force gromacs to fix all bad bonds and angles in a homology model?   Justin A. Lemkul
    • [gmx-users] How to force gromacs to fix all bad bonds and angles in a homology model?   Thomas Evangelidis
• [gmx-users] Re: gmx-users Digest, Vol 80, Issue 64   shiva birgani
• [gmx-users] How to obtain the semi-axis lengths from inertia tensor for an aggregate   sa
• [gmx-users] g_anaeig   pawan raghav
  • [gmx-users] g_anaeig   Justin A. Lemkul
• [gmx-users] CMAP error   Jon Mujika
  • [gmx-users] CMAP error   Justin A. Lemkul
    • [gmx-users] CMAP error   Amit Choubey
      • [gmx-users] CMAP error   Thomas Piggot
• [gmx-users] gb_saltconc in implicit water simulations   Bob Johnson
  • [gmx-users] Re: gb_saltconc in implicit water simulations   Bob Johnson
    • [gmx-users] Re: gb_saltconc in implicit water simulations   devicerandom
      • [gmx-users] Re: gb_saltconc in implicit water simulations   Justin A. Lemkul
      • [gmx-users] Re: gb_saltconc in implicit water simulations   devicerandom
      • [gmx-users] Re: gb_saltconc in implicit water simulations   Per Larsson
      • [gmx-users] Re: gb_saltconc in implicit water simulations   Rogan Carr
      • [gmx-users] Re: gb_saltconc in implicit water simulations   Per Larsson
• [gmx-users] What might be the process if we wanted to sim a peptide + a peptide?   swati shah
  • [gmx-users] What might be the process if we wanted to sim a peptide + a peptide?   Justin A. Lemkul
    • [gmx-users] What might be the process if we wanted to sim a peptide + a peptide?   swati shah
      • [gmx-users] What might be the process if we wanted to sim a peptide + a peptide?   Justin A. Lemkul
• [gmx-users] Seeking advice on how to build Gromacs on Teragrid resources   J. Nathan Scott
  • [gmx-users] Seeking advice on how to build Gromacs on Teragrid resources   Mark Abraham
    • [gmx-users] Seeking advice on how to build Gromacs on Teragrid resources   J. Nathan Scott
  • [gmx-users] Seeking advice on how to build Gromacs on Teragrid resources   Roland Schulz
• [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?   Liu Shiyong
  • [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?   Justin A. Lemkul
    • [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?   Liu Shiyong
    • [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?   Liu Shiyong
      • [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?   Liu Shiyong
    • [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?   Liu Shiyong
      • [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?   Justin A. Lemkul
• [gmx-users] Re: Which FF could be used for protein-RNA MD simulation in GROMACS?   Vitaly Chaban
  • [gmx-users] Re: Which FF could be used for protein-RNA MD simulation in GROMACS?   Justin A. Lemkul
• [gmx-users] g_anaeig   pawan raghav
  • [gmx-users] g_anaeig   Tsjerk Wassenaar
• [gmx-users] Trjcat append error   Rosanne Zeiler
• [gmx-users] Polyglycine simulation   YUVRAJ UBOVEJA
  • [gmx-users] Polyglycine simulation   Erik Marklund
• [gmx-users] CMAP error   Jon Mujika
  • [gmx-users] CMAP error   Justin A. Lemkul
• [gmx-users] g_protonate: Can't find ffgmx2 library files   Jon Kapla
  • [gmx-users] g_protonate: Can't find ffgmx2 library files   Sarath Chandra
    • [gmx-users] g_protonate: Can't find ffgmx2 library files   Jon Kapla
• [gmx-users] g_protonate: Can't find ffgmx2 library files   Jon Kapla
  • [gmx-users] g_protonate: Can't find ffgmx2 library files   Justin A. Lemkul
• [gmx-users] Invalid atom number 101717 in indexfile   Natalie Stephenson
  • [gmx-users] Invalid atom number 101717 in indexfile   Justin A. Lemkul
    • [gmx-users] Invalid atom number 101717 in indexfile   Natalie Stephenson
      • [gmx-users] Invalid atom number 101717 in indexfile   Justin A. Lemkul
      • [gmx-users] Invalid atom number 101717 in indexfile   Natalie Stephenson
• [gmx-users] Re: CMAP error   Pär Bjelkmar
• [gmx-users] Re:Re: Which FF could be used for protein-RNA MD simulation in GROMACS?   lloyd riggs
  • [gmx-users] Re:Re: Which FF could be used for protein-RNA MD simulation in GROMACS?   Thomas Piggot
• [gmx-users] Molecule redefined   Tanos Celmar Costa Franca
  • [gmx-users] Molecule redefined   Justin A. Lemkul
• [gmx-users] extending simulations made with version 3.3.3   Anna Marabotti
  • [gmx-users] extending simulations made with version 3.3.3   Mark Abraham
• [gmx-users] Reg; Surface tension of liquid-liquid interface   vinothkumar mohanakrishnan
• [gmx-users] Normal modes for certain group   Ольга Кононова
• [gmx-users] box length in z dimension keep increasing when using two walls in NPT ensemble   Jianguo Li
