March 2008 Archives by thread

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Starting: Sat Mar 1 01:18:46 CET 2008
Ending: Mon Mar 31 23:53:55 CEST 2008
Messages: 563

• [gmx-users] Gromacs force field discussion   Reay, Andrew
  • [gmx-users] Gromacs force field discussion   David van der Spoel
    • [gmx-users] Gromacs force field discussion   patrick fuchs
      • [gmx-users] Gromacs force field discussion   David van der Spoel
      • [gmx-users] Gromacs force field discussion   Ran Friedman
      • [gmx-users] Gromacs force field discussion   rainer
• [gmx-users] peoblem with water   sudheer babu
  • [gmx-users] peoblem with water   Mark Abraham
• [gmx-users] procedure for creating an S-S bridge   OZGE ENGIN
  • [gmx-users] procedure for creating an S-S bridge   Mark Abraham
• [gmx-users] constraints & cg   V. Tanchuk
  • [gmx-users] constraints & cg   Justin A. Lemkul
  • [gmx-users] constraints & cg   Daniel Larsson
• [gmx-users] number of coordinates in coordinate file   s lal badshah
  • [gmx-users] number of coordinates in coordinate file   David van der Spoel
  • [gmx-users] number of coordinates in coordinate file   Mark Abraham
• [gmx-users] S2 min and S2 max   Lam Y Sonia
• [gmx-users] procedure for creating an S-S bridge   OZGE ENGIN
  • [gmx-users] procedure for creating an S-S bridge   Mark Abraham
• [gmx-users] procedure for creating an S-S bridge   OZGE ENGIN
  • [gmx-users] DPPC lipid model in Gromos 53a5   Andreas
    • [gmx-users] DPPC lipid model in Gromos 53a5   Mark Abraham
      • [gmx-users] DPPC lipid model in Gromos 53a5   David van der Spoel
      • [gmx-users] DPPC lipid model in Gromos 53a5   Andreas
      • [gmx-users] DPPC lipid model in Gromos 53a5   Mark Abraham
    • [gmx-users] DPPC lipid model in Gromos 53a5   Mark Abraham
• [gmx-users] problem with trjconv   sudheer babu
  • [gmx-users] problem with trjconv   Justin A. Lemkul
  • [gmx-users] problem with trjconv   Mark Abraham
• [gmx-users] Electrostatic forces   Georgios Patargias
  • [gmx-users] Electrostatic forces   Mark Abraham
    • [gmx-users] Electrostatic forces   Georgios Patargias
• [gmx-users] problem with mpi configuration.   mario ciappy
  • [gmx-users] problem with mpi configuration.   Diego Enry
    • [gmx-users] problem with mpi configuration.   mario ciappy
      • [gmx-users] problem with mpi configuration.   Diego Enry
      • [gmx-users] problem with mpi configuration.   mario ciappy
      • [gmx-users] problem with mpi configuration.   Diego Enry
• [gmx-users] incorporation of distance restraint into the topology file   OZGE ENGIN
  • [gmx-users] incorporation of distance restraint into the topology file   Mark Abraham
• [gmx-users] GROMACS vs NAMD   Dibyadeep Paul
  • [gmx-users] GROMACS vs NAMD   Mark Abraham
  • [gmx-users] GROMACS vs NAMD   David van der Spoel
    • [gmx-users] GROMACS vs NAMD   Ilya Chorny
• [gmx-users] step.pdb files during EM   JMandumpal
  • [gmx-users] step.pdb files during EM   Mark Abraham
• [gmx-users] peptide MD   Rigden, LucianeVMello
  • [gmx-users] peptide MD   Daniel Larsson
• [gmx-users] Dumping of energies   andersle at stud.ntnu.no
  • [gmx-users] Dumping of energies   Mark Abraham
• [gmx-users] Re: Dumping of energies   andersle at stud.ntnu.no
  • [gmx-users] Re: Dumping of energies   David van der Spoel
• [gmx-users] Relating acceleration to pressure   avinash kumar
• [gmx-users] Relating acceleration to pressure   Alan Dodd
• [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   reich at mpikg.mpg.de
  • [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   Berk Hess
    • [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   Stéphane Téletchéa
      • [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   Berk Hess
      • [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   Berk Hess
• [gmx-users] Data generated by g_sas   mon_sharma at research.iiit.ac.in
  • [gmx-users] Data generated by g_sas   Daniel Larsson
  • [gmx-users] Data generated by g_sas   Mark Abraham
    • [gmx-users] Data generated by g_sas   mon_sharma at research.iiit.ac.in
      • [gmx-users] Data generated by g_sas   Tsjerk Wassenaar
• [gmx-users] ramping force constants   D. Flemming Hansen
  • [gmx-users] ramping force constants   Mark Abraham
• [gmx-users] Coul-14, LJ-14 and RF-excl definitions?   pascal.baillod at epfl.ch
• [gmx-users] Total potential energy: 1/2 protein-solvent interactions??   pascal.baillod at epfl.ch
  • [gmx-users] Total potential energy: 1/2 protein-solvent interactions??   Xavier Periole
    • [gmx-users] Total potential energy: 1/2 protein-solvent interactions??   David van der Spoel
