August 2013 Archives by author

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Starting: Thu Aug 1 03:15:30 CEST 2013
Ending: Sat Aug 31 21:33:43 CEST 2013
Messages: 595

[gmx-users] remd Shine A
[gmx-users] Re: Conserved energy ("Conserved En.") in NVT simulation Mark Abraham
[gmx-users] Potential Energy Scan Mark Abraham
[gmx-users] fatal error with charmm/amber forcefield Mark Abraham
[gmx-users] Potential Energy Scan Mark Abraham
[gmx-users] remd Mark Abraham
[gmx-users] Trying to explain differences in behaviour between 2fs and 5fs timesteps Mark Abraham
[gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher Mark Abraham
[gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1 Mark Abraham
[gmx-users] REMD run on higher nodes. Mark Abraham
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P Mark Abraham
[gmx-users] set charge as 0 in gromacs code Mark Abraham
[gmx-users] set charge as 0 in gromacs code Mark Abraham
Fwd: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P Mark Abraham
[gmx-users] VDW switched off in CHARMM tip3p model Mark Abraham
[gmx-users] plans for mdrun features to deprecate in GROMACS 5.0 Mark Abraham
[gmx-users] VDW switched off in CHARMM tip3p model Mark Abraham
[gmx-users] plans for mdrun features to deprecate in GROMACS 5.0 Mark Abraham
[gmx-users] Running g_tune_pme on a BlueGene/Q cluster Mark Abraham
[gmx-users] Partial incompatibility of pdb2gmx with 4 character residue names? Mark Abraham
[gmx-users] for help about reading xtc file Mark Abraham
[gmx-users] for help about reading xtc file Mark Abraham
[gmx-users] Re: Running g_tune_pme on a BlueGene/Q cluster Mark Abraham
[gmx-users] psf to tpr Mark Abraham
[gmx-users] Restart REMD Mark Abraham
[gmx-users] for help about reading xtc file Mark Abraham
[gmx-users] for help about reading xtc file Mark Abraham
[gmx-users] gromacs installation in mac osx 10.8 Mark Abraham
[gmx-users] Number of SOL/Water in gmx_moltype_t Mark Abraham
[gmx-users] Number of SOL/Water in gmx_moltype_t Mark Abraham
[gmx-users] g_select problem Mark Abraham
[gmx-users] g_select problem Mark Abraham
[gmx-users] NPT, freezegroups and Position Restraints. Mark Abraham
[gmx-users] NPT, freezegroups and Position Restraints. Mark Abraham
[gmx-users] position restraint Mark Abraham
[gmx-users] position restraint Mark Abraham
[gmx-users] position restraint Mark Abraham
[gmx-users] 'Command not found' after installation Mark Abraham
[gmx-users] NPT-REMD Mark Abraham
[gmx-users] Regarding adding ions error Mark Abraham
[gmx-users] 'Command not found' after installation Mark Abraham
[gmx-users] Re: GPU version of Gromacs Mark Abraham
[gmx-users] general question about molecule.rtp and pdb2gmx Mark Abraham
[gmx-users] About script for free energy calculation Mark Abraham
[gmx-users] Long range Lennard Jones Mark Abraham
[gmx-users] Gentle heating with implicit solvent Mark Abraham
[gmx-users] Long range Lennard Jones Mark Abraham
[gmx-users] total charge Mark Abraham
[gmx-users] problem of submitting job in HPC Mark Abraham
[gmx-users] A question about velocity rescaling thermostat and velocity verlet integrator Mark Abraham
[gmx-users] Distance restraints exploding system Mark Abraham
[gmx-users] efficiency in HPC Mark Abraham
[gmx-users] AVX libraries with GMX4.6.3 Mark Abraham
[gmx-users] AVX libraries with GMX4.6.3 Mark Abraham
[gmx-users] Reg mpirun error Mark Abraham
[gmx-users] Cleaning up trajectory files after crash Joshua Adelman
[gmx-users] Cleaning up trajectory files after crash Joshua Adelman
[gmx-users] Unkwown Keyword HILLS Albert
[gmx-users] Re: Unkwown Keyword HILLS Albert
[gmx-users] Re: Unkwown Keyword HILLS Albert
[gmx-users] how can we control output ? Albert
[gmx-users] GPU metadynamics Albert
[gmx-users] GPU metadynamics Albert
[gmx-users] itp problem Albert
[gmx-users] g_select problem Albert
[gmx-users] g_select problem Albert
[gmx-users] g_select problem Albert
[gmx-users] g_select problem Albert
[gmx-users] work in 4.5.5 but failed in 4.6.1 Albert
[gmx-users] problem of submitting job in HPC Albert
[gmx-users] work in 4.5.5 but failed in 4.6.1 Albert
[gmx-users] work in 4.5.5 but failed in 4.6.1 Albert
[gmx-users] work in 4.5.5 but failed in 4.6.1 Albert
[gmx-users] problem of submitting job in HPC Albert
[gmx-users] efficiency in HPC Albert
[gmx-users] efficiency in HPC Albert
[gmx-users] generation of gro file Musharaf Ali
[gmx-users] generation of gro file Musharaf Ali
[gmx-users] generation of gro file Musharaf Ali
[gmx-users] generation of gro file Musharaf Ali
[gmx-users] g_wham error analysis hangs Magnus Andersson
[gmx-users] g_wham error analysis hangs Magnus Andersson
[gmx-users] g_wham error analysis hangs Magnus Andersson
[gmx-users] g_wham error analysis hangs Magnus Andersson
[gmx-users] g_WHAM Shima Arasteh
[gmx-users] g_WHAM Shima Arasteh
[gmx-users] g_wham -sym Shima Arasteh
[gmx-users] g_wham -sym Shima Arasteh
[gmx-users] g_WHAM Shima Arasteh
[gmx-users] position restraint Shima Arasteh
[gmx-users] position restraint Shima Arasteh
[gmx-users] position restraint Shima Arasteh
[gmx-users] position restraint Shima Arasteh
[gmx-users] position restraint Shima Arasteh
[gmx-users] Distribution of an atom along a trajectory Shima Arasteh
[gmx-users] regarding US Abed Askari
[gmx-users] regarding umbrella sampling Abed Askari
[gmx-users] regarding umbrella sampling Abed Askari
[gmx-users] SR-coulomb energy SANTU BISWAS
[gmx-users] Re: energy conservation / frozen atoms S. Alireza Bagherzadeh
[gmx-users] Re: energy conservation / frozen atoms S. Alireza Bagherzadeh
[gmx-users] LINCS Constraints - all-bonds or h-bonds? Barnett, James W.
