July 2007 Archives by author

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Starting: Sun Jul 1 00:10:41 CEST 2007
Ending: Tue Jul 31 23:05:56 CEST 2007
Messages: 567

[gmx-users] Replica Exchange MD ... Exchange rates Mu Yuguang (Dr)
[gmx-users] mdrun -rerun problems George Abadir
[gmx-users] mdrun -rerun problems George Abadir
[gmx-users] Moments of inertia calculation using g_gyrate George Abadir
[gmx-users] How to proceed with energy minimization for Normal Mode Analysis Mark Abraham
[gmx-users] center of mass Mark Abraham
[gmx-users] pdb2gmx not recognizing disulfides Mark Abraham
[gmx-users] [Fwd: How simulate two peptides in a box?] Mark Abraham
[gmx-users] Gromacs Performance mesurement Mark Abraham
[gmx-users] pdb2gmx not recognizing disulfides Mark Abraham
[gmx-users] Applying constant force between two atoms Mark Abraham
[gmx-users] pdb2gmx not recognizing disulfides Mark Abraham
[gmx-users] pdb2gmx not recognizing disulfides Mark Abraham
[gmx-users] which tpr? Mark Abraham
[gmx-users] [Fwd: How simulate two peptides in a box?] Mark Abraham
[gmx-users] g_wham and PMF problem Mark Abraham
[gmx-users] which tpr? Mark Abraham
[gmx-users] g_wham and PMF problem Mark Abraham
[gmx-users] Topology builder Mark Abraham
[gmx-users] error running position restraints Mark Abraham
[gmx-users] g_wham and PMF problem Mark Abraham
[gmx-users] a question about gromacs Mark Abraham
[gmx-users] pdb2gmx not recognizing disulfides Mark Abraham
[gmx-users] Regarding conversion of lipid parapeters to Amber format Mark Abraham
[gmx-users] [Fwd: How simulate two peptides in a box?] Mark Abraham
[gmx-users] [Fwd: a question about your reply] Mark Abraham
[gmx-users] Re: Conversion of gromacs parameters to AMBER parameters Mark Abraham
[gmx-users] Topology builder Mark Abraham
[gmx-users] Regarding neutralization of lipid bilayer Mark Abraham
[gmx-users] get_index Mark Abraham
[gmx-users] get_index Mark Abraham
[gmx-users] Error_message Mark Abraham
[gmx-users] Regarding Na ions Mark Abraham
[gmx-users] Error durign Grompp Mark Abraham
[gmx-users] Re: Regarding Na ions Mark Abraham
[gmx-users] HETATM records of crystallized water Mark Abraham
[gmx-users] Another problem with Stimulated Annealing Mark Abraham
[gmx-users] How to create correct .gro file? Mark Abraham
[gmx-users] a recruit's quention Mark Abraham
[gmx-users] g_enemat Mark Abraham
[gmx-users] Calculations of area per lipid using g_sas Mark Abraham
[gmx-users] Lipid-protein force field problem. Mark Abraham
[gmx-users] Less than Graceful Mark Abraham
[gmx-users] Less than Graceful Mark Abraham
[gmx-users] The Lennard-Jones parameter of Na+? Mark Abraham
[gmx-users] Re: Calculations of area per lipid using g_sas Mark Abraham
[gmx-users] dssp in gromacs Mark Abraham
[gmx-users] Re: The Lennard-Jones parameter of Na+? (Mark Abraham) Mark Abraham
[gmx-users] Re: gmx-users Digest, Vol 39, Issue 37 Mark Abraham
[gmx-users] Replica Exchange MD ... Exchange rates Mark Abraham
[gmx-users] the atomic charges in ligand Mark Abraham
[gmx-users] How to simulate peptide capped with ACE? Mark Abraham
[gmx-users] Solvent_box Mark Abraham
[gmx-users] Regarding D-Alanine paramters Mark Abraham
[gmx-users] [Fwd: conjugate gradients with constraints] Mark Abraham
[gmx-users] pdb file of a crystal lattice of epoxy resin Mark Abraham
[gmx-users] g_energy doubt Mark Abraham
[gmx-users] Sphingomyelin parameters Mark Abraham
[gmx-users] mdp file help Mark Abraham
[gmx-users] mdrun -rerun problems Mark Abraham
[gmx-users] g_rdf dual core Mark Abraham
[gmx-users] restarting a run using tpbconv Mark Abraham
[gmx-users] doubt in minimization Mark Abraham
[gmx-users] regarding the positional restraints Mark Abraham
[gmx-users] adding mixed solvent using genbox Mark Abraham
[gmx-users] regarding the positional restraints Mark Abraham
[gmx-users] simulations using structureless surface Mark Abraham
