October 2013 Archives by thread

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Starting: Tue Oct 1 06:24:29 CEST 2013
Ending: Thu Oct 31 22:17:47 CET 2013
Messages: 520

• [gmx-users] Installing Extended Genbox   Tegar Nurwahyu Wijaya
  • [gmx-users] Installing Extended Genbox   Mark Abraham
    • [gmx-users] Installing Extended Genbox   Tegar Nurwahyu Wijaya
      • [gmx-users] Installing Extended Genbox   Justin Lemkul
      • [gmx-users] Installing Extended Genbox   Mark Abraham
• [gmx-users] OPLS/AA + TIP5P, anybody?   gigo
• [gmx-users] g_hydorder   Nidhi Katyal
  • [gmx-users] Re: g_hydorder   Nidhi Katyal
    • [gmx-users] Re: g_hydorder   David van der Spoel
      • [gmx-users] Re: g_hydorder   Nidhi Katyal
• [gmx-users] ionomer topolgy   Ehsan Sadeghi
  • [gmx-users] ionomer topolgy   Justin Lemkul
• [gmx-users] installing Gromacs4.6.3 with CPMD   Collins Nganou
• [gmx-users] Invalid line in coordinate file (grompp tool)   Andrew Bostick
  • [gmx-users] Invalid line in coordinate file (grompp tool)   Justin Lemkul
• [gmx-users] Invalid line in coordinate file (grompp tool)   Andrew Bostick
  • [gmx-users] Invalid line in coordinate file (grompp tool)   Justin Lemkul
• [gmx-users] Problem running free energy simulations   Jernej Zidar
  • [gmx-users] Problem running free energy simulations   Michael Shirts
• [gmx-users] (no subject)   prithvi raj pandey
• [gmx-users] pulling along hexane-water interface   prithvi raj pandey
• [gmx-users] Re: Problem running free energy simulations   Jernej Zidar
  • [gmx-users] Re: Problem running free energy simulations   Michael Shirts
• [gmx-users] GAFFlipids for Gromacs?   Ollila Samuli
• [gmx-users] Question regarding g_order   sa
  • [gmx-users] Question regarding g_order   Justin Lemkul
• [gmx-users] double bond   Ehsan Sadeghi
  • [gmx-users] double bond   Justin Lemkul
    • [gmx-users] double bond   Ehsan Sadeghi
      • [gmx-users] double bond   Justin Lemkul
• [gmx-users] Membrane is shifted a lot during umbrella sampling   sudipta
• [gmx-users] how to calculate kinetic constant?   Albert
  • [gmx-users] how to calculate kinetic constant?   rajat desikan
  • [gmx-users] how to calculate kinetic constant?   David van der Spoel
• [gmx-users] OPLS/AA + TIP5P, anybody?   Christopher Neale
  • [gmx-users] OPLS/AA + TIP5P, anybody?   gigo
• [gmx-users] Membrane is shifted a lot during umbrella sampling   Christopher Neale
  • [gmx-users] Membrane is shifted a lot during umbrella sampling   Justin Lemkul
• [gmx-users] Verlett buffer drift   Venkatesh Ramakrishnan
• [gmx-users] pull-code constant-force direction gives unexpected error about distance larger than box size   Christopher Neale
• [gmx-users] What are F1~F4 of Equation(4.63) of Gromacs manual-4.5.6   Insung
• [gmx-users] pull-code constant-force direction gives unexpected error about distance larger than box size   Christopher Neale
• [gmx-users] how to calculate kinetic constant?   Christopher Neale
  • [gmx-users] how to calculate kinetic constant?   rajat desikan
• [gmx-users] how to calculate kinetic constant?   Christopher Neale
  • [gmx-users] how to calculate kinetic constant?   rajat desikan
• [gmx-users] Regarding lipid bilayer simulation   hasthi
  • [gmx-users] Regarding lipid bilayer simulation   Justin Lemkul
• [gmx-users] change of bilayer structure during NVT equilibration   shahab shariati
  • [gmx-users] change of bilayer structure during NVT equilibration   Justin Lemkul
• [gmx-users] pair distribution function   Archana Sonawani-Jagtap
  • [gmx-users] pair distribution function   Justin Lemkul
    • [gmx-users] pair distribution function   Archana Sonawani-Jagtap
• [gmx-users] change of bilayer structure during NVT equilibration   shahab shariati
  • [gmx-users] change of bilayer structure during NVT equilibration   Justin Lemkul
• [gmx-users] parallel simulation   pratibha kapoor
  • [gmx-users] parallel simulation   Venkat Reddy
  • [gmx-users] Re: parallel simulation   pratibha kapoor
    • [gmx-users] Re: parallel simulation   Kukol, Andreas
• [gmx-users] some code for writing topologies   Laura Leay
• [gmx-users] Bilayer thickness   Archana Sonawani-Jagtap
  • [gmx-users] Bilayer thickness   Justin Lemkul
• [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box   bipin singh