      • [gmx-users] Total potential energy: 1/2 protein-solvent interactions??   Xavier Periole
      • [gmx-users] Total potential energy: 1/2 protein-solvent interactions??   David van der Spoel
      • [gmx-users] Total potential energy: 1/2 protein-solvent interactions??   Xavier Periole
      • [gmx-users] Total potential energy: 1/2 protein-solvent interactions??   David van der Spoel
      • [gmx-users] Total potential energy: 1/2 protein-solvent interactions??   Xavier Periole
• [gmx-users] Problems with OPLS topology files   Goran Krilov
  • [gmx-users] Problems with OPLS topology files   Mark Abraham
    • [gmx-users] Problems with OPLS topology files   Goran Krilov
      • [gmx-users] Problems with OPLS topology files   Mark Abraham
• [gmx-users] Problem with using distance restraints (disre) with PBC   Grace Li
  • [gmx-users] Problem with using distance restraints (disre) with PBC   D. Flemming Hansen
  • [gmx-users] Problem with using distance restraints (disre) with PBC   Mark Abraham
  • [gmx-users] Problem with using distance restraints (disre) with PBC   TJ Piggot
    • [gmx-users] Problem with using distance restraints (disre) with PBC   Mitchell Stanton-Cook
      • [gmx-users] Problem with using distance restraints (disre) with PBC   TJ Piggot
      • [gmx-users] Problem with using distance restraints (disre) with PBC   Mitchell Stanton-Cook
      • [gmx-users] Problem with using distance restraints (disre) with PBC   TJ Piggot
• [gmx-users] lateral diffusion coefficient of bilayer   LeeHwan-kyu
  • [gmx-users] lateral diffusion coefficient of bilayer   Justin A. Lemkul
• [gmx-users] Checking the Progress of Energy minimization   s lal badshah
  • [gmx-users] Checking the Progress of Energy minimization   Mark Abraham
  • [gmx-users] Checking the Progress of Energy minimization   Berk Hess
• [gmx-users] TIP5P and cg minimization   rob yang
  • [gmx-users] TIP5P and cg minimization   Mark Abraham
    • [gmx-users] TIP5P and cg minimization   rob yang
      • [gmx-users] TIP5P and cg minimization   Mark Abraham
      • [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions   rob yang
      • [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions   David van der Spoel
      • [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions   rob yang
      • [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions   David van der Spoel
      • [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions   rob yang
      • [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions   David van der Spoel
      • [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions   rob yang
• [gmx-users] Querry about NPT simulation with PR   shankari hariharan
• [gmx-users] problem with undistribution of water   sudheer babu
  • [gmx-users] problem with undistribution of water   Justin A. Lemkul
• [gmx-users] Re: gmx-users Digest, Vol 47, Issue 12   Grace Li
• [gmx-users] Re: lateral diffusion coefficient of bilayer   LeeHwan-kyu
• [gmx-users] density calculation of genbox   Tobias Unruh
  • [gmx-users] density calculation of genbox   Mark Abraham
    • [gmx-users] density calculation of genbox   Tobias Unruh
• [gmx-users] Computational efficiency   Ricardo Soares
  • [gmx-users] Computational efficiency   Diego Enry
    • [gmx-users] Computational efficiency   Ricardo Soares
      • [gmx-users] Computational efficiency   Diego Enry
• [gmx-users] query for g_sas   Dilraj Lama
  • [gmx-users] query for g_sas   Xavier Periole
• [gmx-users] Gromacs setup on dual core machine   Ricardo Soares
  • [gmx-users] Gromacs setup on dual core machine   Yang Ye
  • [gmx-users] Gromacs setup on dual core machine   Kpiwara De X-nelo
    • [gmx-users] Gromacs setup on dual core machine   Ricardo Soares
      • [gmx-users] Gromacs setup on dual core machine   Diego Enry
      • [gmx-users] Gromacs setup on dual core machine   Kpiwara De X-nelo
• [gmx-users] TIP5P and cg minimization   JMandumpal
  • [gmx-users] TIP5P and cg minimization   rob yang
• [gmx-users] problem with undistribution of water   sudheer babu
  • [gmx-users] problem with undistribution of water   Mark Abraham
  • [gmx-users] problem with undistribution of water   Maik Goette
• [gmx-users] .gro files generation for a certain time-step interval in a simulation   Huey Ling Tan
  • [gmx-users] .gro files generation for a certain time-step interval in a simulation   rob yang
  • [gmx-users] .gro files generation for a certain time-step interval in a simulation   Yang Ye
• [gmx-users] Position restraints on a lipid bilayer   toma0052
  • [gmx-users] Position restraints on a lipid bilayer   Mark Abraham
  • [gmx-users] Position restraints on a lipid bilayer   Stéphane Téletchéa
