July 2008 Archives by author

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Starting: Tue Jul 1 00:26:06 CEST 2008
Ending: Thu Jul 31 23:51:59 CEST 2008
Messages: 583

[gmx-users] settle issue Mu Yuguang (Dr)
[gmx-users] settle issue Mu Yuguang (Dr)
[gmx-users] energy minimization on a cluster DEEPESH AGARWAL
[gmx-users] How to generate .itp file for a given molecule DEEPESH AGARWAL
[gmx-users] Can GROMACS mutate a residue? DEEPESH AGARWAL
[gmx-users] centering molecule in the water box Fabio Affinito
[gmx-users] centering molecule in the water box Fabio Affinito
[gmx-users] centering molecule in the water box Fabio Affinito
[gmx-users] centering molecule in the water box Fabio Affinito
[gmx-users] minimisation and constraints Alan
[gmx-users] ffamber and ions Alan
[gmx-users] Re: minimisation and constraints Alan
[gmx-users] Re: ffamber and ions Alan
[gmx-users] ffamber and ions Alan
[gmx-users] drawing chemicals 2d sketchs Alan
[gmx-users] Re: ffamber and ions Alan
[gmx-users] steep and md all within one mdp file Alan
[gmx-users] About "Invalid order for directive atomtypes" Alan
[gmx-users] About "Invalid order for directive atomtypes" Alan
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 70 Alan
[gmx-users] Re: CHARMM FF Alan
[gmx-users] a tip to run gromacs from Fink in mac duo core Alan
[gmx-users] Re: a tip to run gromacs from Fink in mac duo core Alan
[gmx-users] ACPYPI announcement Alan
[gmx-users] about gromacs with double precision for FINK in Mac OSX Alan
[gmx-users] definition of J-couplings in g_chi Abil Aliev
[gmx-users] definition of J-couplings in g_chi Abil Aliev
[gmx-users] definition of J-couplings in g_chi Abil Aliev
[gmx-users] definition of J-couplings in g_chi Abil Aliev
[gmx-users] definition of J-couplings in g_chi Abil Aliev
[gmx-users] definition of J-couplings in g_chi Abil Aliev
[gmx-users] Velocity ACF not decaying to zero Vasilii Artyukhov
[gmx-users] Reshaping of triclinic box Cesar Avila
[gmx-users] mdrun -nice integer Nuno Azoia
[gmx-users] simulate Gas Phase system Nuno Azoia
[gmx-users] box size Nuno Azoia
[gmx-users] box size Nuno Azoia
[gmx-users] Where is main() function in GROMACS source? Sangamesh B
[gmx-users] How to do CGMD in GROMACS? Kia Balali-Mood
[gmx-users] Diffusion Cofficient of POPC Jojart Balazs
[gmx-users] tabulated potentials and pairs Michael Brunsteiner
[gmx-users] RE: Have read the manual => How to calculate dihedral Vitaly Chaban
[gmx-users] RE: Covalent bonds breaking formation Vitaly Chaban
[gmx-users] RE: the .mdp format Vitaly Chaban
[gmx-users] RE: about itp file making Vitaly Chaban
[gmx-users] C6 and C12 or sigma and epsilon. Vitaly Chaban
[gmx-users] RE: how to fix molecules and give different temperature Vitaly Chaban
[gmx-users] RE: Using user-tables for simulations in vacuum Vitaly Chaban
[gmx-users] RE: Gromacs and restraints Vitaly Chaban
[gmx-users] RE: how to fix molecules and give different Vitaly Chaban
[gmx-users] RE[2]: how to fix molecules and give different temperature Vitaly Chaban
[gmx-users] RE: problem with using VMD to view the trajectory Vitaly Chaban
[gmx-users] RE: problem with using VMD to view the trajectory Vitaly Chaban
[gmx-users] RE: Gromacs site Vitaly Chaban
[gmx-users] Tyrosine vsite aromatics David Chan
[gmx-users] Tyrosine problems again David Chan
[gmx-users] mdrun producing 0 steps, 0 ps Travis Craddock
[gmx-users] Atom not found in residue while adding hydrogens Travis Craddock
[gmx-users] Atom not found in residue while adding hydrogens Travis Craddock
[gmx-users] GDP Topology Travis Craddock
[gmx-users] Hydrogen Database Format - Control Atoms Travis Craddock
[gmx-users] TEE-REX problem Ramon Crehuet
[gmx-users] Zinc (Zn) parameters Ramon Crehuet
[gmx-users] trjcat -cat skips frames Michel Cuendet
[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling Michel Cuendet
[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling Michel Cuendet
[gmx-users] g_sas, what's it all about? Michel Cuendet
[gmx-users] Possible Bug???? Matthew Danielson
[gmx-users] Possible Bug???? Matthew Danielson
[gmx-users] Correlation-Covariance Dhananjay
[gmx-users] Re: minimize multi-chain protein Florian Dommert
[gmx-users] OPLS-AA methanol model Florian Dommert
[gmx-users] Simulation of silicon oxide surfaces Diego Enry
[gmx-users] Calculating electric field vector at snapshots Aaron Fafarman
[gmx-users] Accuracy of force calculation and doubts on PME parameter choice Nickle Fan
