March 2009 Archives by thread

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Starting: Sun Mar 1 00:08:50 CET 2009
Ending: Tue Mar 31 23:56:22 CEST 2009
Messages: 843

• [gmx-users] atomtype OWT4 not found but OWT3 and OWT5 is ok in amber03 force field....how is that possible?   Mark Abraham
• [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system   GuoGuangjun
  • [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system   David van der Spoel
  • [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system   Berk Hess
    • [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system   Berk Hess
    • [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system   GuoGuangjun
      • [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system   Berk Hess
      • [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system   GuoGuangjun
      • [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system   Jussi Lehtola
      • [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 59, Issue 1   drugdesign
  • [gmx-users] Re: gmx-users Digest, Vol 59, Issue 1   Mark Abraham
• [gmx-users] Question   Elias santos
  • [gmx-users] Question   Mark Abraham
    • [gmx-users] g_order version 4.0.x   Sarah Witzke
      • [gmx-users] g_order version 4.0.x   David van der Spoel
      • SV: [gmx-users] g_order version 4.0.x   Sarah Witzke
      • SV: [gmx-users] g_order version 4.0.x   Justin A. Lemkul
      • SV: SV: [gmx-users] g_order version 4.0.x   Sarah Witzke
      • SV: SV: [gmx-users] g_order version 4.0.x   Sarah Witzke
      • SV: SV: [gmx-users] g_order version 4.0.x   Justin A. Lemkul
      • SV: SV: SV: [gmx-users] g_order version 4.0.x   Sarah Witzke
      • SV: SV: SV: [gmx-users] g_order version 4.0.x   Justin A. Lemkul
      • SV: SV: SV: [gmx-users] g_order version 4.0.x   Justin A. Lemkul
      • SV: SV: SV: [gmx-users] g_order version 4.0.x   Sarah Witzke
• [gmx-users] tool.top does not found   drugdesign
  • [gmx-users] tool.top does not found   Justin A. Lemkul
• [gmx-users] help with FAD topology, please   Miguel Quiliano Meza
  • [gmx-users] help with FAD topology, please   Justin A. Lemkul
• [gmx-users] (no subject)   Sunil Thapa
  • [gmx-users] (no subject)   Mark Abraham
• [gmx-users] regarding dimethylated lysine topology file   prasun kumar
  • [gmx-users] regarding dimethylated lysine topology file   Anil Kumar
  • [gmx-users] regarding dimethylated lysine topology file   Justin A. Lemkul
• [gmx-users] problem in creating .gro file   nitu sharma
  • [gmx-users] problem in creating .gro file   Justin A. Lemkul
  • [gmx-users] problem in creating .gro file   Mark Abraham
• [gmx-users] settingparameters for energy minimization   vivek sharma
  • [gmx-users] settingparameters for energy minimization   Justin A. Lemkul
    • [gmx-users] settingparameters for energy minimization   vivek sharma
      • [gmx-users] settingparameters for energy minimization   Justin A. Lemkul
• [gmx-users] angle restraints in gromacs 4   Brian Novak
• [gmx-users] a question about analysis   oguz gurbulak
  • [gmx-users] a question about analysis   Justin A. Lemkul
• [gmx-users] generalized order parameters S2   Dechang Li
  • [gmx-users] generalized order parameters S2   Justin A. Lemkul
• [gmx-users] How to define protein surface residues   Lee Soin
  • [gmx-users] How to define protein surface residues   David van der Spoel
    • [gmx-users] How to define protein surface residues   Lee Soin
      • [gmx-users] How to define protein surface residues   Mark Abraham
• [gmx-users] Detail of Script.sh in Gromacs-4.0.3?   mhviet at ifpan.edu.pl
  • [gmx-users] Detail of Script.sh in Gromacs-4.0.3?   David van der Spoel
• [gmx-users] regarding dimethylated lysine topology file   prasun kumar
  • [gmx-users] regarding dimethylated lysine topology file   Justin A. Lemkul
• [gmx-users] about LINCS WARNING   mhviet at ifpan.edu.pl
  • [gmx-users] about LINCS WARNING   Roland Schulz
• [gmx-users] Thank Roland   mhviet at ifpan.edu.pl
• [gmx-users] How to handle incomplete PDB file?   Lee Soin
  • [gmx-users] How to handle incomplete PDB file?   Justin A. Lemkul
    • [gmx-users] How to handle incomplete PDB file?   Justin A. Lemkul
      • [gmx-users] How to handle incomplete PDB file?   Lee Soin
      • [gmx-users] How to handle incomplete PDB file?   Tsjerk Wassenaar
• [gmx-users] Can not open file: topol.tpr   drugdesign
  • [gmx-users] Can not open file: topol.tpr   Justin A. Lemkul
  • [gmx-users] Can not open file: topol.tpr   J. Rui Rodrigues
  • [gmx-users] Can not open file: topol.tpr   Mark Abraham
    • [gmx-users] Can not open file: topol.tpr   Tsjerk Wassenaar
• [gmx-users] (no subject)   Antonia Vyrkou
• [gmx-users] (no subject)   Antonia Vyrkou
  • [gmx-users] (no subject)   Mark Abraham
• [gmx-users] regarding dimethylated lysine topology file   Antonia Vyrkou
• [gmx-users] regarding dimethylated lysine topology file   Antonia Vyrkou
• [gmx-users] Polyethylene (PE) simulations in Gromacs - please!   Chansoo Kim
  • [gmx-users] Fwd: Polyethylene (PE) simulations in Gromacs - please!   Chansoo Kim
  • [gmx-users] Polyethylene (PE) simulations in Gromacs - please!   Justin A. Lemkul
    • [gmx-users] Polyethylene (PE) simulations in Gromacs - please!   Chansoo Kim
      • [gmx-users] Polyethylene (PE) simulations in Gromacs - please!   Chansoo Kim
      • [gmx-users] Polyethylene (PE) simulations in Gromacs - please!   Justin A. Lemkul
      • [gmx-users] Polyethylene (PE) simulations in Gromacs - please!   Chansoo Kim
      • [gmx-users] Polyethylene (PE) simulations in Gromacs - please!   Zuzana Benkova
      • [gmx-users] Polyethylene (PE) simulations in Gromacs - please!   Justin A. Lemkul
• [gmx-users] add zinc in gromacs/cpmd   Jacopo Sgrignani
  • [gmx-users] add zinc in gromacs/cpmd   Marius Retegan
• [gmx-users] gromacs-4.0.2, parallel performance in two quadcore xeon machines   Antoine FORTUNE
• [gmx-users] Polyethylene (PE) simulations in Gromacs - please!   Justin A. Lemkul
• [gmx-users] Problem configuring openMPI   Manik Mayur
  • [gmx-users] Problem configuring openMPI   Nicolas
    • [gmx-users] Problem configuring openMPI   Manik Mayur
      • [gmx-users] Problem configuring openMPI   Nicolas
      • [gmx-users] Problem configuring openMPI   Manik Mayur
      • [gmx-users] Problem configuring openMPI   Nicolas
      • [gmx-users] Problem configuring openMPI   Manik Mayur
      • [gmx-users] Problem configuring openMPI   Manik Mayur
      • [gmx-users] Problem configuring openMPI   Roland Schulz
      • [gmx-users] Problem configuring openMPI   Manik Mayur
      • [gmx-users] Problem configuring openMPI   Roland Schulz
      • [gmx-users] Problem configuring openMPI   Manik Mayur
      • [gmx-users] Problem configuring openMPI   Mark Abraham
      • [gmx-users] Problem configuring openMPI   Manik Mayur
• [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3   Claus Valka
  • [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3   Berk Hess
• [gmx-users] box size   noob noob
  • [gmx-users] box size   Ricardo Soares
• [gmx-users] simulation box   noob noob
  • [gmx-users] simulation box   Ricardo Soares
    • [gmx-users] simulation box   Justin A. Lemkul