[gmx-users] 'Command not found' after installation Barnett, James W.
[gmx-users] 'Command not found' after installation Barnett, James W.
[gmx-users] Ok now what? Emanuel Birru
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P Prentice Bisbal
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P Prentice Bisbal
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P Prentice Bisbal
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P Prentice Bisbal
[gmx-users] efficiency in HPC Prentice Bisbal
[gmx-users] Number of SOL/Water in gmx_moltype_t Pradip Biswas
[gmx-users] Number of SOL/Water in gmx_moltype_t Pradip Biswas
[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere? Richard Broadbent
[gmx-users] pdb2gmx breaking bonds Ewa Brylska
[gmx-users] Lateral Diffusion of Lipids Dr. Vitaly Chaban
[gmx-users] Force Field for peptides and proteins Dr. Vitaly Chaban
[gmx-users] psf to tpr Dr. Vitaly Chaban
[gmx-users] Re: periodic_molecule & missing interactions Dr. Vitaly Chaban
[gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1 Guillaume Chevrot
[gmx-users] Re: Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1 Guillaume Chevrot
[gmx-users] Re: Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1 Guillaume Chevrot
[gmx-users] analysis tool of 407 to 46x Chandan Choudhury
[gmx-users] Issue in ligand gyration analysis Chandan Choudhury
[gmx-users] Regarding g_densmap output Chandan Choudhury
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P Bogdan Costescu
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P Bogdan Costescu
[gmx-users] TPIC and GMX_TPI_DUMP João M. Damas
[gmx-users] TPIC and GMX_TPI_DUMP João M. Damas
[gmx-users] TPIC and GMX_TPI_DUMP João M. Damas
[gmx-users] TPIC and GMX_TPI_DUMP João M. Damas
[gmx-users] rvdw, rlist and rcoulomb for Amber03 Rajat Desikan
[gmx-users] Problem in Gyrate analysis Sainitin Donakonda
[gmx-users] Issue in ligand gyration analysis Sainitin Donakonda
[gmx-users] Issue in ligand gyration analysis Sainitin Donakonda
[gmx-users] position restraint Gaurav Goel
[gmx-users] Rescale: Cloud simulation platform research grants Ilea Graedel
[gmx-users] total charge Group Gro
[gmx-users] Bond energy doesn't appear in gromacs rerun Golshan Hejazi
[gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k Golshan Hejazi
[gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k Golshan Hejazi
[gmx-users] CGennFF in gromacs Golshan Hejazi
Re: [gmx-users] Conversion of nm to Å João Henriques
[gmx-users] GPU + surface Berk Hess
[gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy). Heymman
[gmx-users] g_wham -sym Jochen Hub
[gmx-users] g_wham error analysis hangs Jochen Hub
[gmx-users] Lateral Diffusion of Lipids Jochen Hub
[gmx-users] Creating an infinite sheet of graphene #TAN BENG HAU IAN#
[gmx-users] Creating an infinite sheet of grapheme #TAN BENG HAU IAN#
[gmx-users] VDW Cut-off vs Switch with CHARMM force field Gianluca Interlandi
[gmx-users] VDW Cut-off vs Switch with CHARMM force field Gianluca Interlandi
[gmx-users] VDW Cut-off vs Switch with CHARMM force field Gianluca Interlandi
[gmx-users] Wrapping of protein molecules during simulation Gianluca Interlandi
[gmx-users] Gentle heating with implicit solvent Gianluca Interlandi
[gmx-users] Long range Lennard Jones Gianluca Interlandi
[gmx-users] Long range Lennard Jones Gianluca Interlandi
[gmx-users] Long range Lennard Jones Gianluca Interlandi
[gmx-users] Long range Lennard Jones Gianluca Interlandi
[gmx-users] Long range Lennard Jones Gianluca Interlandi
[gmx-users] Long range Lennard Jones Gianluca Interlandi
[gmx-users] Long range Lennard Jones Gianluca Interlandi
[gmx-users] Long range Lennard Jones Gianluca Interlandi
[gmx-users] Long range Lennard Jones Gianluca Interlandi
[gmx-users] grompy and how to call energy routine Gianluca Interlandi
[gmx-users] grompy and how to call energy routine Gianluca Interlandi
[gmx-users] grompy and how to call energy routine Gianluca Interlandi
[gmx-users] grompy and how to call energy routine Gianluca Interlandi
[gmx-users] grompy and how to call energy routine Gianluca Interlandi
[gmx-users] Re: 'Command not found' after installation Christoph Junghans
[gmx-users] g_hydorder error Nidhi Katyal
[gmx-users] question about g_hydorder Nidhi Katyal
[gmx-users] Re: GPU version of Gromacs Dwey Kauffman
[gmx-users] VDW Cut-off vs Switch with CHARMM force field James Krieger