[gmx-users] topology for a membrane + protein Rebeca García Fandiño
[gmx-users] Membrane: anisotropic pressure coupling Rebeca García Fandiño
[gmx-users] amb2gmx for big systems Rebeca García Fandiño
[gmx-users] amb2gmx for big systems Rebeca García Fandiño
[gmx-users] Fitting when structure and reference are slightly different Ran Friedman
[gmx-users] Gromacs and restraints Ran Friedman
[gmx-users] Correlation-Covariance Ran Friedman
[gmx-users] Gromacs site Ran Friedman
[gmx-users] Gromacs site Ran Friedman
[gmx-users] Correlation-Covariance 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] segmentation fault with lincs warning ANINDITA GAYEN
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 77 ANINDITA GAYEN
[gmx-users] (no subject) ANINDITA GAYEN
[gmx-users] antechamber topologies to gromacs format ANINDITA GAYEN
[gmx-users] How to do CGMD in GROMACS? Anirban Ghosh
[gmx-users] How to run on MARTINI Force Field in GROMACS Anirban Ghosh
[gmx-users] Strange dV/dl profile in free energy calculation Maik Goette
[gmx-users] Zinc (Zn) parameters Maik Goette
[gmx-users] Re: QMMM memory problem Gerrit Groenhof
[gmx-users] compilation problem with mopac in gromacs 3.3.3, and x86_64 machine Gerrit Groenhof
[gmx-users] topologies from autodock KAUSHIK H.S.
[gmx-users] g_wham command issues VENKATESH HARIHARAN
[gmx-users] g_wham command issues VENKATESH HARIHARAN
[gmx-users] editconf & genbox for Constraint Pull VENKATESH HARIHARAN
[gmx-users] Force Extension Curve VENKATESH HARIHARAN
[gmx-users] Constraint Pulling - Oscillating Forces VENKATESH HARIHARAN
[gmx-users] g_wham.c VENKATESH HARIHARAN
[gmx-users] drawing chemicals 2d sketchs Florian Haberl
[gmx-users] make_ndx problem Florian Haberl
[gmx-users] Analysis of mutants Florian Haberl
[gmx-users] amb2gmx for big systems Florian Haberl
[gmx-users] dimerization problem Florian Haberl
[gmx-users] plotting displacement of each C-alpha along first eigenvector having largest eigenvalue Florian Haberl
[gmx-users] Berendsen Temperature Coupling and Heat Daniel S. Han
[gmx-users] generating topology for artificial residues Grange Hermitage
[gmx-users] forcefields gaff/ff02EP good solvated with SPCBOX but not POL3BOX Grange Hermitage
FW: [gmx-users] tabulated potential both on pairs and non-bonded interactions / different cutoffs Berk Hess
[gmx-users] Accuracy of force calculation and doubts on PME parameter choice Berk Hess
[gmx-users] rot_diff Berk Hess
[gmx-users] trjcat -cat skips frames Berk Hess
[gmx-users] Constraint Pulling - Oscillating Forces Berk Hess
[gmx-users] cvs version and position restraints... Berk Hess
[gmx-users] How to modify code so that rlist > rcoulomb Berk Hess
[gmx-users] How to modify code so that rlist > rcoulomb Berk Hess
[gmx-users] box size changing during isotropic pressure coupling Berk Hess
[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling (chris.neale at utoronto.ca) Berk Hess
[gmx-users] box size changing during isotropic pressure coupling Berk Hess
[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling (chris.neale at utoronto.ca) Berk Hess
[gmx-users] box size changing during isotropic pressure coupling Berk Hess
[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling Berk Hess
[gmx-users] Possible Bug???? Berk Hess
[gmx-users] tabulated potentials and pairs Berk Hess
[gmx-users] Simulation of silicon oxide surfaces Michael Hirtz
[gmx-users] Re: Simulation of silicon oxide surfaces Michael Hirtz
[gmx-users] Re: Re: Re: Simulation of silicon oxide surfaces Michael Hirtz
[gmx-users] Re: Re: Re: Re: Simulation of silicon oxide surfaces Michael Hirtz
[gmx-users] PDBs for mixed lipid bilayer/membrane Jochen Hub
[gmx-users] Fitting when structure and reference are slightly different Jochen Hub
[gmx-users] problem with using VMD to view the trajectory Martin Höfling
[gmx-users] How to define NVE ensemble in gromacs JMandumpal
[gmx-users] (no subject) JMandumpal
[gmx-users] make_ndx problem JMandumpal
[gmx-users] PBS script for gromacs Gromacs JMandumpal
[gmx-users] cooling the system "NVT" ensemble JMandumpal
[gmx-users] Strange dV/dl profile in free energy calculation Robert Johnson
[gmx-users] Biomolecular Modelling Retreat 8-12th September 2008 Itamar Kass
[gmx-users] Save all MD snapshot Andreas Kring
[gmx-users] Save all MD snapshot Kukol, Andreas
[gmx-users] How to analyze order parameter Kukol, Andreas