      • [gmx-users] simulation box   Lucio Montero
• [gmx-users] gromacs on itanium2   Marius Retegan
  • [gmx-users] gromacs on itanium2   David van der Spoel
    • [gmx-users] gromacs on itanium2   Marius Retegan
      • [gmx-users] gromacs on itanium2   Mark Abraham
    • [gmx-users] gromacs on itanium2   Erik Lindahl
      • [gmx-users] gromacs on itanium2   Marius Retegan
      • [gmx-users] gromacs on itanium2   David van der Spoel
      • [gmx-users] gromacs on itanium2   Marius Retegan
      • [gmx-users] gromacs on itanium2   Justin A. Lemkul
      • GMX-4.0.4 failed test (Re: [gmx-users] gromacs on itanium2)   Tru Huynh
• [gmx-users] Diffusion coefficients ( Exp X Simul )   Eudes Fileti
  • [gmx-users] Diffusion coefficients ( Exp X Simul )   David van der Spoel
  • [gmx-users] Diffusion coefficients ( Exp X Simul )   Omer Markovitch
• [gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons   chris.neale at utoronto.ca
  • [gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons   Mark Abraham
• [gmx-users] g_wham 4..0.x input file: tpr-files.dat ?   Y.C. Huang
  • [gmx-users] g_wham 4..0.x input file: tpr-files.dat ?   Justin A. Lemkul
• [gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons   chris.neale at utoronto.ca
  • [gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons   Roland Schulz
  • [gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons   Mark Abraham
• [gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons   chris.neale at utoronto.ca
• [gmx-users] combination rules -- the part aboutthecombinationrules   Shuangxing Dai
  • [gmx-users] combination rules -- the part aboutthecombinationrules   Mark Abraham
• [gmx-users] RE: Diffusion coefficients ( Exp X Simul )   Vitaly V. Chaban
• [gmx-users] Diffusion coefficients ( Exp X Simul )   Eudes Fileti
  • [gmx-users] Diffusion coefficients ( Exp X Simul )   David van der Spoel
• [gmx-users] exclude intramolecular coulombic   Antonia Vyrkou
• [gmx-users] exclude intramolecular coulombic   Antonia Vyrkou
• [gmx-users] exclude intramolecular coulombic   Antonia Vyrkou
• [gmx-users] exclude intramolecular coulombic   Antonia Vyrkou
• [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3   Claus Valka
  • [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3   Berk Hess
• WG: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3   Claus Valka
  • WG: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3   Berk Hess
    • [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3   Claus Valka
      • [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3   Berk Hess
    • [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3   Claus Valka
      • [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3   Claus Valka
      • [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3   Mark Abraham
• [gmx-users] How g_energy program calculates the averages ?   rashmi_chem at iitb.ac.in
  • [gmx-users] How g_energy program calculates the averages ?   Mark Abraham
• [gmx-users] Fatal error with g_hbond   Grzegorz Jezierski
  • [gmx-users] Fatal error with g_hbond   Justin A. Lemkul
• [gmx-users] How to define "stretch" in ffoplsaabon.itp ?   Tree
  • [gmx-users] How to define "stretch" in ffoplsaabon.itp ?   Justin A. Lemkul
    • [gmx-users] How to define "stretch" in ffoplsaabon.itp ?   Tree
      • [gmx-users] How to define "stretch" in ffoplsaabon.itp ?   Justin A. Lemkul
      • [gmx-users] How to define "stretch" in ffoplsaabon.itp ?   Tree
      • Fwd: [gmx-users] How to define "stretch" in ffoplsaabon.itp ?   Tree
      • Fwd: [gmx-users] How to define "stretch" in ffoplsaabon.itp ?   Justin A. Lemkul
  • [gmx-users] Fwd: How to define "stretch" in ffoplsaabon.itp ?   Tree
• [gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons   chris.neale at utoronto.ca
• [gmx-users] MPI-based errors on the power6 at large parallelization   chris.neale at utoronto.ca
  • [gmx-users] MPI-based errors on the power6 at large parallelization   Roland Schulz
• [gmx-users] about force fields   oguz gurbulak
• [gmx-users] about force fields   chris.neale at utoronto.ca
• [gmx-users] where is the position of the partial charges?   Chih-Ying Lin
• [gmx-users] where is the position of the partial charges?   Chris Neale
• [gmx-users] g_vellac in the last versions   Florian Dommert
• [gmx-users] what is data type the string "rvec" stands for?   Cao, Yang
  • [gmx-users] what is data type the string "rvec" stands for?   Mark Abraham
• [gmx-users] How VMD to display the velocity   Dechang Li
  • [gmx-users] How VMD to display the velocity   Höfling Martin
• [gmx-users] Installing topolbuild   vivek sharma
  • [gmx-users] Installing topolbuild   Bruce D. Ray
    • [gmx-users] Installing topolbuild   vivek sharma
      • [gmx-users] Installing topolbuild   Bruce D. Ray
• [gmx-users] Interpretation of g_chi results   naimah haron naimah
• [gmx-users] eigenvec.trr and eigenval.xvg   Dechang Li
  • [gmx-users] eigenvec.trr and eigenval.xvg   Berk Hess
• [gmx-users] Re: gmx-users Digest, Vol 59, Issue 44   Vitaly V. Chaban
• [gmx-users] Problems with SMD using gromacs   huifang liu
• [gmx-users] Re: Ligand is moving far away after energy minimization   Ms. Aswathy S
  • [gmx-users] Re: Ligand is moving far away after energy minimization   Justin A. Lemkul
• [gmx-users] How to add any new force field to GRMOACS for modelling the system of interest?   wuxiao
  • [gmx-users] How to add any new force field to GRMOACS for modelling the system of interest?   Justin A. Lemkul
• [gmx-users] 1-4 interaction, infinite meanings for energies   drugdesign
  • [gmx-users] 1-4 interaction, infinite meanings for energies   Justin A. Lemkul
• [gmx-users] genion command with PDB files for amber03 force field   drugdesign
  • [gmx-users] genion command with PDB files for amber03 force field   Justin A. Lemkul
  • [gmx-users] genion command with PDB files for amber03 force field   Joshua Ballanco
    • [gmx-users] genion command with PDB files for amber03 force field   Tsjerk Wassenaar
• [gmx-users] Re: gmx-users Digest, Vol 59, Issue 48   Vitaly V. Chaban
• [gmx-users] problem extending simulation 64 proc   Rebeca García Fandiño
  • [gmx-users] problem extending simulation 64 proc   Berk Hess
• [gmx-users] problem in running grompp   victor doss
• [gmx-users] problem running grompp - error message here   victor doss
  • [gmx-users] problem running grompp - error message here   Justin A. Lemkul
• [gmx-users] OXY not found   Andy Torres
  • [gmx-users] OXY not found   Justin A. Lemkul
  • [gmx-users] Re: OXY not found   Andy Torres
• [gmx-users] distance restraints for alpha helix   abhigna polavarapu
• [gmx-users] OXY not found   Chris Neale
• [gmx-users] How to build a coarse grained model and do the simulation with Gromacs   侃
• [gmx-users] How to build a coarse grained model and do the simulation with Gromacs   侃
  • [gmx-users] How to build a coarse grained model and do the simulation with Gromacs   Justin A. Lemkul
    • [gmx-users] How to build a coarse grained model and do the simulation with Gromacs   Justin A. Lemkul
• [gmx-users] Can make_ndx generate indices only for heavy atoms?   Lee Soin
