August 2008 Archives by author

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Starting: Fri Aug 1 00:56:59 CEST 2008
Ending: Sun Aug 31 23:37:47 CEST 2008
Messages: 620

[gmx-users] Different results with and without constraints for pr coupling. A.Rzepiela
[gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X) Alan
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 116 Alan
[gmx-users] amb2gmx for big systems Alan
[gmx-users] water tip3p Alan
[gmx-users] [ atomtypes ] are not case sensitive? Alan
[gmx-users] temperature coupling for complex+ligand+water+ions Alan
[gmx-users] Re: temperature coupling for complex+ligand+water+ions Alan
[gmx-users] RE: [ atomtypes ] are not case sensitive? Alan
[gmx-users] RE: [ atomtypes ] are not case sensitive? Alan
[gmx-users] remove center of mass motion M. Emal Alekozai
[gmx-users] error comm-grps=Protein SOL M. Emal Alekozai
[gmx-users] error comm-grps=Protein SOL M. Emal Alekozai
[gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types" M. Emal Alekozai
[gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types" M. Emal Alekozai
[gmx-users] Vacuum Simulation of Alanine Dipeptide =>production run M. Emal Alekozai
[gmx-users] AMBER and gromacs atoms renaming Shay Amram
[gmx-users] problem with protein secondary structure analysis Shay Amram
[gmx-users] groups to write to trr Shay Amram
[gmx-users] a question about the content in atm-pair.out file Shay Amram
[gmx-users] do_dssp Nuno Azoia
[gmx-users] RE: g_mindist option van Bemmelen
[gmx-users] AFM pulling rate Malin Bergenstråhle
[gmx-users] protein/dmso simulation Bhanu
[gmx-users] Genion failing in parallel runs. Bhanu
[gmx-users] New Gromacs-CPMD QMMM webpage Pradip Biswas
[gmx-users] New Gromacs-CPMD QMMM webpage Pradip Biswas
[gmx-users] QMMM Pradip Biswas
[gmx-users] a question about the content in atm-pair.out file Cao, Yang
[gmx-users] Re: Putting more than one peptide Vitaly Chaban
[gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed Vitaly Chaban
[gmx-users] RE: Umbrella Sampling Vitaly Chaban
[gmx-users] RE: how to extend 1ns Unfolding simulation to 6ns Vitaly Chaban
[gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed Vitaly Chaban
[gmx-users] RE: Define proper set of topology parameters for new molecule in different FF. Vitaly Chaban
[gmx-users] RE: how long simulation takes to get stable when constrains is none in mdp file? Vitaly Chaban
[gmx-users] RE: how to fix the COM of group in the pull. Vitaly Chaban
[gmx-users] RE[4]: Define proper set of topology parameters for new molecule in different FF. Vitaly Chaban
[gmx-users] RE: simulating with air Vitaly Chaban
[gmx-users] RE: grompp and box size Vitaly Chaban
[gmx-users] RE: grompp and box size Vitaly Chaban
[gmx-users] rdf O-H of water from tutorial Vitaly Chaban
[gmx-users] Re: requested for GROMACS package Vitaly Chaban
[gmx-users] Re: Force Field Parameters Nitrogen and Oxygen Vitaly Chaban
[gmx-users] Re: simulating with air Vitaly Chaban
[gmx-users] Re: colour of the molecules Vitaly Chaban
[gmx-users] Re: categorization Vitaly Chaban
[gmx-users] Re: Re: colour of the molecules Vitaly Chaban
[gmx-users] Re: simulating with air Vitaly Chaban
[gmx-users] Re: simulating with air Vitaly Chaban
[gmx-users] Re: about size of group of monomers vs time Vitaly Chaban
[gmx-users] Re: Empty trr file Vitaly Chaban
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 61 Vitaly Chaban
[gmx-users] generating conf.gro Vitaly Chaban
[gmx-users] generating conf.gro Vitaly Chaban
[gmx-users] Re: protein/dmso simulation Vitaly Chaban
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 78 Vitaly Chaban
[gmx-users] Re: tfe.itp Vitaly Chaban
[gmx-users] Re: The WARNING Vitaly Chaban
[gmx-users] Re: Simulations backward in time Vitaly Chaban
[gmx-users] Re: The WARNING Vitaly Chaban
[gmx-users] Re: Using Morse potentials with ENCAD force field Vitaly Chaban
[gmx-users] Re: New Gromacs-CPMD QMMM webpage Vitaly Chaban
[gmx-users] Re: Simulations backward in time Vitaly Chaban
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 89 Vitaly Chaban
[gmx-users] Re: Simulations backward in time Vitaly Chaban
[gmx-users] Re: Simulations backward in time Vitaly Chaban
[gmx-users] Re: Using Morse potentials with ENCAD force field Vitaly Chaban
[gmx-users] Re: Salt molecule - ion bond Vitaly Chaban
[gmx-users] Re: The WARNING Vitaly Chaban
[gmx-users] groups to write to trr Vitaly Chaban
[gmx-users] groups to write to trr Vitaly Chaban
[gmx-users] Re: groups to write to trr Vitaly Chaban
[gmx-users] Re: Using Morse potentials with ENCAD force field Vitaly Chaban
[gmx-users] Re[2]: Using Morse potentials with ENCAD force field Vitaly Chaban
