November 2012 Archives by thread

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Starting: Thu Nov 1 00:34:56 CET 2012
Ending: Fri Nov 30 20:18:53 CET 2012
Messages: 809

• [gmx-users] *** Extended Deadline *** Nov 19 CfP: 3rd International Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim13) part of the Symposium on Theory of Modeling and Simulation SCS SpringSim 2013)   Daniele Gianni
• [gmx-users] steered pulling code on ligand-receptor complex   范聪
• [gmx-users] Re: Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)   Emma Eriksson
• [gmx-users] Cholesterol parameters (Charrm36) in GMX   David van der Spoel
  • [gmx-users] Cholesterol parameters (Charrm36) in GMX   Yorquant Wang
    • [gmx-users] Cholesterol parameters (Charrm36) in GMX   David van der Spoel
• [gmx-users] Getting the constraint force from the LINCS algorith   Tom Kirchner
• [gmx-users] Simulation of charged systems   Felipe Pineda, PhD
  • [gmx-users] Simulation of charged systems (2)   Felipe Pineda, PhD
    • [gmx-users] Simulation of charged systems (2)   XAvier Periole
      • [gmx-users] Simulation of charged systems (2)   Felipe Pineda, PhD
      • [gmx-users] Simulation of charged systems (2)   Justin Lemkul
      • [gmx-users] Simulation of charged systems (2)   Felipe Pineda, PhD
• [gmx-users] Defining strongly interdependent dihedral force constants   mts503
• [gmx-users] fraction of native contacts calculation   Erik Marklund
  • [gmx-users] fraction of native contacts calculation   bipin singh
    • [gmx-users] fraction of native contacts calculation   Justin Lemkul
      • [gmx-users] fraction of native contacts calculation   bipin singh
    • [gmx-users] fraction of native contacts calculation   Sanku M
      • [gmx-users] fraction of native contacts calculation   bipin singh
  • [gmx-users] fraction of native contacts calculation   Oliver Beckstein
    • [gmx-users] fraction of native contacts calculation   bipin singh
• [gmx-users] tc-grps in Temperature coupling   Ali Alizadeh
  • [gmx-users] tc-grps in Temperature coupling   Justin Lemkul
• [gmx-users] regarding converge of system   ahmet yıldırım
• [gmx-users] regarding converge of system   Christopher Neale
  • [gmx-users] regarding converge of system   Tsjerk Wassenaar
  • [gmx-users] regarding converge of system   ahmet yıldırım
    • [gmx-users] regarding converge of system   Tsjerk Wassenaar
• [gmx-users] Regarding g_tune_pme optimization   Venkat Reddy
  • [gmx-users] Regarding g_tune_pme optimization   Carsten Kutzner
• [gmx-users] carbohydrate forcefield in gromacs   Sanku M
  • [gmx-users] carbohydrate forcefield in gromacs   Sai Kumar Ramadugu
• [gmx-users] are wall atoms virtual ?   harshaljain950
• [gmx-users] Re, g_rdf   Ali Alizadeh
  • [gmx-users] Re, g_rdf   Justin Lemkul
• [gmx-users] About APL And Shrunken System Size   vidhya sankar
  • [gmx-users] About APL And Shrunken System Size   Justin Lemkul
• [gmx-users] why it is so slow   Albert
  • [gmx-users] why it is so slow   Justin Lemkul
    • [gmx-users] why it is so slow   Albert
      • [gmx-users] why it is so slow   Justin Lemkul
      • [gmx-users] why it is so slow   Albert
      • [gmx-users] why it is so slow   Justin Lemkul
• [gmx-users] Re: are wall atoms virtual ?   Dr. Vitaly Chaban
  • [gmx-users] Re: are wall atoms virtual ?   harshaljain950
    • [gmx-users] Re: are wall atoms virtual ?   Peter C. Lai
      • [gmx-users] Re: are wall atoms virtual ?   harshaljain950
      • [gmx-users] a question on g_hbond   Acoot Brett
      • [gmx-users] a question on g_hbond   David van der Spoel
      • [gmx-users] a question on g_hbond   Justin Lemkul
• [gmx-users] Hessian Unit   Yao Yao
• [gmx-users] Re: are wall atoms virtual ?   Dr. Vitaly Chaban
• [gmx-users] T - Annealing at NP - cell expands   Steven Neumann
  • [gmx-users] T - Annealing at NP - cell expands   Justin Lemkul
    • [gmx-users] T - Annealing at NP - cell expands   Steven Neumann
      • [gmx-users] T - Annealing at NP - cell expands   Justin Lemkul
• [gmx-users] Freeze group atoms changing position   Alex Marshall
  • [gmx-users] Freeze group atoms changing position   Justin Lemkul
    • [gmx-users] Freeze group atoms changing position   Alex Marshall
• [gmx-users] I have a problem with my biphasic system   Ali Alizadeh
  • [gmx-users] I have a problem with my biphasic system   Justin Lemkul
• [gmx-users] Re: Why potential energy not in negative value?   shika
  • [gmx-users] Re: Why potential energy not in negative value?   Justin Lemkul
• [gmx-users] About BoxVector and APL   vidhya sankar
  • [gmx-users] About BoxVector and APL   Justin Lemkul
• [gmx-users] about tc_grps in mdp file...   rama david
  • [gmx-users] about tc_grps in mdp file...   Justin Lemkul
    • [gmx-users] about tc_grps in mdp file...   rama david
• [gmx-users] Re,I have a problem with my biphasic system   Ali Alizadeh
  • [gmx-users] Re,I have a problem with my biphasic system   Justin Lemkul
• [gmx-users] Free energy calculations with BAR and TI   Ignacio Fernández Galván
  • [gmx-users] Free energy calculations with BAR and TI   Tom Kirchner
    • [gmx-users] Free energy calculations with BAR and TI   Ignacio Fernández Galván
  • [gmx-users] a question related to tpbconv and trjcat   Acoot Brett
    • [gmx-users] a question related to tpbconv and trjcat   Justin Lemkul
  • [gmx-users] Error of violate the Second Law of Thermodynamics in Free energy calculation with BAR   badamkhatan togoldor
• [gmx-users] Multiple protein simulations in a box   Rajeswari A.
  • [gmx-users] Multiple protein simulations in a box   rama david
  • [gmx-users] Multiple protein simulations in a box   Justin Lemkul
• [gmx-users] Re,I have a problem with my biphasic system   Ali Alizadeh
  • [gmx-users] Re,I have a problem with my biphasic system   Justin Lemkul
• [gmx-users] cosine content and nonconverged trajectory   ahmet yıldırım
  • [gmx-users] cosine content and nonconverged trajectory   Justin Lemkul
• [gmx-users] Pull code, Velocity distribution   Samadashvili Nino
  • [gmx-users] Pull code, Velocity distribution   Justin Lemkul
    • [gmx-users] Pull code, Velocity distribution   Samadashvili Nino
    • [gmx-users] Pull code, Velocity distribution   Samadashvili Nino
• [gmx-users] Setting up a complex membrane simulation   jonas87
  • [gmx-users] Setting up a complex membrane simulation   Justin Lemkul
    • [gmx-users] Setting up a complex membrane simulation   Tsjerk Wassenaar
  • [gmx-users] Re: Setting up a complex membrane simulation   jonas87
    • [gmx-users] Re: Setting up a complex membrane simulation   Justin Lemkul
• [gmx-users] Re: why it is so slow   Dr. Vitaly Chaban
  • [gmx-users] Re: why it is so slow   Albert
    • [gmx-users] Re: why it is so slow   Justin Lemkul
      • [gmx-users] Re: why it is so slow   Albert
      • [gmx-users] Re: why it is so slow   Justin Lemkul
    • [gmx-users] Re: why it is so slow   Dr. Vitaly Chaban
• [gmx-users] Total energy for a group of molecule   Hanne Antila
  • [gmx-users] Total energy for a group of molecule   Justin Lemkul
    • [gmx-users] Total energy for a group of molecule   Hanne Antila
• [gmx-users] Re: Re,I have a problem with my biphasic system   Ali Alizadeh
  • [gmx-users] Re: Re,I have a problem with my biphasic system   Justin Lemkul
• [gmx-users] Setting up a complex membrane simulation   Christopher Neale
• [gmx-users] Re: Re,I have a problem with my biphasic system   Ali Alizadeh
  • [gmx-users] Re: Re,I have a problem with my biphasic system   Justin Lemkul
• [gmx-users] g_rms/rmsf: fit vs. nofit   Peter C. Lai
  • [gmx-users] g_rms/rmsf: fit vs. nofit   Justin Lemkul
• [gmx-users] Re: Multiple protein simulations in a box   Rajeswari A.