  • [gmx-users] Can make_ndx generate indices only for heavy atoms?   Justin A. Lemkul
• [gmx-users] How to break a disulfide bond ???   Venkat Reddy
  • [gmx-users] How to break a disulfide bond ???   sharada
    • [gmx-users] How to break a disulfide bond ???   Venkat Reddy
      • [gmx-users] How to break a disulfide bond ???   sharada
      • [gmx-users] How to break a disulfide bond ???   sharada
      • [gmx-users] How to break a disulfide bond ???   Venkat Reddy
      • [gmx-users] How to break a disulfide bond ???   Mark Abraham
      • [gmx-users] How to break a disulfide bond ???   Justin A. Lemkul
• [gmx-users] Change only one atom pair VdW interaction   Gaurav Chopra
  • [gmx-users] Change only one atom pair VdW interaction   Mark Abraham
• [gmx-users] running GROMACS-MPI on Rocks cluster- strange results   kala
  • [gmx-users] running GROMACS-MPI on Rocks cluster- strange results   Diego Enry Gomes
• [gmx-users] Positive energy for Coulumb term. Does this mean Coulumb interaction destabilizes protein?   Seungpyo Hong
• [gmx-users] Re: Positive energy for Coulumb term. Does this mean Coulumb, interaction destabilizes protein? (Seungpyo Hong)   Gerrit Groenhof
  • [gmx-users] Re: Positive energy for Coulumb term. Does this mean Coulumb, interaction destabilizes protein? (Seungpyo Hong)   Seungpyo Hong
• [gmx-users] RE: g_vellac   Vitaly V. Chaban
  • [gmx-users] Re: g_vellac   Florian Dommert
    • [gmx-users] Re: g_vellac   Vitaly V. Chaban
      • [gmx-users] Re: g_vellac   Florian Dommert
• [gmx-users] (no subject)   ANINDITA GAYEN
• [gmx-users] gromacs in parallel version   ANINDITA GAYEN
  • [gmx-users] gromacs in parallel version   Justin A. Lemkul
  • [gmx-users] gromacs in parallel version   Diego Enry Gomes
• [gmx-users] Error in pdb2gmx   Robert Kretschmer
  • [gmx-users] Error in pdb2gmx   Justin A. Lemkul
• [gmx-users] using pdb2gmx   oguz gurbulak
  • [gmx-users] using pdb2gmx   Justin A. Lemkul
• [gmx-users] .gro files problems   Andrew Voronkov
  • [gmx-users] .gro files problems   Justin A. Lemkul
• [gmx-users] gromac 4.0.4 g utilities freeze the OS with Out of Memory   nam kim
  • [gmx-users] gromac 4.0.4 g utilities freeze the OS with Out of Memory   Mark Abraham
    • [gmx-users] gromac 4.0.4 g utilities freeze the OS with Out of Memory   Justin A. Lemkul
• [gmx-users] A Question About gmxtest   Reza Salari
• [gmx-users] pbc interference with g_dist   Suman Chakrabarty
  • [gmx-users] pbc interference with g_dist   Mark Abraham
• [gmx-users] maintaining the overall conformation of a protein during simulation   Lee Soin
  • [gmx-users] maintaining the overall conformation of a protein during simulation   Mark Abraham
• [gmx-users] pdb files   oguz gurbulak
  • [gmx-users] pdb files   Justin A. Lemkul
• [gmx-users] Polymer entanglement simulation   Tree
  • [gmx-users] Polymer entanglement simulation   Justin A. Lemkul
    • [gmx-users] Polymer entanglement simulation   Tree
      • [gmx-users] Polymer entanglement simulation   Mark Abraham
      • [gmx-users] Polymer entanglement simulation   Justin A. Lemkul
      • [gmx-users] Polymer entanglement simulation   Tree
      • [gmx-users] Polymer entanglement simulation   Justin A. Lemkul
• [gmx-users] K+ ion missing from gromos96ff in ions.itp file   Dean Cuebas
  • [gmx-users] K+ ion missing from gromos96ff in ions.itp file   Mark Abraham
• [gmx-users] Simulated annealing   jayant james
  • [gmx-users] Simulated annealing   Justin A. Lemkul
    • [gmx-users] Simulated annealing   jayant james
      • [gmx-users] Simulated annealing   Justin A. Lemkul
• [gmx-users] Invitation to connect on LinkedIn   himanshu khandelia
• [gmx-users] initial velocities Langevin dynamics   Loris Moretti
• [gmx-users] editconf and genbox using method   Marian Butu
  • [gmx-users] editconf and genbox using method   Mark Abraham
  • [gmx-users] editconf and genbox using method   Nuno Azoia
    • [gmx-users] editconf and genbox using method   Mark Abraham
      • [gmx-users] editconf and genbox using method   Justin A. Lemkul
      • [gmx-users] editconf and genbox using method   Nuno Azoia
      • [gmx-users] editconf and genbox using method   Marian Butu
• [gmx-users] solvent temperature   imparato at na.infn.it
  • [gmx-users] solvent temperature   Justin A. Lemkul
• [gmx-users] The gromacs4 run err!   li bai
  • [gmx-users] The gromacs4 run err!   Justin A. Lemkul
• [gmx-users] Re: Job Crash   Ilya Chorny
  • [gmx-users] Re: Job Crash   Mark Abraham
    • [gmx-users] Re: Job Crash   Ilya Chorny
• [gmx-users] question about parallel runing of gromacs   Xiang Mao
  • [gmx-users] question about parallel runing of gromacs   Mark Abraham
    • [gmx-users] question about parallel runing of gromacs   Xiang Mao
      • [gmx-users] question about parallel runing of gromacs   Mark Abraham
      • [gmx-users] question about parallel runing of gromacs   Diego Enry Gomes
      • [gmx-users] question about parallel runing of gromacs   Xiang Mao
      • [gmx-users] question about parallel runing of gromacs   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 59, Issue 58   Andrew Voronkov
  • [gmx-users] Re: gmx-users Digest, Vol 59, Issue 58   Jack Shultz
    • [gmx-users] Re: gmx-users Digest, Vol 59, Issue 58   Jack Shultz
• [gmx-users] pdb2gmx -vsite h hangs   Ilya Chorny
  • [gmx-users] pdb2gmx -vsite h hangs   Mark Abraham
  • [gmx-users] pdb2gmx -vsite h hangs   Justin A. Lemkul
    • [gmx-users] pdb2gmx -vsite h hangs   Ilya Chorny
      • [gmx-users] pdb2gmx -vsite h hangs   Justin A. Lemkul
• [gmx-users] problem in pdb file after SA   Homa Azizian
  • [gmx-users] problem in pdb file after SA   Diego Enry Gomes
• [gmx-users] About pull force in COM pulling   Lee Soin
• [gmx-users] Isn't dt=0.0001 very small?   Andrew Voronkov
  • [gmx-users] Isn't dt=0.0001 very small?   Tsjerk Wassenaar
  • [gmx-users] Isn't dt=0.0001 very small?   Diego Enry Gomes
• [gmx-users] do_dssp fatal error   Homa Azizian
  • [gmx-users] do_dssp fatal error   Diego Enry Gomes
• [gmx-users] problems with pulling direction and the initial spring position   huifang liu
• [gmx-users] Gromac4 grompp -v Err   li bai
  • [gmx-users] Gromac4 grompp -v Err   Tsjerk Wassenaar
  • [gmx-users] Gromac4 grompp -v Err   Mark Abraham
• [gmx-users] "Gromacs 4 grompp -v" err   li bai
• [gmx-users] Potential energy of a single amino acid residu   Tom Venken
  • [gmx-users] Potential energy of a single amino acid residu   Mark Abraham
• [gmx-users] Problem to simulate silica melts and amorphous silica with BKS potentials   David Waroquiers
  • [gmx-users] Problem to simulate silica melts and amorphous silica with BKS potentials   Mark Abraham
• [gmx-users] Re: problems with editconf command   Justin A. Lemkul
  • [gmx-users] Re: problems with editconf command   Justin A. Lemkul
• [gmx-users] relative constraint deviation after lincs   Alessandro Casoni
  • [gmx-users] relative constraint deviation after lincs   Justin A. Lemkul
• [gmx-users] Re: Fwd: gmx-users Digest, Vol 59, Issue 74   li bai
• [gmx-users] g_sdf gives wrong refmol with multiple center molecules   Atte Sillanpää
• [gmx-users] Potential energy of a single amino acid residu   Tom Venken