  • [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box   Justin Lemkul
    • [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box   bipin singh
      • [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box   Justin Lemkul
      • [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box   Trayder Thomas
      • [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box   bipin singh
      • [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box   Trayder Thomas
• [gmx-users] pdb2gmx takes phosphoserine as terminal ends   Villarealed
  • [gmx-users] pdb2gmx takes phosphoserine as terminal ends   Justin Lemkul
    • [gmx-users] Re: pdb2gmx takes phosphoserine as terminal ends   Villarealed
• [gmx-users] Can I generate Pulf files after mD running?   Yoochan,Myung
  • [gmx-users] Can I generate Pulf files after mD running?   Justin Lemkul
• [gmx-users] Regarding lipid bilayer   hasthi
  • [gmx-users] Regarding lipid bilayer   Kukol, Andreas
• [gmx-users] On the usage of g_sas   Jernej Zidar
  • [gmx-users] On the usage of g_sas   Justin Lemkul
• [gmx-users] Question about installing DSSP on Ubuntu 12.10   Mass
  • [gmx-users] Question about installing DSSP on Ubuntu 12.10   Justin Lemkul
• [gmx-users] Re: questions   Tsjerk Wassenaar
• [gmx-users] Is Gromos force field 45a3 out of dated?   Chih-Ying Lin
  • [gmx-users] Is Gromos force field 45a3 out of dated?   Tsjerk Wassenaar
• [gmx-users] Iron(III) Chloride in water   Jonathan Saboury
• [gmx-users] CHARMM36 force field available for GROMACS   Justin Lemkul
  • [gmx-users] CHARMM36 force field available for GROMACS   Mark Abraham
  • [gmx-users] CHARMM36 force field available for GROMACS   rajat desikan
    • [gmx-users] CHARMM36 force field available for GROMACS   Justin Lemkul
      • [gmx-users] CHARMM36 force field available for GROMACS   rajat desikan
      • [gmx-users] CHARMM36 force field available for GROMACS   Justin Lemkul
    • [gmx-users] CHARMM36 force field available for GROMACS   CHEN Pan
      • [gmx-users] CHARMM36 force field available for GROMACS   Justin Lemkul
      • [gmx-users] CHARMM36 force field available for GROMACS   Justin Lemkul
• [gmx-users] Re:On the usage of g_sas   Jernej Zidar
  • [gmx-users] Re:On the usage of g_sas   Justin Lemkul
• [gmx-users] Question about installing DSSP on Ubuntu 12.10   Justin Lemkul
• [gmx-users] pressure coupling without pbc   MURAT OZTURK
• [gmx-users] Steered MD   Steven Neumann
• [gmx-users] problem with the amb2gmx.pl   xiao
  • [gmx-users] problem with the amb2gmx.pl   Alan
    • [gmx-users] problem with the amb2gmx.pl   xiao
      • [gmx-users] problem with the amb2gmx.pl   Alan
• [gmx-users] time evaluation of dimensions of the simulation cell   Atila Petrosian
  • [gmx-users] time evaluation of dimensions of the simulation cell   Justin Lemkul
  • [gmx-users] time evaluation of dimensions of the simulation cell   Baptiste Demoulin
• [gmx-users] Re: CHARMM36 force field available for GROMACS   ABEL Stephane 175950
  • [gmx-users] Re: CHARMM36 force field available for GROMACS   Justin Lemkul
• [gmx-users] CHARMM36 force field available for GROMACS   Roland Schulz
  • [gmx-users] CHARMM36 force field available for GROMACS   Justin Lemkul
• [gmx-users] RE : gmx-users Digest, Vol 114, Issue 21   ABEL Stephane 175950
• [gmx-users] RMSF analysis   Sainitin Donakonda
  • [gmx-users] RMSF analysis   Justin Lemkul
    • [gmx-users] RMSF analysis   Sainitin Donakonda
      • [gmx-users] RMSF analysis   Justin Lemkul
  • [gmx-users] RMSF analysis   Gianluca Interlandi
• [gmx-users] Adding proton using genion to study proton transfer reaction   Deepak Ojha
  • [gmx-users] Adding proton using genion to study proton transfer reaction   Tsjerk Wassenaar
• [gmx-users] Gromacs on Stampede   Arun Sharma
  • [gmx-users] Gromacs on Stampede   Szilárd Páll
• [gmx-users] DSSP installation on Ubuntu 12.10   Mass
  • [gmx-users] DSSP installation on Ubuntu 12.10   Mark Abraham
    • [gmx-users] DSSP installation on Ubuntu 12.10   Mass
      • [gmx-users] DSSP installation on Ubuntu 12.10   Justin Lemkul
      • [gmx-users] DSSP installation on Ubuntu 12.10   Mass
      • [gmx-users] DSSP installation on Ubuntu 12.10   Justin Lemkul