    • [gmx-users] Position restraints on a lipid bilayer   Mark Abraham
• [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   reich at mpikg.mpg.de
• [gmx-users] ED analysis, domain rotation, DynDom   jo hanna
  • [gmx-users] ED analysis, domain rotation, DynDom   Tsjerk Wassenaar
    • [gmx-users] ED analysis, domain rotation, DynDom   jo hanna
      • [gmx-users] ED analysis, domain rotation, DynDom   Tsjerk Wassenaar
• [gmx-users] Noive to gromacs : MD for zeolitic system   anjaiah Nalaparaju
  • [gmx-users] Noive to gromacs : MD for zeolitic system   Mark Abraham
• [gmx-users] Error of moleculetype   s lal badshah
  • [gmx-users] Error of moleculetype   Mark Abraham
• [gmx-users] Coul-14, LJ-14 and RF-excl definitions (2)   pascal.baillod at epfl.ch
  • [gmx-users] Coul-14, LJ-14 and RF-excl definitions (2)   David van der Spoel
    • [gmx-users] Coul-14, LJ-14 and RF-excl definitions (2)   Xavier Periole
    • [gmx-users] Coul-14, LJ-14 and RF-excl definitions (2)   Berk Hess
• [gmx-users] A question about quenching   Kristina Woods
  • [gmx-users] A question about quenching   L. Michel Espinoza-Fonseca
    • [gmx-users] A question about quenching   David van der Spoel
• [gmx-users] minimized on protein-protein decoys   Liu Shiyong
  • [gmx-users] minimized on protein-protein decoys   Mark Abraham
    • [gmx-users] minimized on protein-protein decoys   Liu Shiyong
      • [gmx-users] minimized on protein-protein decoys   Justin A. Lemkul
• [gmx-users] problem of nvt and npt   sudheer babu
  • [gmx-users] problem of nvt and npt   Mark Abraham
• [gmx-users] pbc on the "xy" direction   OZGE ENGIN
  • [gmx-users] pbc on the "xy" direction   Berk Hess
• [gmx-users] Ki estimation   V. Tanchuk
  • [gmx-users] Ki estimation   Ran Friedman
  • [gmx-users] Ki estimation   Maik Goette
• [gmx-users] no peak in rdf graph   zhuliang at tju.edu.cn
  • [gmx-users] no peak in rdf graph   Xavier Periole
• [gmx-users] Free energy of dihedral restraint   Robert Johnson
• [gmx-users] Error of atomtype before minimization   s lal badshah
  • [gmx-users] Error of atomtype before minimization   Mark Abraham
• [gmx-users] Problem of *tpbconv   sudheer babu
  • [gmx-users] Problem of *tpbconv   Mark Abraham
• [gmx-users] Error of atomtype not found   s lal badshah
  • [gmx-users] Error of atomtype not found   Justin A. Lemkul
• [gmx-users] ligand-protein interaction using gromacs   #NGUYEN CONG TRI#
  • [gmx-users] ligand-protein interaction using gromacs   Justin A. Lemkul
  • [gmx-users] ligand-protein interaction using gromacs   David Mobley
• [gmx-users] Avoiding parameterization step   Abu Naser
• [gmx-users] Avoiding parameterization step   Abu Naser
• [gmx-users] Avoiding parameterization step   Abu Naser
• [gmx-users] Avoiding parameterization step   Abu Naser
• [gmx-users] Avoiding parameterization step   Gerrit Groenhof
  • [gmx-users] Avoiding parameterization step   Abu Naser
    • [gmx-users] Avoiding parameterization step   Mark Abraham
• [gmx-users] Avoiding parameterization step   Gerrit Groenhof
• [gmx-users] Calculation of Dihedral angles   Anirban Ghosh
  • [gmx-users] Calculation of Dihedral angles   Justin A. Lemkul
• [gmx-users] size of the system   V.V. Chaban
  • [gmx-users] size of the system   Justin A. Lemkul
    • [gmx-users] size of the system   V.V. Chaban
• [gmx-users] size of the system   V.V. Chaban
• [gmx-users] parameter on Energy Minimization   Liu Shiyong
  • [gmx-users] parameter on Energy Minimization   Justin A. Lemkul
  • [gmx-users] parameter on Energy Minimization   Mark Abraham
    • [gmx-users] parameter on Energy Minimization   Liu Shiyong
      • [gmx-users] parameter on Energy Minimization   Justin A. Lemkul
• [gmx-users] size of the system   V.V. Chaban
  • [gmx-users] size of the system   Mark Abraham
• [gmx-users] size of the system   Justin A. Lemkul
• [gmx-users] pdb2gmx error   shyamala iyer
• [gmx-users] Gromacs setup on dual core machine   Jens Pohl
  • [gmx-users] Gromacs setup on dual core machine   David van der Spoel
  • [gmx-users] Gromacs setup on dual core machine   Mark Abraham
• [gmx-users] Gromacs setup on dual core machine   Jens Pohl
• [gmx-users] How to judge the system was equilibrated   Rui Li
• [gmx-users] results of energy minimization   s lal badshah
  • [gmx-users] results of energy minimization   Per Larsson
  • [gmx-users] results of energy minimization   Justin A. Lemkul
• [gmx-users] DMSO G53a6 FF in Gromacs   Andreas Boozo Frank
  • [gmx-users] DMSO G53a6 FF in Gromacs   Berk Hess
    • [gmx-users] DMSO G53a6 FF in Gromacs   Xavier Periole
      • [gmx-users] DMSO G53a6 FF in Gromacs   Andreas Boozo Frank