  • [gmx-users] Potential energy of a single amino acid residu   Justin A. Lemkul
• [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.   Chitrita Dutta Roy
  • [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.   Justin A. Lemkul
  • [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.   Tsjerk Wassenaar
    • [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.   Chitrita Dutta Roy
      • [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.   Tsjerk Wassenaar
      • [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.   Justin A. Lemkul
      • [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.   Chitrita Dutta Roy
• [gmx-users] Problems with pulling code   Marisa Roman
• [gmx-users] Cuda support   Jack Shultz
  • [gmx-users] Cuda support   Mark Abraham
• [gmx-users] Calculate asphericity of a group of atoms   loan.huynh at utoronto.ca
  • [gmx-users] Calculate asphericity of a group of atoms   Suman Chakrabarty
• [gmx-users] Infiniband Hardware   Ilya Chorny
• [gmx-users] Energy Drift in Gromacs 4.0   Ilya Chorny
  • [gmx-users] Re: Energy Drift in Gromacs 4.0   Ilya Chorny
    • [gmx-users] Re: Energy Drift in Gromacs 4.0   Mark Abraham
      • [gmx-users] Re: Energy Drift in Gromacs 4.0   Ilya Chorny
      • [gmx-users] Re: Energy Drift in Gromacs 4.0   Ilya Chorny
      • [gmx-users] Re: Energy Drift in Gromacs 4.0   David van der Spoel
      • [gmx-users] Re: Energy Drift in Gromacs 4.0   Mark Abraham
• [gmx-users] g_analylse and g_energy give different average value   Li Jianguo
  • [gmx-users] g_analylse and g_energy give different average value   Mark Abraham
• [gmx-users] how could have integrated structure after sa.   Homa Azizian
  • [gmx-users] how could have integrated structure after sa.   Mark Abraham
• [gmx-users] metal ion go out of protein after md   Homa Azizian
  • [gmx-users] metal ion go out of protein after md   #NGUYEN CONG TRI#
• [gmx-users] metal ion go out of protein after md   Homa Azizian
  • [gmx-users] metal ion go out of protein after md   Tsjerk Wassenaar
• [gmx-users] is there a possibility to convert .gro files directly to PDB?   Andrew Voronkov
  • [gmx-users] is there a possibility to convert .gro files directly to PDB?   Mark Abraham
  • [gmx-users] is there a possibility to convert .gro files directly to PDB?   Andrea Muntean
    • [gmx-users] is there a possibility to convert .gro files directly to PDB?   Omer Markovitch
      • [gmx-users] is there a possibility to convert .gro files directly to PDB?   David van der Spoel
• [gmx-users] initial velocities Langevin dynamics   Loris Moretti
  • [gmx-users] initial velocities Langevin dynamics   Mark Abraham
    • [gmx-users] initial velocities Langevin dynamics   Loris Moretti
      • [gmx-users] initial velocities Langevin dynamics   Mark Abraham
      • [gmx-users] initial velocities Langevin dynamics   Omer Markovitch
      • [gmx-users] initial velocities Langevin dynamics   Loris Moretti
      • [gmx-users] initial velocities Langevin dynamics   Ran Friedman
• [gmx-users] Broken trr-file   Hansjoerg Jerabek
  • [gmx-users] Broken trr-file   Mark Abraham
    • [gmx-users] phi / psi values using g_chi   XAvier Periole
    • [gmx-users] Broken trr-file   Hansjoerg Jerabek
      • [gmx-users] Broken trr-file   Justin A. Lemkul
      • [gmx-users] Broken trr-file   Mark Abraham
      • [gmx-users] Broken trr-file   Hansjoerg Jerabek
• [gmx-users] big system   noob noob
  • [gmx-users] big system   Justin A. Lemkul
• [gmx-users] redirect md.log to standard ourput   Jack Shultz
  • [gmx-users] redirect md.log to standard ourput   Mark Abraham
    • [gmx-users] redirect md.log to standard ourput   Jack Shultz
• [gmx-users] get a box of 100 molecules   Adrien Delmont
  • [gmx-users] get a box of 100 molecules   Justin A. Lemkul
• [gmx-users] phi / psi values using g_chi   chris.neale at utoronto.ca
  • [gmx-users] phi / psi values using g_chi   XAvier Periole
• [gmx-users] get a box of 100 molecules   Adrien Delmont
  • [gmx-users] get a box of 100 molecules   Mark Abraham
    • [gmx-users] get a box of 100 molecules   Adrien Delmont
      • [gmx-users] get a box of 100 molecules   Justin A. Lemkul
• [gmx-users] problem about compiling mdrun_mpi under cygwin   Xiang Mao
  • [gmx-users] problem about compiling mdrun_mpi under cygwin   Mark Abraham
• [gmx-users] problems with gmxtest.pl   Bernhard Bandow
  • [gmx-users] problems with gmxtest.pl   David van der Spoel
  • [gmx-users] problems with gmxtest.pl   Justin A. Lemkul
  • [gmx-users] problems with gmxtest.pl   Mark Abraham
• [gmx-users] RE : big system   noob noob
  • [gmx-users] RE : big system   Mark Abraham
• [gmx-users] phi / psi values using g_chi   chris.neale at utoronto.ca
  • [gmx-users] phi / psi values using g_chi   XAvier Periole
• [gmx-users] get a box of 100 molecules   Adrien Delmont
• [gmx-users] get a box of 100 molecules   Justin A. Lemkul
  • [gmx-users] get a box of 100 molecules   Adrien Delmont
    • [gmx-users] get a box of 100 molecules   Justin A. Lemkul
      • [gmx-users] get a box of 100 molecules   Adrien Delmont
      • [gmx-users] get a box of 100 molecules   Justin A. Lemkul
• [gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION   Jack Shultz
  • [gmx-users] Re: mdrun dies with STATUS_ACCESS_VIOLATION   Jack Shultz
    • [gmx-users] Re: mdrun dies with STATUS_ACCESS_VIOLATION   Justin A. Lemkul
  • [gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION   Mark Abraham
    • [gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION   Jack Shultz
      • [gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION   Mark Abraham
• [gmx-users] viscosity calculation using g_energy (3.3.3)   JMandumpal
  • [gmx-users] viscosity calculation using g_energy (3.3.3)   David van der Spoel
• [gmx-users] Height of the box   naimah haron naimah
  • [gmx-users] Height of the box   Mark Abraham
    • [gmx-users] Height of the box   Ilya Chorny
• [gmx-users] Questions about urea.itp   Lee Soin
  • [gmx-users] Questions about urea.itp   David van der Spoel
• [gmx-users] viscosity calculation using g_energy (3.3.3)   JMandumpal
  • [gmx-users] viscosity calculation using g_energy (3.3.3)   Berk Hess
• [gmx-users] about the restart of the mdrun   sheerychen
  • [gmx-users] about the restart of the mdrun   Mark Abraham
• [gmx-users] Re: Energy Drift in Gromacs 4.0   Luca De Gaetani
  • [gmx-users] Re: Energy Drift in Gromacs 4.0   Berk Hess
• [gmx-users] Karplus parameterization   XAvier Periole
  • [gmx-users] Karplus parameterization   David van der Spoel
• [gmx-users] How to carry out rigid body   lammps lammps
  • [gmx-users] How to carry out rigid body   XAvier Periole
• [gmx-users] Minimization not converging   Jack Shultz
  • [gmx-users] Re: Minimization not converging   Jack Shultz
    • [gmx-users] Re: Minimization not converging   Justin A. Lemkul
• [gmx-users] pdb files   oguz gurbulak
  • [gmx-users] pdb files   Justin A. Lemkul
    • [gmx-users] pdb files   Justin A. Lemkul
• [gmx-users] Variance in ED   andrea carotti
  • [gmx-users] Variance in ED   Tsjerk Wassenaar
• [gmx-users] Problem to simulate silica melts and amorphous silica with BKS potentials   David Waroquiers