      • [gmx-users] DSSP installation on Ubuntu 12.10   Mass
      • [gmx-users] DSSP installation on Ubuntu 12.10   Justin Lemkul
      • [gmx-users] DSSP installation on Ubuntu 12.10   Mark Abraham
• [gmx-users] jwe1050i + jwe0019i errors = SIGSEGV (Fujitsu)   James
  • [gmx-users] jwe1050i + jwe0019i errors = SIGSEGV (Fujitsu)   Mark Abraham
• [gmx-users] non-bonded interaction for molecule contain virtual site   zhonghe xu
• [gmx-users] carbon nanotube - ifnite in length ?   Steven Neumann
  • [gmx-users] carbon nanotube - ifnite in length ?   Justin Lemkul
    • [gmx-users] carbon nanotube - ifnite in length ?   Steven Neumann
      • [gmx-users] carbon nanotube - ifnite in length ?   Justin Lemkul
      • [gmx-users] carbon nanotube - ifnite in length ?   Steven Neumann
      • [gmx-users] carbon nanotube - ifnite in length ?   Justin Lemkul
      • [gmx-users] carbon nanotube - ifnite in length ?   Steven Neumann
      • [gmx-users] carbon nanotube - ifnite in length ?   Justin Lemkul
      • [gmx-users] carbon nanotube - ifnite in length ?   Steven Neumann
      • [gmx-users] carbon nanotube - ifnite in length ?   Justin Lemkul
      • [gmx-users] carbon nanotube - ifnite in length ?   Steven Neumann
      • [gmx-users] carbon nanotube - ifnite in length ?   Steven Neumann
      • [gmx-users] carbon nanotube - ifnite in length ?   Justin Lemkul
      • [gmx-users] carbon nanotube - ifnite in length ?   Steven Neumann
      • [gmx-users] carbon nanotube - ifnite in length ?   Justin Lemkul
• [gmx-users] Unstable System   Nikhil Agrawal
  • [gmx-users] Unstable System   Justin Lemkul
    • [gmx-users] Unstable System   massimo sandal
• [gmx-users] question about OPLS-AA force field -required bond constraints   Martin, Erik W
  • [gmx-users] question about OPLS-AA force field -required bond constraints   Justin Lemkul
    • [gmx-users] question about OPLS-AA force field -required bond constraints   Michael Shirts
• [gmx-users] Gromacs on Stampede   Christopher Neale
  • [gmx-users] Gromacs on Stampede   Arun Sharma
    • [gmx-users] Gromacs on Stampede   Arun Sharma
• [gmx-users] Building lipid bilayers topology   superpc
  • [gmx-users] Building lipid bilayers topology   Justin Lemkul
• [gmx-users] bonded interactions in Gromos96   Ehsan Sadeghi
  • [gmx-users] bonded interactions in Gromos96   Justin Lemkul
    • [gmx-users] bonded interactions in Gromos96   Ehsan Sadeghi
      • [gmx-users] bonded interactions in Gromos96   Justin Lemkul
• [gmx-users] energy drift - comparison of double and single precision   Guillaume Chevrot
  • [gmx-users] energy drift - comparison of double and single precision   Michael Shirts
  • [gmx-users] energy drift - comparison of double and single precision   Mark Abraham
    • [gmx-users] energy drift - comparison of double and single precision   Guillaume Chevrot
      • [gmx-users] energy drift - comparison of double and single precision   Mark Abraham
      • [gmx-users] energy drift - comparison of double and single precision   XAvier Periole
      • [gmx-users] energy drift - comparison of double and single precision   Guillaume Chevrot
      • [gmx-users] energy drift - comparison of double and single precision   Guillaume Chevrot
      • [gmx-users] energy drift - comparison of double and single precision   Michael Shirts
      • [gmx-users] energy drift - comparison of double and single precision   Guillaume Chevrot
      • [gmx-users] energy drift - comparison of double and single precision   Mark Abraham
• [gmx-users] DSSP problem   Mass
  • [gmx-users] DSSP problem   Justin Lemkul
    • [gmx-users] DSSP problem   Mass
      • [gmx-users] DSSP problem   Justin Lemkul
• [gmx-users] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?)   Jonathan Saboury
• [gmx-users] Gromacs on Stampede   Christopher Neale
• [gmx-users] Number of ligand contacts over the trajectories   anu chandra
  • [gmx-users] Number of ligand contacts over the trajectories   bipin singh
    • [gmx-users] Number of ligand contacts over the trajectories   anu chandra
• [gmx-users] KALP in DPPC tutorial reg   Sathya
  • [gmx-users] KALP in DPPC tutorial reg   Justin Lemkul
• [gmx-users] Re: Steered MD   Thomas Schlesier
• [gmx-users] KALP in DPPC tutorial reg   Sathya