[gmx-users] VDW Cut-off vs Switch with CHARMM force field James Krieger
[gmx-users] GPU + surface Ondrej Kroutil
[gmx-users] Regarding TCoupling and position restraints HANNIBAL LECTER
[gmx-users] Regarding TCoupling and position restraints HANNIBAL LECTER
[gmx-users] NPT, freezegroups and Position Restraints. HANNIBAL LECTER
[gmx-users] NPT, freezegroups and Position Restraints. HANNIBAL LECTER
[gmx-users] NPT, freezegroups and Position Restraints. HANNIBAL LECTER
[gmx-users] NPT, freezegroups and Position Restraints. HANNIBAL LECTER
[gmx-users] NPT, freezegroups and Position Restraints. HANNIBAL LECTER
[gmx-users] NPT, freezegroups and Position Restraints. HANNIBAL LECTER
[gmx-users] NPT, freezegroups and Position Restraints. HANNIBAL LECTER
[gmx-users] NPT, freezegroups and Position Restraints. HANNIBAL LECTER
[gmx-users] Gromacs 4.6.3 Installation Issues, HANNIBAL LECTER
[gmx-users] segmentation fault on g_protonate Pedro Lacerda
[gmx-users] Yet another question about what force field to use Pedro Lacerda
[gmx-users] Trying to replicate Aqvist's results (solvation free energy). Francis de Lasalle
[gmx-users] Re: inconsistent energy drops Justin Lemkul
[gmx-users] concatenating 2 xtc files Justin Lemkul
[gmx-users] Box dimension size errors in MARTINI soft core simulation Justin Lemkul
[gmx-users] concatenating 2 xtc files Justin Lemkul
[gmx-users] Regarding g_order Justin Lemkul
[gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher Justin Lemkul
[gmx-users] 1. Re: Interaction energy between specific residue in a set of residues (Justin Lemkul) Justin Lemkul
[gmx-users] Re: inconsistent energy drops Justin Lemkul
[gmx-users] Re: inconsistent energy drops Justin Lemkul
[gmx-users] Re: inconsistent energy drops Justin Lemkul
[gmx-users] g_potential and trjconv: problems with bilayer simulation analysis Justin Lemkul
[gmx-users] Re: topology and coordinate file not matching after grompp Justin Lemkul
[gmx-users] Regarding g_order Justin Lemkul
[gmx-users] g_potential and trjconv: problems with bilayer simulation analysis Justin Lemkul
[gmx-users] Re: energy conservation / frozen atoms Justin Lemkul
[gmx-users] Re: energy conservation / frozen atoms Justin Lemkul
[gmx-users] g_wham error analysis hangs Justin Lemkul
[gmx-users] Re: topology and coordinate file not matching after grompp Justin Lemkul
[gmx-users] REMD run on higher nodes. Justin Lemkul
[gmx-users] Unphysical conformations in decoupled free energy simulation Justin Lemkul
[gmx-users] g_wham error analysis hangs Justin Lemkul
[gmx-users] Unphysical conformations in decoupled free energy simulation Justin Lemkul
[gmx-users] g_wham error analysis hangs Justin Lemkul
[gmx-users] Adding charges to a protein to observe interaction Justin Lemkul
[gmx-users] Unphysical conformations in decoupled free energy simulation Justin Lemkul
[gmx-users] The sum of the two largest charge group radii ..is larger than rlist Justin Lemkul
[gmx-users] starting temperature equilibration phase Justin Lemkul
[gmx-users] Re: starting temperature equilibration phase Justin Lemkul
[gmx-users] g_angle bin centers Justin Lemkul
[gmx-users] Bond energy doesn't appear in gromacs rerun Justin Lemkul
[gmx-users] Bond energy doesn't appear in gromacs rerun Justin Lemkul
[gmx-users] Re: starting temperature equilibration phase Justin Lemkul
[gmx-users] Re: inconsistent energy drops Justin Lemkul
[gmx-users] g_WHAM Justin Lemkul
[gmx-users] g_WHAM Justin Lemkul
[gmx-users] Umbrella sampling - position restraints Justin Lemkul
[gmx-users] Use pull code to restrain the COM Justin Lemkul
[gmx-users] g_wham -sym Justin Lemkul
[gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k Justin Lemkul
[gmx-users] segmentation fault on g_protonate Justin Lemkul
[gmx-users] Re: Use pull code to restrain the COM Justin Lemkul
[gmx-users] About running gromacs in GPU Justin Lemkul
[gmx-users] About running Production simulation in GPU with twinrange cut-off Justin Lemkul
[gmx-users] About Running production simualtion in GPU Justin Lemkul
[gmx-users] Cleaning up trajectory files after crash Justin Lemkul
[gmx-users] Cleaning up trajectory files after crash Justin Lemkul
[gmx-users] Lateral Diffusion of Lipids Justin Lemkul
[gmx-users] Force Field for peptides and proteins Justin Lemkul
[gmx-users] Implement a modified pull module to mdrun Justin Lemkul
[gmx-users] Implement a modified pull module to mdrun Justin Lemkul