• [gmx-users] pdb files   oguz gurbulak
  • [gmx-users] pdb files   Justin A. Lemkul
• [gmx-users] problems with gmxtest.pl   Bernhard Bandow
• [gmx-users] problem in energy minimization   Abhik Mukhopadhyay
  • [gmx-users] problem in energy minimization   Justin A. Lemkul
    • [gmx-users] problem in energy minimization   Abhik Mukhopadhyay
      • [gmx-users] problem in energy minimization   Mark Abraham
• [gmx-users] removal of COM   Sun Joo Lee
  • [gmx-users] removal of COM   Mark Abraham
• [gmx-users] Reducing Size of Data   Jack Shultz
  • [gmx-users] Reducing Size of Data   Justin A. Lemkul
  • [gmx-users] Reducing Size of Data   Mark Abraham
• [gmx-users] problems with gmxtest.pl   bandow
  • [gmx-users] problems with gmxtest.pl   David van der Spoel
    • [gmx-users] problems with gmxtest.pl   Bernhard Bandow
• [gmx-users] Force Field - Gromos96   tree
  • [gmx-users] Fwd: Force Field - Gromos96   Tree
    • [gmx-users] Fwd: Force Field - Gromos96   Tsjerk Wassenaar
  • [gmx-users] Force Field - Gromos96   XAvier Periole
• [gmx-users] free energy coupling/decoupling equivalence   chris.neale at utoronto.ca
  • [gmx-users] free energy coupling/decoupling equivalence   Berk Hess
• [gmx-users] gmx in GPU calculation   li ming
  • [gmx-users] Re: gmx in GPU calculation   li ming
• [gmx-users] gmx in GPU calculation   chris.neale at utoronto.ca
• [gmx-users] Re: Hardware suggestion   David van der Spoel
• [gmx-users] viscosity calculation using g_energy (3.3.3)   JMandumpal
  • [gmx-users] viscosity calculation using g_energy (3.3.3)   Berk Hess
• [gmx-users] how to parametrize Phos. Thr TPO   nahren manuel
  • [gmx-users] how to parametrize Phos. Thr TPO   Justin A. Lemkul
  • [gmx-users] how to parametrize Phos. Thr TPO   Lucio Ricardo Montero Valenzuela
• [gmx-users] gtkmm Code Demos?   Stephen P. Molnar
  • [gmx-users] gtkmm Code Demos?   Mark Abraham
    • [gmx-users] gtkmm Code Demos?   Stephen P. Molnar
      • [gmx-users] gtkmm Code Demos?   Mark Abraham
      • [gmx-users] gtkmm Code Demos?   Stephen P. Molnar
• [gmx-users] wall modelling   avinash kumar
• [gmx-users] Re: Fwd: Ligand is moving far away after energy minimization   Justin A. Lemkul
• [gmx-users] get a top file to run md simulation   oguz gurbulak
  • [gmx-users] get a top file to run md simulation   Justin A. Lemkul
• [gmx-users] make hole with gromacs 3.1.4 error : Unknown left-hand iconstraint_algorithm in parameter file   sitiazma
  • [gmx-users] make hole with gromacs 3.1.4 error : Unknown left-hand iconstraint_algorithm in parameter file   Justin A. Lemkul
  • [gmx-users] make hole with gromacs 3.1.4 error : Unknown left-hand iconstraint_algorithm in parameter file   Mark Abraham
• [gmx-users] Variance in ED   andrea carotti
  • [gmx-users] Variance in ED   Tsjerk Wassenaar
• [gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1   Pietro Amodeo
  • [gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1   David van der Spoel
    • [gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1   Pietro Amodeo
    • [gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1   Pietro Amodeo
      • [gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1   David van der Spoel
• [gmx-users] Triclinic water box for a protein MD   Lucio Montero
  • [gmx-users] Triclinic water box for a protein MD   Justin A. Lemkul
    • [gmx-users] Triclinic water box for a protein MD   Tsjerk Wassenaar
      • [gmx-users] Triclinic water box for a protein MD   TJ Piggot
      • [gmx-users] Triclinic water box for a protein MD   Tsjerk Wassenaar
      • [gmx-users] Triclinic water box for a protein MD   TJ Piggot
• [gmx-users] using more than one type of molecules   Molecular Dynamics
  • [gmx-users] using more than one type of molecules   Justin A. Lemkul
    • [gmx-users] using more than one type of molecules   Molecular Dynamics
      • [gmx-users] using more than one type of molecules   Justin A. Lemkul
      • [gmx-users] using more than one type of molecules   Justin A. Lemkul
• [gmx-users] Matching atom name and types in OPLS-aa FF   Tree
  • [gmx-users] Fwd: Matching atom name and types in OPLS-aa FF   Tree
  • [gmx-users] Matching atom name and types in OPLS-aa FF   Justin A. Lemkul
    • [gmx-users] Matching atom name and types in OPLS-aa FF   tree
      • [gmx-users] Matching atom name and types in OPLS-aa FF   XAvier Periole
      • [gmx-users] Matching atom name and types in OPLS-aa FF   Tree
      • [gmx-users] Matching atom name and types in OPLS-aa FF   Justin A. Lemkul
      • [gmx-users] Matching atom name and types in OPLS-aa FF   tree
      • [gmx-users] Matching atom name and types in OPLS-aa FF   XAvier Periole
      • [gmx-users] Matching atom name and types in OPLS-aa FF   Tree
• [gmx-users] problem with pull direction   huifang liu
• [gmx-users] about MARTINI forcefield   lammps lammps
  • [gmx-users] about MARTINI forcefield   XAvier Periole
• [gmx-users] (no subject)   Homa Azizian
  • [gmx-users] (no subject)   Omer Markovitch
• [gmx-users] Triclinic water box for a protein MD   Tsjerk Wassenaar
• [gmx-users] "Now there are 16 atoms. Deleted 304 duplicates."   xiaowu759 at hotmail.com
  • [gmx-users] "Now there are 16 atoms. Deleted 304 duplicates."   David van der Spoel
  • [gmx-users] "Now there are 16 atoms. Deleted 304 duplicates."   Berk Hess
• [gmx-users] ion jump out of protein   Homa Azizian
  • [gmx-users] ion jump out of protein   Justin A. Lemkul
• [gmx-users] pdb2gmx error   Ilya Chorny
  • [gmx-users] pdb2gmx error   Justin A. Lemkul
    • [gmx-users] pdb2gmx error   Ilya Chorny
      • [gmx-users] pdb2gmx error   Justin A. Lemkul
      • [gmx-users] pdb2gmx error   Tsjerk Wassenaar
      • [gmx-users] pdb2gmx error   Justin A. Lemkul
      • [gmx-users] pdb2gmx error   Ilya Chorny
• [gmx-users] Fwd: using oplsaa in Gromacs   Tsjerk Wassenaar
• [gmx-users] How can I record only molecule trajectory ?   Chih-Ying Lin
  • [gmx-users] How can I record only molecule trajectory ?   David van der Spoel
  • [gmx-users] How can I record only molecule trajectory ?   Justin A. Lemkul
• [gmx-users] GPU calculation of GROMACS in Windows System   li ming
  • [gmx-users] GPU calculation of GROMACS in Windows System   Mark Abraham
• [gmx-users] supti mukherjee sent you a Friend Request on Yaari   supti mukherjee
• [gmx-users] open positions   Gerrit Groenhof
• [gmx-users] problem with pull direction   Thomas Schlesier
• [gmx-users] Wrong Shake Tolerance   Andreas Boozo Frank
  • [gmx-users] Wrong Shake Tolerance   Berk Hess
• [gmx-users] Wrong Shake Tolerance   Andreas Boozo Frank
  • [gmx-users] Wrong Shake Tolerance   Berk Hess
• [gmx-users] angular removal of COM and domain decomposition   XAvier Periole
  • [gmx-users] angular removal of COM and domain decomposition   Berk Hess
    • [gmx-users] angular removal of COM and domain decomposition   XAvier Periole
      • [gmx-users] angular removal of COM and domain decomposition   Berk Hess
      • [gmx-users] angular removal of COM and domain decomposition   XAvier Periole
• [gmx-users] no ngmx?   Dr. Barbara Gioffreda
  • [gmx-users] no ngmx?   Justin A. Lemkul
  • [gmx-users] no ngmx?   Abu Naser
• [gmx-users] center of mass   Antonia V.