• [gmx-users] Extreme   pawan raghav
  • [gmx-users] Extreme   Justin A. Lemkul
• [gmx-users] Forces in source code   Петр Попов
  • [gmx-users] Forces in source code   David van der Spoel
    • [gmx-users] Forces in source code   Петр Попов
• [gmx-users] Forces in source code   Mark Abraham
  • [gmx-users] Forces in source code   Петр Попов
    • [gmx-users] Forces in source code   Berk Hess
• [gmx-users] -ve value of z in g_wham   Nilesh Dhumal
  • [gmx-users] -ve value of z in g_wham   Justin A. Lemkul
    • [gmx-users] -ve value of z in g_wham   Nilesh Dhumal
      • [gmx-users] -ve value of z in g_wham   Justin A. Lemkul
      • [gmx-users] -ve value of z in g_wham   Nilesh Dhumal
• [gmx-users] Binary lennard jones   leila separdar
  • [gmx-users] Binary lennard jones   Mark Abraham
    • [gmx-users] Binary lennard jones   leila separdar
      • [gmx-users] Binary lennard jones   Mark Abraham
• [gmx-users] Setting up e-mail notifications   boaz kan-tor
  • [gmx-users] Setting up e-mail notifications   Erik Marklund
• [gmx-users] g_energy: Energy names magic number mismatch   Mikhail Stukan
  • [gmx-users] g_energy: Energy names magic number mismatch   Justin A. Lemkul
• [gmx-users] Extreme   pawan raghav
  • [gmx-users] Extreme   Tsjerk Wassenaar
• [gmx-users] RMSF or RMSD per residues   shiva birgani
  • [gmx-users] RMSF or RMSD per residues   Justin A. Lemkul
• [gmx-users] Re: g_energy: Energy names magic number mismatch   Mikhail Stukan
  • [gmx-users] Re: g_energy: Energy names magic number mismatch   Justin A. Lemkul
• [gmx-users] perl script for g_hbond   Olga Ivchenko
  • [gmx-users] perl script for g_hbond   Justin A. Lemkul
• [gmx-users] HBOND probability   Poojari, Chetan
  • [gmx-users] HBOND probability   Justin A. Lemkul
    • [gmx-users] HBOND probability   Poojari, Chetan
      • [gmx-users] HBOND probability   Justin A. Lemkul
      • [gmx-users] HBOND probability   Poojari, Chetan
      • [gmx-users] HBOND probability   Justin A. Lemkul
      • [gmx-users] HBOND probability   Poojari, Chetan
      • [gmx-users] HBOND probability   Justin A. Lemkul
      • [gmx-users] HBOND probability   Poojari, Chetan
      • [gmx-users] HBOND probability   Justin A. Lemkul
• [gmx-users] [Fwd: g_sas for each residu]   Stephane Abel
  • [gmx-users] [Fwd: g_sas for each residu]   Justin A. Lemkul
    • [gmx-users] [Fwd: g_sas for each residu]   Austin B. Yongye
• [gmx-users] problem building Gromacs 4.5.3 using the Intel compiler   Miah Wadud Dr (ITCS)
• [gmx-users] [Fwd: g_sas for each residu]   Mark Abraham
• [gmx-users] problem building Gromacs 4.5.3 using the Intel compiler   Mark Abraham
  • [gmx-users] problem building Gromacs 4.5.3 using the Intel compiler   Carsten Kutzner
  • [gmx-users] problem building Gromacs 4.5.3 using the Intel compiler   Miah Wadud Dr (ITCS)
• [gmx-users] Question about COM-Pulling   Christian Mücksch
• [gmx-users] Not have PDB file of peptide   swati shah
  • [gmx-users] Not have PDB file of peptide   Justin A. Lemkul
• [gmx-users] ERROR: Source code file: statutil.c, line: 727   udaya kiran
  • [gmx-users] ERROR: Source code file: statutil.c, line: 727   Justin A. Lemkul
  • [gmx-users] ERROR: Source code file: statutil.c, line: 727   sharada
• [gmx-users] tpbconv extension   ram bio
  • [gmx-users] Re: tpbconv extension   ram bio
    • [gmx-users] Re: tpbconv extension   Justin A. Lemkul
      • [gmx-users] Re: tpbconv extension   ram bio
      • [gmx-users] Re: tpbconv extension   Justin A. Lemkul
      • [gmx-users] Re: tpbconv extension   Berk Hess
      • [gmx-users] Re: tpbconv extension   Berk Hess
      • [gmx-users] Re: tpbconv extension   ram bio
      • [gmx-users] Re: tpbconv extension   Berk Hess
      • [gmx-users] Re: tpbconv extension   ram bio
      • [gmx-users] Re: tpbconv extension   Berk Hess
• [gmx-users] Question about COM-Pulling   chris.neale at utoronto.ca
• [gmx-users] Question about COM-Pulling   Christian Mücksch
• [gmx-users] Question about COM-Pulling   chris.neale at utoronto.ca
• [gmx-users] Re: gmx-users Digest, Vol 80, Issue 88   Thomas Schlesier
• [gmx-users] Question about COM-Pulling   Christian Mücksch
• [gmx-users] Re: gmx-users Digest, Vol 80, Issue 90   Chris Neale
• [gmx-users] Question about COM-Pulling   Christian Mücksch
• [gmx-users] mpi run in Gromacs 4.5.3   Te, Jerez A., Ph.D.
  • [gmx-users] mpi run in Gromacs 4.5.3   Mark Abraham
    • [gmx-users] mpi run in Gromacs 4.5.3   Te, Jerez A., Ph.D.
      • [gmx-users] mpi run in Gromacs 4.5.3   Justin A. Lemkul
      • [gmx-users] mpi run in Gromacs 4.5.3   Te, Jerez A., Ph.D.