  • [gmx-users] Re: Multiple protein simulations in a box   Davide Mercadante
  • [gmx-users] Re: Multiple protein simulations in a box   Justin Lemkul
    • [gmx-users] Re: Multiple protein simulations in a box   Rajeswari A.
• [gmx-users] Re: Re,I have a problem with my biphasic system   Ali Alizadeh
• [gmx-users] part of protein in protein complex out of the box (system preparation) -reg   venkatesh s
  • [gmx-users] part of protein in protein complex out of the box (system preparation) -reg   Justin Lemkul
• [gmx-users] GPU warnings   Albert
  • [gmx-users] GPU warnings   Justin Lemkul
    • [gmx-users] GPU warnings   Thomas Evangelidis
    • [gmx-users] GPU warnings   Albert
      • [gmx-users] GPU warnings   Szilárd Páll
      • [gmx-users] GPU warnings   Thomas Evangelidis
      • [gmx-users] GPU warnings   Szilárd Páll
  • [gmx-users] GPU warnings   Szilárd Páll
    • [gmx-users] GPU warnings   Szilárd Páll
      • [gmx-users] GPU warnings   Thomas Evangelidis
      • [gmx-users] GPU warnings   Szilárd Páll
      • [gmx-users] GPU warnings   Szilárd Páll
      • [gmx-users] GPU warnings   Thomas Evangelidis
      • [gmx-users] GPU warnings   Szilárd Páll
• [gmx-users] Re: Error in DNA-Simulation   Mehdi Bagherpour
  • [gmx-users] Re: Error in DNA-Simulation   Justin Lemkul
• [gmx-users] Error in DNA Simulation   Mehdi Bagherpour
  • [gmx-users] Error in DNA Simulation   Justin Lemkul
  • [gmx-users] on energygrp_excl   Acoot Brett
    • [gmx-users] on energygrp_excl   Justin Lemkul
      • [gmx-users] a question on trajcat settime   Acoot Brett
      • [gmx-users] a question on trajcat settime   Peter C. Lai
• [gmx-users] libfftw3f.so.3 error known but not able to solve   gromacs query
  • [gmx-users] libfftw3f.so.3 error known but not able to solve   Justin Lemkul
    • [gmx-users] libfftw3f.so.3 error known but not able to solve   gromacs query
      • [gmx-users] libfftw3f.so.3 error known but not able to solve   Justin Lemkul
      • [gmx-users] libfftw3f.so.3 error known but not able to solve   gromacs query
• [gmx-users] g_wham with pull_geometry=position   David Peeler
  • [gmx-users] g_wham with pull_geometry=position   Jochen Hub
    • [gmx-users] g_wham with pull_geometry=position   David Peeler
• [gmx-users] tail correction   tarak karmakar
  • [gmx-users] tail correction   Justin Lemkul
• [gmx-users] g_sgangle   akn
  • [gmx-users] g_sgangle   Justin Lemkul
    • [gmx-users] Re: g_sgangle   akn
• [gmx-users] About The Diffusion of Water molecules in Protein Lipid Simulation   vidhya sankar
  • [gmx-users] About The Diffusion of Water molecules in Protein Lipid Simulation   Justin Lemkul
• [gmx-users] About The Diffusion of Water molecules in Protein Lipid Simulation   vidhya sankar
  • [gmx-users] About The Diffusion of Water molecules in Protein Lipid Simulation   Justin Lemkul
    • [gmx-users] Re:Ka/Kd   lloyd riggs
      • [gmx-users] Re:Ka/Kd   Justin Lemkul
      • [gmx-users] Re:Ka/Kd   lloyd riggs
      • [gmx-users] Re:Ka/Kd   lloyd riggs
      • [gmx-users] Re:Ka/Kd   lloyd riggs
      • [gmx-users] Re:Ka/Kd   Justin Lemkul
      • [gmx-users] Re:Ka/Kd   lloyd riggs
      • [gmx-users] Re:Ka/Kd   Justin Lemkul
• [gmx-users] charge groups   akn
  • [gmx-users] charge groups   Justin Lemkul
    • [gmx-users] Re: charge groups   akn
      • [gmx-users] Re: charge groups   Justin Lemkul
• [gmx-users] why not double precision?   Szilárd Páll
• [gmx-users] Question about OPLS atomtypes   Andrew DeYoung
• [gmx-users] Converting trajectory into tpr file   rainy908
  • [gmx-users] Converting trajectory into tpr file   Justin Lemkul
• [gmx-users] simulated annealing   tarak karmakar
• [gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us   benjfitz
  • [gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us   Justin Lemkul
    • [gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us   benjfitz
      • [gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us   Justin Lemkul
      • [gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us   benjfitz
      • [gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us   benjfitz
      • [gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us   Justin Lemkul
• [gmx-users] Creating layers of atoms in the BOX   harshaljain950
  • [gmx-users] Creating layers of atoms in the BOX   Justin Lemkul
• [gmx-users] simulated annealing   Christopher Neale
• [gmx-users] PCA   Tuba Kilinc
  • [gmx-users] PCA   francesco oteri
  • [gmx-users] PCA   vijaya subramanian
• [gmx-users] NPT with md-vv + Nose-Hoover + Parinello-Rehman   tarak karmakar
  • [gmx-users] Re: NPT with md-vv + Nose-Hoover + Parinello-Rehman   dakoenig
    • [gmx-users] Re: NPT with md-vv + Nose-Hoover + Parinello-Rehman   Justin Lemkul
• [gmx-users] gromos 45a3 ff   Ali Alizadeh
  • [gmx-users] gromos 45a3 ff   Justin Lemkul
• [gmx-users] Converting trajectory into tpr file   rainy908
  • [gmx-users] Converting trajectory into tpr file   Justin Lemkul
• [gmx-users] gromos 45a3 ff   Ali Alizadeh
  • [gmx-users] gromos 45a3 ff   Justin Lemkul
• [gmx-users] EM and an error: Water molecule starting at atom 5113 can not be settled.   Ali Alizadeh
  • [gmx-users] EM and an error: Water molecule starting at atom 5113 can not be settled.   Justin Lemkul
• [gmx-users] Converting trajectory into tpr file   rainy908
• [gmx-users] Water molecule starting at atom 5113 can not be settled.   Ali Alizadeh
  • [gmx-users] Water molecule starting at atom 5113 can not be settled.   Justin Lemkul
• [gmx-users] Water molecule starting at atom 5113 can not be settled.   Ali Alizadeh
  • [gmx-users] Water molecule starting at atom 5113 can not be settled.   Justin Lemkul
• [gmx-users] Water molecule starting at atom 5113 can not be settled.   Ali Alizadeh
• [gmx-users] QM-MM Minimization   Jose Tusell
• [gmx-users] Problem building Gromacs-4.5.5 on BlueGene/Q   Lin, Dejun
• [gmx-users] A charge group moved too far between two domain decomposition steps   Ali Alizadeh
  • [gmx-users] A charge group moved too far between two domain decomposition steps   Justin Lemkul
• [gmx-users] What algorithm does g_sas use?   jia jia
  • [gmx-users] What algorithm does g_sas use?   Justin Lemkul
    • [gmx-users] What algorithm does g_sas use?   jia jia
      • [gmx-users] What algorithm does g_sas use?   Matthew Zwier
      • [gmx-users] What algorithm does g_sas use?   jia jia
• [gmx-users] converting amber distributed parameters to gromacs.   Rajiv Gandhi
  • [gmx-users] converting amber distributed parameters to gromacs.   Felipe Pineda, PhD
    • [gmx-users] converting amber distributed parameters to gromacs.   Rajiv Gandhi