[gmx-users] Re: M*tif installation Vitaly Chaban
[gmx-users] Re: g_msd Vitaly Chaban
[gmx-users] Re: g_velacc Vitaly Chaban
[gmx-users] Re: g_velacc Vitaly Chaban
[gmx-users] Re: g_velacc Vitaly Chaban
[gmx-users] Questions about brownian/langevin dynamics of bead-spring polymers Suman Chakrabarty
[gmx-users] How to display simulation box in VMD? Suman Chakrabarty
[gmx-users] M*tif installation Suman Chakrabarty
[gmx-users] Testing David Chan
[gmx-users] re: ensuring that compilation used gcc 3.x David Chan
[gmx-users] Differences in version 3.0 and 3.3 Cheong Wee Loong, Daniel
[gmx-users] LJ question Anthony Cruz
[gmx-users] LJ question Anthony Cruz
[gmx-users] FFTW & Gromacs installation on AIX 5.3 Dimitris Dellis
[gmx-users] catastrophic error: "timer not defined" DimitryASuplatov
[gmx-users] Order parameters of lipid Alan Dodd
[gmx-users] Corrupt TRR file -- skipping a bad frame? Alan Dodd
[gmx-users] when gen_vel should be "no" Florian Dommert
[gmx-users] Re: g_velacc Florian Dommert
[gmx-users] membrane with OPLS force field Rebeca García Fandiño
[gmx-users] membrane with OPLS force field Rebeca García Fandiño
[gmx-users] gmx does not recognize HIE as protein Rebeca García Fandiño
[gmx-users] error: 1 particles communicated to PME node 3 (...) Rebeca García Fandiño
[gmx-users] Problems extending a calculation (in steps and Benchmark) Rebeca García Fandiño
[gmx-users] invalid number of nodes Rebeca García Fandiño
[gmx-users] invalid number of nodes Rebeca García Fandiño
[gmx-users] problems with PBC in editconf Rebeca García Fandiño
[gmx-users] problems creating mixed solvent systems Ted Fischer
[gmx-users] problems creating mixed solvent systems Ted Fischer
[gmx-users] Normal Mode Analysis in Double-Precision Ran Friedman
[gmx-users] Normal Mode Analysis in Double-Precision Ran Friedman
[gmx-users] Normal Mode Analysis in Double-Precision Ran Friedman
[gmx-users] Normal Mode Analysis in Double-Precision Ran Friedman
[gmx-users] Normal Mode Analysis in Double-Precision Ran Friedman
[gmx-users] single-precision *.tpr data after a double-precision run Ran Friedman
[gmx-users] g_covar with correlation matrix Ran Friedman
[gmx-users] single-precision *.tpr data after a double-precision run Ran Friedman
[gmx-users] single-precision *.tpr data after a double-precision run Ran Friedman
[gmx-users] about size of group of monomers vs time Ran Friedman
[gmx-users] Cluster Size Distribution Ran Friedman
[gmx-users] Define proper set of topology parameters for new molecule in different FF. Andrey Frolov
[gmx-users] RE: Define proper set of topology parameters for new molecule in different FF. Andrey Frolov
[gmx-users] pdb2gmx -inter automatised ? Christian Fufezan
[gmx-users] pdb2gmx -inter automatised ? Christian Fufezan
[gmx-users] (no subject) Anjelika Gasilina
[gmx-users] mdrun failing with error message "reading tpx file (em.tpr) version 40 with version 31 program" Anjelika Gasilina
[gmx-users] how to fix a position in the single eigenvector in essential dynamics sampling? Bert de Groot
[gmx-users] analysizing the sam.edo script? Bert de Groot
[gmx-users] Re: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue Bert de Groot
[gmx-users] Force Distance Curve from .trr .xtc VENKATESH HARIHARAN
[gmx-users] Please help: POPC membrane simulation Florian Haberl
[gmx-users] colour of the molecules Florian Haberl
[gmx-users] g_hbond output analysis Florian Haberl
[gmx-users] Genion failing in parallel runs. Florian Haberl
[gmx-users] M*tif installation Florian Haberl
[gmx-users] problem with parallelization on a dual quad-core machine Hongxian He
[gmx-users] AMOEBA in gromacs Grange Hermitage
[gmx-users] Imposing distance restraints between two Grange Hermitage
[gmx-users] quantum chemistry to gromacs topology approaches Grange Hermitage
[gmx-users] about size of group of monomers vs time Rogelio Hernández
[gmx-users] about size of group of monomers vs time Rogelio Hernández
[gmx-users] A bug of trjconv for force output? Berk Hess
[gmx-users] invalid number of nodes Berk Hess
[gmx-users] error: 1 particles communicated to PME node 3 (...) Berk Hess
[gmx-users] invalid number of nodes Berk Hess
[gmx-users] invalid number of nodes Berk Hess
[gmx-users] AFM pulling rate Berk Hess
[gmx-users] Dielectric constant Berk Hess
[gmx-users] Dielectric constant Berk Hess
[gmx-users] catastrophic error: "timer not defined" Berk Hess
[gmx-users] [ atomtypes ] are not case sensitive? Berk Hess
[gmx-users] RE: [ atomtypes ] are not case sensitive? Berk Hess
FW: [gmx-users] charmm and oplsaa simulation results don't match Berk Hess
FW: [gmx-users] Re: Simulations backward in time Berk Hess