      • [gmx-users] mpi run in Gromacs 4.5.3   Mark Abraham
• [gmx-users] Question about COM-Pulling   Chris Neale
• [gmx-users] pathologically expanding box   Greg Bowman
  • [gmx-users] pathologically expanding box   Justin A. Lemkul
    • [gmx-users] pathologically expanding box   Berk Hess
• [gmx-users] Question about COM-Pulling   Christian Mücksch
• [gmx-users] Re: pathologically expanding box   Vitaly Chaban
• [gmx-users] md.log   Ramachandran G
  • [gmx-users] md.log   Justin A. Lemkul
  • [gmx-users] md.log   Itamar Kass
    • [gmx-users] md.log   Ramachandran G
    • [gmx-users] md.log   Ramachandran G
      • [gmx-users] md.log   Mark Abraham
• [gmx-users] Coarse-grained simulation with MARTINI   samio
  • [gmx-users] Coarse-grained simulation with MARTINI   XAvier Periole
• [gmx-users] free energy calculation problem   Jin Wen
• [gmx-users] Terminal_ARG_residue causing problem in pdb2gmx   shahid nayeem
  • [gmx-users] Terminal_ARG_residue causing problem in pdb2gmx   Mark Abraham
• [gmx-users] what do you do?   mohsen ramezanpour
• [gmx-users] Umberella sampling   mohsen ramezanpour
• [gmx-users] g-WHAM   mohsen ramezanpour
  • [gmx-users] g-WHAM   Carsten Kutzner
• [gmx-users] gmx-4.5.3 CMake build fails   Reinhold Bader
  • [gmx-users] gmx-4.5.3 CMake build fails   Mark Abraham
• [gmx-users] ERROR: Source code file: statutil.c, line: 727   udaya kiran
  • [gmx-users] ERROR: Source code file: statutil.c, line: 727   Sarath Chandra
    • [gmx-users] ERROR: Source code file: statutil.c, line: 727   udaya kiran
      • [gmx-users] ERROR: Source code file: statutil.c, line: 727   Sarath Chandra
      • [gmx-users] ERROR: Source code file: statutil.c, line: 727   T.M.D. Graen
      • [gmx-users] ERROR: Source code file: statutil.c, line: 727   sharada
• [gmx-users] How to define Center of Mass velocity of a specific group   Tomy van Batis
  • [gmx-users] How to define Center of Mass velocity of a specific group   Justin A. Lemkul
    • [gmx-users] How to define Center of Mass velocity of a specific group   Tomy van Batis
      • [gmx-users] How to define Center of Mass velocity of a specific group   Justin A. Lemkul
• [gmx-users] Umberella sampling   chris.neale at utoronto.ca
• [gmx-users] "freezegrps" concept   YUVRAJ UBOVEJA
  • [gmx-users] "freezegrps" concept   Justin A. Lemkul
  • [gmx-users] "freezegrps" concept   Sarath Chandra Dantu
• [gmx-users] HPC mpi how to run   gromacs
  • [gmx-users] HPC mpi how to run   Justin A. Lemkul
  • [gmx-users] HPC mpi how to run   Shi Wenxiong (Dr)
• [gmx-users] Appropriate (desktop) hardware for Gromacs   Tom Dupree
  • [gmx-users] Appropriate (desktop) hardware for Gromacs   Mark Abraham
• [gmx-users] NaN error using mdrun-gpu   Bongkeun Kim
• Antw: [gmx-users] NaN error using mdrun-gpu   Emanuel Peter
  • Antw: [gmx-users] NaN error using mdrun-gpu   Bongkeun Kim
    • Antw: [gmx-users] NaN error using mdrun-gpu   Justin A. Lemkul
    • Antw: [gmx-users] NaN error using mdrun-gpu   Szilárd Páll
      • Antw: [gmx-users] NaN error using mdrun-gpu   Bongkeun Kim
      • Antw: [gmx-users] NaN error using mdrun-gpu   Szilárd Páll
• Antw: Re: Antw: [gmx-users] NaN error using mdrun-gpu   Emanuel Peter
• [gmx-users] Question about Extention simulation in REMD   Qin Qiao
  • [gmx-users] Question about Extention simulation in REMD   Justin A. Lemkul
    • [gmx-users] Question about Extention simulation in REMD   Qin Qiao
• [gmx-users] g_rotacf NH vector relaxation   Olga Ivchenko
• [gmx-users] pullx.xvg / pullf.xvg   Poojari, Chetan
• [gmx-users] RE: Log files   Nimesh Jain
  • [gmx-users] RE: Log files   Justin A. Lemkul
  • [gmx-users] RE: Log files   Javier Cerezo
• [gmx-users] Re: Com Pulling   lloyd riggs
• [gmx-users] pullx.xvg / pullf.xvg   chris.neale at utoronto.ca
  • [gmx-users] pullx.xvg / pullf.xvg   Poojari, Chetan
    • [gmx-users] pullx.xvg / pullf.xvg   Carsten Kutzner
      • [gmx-users] pullx.xvg / pullf.xvg   Poojari, Chetan
• [gmx-users] Com Pulling   chris.neale at utoronto.ca
• [gmx-users] Re: RE:Com Pulling   lloyd riggs
• [gmx-users] Com Pulling   chris.neale at utoronto.ca
• [gmx-users] NMA   Yao Yao
  • [gmx-users] NMA   Justin A. Lemkul
• [gmx-users] different output generated by continue and discontinue simulation   Hsin-Lin Chiang
• [gmx-users] different output generated by continue and discontinue simulation   Hsin-Lin Chiang
  • [gmx-users] different output generated by continue and discontinue simulation   Hsin-Lin Chiang
• [gmx-users] water genbox 3x3x0.8 EM not successful T not high   gromacs
  • [gmx-users] water genbox 3x3x0.8 EM not successful T not high   Javier Cerezo
• [gmx-users] different output generated by continue and discontinue simulation   Mark Abraham
• [gmx-users] water genbox 3x3x0.8 EM not successful T not high   Mark Abraham
• [gmx-users] different output generated by continue and discontinue > simulation   Hsin-Lin Chiang
  • [gmx-users] different output generated by continue and discontinue > simulation   Justin A. Lemkul
• [gmx-users] Brownian Dynamics Simulations generating huge log files   Nimesh Jain
  • [gmx-users] Brownian Dynamics Simulations generating huge log files   Justin A. Lemkul
    • [gmx-users] Brownian Dynamics Simulations generating huge log files   Nimesh Jain
      • [gmx-users] Brownian Dynamics Simulations generating huge log files   Justin A. Lemkul
• [gmx-users] Simulated Annealing parameters   Ehud Schreiber