  • [gmx-users] center of mass   XAvier Periole
    • [gmx-users] center of mass   Antonia V.
• [gmx-users] FOMMS 2009 2nd Circular   Jonathan Moore
• [gmx-users] Pull code using two reaction coordinates??   rversace at ccny.cuny.edu
  • [gmx-users] Pull code using two reaction coordinates??   XAvier Periole
• [gmx-users] virtual atoms: hydrogens on sugars   Relly Brandman
• [gmx-users] Pull code using two reaction coordinates??   Chris Neale
• [gmx-users] g_dipoles   rams rams
  • [gmx-users] g_dipoles   David van der Spoel
    • [gmx-users] g_dipoles   rams rams
      • [gmx-users] g_dipoles   Berk Hess
      • [gmx-users] g_dipoles   rams rams
• [gmx-users] non-harmonic position restraints   Makoto Yoneya
• [gmx-users] two peptides in same water box   Bhawana Gupta
  • [gmx-users] two peptides in same water box   Mark Abraham
• [gmx-users] how to save grace out put to jpeg or grafifal pic   Homa Azizian
  • [gmx-users] how to save grace out put to jpeg or grafifal pic   David van der Spoel
  • [gmx-users] how to save grace out put to jpeg or grafifal pic   Jochen Hub
• [gmx-users] how to save grace out put to jpeg or grafical pic   Homa Azizian
• [gmx-users] do_dssp fatal error   Homa Azizian
  • [gmx-users] do_dssp fatal error   Justin A. Lemkul
• [gmx-users] gromacs 4 mpi weirdness   Tsjerk Wassenaar
  • [gmx-users] gromacs 4 mpi weirdness   Ran Friedman
    • [gmx-users] gromacs 4 mpi weirdness   Tsjerk Wassenaar
• [gmx-users] OS - Compiler - GROMACS compatibility   alkasrivastava at iitb.ac.in
  • [gmx-users] OS - Compiler - GROMACS compatibility   Alexey Shvetsov
• [gmx-users] Softcores: sc-power = 1 ou 2 ?   Eudes Fileti
  • [gmx-users] Softcores: sc-power = 1 ou 2 ?   Berk Hess
• [gmx-users] mdrun hangs with the pull option   Manik Mayur
  • [gmx-users] mdrun hangs with the pull option   Berk Hess
    • [gmx-users] mdrun hangs with the pull option   Manik Mayur
      • [gmx-users] mdrun hangs with the pull option   Manik Mayur
• [gmx-users] Equilibration   Emanuel Peter
  • [gmx-users] Equilibration   Justin A. Lemkul
• [gmx-users] grompp segmentation fault when trying to position restrain water along bilayer normal   maria goranovic
  • [gmx-users] grompp segmentation fault when trying to position restrain water along bilayer normal   XAvier Periole
• [gmx-users] Range checking error: only on double precision   Jack Shultz
  • [gmx-users] Range checking error: only on double precision   Justin A. Lemkul
    • [gmx-users] Range checking error: only on double precision   Jack Shultz
      • [gmx-users] Range checking error: only on double precision   Justin A. Lemkul
      • [gmx-users] Range checking error: only on double precision   Jack Shultz
• [gmx-users] Softcores: sc-power = 1 or 2 ? again   Eudes Fileti
  • [gmx-users] Softcores: sc-power = 1 or 2 ? again   Berk Hess
• [gmx-users] RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess)   Eudes Fileti
  • [gmx-users] RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess)   Berk Hess
• [gmx-users] make-hole   Urszula Uciechowska
  • [gmx-users] make-hole   Justin A. Lemkul
• [gmx-users] Venkat C has sent you a private message   Venkat C
• [gmx-users] Gromacs on SPARC   Andrey Gurtovenko
• [gmx-users] Re: Free energy with Gromacs.   Justin A. Lemkul
• [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems   Claus Valka
  • [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems   Berk Hess
    • [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems   Claus Valka
      • [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems   Berk Hess
• [gmx-users] g_rdf program   Pablo Umazano
  • [gmx-users] g_rdf program   Dallas B. Warren
• [gmx-users] Re: Free energy with Gromacs.   Justin A. Lemkul
• [gmx-users] Help parameterizing ddb to work with vsite -h option of pdb2gmx   Ilya Chorny
• [gmx-users] Questions About Gromacs   Xi Ouyang
  • [gmx-users] Questions About Gromacs   Antonia V.
  • [gmx-users] Questions About Gromacs   Mark Abraham
• [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
  • [gmx-users] Doubt regarding membrane protein in POPC bilayer   XAvier Periole
• [gmx-users] how to get the the force plot after pulling dynamic simulation using GMX-3.3   huifang liu
• [gmx-users] Re: Softcores: sc-power = 1 or 2 ? again (Berk and Justin)   Eudes Fileti
• [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
  • [gmx-users] Doubt regarding membrane protein in POPC bilayer   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 59, Issue 136   Pawan Kumar
  • [gmx-users] Re: gmx-users Digest, Vol 59, Issue 136   Justin A. Lemkul
• [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
• [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
  • [gmx-users] Doubt regarding membrane protein in POPC bilayer   Justin A. Lemkul
• [gmx-users] how to get the the force plot after pulling, dynamic simulation using GMX-3.3   Thomas Schlesier
• [gmx-users] inertia   Antonia V.
  • [gmx-users] inertia   Justin A. Lemkul
• [gmx-users] Nomenclature Inconsistency between *.rtp and *nb.itp in ffG53a5 and ffG53a6 (CH2r vs CH2R)   Diana Lousa
• [gmx-users] hydrophobicity   Sunjoo Lee
• [gmx-users] Continue run in Gromacs-4 with check point file   xuji
  • [gmx-users] Continue run in Gromacs-4 with check point file   Mark Abraham
    • [gmx-users] One more broken .trr file   Sarah Witzke
      • [gmx-users] One more broken .trr file   Sarah Witzke
      • [gmx-users] One more broken .trr file   Justin A. Lemkul
      • FW: [gmx-users] One more broken .trr file   Sarah Witzke
      • FW: [gmx-users] One more broken .trr file   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 59, Issue 138   Pawan Kumar
  • [gmx-users] Re: gmx-users Digest, Vol 59, Issue 138   Justin A. Lemkul
    • [gmx-users] Re: gmx-users Digest, Vol 59, Issue 138   Pawan Kumar
      • [gmx-users] Re: gmx-users Digest, Vol 59, Issue 138 (Doubt regarding membrane protein in POPC bilayer)   Justin A. Lemkul
• [gmx-users] g_principal   Antonia V.