[gmx-users] Some Issues on Substrates/PBC Michael Hirtz
[gmx-users] Some Issues on Substrates/PBC Michael Hirtz
[gmx-users] Some Issues on Substrates/PBC Michael Hirtz
[gmx-users] dihedral potential OPLSAA force field David Huang
[gmx-users] dihedral potential OPLSAA force field (correction) David Huang
[gmx-users] Re: Simulations backward in time Jochen Hub
[gmx-users] Visualizing gromacs result Jochen Hub
[gmx-users] when gen_vel should be "no" Jochen Hub
[gmx-users] How to use g_energy after parellal mdrun Jochen Hub
[gmx-users] Warnings while grompp_d Jochen Hub
[gmx-users] How to use g_energy after parellal mdrun Jochen Hub
[gmx-users] genbox and triclinic boxes. Problem an workaround. Jochen Hub
[gmx-users] debian packages from CVS versions Martin Höfling
[gmx-users] Simulations backward in time. Sumanth Jamadagni
[gmx-users] simulations backward in time Sumanth Jamadagni
[gmx-users] not running on higher no of nodes Anupam Nath Jha
[gmx-users] one component plasma simulations (OCP) Argyrios Karatrantos
[gmx-users] OCP simulations Argyrios Karatrantos
[gmx-users] Disappear my solution Morteza Khabiri
[gmx-users] Disappear my solution Morteza Khabiri
[gmx-users] Disappear my solution Morteza Khabiri
[gmx-users] Disappear my solution Morteza Khabiri
[gmx-users] Re: Energy minimization output Kukol, Andreas
[gmx-users] flexible organic solvents Kukol, Andreas
[gmx-users] MDRUN with MPIRUN Kukol, Andreas
[gmx-users] dmso/peptide simulation Anil Kumar
[gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X) Carsten Kutzner
[gmx-users] invalid number of nodes Carsten Kutzner
[gmx-users] invalid number of nodes Carsten Kutzner
[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens Per Larsson
[gmx-users] Cluster Size Distribution Alif M Latif
[gmx-users] charge density Sunjoo Lee
[gmx-users] charge density Sunjoo Lee
[gmx-users] simulations backward in time Jussi Lehtola
[gmx-users] Re: Putting more than one peptide Justin A. Lemkul
[gmx-users] Testing Justin A. Lemkul
[gmx-users] Order parameters of lipid Justin A. Lemkul
[gmx-users] Order parameters of lipid Justin A. Lemkul
[gmx-users] how to extend 1ns Unfolding simulation to 6ns Justin A. Lemkul
[gmx-users] Please help: POPC membrane simulation Justin A. Lemkul
[gmx-users] Question about octahedral boxes Justin A. Lemkul
[gmx-users] Re: Question about octahedral boxes (solved) Justin A. Lemkul
[gmx-users] table force-field Justin A. Lemkul
[gmx-users] table force-field Justin A. Lemkul
[gmx-users] table force-field Justin A. Lemkul
[gmx-users] membrane with OPLS force field Justin A. Lemkul
[gmx-users] force feield paremeters for magnesium Justin A. Lemkul
[gmx-users] RE: Define proper set of topology parameters for new molecule in different FF. Justin A. Lemkul
[gmx-users] membrane with OPLS force field Justin A. Lemkul
[gmx-users] Some Issues on Substrates/PBC Justin A. Lemkul
[gmx-users] membrane with OPLS force field Justin A. Lemkul
[gmx-users] top file definitions_1 Justin A. Lemkul
[gmx-users] remove center of mass motion Justin A. Lemkul
[gmx-users] Some Issues on Substrates/PBC Justin A. Lemkul
[gmx-users] error comm-grps=Protein SOL Justin A. Lemkul
[gmx-users] gromos function type assigned by grompp Justin A. Lemkul
[gmx-users] simulating with air Justin A. Lemkul
[gmx-users] error comm-grps=Protein SOL Justin A. Lemkul
[gmx-users] gromos function type assigned by grompp Justin A. Lemkul
[gmx-users] gromos function type assigned by grompp Justin A. Lemkul
[gmx-users] regarding grompp warning Justin A. Lemkul
[gmx-users] grompp and box size Justin A. Lemkul
[gmx-users] AMBER and gromacs atoms renaming Justin A. Lemkul
[gmx-users] Residue specific secondary structure analysis Justin A. Lemkul
[gmx-users] pdb2gmx -inter automatised ? Justin A. Lemkul
[gmx-users] translation Justin A. Lemkul
[gmx-users] translation Justin A. Lemkul
[gmx-users] requested for GROMACS package Justin A. Lemkul
[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens Justin A. Lemkul
[gmx-users] Error in pdb2gmx Justin A. Lemkul
[gmx-users] ASP-LIG Interaction Energy : MDRUN Justin A. Lemkul
[gmx-users] error: 1 particles communicated to PME node 3 (...) Justin A. Lemkul
[gmx-users] Force Field Parameters Nitrogen and Oxygen Justin A. Lemkul
[gmx-users] Re: requested for GROMACS package Justin A. Lemkul
[gmx-users] mistake!! Justin A. Lemkul
[gmx-users] colour of the molecules Justin A. Lemkul
[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens Justin A. Lemkul
[gmx-users] Re: Energy minimization output Justin A. Lemkul
[gmx-users] Problems extending a calculation (in steps and Benchmark) Justin A. Lemkul
[gmx-users] Re: categorization Justin A. Lemkul