      • [gmx-users] orires energy terms   Berk Hess
• [gmx-users] Re: DMSO G53a6 FF in Gromacs   Andreas Boozo Frank
  • [gmx-users] Re: DMSO G53a6 FF in Gromacs   Berk Hess
    • [gmx-users] Re: DMSO G53a6 FF in Gromacs   Andreas Boozo Frank
    • [gmx-users] Re: DMSO G53a6 FF in Gromacs   Andreas Boozo Frank
      • [gmx-users] Re: DMSO G53a6 FF in Gromacs   Berk Hess
• [gmx-users] size of the system   V.V. Chaban
• [gmx-users] RE: Coul-14, LJ-14 and RF-excl definitions (2)   pascal.baillod at epfl.ch
  • [gmx-users] RE: Coul-14, LJ-14 and RF-excl definitions (2)   Berk Hess
• [gmx-users] trjconv output at a specified time   Liu Shiyong
• [gmx-users] trjconv output at a specified time   Alan Dodd
  • [gmx-users] trjconv output at a specified time   Liu Shiyong
• [gmx-users] trjconv output at a specified time   Alan Dodd
• [gmx-users] problem with mpi configuration.   Jens Pohl
  • [gmx-users] problem with mpi configuration.   Dr. Niharendu Choudhury
    • [gmx-users] problem with mpi configuration.   Mark Abraham
    • [gmx-users] downloading problem   Siavoush Dastmalchi
      • [gmx-users] downloading problem   David van der Spoel
• [gmx-users] Problem about *pdbgmx   sudheer babu
  • [gmx-users] Problem about *pdbgmx   David van der Spoel
• [gmx-users] selecting residues which are within cutoff distances   maria goranovic
  • [gmx-users] selecting residues which are within cutoff distances   TJ Piggot
• [gmx-users] Re: gmx-users Digest, Vol 47, Issue 41   sudheer babu
• [gmx-users] Acetyl capping and Range checking error   Mauro Puppett
  • [gmx-users] Acetyl capping and Range checking error   Justin A. Lemkul
• [gmx-users] Umbrella sampling using 3-dimensions   Mirijanian, Dina Tigranui
• [gmx-users] How to change the default value for pbc ?   Liu Shiyong
• [gmx-users] How to change the default value for pbc ?   Alan Dodd
  • [gmx-users] How to change the default value for pbc ?   Liu Shiyong
• [gmx-users] converged to Epot   Liu Shiyong
  • [gmx-users] converged to Epot   Mark Abraham
• [gmx-users] how to run a gases diffusiion simulation   vips g
  • [gmx-users] how to run a gases diffusiion simulation   David van der Spoel
    • [gmx-users] running multiprocessor jobs on leopard 10.5.2   Syma Khalid
      • [gmx-users] running multiprocessor jobs on leopard 10.5.2   Marc Baaden
• [gmx-users] Help needed on using general amber force field (GAFF) in Gromacs   Xiangyu Fan
  • [gmx-users] Help needed on using general amber force field (GAFF) in Gromacs   Yang Ye
• [gmx-users] mgxtest failed.   Dr. Niharendu Choudhury
  • [gmx-users] mgxtest failed.   David van der Spoel
    • [gmx-users] mgxtest failed.   Dr. Niharendu Choudhury
      • [gmx-users] mgxtest failed.   David van der Spoel
• [gmx-users] traj.trr   s lal badshah
  • [gmx-users] traj.trr   Maik Goette
• [gmx-users] ambconv again   Alan
  • [gmx-users] ambconv again   Bruce Ray
• [gmx-users] Re: Help needed on using general amber force field (GAFF) in Gromacs   servaas michielssens
  • [gmx-users] Re: Help needed on using general amber force field (GAFF) in Gromacs   Xiangyu Fan
• [gmx-users] Black whole simluations   roger han
  • [gmx-users] Black whole simluations   Steffen Wolf
  • [gmx-users] Black whole simluations   Mark Abraham
    • [gmx-users] Black whole simluations   David van der Spoel
  • [gmx-users] Black whole simluations   Kpiwara De X-nelo
    • [gmx-users] Black whole simluations   #NGUYEN CONG TRI#
  • [gmx-users] Black whole simluations   Maik Goette
• [gmx-users] g_msd, REMD, trestart...   Julián GC
  • [gmx-users] g_msd, REMD, trestart...   Mark Abraham
• [gmx-users] Whereabouts of NDLP???   Alan Chen
  • [gmx-users] Whereabouts of NDLP???   Tsjerk Wassenaar
• [gmx-users] kinetically trapped in a local minimum???   #NGUYEN CONG TRI#
  • [gmx-users] kinetically trapped in a local minimum???   Mark Abraham
    • [gmx-users] kinetically trapped in a local minimum???   #NGUYEN CONG TRI#
• [gmx-users] Force field   Dr. Niharendu Choudhury
  • [gmx-users] Force field   Ángel Piñeiro
    • [gmx-users] Force field   Dr. Niharendu Choudhury
      • [gmx-users] Force field   Ángel Piñeiro
• [gmx-users] SGI installation problem   Siavoush Dastmalchi
  • [gmx-users] SGI installation problem   David van der Spoel
    • [gmx-users] SGI installation problem   Siavoush Dastmalchi
      • [gmx-users] SGI installation problem   David van der Spoel
      • [gmx-users] SGI installation problem   Siavoush Dastmalchi
      • [gmx-users] SGI installation problem   Erik Lindahl
      • [gmx-users] SGI installation problem   Siavoush Dastmalchi
      • [gmx-users] SGI installation problem   Siavoush Dastmalchi