[gmx-users] Implement a modified pull module to mdrun Justin Lemkul
[gmx-users] Problem running do_dssp Justin Lemkul
[gmx-users] Yet another question about what force field to use Justin Lemkul
[gmx-users] how can we control output ? Justin Lemkul
[gmx-users] charmm36 proteins Justin Lemkul
[gmx-users] "Sign convention" g_energy total energies Justin Lemkul
[gmx-users] what is sigma in gromacs? the radius of a sphere or the diameter of a sphere? Justin Lemkul
[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere? Justin Lemkul
[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere? Justin Lemkul
[gmx-users] Molecule removal by g_membed Justin Lemkul
[gmx-users] About Error in mdrun Justin Lemkul
[gmx-users] Regarding TCoupling and position restraints Justin Lemkul
[gmx-users] Regarding TCoupling and position restraints Justin Lemkul
[gmx-users] generation of gro file Justin Lemkul
[gmx-users] generation of gro file Justin Lemkul
[gmx-users] Lennard jones energy Justin Lemkul
[gmx-users] generation of gro file Justin Lemkul
[gmx-users] itp problem Justin Lemkul
[gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand? Justin Lemkul
[gmx-users] want to apply electric field in membrane system Justin Lemkul
[gmx-users] GPU version of Gromacs Justin Lemkul
[gmx-users] Query regarding membrane-peptide simulation Justin Lemkul
[gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand? Justin Lemkul
[gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand? Justin Lemkul
[gmx-users] NPT, freezegroups and Position Restraints. Justin Lemkul
[gmx-users] NPT, freezegroups and Position Restraints. Justin Lemkul
[gmx-users] NPT, freezegroups and Position Restraints. Justin Lemkul
[gmx-users] PMF calculation Justin Lemkul
[gmx-users] want to apply electric field in membrane system Justin Lemkul
[gmx-users] want to apply electric field in membrane system Justin Lemkul
[gmx-users] regarding umbrella sampling Justin Lemkul
[gmx-users] regarding umbrella sampling Justin Lemkul
[gmx-users] want to apply electric field in membrane system Justin Lemkul
[gmx-users] Re: GPU version of Gromacs Justin Lemkul
[gmx-users] g_WHAM Justin Lemkul
[gmx-users] g_select problem Justin Lemkul
[gmx-users] GROMACS-CYSTEINE PROTEASES Justin Lemkul
[gmx-users] NPT, freezegroups and Position Restraints. Justin Lemkul
[gmx-users] position restraint Justin Lemkul
[gmx-users] Interpreting dihedrals in topology file Justin Lemkul
[gmx-users] Re: GROMACS-CYSTEINE PROTEASES Justin Lemkul
[gmx-users] Issue in ligand gyration analysis Justin Lemkul
[gmx-users] Invalid order for directive atomtypes Justin Lemkul
[gmx-users] DMPC Bilayer Justin Lemkul
[gmx-users] Issue in ligand gyration analysis Justin Lemkul
[gmx-users] VDW Cut-off vs Switch with CHARMM force field Justin Lemkul
[gmx-users] Help with Error Message Justin Lemkul
[gmx-users] VDW Cut-off vs Switch with CHARMM force field Justin Lemkul
[gmx-users] rvdw, rlist and rcoulomb for Amber03 Justin Lemkul
[gmx-users] Re: GROMACS-CYSTEINE PROTEASES Justin Lemkul
[gmx-users] 'Command not found' after installation Justin Lemkul
[gmx-users] g_hydorder error Justin Lemkul
[gmx-users] error with g_dist Justin Lemkul
[gmx-users] Re: error with g_dist Justin Lemkul
[gmx-users] Re: error with g_dist Justin Lemkul
[gmx-users] Re: error with g_dist Justin Lemkul
[gmx-users] Re: error with g_dist Justin Lemkul
[gmx-users] Re: error with g_dist Justin Lemkul
[gmx-users] Re: error with g_dist Justin Lemkul
[gmx-users] LIGAND TOPOLOGY Justin Lemkul
[gmx-users] Regarding coordinate mismatching. Justin Lemkul
[gmx-users] general question about molecule.rtp and pdb2gmx Justin Lemkul
[gmx-users] Re: general question about molecule.rtp and pdb2gmx Justin Lemkul
[gmx-users] Wrapping of protein molecules during simulation Justin Lemkul
[gmx-users] DMPC Bilayer Justin Lemkul
[gmx-users] problem of submitting job in HPC Justin Lemkul
[gmx-users] work in 4.5.5 but failed in 4.6.1 Justin Lemkul
[gmx-users] work in 4.5.5 but failed in 4.6.1 Justin Lemkul
[gmx-users] work in 4.5.5 but failed in 4.6.1 Justin Lemkul
[gmx-users] Long range Lennard Jones Justin Lemkul
[gmx-users] CGennFF in gromacs Justin Lemkul
[gmx-users] Long range Lennard Jones Justin Lemkul
[gmx-users] Long range Lennard Jones Justin Lemkul
[gmx-users] MD vs. free energy simulations Justin Lemkul