• [gmx-users] installation gromacs-3.2.1 in redhat-6   akalabya bissoyi
  • [gmx-users] installation gromacs-3.2.1 in redhat-6   Justin A. Lemkul
• [gmx-users] Re:how to get the the force plot after pulling   huifang liu
• [gmx-users] Non-equilibraium MD: simulating a moving plate.   Vitaly V. Chaban
• [gmx-users] Simulated annealing   jayant james
  • [gmx-users] Simulated annealing   Justin A. Lemkul
    • [gmx-users] Simulated annealing   jayant james
      • [gmx-users] Simulated annealing   Justin A. Lemkul
• [gmx-users] Binding Copper to Protein   DimitryASuplatov
  • [gmx-users] Binding Copper to Protein   Justin A. Lemkul
    • [gmx-users] Binding Copper to Protein   Tsjerk Wassenaar
• [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems   Claus Valka
  • [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems   Berk Hess
• [gmx-users] problem in running simulation   nitu sharma
  • [gmx-users] problem in running simulation   Justin A. Lemkul
• [gmx-users] nitu sharma has invited you to open a Google mail account   nitu sharma
• [gmx-users] Non-equilibraium MD: simulating a moving plate.   Vitaly V. Chaban
• [gmx-users] Timestep and force field   varsha gautham
  • [gmx-users] Timestep and force field   Jussi Lehtola
  • [gmx-users] Timestep and force field   David van der Spoel
• [gmx-users] Timestep and force field   varsha gautham
  • [gmx-users] Timestep and force field   Manik Mayur
• [gmx-users] Questions about energy groups!   Zhong Zheng
  • [gmx-users] Questions about energy groups!   Justin A. Lemkul
• [gmx-users] grompp vel_gen = seg fault   KS Rotondi
  • [gmx-users] grompp vel_gen = seg fault   Roland Schulz
• [gmx-users] Re: Non-equilibraium MD: simulating a moving plate.   Hu Zhongqiao
• [gmx-users] some peoblems about modeling...   li ming
• [gmx-users] three questions about GMX modeling...   li ming
• [gmx-users] not referencing ffamber03.hdb   Jack Shultz
  • [gmx-users] not referencing ffamber03.hdb   Höfling Martin
• [gmx-users] Cross-linking of polymers   Tree
  • [gmx-users] Cross-linking of polymers   Dallas B. Warren
    • [gmx-users] Cross-linking of polymers   Tree
• [gmx-users] Compiler and OS issue in gromacs   alkasrivastava at iitb.ac.in
  • [gmx-users] Compiler and OS issue in gromacs   Manik Mayur
• [gmx-users] some peoblems about modeling...   chris.neale at utoronto.ca
• [gmx-users] incorporate multi proteins into a cell?   li ming
• [gmx-users] how to merge the protein and lipid bilayer in a cell?   li ming
  • [gmx-users] how to merge the protein and lipid bilayer in a cell?   Justin A. Lemkul
• [gmx-users] (no subject)   Antonia V.
  • [gmx-users] (no subject) - fluctuations   David van der Spoel
    • [gmx-users] (no subject) - fluctuations   Dallas B. Warren
      • [gmx-users] (no subject) - fluctuations   Antonia V.
      • [gmx-users] (no subject) - fluctuations   David van der Spoel
      • [gmx-users] (no subject) - fluctuations   Antonia V.
      • [gmx-users] (no subject) - fluctuations   David van der Spoel
      • [gmx-users] (no subject) - fluctuations   Antonia V.
• [gmx-users] PBC dodecahedron   meetnahren at yahoo.com
  • [gmx-users] PBC dodecahedron   Tsjerk Wassenaar
• [gmx-users] Trying to link C++ code with libgmx. Please help!   Semen Esilevsky
  • [gmx-users] Trying to link C++ code with libgmx. Please help!   David van der Spoel
    • [gmx-users] Trying to link C++ code with libgmx. Please help!   Semen Esilevsky
      • [gmx-users] Trying to link C++ code with libgmx. Please help!   Mark Abraham
• [gmx-users] PBC dodecahedron (corrected)   nahren manuel
• [gmx-users] Announcement of Model(l)ing'09 - The annual 2009 MGMS Meeting in Erlangen, Germany   Harald Lanig
• [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
  • [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer   Justin A. Lemkul
    • [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
      • [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer   Justin A. Lemkul
      • [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
      • [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer   Justin A. Lemkul
• [gmx-users] Re: Non-equilibraium MD: simulating a moving   Vitaly V. Chaban
• [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
• [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer   Justin A. Lemkul
• [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
  • [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
    • [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer   Justin A. Lemkul
      • [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
      • [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
      • [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer   Justin A. Lemkul
      • [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
      • [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer   Justin A. Lemkul
      • [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer   Justin A. Lemkul
      • [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
      • [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer   Justin A. Lemkul
      • [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer   Marc F. Lensink
      • [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
• [gmx-users] How to add another electrostatic summation method in Gromacs   Shuangxing Dai
  • [gmx-users] How to add another electrostatic summation method in Gromacs   Mark Abraham
    • [gmx-users] How to add another electrostatic summation method in Gromacs   Shuangxing Dai
      • [gmx-users] How to add another electrostatic summation method in Gromacs   Mark Abraham
      • [gmx-users] How to add another electrostatic summation method in Gromacs   Berk Hess
      • [gmx-users] How to add another electrostatic summation methodin Gromacs   Shuangxing Dai
      • [gmx-users] How to add another electrostatic summation methodin Gromacs   Mark Abraham
      • [gmx-users] How to add another electrostatic summation methodinGromacs   Shuangxing Dai
      • [gmx-users] How to add another electrostatic summation methodinGromacs   Mark Abraham
• [gmx-users] Re: Non-equilibraium MD: simulating a moving   Hu Zhongqiao
• [gmx-users] problem in DMPC lipid bilayer   nitu sharma
• [gmx-users] Re:problem in DMPC lipid bilayer   huifang liu
• [gmx-users] Re: About Gromacs   Mark Abraham
  • [gmx-users] Re: About Gromacs   Tsjerk Wassenaar
• [gmx-users] Reminder: Please Respond to supti's Invitation   supti mukherjee
• [gmx-users] rotate trajectory from self-assembly of lipid bilayer   maria goranovic
• [gmx-users] Drug-Enzyme tutorial- LIE energies in gromacs   Neha Gandhi
  • [gmx-users] Drug-Enzyme tutorial- LIE energies in gromacs   David van der Spoel
  • [gmx-users] Drug-Enzyme tutorial- LIE energies in gromacs   Alexandre Suman de Araujo
  • [gmx-users] Re: Drug-Enzyme tutorial- LIE energies in gromacs   Neha Gandhi
• [gmx-users] Re: Non-equilibrium MD: simulating a moving plate   Vitaly V. Chaban
• [gmx-users] grompp command: The solvent group SOL is not continuous   Halie Shah
  • [gmx-users] grompp command: The solvent group SOL is not continuous   Justin A. Lemkul
• [gmx-users] viscosity calculation using g_energy (3.3.3)   JMandumpal
• [gmx-users] how to make whole trajectory Pdb files   Bhawana Gupta
  • [gmx-users] how to make whole trajectory Pdb files   David van der Spoel
• [gmx-users] problem in simulation of DMPC lipid bilayer   nitu sharma
  • [gmx-users] problem in simulation of DMPC lipid bilayer   Mark Abraham
    • [gmx-users] problem in simulation of DMPC lipid bilayer   Justin A. Lemkul
• [gmx-users] k- means clustering   sarbani chattopadhyay
  • [gmx-users] k- means clustering   Mark Abraham
• [gmx-users] How to avoid the error: "Shake block crossing node boundaries"   Leontyev Igor
  • [gmx-users] How to avoid the error: "Shake block crossing node boundaries"   Mark Abraham