[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens Justin A. Lemkul
[gmx-users] colour of the molecules Justin A. Lemkul
[gmx-users] more than one drug in lipid? Justin A. Lemkul
[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens Justin A. Lemkul
[gmx-users] tfe Justin A. Lemkul
[gmx-users] tfe Justin A. Lemkul
[gmx-users] problems with PBC in editconf Justin A. Lemkul
[gmx-users] LINCS warning Justin A. Lemkul
[gmx-users] Empty trr file !!?? Justin A. Lemkul
[gmx-users] Imposing distance restraints between two residues Justin A. Lemkul
[gmx-users] tfe Justin A. Lemkul
[gmx-users] do_dssp Justin A. Lemkul
[gmx-users] do_dssp Justin A. Lemkul
[gmx-users] do_dssp Justin A. Lemkul
[gmx-users] Position restraints on a pentamer Justin A. Lemkul
[gmx-users] problem with protein secondary structure analysis Justin A. Lemkul
[gmx-users] tfe Justin A. Lemkul
[gmx-users] tfe Justin A. Lemkul
[gmx-users] problem with protein secondary structure analysis Justin A. Lemkul
[gmx-users] temperature coupling for complex+ligand+water+ions Justin A. Lemkul
[gmx-users] tfe Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 66 Justin A. Lemkul
[gmx-users] protein/dmso simulation Justin A. Lemkul
[gmx-users] dmso/peptide simulation Justin A. Lemkul
[Fwd: Re: [gmx-users]build topology file for a molecule define with new residues] Justin A. Lemkul
[gmx-users] Re: temperature coupling for complex+ligand+water+ions Justin A. Lemkul
[gmx-users] Help with grompp with amber99 forcefield Justin A. Lemkul
[gmx-users] tfe.itp Justin A. Lemkul
[gmx-users] FFTW & Gromacs installation on AIX 5.3 Justin A. Lemkul
[gmx-users] tfe Justin A. Lemkul
[gmx-users] HELP::Running Gromacs in parellel Justin A. Lemkul
[gmx-users] [Fwd: WARNING: Found more than 12 triclinic correction vectors, ignoring some.] Justin A. Lemkul
[gmx-users] tfe and gromos9653a Justin A. Lemkul
[gmx-users] Salt molecule - ion bond Justin A. Lemkul
[gmx-users] rb1 test failed after recompiling gromacs 3.3.2 Justin A. Lemkul
[gmx-users] Help - No default Bond types dna Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 96 Justin A. Lemkul
[gmx-users] groups to write to trr Justin A. Lemkul
[gmx-users] g_sgangle Justin A. Lemkul
[gmx-users] g_energy Justin A. Lemkul
[gmx-users] Re: groups to write to trr Justin A. Lemkul
[gmx-users] #include "ffG45a3.itp" Justin A. Lemkul
[gmx-users] Genion failing in parallel runs. Justin A. Lemkul
[gmx-users] Re:g_mindist option Justin A. Lemkul
[gmx-users] Re[2]: Using Morse potentials with ENCAD force field Justin A. Lemkul
[gmx-users] The molecular structure Justin A. Lemkul
[gmx-users] Corrupt TRR file -- skipping a bad frame? Justin A. Lemkul
[gmx-users] Re: Help Justin A. Lemkul
[gmx-users] when gen_vel should be "no" Justin A. Lemkul
[gmx-users] ffg53a5 Justin A. Lemkul
[gmx-users] Error with LINC warning Justin A. Lemkul
[gmx-users] Re: Help Justin A. Lemkul
[gmx-users] error ffg53a5 Justin A. Lemkul
[gmx-users] error ffg53a Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 97 Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 97 Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 97 (Justin A. Lemkul) Justin A. Lemkul
[gmx-users] Keeping portions of a protein fixed during energy minimization and MD simulations Justin A. Lemkul
[gmx-users] M*tif installation Justin A. Lemkul
[gmx-users] problems creating mixed solvent systems Justin A. Lemkul
[gmx-users] M*tif installation Justin A. Lemkul
[gmx-users] g_hbond + invalid command line argument -g Justin A. Lemkul
[gmx-users] Disappear my solution Justin A. Lemkul
[gmx-users] g_hbond + invalid command line argument -g Justin A. Lemkul
[gmx-users] Disappear my solution Justin A. Lemkul
[gmx-users] Disappear my solution Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 109 Justin A. Lemkul
[gmx-users] Disappear my solution Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 118 Justin A. Lemkul
[gmx-users] using gromacs for protein site-mutagenesis study Justin A. Lemkul
[gmx-users] NPT restarts without .edr, can the simulations be used anyway? Justin A. Lemkul
[gmx-users] Re: g_hbond in version 3.4.1 vs rest (Especially higher one) Justin A. Lemkul
[gmx-users] LINCS error Justin A. Lemkul
[gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein? Justin A. Lemkul
[gmx-users] M*tif installation Ross KK Leung
[gmx-users] M*tif installation Ross KK Leung
[gmx-users] how to define small in RMSD Ross KK Leung
[gmx-users] using gromacs for protein site-mutagenesis study Ross KK Leung
[gmx-users] pdb file ??? Chih-Ying Lin
[gmx-users] The WARNING Chih-Ying Lin
[gmx-users] cgnr Chih-Ying Lin
[gmx-users] Salt molecule - ion bond Chih-Ying Lin