[gmx-users] pdb2gmx breaking bonds Justin Lemkul
[gmx-users] Creating an infinite sheet of graphene Justin Lemkul
[gmx-users] Re: Creating an infinite sheet of graphene Justin Lemkul
[gmx-users] periodic_molecule & missing interactions Justin Lemkul
[gmx-users] Long range Lennard Jones Justin Lemkul
[gmx-users] Regarding Position restraint and freezegroups Justin Lemkul
[gmx-users] Long range Lennard Jones Justin Lemkul
[gmx-users] Regarding Position restraint and freezegroups Justin Lemkul
[gmx-users] Long range Lennard Jones Justin Lemkul
[gmx-users] Long range Lennard Jones Justin Lemkul
[gmx-users] Distribution of an atom along a trajectory Justin Lemkul
[gmx-users] Reg Mpi run Error Justin Lemkul
[gmx-users] grompy and how to call energy routine Justin Lemkul
[gmx-users] grompy and how to call energy routine Justin Lemkul
[gmx-users] grompy and how to call energy routine Justin Lemkul
[gmx-users] grompy and how to call energy routine Justin Lemkul
[gmx-users] Restrain lipid in a bilayer Li, Hualin
[gmx-users] Implement a modified pull module to mdrun Li, Hualin
[gmx-users] Implement a modified pull module to mdrun Li, Hualin
[gmx-users] Implement a modified pull module to mdrun Li, Hualin
[gmx-users] restraint-lambdas for position restraints in hamiltonian exchange Dejun Lin
[gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange Dejun Lin
[gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange Dejun Lin
[gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange Dejun Lin
[gmx-users] Use pull code to restrain the COM Bin Liu
[gmx-users] Re: Use pull code to restrain the COM Bin Liu
[gmx-users] Molecule removal by g_membed Bin Liu
[gmx-users] concatenating 2 xtc files Kavyashree M
[gmx-users] concatenating 2 xtc files Kavyashree M
[gmx-users] concatenating 2 xtc files Kavyashree M
[gmx-users] concatenating 2 xtc files Kavyashree M
[gmx-users] The sum of the two largest charge group radii ..is larger than rlist Kavyashree M
[gmx-users] The sum of the two largest charge group radii ..is larger than rlist Kavyashree M
[gmx-users] Hamiltonian replica exchange not working in 4.6 Sanku M
[gmx-users] LINCS Constraints - all-bonds or h-bonds? Erik Marklund
[gmx-users] COM of a molecule Sikandar Mashayak
[gmx-users] 'Command not found' after installation Nimmy McNimmerson
[gmx-users] 'Command not found' after installation Nimmy McNimmerson
[gmx-users] 'Command not found' after installation Nimmy McNimmerson
[gmx-users] 'Command not found' after installation Nimmy McNimmerson
[gmx-users] charmm36 proteins Dina Mirijanian
[gmx-users] charmm36 proteins Dina Mirijanian
[gmx-users] GPU + surface Lucio Montero
[gmx-users] Trying to replicate Aqvist's results (solvation free energy). André Farias de Moura
[gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy). André Farias de Moura
[gmx-users] g_select problem Teemu Murtola
[gmx-users] Re: Hai friends (balu) Muhammad Naqvi
[gmx-users] VDW switched off in CHARMM tip3p model Christopher Neale
[gmx-users] charmm36 proteins Christopher Neale
[gmx-users] 1. Re: Interaction energy between specific residue in a set of residues (Justin Lemkul) Collins Nganou
[gmx-users] Lateral Diffusion of Lipids Kieu Thu Nguyen
[gmx-users] Lateral Diffusion of Lipids Kieu Thu Nguyen
[gmx-users] Force Field for peptides and proteins Kieu Thu Nguyen
[gmx-users] Genion command not working Deepak Ojha
[gmx-users] Gromacs 4.6.3 Installation Issues, No One
[gmx-users] Help with Error Message The One And Only
[gmx-users] Help with Error Message The One And Only
[gmx-users] Help with Error Message The One And Only
[gmx-users] Help with Error Message The One And Only
[gmx-users] Ok now what? The One And Only
[gmx-users] #coordinates do not match The One And Only
[gmx-users] #coordinates do not match The One And Only
[gmx-users] Help with Error Message The One And Only
[gmx-users] Help with Error Message The One And Only
[gmx-users] Re: inconsistent energy drops Brad Van Oosten
[gmx-users] Re: inconsistent energy drops Brad Van Oosten
[gmx-users] Re: inconsistent energy drops Brad Van Oosten
[gmx-users] Re: COM of a molecule Brad Van Oosten
[gmx-users] Re: Gromacs 4.6.3 installation Issue with Intel & CUDA Brad Van Oosten
[gmx-users] Re: inconsistent energy drops Brad Van Oosten
[gmx-users] Re: Gromacs: GPU detection Brad Van Oosten
[gmx-users] Query regarding membrane-peptide simulation Aditya Padhi