  • [gmx-users] Simulated Annealing parameters   Mark Abraham
• [gmx-users] Re: water genbox 3x3x0.8 EM not successful T not high   Vitaly Chaban
• [gmx-users] g_bundle question   Rebeca García Fandiño
  • [gmx-users] g_bundle question   Justin A. Lemkul
    • [gmx-users] g_bundle question   Rebeca García Fandiño
      • [gmx-users] g_bundle question   Justin A. Lemkul
      • [gmx-users] g_bundle question   Rebeca García Fandiño
• [gmx-users] tpr-files.dat and pullf-files.dat   Poojari, Chetan
  • [gmx-users] tpr-files.dat and pullf-files.dat   Justin A. Lemkul
    • [gmx-users] tpr-files.dat and pullf-files.dat   Poojari, Chetan
      • [gmx-users] tpr-files.dat and pullf-files.dat   Justin A. Lemkul
• [gmx-users] Brownian Dynamics Simulations generating huge log files   Justin A. Lemkul
• [gmx-users] water genbox 3x3x0.8 EM not successful T too high   gromacs
• [gmx-users] RE: pathologically expanding box   Greg Bowman
• [gmx-users] water genbox 3x3x0.8 EM not successful T too high   Dallas Warren
• [gmx-users] Re: water genbox 3x3x0.8 EM not successful T not high   Vitaly Chaban
  • [gmx-users] Re:Re: water genbox 3x3x0.8 EM not successful T not high   gromacs
    • [gmx-users] Re: Re: water genbox 3x3x0.8 EM not successful T not high   Vitaly Chaban
      • [gmx-users] Re:Re: Re: water genbox 3x3x0.8 EM not successful T not high   gromacs
      • [gmx-users] Re: Re: Re: water genbox 3x3x0.8 EM not successful T not high   Vitaly Chaban
      • [gmx-users] Re: Re: Re: water genbox 3x3x0.8 EM not successful T not high   Vitaly Chaban
• [gmx-users] water genbox 3x3x0.8 EM not successful T not high   gromacs
• [gmx-users] Re:Re: Re: water genbox 3x3x0.8 EM not successful T not high   Mark Abraham
• [gmx-users] Re:Re: Re: water genbox 3x3x0.8 EM not successful T not high   Mark Abraham
• [gmx-users] Question about Extention simulation in REMD   Mark Abraham
  • [gmx-users] Question about Extention simulation in REMD   Qin Qiao
• [gmx-users] multiple dihedrals   Jarmila Husby
  • [gmx-users] multiple dihedrals   Mark Abraham
• [gmx-users] Segmentation fault in g_hbond   leila karami
• [gmx-users] Segmentation fault in g_hbond   leila karami
  • [gmx-users] Segmentation fault in g_hbond   Erik Marklund
• [gmx-users] Segmentation fault in g_hbond   leila karami
  • [gmx-users] Segmentation fault in g_hbond   Erik Marklund
    • [gmx-users] Segmentation fault in g_hbond   Erik Marklund
• [gmx-users] Segmentation fault in g_hbond   leila karami
  • [gmx-users] Segmentation fault in g_hbond   Erik Marklund
    • [gmx-users] Segmentation fault in g_hbond   Erik Marklund
• [gmx-users] Segmentation fault in g_hbond   leila karami
  • [gmx-users] Segmentation fault in g_hbond   Erik Marklund
    • [gmx-users] Segmentation fault in g_hbond   Erik Marklund
      • [gmx-users] Segmentation fault in g_hbond   Erik Marklund
• [gmx-users] Segmentation fault in g_hbond   leila karami
  • [gmx-users] Segmentation fault in g_hbond   Erik Marklund
    • [gmx-users] Segmentation fault in g_hbond   Erik Marklund
    • [gmx-users] Segmentation fault in g_hbond   Justin A. Lemkul
• [gmx-users] Is there an easy way to increase the energy of bonds, angles, etc?   Arthur Roberts
  • [gmx-users] Is there an easy way to increase the energy of bonds, angles, etc?   Justin A. Lemkul
• [gmx-users] .psf and .dcd files   atila petrosian
  • [gmx-users] .psf and .dcd files   Ran Friedman
• [gmx-users] .psf and .dcd files   atila petrosian
  • [gmx-users] .psf and .dcd files   Ran Friedman
• [gmx-users] RE: multiple dihedrals   Jarmila Husby
  • [gmx-users] RE: multiple dihedrals   Mark Abraham
• [gmx-users] umberella sampling   mohsen ramezanpour
  • [gmx-users] umberella sampling   Justin A. Lemkul
• [gmx-users] water models add polarization, water film   gromacs
  • [gmx-users] water models add polarization, water film   Justin A. Lemkul
• [gmx-users] Re: water models add polarization, water film   Vitaly Chaban
• [gmx-users] (no subject)   Katerina Hynstova
• [gmx-users] reagarding polarisable force field in gromacs   sreelakshmi ramesh
  • [gmx-users] reagarding polarisable force field in gromacs   Justin A. Lemkul
    • [gmx-users] reagarding polarisable force field in gromacs   sreelakshmi ramesh
      • [gmx-users] reagarding polarisable force field in gromacs   Justin A. Lemkul
      • [gmx-users] reagarding polarisable force field in gromacs   sreelakshmi ramesh
      • [gmx-users] reagarding polarisable force field in gromacs   Justin A. Lemkul
      • [gmx-users] reagarding polarisable force field in gromacs   Mark Abraham
• [gmx-users] reagarding polarisable force field in gromacs   Dallas Warren
• [gmx-users] Reg: fatal error pdb2gmx   vinothkumar mohanakrishnan
  • [gmx-users] Reg: fatal error pdb2gmx   Justin A. Lemkul
    • [gmx-users] Reg: fatal error pdb2gmx   vinothkumar mohanakrishnan
      • [gmx-users] Reg: fatal error pdb2gmx   Justin A. Lemkul
      • [gmx-users] Reg: fatal error pdb2gmx   vinothkumar mohanakrishnan
  • [gmx-users] Reg: fatal error pdb2gmx   Mark Abraham
• [gmx-users] search for help   松啸天
• [gmx-users] how to add a electric field to the water box when do a simulation   松啸天
  • [gmx-users] how to add a electric field to the water box when do a simulation   Carsten Kutzner
• [gmx-users] Reg: Dihedral conversion from fourier to RB form   vinothkumar mohanakrishnan
• [gmx-users] how to add a electric field to the water box when do a simulation   Daniel P. Luis J.