      • [gmx-users] SGI installation problem   David van der Spoel
      • [gmx-users] SGI installation problem   Siavoush Dastmalchi
      • [gmx-users] SGI installation problem   Erik Lindahl
      • [gmx-users] SGI installation problem   Siavoush Dastmalchi
      • [gmx-users] SGI installation problem - make_edi   David van der Spoel
• [gmx-users] Re: kinetically trapped in a local minimum???   Alan Chen
• [gmx-users] g_msd, REMD, trestart...   Julián GC
  • [gmx-users] g_msd, REMD, trestart...   David van der Spoel
• [gmx-users] Postdoc/staff scientist opportunities: Gromacs & free energy   Erik Lindahl
• e: [gmx-users] ambconv again   Alan
  • e: [gmx-users] ambconv again   Bruce Ray
• [gmx-users] *.itp files   Sagittarius
  • [gmx-users] *.itp files   Justin A. Lemkul
• [gmx-users] equilibration   s lal badshah
  • [gmx-users] equilibration   Mark Abraham
• [gmx-users] total energy   Daniel P. Luis Jimenez
  • [gmx-users] total energy   Mark Abraham
• [gmx-users] Problem about Forcefield   sudheer babu
  • [gmx-users] Problem about Forcefield   Mark Abraham
• [gmx-users] understanding of difference between gromacs procedures   pragya chohan
  • [gmx-users] understanding of difference between gromacs procedures   Mark Abraham
    • [gmx-users] understanding of difference between gromacs procedures   pragya chohan
      • [gmx-users] understanding of difference between gromacs procedures   Justin A. Lemkul
      • [gmx-users] understanding of difference between gromacs procedures   pragya chohan
      • [gmx-users] understanding of difference between gromacs procedures   Justin A. Lemkul
      • [gmx-users] understanding of difference between gromacs procedures   pragya chohan
      • [gmx-users] understanding of difference between gromacs procedures   Justin A. Lemkul
• [gmx-users] equilibration   s lal badshah
  • [gmx-users] equilibration   Tsjerk Wassenaar
• [gmx-users] RE:Problem about *FF   sudheer babu
  • [gmx-users] RE:Problem about *FF   Andreas
• [gmx-users] Problem about *FF   sudheer babu
  • [gmx-users] Problem about *FF   Justin A. Lemkul
• [gmx-users] Free energy of dihedral restraint   Robert Johnson
  • [gmx-users] Free energy of dihedral restraint   David Mobley
• [gmx-users] pdb2gmx error   Gadzikano Munyuki
  • [gmx-users] pdb2gmx error   Mark Abraham
• [gmx-users] problem of FF   sudheer babu
• [gmx-users] average structure with ligand   Anna Marabotti
  • [gmx-users] average structure with ligand   #NGUYEN CONG TRI#
  • [gmx-users] average structure with ligand   Ran Friedman
    • [gmx-users] average structure with ligand   David Mobley
• [gmx-users] nstcomm value   avinash kumar
• [gmx-users] g_anaeig   SWAPNA
  • [gmx-users] g_anaeig   Mark Abraham
    • [gmx-users] g_anaeig   SWAPNA
      • [gmx-users] g_anaeig   Mark Abraham
• [gmx-users] Definition of mol2 file used by topolbuild   Bruce Ray
• [gmx-users] RE: gmx-users Digest, Vol 47, Issue 58   Evanildo Júnior
• [gmx-users] How to create three different zones to minimize energy of a enzyme?   Evanildo Júnior
  • [gmx-users] How to create three different zones to minimize energy of a enzyme?   Mark Abraham
    • [gmx-users] How to create three different zones to minimize energy of a enzyme?   Tsjerk Wassenaar
      • [gmx-users] How to create three different zones to minimize energy of a enzyme?   TJ Piggot
• [gmx-users] center of mass removal   baloilgiullare at interfree.it
  • [gmx-users] center of mass removal   Tsjerk Wassenaar
    • [gmx-users] center of mass removal   Giordano Mancini
• [gmx-users] Remove COM of group only in x & y direction   Mirijanian, Dina Tigranui
  • [gmx-users] Remove COM of group only in x & y direction   Berk Hess
    • [gmx-users] tutorial for membrane-bound systems   serdar durdagi
• [gmx-users] ions different   s lal badshah
  • [gmx-users] ions different   Mark Abraham
• [gmx-users] complete energy minimization   s lal badshah
  • [gmx-users] complete energy minimization   Justin A. Lemkul
    • [gmx-users] complete energy minimization   Mark Abraham
• [gmx-users] configure error (lam-mpi installation)   Andreas Kring
  • [gmx-users] configure error (lam-mpi installation)   Mark Abraham
• [gmx-users] Black whole simluations   Jiang ran
• [gmx-users] pdb2gmx error   Gadzikano Munyuki
  • [gmx-users] pdb2gmx error   Tsjerk Wassenaar
  • [gmx-users] pdb2gmx error   Justin A. Lemkul
• [gmx-users] construct electron density from file WANNIER_CENTER   Yunan Yan
• [gmx-users] wants to simulate for more timesteps   Anamika Awasthi
  • [gmx-users] wants to simulate for more timesteps   Siavoush Dastmalchi
  • [gmx-users] wants to simulate for more timesteps   Mark Abraham