  • [gmx-users] KALP in DPPC tutorial reg   Justin Lemkul
• [gmx-users] g_sham   pratibha kapoor
  • [gmx-users] g_sham   Justin Lemkul
  • Aw: [gmx-users] g_sham   lloyd riggs
• [gmx-users] Wall option with 12-6 LJ   Yutian Yang
• [gmx-users] problem in NPT equilibration step   Preeti Choudhary
  • [gmx-users] problem in NPT equilibration step   Baptiste Demoulin
  • [gmx-users] problem in NPT equilibration step   srinathchowdary
    • [gmx-users] problem in NPT equilibration step   Mark Abraham
• [gmx-users] LJ - SR and Coulbom - SR mdp options   Steven Neumann
  • [gmx-users] LJ - SR and Coulbom - SR mdp options   Justin Lemkul
• [gmx-users] recalculating .trr from .xtc   Leandro Bortot
  • [gmx-users] recalculating .trr from .xtc   Justin Lemkul
    • [gmx-users] recalculating .trr from .xtc   Mark Abraham
      • [gmx-users] recalculating .trr from .xtc   XAvier Periole
• [gmx-users] topology file of ligand   sunyeping
  • [gmx-users] topology file of ligand   Justin Lemkul
    • 答复: [gmx-users] topology file of ligand   sunyeping
      • 答复: [gmx-users] topology file of ligand   Justin Lemkul
• [gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102   Mark Abraham
• [gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102   Nikolay Alemasov
  • [gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102   Mark Abraham
    • [gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102   Nikolay Alemasov
    • [gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102   Nikolay Alemasov
• [gmx-users] Centering the system   Shima Arasteh
  • [gmx-users] Centering the system   Justin Lemkul
    • [gmx-users] Centering the system   Shima Arasteh
      • [gmx-users] Centering the system   Justin Lemkul
  • [gmx-users] Centering the system   Андрей Гончар
• [gmx-users] Re: gro file formate error   Justin Lemkul
• [gmx-users] Constraint bonds and contribution to pressure   Chrisostomos Batistakis
• [gmx-users] KALP-15 in DPPC tutorial   Sathya
  • [gmx-users] KALP-15 in DPPC tutorial   Justin Lemkul
• [gmx-users] Is the website of Martini Force Field down for maintenance?   朱文鹏
  • [gmx-users] Is the website of Martini Force Field down for maintenance?   Justin Lemkul
  • [gmx-users] Is the website of Martini Force Field down for maintenance?   XAvier Periole
• [gmx-users] Gibbs Energy Calculation and charges   Dallas Warren
  • [gmx-users] RE: Gibbs Energy Calculation and charges   Dallas Warren
• [gmx-users] Gibbs Energy Calculation and charges   Christopher Neale
  • [gmx-users] RE: Gibbs Energy Calculation and charges   Dallas Warren
• [gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm   Nilesh Dhumal
  • [gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm   Trayder Thomas
    • [gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm   Nilesh Dhumal
      • [gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm   Mark Abraham
• [gmx-users] MD of lipid bilayer   Sathya
  • [gmx-users] MD of lipid bilayer   Justin Lemkul
• [gmx-users] Gibbs Energy Calculation and charges   Christopher Neale
  • [gmx-users] RE: Gibbs Energy Calculation and charges   Dallas Warren
    • [gmx-users] RE: Gibbs Energy Calculation and charges   Dallas Warren
      • [gmx-users] RE: Gibbs Energy Calculation and charges   Dallas Warren
      • [gmx-users] RE: Gibbs Energy Calculation and charges   Michael Shirts
      • [gmx-users] RE: Gibbs Energy Calculation and charges   Dallas Warren
      • [gmx-users] RE: Gibbs Energy Calculation and charges   Michael Shirts
• [gmx-users] default -rdd with distance restraints seems too large   Christopher Neale
  • [gmx-users] default -rdd with distance restraints seems too large   Mark Abraham
• [gmx-users] mistake occured in Gromacs install   张海平
  • [gmx-users] mistake occured in Gromacs install   Mark Abraham
• [gmx-users] Free energy of solvation of large molecule   Jernej Zidar
• [gmx-users] lipid tail order   Archana Sonawani-Jagtap
  • [gmx-users] lipid tail order   Justin Lemkul
• [gmx-users] postdoctoral position in computational biophysics in Denmark   himanshu khandelia
• [gmx-users] (no subject)   Archana Sonawani-Jagtap
• [gmx-users] parallelization   pratibha kapoor
  • [gmx-users] parallelization   Carsten Kutzner
• [gmx-users] default -rdd with distance restraints seems too large   Christopher Neale