  • [gmx-users] how to add a electric field to the water box when do a simulation   Mark Abraham
• [gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC   Chris Neale
  • [gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC   Roland Schulz
• [gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object;   chris.neale at utoronto.ca
  • [gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object;   Roland Schulz
• [gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites   chris.neale at utoronto.ca
  • [gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites   Roland Schulz
• [gmx-users] Question regarding g_rdf   rainy908 at yahoo.com
  • [gmx-users] Question regarding g_rdf   Justin A. Lemkul
• [gmx-users] reagrding huggins meyer potential   sreelakshmi ramesh
  • [gmx-users] reagrding huggins meyer potential   Justin A. Lemkul
• [gmx-users] free energy of methan disappearing:tutorial   mohsen ramezanpour
  • [gmx-users] free energy of methan disappearing:tutorial   TJ Mustard
    • [gmx-users] free energy of methan disappearing:tutorial   mohsen ramezanpour
      • [gmx-users] Speed up my jobs with PME and grid spacing?   TJ Mustard
      • [gmx-users] Speed up my jobs with PME and grid spacing?   Justin A. Lemkul
      • [gmx-users] Speed up my jobs with PME and grid spacing?   Mark Abraham
      • [gmx-users] Speed up my jobs with PME and grid spacing?   Florian Dommert
      • [gmx-users] Speed up my jobs with PME and grid spacing?   Mark Abraham
• [gmx-users] buckingham potentials   sreelakshmi ramesh
  • [gmx-users] buckingham potentials   Justin A. Lemkul
    • [gmx-users] buckingham potentials   sreelakshmi ramesh
      • [gmx-users] buckingham potentials   Justin A. Lemkul
      • [gmx-users] buckingham potentials   sreelakshmi ramesh
      • [gmx-users] buckingham potentials   Justin A. Lemkul
      • [gmx-users] buckingham potentials   sreelakshmi ramesh
      • [gmx-users] buckingham potentials   Justin A. Lemkul
      • [gmx-users] buckingham potentials   Justin A. Lemkul
      • [gmx-users] buckingham potentials   sreelakshmi ramesh
      • [gmx-users] buckingham potentials   Justin A. Lemkul
      • [gmx-users] buckingham potentials   sreelakshmi ramesh
      • [gmx-users] buckingham potentials   Justin A. Lemkul
      • [gmx-users] buckingham potentials   sreelakshmi ramesh
      • [gmx-users] buckingham potentials   Justin A. Lemkul
      • [gmx-users] buckingham potentials   sreelakshmi ramesh
      • [gmx-users] buckingham potentials   delara aghaie
      • [gmx-users] location of aminoacids.dat   Justin A. Lemkul
      • [gmx-users] location of aminoacids.dat   delara aghaie
      • [gmx-users] location of aminoacids.dat   Mark Abraham
• [gmx-users] Nose-hoover T-coupling nsttcouple   Qin Qiao
• [gmx-users] g-dist   mohsen ramezanpour
  • [gmx-users] g-dist   Justin A. Lemkul
    • [gmx-users] g-dist   mohsen ramezanpour
      • [gmx-users] g-dist   Justin A. Lemkul
      • [gmx-users] g-dist   mohsen ramezanpour
      • [gmx-users] g-dist   Justin A. Lemkul
      • [gmx-users] g-dist   mohsen ramezanpour
      • [gmx-users] g-dist   Justin A. Lemkul
• [gmx-users] fac value for distance or h-bonding restraints   udaya kiran
  • [gmx-users] fac value for distance or h-bonding restraints   Justin A. Lemkul
• [gmx-users] Umbrella sampling   Nilesh Dhumal
  • [gmx-users] Umbrella sampling   Justin A. Lemkul
• [gmx-users] Re:Crash error   lloyd riggs
  • [gmx-users] Re:Crash error   Justin A. Lemkul
• [gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites   chris.neale at utoronto.ca
  • [gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites   Justin A. Lemkul
    • [gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites   Rossen Apostolov
• [gmx-users] Nose-hoover T-coupling in REMD   Qin Qiao
  • [gmx-users] Nose-hoover T-coupling in REMD   Mark Abraham
    • [gmx-users] Nose-hoover T-coupling in REMD   David van der Spoel
      • [gmx-users] Nose-hoover T-coupling in REMD   ms
      • [gmx-users] Nose-hoover T-coupling in REMD   David van der Spoel
      • [gmx-users] Nose-hoover T-coupling in REMD   ms
      • [gmx-users] Nose-hoover T-coupling in REMD   David van der Spoel
      • [gmx-users] Nose-hoover T-coupling in REMD   Qin Qiao
      • [gmx-users] Nose-hoover T-coupling in REMD   ms
      • [gmx-users] Nose-hoover T-coupling in REMD   Qin Qiao
      • [gmx-users] Nose-hoover T-coupling in REMD   ms
      • [gmx-users] Nose-hoover T-coupling in REMD   Mark Abraham
• [gmx-users] Re:RE:Crash error   lloyd riggs
• [gmx-users] adding Na and cl ions to pdb structure   mohsen ramezanpour
  • [gmx-users] adding Na and cl ions to pdb structure   Justin A. Lemkul
  • [gmx-users] adding Na and cl ions to pdb structure   TJ Mustard
• [gmx-users] simulation of membrane protein   shikha agarwal
• [gmx-users] simulation of membrane protein   shikha agarwal
  • [gmx-users] simulation of membrane protein   Sarath Chandra Dantu
• [gmx-users] simulation of membrane protein   shikha agarwal
  • [gmx-users] simulation of membrane protein   Justin A. Lemkul