• [gmx-users] How to avoid the error: "Shake block crossing nodeboundaries"   Igor Leontyev
  • [gmx-users] How to avoid the error: "Shake block crossing nodeboundaries"   David van der Spoel
    • [gmx-users] How to avoid the error: "Shake blockcrossing nodeboundaries"   Igor Leontyev
      • [gmx-users] How to avoid the error: "Shake blockcrossing nodeboundaries"   David van der Spoel
      • [gmx-users] How to avoid the error:"Shake blockcrossing nodeboundaries"   Igor Leontyev
• [gmx-users] How to make pdb file of whole trajectory   Bhawana Gupta
  • [gmx-users] How to make pdb file of whole trajectory   David van der Spoel
  • [gmx-users] How to make pdb file of whole trajectory   Mark Abraham
• [gmx-users] k means cluster   sarbani chattopadhyay
• [gmx-users] pulling of molecule in GROMACS 4.03   anirban polley
• [gmx-users] Explicit \ implicit   Bhawana Gupta
  • [gmx-users] Explicit \ implicit   Mark Abraham
  • [gmx-users] Explicit \ implicit   David van der Spoel
• [gmx-users] what factors effetc the simulation during energy minimization   bhargavi ch
  • [gmx-users] what factors effetc the simulation during energy minimization   Mark Abraham
• [gmx-users] (no subject)   bhargavi ch
• [gmx-users] what factors effetc the simulation during energy minimization   bhargavi ch
  • [gmx-users] what factors effetc the simulation during energy minimization   Justin A. Lemkul
• [gmx-users] factors effecting the simulation   bhargavi ch
• [gmx-users] Calculation of fraction of native contacts   Camilo Velez
• [gmx-users] Rosetta Academic Training Webinar   Nir London
• [gmx-users] Applying an improper to S-S bond   DimitryASuplatov
  • [gmx-users] Applying an improper to S-S bond   Justin A. Lemkul
  • [gmx-users] Applying an improper to S-S bond   Mark Abraham
• [gmx-users] Using R.E.D. charges with OPLS AA   DimitryASuplatov
  • [gmx-users] Using R.E.D. charges with OPLS AA   Mark Abraham
  • [gmx-users] Using R.E.D. charges with OPLS AA   Ran Friedman
• [gmx-users] RE: Question for pulling in GROMACS 4.0   Thomas Schlesier
• [gmx-users] Usually how do you decide the salt concentration?   Peggy Yao
  • [gmx-users] Usually how do you decide the salt concentration?   Justin A. Lemkul
• [gmx-users] How to calculate PMF after AFM pulling   huifang liu
  • [gmx-users] How to calculate PMF after AFM pulling   Justin A. Lemkul
• [gmx-users] Re: g_covar   Ran Friedman
  • [gmx-users] Re: g_covar   Tsjerk Wassenaar
• [gmx-users] How to calculate PMF after AFM pulling   huifang liu
• [gmx-users] How to calculate PMF after AFM pulling   Justin A. Lemkul
• [gmx-users] about parallel run   Mahnam
  • [gmx-users] about parallel run   Justin A. Lemkul
• [gmx-users] Integrating with BOINC: failing at minimization   Jack Shultz
  • [gmx-users] Integrating with BOINC: failing at minimization   Mark Abraham
• [gmx-users] How to calculate PMF after AFM pulling   huifang liu
  • [gmx-users] How to calculate PMF after AFM pulling   Justin A. Lemkul
• [gmx-users] how to deal with the hydrogen bonding interactions between bases   He, Yang
• [gmx-users] question in pulling in gromacs 4.0   anirban polley
  • [gmx-users] question in pulling in gromacs 4.0   Mark Abraham
  • [gmx-users] question in pulling in gromacs 4.0   Justin A. Lemkul
• [gmx-users] localp   Jose Javier Lopez Cascales
• [gmx-users] [Fwd: Problems in pulling a molecule from the membrane]   Thomas Schlesier
  • [gmx-users] [Fwd: Problems in pulling a molecule from the membrane]   Berk Hess
• [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones   Josmar R. da Rocha
  • [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones   Ran Friedman, Biochemisches Inst.
    • [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones   Lucio Montero
      • [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones   Justin A. Lemkul
    • [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones   Lucio Montero
      • [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones   Justin A. Lemkul
• [gmx-users] about martini forcefield(MFF)   lammps lammps
• [gmx-users] drug-enzyme simulation.   Neha Gandhi
  • [gmx-users] drug-enzyme simulation.   Justin A. Lemkul
    • [gmx-users] drug-enzyme simulation.   Neha Gandhi
      • [gmx-users] drug-enzyme simulation.   Tsjerk Wassenaar
• [gmx-users] using Gaussian with Gromacs   oguz gurbulak
  • [gmx-users] using Gaussian with Gromacs   Justin A. Lemkul
• [gmx-users] rmsd   shahrbanoo karbalaee
  • [gmx-users] rmsd   Justin A. Lemkul
• [gmx-users] parallel install gromacs-4.0.4   Hongyan Xiao
  • [gmx-users] parallel install gromacs-4.0.4   Mark Abraham
• [gmx-users] parallel install gromacs-4.0.4   Hongyan Xiao
  • [gmx-users] parallel install gromacs-4.0.4   Justin A. Lemkul
• [gmx-users] Alert for Open MPI bug v1.3.0 and v1.3.1   chris.neale at utoronto.ca
• [gmx-users] Water models for amber03   Jack Shultz
  • [gmx-users] Water models for amber03   Justin A. Lemkul
• [gmx-users] grompp error in running simulation of lipid bilayer   nitu sharma
  • [gmx-users] grompp error in running simulation of lipid bilayer   Pawan Kumar
• [gmx-users] Re: Water models for amber03 (Justin A. Lemkul)   Alan
• [gmx-users] Error with equilibration of DPPC membrane with protein   Edvin Erdtman
  • [gmx-users] Error with equilibration of DPPC membrane with protein   Justin A. Lemkul
    • [gmx-users] Error with equilibration of DPPC membrane with protein   Edvin Erdtman
• [gmx-users] grompp error in running simulation of lipid bilayer   nitu sharma
  • [gmx-users] grompp error in running simulation of lipid bilayer   Pawan Kumar
  • [gmx-users] grompp error in running simulation of lipid bilayer   Dallas B. Warren
• [gmx-users] grompp errors   andrea.borgogno at unipd.it
  • [gmx-users] grompp errors   Tsjerk Wassenaar
• [gmx-users] water model and force field   varsha gautham
  • [gmx-users] water model and force field   Justin A. Lemkul
• [gmx-users] POPE setup   Peter Tieleman
  • [gmx-users] POPE setup   Marc F. Lensink
• [gmx-users] new block lactitol   cesteban at unsl.edu.ar
  • [gmx-users] new block lactitol   Justin A. Lemkul
    • [gmx-users] new block lactitol   cesteban at unsl.edu.ar
      • [gmx-users] new block lactitol   Justin A. Lemkul
• [gmx-users] No plot found running .xvg files using xmgrace produced by g_helix.   Chitrita Dutta Roy
  • [gmx-users] Fwd: No plot found running .xvg files using xmgrace produced by g_helix.   Chitrita Dutta Roy
• [gmx-users] Prepping Docking Complexes   Jack Shultz
  • [gmx-users] Prepping Docking Complexes   Justin A. Lemkul
• [gmx-users] Missing atom in residue   Jack Shultz
  • [gmx-users] Missing atom in residue   Justin A. Lemkul
• [gmx-users] how to define the dummy atoms in gromacs   He, Yang
  • [gmx-users] how to define the dummy atoms in gromacs   Jochen Hub
• [gmx-users] solvent box outside protein   Halie Shah
  • [gmx-users] solvent box outside protein   Tsjerk Wassenaar
• [gmx-users] Elastic Network Model   Joshua Adelman
• [gmx-users] problem in simulation of lipid bilayer   nitu sharma
  • [gmx-users] problem in simulation of lipid bilayer   Pawan Kumar
  • [gmx-users] problem in simulation of lipid bilayer   XAvier Periole
• [gmx-users] Announcing NMR validation web interface iCing   Alan
• [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
  • [gmx-users] Doubt regarding membrane protein in POPC bilayer   Justin A. Lemkul
    • [gmx-users] Doubt regarding membrane protein in POPC bilayer   Pawan Kumar
      • [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer   Justin A. Lemkul
• [gmx-users] Lipid models for GROMOS96 53a6   Kukol, Andreas
• [gmx-users] Does andersen thermostat work?   Camilo Velez

Last message date: Tue Mar 31 23:56:22 CEST 2009
Archived on: Thu Nov 14 12:06:31 CET 2013

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