  • [gmx-users] default -rdd with distance restraints seems too large   XAvier Periole
• [gmx-users] default -rdd with distance restraints seems too large   Christopher Neale
  • [gmx-users] default -rdd with distance restraints seems too large   XAvier Periole
• [gmx-users] genion doesn't recognize SOL in top file   sunyeping
  • [gmx-users] genion doesn't recognize SOL in top file   Justin Lemkul
• [gmx-users] OPLS-AA parameters for Phospho-threonine and serine   Martin, Erik W
  • [gmx-users] OPLS-AA parameters for Phospho-threonine and serine   Andrea Spitaleri
• [gmx-users] Problem with reading AMBER trajectories   anu chandra
  • [gmx-users] Problem with reading AMBER trajectories   Mark Abraham
    • [gmx-users] Problem with reading AMBER trajectories   anu chandra
      • [gmx-users] Problem with reading AMBER trajectories   Mark Abraham
      • [gmx-users] Problem with reading AMBER trajectories   anu chandra
      • [gmx-users] Problem with reading AMBER trajectories   anu chandra
      • [gmx-users] Problem with reading AMBER trajectories   Mark Abraham
• [gmx-users] Bilayer thickness error   Archana Sonawani-Jagtap
  • [gmx-users] Bilayer thickness error   Justin Lemkul
    • [gmx-users] Bilayer thickness error   Archana Sonawani-Jagtap
• [gmx-users] modification of LJ potential   Zuzana Benkova
• [gmx-users] Molecular dynamics with LEGO?   Tsjerk Wassenaar
  • [gmx-users] Molecular dynamics with LEGO?   jkrieger at mrc-lmb.cam.ac.uk
    • [gmx-users] Molecular dynamics with LEGO?   Tsjerk Wassenaar
• [gmx-users] (no subject)   Raj K
• [gmx-users] Insertion of chromium III ion into lipid bilayer   Sathya
  • [gmx-users] Insertion of chromium III ion into lipid bilayer   Mark Abraham
  • [gmx-users] Insertion of chromium III ion into lipid bilayer   Justin Lemkul
    • [gmx-users] Re: Insertion of chromium III ion into lipid bilayer   Sathya
      • [gmx-users] Re: Insertion of chromium III ion into lipid bilayer   Justin Lemkul
• [gmx-users] The box of umbrella sampling   sunyeping
  • [gmx-users] The box of umbrella sampling   Justin Lemkul
• [gmx-users] Ligand breaking in to two   MUSYOKA THOMMAS
  • [gmx-users] Ligand breaking in to two   Alan
  • [gmx-users] Ligand breaking in to two   Mark Abraham
• [gmx-users] Entering ions   Mohsen Ramezanpour
  • [gmx-users] Entering ions   Justin Lemkul
    • [gmx-users] Entering ions   Mohsen Ramezanpour
      • [gmx-users] Entering ions   Justin Lemkul
      • [gmx-users] Entering ions   Mohsen Ramezanpour
• [gmx-users] The box of umbrella sampling   Justin Lemkul
• [gmx-users] CHARMM-GUI to GROMACS   Zhi Yue
  • [gmx-users] CHARMM-GUI to GROMACS   Justin Lemkul
    • [gmx-users] CHARMM-GUI to GROMACS   Zhi Yue
• [gmx-users] regarding charge group   Sathish Kumar
  • [gmx-users] regarding charge group   Mark Abraham
• [gmx-users] Minimum distance between periodic images   Nidhi Katyal
  • [gmx-users] Minimum distance between periodic images   Tsjerk Wassenaar
    • [gmx-users] Minimum distance between periodic images   Nidhi Katyal
• [gmx-users] Regarding membrane(DMPC) simulations with fullerene   Sathish Kumar
  • [gmx-users] Regarding membrane(DMPC) simulations with fullerene   Justin Lemkul
• [gmx-users] a new GROMACS simulation tool   Kevin Chen
  • [gmx-users] a new GROMACS simulation tool   Michael Shirts
    • [gmx-users] a new GROMACS simulation tool   Kevin Chen
  • [gmx-users] a new GROMACS simulation tool   Gloria Saracino
    • [gmx-users] a new GROMACS simulation tool   Thales Kronenberger
      • [gmx-users] a new GROMACS simulation tool   Jeya vimalan
  • [gmx-users] a new GROMACS simulation tool   Mark Abraham
  • [gmx-users] a new GROMACS simulation tool   Ehsan Sadeghi
    • [gmx-users] a new GROMACS simulation tool   Gabriele Lanaro
  • [gmx-users] a new GROMACS simulation tool   jkrieger at mrc-lmb.cam.ac.uk
  • [gmx-users] a new GROMACS simulation tool   Ashutosh singh
  • [gmx-users] Re: a new GROMACS simulation tool   Villarealed
    • [gmx-users] Re: a new GROMACS simulation tool   houyang chen
      • [gmx-users] Re: a new GROMACS simulation tool   Kieu Thu Nguyen
  • [gmx-users] Re: a new GROMACS simulation tool   sri2201
    • [gmx-users] Re: a new GROMACS simulation tool   houyang chen