• [gmx-users] stopping mdrun without error massage   Mahnam
  • [gmx-users] stopping mdrun without error massage   Carsten Kutzner
• [gmx-users] center the protein to the origin   Asmaa Elsheshiny
  • [gmx-users] center the protein to the origin   Justin A. Lemkul
• [gmx-users] atom type errer   mohsen ramezanpour
  • [gmx-users] atom type errer   Justin A. Lemkul
• [gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites   chris.neale at utoronto.ca
• [gmx-users] "Atomtype OW not found"   shikha agarwal
  • [gmx-users] "Atomtype OW not found"   Justin A. Lemkul
    • [gmx-users] "Atomtype OW not found"   Justin A. Lemkul
• [gmx-users] deciphering the output of g_helixorient ?   maria goranovic
• [gmx-users] Silly question?   Sergio Manzetti
  • [gmx-users] Silly question?   Justin A. Lemkul
    • [gmx-users] Silly question?   Sergio Manzetti
      • [gmx-users] Silly question?   Justin A. Lemkul
• [gmx-users] Silly question?   chris.neale at utoronto.ca
• [gmx-users] interfacial water molecules   chris.neale at utoronto.ca
• [gmx-users] PME or Reaction field suitable for Gromos forcefield ?   Sanku M
  • [gmx-users] PME or Reaction field suitable for Gromos forcefield ?   David van der Spoel
    • [gmx-users] PME or Reaction field suitable for Gromos forcefield ?   Sanku M
      • [gmx-users] PME or Reaction field suitable for Gromos forcefield ?   David van der Spoel
• [gmx-users] How to count the number of waters in the first hydration shell of a macromolecule   chris.neale at utoronto.ca
• [gmx-users] Unknown bond_atomtype MNH3   shikha agarwal
  • [gmx-users] Unknown bond_atomtype MNH3   Justin A. Lemkul
• [gmx-users] amber convert gromacs input files   gromacs564
  • [gmx-users] amber convert gromacs input files   Mark Abraham
  • [gmx-users] amber convert gromacs input files   Alan Wilter Sousa da Silva
    • [gmx-users] amber convert gromacs input files   Oliver Grant
      • [gmx-users] amber convert gromacs input files   Alan Wilter Sousa da Silva
• [gmx-users] HPC mpi how to run batch system   gromacs
  • [gmx-users] HPC mpi how to run batch system   Mark Abraham
• [gmx-users] Illegal division by zero at inflategro   shikha agarwal
  • [gmx-users] Illegal division by zero at inflategro   NG HUI WEN
• [gmx-users] Installation GROMACS UBUNTU   Sergio Manzetti
  • [gmx-users] Installation GROMACS UBUNTU   Rodrigo Faccioli
  • [gmx-users] Installation GROMACS UBUNTU   Mark Abraham
    • [gmx-users] Installation GROMACS UBUNTU   Sergio Manzetti
      • [gmx-users] Installation GROMACS UBUNTU   Terry
      • [gmx-users] Installation GROMACS UBUNTU   Mark Abraham
      • [gmx-users] Installation GROMACS UBUNTU   Sergio Manzetti
      • [gmx-users] Installation GROMACS UBUNTU   Justin A. Lemkul
      • [gmx-users] Installation GROMACS UBUNTU   Sergio Manzetti
      • [gmx-users] Installation GROMACS UBUNTU   Justin A. Lemkul
      • [gmx-users] Installation GROMACS UBUNTU   Sergio Manzetti
      • [gmx-users] Installation GROMACS UBUNTU   Justin A. Lemkul
      • [gmx-users] Installation GROMACS UBUNTU   Sergio Manzetti
      • [gmx-users] Installation GROMACS UBUNTU   Sergio Manzetti
      • [gmx-users] Installation GROMACS UBUNTU   Sergio Manzetti
      • [gmx-users] Installation GROMACS UBUNTU   Justin A. Lemkul
      • [gmx-users] Installation GROMACS UBUNTU   Sergio Manzetti
• [gmx-users] mdrun mpi segmentation fault in high load situation   Wojtyczka, André
  • [gmx-users] mdrun mpi segmentation fault in high load situation   Mark Abraham
    • AW: [gmx-users] mdrun mpi segmentation fault in high load situation   Wojtyczka, André
      • AW: [gmx-users] mdrun mpi segmentation fault in high load situation   Mark Abraham
      • AW: [gmx-users] mdrun mpi segmentation fault in high load situation   Mark Abraham
• [gmx-users] 25th Molecular Modelling Workshop 2011 Announcement   Tatyana Shubina
• [gmx-users] Re: "moleculetype DRG is redefined"   Justin A. Lemkul
• [gmx-users] Fatal error (g_polystat)   Chandan Choudhury
  • [gmx-users] Fatal error (g_polystat)   Mark Abraham
    • [gmx-users] Fatal error (g_polystat)   Chandan Choudhury
• [gmx-users] Optimization of the box size during an energy minimization?   MyLinkka
  • [gmx-users] Optimization of the box size during an energy minimization?   Mark Abraham
    • [gmx-users] Optimization of the box size during an energy minimization?   Terry
      • [gmx-users] Optimization of the box size during an energy minimization?   MyLinkka
      • [gmx-users] Optimization of the box size during an energy minimization?   Justin A. Lemkul
      • [gmx-users] Optimization of the box size during an energy minimization?   MyLinkka
      • [gmx-users] Optimization of the box size during an energy minimization?   Justin A. Lemkul
      • [gmx-users] Optimization of the box size during an energy minimization?   MyLinkka
    • [gmx-users] Optimization of the box size during an energy minimization?   MyLinkka
  • [gmx-users] Optimization of the box size during an energy minimization?   Jussi Lehtola
• [gmx-users] Grompp error message   Sergio Manzetti
  • [gmx-users] Grompp error message   Mark Abraham