[gmx-users] about deuterium order parameter Kukol, Andreas
[gmx-users] Re: a tip to run gromacs from Fink in mac duo core Carsten Kutzner
[gmx-users] Where is main() function in GROMACS source? Carsten Kutzner
[gmx-users] (no subject) Per Larsson
[gmx-users] Error with polymer surface modeling Justin A. Lemkul
[gmx-users] centering molecule in the water box Justin A. Lemkul
[gmx-users] Heme-O2 parameters Justin A. Lemkul
[gmx-users] Partial Vs Formal Charges Justin A. Lemkul
[gmx-users] segmentation fault Justin A. Lemkul
[gmx-users] Abnormal popc struture after inserting protein Justin A. Lemkul
[gmx-users] Re: How to calculate dihedral angle ?? Justin A. Lemkul
[gmx-users] Abnormal popc struture after inserting protein Justin A. Lemkul
[gmx-users] PDBs for mixed lipid bilayer/membrane Justin A. Lemkul
[gmx-users] segmentation fault Justin A. Lemkul
[gmx-users] minimisation and constraints Justin A. Lemkul
[gmx-users] about itp file making Justin A. Lemkul
[gmx-users] RE: the .mdp format Justin A. Lemkul
[gmx-users] Re: .mdp format Justin A. Lemkul
[gmx-users] Force Field: A new chemical compound Justin A. Lemkul
[gmx-users] segmentation fault during MD Justin A. Lemkul
[gmx-users] simulate Gas Phase system Justin A. Lemkul
[gmx-users] Re: segmentation fault during MD and develop parameter Justin A. Lemkul
[gmx-users] Atom CD in residue ILE 1 not found in rtp entry with 19 atoms Justin A. Lemkul
[gmx-users] Re: segmentation fault during MD and develop parameter Justin A. Lemkul
[gmx-users] .mdp format Justin A. Lemkul
[gmx-users] Re: Re: topology using prodrg (Diego Nolasco) Justin A. Lemkul
[gmx-users] Help Justin A. Lemkul
[gmx-users] lipid itp file problem Justin A. Lemkul
[gmx-users] lipid itp problem Justin A. Lemkul
[gmx-users] about some question on gromacs Justin A. Lemkul
[gmx-users] lipid itp problem Justin A. Lemkul
[gmx-users] lipid itp file problem Justin A. Lemkul
[gmx-users] simulating two peptides in a box Justin A. Lemkul
[gmx-users] simulating two peptides in a box Justin A. Lemkul
[gmx-users] simulating two peptides in a box Justin A. Lemkul
[gmx-users] Error:Cannot determine precision of trn file Justin A. Lemkul
[gmx-users] Including itp files Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 32 Justin A. Lemkul
[gmx-users] why temperature result of DMSO simulation is so low Justin A. Lemkul
[gmx-users] various files generated using prodrg Justin A. Lemkul
[gmx-users] Error: number of atoms do not match Justin A. Lemkul
[gmx-users] generating topology for artificial residues Justin A. Lemkul
[gmx-users] Charging one layer of 3-layer slabs Justin A. Lemkul
[gmx-users] total charge of the system Justin A. Lemkul
[gmx-users] How to get LJ potential Energy at any time(not average) Justin A. Lemkul
AW: [gmx-users] topology for a membrane + protein Justin A. Lemkul
[gmx-users] The negative state of a Phe molecule is not parametrized in gromos96 FF? Justin A. Lemkul
[gmx-users] error... plz help Justin A. Lemkul
[gmx-users] Partial charges QM to GROMACS Justin A. Lemkul
[gmx-users] Partial charges QM to GROMACS Justin A. Lemkul
[gmx-users] error in grompp Justin A. Lemkul
[gmx-users] How to generate .itp file for a given molecule Justin A. Lemkul
[gmx-users] How to generate .itp file for a given molecule Justin A. Lemkul
[gmx-users] tfe.gro file and generation of .itp file Justin A. Lemkul
[gmx-users] Molecule which is not defined in the rtp file Justin A. Lemkul
[gmx-users] Can GROMACS mutate a residue? Justin A. Lemkul
[gmx-users] error in g_hbond Justin A. Lemkul
[gmx-users] gromacs bond type Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 50 Justin A. Lemkul
[gmx-users] segmentation fault with lincs warning Justin A. Lemkul
[gmx-users] deuterim order parameter Justin A. Lemkul
[gmx-users] definition of J-couplings in g_chi Justin A. Lemkul
[gmx-users] g_msd Justin A. Lemkul
[gmx-users] editconf & genbox for Constraint Pull Justin A. Lemkul
[gmx-users] help Justin A. Lemkul
[gmx-users] Still :Partial charges QM to GROMACS Justin A. Lemkul
[gmx-users] make_ndx problem Justin A. Lemkul
[gmx-users] make_ndx problem Justin A. Lemkul
[gmx-users] make_ndx problem Justin A. Lemkul
[gmx-users] Atom not found in residue while adding hydrogens Justin A. Lemkul
[gmx-users] Atom not found in residue while adding hydrogens Justin A. Lemkul
[gmx-users] About "Invalid order for directive atomtypes" error Justin A. Lemkul