      • [gmx-users] converting amber distributed parameters to gromacs.   Felipe Pineda, PhD
• [gmx-users] Protein at given pH   Steven Neumann
  • [gmx-users] Protein at given pH   Justin Lemkul
    • [gmx-users] Protein at given pH   Steven Neumann
      • [gmx-users] Protein at given pH   Justin Lemkul
      • [gmx-users] Protein at given pH   Steven Neumann
  • [gmx-users] Protein at given pH   Erik Marklund
    • [gmx-users] Protein at given pH   Steven Neumann
      • [gmx-users] Protein at given pH   Erik Marklund
      • [gmx-users] Protein at given pH   Tsjerk Wassenaar
• [gmx-users] Polarisation model   Volker Lesch
  • [gmx-users] Polarisation model   David van der Spoel
    • [gmx-users] Polarisation model   Volker Lesch
      • [gmx-users] Polarisation model   David van der Spoel
• [gmx-users] Double entries in block structure--problem with SHAKE   tarak karmakar
  • [gmx-users] Double entries in block structure--problem with SHAKE   Justin Lemkul
    • [gmx-users] Double entries in block structure--problem with SHAKE   tarak karmakar
• [gmx-users] Running Gromacs in Clusters   Marcelo Depolo
  • [gmx-users] Running Gromacs in Clusters   Erik Marklund
    • [gmx-users] Running Gromacs in Clusters   Marcelo Depolo
      • [gmx-users] Running Gromacs in Clusters   Erik Marklund
      • [gmx-users] Running Gromacs in Clusters   Marcelo Depolo
      • [gmx-users] Running Gromacs in Clusters   Erik Marklund
    • [gmx-users] Running Gromacs in Clusters   Szilárd Páll
      • [gmx-users] Running Gromacs in Clusters   Erik Marklund
• [gmx-users] Temperature Histogram   Samadashvili Nino
  • [gmx-users] Temperature Histogram   Justin Lemkul
    • [gmx-users] Temperature Histogram   Samadashvili Nino
      • [gmx-users] Temperature Histogram   Justin Lemkul
      • [gmx-users] Temperature Histogram   Samadashvili Nino
    • [gmx-users] Temperature Histogram   cuong nguyen
      • [gmx-users] Temperature Histogram   Justin Lemkul
• [gmx-users] Re: Self-diffusion in high temperature water   Jose Ignacio Marquez
• [gmx-users] Re: Running Gromacs in Clusters   Dr. Vitaly Chaban
• [gmx-users] Re: Running Gromacs in Clusters   Dr. Vitaly Chaban
  • [gmx-users] Re: Running Gromacs in Clusters   Marcelo Depolo
• Fwd: [gmx-users] Re: Running Gromacs in Clusters   Dr. Vitaly Chaban
  • [gmx-users] Re: Running Gromacs in Clusters   Dr. Vitaly Chaban
    • [gmx-users] Re: Running Gromacs in Clusters   Marcelo Depolo
• [gmx-users] comparing gmx GB energy with Amber11   Sandeep Somani
  • [gmx-users] comparing gmx GB energy with Amber11   Per Larsson
    • [gmx-users] comparing gmx GB energy with Amber11   Sandeep Somani
      • [gmx-users] comparing gmx GB energy with Amber11   Per Larsson
      • [gmx-users] comparing gmx GB energy with Amber11   Sandeep Somani
      • [gmx-users] comparing gmx GB energy with Amber11   Per Larsson
      • [gmx-users] comparing gmx GB energy with Amber11   Sandeep Somani
• [gmx-users] area per lipid   Shima Arasteh
  • [gmx-users] area per lipid   Justin Lemkul
    • [gmx-users] area per lipid   Shima Arasteh
• [gmx-users] GROMACS with different gcc and FFT versions but one unique *tpr file   Thomas Schlesier
  • [gmx-users] GROMACS with different gcc and FFT versions but one unique *tpr file   Carsten Kutzner
• [gmx-users] constraining multiple types of bonds   tarak karmakar
  • [gmx-users] constraining multiple types of bonds   Justin Lemkul
    • [gmx-users] constraining multiple types of bonds   tarak karmakar
      • [gmx-users] constraining multiple types of bonds   Justin Lemkul
      • [gmx-users] constraining multiple types of bonds   tarak karmakar
      • [gmx-users] constraining multiple types of bonds   Justin Lemkul
      • [gmx-users] constraining multiple types of bonds   tarak karmakar
• [gmx-users] Need parameter file of heme with ligated form   Rajiv Gandhi
• [gmx-users] line longer than 4095 characters - help   Steven Neumann
  • [gmx-users] line longer than 4095 characters - help   Justin Lemkul
    • [gmx-users] line longer than 4095 characters - help   Steven Neumann
      • [gmx-users] line longer than 4095 characters - help   Justin Lemkul
• [gmx-users] how to check the intermediate coordinated even when the simulation is running   ananyachatterjee
  • [gmx-users] how to check the intermediate coordinated even when the simulation is running   Kavyashree M
    • [gmx-users] how to check the intermediate coordinated even when the simulation is running   Justin Lemkul
• [gmx-users] pdb2gmx fatal error   Marco Gerolin
• [gmx-users] How to avoid dumping trr file?   Bao Kai
• [gmx-users] REMD with Frozen DNA and Moving Protein   saber naderi
  • [gmx-users] REMD with Frozen DNA and Moving Protein   Justin Lemkul
    • [gmx-users] REMD with Frozen DNA and Moving Protein   Erik Marklund
• [gmx-users] Problem building Gromacs-4.5.5 on BlueGene/Q   Christopher Neale
  • [gmx-users] Problem building Gromacs-4.5.5 on BlueGene/Q   Mark Abraham
• [gmx-users] How to avoid dumping trr file?   Christopher Neale
• [gmx-users] Calculating the dipole moment vectors of functional groups   Andrew DeYoung
• [gmx-users] Re: Calculating the dipole moment vectors of functional groups   Andrew DeYoung
• [gmx-users] rigid structure   afsaneh maleki
  • [gmx-users] rigid structure   Erik Marklund
• [gmx-users] GPU warnings   Szilárd Páll
  • [gmx-users] GPU warnings   Thomas Evangelidis
    • [gmx-users] GPU warnings   Szilárd Páll
      • [gmx-users] GPU warnings   Thomas Evangelidis
      • [gmx-users] GPU warnings   Justin Lemkul
      • [gmx-users] GPU warnings   Szilárd Páll
• [gmx-users] Re: g_mindist - reg   Raj
  • [gmx-users] Re: g_mindist - reg   Justin Lemkul
• [gmx-users] ff parameters   Ali Alizadeh
  • [gmx-users] ff parameters   rama david
• [gmx-users] About periodic image of system.......   rama david
  • [gmx-users] About periodic image of system.......   Justin Lemkul
    • [gmx-users] About periodic image of system.......   rama david
      • [gmx-users] About periodic image of system.......   Justin Lemkul
      • [gmx-users] About periodic image of system.......   rama david
      • [gmx-users] About periodic image of system.......   Justin Lemkul
      • [gmx-users] About periodic image of system.......   rama david
      • [gmx-users] About periodic image of system.......   Justin Lemkul
      • [gmx-users] About periodic image of system.......   rama david
      • [gmx-users] About periodic image of system.......   Justin Lemkul
      • [gmx-users] About periodic image of system.......   rama david
• [gmx-users] problem with MPI   Bahar Mehrpuyan
  • [gmx-users] problem with MPI   Szilárd Páll
• [gmx-users] ff parameters,   Ali Alizadeh