• [gmx-users] Problems about the output force   Qianqian Cao
• [gmx-users] Conflicting atom names when using g_density   Bin Liu
  • [gmx-users] Conflicting atom names when using g_density   Justin Lemkul
• [gmx-users] Energy minimizations taking really, really long?   Nimmy McNimmerson
  • [gmx-users] Re: Energy minimizations taking really, really long?   shika
  • [gmx-users] Energy minimizations taking really, really long?   Justin Lemkul
• [gmx-users] Box size increases in NPT   Nilesh Dhumal
  • [gmx-users] Box size increases in NPT   Mark Abraham
    • [gmx-users] Box size increases in NPT   Dr. Vitaly Chaban
      • [gmx-users] Box size increases in NPT   Mark Abraham
• [gmx-users] Continuing runs from 4.5.4 in 4.6.3   rajat desikan
  • [gmx-users] Continuing runs from 4.5.4 in 4.6.3   Mark Abraham
    • [gmx-users] Continuing runs from 4.5.4 in 4.6.3   rajat desikan
  • [gmx-users] Continuing runs from 4.5.4 in 4.6.3   Kevin Chen
    • Aw: RE: [gmx-users] Continuing runs from 4.5.4 in 4.6.3   lloyd riggs
• [gmx-users] TFE-water simulation   Archana Sonawani-Jagtap
  • [gmx-users] TFE-water simulation   Justin Lemkul
    • [gmx-users] TFE-water simulation   Archana Sonawani-Jagtap
      • [gmx-users] TFE-water simulation   Justin Lemkul
• [gmx-users] pbc problem   shahab shariati
  • [gmx-users] pbc problem   jkrieger at mrc-lmb.cam.ac.uk
  • [gmx-users] pbc problem   Mark Abraham
• [gmx-users] list   Michelangelo Scordino
  • [gmx-users] list   Justin Lemkul
• [gmx-users] converting pdb of protein+ATP+water+ion into gromacs files   Dina Mirijanian
  • [gmx-users] converting pdb of protein+ATP+water+ion into gromacs files   Justin Lemkul
    • [gmx-users] converting pdb of protein+ATP+water+ion into gromacs files   Dina Mirijanian
• [gmx-users] cant find certain atomtypes from atomtype database   JuYeon
  • [gmx-users] cant find certain atomtypes from atomtype database   Justin Lemkul
• [gmx-users] pbc problem   shahab shariati
  • [gmx-users] pbc problem   Mark Abraham
• [gmx-users] g_hbond and g_rdf in vacuum   Santu Biswas
  • [gmx-users] g_hbond and g_rdf in vacuum   Mark Abraham
• [gmx-users] Output pinning for mdrun   Carsten Kutzner
  • [gmx-users] Output pinning for mdrun   Mark Abraham
    • [gmx-users] Output pinning for mdrun   Carsten Kutzner
      • [gmx-users] Output pinning for mdrun   Szilárd Páll
      • [gmx-users] Output pinning for mdrun   Mark Abraham
• [gmx-users] Gromos54a8   rajat desikan
  • [gmx-users] Gromos54a8   Justin Lemkul
    • [gmx-users] Gromos54a8   rajat desikan
      • [gmx-users] Gromos54a8   Justin Lemkul
      • [gmx-users] Gromos54a8   rajat desikan
      • [gmx-users] Gromos54a8   Djurre de Jong-Bruinink
      • [gmx-users] Gromos54a8   rajat desikan
• [gmx-users] Genion error   felipe vasquez
  • [gmx-users] Genion error   Justin Lemkul
    • [gmx-users] Genion error   felipe vasquez
      • [gmx-users] Genion error   Justin Lemkul
• [gmx-users] pbc problem   shahab shariati
  • [gmx-users] pbc problem   Justin Lemkul
  • [gmx-users] pbc problem   Mark Abraham
• [gmx-users] nstcalclr bug?   Andrea Spitaleri
  • [gmx-users] nstcalclr bug?   jkrieger at mrc-lmb.cam.ac.uk
    • [gmx-users] nstcalclr bug?   Mark Abraham
      • [gmx-users] nstcalclr bug?   Andrea Spitaleri
• [gmx-users] meaning of the parameters in gbsa.itp   Corina Mo
  • [gmx-users] meaning of the parameters in gbsa.itp   Justin Lemkul
    • [gmx-users] meaning of the parameters in gbsa.itp   Coco Mo
      • [gmx-users] meaning of the parameters in gbsa.itp   Justin Lemkul
      • [gmx-users] Re: meaning of the parameters in gbsa.itp   Corina Mo
      • [gmx-users] Re: meaning of the parameters in gbsa.itp   Mark Abraham
• [gmx-users] gmxdump segmentation fault   Sarlo, Jeffrey S
• [gmx-users] 2D umbrella sampling simulation   mjyang
• [gmx-users] 2D umbrella sampling simulation   Christopher Neale
  • [gmx-users] RE: 2D umbrella sampling simulation   mjyang
• [gmx-users] Optimizing performance mac osx   Tiago Gomes
  • [gmx-users] Optimizing performance mac osx   Mark Abraham
• [gmx-users] Wall potential for a membrane-simulation   Marianne Schulte
• [gmx-users] 2D umbrella sampling simulation   Christopher Neale
  • [gmx-users] RE: 2D umbrella sampling simulation   mjyang