    • [gmx-users] Install on a 64 bit dual core machine - Debian linux   Ricardo Soares
      • [gmx-users] Install on a 64 bit dual core machine - Debian linux   Kpiwara De X-nelo
      • [gmx-users] Install on a 64 bit dual core machine - Debian linux   Diego Enry
• [gmx-users] tutorial for membrane-bound systems   Alan Dodd
  • [gmx-users] tutorial for membrane-bound systems   serdar durdagi
    • [gmx-users] tutorial for membrane-bound systems   Andreas
• [gmx-users] tutorial for membrane-bound systems   Alan Dodd
• [gmx-users] help for dynamic in TFE/H2O   Luisa Calvanese
• [gmx-users] problem with TFE in GROMOS96 53a6   Luisa Calvanese
• [gmx-users] problem with TFE in GROMOS96 53a6   Luisa Calvanese
• [gmx-users] help for file .itp   Luisa Calvanese
  • [gmx-users] help for file .itp   Mark Abraham
• [gmx-users] Problem about tpbconv   sudheer babu
  • [gmx-users] Problem about tpbconv   Mark Abraham
• [gmx-users] information about tau_p   pragya chohan
  • [gmx-users] information about tau_p   Mark Abraham
• [gmx-users] popc   Chiara Parravicini
  • [gmx-users] popc   Justin A. Lemkul
    • [gmx-users] popc   Chiara Parravicini
      • [gmx-users] popc   Justin A. Lemkul
• [gmx-users] changing the time step with tpbconv   OZGE ENGIN
  • [gmx-users] changing the time step with tpbconv   David van der Spoel
• [gmx-users] problem about rmsd   sudheer babu
  • [gmx-users] problem about rmsd   Justin A. Lemkul
• [gmx-users] changing the time step with tpbconv   OZGE ENGIN
  • [gmx-users] changing the time step with tpbconv   David van der Spoel
• [gmx-users] popc   chris.neale at utoronto.ca
• [gmx-users] problem about rmsd   sudheer babu
  • [gmx-users] problem about rmsd   Justin A. Lemkul
    • [gmx-users] problem about rmsd   bharat v. adkar
  • [gmx-users] problem about rmsd   Mark Abraham
• [gmx-users] problem with grompp (that is used instead of tpbconv)   OZGE ENGIN
  • [gmx-users] problem with grompp (that is used instead of tpbconv)   Mark Abraham
  • [gmx-users] problem with grompp (that is used instead of tpbconv)   David van der Spoel
• [gmx-users] Simulated Annealing problem   mon_sharma at research.iiit.ac.in
  • [gmx-users] Simulated Annealing problem   Mark Abraham
    • [gmx-users] Simulated Annealing problem   mon_sharma at research.iiit.ac.in
• [gmx-users] lipid parameters for ffG43a1   pragya chohan
  • [gmx-users] lipid parameters for ffG43a1   Justin A. Lemkul
  • [gmx-users] lipid parameters for ffG43a1   Mark Abraham
• [gmx-users] Simulated Annealing problem   mon_sharma at research.iiit.ac.in
• [gmx-users] error of equilibration   s lal badshah
  • [gmx-users] error of equilibration   Mark Abraham
• [gmx-users] pr.mdp file   s lal badshah
  • [gmx-users] pr.mdp file   Justin A. Lemkul
• [gmx-users] LINCS problem   s lal badshah
  • [gmx-users] LINCS problem   Mark Abraham
• [gmx-users] FF for membrane protein simulation in water   sudheer babu
  • [gmx-users] FF for membrane protein simulation in water   Justin A. Lemkul
• [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours   maria goranovic
  • [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours   Carsten Kutzner
    • [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours   maria goranovic
      • [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours   maria goranovic
      • [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours   Mark Abraham
• [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours   Alan Dodd
• [gmx-users] OPLS-FF   sudheer babu
• [gmx-users] amber force field problem: ignh doesnot work   Liu Shiyong
  • [gmx-users] amber force field problem: ignh doesnot work   Justin A. Lemkul
• [gmx-users] OPLS-FF   chris.neale at utoronto.ca
• [gmx-users] Error in equilibration   s lal badshah
  • [gmx-users] Error in equilibration   Justin A. Lemkul
  • [gmx-users] Error in equilibration   Mark Abraham
• [gmx-users] error oxo   s lal badshah
• [gmx-users] .itp file for polymer (Polystyrene)   Rohit
  • [gmx-users] .itp file for polymer (Polystyrene)   Mark Abraham
    • [gmx-users] .itp file for polymer (Polystyrene)   Rohit
• [gmx-users] query about itp file of sugar   SHREYA RAY CHAUDHURI
  • [gmx-users] query about itp file of sugar   Mark Abraham
• [gmx-users] Re: Hi   Justin A. Lemkul
• [gmx-users] Re: Informatin about Force field for Protein in POPC   Chris Neale
• [gmx-users] POL3 polarizable water model   Bo Zhou
  • [gmx-users] POL3 polarizable water model   Vasilii Artyukhov
  • [gmx-users] POL3 polarizable water model   David van der Spoel
• [gmx-users] combining the OPLS-AA forcefield with the Berger lipids   Chris Neale