  • [gmx-users] ff parameters,   Justin Lemkul
    • [gmx-users] ff parameters,   rama david
      • [gmx-users] ff parameters,   Justin Lemkul
• [gmx-users] representation of ice structure   Ali Alizadeh
• [gmx-users] About Box VEctor   vidhya sankar
  • [gmx-users] About Box VEctor   Justin Lemkul
• [gmx-users] About Box Vector   vidhya sankar
  • [gmx-users] About Box Vector   Justin Lemkul
• [gmx-users] About Usage of maxwarn option in EM Afer first first Shrinking   vidhya sankar
  • [gmx-users] About Usage of maxwarn option in EM Afer first first Shrinking   Justin Lemkul
• [gmx-users] problem with simulation of freezing of water   Ali Alizadeh
  • [gmx-users] problem with simulation of freezing of water   Justin Lemkul
  • [gmx-users] problem with simulation of freezing of water   Erik Marklund
• [gmx-users] Re:problem with simulation of freezing of water   Ali Alizadeh
  • [gmx-users] Re:problem with simulation of freezing of water   Justin Lemkul
    • [gmx-users] Re:problem with simulation of freezing of water   David van der Spoel
• [gmx-users] (no subject)   Ali Alizadeh
• [gmx-users] Re:problem with simulation of freezing of water   ran friedman
• [gmx-users] how to restart a stopped simulation   ananyachatterjee
  • [gmx-users] how to restart a stopped simulation   Kavyashree M
    • [gmx-users] how to restart a stopped simulation   ananyachatterjee
      • [gmx-users] how to restart a stopped simulation   Venkat Reddy
• [gmx-users] Continuous mdrun vs step-by-step mdrun   Venkat Reddy
  • [gmx-users] Continuous mdrun vs step-by-step mdrun   francesco oteri
    • [gmx-users] Continuous mdrun vs step-by-step mdrun   Venkat Reddy
• [gmx-users] do_dssp Segmentation fault   mshappy1986
  • [gmx-users] do_dssp Segmentation fault   João Henriques
    • [gmx-users] do_dssp Segmentation fault   Erik Marklund
• [gmx-users] problem with simulation of freezing of water   Ali Alizadeh
• [gmx-users] Dihedral Parameters for FEP   Jose Tusell
• [gmx-users] About Presence of Water in Hydrophobic core of lipids in NPT equlibration   vidhya sankar
  • [gmx-users] About Presence of Water in Hydrophobic core of lipids in NPT equlibration   Justin Lemkul
• [gmx-users] How to launch mdrun_mpi using g_tune_pme on a cluster   Venkat Reddy
  • [gmx-users] How to launch mdrun_mpi using g_tune_pme on a cluster   Justin Lemkul
• [gmx-users] Gromacs 4.6 segmentation fault with mdrun   sebastian
  • [gmx-users] Gromacs 4.6 segmentation fault with mdrun   sebastian
    • [gmx-users] Gromacs 4.6 segmentation fault with mdrun   Szilárd Páll
      • [gmx-users] Gromacs 4.6 segmentation fault with mdrun   Raf Ponsaerts
• [gmx-users] is it possible?   Albert
  • [gmx-users] is it possible?   Justin Lemkul
• [gmx-users] Question about scaling   Thomas Schlesier
  • [gmx-users] Question about scaling   Carsten Kutzner
• [gmx-users] compressibility water - TFE mixture   jojartb at jgypk.u-szeged.hu
• [gmx-users] Modifying the force field to recognize iron with ligand atoms?   Rajiv Gandhi
  • [gmx-users] Modifying the force field to recognize iron with ligand atoms?   Justin Lemkul
• [gmx-users] mdrun and orca fatal error   Anastasia Maslova
• [gmx-users] Re: Setting up a complex membrane simulation   Christopher Neale
• [gmx-users] error : One of the box lengths is smaller than twice the cut-off length   sri2201
  • [gmx-users] error : One of the box lengths is smaller than twice the cut-off length   Justin Lemkul
• [gmx-users] calculating lennard-jones interaction   Zahra M
  • [gmx-users] calculating lennard-jones interaction   Erik Marklund
• [gmx-users] Re: Question about scaling   Thomas Schlesier
• [gmx-users] Re: Question about scaling   Thomas Schlesier
  • [gmx-users] Re: Question about scaling   Carsten Kutzner
• [gmx-users] Re: error : One of the box lengths is smaller than twice the cut-off length   Dr. Vitaly Chaban
  • [gmx-users] Re: error : One of the box lengths is smaller than twice the cut-off length   Justin Lemkul
• [gmx-users] position / distance restraint involving more than one molecule   Dr. Vitaly Chaban
  • [gmx-users] position / distance restraint involving more than one molecule   Justin Lemkul
    • [gmx-users] Re: position / distance restraint involving more than one molecule   Dr. Vitaly Chaban
• [gmx-users] Re: Segmentation fault, mdrun_mpi   Taudt
• [gmx-users] Umbrella sampling question   Gmx QA
• [gmx-users] Ryckeat-Bellemans Potential in Charmm forcefield   XUEMING TANG
• [gmx-users] calculating lennard-jones interaction   Erik Marklund
• [gmx-users] Umbrella sampling question   Christopher Neale
• [gmx-users] Re: hydrophobic contacts   Raj
  • [gmx-users] Re: hydrophobic contacts   Justin Lemkul
    • [gmx-users] Re: hydrophobic contacts   francesco oteri
    • [gmx-users] Re: hydrophobic contacts   Raj
• [gmx-users] Ryckeat-Bellemans Potential in Charmm forcefield (XUEMING TANG)   ABEL Stephane 175950
  • [gmx-users] Ryckeat-Bellemans Potential in Charmm forcefield (XUEMING TANG)   XUEMING TANG
    • [gmx-users] Ryckeat-Bellemans Potential in Charmm forcefield (XUEMING TANG)   Justin Lemkul
      • [gmx-users] Ryckeat-Bellemans Potential in Charmm forcefield (XUEMING TANG)   XUEMING TANG
• [gmx-users] amino acid color   tarak karmakar
  • [gmx-users] amino acid color   Erik Marklund
• [gmx-users] Weird result of WHAM   Netaly Khazanov
  • [gmx-users] Weird result of WHAM   Justin Lemkul
    • [gmx-users] Weird result of WHAM   Netaly Khazanov
      • [gmx-users] Weird result of WHAM   Jianguo Li
      • [gmx-users] Weird result of WHAM   Netaly Khazanov
• [gmx-users] Re: Umbrella sampling question   Gmx QA
  • [gmx-users] Re: Umbrella sampling question   Erik Marklund
    • [gmx-users] Re: Umbrella sampling question   Gmx QA
  • [gmx-users] Re: Umbrella sampling question   Gmx QA
    • [gmx-users] Re: Umbrella sampling question   Erik Marklund
      • [gmx-users] Re: Umbrella sampling question   Gmx QA
• [gmx-users] Re: Umbrella sampling question   Christopher Neale
• [gmx-users] is it compatable?   Albert
  • [gmx-users] is it compatable?   Mark Abraham
• [gmx-users] position restraints & domain decomposition & Some interactions seem to be assigned multiple times : deadly combination   Dr. Vitaly Chaban
• [gmx-users] problem in running md simulation   ananyachatterjee
  • [gmx-users] problem in running md simulation   Venkat Reddy
    • [gmx-users] problem in running md simulation   ananyachatterjee
      • [gmx-users] problem in running md simulation   Kavyashree M
      • [gmx-users] problem in running md simulation   Justin Lemkul
      • [gmx-users] problem in running md simulation   Kavyashree M