[gmx-users] The WARNING Chih-Ying Lin
[gmx-users] g_sgangle Chih-Ying Lin
[gmx-users] g_angle , g_bond distribution Chih-Ying Lin
[gmx-users] g_energy Chih-Ying Lin
[gmx-users] #include "ffG45a3.itp" Chih-Ying Lin
[gmx-users] #include "ffG45a3.itp" Chih-Ying Lin
[gmx-users] The molecular structure Chih-Ying Lin
[gmx-users] Pressure coupling Matteus Lindgren
[gmx-users] Choose groups for force output Matteus Lindgren
[gmx-users] NPT restarts without .edr, can the simulations be used anyway? Matteus Lindgren
[gmx-users] A bug of trjconv for force output? LuLanyuan
[gmx-users] cgnr LuLanyuan
[gmx-users] FFTW & Gromacs installation on AIX 5.3 Senthil Kumar M
[gmx-users] Error in trjconv M.Parthiban
[gmx-users] Re:Error in trjconv M.Parthiban
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 77 M.Parthiban
[gmx-users] Error in trjconv M.Parthiban
[gmx-users] force feield paremeters for magnesium Mahnam
[gmx-users] Umbrella Sampling Alexandr Malafeev
[gmx-users] Re: Umbrella Sampling Alexandr Malafeev
[gmx-users] table force-field Alexandr Malafeev
[gmx-users] table force-field Alexandr Malafeev
[gmx-users] table force-field Alexandr Malafeev
[gmx-users] table force-field Alexandr Malafeev
[gmx-users] Residue specific secondary structure analysis Biswaranjan Meher
[gmx-users] Some Issues on Substrates/PBC André Farias de Moura
[gmx-users] membrane with OPLS force field Chris Neale
[gmx-users] membrane with OPLS force field Chris Neale
[gmx-users] ensuring that compilation used gcc 3.x Chris Neale
[gmx-users] ensuring that compilation used gcc 3.x Chris Neale
[gmx-users] charmm and oplsaa simulation results don't match Chris Neale
[gmx-users] charmm and oplsaa simulation results don't match Chris Neale
[gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types" Chris Neale
[gmx-users] Re: Putting more than one peptide Sheyore Omovie
[gmx-users] single-precision *.tpr data after a double-precision run David Osguthorpe
[gmx-users] REMD trjcat -demux problem Di Pan
[gmx-users] heat_capacity_&_viscosity Sang-Min Park
[gmx-users] g_msd Xavier Periole
[gmx-users] G_SDF if reference atoms are in different residues Hawtin R.
[gmx-users] flexible organic solvents Sascha Rehm
[gmx-users] gromos function type assigned by grompp Romelia Salomon
[gmx-users] gromos function type assigned by grompp Romelia Salomon
[gmx-users] gromos function type assigned by grompp Romelia Salomon
[gmx-users] gromos function type assigned by grompp Romelia Salomon
[gmx-users] CHARMM FF Nicolas Sapay
[gmx-users] rb1 test failed after recompiling gromacs 3.3.2 Nicolas Sapay
[gmx-users] rb1 test failed after recompiling gromacs 3.3.2 Nicolas Sapay
[gmx-users] rb1 test failed after recompiling gromacs 3.3.2 Nicolas Sapay
[gmx-users] How to display simulation box in VMD? Nicolas Sapay
[gmx-users] AFM pulling: after bond-breakage force does not drop to zero Thomas Schlesier
[gmx-users] AFM pulling: after bond-breakage force does not drop to zero Thomas Schlesier
[gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X) Roland Schulz
[gmx-users] Testing (was: Tyrosine problems again) Roland Schulz
[gmx-users] Testing Roland Schulz
[gmx-users] Re: CHARMM FF Roland Schulz
[gmx-users] CHARMM FF Roland Schulz
[gmx-users] Normal Mode Analysis in Double-Precision Inon Sharony
[gmx-users] segmentation fault in g_anaeig Inon Sharony
[gmx-users] segmentation fault in g_anaeig Inon Sharony
[gmx-users] Normal Mode Analysis in Double-Precision Inon Sharony
[gmx-users] Normal Mode Analysis in Double-Precision Inon Sharony
[gmx-users] Normal Mode Analysis in Double-Precision Inon Sharony
[gmx-users] Normal Mode Analysis in Double-Precision Inon Sharony
[gmx-users] single-precision *.tpr data after a double-precision run Inon Sharony
[gmx-users] single-precision *.tpr data after a double-precision run Inon Sharony
[gmx-users] single-precision *.tpr data after a double-precision run Inon Sharony
[gmx-users] Determining temperature from velocities Andy Shelley
[gmx-users] simulating with air Andy Shelley
[gmx-users] Force Field Parameters Nitrogen and Oxygen Andy Shelley
[gmx-users] Re: simulating with air Andy Shelley
[gmx-users] Re: simulating with air Andy Shelley
[gmx-users] Using Morse potentials with ENCAD force field Andy Shelley
[gmx-users] Using Morse potentials with ENCAD force field Andy Shelley
[gmx-users] Re: Using Morse potentials with ENCAD force field Andy Shelley
[gmx-users] G_RMS for different simulations Ricardo Soares
[gmx-users] G_RMS for different simulations Ricardo Soares
[gmx-users] Testing (was: Tyrosine problems again) David van der Spoel
[gmx-users] Testing David van der Spoel
[gmx-users] Testing David van der Spoel