• [gmx-users] Distance constrained energy minimization and MD   jayant james
  • [gmx-users] Distance constrained energy minimization and MD   Mark Abraham
• [gmx-users] looking for help about the generating of opls forcefield   zhuliang at tju.edu.cn
  • [gmx-users] looking for help about the generating of opls forcefield   Mark Abraham
• [gmx-users] OPLS-AA/L   sudheer babu
• [gmx-users] System   s lal badshah
• [gmx-users] OPLS-AA/L   chris.neale at utoronto.ca
• [gmx-users] Error in equilibration   s lal badshah
  • [gmx-users] Error in equilibration   Mark Abraham
• [gmx-users] Basic questions.   fabracht sdf
  • [gmx-users] Basic questions.   Justin A. Lemkul
• [gmx-users] gmxtest failure on a phenom machine   Giovanni Settanni
• [gmx-users] minimization -- bugzilla or general advice?   David Mobley
  • [gmx-users] minimization -- bugzilla or general advice?   Xavier Periole
    • [gmx-users] minimization -- bugzilla or general advice?   David Mobley
      • [gmx-users] minimization -- bugzilla or general advice?   Mark Abraham
      • [gmx-users] minimization -- bugzilla or general advice?   David Mobley
      • [gmx-users] minimization -- bugzilla or general advice?   Christian Burisch
      • [gmx-users] minimization -- bugzilla or general advice?   David Mobley
      • [gmx-users] minimization -- bugzilla or general advice?   David van der Spoel
      • [gmx-users] minimization -- bugzilla or general advice?   Berk Hess
      • [gmx-users] minimization -- bugzilla or general advice?   David Mobley
      • [gmx-users] minimization -- bugzilla or general advice?   Berk Hess
      • [gmx-users] minimization -- bugzilla or general advice?   David Mobley
      • [gmx-users] minimization -- bugzilla or general advice?   David Mobley
      • [gmx-users] minimization -- bugzilla or general advice?   Berk Hess
      • [gmx-users] gromacs 4.0   Xavier Periole
      • [gmx-users] gromacs 4.0   Berk Hess
      • [gmx-users] restarting MD simulation   serdar durdagi
      • [gmx-users] restarting MD simulation   David van der Spoel
      • [gmx-users] restarting MD simulation   Diego Enry
• [gmx-users] system collapsed   Gitanjali tandon
  • [gmx-users] system collapsed   Mark Abraham
• [gmx-users] Re:writing xtc file from trr file   JMandumpal
  • [gmx-users] Re:writing xtc file from trr file   Florian Dommert
  • [gmx-users] Re:writing xtc file from trr file   Florian Dommert
  • [gmx-users] Re:writing xtc file from trr file   Florian Dommert
• [gmx-users] about g_bond   Rui Li
  • [gmx-users] about g_bond   David van der Spoel
• [gmx-users] MInimization with frozen atoms   Georgios Patargias
• [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   reich at mpikg.mpg.de
  • [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   Berk Hess
• [gmx-users] why trjconv cannot split a file more than 1020 parts   齐文鹏
  • [gmx-users] why trjconv cannot split a file more than 1020 parts   Yang Ye
• [gmx-users] Minimisation with frozen groups   reich at mpikg.mpg.de
• [gmx-users] Alkane dihedral from OPLS to Ryckaert-Bellemans   Sung Hyun Park
• [gmx-users] Install on a 64 bit dual core machine - Debian linux   Rodrigo faccioli
• [gmx-users] OPLS-AA/L   sudheer babu
  • [gmx-users] OPLS-AA/L   Justin A. Lemkul
• [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   reich at mpikg.mpg.de
  • [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   Berk Hess
• [gmx-users] How to decrease the temperature during a MD?   Priscila Capriles Goliatt
  • [gmx-users] How to decrease the temperature during a MD?   Martin Höfling
• [gmx-users] OPLS-AA/L   Chris Neale
• [gmx-users] gmx-users   Luis Javier Alvarez Noguera
  • [gmx-users] gmx-users   Mark Abraham
• [gmx-users] why trjconv cannot split a file more than 1020 parts   齐文鹏
• [gmx-users] NVT and NVE   JMandumpal
  • [gmx-users] NVT and NVE   Mark Abraham
• [gmx-users] how to calculate redisue wise RMSD in gromacs?   yren at home.ipe.ac.cn
  • [gmx-users] how to calculate redisue wise RMSD in gromacs?   Mark Abraham
    • [gmx-users] how to calculate redisue wise RMSD in gromacs?   TJ Piggot
• [gmx-users] NVT and NVE   JMandumpal
• [gmx-users] NVT and NVE   JMandumpal
• [gmx-users] Question about different versions of gromacs   Nicolas Martinez
  • [gmx-users] Question about different versions of gromacs   Mark Abraham
  • [gmx-users] Question about different versions of gromacs   Carsten Kutzner
    • [gmx-users] Question about different versions of gromacs   Berk Hess
      • [gmx-users] Question about different versions of gromacs   pragya chohan
      • [gmx-users] Question about different versions of gromacs   Berk Hess
• [gmx-users] NVT and NVE   JMandumpal