• [gmx-users] GPU-gromacs   aixintiankong
  • [gmx-users] GPU-gromacs   Carsten Kutzner
• [gmx-users] Lie method for binding free energy calculations   Sajad Ahrari
  • [gmx-users] Lie method for binding free energy calculations   Justin Lemkul
• [gmx-users] Lie method for binding free energy calculations   Justin Lemkul
• [gmx-users] Lie method for binding free energy calculations   Justin Lemkul
  • [gmx-users] Lie method for binding free energy calculations   Andrea Spitaleri
• [gmx-users] Re: gmx-users Digest, Vol 114, Issue 64   Santu Biswas
  • [gmx-users] Re: gmx-users Digest, Vol 114, Issue 64   Mark Abraham
• [gmx-users] two warnings in umbralla sampling step 6   sunyeping
• [gmx-users] error in umbralla sampling step 6   sunyeping
  • [gmx-users] error in umbralla sampling step 6   Justin Lemkul
• [gmx-users] Replica Exchange with Solute Tempering   David Osguthorpe
  • [gmx-users] Replica Exchange with Solute Tempering   Michael Shirts
    • [gmx-users] Replica Exchange with Solute Tempering   David Osguthorpe
      • [gmx-users] Replica Exchange with Solute Tempering   HANNIBAL LECTER
      • [gmx-users] Replica Exchange with Solute Tempering   Andrew Ritchie
• [gmx-users] RE:Requests   lloyd riggs
• [gmx-users] pbc problem   shahab shariati
  • [gmx-users] pbc problem   Justin Lemkul
• 答复: [gmx-users] error in umbralla sampling step 6   Justin Lemkul
  • [gmx-users] error in umbralla sampling step 6   sunyeping
    • [gmx-users] error in umbralla sampling step 6   Justin Lemkul
• [gmx-users] pbc problem   shahab shariati
• [gmx-users] mdrun cpt   Pavan Ghatty
  • [gmx-users] mdrun cpt   Justin Lemkul
    • [gmx-users] mdrun cpt   Pavan Ghatty
      • [gmx-users] mdrun cpt   Mark Abraham
      • [gmx-users] mdrun cpt   Pavan Ghatty
      • [gmx-users] mdrun cpt   jkrieger at mrc-lmb.cam.ac.uk
      • [gmx-users] mdrun cpt   Pavan Ghatty
      • [gmx-users] mdrun cpt   jkrieger at mrc-lmb.cam.ac.uk
      • [gmx-users] mdrun cpt   Mark Abraham
      • [gmx-users] mdrun cpt   Pavan Ghatty
      • [gmx-users] mdrun cpt   Mark Abraham
• [gmx-users] pbc problem   shahab shariati
  • [gmx-users] pbc problem   Tsjerk Wassenaar
• [gmx-users] pbc problem   shahab shariati
  • [gmx-users] pbc problem   Justin Lemkul
    • [gmx-users] pbc problem   Mark Abraham
• [gmx-users] *** Extended deadline *** CfP: 4th International Workshop on Model-driven Approaches for Simulation Engineering part of the Symposium on Theory of Modeling and Simulation (SCS SpringSim 2014)   Daniele Gianni
• [gmx-users] How To SOLVATE   Hari Pandey
  • [gmx-users] How To SOLVATE   Justin Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 114, Issue 75   Santu Biswas
  • [gmx-users] g_hbond and g_rdf in vacuum   Justin Lemkul
• [gmx-users] Charges in vacuum simulation   Richa Singh
  • [gmx-users] Charges in vacuum simulation   Dr. Vitaly Chaban
• [gmx-users] pdb2gmx conversion   MUSYOKA THOMMAS
  • [gmx-users] pdb2gmx conversion   Tsjerk Wassenaar
• [gmx-users] Gromacs tutorials for binding free energy analysis   Sajad Ahrari
  • [gmx-users] Gromacs tutorials for binding free energy analysis   Justin Lemkul
• [gmx-users] PLUMED2 official release   Carlo Camilloni
• [gmx-users] Suggestion for a project   Asaf Farhi
• [gmx-users] parmbsc0 force field   kiana moghaddam
  • [gmx-users] parmbsc0 force field   Justin Lemkul
• [gmx-users] How can I increase maximum number of pulling step for energy minimization?   Gwonchan Yoon
  • [gmx-users] How can I increase maximum number of pulling step for energy minimization?   Justin Lemkul
• [gmx-users] Obtaining trajectory coordinates at all dt   Xu Dong Huang
  • [gmx-users] Obtaining trajectory coordinates at all dt   Mark Abraham
• [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15   Hari Pandey
  • [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15   Mark Abraham
    • [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15   Hari Pandey
      • [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15   Justin Lemkul
      • [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15   Hari Pandey
      • [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15   Justin Lemkul
• [gmx-users] Failure in MD run without any error   niloofar niknam