[gmx-users] Testing (was: Tyrosine problems again) David van der Spoel
[gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed David van der Spoel
[gmx-users] how long simulation takes to get stable when constrains is none in mdp file? David van der Spoel
[gmx-users] nature of gromacs / gcc-4.x problem David van der Spoel
[gmx-users] ACE patch in FFG43a1 David van der Spoel
[gmx-users] RMSD between David van der Spoel
[gmx-users] PROBLEM : rdf O-H of water from tutorial David van der Spoel
[gmx-users] Error in pdb2gmx David van der Spoel
[gmx-users] Error in pdb2gmx David van der Spoel
[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens David van der Spoel
[gmx-users] one component plasma simulations (OCP) David van der Spoel
[gmx-users] XTC error David van der Spoel
[gmx-users] REMD trjcat -demux problem David van der Spoel
[gmx-users] Using Morse potentials with ENCAD force field David van der Spoel
[gmx-users] The WARNING David van der Spoel
[gmx-users] Simulations backward in time. David van der Spoel
[gmx-users] Re: Simulations backward in time David van der Spoel
[gmx-users] regarding 2002 post showing protein unfolding with long timesteps David van der Spoel
[gmx-users] #include "ffG45a3.itp" David van der Spoel
[gmx-users] g_hbond output analysis David van der Spoel
[gmx-users] LJ question David van der Spoel
[gmx-users] LJ question David van der Spoel
[gmx-users] g_hbond + invalid command line argument -g David van der Spoel
[gmx-users] FENE potential (Finitely extensible Nonlinear elastic model) David van der Spoel
[gmx-users] Different results with and without constraints for pr coupling. David van der Spoel
[gmx-users] g_velacc David van der Spoel
[gmx-users] Re: g_velacc David van der Spoel
[gmx-users] dimerization problem Tsjerk Wassenaar
[gmx-users] Re: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue Tsjerk Wassenaar
[gmx-users] Fwd: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue Tsjerk Wassenaar
[gmx-users] segmentation fault in g_anaeig Tsjerk Wassenaar
[gmx-users] how long simulation takes to get stable when constrains is none in mdp file? Tsjerk Wassenaar
[gmx-users] RE: grompp and box size Tsjerk Wassenaar
[gmx-users] AMBER and gromacs atoms renaming Tsjerk Wassenaar
[gmx-users] pdb2gmx -inter automatised ? Tsjerk Wassenaar
[gmx-users] Error in pdb2gmx Tsjerk Wassenaar
[gmx-users] gmx does not recognize HIE as protein Tsjerk Wassenaar
[gmx-users] Error in pdb2gmx Tsjerk Wassenaar
[gmx-users] Error in pdb2gmx Tsjerk Wassenaar
[gmx-users] addition of all hydrogens in pdb2gmx Tsjerk Wassenaar
[gmx-users] about how to set the environment variable Tsjerk Wassenaar
[gmx-users] problem with protein secondary structure analysis Tsjerk Wassenaar
[gmx-users] Error in trjconv Tsjerk Wassenaar
[gmx-users] generating conf.gro Tsjerk Wassenaar
[gmx-users] Re:Error in trjconv Tsjerk Wassenaar
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 66 Tsjerk Wassenaar
[gmx-users] Error in trjconv Tsjerk Wassenaar
[gmx-users] pdb file ??? Tsjerk Wassenaar
[gmx-users] Re: The WARNING Tsjerk Wassenaar
[gmx-users] Re: The WARNING Tsjerk Wassenaar
[gmx-users] Re: groups to write to trr Tsjerk Wassenaar
[gmx-users] Re: Re:Re:g_mindist option Tsjerk Wassenaar
[gmx-users] trjconv error Tsjerk Wassenaar
[gmx-users] ffg53a5 Tsjerk Wassenaar
[gmx-users] Corrupt TRR file -- skipping a bad frame? Tsjerk Wassenaar
[gmx-users] trjconv error Tsjerk Wassenaar
[gmx-users] Re: trjconv error Tsjerk Wassenaar
[gmx-users] M*tif installation Tsjerk Wassenaar
[gmx-users] (no subject) Tsjerk Wassenaar
[gmx-users] Mailman CGI error!!! The Mailman CGI wrapper encountered a fatal error. This entry is being stored in your syslog: Group mismatch error. Mailman expected the CGI wrapper script to be executed as group "nobody", but the system's web server executed the CGI script as group "apache". Try tweaking the web server to run the script as group "nobody", or re-run configure, providing the command line option `--with-cgi-gid=apache'. Brian Wengerter
[gmx-users] membrane with OPLS force field Volker Wirth
[gmx-users] membrane with OPLS force field Volker Wirth
[gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X) Steffen Wolf
[gmx-users] Corrupt TRR file -- skipping a bad frame? Matt Wyczalkowski
[gmx-users] Creating a new topology using OPLSAA Mike Wykes
[gmx-users] some questions about gmx_density.c Yang Ye
[gmx-users] Run test in parallel Yang Ye
[gmx-users] Run test in parallel Yang Ye
[gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein? Limei Zhang
[gmx-users] addition of all hydrogens in pdb2gmx sridhar acharya
[gmx-users] simulation problems baloilgiullare