• [gmx-users] Ryckeat-Bellemans Potential in Charmm forcefield   ABEL Stephane 175950
• [gmx-users] Dihedral form   Laura Leay
  • [gmx-users] Dihedral form   Erik Marklund
    • [gmx-users] Dihedral form   Laura Leay
      • [gmx-users] Dihedral form   Erik Marklund
      • [gmx-users] Dihedral form   Mark Abraham
• [gmx-users] Cannot minimiza - vdwradii.dat ???   Steven Neumann
  • [gmx-users] Cannot minimiza - vdwradii.dat ???   Justin Lemkul
    • [gmx-users] Cannot minimiza - vdwradii.dat ???   Steven Neumann
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Justin Lemkul
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Steven Neumann
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Steven Neumann
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Justin Lemkul
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Steven Neumann
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Steven Neumann
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Justin Lemkul
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Steven Neumann
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Justin Lemkul
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Steven Neumann
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Justin Lemkul
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Steven Neumann
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Justin Lemkul
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Steven Neumann
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Steven Neumann
      • [gmx-users] Cannot minimiza - vdwradii.dat ???   Justin Lemkul
• [gmx-users] About the biotin parameter.....   rama david
  • [gmx-users] About the biotin parameter.....   Justin Lemkul
    • [gmx-users] About the biotin parameter.....   rama david
      • [gmx-users] About the biotin parameter.....   rama david
      • [gmx-users] About the biotin parameter.....   Justin Lemkul
      • [gmx-users] About the biotin parameter.....   rama david
      • [gmx-users] About the biotin parameter.....   Justin Lemkul
      • [gmx-users] About the biotin parameter.....   rama david
      • [gmx-users] About the biotin parameter.....   Justin Lemkul
      • [gmx-users] About the biotin parameter.....   rama david
• [gmx-users] Atoms in the .top are not numbered consecutively from 1   Rajiv Gandhi
  • [gmx-users] Atoms in the .top are not numbered consecutively from 1   Justin Lemkul
• [gmx-users] Fe(2+) nonbonded parameters   Steven Neumann
  • [gmx-users] Fe(2+) nonbonded parameters   Justin Lemkul
    • [gmx-users] Fe(2+) nonbonded parameters   Steven Neumann
      • [gmx-users] Fe(2+) nonbonded parameters   Justin Lemkul
      • [gmx-users] Fe(2+) nonbonded parameters   Steven Neumann
      • [gmx-users] Fe(2+) nonbonded parameters   Justin Lemkul
• [gmx-users] Strange form of RDF curve   shch406
  • [gmx-users] Strange form of RDF curve   David van der Spoel
• [gmx-users] Re: Strange form of RDF curve   Dr. Vitaly Chaban
  • [gmx-users] Re: Strange form of RDF curve   Justin Lemkul
    • [gmx-users] Re: Strange form of RDF curve   shch406
      • [gmx-users] Re: Strange form of RDF curve   Justin Lemkul
      • [gmx-users] Re: Strange form of RDF curve   shch406
      • [gmx-users] Re: Strange form of RDF curve   André Farias de Moura
      • [gmx-users] Re: Strange form of RDF curve   André Farias de Moura
      • [gmx-users] Re: Strange form of RDF curve   Justin Lemkul
      • [gmx-users] Re: Strange form of RDF curve   André Farias de Moura
• [gmx-users] Water flow over carbon nanotube   shsubram
• [gmx-users] Re: Water flow over carbon nanotube   Dr. Vitaly Chaban
  • [gmx-users] Re: Water flow over carbon nanotube   Shankar Subramaniam
• [gmx-users] partial charges and radius setting   Rajiv Gandhi
  • [gmx-users] partial charges and radius setting   Justin Lemkul
• [gmx-users] g(r) does not go to 1 at long r -- bug in g_rdf?   Pablo Englebienne
  • [gmx-users] g(r) does not go to 1 at long r -- bug in g_rdf?   David van der Spoel
    • [gmx-users] Re: g(r) does not go to 1 at long r -- bug in g_rdf?   penglebienne
• [gmx-users] Bug (?) with FEP while using particle decomposition in charge transformation   Alexey Zeifman
• [gmx-users] Force vs distance plot in pulling simulation?   Gmx QA
  • [gmx-users] Force vs distance plot in pulling simulation?   Justin Lemkul
    • [gmx-users] Force vs distance plot in pulling simulation?   Erik Marklund
      • [gmx-users] Re: Force vs distance plot in pulling simulation?   Gmx QA
      • [gmx-users] Re: Force vs distance plot in pulling simulation?   Gmx QA
• [gmx-users] NMA Fatal Error   Yao Yao
  • [gmx-users] NMA Fatal Error   Justin Lemkul
• [gmx-users] NMA proctocol   Yao Yao
  • [gmx-users] NMA proctocol   Justin Lemkul
• [gmx-users] Gromacs 4.6 segmentation fault with mdrun   Roland Schulz
  • [gmx-users] Gromacs 4.6 segmentation fault with mdrun   Szilárd Páll
    • [gmx-users] Gromacs 4.6 segmentation fault with mdrun   Raf Ponsaerts
• [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus   Atila Petrosian
  • [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus   David van der Spoel
• [gmx-users] simulation with two different force fields   shahab shariati
  • [gmx-users] simulation with two different force fields   Justin Lemkul
• [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus   Atila Petrosian
  • [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus   David van der Spoel
• [gmx-users] simulation with two different force fields   shahab shariati
  • [gmx-users] simulation with two different force fields   Justin Lemkul
• [gmx-users] (no subject)   behnoosh Bahadori
• [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus   Atila Petrosian
  • [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus   David van der Spoel
• [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus   Atila Petrosian
• [gmx-users] (no subject)   behnoosh Bahadori
• [gmx-users] Force vs distance plot in pulling simulation?   Thomas Schlesier
• [gmx-users] (no subject)   sangeeta kundu
• [gmx-users] strange protonate state   Albert
  • [gmx-users] strange protonate state   David van der Spoel
    • [gmx-users] strange protonate state   Albert
      • [gmx-users] strange protonate state   David van der Spoel
• [gmx-users] Save frames of trajectory file   Shima Arasteh
  • [gmx-users] Save frames of trajectory file   Erik Marklund
• [gmx-users] (no subject)   behnoosh Bahadori
• [gmx-users] min + capped peptide   Bahar Mehrpuyan
  • [gmx-users] min + capped peptide   Justin Lemkul
    • [gmx-users] min + capped peptide   Bahar Mehrpuyan
      • [gmx-users] min + capped peptide   Justin Lemkul
• [gmx-users] which version it is?   Albert