• [gmx-users] box size & continuing the previous energy minimization   mustafa bilsel
  • [gmx-users] box size & continuing the previous energy minimization   Amit Choubey
    • [gmx-users] box size & continuing the previous energy minimization   Terry
• [gmx-users] RE: "moleculetype DRG is redefined"   Vitaly Chaban
• [gmx-users] dssp problem   mustafa bilsel
  • [gmx-users] dssp problem   Terry
• [gmx-users] dssp   mustafa bilsel
  • [gmx-users] dssp   Justin A. Lemkul
• [gmx-users] reading tpx file version 73 with version 58 program   shikha agarwal
  • [gmx-users] reading tpx file version 73 with version 58 program   maria goranovic
  • [gmx-users] reading tpx file version 73 with version 58 program   Mark Abraham
• [gmx-users] Updating Ubuntu   Sergio Manzetti
  • [gmx-users] Updating Ubuntu   Mark Abraham
• [gmx-users] Reg: Simulating large number of molecules   vinothkumar mohanakrishnan
  • [gmx-users] Reg: Simulating large number of molecules   David van der Spoel
  • [gmx-users] Reg: Simulating large number of molecules   Mark Abraham
• [gmx-users] mdrun mpi segmentation fault in high load situation   Wojtyczka, André
  • [gmx-users] mdrun mpi segmentation fault in high load situation   Mark Abraham
• [gmx-users] nve simulation   sreelakshmi ramesh
• [gmx-users] simulation at constant temprature   sreelakshmi ramesh
  • [gmx-users] simulation at constant temprature   Jussi Lehtola
• [gmx-users] number of coordinates in coordinate file does not match topology   shikha agarwal
  • [gmx-users] number of coordinates in coordinate file does not match topology   Justin A. Lemkul
• [gmx-users] velocity rescaling   sreelakshmi ramesh
  • [gmx-users] velocity rescaling   Justin A. Lemkul
• [gmx-users] minimization   mustafa bilsel
  • [gmx-users] minimization   Justin A. Lemkul
• [gmx-users] minimization   mustafa bilsel
  • [gmx-users] minimization   Justin A. Lemkul
• [gmx-users] generate .top file   shikha agarwal
  • [gmx-users] generate .top file   Mark Abraham
    • [gmx-users] generate .top file   Justin A. Lemkul
• [gmx-users] pulling   mohsen ramezanpour
  • [gmx-users] Fwd: pulling   mohsen ramezanpour
• [gmx-users] Re:gmx-users Digest, Vol 80, Issue 164   gromacs564
• [gmx-users] dssp problem   mustafa bilsel
  • [gmx-users] dssp problem   Mark Abraham
    • [gmx-users] dssp problem   lina zhao
• [gmx-users] How can I ...?   mohsen ramezanpour
  • [gmx-users] How can I ...?   Mark Abraham
• [gmx-users] Fwd: Help regarding Membrane simulation   Mark Abraham
• [gmx-users] g-dist   mohsen ramezanpour
  • [gmx-users] Fwd: g-dist   mohsen ramezanpour
  • [gmx-users] g-dist   Tsjerk Wassenaar
• [gmx-users] Replicating an experiment   NG HUI WEN
  • [gmx-users] Replicating an experiment   David van der Spoel
    • [gmx-users] Replicating an experiment   NG HUI WEN
      • [gmx-users] Replicating an experiment   David van der Spoel
      • [gmx-users] Replicating an experiment   NG HUI WEN
      • [gmx-users] Replicating an experiment   Mark Abraham
      • [gmx-users] Replicating an experiment   NG HUI WEN
• [gmx-users] amb2gmx.pl file   gromacs564
  • [gmx-users] amb2gmx.pl file   Oliver Grant
• [gmx-users] average pressure too high   sreelakshmi ramesh
  • [gmx-users] average pressure too high   Roland Schulz
• [gmx-users] No such moleculetype NA+   shikha agarwal
  • [gmx-users] No such moleculetype NA+   John Wesly . J
• [gmx-users] No such moleculetype NA+   YUVRAJ UBOVEJA
• [gmx-users] topolbuild1_3 install problem   gromacs564
• [gmx-users] topolbuild1_3 install problem   gromacs564
  • [gmx-users] topolbuild1_3 install problem   Mark Abraham
  • [gmx-users] topolbuild1_3 install problem   Bruce D. Ray
• [gmx-users] Re: average pressure too high   Vitaly Chaban
• [gmx-users] number of DD cells   Poojari, Chetan
  • [gmx-users] number of DD cells   Mark Abraham
    • [gmx-users] number of DD cells   Poojari, Chetan
      • [gmx-users] number of DD cells   Justin A. Lemkul
• [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group   WU Yanbin
  • [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group   Mark Abraham
• [gmx-users] number of DD cells   Poojari, Chetan
• [gmx-users] umbrella sampling   Poojari, Chetan
  • [gmx-users] umbrella sampling   Justin A. Lemkul
• [gmx-users] topolbuild1_3 install problem   gromacs564
  • [gmx-users] topolbuild1_3 install problem   Bruce D. Ray
• [gmx-users] Energy due to Hydrogen bonds   Anirban Ghosh
  • [gmx-users] Energy due to Hydrogen bonds   Justin A. Lemkul
• [gmx-users] Potential Energy = -nan   shikha agarwal
  • [gmx-users] Potential Energy = -nan   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 76, Issue 59   farideh zergani
• [gmx-users] Fwd: pulling   chris.neale at utoronto.ca
• [gmx-users] glycam force field problem   gromacs564
  • [gmx-users] glycam force field problem   Oliver Grant
• [gmx-users] coarse grainig with Martini ff???   Faezeh Kargar
  • [gmx-users] coarse grainig with Martini ff???   Justin A. Lemkul
    • [gmx-users] coarse grainig with Martini ff???   Faezeh Kargar