  • [gmx-users] NVT and NVE   David van der Spoel
• [gmx-users] H Atom type modification of POPC and double pair   sudheer babu
• [gmx-users] Re: Re: How to decrease the temperature during a MD?   Priscila Capriles Goliatt
• [gmx-users] Position restraint and distance restraints   jayant james
  • [gmx-users] Position restraint and distance restraints   Yang Ye
• [gmx-users] Re: Starting configuration for gromacs   Mark Abraham
  • [gmx-users] Converting Tripos FF to Gromacs?   serdar durdagi
    • [gmx-users] Converting Tripos FF to Gromacs?   Mark Abraham
    • [gmx-users] Converting Tripos FF to Gromacs?   Bruce Ray
• [gmx-users] modify H atom type from opls_369   sudheer babu
• [gmx-users] Command for MD   s lal badshah
  • [gmx-users] Command for MD   Tsjerk Wassenaar
• [gmx-users] g_sas WARNING: could not find a Van der Waals radius   jo hanna
  • [gmx-users] g_sas WARNING: could not find a Van der Waals radius   Mark Abraham
    • [gmx-users] g_sas WARNING: could not find a Van der Waals radius   Tsjerk Wassenaar
• [gmx-users] transfer of AMBER ion definitions to the ions.itp file   OZGE ENGIN
  • [gmx-users] transfer of AMBER ion definitions to the ions.itp file   Justin A. Lemkul
• [gmx-users] g_analyze   A Heddell
  • [gmx-users] g_analyze   David van der Spoel
• [gmx-users] transfer of AMBER ion definitions to the ions.itp file   OZGE ENGIN
• [gmx-users] simulation of gases diffusion pathways   vips g
  • [gmx-users] simulation of gases diffusion pathways   David van der Spoel
• [gmx-users] table-extension   jayant james
  • [gmx-users] table-extension   Mark Abraham
• [gmx-users] How to analyse the number of atom around the protein?   fufengliu at tju.edu.cn
  • [gmx-users] How to analyse the number of atom around the protein?   David van der Spoel
• [gmx-users] Help with water decane interface   fabracht sdf
  • [gmx-users] Help with water decane interface   Justin A. Lemkul
  • [gmx-users] Help with water decane interface   Ángel Piñeiro
• [gmx-users] An error in parallel   shuai lu
  • [gmx-users] An error in parallel   Justin A. Lemkul
    • [gmx-users] An error in parallel   shuai lu
• [gmx-users] to create a simulation box containing only oxygen gas   vips g
  • [gmx-users] to create a simulation box containing only oxygen gas   Justin A. Lemkul
• [gmx-users] residue names for AMBER ff in GROMACS   OZGE ENGIN
  • [gmx-users] residue names for AMBER ff in GROMACS   Justin A. Lemkul
• [gmx-users] Entropy correction in PMF   Ángel Piñeiro
• [gmx-users] Pressure negative after NVT simulation   Alif M Latif
  • [gmx-users] Pressure negative after NVT simulation   Mark Abraham
• [gmx-users] How to modify H atom type from opls_369 to match H expected by popc.itp   sudheer babu
  • [gmx-users] How to modify H atom type from opls_369 to match H expected by popc.itp   Justin A. Lemkul
• [gmx-users] Simulation at different temperature   s lal badshah
  • [gmx-users] Simulation at different temperature   David van der Spoel
• [gmx-users] Please let me know where can I found parameters for Phosphorylated amino acids.   SeungPyo Hong
  • [gmx-users] Please let me know where can I found parameters for Phosphorylated amino acids.   Justin A. Lemkul
• [gmx-users] Simulation at different temperature   Yang Ye
• [gmx-users] problem with bilayer PBC. after dynamics, bilayer becomes 2 monolayers (shift in box center?)   maria goranovic
• [gmx-users] problem with bilayer PBC. after dynamics, bilayer becomes 2 monolayers (shift in box center?)   Alan Dodd
• [gmx-users] how can I restart simulation   Anamika Awasthi
  • [gmx-users] how can I restart simulation   Justin A. Lemkul
• [gmx-users] How to modify H atom type from opls_369 to match H expected by popc.itp   Chris Neale
• [gmx-users] Re: Help needed on using general amber force field (GAFF)   servaas michielssens
• [gmx-users] anisotropic coupling tau_p values   pragya chohan
  • [gmx-users] anisotropic coupling tau_p values   Justin A. Lemkul
• [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS   OZGE ENGIN
  • [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS   Justin A. Lemkul
• [gmx-users] g_sas and vdwradii.dat   Justin A. Lemkul
  • [gmx-users] Re: g_sas and vdwradii.dat   Justin A. Lemkul
• [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS   OZGE ENGIN
  • [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS   Justin A. Lemkul
• [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS   OZGE ENGIN
  • [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS   Justin A. Lemkul

Last message date: Mon Mar 31 23:53:55 CEST 2008
Archived on: Thu Nov 14 12:04:21 CET 2013

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