[gmx-users] Re Re Re: charge group in topology file Justin A. Lemkul
[gmx-users] About "Invalid order for directive atomtypes" Justin A. Lemkul
[gmx-users] trjconv pbc membrane Justin A. Lemkul
[gmx-users] Re: Removal of pbc for analysis Justin A. Lemkul
[gmx-users] energy groups Justin A. Lemkul
[gmx-users] How to do CGMD in GROMACS? Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] segmentation fault with lincs warning Justin A. Lemkul
[gmx-users] segmentation fault with lincs warning Justin A. Lemkul
[gmx-users] problem with charmm Justin A. Lemkul
[gmx-users] Re: Simulation of silicon oxide surfaces Justin A. Lemkul
[gmx-users] [Fwd: deprotonated systeine] Justin A. Lemkul
[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling Justin A. Lemkul
[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling Justin A. Lemkul
[gmx-users] new version of C terminus database for charmm Justin A. Lemkul
[gmx-users] Is it correct Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 85 Justin A. Lemkul
[gmx-users] Membrane: anisotropic pressure coupling Justin A. Lemkul
[gmx-users] topologies from autodock Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 89 Justin A. Lemkul
[gmx-users] what is cgnr ? Justin A. Lemkul
[gmx-users] How to run on MARTINI Force Field in GROMACS Justin A. Lemkul
[gmx-users] help Justin A. Lemkul
[gmx-users] energy minimization Justin A. Lemkul
[gmx-users] What's the default pbc of Gromacs trajectories? Justin A. Lemkul
[gmx-users] g_rmsf Justin A. Lemkul
[gmx-users] What's the default pbc of Gromacs trajectories? Justin A. Lemkul
[gmx-users] Re: adding gas by Gromacs Justin A. Lemkul
[gmx-users] CH3 group and units of POPC? Justin A. Lemkul
[gmx-users] Order parameters of lipid Justin A. Lemkul
[gmx-users] RE: value of d in editconf Justin A. Lemkul
[gmx-users] g_sas, what's it all about? Justin A. Lemkul
[gmx-users] Order parameters of lipid Justin A. Lemkul
[gmx-users] g_sas, what's it all about? Justin A. Lemkul
[gmx-users] dimerization problem Justin A. Lemkul
[gmx-users] error in grompp Serena Leone
[gmx-users] Re: How to calculate dihedral angle ?? Chih-Ying Lin
[gmx-users] Have read the manual => How to calculate dihedral angle?????? Chih-Ying Lin
[gmx-users] The dihedral angles from 192 elements ?? Chih-Ying Lin
[gmx-users] Dynamics : ONE dihedral angle time resolution Chih-Ying Lin
[gmx-users] the .mdp format Chih-Ying Lin
[gmx-users] .mdp format Chih-Ying Lin
[gmx-users] Re: .mdp format Chih-Ying Lin
[gmx-users] Force Field: A new chemical compound Chih-Ying Lin
[gmx-users] mdrun -nice integer Chih-Ying Lin
[gmx-users] box size Chih-Ying Lin
[gmx-users] simulate Gas Phase system Chih-Ying Lin
[gmx-users] .mdp format Chih-Ying Lin
[gmx-users] Wilson angle Chih-Ying Lin
[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling Chih-Ying Lin
[gmx-users] what is cgnr ? Chih-Ying Lin
[gmx-users] Re: CHARMM FF Erik Lindahl
[gmx-users] Gromacs and restraints Matteus Lindgren
[gmx-users] Gromacs and system building Matteus Lindgren
[gmx-users] g_wham command issues LuLanyuan
[gmx-users] What's the default pbc of Gromacs trajectories? LuLanyuan
[gmx-users] What's the default pbc of Gromacs trajectories? LuLanyuan
[gmx-users] total charge of the system Daniel Adriano Silva M
[gmx-users] release of GROMACS 4 Anna Marabotti
[gmx-users] error in g_hbond Biswaranjan Meher
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 50 Biswaranjan Meher
[gmx-users] Where is gmxtest gmxtest-3.3.3... Kent F. Milfeld
[gmx-users] simulating two peptides in a box Rakesh Mishra
[gmx-users] How to modify code so that rlist > rcoulomb Jeetain Mittal
[gmx-users] How to modify code so that rlist > rvdw > rcoulomb Jeetain Mittal
[gmx-users] How to modify code so that rlist > rcoulomb Jeetain Mittal
[gmx-users] How to modify code so that rlist > rcoulomb Jeetain Mittal
[gmx-users] mass changes in free energy calculations David Mobley
[gmx-users] compilation problem with mopac in gromacs 3.3.3 and x86_64 machine Abu Naser
[gmx-users] compilation problem with mopac in gromacs 3.3.3, and x86_64 machine Abu Naser
[gmx-users] compilation problem with mopac in gromacs 3.3.3 Abu Naser
[gmx-users] box size changing during isotropic pressure coupling Chris Neale
[gmx-users] box size changing during isotropic pressure coupling Chris Neale
[gmx-users] box size changing during isotropic pressure coupling Chris Neale