[gmx-users] some questions about gmx_density.c beibei
[gmx-users] about how to set the environment variable beibei
[gmx-users] requested for GROMACS package shiny chandy
[gmx-users] Out of office AutoReply charloteaux.b
[gmx-users] Out of office AutoReply charloteaux.b
[gmx-users] Out of office AutoReply charloteaux.b
[gmx-users] Out of office AutoReply charloteaux.b
[gmx-users] Out of office AutoReply charloteaux.b
[gmx-users] Out of office AutoReply charloteaux.b
[gmx-users] Out of office AutoReply charloteaux.b
[gmx-users] Out of office AutoReply charloteaux.b
[gmx-users] Out of office AutoReply charloteaux.b
[gmx-users] Out of office AutoReply charloteaux.b
[gmx-users] Out of office AutoReply charloteaux.b
[gmx-users] Out of office AutoReply charloteaux.b
[gmx-users] mistake!! sarbani chattopadhyay
[gmx-users] charmm and oplsaa simulation results don't match sarbani chattopadhyay
FW: [gmx-users] charmm and oplsaa simulation results don't match sarbani chattopadhyay
[gmx-users] when gen_vel should be "no" sarbani chattopadhyay
[gmx-users] LINCS error sarbani chattopadhyay
[gmx-users] PROBLEM : rdf O-H of water from tutorial niharendu choudhury
[gmx-users] more than one drug in lipid? serdar durdagi
[gmx-users] LINCS warning serdar durdagi
[gmx-users] all-bonds option serdar durdagi
[gmx-users] AW: all-bonds option serdar durdagi
[gmx-users] A fix to eigio.c ? eladp at elaine.tau.ac.il
[gmx-users] topology for Amyloid beta peptide ffavela at fis.cinvestav.mx
[gmx-users] flexible organic solvents patrick fuchs
[gmx-users] compare 3.3.3 vs 3.99.4 (bit long) spitaleri.andrea at hsr.it
[gmx-users] colour of the molecules hhhh huan
[gmx-users] colour of the molecules hhhh huan
[gmx-users] XTC error hhhh huan
[gmx-users] Re: Putting more than one peptide alkasrivastava at iitb.ac.in
[gmx-users] Re: Energy minimization output alkasrivastava at iitb.ac.in
[gmx-users] Re:g_mindist option alkasrivastava at iitb.ac.in
[gmx-users] Re: Re:Re:g_mindist option alkasrivastava at iitb.ac.in
[gmx-users] Run test in parallel ikedaike
[gmx-users] Run test in parallel ikedaike
[gmx-users] Run test in parallel ikedaike
[gmx-users] Keeping portions of a protein fixed during energy minimization and MD simulations shyamala iyer
[gmx-users] RMSD between jayant james
[gmx-users] tfe shahrbanoo karbalaee
[gmx-users] tfe shahrbanoo karbalaee
[gmx-users] tfe shahrbanoo karbalaee
[gmx-users] tfe shahrbanoo karbalaee
[gmx-users] tfe shahrbanoo karbalaee
[gmx-users] tfe shahrbanoo karbalaee
[gmx-users] tfe.itp shahrbanoo karbalaee
[gmx-users] tfe.itp shahrbanoo karbalaee
[gmx-users] tfe shahrbanoo karbalaee
[gmx-users] tfe and gromos9653a shahrbanoo karbalaee
[gmx-users] ffg53a5 shahrbanoo karbalaee
[gmx-users] error ffg53a5 shahrbanoo karbalaee
[gmx-users] error ffg53a shahrbanoo karbalaee
[gmx-users] error ffg53a and thanks shahrbanoo karbalaee
[gmx-users] how long simulation takes to get stable when constrains is none in mdp file? wang kelvin
[gmx-users] how long simulation takes to get stable when constrains is none in mdp file? wang kelvin
[gmx-users] Please help: POPC membrane simulation mahesh kulharia
[gmx-users] Dielectric constant avinash kumar
[gmx-users] Dielectric constant avinash kumar
[gmx-users] FENE potential (Finitely extensible Nonlinear elastic model) avinash kumar
[gmx-users] regarding grompp warning prasun kumar
[gmx-users] grompp and box size prasun kumar
[gmx-users] protein/dmso simulation prasun kumar
[gmx-users] dmso/peptide simulation prasun kumar
[gmx-users] dmso/peptide simulation prasun kumar
[gmx-users] query about essential dynamics sangeeta kundu
[gmx-users] Imposing distance restraints between two residues plmallip at mail.uh.edu
[gmx-users] Imposing distance restraints between two residues plmallip at mail.uh.edu
[gmx-users] Imposing distance restraints between two plmallip at mail.uh.edu
[gmx-users] Position restraints on a pentamer plmallip at mail.uh.edu
[gmx-users] Position restraints on a pentamer plmallip at mail.uh.edu
[gmx-users] ASP-LIG Interaction Energy : MDRUN nahren manuel
[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens nahren manuel
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 5 minnale
[gmx-users] do_dssp minnale
[gmx-users] do_dssp minnale
[gmx-users] problem with protein secondary structure analysis minnale
[gmx-users] problem with protein secondary structure analysis minnale
[gmx-users] problem with protein secondary structure analysis minnale
[gmx-users] problem with protein secondary structure analysis minnale
[gmx-users] problem with protein secondary structure analysis minnale
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 66 minnale