• [gmx-users] which version it is   ABEL Stephane 175950
  • [gmx-users] which version it is   Thomas Piggot
    • [gmx-users] which version it is   Justin Lemkul
      • [gmx-users] which version it is   Thomas Piggot
      • [gmx-users] which version it is   Albert
• [gmx-users] reaction field   wmiranda at fbio.uh.cu
• [gmx-users] REMD simulation   Kenny Bravo Rodriguez
  • [gmx-users] REMD simulation   XAvier Periole
• [gmx-users] mpirun error   Parisa Rahmani
  • [gmx-users] mpirun error   Justin Lemkul
    • [gmx-users] mpirun error   Parisa Rahmani
      • [gmx-users] mpirun error   Justin Lemkul
      • [gmx-users] mpirun error   Parisa Rahmani
      • [gmx-users] mpirun error   Justin Lemkul
• [gmx-users] which version it is   ABEL Stephane 175950
  • [gmx-users] which version it is   Thomas Piggot
• [gmx-users] gmx 4.6: incompatible gpu device   Oliver Mirus
  • [gmx-users] gmx 4.6: incompatible gpu device   Justin Lemkul
• [gmx-users] REMD simulation   Christopher Neale
  • [gmx-users] REMD simulation   Mark Abraham
• [gmx-users] maruthi.sena at gmail.com wants to follow you. Accept?   maruthi.sena at gmail.com
• [gmx-users] Regarding the charge group radii   rama david
  • [gmx-users] Regarding the charge group radii   Justin Lemkul
• [gmx-users] Charge group radii...   rama david
• [gmx-users] problem with EM   Ali Alizadeh
  • [gmx-users] problem with EM   Justin Lemkul
• [gmx-users] About HPO4   闪耀星空
  • [gmx-users] About HPO4   Justin Lemkul
• [gmx-users] Re: Regarding the charge group radii   Dr. Vitaly Chaban
• [gmx-users] enthalpy changes (ΔH) and entropy changes (ΔS)   shahab shariati
• 回复： [gmx-users] About HPO4   闪耀星空
  • 回复： [gmx-users] About HPO4   Justin Lemkul
• [gmx-users] Re: Strange form of RDF curve   Thomas Schlesier
  • [gmx-users] Re: Strange form of RDF curve   André Farias de Moura
• [gmx-users] Own Coarse Grained ff   Steven Neumann
  • [gmx-users] Own Coarse Grained ff   Justin Lemkul
• [gmx-users] pressure_coupling   tarak karmakar
  • [gmx-users] pressure_coupling   Justin Lemkul
    • [gmx-users] pressure_coupling   tarak karmakar
      • [gmx-users] pressure_coupling   Justin Lemkul
      • AW: [gmx-users] pressure_coupling   Florian Dommert
      • [gmx-users] pressure_coupling   tarak karmakar
      • AW: [gmx-users] pressure_coupling   Florian Dommert
      • [gmx-users] pressure_coupling   tarak karmakar
      • AW: [gmx-users] pressure_coupling   Florian Dommert
      • [gmx-users] pressure_coupling   Michael Shirts
• [gmx-users] Re, problem with EM   Ali Alizadeh
  • [gmx-users] Re, problem with EM   Justin Lemkul
• [gmx-users] Re, problem with EM   Ali Alizadeh
  • [gmx-users] Re, problem with EM   Justin Lemkul
• [gmx-users] Some notes on parameterising dreiding   Laura Leay
• [gmx-users] Re: pressure_coupling   Dr. Vitaly Chaban
• [gmx-users] Re,problem with EM   Ali Alizadeh
  • [gmx-users] Re,problem with EM   Justin Lemkul
• [gmx-users] i don't know how can i determine emtol   Ali Alizadeh
  • [gmx-users] i don't know how can i determine emtol   Justin Lemkul
• [gmx-users] About Temperature coupling and Energy Transfer....   jhon michael espinosa duran
  • [gmx-users] About Temperature coupling and Energy Transfer....   Justin Lemkul
    • [gmx-users] Re: About Temperature coupling and Energy Transfer....   cyberjhon
      • [gmx-users] Re: About Temperature coupling and Energy Transfer....   Justin Lemkul
• [gmx-users] Re,i don't know how can i determine emtol   Ali Alizadeh
  • [gmx-users] Re,i don't know how can i determine emtol   Ivan Gladich
    • [gmx-users] Re,i don't know how can i determine emtol   Ivan Gladich
• [gmx-users] how to repeat simulation correctly?   Albert
  • [gmx-users] how to repeat simulation correctly?   Mark Abraham
    • [gmx-users] how to repeat simulation correctly?   Felipe Pineda, PhD
      • [gmx-users] how to repeat simulation correctly?   Mark Abraham
      • [gmx-users] how to repeat simulation correctly?   Felipe Pineda, PhD
      • [gmx-users] how to repeat simulation correctly?   Erik Marklund
      • [gmx-users] how to repeat simulation correctly?   Felipe Pineda, PhD
      • [gmx-users] how to repeat simulation correctly?   Erik Marklund
      • [gmx-users] how to repeat simulation correctly?   Felipe Pineda, PhD
      • [gmx-users] how to repeat simulation correctly?   Erik Marklund
      • [gmx-users] how to repeat simulation correctly?   Mark Abraham
• [gmx-users] Re: hpo4   Justin Lemkul
• [gmx-users] (no subject)   Emanuele Coccia
• [gmx-users] Gromacs GPU   Emanuele Coccia
  • [gmx-users] Gromacs GPU   Justin Lemkul
    • [gmx-users] Gromacs GPU   Emanuele Coccia
      • [gmx-users] Gromacs GPU   Justin Lemkul
      • [gmx-users] Gromacs GPU   Emanuele Coccia
      • [gmx-users] Gromacs GPU   Justin Lemkul
• [gmx-users] Vizualization with VMD: no image appears   shch406
  • [gmx-users] Vizualization with VMD: no image appears   Justin Lemkul
  • AW: [gmx-users] Vizualization with VMD: no image appears   Rausch, Felix
    • [gmx-users] Vizualization with VMD: no image appears   rama david
      • [gmx-users] Vizualization with VMD: no image appears   tarak karmakar
• [gmx-users] Re,i don't know how can i determine emtol   Ali Alizadeh
  • [gmx-users] Re,i don't know how can i determine emtol   Ivan Gladich
• [gmx-users] REMD with umbrella sampling in Gromacs 4.5.5   dejun_lin at urmc.rochester.edu
• [gmx-users] REMD with umbrella sampling in Gromacs 4.5.5   Lin, Dejun
• [gmx-users] g_select   akn
• [gmx-users] RE: GROMACS96 proper dihetral parameters/OPLS   Junfang.Zhang at csiro.au
  • [gmx-users] RE: GROMACS96 proper dihetral parameters/OPLS   Justin Lemkul
    • [gmx-users] RE: GROMACS96 proper dihetral parameters/OPLS   Junfang.Zhang at csiro.au
      • [gmx-users] RE: GROMACS96 proper dihetral parameters/OPLS   Justin Lemkul
• [gmx-users] G_sas change in hydrophilic and hydrophobic surface area   rama david
  • [gmx-users] G_sas change in hydrophilic and hydrophobic surface area   Justin Lemkul
    • [gmx-users] G_sas change in hydrophilic and hydrophobic surface area   rama david
      • [gmx-users] G_sas change in hydrophilic and hydrophobic surface area   Justin Lemkul
      • [gmx-users] G_sas change in hydrophilic and hydrophobic surface area   rama david
• [gmx-users] Question about conserved energy in MTTK   Shun Sakuraba
  • [gmx-users] Question about conserved energy in MTTK   tarak karmakar
    • [gmx-users] Question about conserved energy in MTTK   Michael Shirts
      • [gmx-users] Question about conserved energy in MTTK   Shun Sakuraba
• [gmx-users] How to obtain MSD trajectory for only one direction from g_msd ??   Kiwoong Kim