[gmx-users] Doubt regarding popc simulations Chris Neale
[gmx-users] Possible Bug???? Chris Neale
[gmx-users] deprotonated cys Chris Neale
[gmx-users] DPPC bilayer Chris Neale
[gmx-users] Save all MD snapshot Collins Nganou
[gmx-users] QMMM memory problem Alcides Nicastro
[gmx-users] Re: QMMM memory problem Alcides Nicastro
[gmx-users] CHARMM FF Nicolas
[gmx-users] Help Maryam Nikoosaleh
[gmx-users] topology using prodrg Diego Nolasco
[gmx-users] Re: Re: topology using prodrg (Diego Nolasco) Diego Nolasco
[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling David Osguthorpe
[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling David Osguthorpe
[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling (chris.neale at utoronto.ca) David Osguthorpe
[gmx-users] Normal Mode Analysis in Double-Precision David Osguthorpe
[gmx-users] PME-User Sang-Min Park
[gmx-users] PME User Sang-Min Park
[gmx-users] initial_configuration_sw_water Sang-Min Park
[gmx-users] hydrogen bonds in water tutorial Sung Hyun Park
[gmx-users] Re: hydrogen bonds in water tutorial Sung Hyun Park
[gmx-users] Dynamics : ONE dihedral angle time resolution Xavier Periole
[gmx-users] rot_diff Xavier Periole
[gmx-users] .mdp format Xavier Periole
[gmx-users] rot_diff Xavier Periole
[gmx-users] steep and md all within one mdp file Xavier Periole
[gmx-users] Diffusion Cofficient of POPC Xavier Periole
[gmx-users] About "Invalid order for directive atomtypes" error Xavier Periole
[gmx-users] About "Invalid order for directive atomtypes" error Xavier Periole
[gmx-users] Re: ffamber and ions Damian Gregory Allis Ph.D.
[gmx-users] number of grid cells is zero N. Sundar Ram
[gmx-users] number of grid cells is zero N. Sundar Ram
[gmx-users] Analysis of mutants N. Sundar Ram
[gmx-users] ffamber and ions Vigneshwar Ramakrishnan
[gmx-users] topolbuild 1.1.2, further revisions to an all-atoms model gromacs topology generator Bruce D. Ray
[gmx-users] force constants of improper dihedrals in .itp file from prodrg Joaquim Rui Rodrigues
[gmx-users] Covalent bonds breaking formation Sagittarius
[gmx-users] Have read the manual => How to calculate dihedral angle?????? Y. U. Sasidhar
[gmx-users] CHARMM FF Roland Schulz
[gmx-users] PBS script for gromacs Gromacs Roland Schulz
[gmx-users] GDP Topology Christian Seifert
[gmx-users] About "Invalid order for directive atomtypes" error Hans Martin Senn
[gmx-users] About "Invalid order for directive atomtypes" error Hans Martin Senn
[gmx-users] About "Invalid order for directive atomtypes" error Hans Martin Senn
[gmx-users] About "Invalid order for directive atomtypes" Hans Martin Senn
[gmx-users] genion strips +, -, digits. Bug or feature? Hans Martin Senn
[gmx-users] genion strips +, -, digits. Bug or feature? Hans Martin Senn
[gmx-users] Re: Question about Berendsen thermostat and Hans Martin Senn
[gmx-users] Re: Question about Berendsen thermostat and Hans Martin Senn
[gmx-users] Heme-O2 parameters Rotem Sertchook
[gmx-users] Restraining molecular symmetry Alok Sharma
[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] Covalent bonds breaking formation Nizamov Shawkat
[gmx-users] compilation problem with mopac in gromacs 3.3.3 and x86_64 machine Nizamov Shawkat
[gmx-users] cannot print velocity information to trr/xtc files (Carbon Nanotube inside water) Andy Shelley
[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling (chris.neale at utoronto.ca) Michael Shirts
[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling (chris.neale at utoronto.ca) Michael Shirts
[gmx-users] Re: Question about Berendsen thermostat and Michael Shirts
[gmx-users] Re: Question about Berendsen thermostat and Michael Shirts
[gmx-users] PBS script for gromacs Gromacs Manoj Kumar Singh
[gmx-users] Can GROMACS mutate a residue? Lee Soin
[gmx-users] Can GROMACS mutate a residue? Lee Soin
[gmx-users] Mail problemos David van der Spoel
[gmx-users] mail problems David van der Spoel
[gmx-users] mail problems David van der Spoel
[gmx-users] Charge transfer David van der Spoel
[gmx-users] PME User David van der Spoel
[gmx-users] gromacs bond type David van der Spoel
[gmx-users] definition of J-couplings in g_chi David van der Spoel
[gmx-users] Calculating electric field vector at snapshots David van der Spoel
[gmx-users] Microcanonical MD with PBC David van der Spoel
[gmx-users] Diffusion Cofficient of POPC David van der Spoel
[gmx-users] Re: charge group in topology file David van der Spoel