[gmx-users] Box dimension size errors in MARTINI soft core simulation Scott Pendley
[gmx-users] PMF calculation Za Pour
[gmx-users] Re: CUDA with QUADRO GPUs Szilárd Páll
[gmx-users] GPU-based workstation Szilárd Páll
[gmx-users] Intel vs gcc compilers Szilárd Páll
[gmx-users] Gromacs: GPU detection Szilárd Páll
[gmx-users] mixing of PCs for generating reduced free energy profile using g_sham R.S.K.Vijayan
[gmx-users] DMPC Bilayer Rama
[gmx-users] DMPC Bilayer Rama
[gmx-users] Re: fftw Andrish Reddy
[gmx-users] Regarding g_order Venkat Reddy
[gmx-users] Regarding g_order Venkat Reddy
[gmx-users] psf to tpr Venkat Reddy
[gmx-users] Coordination number Venkat Reddy
[gmx-users] Coordination number Venkat Reddy
[gmx-users] Regarding g_densmap output Venkat Reddy
[gmx-users] Regarding g_densmap output Venkat Reddy
[gmx-users] Problem running do_dssp Dipankar Roy
[gmx-users] gromacs installation in mac osx 10.8 Sudip Roy
[gmx-users] Invalid order for directive atomtypes Jonathan Saboury
[gmx-users] A question about velocity rescaling thermostat and velocity verlet integrator Ali Sinan Saglam
[gmx-users] AVX libraries with GMX4.6.3 Ali Sinan Saglam
[gmx-users] A question about velocity rescaling thermostat and velocity verlet integrator Ali Sinan Saglam
[gmx-users] AVX libraries with GMX4.6.3 Ali Sinan Saglam
[gmx-users] charmm2gromacs.py error Revthi Sanker
[gmx-users] converting Charmm36 lipidds to gromacs Revthi Sanker
[gmx-users] perl scripts to convert CHARMM ff in GROMACS Revthi Sanker
[gmx-users] Unphysical conformations in decoupled free energy simulation Joerg Sauter
[gmx-users] Unphysical conformations in decoupled free energy simulation Joerg Sauter
[gmx-users] Unphysical conformations in decoupled free energy simulation Joerg Sauter
[gmx-users] Partial incompatibility of pdb2gmx with 4 character residue names? Joerg Sauter
[gmx-users] Partial incompatibility of pdb2gmx with 4 character residue names? Joerg Sauter
[gmx-users] Re: general question about molecule.rtp and pdb2gmx Sergey
[gmx-users] Force Field for peptides and proteins Maria Astón Serrano
[gmx-users] GPU metadynamics Jacopo Sgrignani
[gmx-users] Free Energy Ion Pair Decoupling Quintin Sheridan
[gmx-users] set charge as 0 in gromacs code Shi, Yu (shiy4)
[gmx-users] set charge as 0 in gromacs code Shi, Yu (shiy4)
[gmx-users] Conversion of nm to Å Arunima Shilpi
[gmx-users] restraint-lambdas for position restraints in hamiltonian exchange Michael Shirts
[gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange Michael Shirts
[gmx-users] Unphysical conformations in decoupled free energy simulation Michael Shirts
[gmx-users] Hamiltonian replica exchange not working in 4.6 Michael Shirts
[gmx-users] Re: Unkwown Keyword HILLS Michael Shirts
[gmx-users] Re: Unkwown Keyword HILLS Michael Shirts
[gmx-users] LINCS Constraints - all-bonds or h-bonds? Michael Shirts
[gmx-users] Early registration period ending for 2013 GROMACS USA Workshop and Conference Michael Shirts
[gmx-users] Early registration period ending for 2013 GROMACS USA Workshop and Conference Michael Shirts
[gmx-users] NPT-REMD Michael Shirts
[gmx-users] Re: NPT-REMD Michael Shirts
[gmx-users] Long range Lennard Jones Michael Shirts
[gmx-users] A question about velocity rescaling thermostat and velocity verlet integrator Michael Shirts
[gmx-users] Lipid Bilayer on the Graphene or GO substrate David van der Spoel
[gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k David van der Spoel
[gmx-users] Lipid Bilayer on the Graphene or GO substrate David van der Spoel
[gmx-users] Lipid Bilayer on the Graphene or GO substrate David van der Spoel
[gmx-users] hessian calculation with periodic boundary condition David van der Spoel
[gmx-users] perl scripts to convert CHARMM ff in GROMACS David van der Spoel
[gmx-users] Long range Lennard Jones David van der Spoel
[gmx-users] Gromacs 4.6.3 installation Issue with Intel & CUDA Jim Strong
[gmx-users] GROMACS-CYSTEINE PROTEASES MUSYOKA THOMMAS
[gmx-users] GROMACS-CYSTEINE PROTEASES MUSYOKA THOMMAS
[gmx-users] Re: GROMACS-CYSTEINE PROTEASES MUSYOKA THOMMAS
[gmx-users] Re: GROMACS-CYSTEINE PROTEASES MUSYOKA THOMMAS
[gmx-users] Re: GROMACS-CYSTEINE PROTEASES MUSYOKA THOMMAS
[gmx-users] LIGAND TOPOLOGY MUSYOKA THOMMAS
[gmx-users] hessian calculation with periodic boundary condition John Travers
[gmx-users] hessian calculation with periodic boundary condition John Travers