      • [gmx-users] coarse grainig with Martini ff???   Justin A. Lemkul
• [gmx-users] Potential Energy = -nan   shikha agarwal
  • [gmx-users] Potential Energy = -nan   Justin A. Lemkul
• [gmx-users] MPIRUN on Ubontu   גדעון לפידות
  • [gmx-users] MPIRUN on Ubontu   Justin A. Lemkul
    • [gmx-users] MPIRUN on Ubontu   Linus Östberg
  • [gmx-users] MPIRUN on Ubontu   Hassan Shallal
• [gmx-users] Potential Energy = -nan   shikha agarwal
• [gmx-users] g_lie query   Anirban Ghosh
  • [gmx-users] g_lie query   Justin A. Lemkul
    • [gmx-users] g_lie query   Anirban Ghosh
      • [gmx-users] g_lie query   Justin A. Lemkul
      • [gmx-users] g_lie query   Anirban Ghosh
      • [gmx-users] g_lie query   Justin A. Lemkul
      • [gmx-users] g_lie query   Anirban Ghosh
      • [gmx-users] g_lie query   Anirban Ghosh
      • [gmx-users] g_lie query   Justin A. Lemkul
      • [gmx-users] g_lie query   Anirban Ghosh
      • [gmx-users] g_lie query   Justin A. Lemkul
• [gmx-users] Potential Energy = -nan   shikha agarwal
  • [gmx-users] Potential Energy = -nan   Justin A. Lemkul
• [gmx-users] Potential Energy = -nan   shikha agarwal
  • [gmx-users] Potential Energy = -nan   Justin A. Lemkul
• [gmx-users] minimization   mustafa bilsel
  • [gmx-users] minimization   Justin A. Lemkul
• [gmx-users] MD simulation at 318K   swagata chakraborty
  • [gmx-users] MD simulation at 318K   Shi Wenxiong (Dr)
• [gmx-users] Re:Energy dur to Hydrogen Bonds   lloyd riggs
  • [gmx-users] Re:Energy dur to Hydrogen Bonds   Justin A. Lemkul
• [gmx-users] Energy minimisation query   nikhil damle
  • [gmx-users] Energy minimisation query   Justin A. Lemkul
    • [gmx-users] making maxwarn a hidden option   Mark Abraham
• [gmx-users] Energy minimization query   nikhil damle
  • [gmx-users] Energy minimization query   TJ Mustard
  • [gmx-users] Allitle stumped about FEP, and my setup for calculating energies...   TJ Mustard
• [gmx-users] work calculation   Aswathy
• [gmx-users] Fatal error:Chain identifier   ahmet yıldırım
  • [gmx-users] Fatal error:Chain identifier   Mark Abraham
    • [gmx-users] Fatal error:Chain identifier   ahmet yıldırım
      • [gmx-users] Fatal error:Chain identifier   Justin A. Lemkul
      • [gmx-users] Fatal error:Chain identifier   ahmet yıldırım
      • [gmx-users] Fatal error:Chain identifier   Justin A. Lemkul
      • [gmx-users] Fatal error:Chain identifier   ahmet yıldırım
      • [gmx-users] Fatal error:Chain identifier   Justin A. Lemkul
      • [gmx-users] Fatal error:Chain identifier   ahmet yıldırım
      • [gmx-users] Fatal error:Chain identifier   Justin A. Lemkul
      • [gmx-users] Fatal error:Chain identifier   ahmet yıldırım
      • [gmx-users] Fatal error:Chain identifier   Mark Abraham
• [gmx-users] force field for simulation of BCN   mina Madah
  • [gmx-users] force field for simulation of BCN   Mark Abraham
• [gmx-users] adequate program for simulation of BCN graphen ?   mina Madah
  • [gmx-users] adequate program for simulation of BCN graphen ?   Justin A. Lemkul
• [gmx-users] Remove COM of a group or of the whole system   Xiaohua Zhang
• [gmx-users] making maxwarn a hidden option   chris.neale at utoronto.ca
  • [gmx-users] making maxwarn a hidden option   Justin A. Lemkul
    • [gmx-users] making maxwarn a hidden option   Mark Abraham
• [gmx-users] work calculation   chris.neale at utoronto.ca
• [gmx-users] -ve value of z in g_wham   Justin A. Lemkul
• [gmx-users] -ve value of z in g_wham   Justin A. Lemkul
• [gmx-users] pulling   mohsen ramezanpour
  • [gmx-users] pulling   Justin A. Lemkul
• [gmx-users] Free energy   mohsen ramezanpour
  • [gmx-users] Free energy   Justin A. Lemkul
  • [gmx-users] Free energy   Floris Buelens
• [gmx-users] Free energy   chris.neale at utoronto.ca
• [gmx-users] making maxwarn a hidden option   chris.neale at utoronto.ca
  • [gmx-users] making maxwarn a hidden option   ms
    • [gmx-users] making maxwarn a hidden option   Justin A. Lemkul
      • [gmx-users] making maxwarn a hidden option   ms
      • [gmx-users] making maxwarn a hidden option   Justin A. Lemkul
      • [gmx-users] making maxwarn a hidden option   ms
• [gmx-users] making maxwarn a hidden option   chris.neale at utoronto.ca
• [gmx-users] Add gromacs forcefield w/ virtual site   Marcelo Silva
• [gmx-users] Add gromacs forcefield w/ virtual site   chris.neale at utoronto.ca
  • [gmx-users] Add gromacs forcefield w/ virtual site   Marcelo Silva
    • [gmx-users] Add gromacs forcefield w/ virtual site   Mark Abraham
• [gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file   leila karami
• [gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file   chris.neale at utoronto.ca
• [gmx-users] Major code reorganization in git coming up   Erik Lindahl
• [gmx-users] Major code reorganization in git coming up   Erik Lindahl
• [gmx-users] Add gromacs forcefield w/ virtual site   chris.neale at utoronto.ca
• [gmx-users] g_tune_pme big standard deviation in perf.out output   WU Yanbin

Last message date: Fri Dec 31 15:28:15 CET 2010
Archived on: Thu Nov 14 12:09:55 CET 2013

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