[gmx-users] definition of J-couplings in g_chi David van der Spoel
[gmx-users] Using user-tables for simulations in vacuum David van der Spoel
[gmx-users] Using user-tables for simulations in vacuum David van der Spoel
[gmx-users]D Gsol from g_sas calculation David van der Spoel
[gmx-users] [Fwd: questions about surface tension] David van der Spoel
[gmx-users] Using user-tables for simulations in vacuum David van der Spoel
[gmx-users] [Fwd: deprotonated systeine] David van der Spoel
[gmx-users] a tip to run gromacs from Fink in mac duo core David van der Spoel
[gmx-users] Tyrosine vsite aromatics David van der Spoel
[gmx-users] Re: Re: Re: Simulation of silicon oxide surfaces David van der Spoel
[gmx-users] How to build boxes with constant number of solvent molecules? David van der Spoel
[gmx-users] (no subject) David van der Spoel
[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling David van der Spoel
[gmx-users] box size changing during isotropic pressure coupling David van der Spoel
[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling (chris.neale at utoronto.ca) David van der Spoel
[gmx-users] Re: Question about Berendsen thermostat and David van der Spoel
[gmx-users] Possible Bug???? David van der Spoel
[gmx-users] Possible Bug???? David van der Spoel
[gmx-users] number of grid cells is zero David van der Spoel
[gmx-users] deprotonated cys (fw) David van der Spoel
[gmx-users] settle issue David van der Spoel
[gmx-users] [Fwd: question] David van der Spoel
[gmx-users] Is there a bug for g_anaeig? David van der Spoel
[gmx-users] Berendsen Temperature Coupling and Heat David van der Spoel
[gmx-users] definition of J-couplings in g_chi David van der Spoel
[gmx-users] g_sas, what's it all about? David van der Spoel
[gmx-users] hydrogen bonds in water tutorial David van der Spoel
[gmx-users] initial_configuration_sw_water David van der Spoel
[gmx-users] g_sas, what's it all about? David van der Spoel
[gmx-users] Tyrosine problems again David van der Spoel
[gmx-users] antechamber topologies to gromacs format #NGUYEN CONG TRI#
[gmx-users] Error problem in free energy calculation Jianhui Tian
[gmx-users] Charging one layer of 3-layer slabs Shaghayegh Vafaei
[gmx-users] cvs version and position restraints... Andrea Vaiana
[gmx-users] cvs version and position restraints... Andrea Vaiana
[gmx-users] tabulated potential both on pairs and non-bonded interactions / different cutoffs Claus Valka
[gmx-users] pairs potential Claus Valka
[gmx-users] pairs potential Claus Valka
[gmx-users]Re: pairs potential Claus Valka
[gmx-users] switch potential function gromacs 3.3.2 Claus Valka
[gmx-users] switch potential function gromacs 3.3.2 Claus Valka
[gmx-users] Microcanonical MD with PBC Lee-Ping Wang
[gmx-users] Re: Microcanonical MD with PBC Lee-Ping Wang
[gmx-users] yet another question about PBC... Tsjerk Wassenaar
[gmx-users] Missing H's in NADH topology? Tsjerk Wassenaar
[gmx-users] mdrun producing 0 steps, 0 ps Tsjerk Wassenaar
[gmx-users] The dihedral angles from 192 elements ?? Tsjerk Wassenaar
[gmx-users] about itp file making Tsjerk Wassenaar
[gmx-users] about itp file making Tsjerk Wassenaar
[gmx-users] box size Tsjerk Wassenaar
[gmx-users] Restraining molecular symmetry Tsjerk Wassenaar
[gmx-users] lipid itp file problem Tsjerk Wassenaar
[gmx-users] lipid itp file problem Tsjerk Wassenaar
[gmx-users] generation of tfe solvent box Tsjerk Wassenaar
[gmx-users] Error: number of atoms do not match Tsjerk Wassenaar
[gmx-users] tfe.gro file and generation of .itp file Tsjerk Wassenaar
[gmx-users] How to generate .itp file for a given molecule Tsjerk Wassenaar
[gmx-users] Zinc (Zn) parameters Tsjerk Wassenaar
[gmx-users] problem with using VMD to view the trajectory Tsjerk Wassenaar
[gmx-users] Fwd: Assistance Tsjerk Wassenaar
[gmx-users] Is there a bug for g_anaeig? Tsjerk Wassenaar
[gmx-users] Correlation-Covariance Tsjerk Wassenaar
[gmx-users] how to fix molecules and give different temperature Santan William
[gmx-users] how to fix molecules and give different temperature Santan William
[gmx-users] RE: how to fix molecules and give different temperature Santan William
[gmx-users] RE: how to fix molecules and give different temperature Santan William
[gmx-users] PDBs for mixed lipid bilayer/membrane Volker Wirth
[gmx-users] Atom CD in residue ILE 1 not found in rtp entry with 19 atoms Volker Wirth
[gmx-users] Including itp files Volker Wirth