[gmx-users] hessian calculation with periodic boundary condition John Travers
[gmx-users] Trying to explain differences in behaviour between 2fs and 5fs timesteps Trayder
[gmx-users] Distance restraints exploding system Trayder
[gmx-users] general question about molecule.rtp and pdb2gmx Valentina
[gmx-users] Re: general question about molecule.rtp and pdb2gmx Valentina
[gmx-users] Re: general question about molecule.rtp and pdb2gmx Valentina
[gmx-users] Re: Creating an infinite sheet of graphene Valentina
[gmx-users] periodic_molecule & missing interactions Valentina
[gmx-users] Re: periodic_molecule & missing interactions Valentina
[gmx-users] Help with Error Message Rafael I. Silverman y de la Vega
[gmx-users] Help with Error Message Rafael I. Silverman y de la Vega
[gmx-users] TPIC and GMX_TPI_DUMP Rafael I. Silverman y de la Vega
[gmx-users] TPIC and GMX_TPI_DUMP Rafael I. Silverman y de la Vega
[gmx-users] TPIC and GMX_TPI_DUMP Rafael I. Silverman y de la Vega
[gmx-users] TPIC and GMX_TPI_DUMP Rafael I. Silverman y de la Vega
[gmx-users] TPIC and GMX_TPI_DUMP Rafael I. Silverman y de la Vega
[gmx-users] Coordination number Dallas Warren
RE: [gmx-users] Conversion of nm to Å Dallas Warren
[gmx-users] Coordination number Dallas Warren
[gmx-users] Long range Lennard Jones Dallas Warren
[gmx-users] concatenating 2 xtc files Tsjerk Wassenaar
[gmx-users] Invalid order for directive atomtypes Tsjerk Wassenaar
[gmx-users] script to add water in protein Tsjerk Wassenaar
[gmx-users] Help with Error Message Tsjerk Wassenaar
[gmx-users] Help with Error Message Tsjerk Wassenaar
[gmx-users] Help with Error Message Tsjerk Wassenaar
[gmx-users] Genion command not working Tsjerk Wassenaar
[gmx-users] ERROR : GROMACS finsihed with error 74 Tsjerk Wassenaar
[gmx-users] g_angle bin centers Brandon Wiebe
[gmx-users] Restart REMD Min Wu
[gmx-users] for help about reading xtc file Xu, Yechuan
[gmx-users] for help about reading xtc file Xu, Yechuan
[gmx-users] for help about reading xtc file Xu, Yechuan
[gmx-users] for help about reading xtc file Xu, Yechuan
[gmx-users] VDW switched off in CHARMM tip3p model Weilong Zhao
[gmx-users] Gromacs: GPU detection Jernej Zidar
[gmx-users] Running g_tune_pme on a BlueGene/Q cluster Jernej Zidar
[gmx-users] Re: Running g_tune_pme on a BlueGene/Q cluster Jernej Zidar
[gmx-users] MD vs. free energy simulations Jernej Zidar
[gmx-users] All molecules being coupled for free energy of self solvation simulation Brittany Zimmerman
[gmx-users] Re: All molecules being coupled for free energy of self solvation simulation Brittany Zimmerman
[gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher akk5r
[gmx-users] QM/MM with gromacs 4.5.5-gaussian03 azeif
[gmx-users] Hai friends balu
[gmx-users] Insertion Events balu
[gmx-users] want to apply electric field in membrane system udels can
[gmx-users] Re: topology and coordinate file not matching after grompp chinnu657
[gmx-users] Re: topology and coordinate file not matching after grompp chinnu657
[gmx-users] Re: topology and coordinate file not matching after grompp chinnu657
[gmx-users] Re: topology and coordinate file not matching after grompp chinnu657
[gmx-users] Adding charges to a protein to observe interaction chinnu657
[gmx-users] Lennard jones energy chinnu657
[gmx-users] error with g_dist chinnu657
[gmx-users] Re: error with g_dist chinnu657
[gmx-users] Re: error with g_dist chinnu657
[gmx-users] Re: error with g_dist chinnu657
[gmx-users] Re: error with g_dist chinnu657
[gmx-users] Re: error with g_dist chinnu657
[gmx-users] Re: error with g_dist chinnu657
[gmx-users] Re: error with g_dist chinnu657
[gmx-users] Re: error with g_dist chinnu657
[gmx-users] Re: error with g_dist chinnu657
[gmx-users] Regarding adding ions error sanjay choubey
[gmx-users] Regarding coordinate mismatching. sanjay choubey
[gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1 rajat desikan
[gmx-users] Force Field for peptides and proteins rajat desikan
[gmx-users] plans for mdrun features to deprecate in GROMACS 5.0 rajat desikan
[gmx-users] Early registration period ending for 2013 GROMACS USA Workshop and Conference rajat desikan
[gmx-users] #coordinates do not match rajat desikan
[gmx-users] Long range Lennard Jones rajat desikan
[gmx-users] Question about HREMD in .log file drew.w.ritchie
[gmx-users] Energies in MM scanning using gmx fantasticqhl