  • [gmx-users] How to obtain MSD trajectory for only one direction from g_msd ??   Justin Lemkul
    • [gmx-users] How to obtain MSD trajectory for only one direction from g_msd ??   Kiwoong Kim
• [gmx-users] top2psf with Amber99SB-ILDN   Steven Neumann
  • [gmx-users] top2psf with Amber99SB-ILDN   francesco oteri
    • [gmx-users] top2psf with Amber99SB-ILDN   Steven Neumann
      • [gmx-users] top2psf with Amber99SB-ILDN   francesco oteri
• [gmx-users] Bonded parametrs for CG   Steven Neumann
  • [gmx-users] Bonded parametrs for CG   Elton Carvalho
• [gmx-users] trjconv -pbc nojump across multiple trajectories   Pablo Englebienne
  • [gmx-users] trjconv -pbc nojump across multiple trajectories   Tsjerk Wassenaar
• [gmx-users] On the usage of SD integrator as the thermostat   James Starlight
• [gmx-users] Re: trjconv -pbc nojump across multiple trajectories   Pablo Englebienne
  • [gmx-users] Re: trjconv -pbc nojump across multiple trajectories   Tsjerk Wassenaar
• [gmx-users] Re: pressure_coupling   ABEL Stephane 175950
  • [gmx-users] Re: pressure_coupling   Michael Shirts
• [gmx-users] Re,i don't know how can i determine emtol   Ali Alizadeh
  • [gmx-users] Re,i don't know how can i determine emtol   Ivan Gladich
• [gmx-users] Re,i don't know how can i determine emtol   Ali Alizadeh
• [gmx-users] trjconv -seq does not work?   Yun Shi
  • [gmx-users] trjconv -seq does not work?   Justin Lemkul
• [gmx-users] Reminder: maruthi.sena at gmail.com wants to follow you. Accept?   maruthi.sena at gmail.com
• [gmx-users] Adding His tag to N-ter of a protein   Jong Wha Lee
• [gmx-users] strange lincs warning with version 4.6   sebastian
  • [gmx-users] strange lincs warning with version 4.6   Szilárd Páll
• [gmx-users] Query about GPU version of Gromacs   Pruthvi Bejugam
  • [gmx-users] Query about GPU version of Gromacs   Mark Abraham
• [gmx-users] Bonded parameters from all atom to CG   Steven Neumann
• [gmx-users] Re,i don't know how can i determine emtol   Ali Alizadeh
• [gmx-users] REGARDING DOUBT   Subramaniam Boopathi
  • [gmx-users] REGARDING DOUBT   Justin Lemkul
• [gmx-users] Energy minimization with walls   harshaljain950
• [gmx-users] On the usage of SD integrator as the thermostat   Christopher Neale
  • [gmx-users] On the usage of SD integrator as the thermostat   Krzysztof Murzyn
• [gmx-users] Different average H bonds with different g_hbond releases   Luigi CAVALLO
  • [gmx-users] Different average H bonds with different g_hbond releases   Justin Lemkul
    • [gmx-users] Different average H bonds with different g_hbond releases   Acoot Brett
      • [gmx-users] Different average H bonds with different g_hbond releases   David van der Spoel
      • [gmx-users] Is any command to distinguish gromacs 4.5.4 and 4.5.5   Acoot Brett
      • [gmx-users] Is any command to distinguish gromacs 4.5.4 and 4.5.5   Mark Abraham
      • [gmx-users] Is any command to distinguish gromacs 4.5.4 and 4.5.5   Szilárd Páll
• [gmx-users] Re: gmx-users Digest, Vol 103, Issue 111   Pruthvi Bejugam
• [gmx-users] force vs time plot   Paula Andrea Delgado Pinzon
  • [gmx-users] force vs time plot   Justin Lemkul
• [gmx-users] Group selection for the output in trjconv command   Shima Arasteh
  • [gmx-users] Group selection for the output in trjconv command   Justin Lemkul
• [gmx-users] shall we use Charmm_t3p water model?   Albert
  • [gmx-users] shall we use Charmm_t3p water model?   Mark Abraham
    • [gmx-users] shall we use Charmm_t3p water model?   Albert
• [gmx-users] Principal Component Analysis (PCA)   harshaljain950
  • [gmx-users] Principal Component Analysis (PCA)   Tsjerk Wassenaar
• [gmx-users] maruthi.sena at gmail.com is awaiting your reply. Accept?   maruthi.sena at gmail.com
• [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0   Venkat Reddy
  • [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0   Justin Lemkul
    • [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0   Venkat Reddy
      • [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0   Justin Lemkul
      • [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0   Venkat Reddy
      • [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0   Venkat Reddy
      • [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0   Justin Lemkul
      • [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0   Venkat Reddy
      • [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0   Justin Lemkul
• [gmx-users] Umbrella sampling - regd   ramesh cheerla
  • [gmx-users] Umbrella sampling - regd   Justin Lemkul
    • [gmx-users] Umbrella sampling - regd   ramesh cheerla
• [gmx-users] where is the script?   Albert
  • [gmx-users] where is the script?   David van der Spoel
    • [gmx-users] where is the script?   Albert
• [gmx-users] Re: energy-mimisation-problem   SANTU BISWAS
  • [gmx-users] Re: energy-mimisation-problem   Justin Lemkul
• [gmx-users] Re: force vs time plot   Thomas Schlesier
• [gmx-users] maxwell-boltzmann distribution   Zahra M
• [gmx-users] Installation problems with MacOS 10.7.5   Stefan Jasconek
  • [gmx-users] Installation problems with MacOS 10.7.5   Mark Abraham
• [gmx-users] Bonds - force constant for given Beads   Steven Neumann
  • [gmx-users] Bonds - force constant for given Beads   André Farias de Moura
• [gmx-users] g_select error   Albert
  • [gmx-users] g_select error   Albert
    • [gmx-users] g_select error   Justin Lemkul
      • [gmx-users] g_select error   Albert
      • [gmx-users] g_select error   Justin Lemkul
      • [gmx-users] g_select error   Albert
• [gmx-users] Re: Bonds - force constant for given Beads   Thomas Schlesier
• [gmx-users] How to avoid adding ions close to ligand   Yun Shi
  • [gmx-users] How to avoid adding ions close to ligand   David van der Spoel
    • [gmx-users] How to avoid adding ions close to ligand   Yun Shi
      • [gmx-users] How to avoid adding ions close to ligand   Peter C. Lai
• [gmx-users] itp atomtypes section   James Cannon
  • [gmx-users] itp atomtypes section   Tsjerk Wassenaar
    • [gmx-users] itp atomtypes section   James Cannon
• [gmx-users] Validation of topology ....   rama david
  • [gmx-users] Fwd: Validation of topology ....   rama david
• [gmx-users] error during minimization   Shine A
  • [gmx-users] error during minimization   Venkat Reddy
  • [gmx-users] error during minimization   Justin Lemkul
• [gmx-users] Calculation Population densities on the PCA projections   James Starlight
• [gmx-users] Error in gromacs installation in cygwin   ashutosh srivastava
• [gmx-users] g_bar and second law violations   Sanku M
  • [gmx-users] g_bar and second law violations   Justin Lemkul