[gmx-users] Analysis of mutants Steffen Wolf
[gmx-users] The g_sdf in gromacs 3.3.3 Rongliang Wu
[gmx-users] Umbrella Sampling and .pdo format file Chenyue Xing
[gmx-users] centering molecule in the water box Peyman Yamin
[gmx-users] Error with polymer surface modeling Peyman Yamin
[gmx-users] centering molecule in the water box Peyman Yamin
[gmx-users] minimisation and constraints Peyman Yamin
[gmx-users] How to build boxes with constant number of solvent molecules? Peyman Yamin
[gmx-users] doesn't match coordinate file with topology Peyman Yamin
[gmx-users] g_sas, what's it all about? Peyman Yamin
[gmx-users] g_sas, what's it all about? Peyman Yamin
[gmx-users] g_sas, what's it all about? Peyman Yamin
[gmx-users] how to measure the surface tension of membrane by inclusion Li Yang
[gmx-users] Error:Cannot determine precision of trn file Yang Ye
[gmx-users] settle issue Yang Ye
[gmx-users] The negative state of a Phe molecule is not parametrized in gromos96 FF? Hu Zhongqiao
[gmx-users] Is there a bug for g_anaeig? G.H. Zuo
[gmx-users] Error with polymer surface modeling h a
[gmx-users] topology using prodrg h a
[gmx-users] Re: Re: topology using prodrg (Diego Nolasco) h a
[gmx-users] Error: number of atoms do not match h a
[gmx-users] various files generated using prodrg h a
[gmx-users] OPLS-AA methanol model auryn_valemig
[gmx-users] OPLS-AA methanol model auryn_valemig
[gmx-users] g_rmsf sudheer babu
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 102 sudheer babu
[gmx-users] CH3 group and units of POPC? sudheer babu
[gmx-users] Re: sudheer babu
[gmx-users] How to define NVE ensemble in gromacs beibei
[gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X) swolf at bph.rub.de
[gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X) swolf at bph.rub.de
[gmx-users] trjconv pbc membrane maite lopez cabezas
[gmx-users] trjconv pbc membrane maite lopez cabezas
[gmx-users] problem with charmm sarbani chattopadhyay
[gmx-users] new version of C terminus database for charmm sarbani chattopadhyay
[gmx-users] Umbrella Sampling and .pdo format file crascgap
[gmx-users] error... plz help nikhil damle
[gmx-users] help najwa drici
[gmx-users] number of grid cells is zero najwa drici
[gmx-users] antechamber topologies to gromacs format najwa drici
AW: [gmx-users] Have read the manual => How to calculate dihedral angle?????? serdar durdagi
[gmx-users] lipid itp file problem serdar durdagi
[gmx-users] lipid itp problem serdar durdagi
[gmx-users] lipid itp file problem serdar durdagi
[gmx-users] lipid itp file problem serdar durdagi
[gmx-users] NMR refinement serdar durdagi
[gmx-users] total charge of the system serdar durdagi
AW: [gmx-users] topology for a membrane + protein serdar durdagi
[gmx-users] Re: QMMM memory problem ggroenh
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 75 ggroenh
[gmx-users] OPLS parameters for phosphotyrosine? maria goranovic
[gmx-users] OPLS parameters for phospho-tyrosine maria goranovic
[gmx-users] plotting displacement of each C-alpha along first eigenvector having largest eigenvalue sunita gupta
[gmx-users] force field hhhh huan
[gmx-users] segmentation fault during MD hhhh huan
[gmx-users] segmentation fault during MD hhhh huan
[gmx-users] segmentation fault during MD and develop parameter hhhh huan
[gmx-users] segmentation fault during MD and develop parameter hhhh huan
[gmx-users] Re: segmentation fault during MD and develop parameter hhhh huan
[gmx-users] Re: charge group in topology file alkasrivastava at iitb.ac.in
[gmx-users] Re Re Re: charge group in topology file alkasrivastava at iitb.ac.in
[gmx-users] Re: Removal of pbc for analysis alkasrivastava at iitb.ac.in
[gmx-users] (no subject) alkasrivastava at iitb.ac.in
[gmx-users] Re:continuation of run alkasrivastava at iitb.ac.in
[gmx-users] Re: tpr file problem with analysis and merged trajectories alkasrivastava at iitb.ac.in
[gmx-users] RE: value of d in editconf alkasrivastava at iitb.ac.in
[gmx-users] Re: Question about Berendsen thermostat and baptista at itqb.unl.pt
[gmx-users] DPPC bilayer jennifer johnston
[gmx-users] Is it correct shahrbanoo karbalaee
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 85 shahrbanoo karbalaee
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 85 shahrbanoo karbalaee
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 89 shahrbanoo karbalaee