[gmx-users] Re: Energies in MM scanning using gmx fantasticqhl
[gmx-users] what is sigma in gromacs? the radius of a sphere or the diameter of a sphere? grita
[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere? grita
[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere? grita
[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere? grita
[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere? grita
[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere? grita
[gmx-users] GPU version of Gromacs grita
[gmx-users] Re: GPU version of Gromacs grita
[gmx-users] Re: GPU version of Gromacs grita
[gmx-users] script to add water in protein bharat gupta
[gmx-users] Cyclodextrin_Ligand_Protein System marawan hussain
[gmx-users] g_potential and trjconv: problems with bilayer simulation analysis wood irene
[gmx-users] g_potential and trjconv: problems with bilayer simulation analysis wood irene
[gmx-users] "Sign convention" g_energy total energies gg jj
[gmx-users] Potential Energy Scan tarak karmakar
[gmx-users] Potential Energy Scan tarak karmakar
[gmx-users] gromacs-4.5.5 CPMD QM/MM tarak karmakar
[gmx-users] gromacs-4.5.5 cpmd QM/MM versions tarak karmakar
[gmx-users] Invalid order for directive atomtypes afsaneh maleki
[gmx-users] Restart REMD minwuh081
[gmx-users] Re: Hai friends (balu) jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] REMD run on higher nodes. suhani nagpal
[gmx-users] REMD run on higher nodes. suhani nagpal
[gmx-users] script to add water in protein pooja_gupta at nccs.res.in
[gmx-users] script to add water in protein pooja_gupta at nccs.res.in
[gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher francesco oteri
[gmx-users] Re: VDW switched off in CHARMM tip3p model qiuxing
[gmx-users] Re: NPT-REMD rahul.seth.gromacs
[gmx-users] Interpreting dihedrals in topology file rdwducl
Aw: [gmx-users] Umbrella sampling - position restraints lloyd riggs
Aw: [gmx-users] Force Field for peptides and proteins lloyd riggs
[gmx-users] Question about HREMD in .log file andrew ritchie
[gmx-users] Umbrella sampling - position restraints rookie417
[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere? massimo sandal
[gmx-users] Hai friends massimo sandal
[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere? massimo sandal
[gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand? massimo sandal
[gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand? massimo sandal
[gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand? massimo sandal
[gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand? massimo sandal
[gmx-users] About running gromacs in GPU vidhya sankar
[gmx-users] About running Production simulation in GPU with twinrange cut-off vidhya sankar
[gmx-users] About Running production simualtion in GPU vidhya sankar
[gmx-users] About Error in mdrun vidhya sankar
[gmx-users] About script for free energy calculation vidhya sankar
[gmx-users] Reg Mpi run Error vidhya sankar
[gmx-users] Reg mpirun error vidhya sankar
[gmx-users] NPT-REMD rahul seth
[gmx-users] Re: NPT-REMD rahul seth
[gmx-users] Regarding Position restraint and freezegroups rahul seth
[gmx-users] Regarding Position restraint and freezegroups rahul seth
[gmx-users] ERROR : GROMACS finsihed with error 74 sri2201
[gmx-users] want to apply electric field in membrane system sudipta
[gmx-users] want to apply electric field in membrane system sudipta
[gmx-users] want to apply electric field in membrane system sudipta
[gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy). sumanc
Aw: [gmx-users] Umbrella sampling - position restraints suram417
[gmx-users] question mjm136525 at yahoo.com
[gmx-users] question mjm136525 at yahoo.com
[gmx-users] starting temperature equilibration phase ypca
[gmx-users] Re: starting temperature equilibration phase ypca
[gmx-users] Re: starting temperature equilibration phase ypca
[gmx-users] Re: starting temperature equilibration phase ypca
[gmx-users] Re: how is the pulling force measured zhuswf
[gmx-users] question Андрей Гончар
[gmx-users] question Андрей Гончар
[gmx-users] Lipid Bilayer on the Graphene or GO substrate 朱文鹏
[gmx-users] Lipid Bilayer on the Graphene or GO substrate 朱文鹏
[gmx-users] Lipid Bilayer on the Graphene or GO substrate 朱文鹏

Last message date: Sat Aug 31 21:33:43 CEST 2013
Archived on: Thu Nov 14 12:14:44 CET 2013

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