[gmx-users] g_hbond + invalid command line argument -g minnale
[gmx-users] g_hbond + invalid command line argument -g minnale
[gmx-users] g_hbond + invalid command line argument -g minnale
[gmx-users] g_hbond + invalid command line argument -g minnale
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 118 minnale
[gmx-users] g_hbond output analysis parthiban at ncbs.res.in
[gmx-users] g_hbond output analysis parthiban at ncbs.res.in
[gmx-users] trjconv error parthiban at ncbs.res.in
[gmx-users] trjconv error parthiban at ncbs.res.in
[gmx-users] Re: trjconv error parthiban at ncbs.res.in
[gmx-users] top file definitions_1 rosip at qb.ffyb.uba.ar
[gmx-users] g_msd ram ram
[gmx-users] g_rotacf rams rams
[gmx-users] g_rotacf rams rams
[gmx-users] g_velacc rams rams
[gmx-users] Re: g_velacc rams rams
[gmx-users] Re: g_velacc rams rams
[gmx-users] QMMM ha salem
[gmx-users] New Gromacs-CPMD QMMM webpage vidhya sankar
[gmx-users] AMBER and gromacs atoms renaming Ragnarok sdf
[gmx-users] Help with grompp with amber99 forcefield Ragnarok sdf
[gmx-users] Help - No default Bond types dna Ragnarok sdf
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 96 Ragnarok sdf
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 97 Ragnarok sdf
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 97 Ragnarok sdf
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 97 (Justin A. Lemkul) Ragnarok sdf
[gmx-users] Re: gmx-users Digest, Vol 52, Issue 109 Ragnarok sdf
[gmx-users] how to extend 1ns Unfolding simulation to 6ns ravi sharma
[gmx-users] about connections ravi sharma
[gmx-users] Error in pdb2gmx vivek sharma
[gmx-users] Error in pdb2gmx vivek sharma
[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens vivek sharma
[gmx-users] Error in pdb2gmx vivek sharma
[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens vivek sharma
[gmx-users] Error in pdb2gmx vivek sharma
[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens vivek sharma
[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens vivek sharma
[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens vivek sharma
[gmx-users] MDRUN with MPIRUN vivek sharma
[gmx-users] MDRUN with MPIRUN vivek sharma
[gmx-users] HELP::Running Gromacs in parellel vivek sharma
[gmx-users] Visualizing gromacs result vivek sharma
[gmx-users] Error while running gromacs in parellel vivek sharma
[gmx-users] How to use g_energy after parellal mdrun vivek sharma
[gmx-users] Error with LINC warning vivek sharma
[gmx-users] How to use g_energy after parellal mdrun vivek sharma
[gmx-users] Warnings while grompp_d vivek sharma
[gmx-users] peptide translation priyanka srivastava
[gmx-users] ACE patch in FFG43a1 priyanka srivastava
[gmx-users] translation priyanka srivastava
[gmx-users] translation priyanka srivastava
[gmx-users] translation priyanka srivastava
[gmx-users] Testing (was: Tyrosine problems again) dichan at ucalgary.ca
[Fwd: Re: [gmx-users]build topology file for a molecule define with new residues] cilpa at users.csc.fi
[Fwd: Re: [gmx-users]build topology file for a molecule define with new residues] cilpa at users.csc.fi
[gmx-users] Tyrosine problems again chris.neale at utoronto.ca
[gmx-users] Tyrosine problems again chris.neale at utoronto.ca
[gmx-users] Testing chris.neale at utoronto.ca
[gmx-users] Testing chris.neale at utoronto.ca
[gmx-users] Fwd: membrane simulations with gromacs chris.neale at utoronto.ca
[gmx-users] nature of gromacs / gcc-4.x problem chris.neale at utoronto.ca
[gmx-users] nature of gromacs / gcc-4.x problem chris.neale at utoronto.ca
[gmx-users] FFTW & Gromacs installation on AIX 5.3 chris.neale at utoronto.ca
[gmx-users] regarding 2002 post showing protein unfolding with long timesteps chris.neale at utoronto.ca
[gmx-users] G_SDF if reference atoms are in different residues chris.neale at utoronto.ca
[gmx-users] Differences in version 3.0 and 3.3 chris.neale at utoronto.ca
[gmx-users] Multiple ppa files from a single parallel mdrun_mpi job chris.neale at utoronto.ca
[gmx-users] analysizing the sam.edo script? xi zhao
[gmx-users] how to fix a position in the single eigenvector in essential dynamics sampling? xi zhao
[gmx-users] how to fix the COM of group in the pull. xi zhao
[gmx-users] how to fix the center of mass of the protein in the pull simulation xi zhao
[gmx-users] AFM and g_wham xi zhao
[gmx-users] pull.pdo and AFM force xi zhao
[gmx-users] Empty trr file !!?? ranqi zhu
[gmx-users] call for help 曹臻
[gmx-users] parameters for protonated nitrogen Samuel Coulbourn Flores 花山

Last message date: Sun Aug 31 23:37:47 CEST 2008
Archived on: Thu Nov 14 12:05:01 CET 2013

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