[gmx-users] why temperature result of DMSO simulation is so low wang kelvin
[gmx-users] why temperature result of DMSO simulation is so low wang kelvin
[gmx-users] simulate Gas Phase system wang kelvin
[gmx-users] So how is the terminal methyl order parameter calculated, and about unsaturated carbons ? himanshu khandelia
[gmx-users] g_spatial installation problem. Points to g_cluster? himanshu khandelia
[gmx-users] generation of tfe solvent box prasun kumar
[gmx-users] How to generate .itp file for a given molecule prasun kumar
[gmx-users] tfe.gro file and generation of .itp file prasun kumar
[gmx-users] Molecule which is not defined in the rtp file prasun kumar
[gmx-users] gromacs bond type prasun kumar
[gmx-users] energy minimization prasun kumar
[gmx-users] dimerization problem prasun kumar
[gmx-users] energy minimization prasun kumar
[gmx-users] Error:Cannot determine precision of trn file plmallip at mail.uh.edu
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 32 plmallip at mail.uh.edu
[gmx-users] help qwang at mail.uh.edu
[gmx-users] Partial Vs Formal Charges nahren manuel
[gmx-users] Partial Charge of 1.11 ??? nahren manuel
[gmx-users] Partial charges QM to GROMACS nahren manuel
[gmx-users] Partial charges QM to GROMACS nahren manuel
[gmx-users] Still :Partial charges QM to GROMACS nahren manuel
[gmx-users] Seperate rlist - Coulomb & vdw nahren manuel
[gmx-users] simulating two peptides in a box kartik mehra
[gmx-users] simulating two peptides in a box kartik mehra
[gmx-users] simulating two peptides in a box kartik mehra
[gmx-users] Re: centering molecule in the water box servaas michielssens
[gmx-users] Re: Dynamics : ONE dihedral angle time resolution servaas michielssens
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 21 servaas michielssens
[gmx-users] Abnormal popc struture after inserting protein minnale
[gmx-users] Abnormal popc struture after inserting protein minnale
[gmx-users] Abnormal popc struture after inserting protein minnale
[gmx-users] g_msd minnale
[gmx-users] Diffusion Cofficient of POPC minnale
[gmx-users] make_ndx problem minnale
[gmx-users] make_ndx problem minnale
[gmx-users] make_ndx problem minnale
[gmx-users] doesn't match coordinate file with topology minnale
[gmx-users] doesn't match coordinate file with topology minnale
[gmx-users] Doubt regarding popc simulations minnale
[gmx-users] Order parameters of lipid minnale
[gmx-users] Order parameters of lipid minnale
[gmx-users] about itp file making anirban polley
[gmx-users] How to analyze order parameter anirban polley
[gmx-users] about deuterium order parameter anirban polley
[gmx-users] about some question on gromacs anirban polley
[gmx-users] deuterim order parameter anirban polley
[gmx-users] AFM by using mdrun in gromacs anirban polley
[gmx-users] segmentation fault rams rams
[gmx-users] segmentation fault rams rams
[gmx-users] rot-diffusion rams rams
[gmx-users] rot_diff rams rams
[gmx-users] rot_diff rams rams
[gmx-users] energy groups rams rams
[gmx-users] energy groups rams rams
[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling mon_sharma at research.iiit.ac.in
[gmx-users] AFM: .pdo output format mon_sharma at research.iiit.ac.in
[gmx-users] Charge transfer Alessandro.Maiorana at roma2.infn.it
[gmx-users] Using user-tables for simulations in vacuum sapna sarupria
[gmx-users] Using user-tables for simulations in vacuum sapna sarupria
[gmx-users] Using user-tables for simulations in vacuum sapna sarupria
[gmx-users] Using user-tables for simulations in vacuum sapna sarupria
[gmx-users] problem with using VMD to view the trajectory hui sun
[gmx-users] Tyrosine problems again dichan at ucalgary.ca
[gmx-users] box size changing during isotropic pressure coupling chris.neale at utoronto.ca
[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling chris.neale at utoronto.ca
[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling chris.neale at utoronto.ca
[gmx-users] -pbc cluster with -center in trjconv 3.3.1 chris.neale at utoronto.ca
[gmx-users] How to get LJ potential Energy at any time(not average) ting wei
[gmx-users] Re: minimize multi-chain protein amit.oberai at yale.edu
[gmx-users]D Gsol from g_sas calculation limei zhang
[gmx-users] how to constrain water with SETTLE 火枪手
[gmx-users] About the "DispCorr" 火枪手

Last message date: Thu Jul 31 23:51:59 CEST 2008
Archived on: Thu Nov 14 12:04:53 CET 2013

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