  • [gmx-users] Failure in MD run without any error   Mark Abraham
• [gmx-users] lmc-stats   Andrew S. Paluch
  • [gmx-users] lmc-stats   Michael Shirts
• [gmx-users] virtual sites   Neha Gandhi
  • [gmx-users] virtual sites   Justin Lemkul
• [gmx-users] Constant-Force Pulling of Ubiquitin   Weiwei Tao
• [gmx-users] pbc problem   shahab shariati
  • [gmx-users] pbc problem   Mark Abraham
  • [gmx-users] pbc problem   Justin Lemkul
• [gmx-users] Constant-Force Pulling of Ubiquitin   Vivian
  • [gmx-users] Constant-Force Pulling of Ubiquitin   XAvier Periole
    • Aw: Re: [gmx-users] Constant-Force Pulling of Ubiquitin   lloyd riggs
• [gmx-users] g_rotacf error   Tiago Gomes
  • [gmx-users] g_rotacf error   Justin Lemkul
• [gmx-users] virtual sites   Roland Schulz
• [gmx-users] hydrogen bond analysis   larif sofiene
  • [gmx-users] hydrogen bond analysis   Justin Lemkul
• [gmx-users] Simulate partially hydrolized polyacrylamide in solutions   qugm110 at 126.com
• [gmx-users] continuing the terminated simulation   delara aghaie
  • [gmx-users] continuing the terminated simulation   Ankita Naithani
    • [gmx-users] continuing the terminated simulation   Pavan Ghatty
• [gmx-users] Re: periodic surface minimization   escajarro
• [gmx-users] Lysozime in Water   Negar Parvizi
  • [gmx-users] Lysozime in Water   jkrieger at mrc-lmb.cam.ac.uk
• [gmx-users] single point calculation with gromacs   fantasticqhl
  • [gmx-users] single point calculation with gromacs   Justin Lemkul
    • [gmx-users] Re: single point calculation with gromacs   fantasticqhl
    • [gmx-users] Re: single point calculation with gromacs   fantasticqhl
      • [gmx-users] Re: single point calculation with gromacs   Justin Lemkul
• [gmx-users] binding energy (score) of single trajectory frames   Knapp Bernhard
  • [gmx-users] binding energy (score) of single trajectory frames   Justin Lemkul
• [gmx-users] pbc off   jwillcox at andrew.cmu.edu
  • [gmx-users] pbc off   Justin Lemkul
• [gmx-users] SHAKE for water   Guillaume Chevrot
  • [gmx-users] SHAKE for water   Justin Lemkul
    • [gmx-users] SHAKE for water   Guillaume Chevrot
      • [gmx-users] SHAKE for water   Justin Lemkul
• [gmx-users] (no subject)   Hari Pandey
• [gmx-users] "editconf" displays incorrect mass of input, GROMACS version 4.5.4   Hari Pandey
  • [gmx-users] "editconf" displays incorrect mass of input, GROMACS version 4.5.4   Justin Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 114, Issue 91   Knapp Bernhard
  • [gmx-users] Re: gmx-users Digest, Vol 114, Issue 91   jkrieger at mrc-lmb.cam.ac.uk
• [gmx-users] RNA simulation   Hossein Lanjanian
  • [gmx-users] RNA simulation   Justin Lemkul
• [gmx-users] cool down problem   Riccardo Concu
  • [gmx-users] cool down problem   Justin Lemkul
    • [gmx-users] cool down problem   Riccardo Concu
• [gmx-users] Grompp note   Nilesh Dhumal
  • [gmx-users] Grompp note   Justin Lemkul
    • [gmx-users] Grompp note   Nilesh Dhumal
      • [gmx-users] Grompp note   Justin Lemkul
• [gmx-users] No group in index file?   Xu Dong Huang
  • [gmx-users] No group in index file?   Justin Lemkul
    • [gmx-users] No group in index file?   Xu Dong Huang
      • [gmx-users] No group in index file?   Riccardo Concu
      • [gmx-users] No group in index file?   Justin Lemkul
      • [gmx-users] No group in index file?   Xu Dong Huang
      • [gmx-users] No group in index file?   Justin Lemkul
      • [gmx-users] No group in index file?   Xu Dong Huang
      • [gmx-users] No group in index file?   Justin Lemkul
      • [gmx-users] No group in index file?   Xu Dong Huang
      • [gmx-users] No group in index file?   Justin Lemkul
      • [gmx-users] No group in index file?   Justin Lemkul
• [gmx-users] All-bonds vs. H-bonds using CHARMM36   rajat desikan
  • [gmx-users] All-bonds vs. H-bonds using CHARMM36   Justin Lemkul
    • [gmx-users] All-bonds vs. H-bonds using CHARMM36   rajat desikan
• [gmx-users] problem vwith ethanol-water solution   Ehsan Sadeghi
  • [gmx-users] problem vwith ethanol-water solution   Riccardo Concu
  • [gmx-users] problem vwith ethanol-water solution   Justin Lemkul

Last message date: Thu Oct 31 22:17:47 CET 2013
Archived on: Thu Nov 14 12:14:56 CET 2013

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