• [gmx-users] how to run charmm2gromacs-pvm.py correctly?   Albert
  • [gmx-users] how to run charmm2gromacs-pvm.py correctly?   David van der Spoel
    • [gmx-users] how to run charmm2gromacs-pvm.py correctly?   Albert
• [gmx-users] Gromacs 4.6 segmentation fault with mdrun   Makoto Yoneya
  • [gmx-users] Gromacs 4.6 segmentation fault with mdrun   Szilárd Páll
• [gmx-users] convergence problem   Shine A
  • [gmx-users] convergence problem   Justin Lemkul
• [gmx-users] About Diffusion of water Towards Tail part of Lipids   vidhya sankar
  • [gmx-users] About Diffusion of water Towards Tail part of Lipids   Justin Lemkul
• [gmx-users] AU-S bonded parameter   fatemeh ramezani
  • [gmx-users] AU-S bonded parameter   Justin Lemkul
• [gmx-users] On the usage of SD integrator as the thermostat   Christopher Neale
• [gmx-users] Hbonds between Adenine and Thymine   Hovakim Grabski
  • [gmx-users] Hbonds between Adenine and Thymine   Justin Lemkul
    • [gmx-users] Hbonds between Adenine and Thymine   Erik Marklund
• [gmx-users] mixed single-precision GPU and double-precision CPU calculation   Makoto Yoneya
  • [gmx-users] mixed single-precision GPU and double-precision CPU calculation   Berk Hess
    • [gmx-users] RE: mixed single-precision GPU and double-precision CPU calculation   Makoto Yoneya
• [gmx-users] gromacs 4.5.5 Do_dssp segment fault   Kdead
  • [gmx-users] gromacs 4.5.5 Do_dssp segment fault   Justin Lemkul
• [gmx-users] what does it mean by 'started run on node 0'   Yihua Zhou
• [gmx-users] what does it mean by 'started mdrun on node 0'   Yihua Zhou
  • [gmx-users] what does it mean by 'started mdrun on node 0'   Tsjerk Wassenaar
• [gmx-users] error during nvt equilibration   Shine A
  • [gmx-users] error during nvt equilibration   Justin Lemkul
• [gmx-users] MM-GB/SA analysis in Gromacs   Anna Marabotti
  • [gmx-users] MM-GB/SA analysis in Gromacs   andrea spitaleri
• [gmx-users] gromacs 4.5.5 Do_dssp segment fault   Kdead
• [gmx-users] Hbonds between Adenine and Thymine   Justin Lemkul
• [gmx-users] error during mdrun   Shine A
  • [gmx-users] error during mdrun   Justin Lemkul
• [gmx-users] Electrostatic field in atoms - GROMACS is not reading table interaction functions for bonded interactions   Ariana Torres Knoop
  • [gmx-users] Electrostatic field in atoms - GROMACS is not reading table interaction functions for bonded interactions   Justin Lemkul
    • [gmx-users] Re:Energy landscapes   lloyd riggs
    • [gmx-users] Electrostatic field in atoms - GROMACS is not reading table interaction functions for bonded interactions   Berk Hess
• [gmx-users] g_velacc   Dr. Vitaly Chaban
• [gmx-users] g_tune_pme for multiple nodes   Chandan Choudhury
  • AW: [gmx-users] g_tune_pme for multiple nodes   Florian Dommert
  • [gmx-users] g_tune_pme for multiple nodes   Carsten Kutzner
• [gmx-users] Potential energy from a previous configuration mismatch   juan-manuel.castillo at mv.uni-kl.de
  • [gmx-users] Potential energy from a previous configuration mismatch   Justin Lemkul
    • [gmx-users] Re: Potential energy from a previous configuration mismatch   escajarro
      • [gmx-users] Re: Potential energy from a previous configuration mismatch   Justin Lemkul
      • [gmx-users] Re: Potential energy from a previous configuration mismatch   escajarro
      • [gmx-users] Re: Potential energy from a previous configuration mismatch   Justin Lemkul
      • [gmx-users] Re: Potential energy from a previous configuration mismatch   escajarro
      • [gmx-users] Re: Potential energy from a previous configuration mismatch   Justin Lemkul
      • [gmx-users] Re: Potential energy from a previous configuration mismatch   Mark Abraham
      • [gmx-users] Re: Potential energy from a previous configuration mismatch   Justin Lemkul
      • [gmx-users] Re: Potential energy from a previous configuration mismatch   Mark Abraham
• [gmx-users] About Diffusion of Water towards Protein in ceter of box   vidhya sankar
  • [gmx-users] About Diffusion of Water towards Protein in ceter of box   Justin Lemkul
• [gmx-users] water mediated hydrogen bond   Raj
  • [gmx-users] water mediated hydrogen bond   Justin Lemkul
• [gmx-users] segmentation fault   Shine A
  • [gmx-users] segmentation fault   Justin Lemkul
• [gmx-users] Does GPU support ATI card?   Albert
  • [gmx-users] Does GPU support ATI card?   Szilárd Páll
    • [gmx-users] Does GPU support ATI card?   Albert
      • [gmx-users] Does GPU support ATI card?   Szilárd Páll
      • [gmx-users] Does GPU support ATI card?   Albert
      • [gmx-users] Does GPU support ATI card?   Justin Lemkul
      • [gmx-users] Does GPU support ATI card?   Szilárd Páll
      • [gmx-users] Does GPU support ATI card?   Justin Lemkul
• [gmx-users] Computing energies using g_energy (is -nmol mandatory?)   André Ferreira
  • [gmx-users] Computing energies using g_energy (is -nmol mandatory?)   Justin Lemkul
• [gmx-users] query regarding PMF calculation   Timir Hajari
  • [gmx-users] query regarding PMF calculation   Justin Lemkul
• Отв: [gmx-users] Hbonds between Adenine and Thymine   Justin Lemkul
• [gmx-users] (no subject)   Mark Abraham
• [gmx-users] GROMACS 4.6 beta1 released!   Mark Abraham
  • [gmx-users] Re: GROMACS 4.6 beta1 released!   Mark Abraham
• [gmx-users] How are the charges of the gromos96 forcefiel calculated ?   Tanos Franca
  • [gmx-users] How are the charges of the gromos96 forcefiel calculated ?   Justin Lemkul
• [gmx-users] Build problem with 4.6beta1   Justin Lemkul
  • [gmx-users] Build problem with 4.6beta1   Szilárd Páll
    • [gmx-users] Build problem with 4.6beta1   Justin Lemkul
  • [gmx-users] Build problem with 4.6beta1   Mark Abraham
• [gmx-users] Build problem with 4.6beta1   Roland Schulz
  • [gmx-users] Build problem with 4.6beta1   Justin Lemkul
• [gmx-users] is it possible?   Albert
  • [gmx-users] is it possible?   Mark Abraham
• [gmx-users] Build on OSX with 4.6beta1   Carlo Camilloni
• [gmx-users] Observations about g_hbond -dist and -ang   Cara Kreck
  • [gmx-users] Observations about g_hbond -dist and -ang   Erik Marklund
• [gmx-users] Build on OSX with 4.6beta1   Roland Schulz
• [gmx-users] Invitation to connect on LinkedIn   Vasilis Georgilas via LinkedIn
• [gmx-users] Build on OSX with 4.6beta1   Roland Schulz
• [gmx-users] g_hbond routine   Velia Minicozzi
  • [gmx-users] g_hbond routine   Justin Lemkul
• [gmx-users] COLVAR not printing   tarak karmakar
• [gmx-users] Re: Build on OSX with 4.6beta1   Carlo Camilloni
• [gmx-users] Re: Build on OSX with 4.6beta1   Roland Schulz

Last message date: Fri Nov 30 20:18:53 CET 2012
Archived on: Thu Nov 14 12:13:36 CET 2013

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