[gmx-users] problem regarding total time elapsed Mark Abraham
[gmx-users] dissociative water models Mark Abraham
[gmx-users] regarding g_energy Mark Abraham
[gmx-users] charge_calculation Mark Abraham
[gmx-users] Re: Carbon Nanotube Simulation Issues Mark Abraham
[gmx-users] Atomtype:CB Mark Abraham
[gmx-users] About Temperature Gradient Mark Abraham
[gmx-users] simulations using structureless surface-2 Mark Abraham
[gmx-users] Help with RB dihedrals implementation Mark Abraham
[gmx-users] Help with RB dihedrals implementation Mark Abraham
[gmx-users] C500 Configuration and parameters help Mark Abraham
[gmx-users] mdrun_problem Mark Abraham
[gmx-users] Error in pr Mark Abraham
[gmx-users] Re:mdrun_problem Mark Abraham
[gmx-users] Buckingham Potential Doubt. Jones de Andrade
[gmx-users] Help with RB dihedrals implementation Jones de Andrade
[gmx-users] Help with RB dihedrals implementation Jones de Andrade
[gmx-users] Help with RB dihedrals implementation Jones de Andrade
[gmx-users] dihedral doubts, again Jones de Andrade
[gmx-users] More dihedral doubts Jones de Andrade
[gmx-users] Chitosan topology Antonello
[gmx-users] g_wham and PMF problem Arneh Babakhani
[gmx-users] Xenon non-bonded parameterization Arneh Babakhani
[gmx-users] which tool to use a measure a user-defined angle in a traj Arneh Babakhani
[gmx-users] which tool to use a measure a user-defined angle in a traj Arneh Babakhani
[gmx-users] which tool to use a measure a user-defined angle in a traj Arneh Babakhani
[gmx-users] Replica Exchange MD ... Exchange rates Carsten Baldauf
[gmx-users] Regarding polymer equillibration (pressure changes) Jeroen van Bemmelen
[gmx-users] Sphingomyelin parameters Jian Dai
[gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet Siavoush Dastmalchi
[gmx-users] Error in pr Dhananjay
[gmx-users] How to simulate peptide capped with ACE? Alan Dodd
[gmx-users] which tool to use a measure a user-defined angle in a traj Alan Dodd
[gmx-users] restarting a run using tpbconv Alan Dodd
[gmx-users] problem regarding total time elapsed Alan Dodd
[gmx-users] Error during grompp Yulia Einav
[gmx-users] free energy perturbations and B-parameter specifications Soren Enemark
[gmx-users] Reading xtc in fortran-90 Semen Esilevsky
[gmx-users] OpenMosix and Gromacs Ansgar Esztermann
[gmx-users] the atomic charges in ligand Ran Friedman
[gmx-users] Implicit solvent simulation Ran Friedman
[gmx-users] protein structural alignment Ran Friedman
[gmx-users] How Long to Equlibrate? Ran Friedman
[gmx-users] Normal Mode Analysis Anirban Ghosh
[gmx-users] free energy calculation and constraint distance? Maik Goette
[gmx-users] pdb2gmx not recognizing disulfides Russell Green
[gmx-users] pdb2gmx not recognizing disulfides Russell Green
[gmx-users] pdb2gmx not recognizing disulfides Russell Green
[gmx-users] pdb2gmx not recognizing disulfides Russell Green
[gmx-users] pdb2gmx not recognizing disulfides Russell Green
[gmx-users] pdb2gmx not recognizing disulfides Russell Green
[gmx-users] GAMESS-US for Hybrid QM/MM ( gmx-users Digest, Vol 39, Issue 71 ) Gerrit Groenhof
[gmx-users] Error running grompp Florian Haberl
[gmx-users] Is there a way to compile gromacs with MPICH instead of LAM? Florian Haberl
[gmx-users] GRomacs 3.3.1 parallel run Florian Haberl
[gmx-users] pb with temperature in bd (2) Berk Hess
[gmx-users] Less than Graceful Berk Hess
[gmx-users] Replica Exchange MD ... Exchange rates Berk Hess
[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units Berk Hess
[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units Berk Hess
[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units Berk Hess
[gmx-users] FW: rvdw Berk Hess
[gmx-users] FW: rvdw Berk Hess
[gmx-users] FW: rvdw Berk Hess
[gmx-users] FW: rvdw Berk Hess
[gmx-users] Problems about sigma & epsilon to C6 & C12 Janne Hirvi
[gmx-users] Applying constant force between two atoms SeungPyo Hong
[gmx-users] Applying constant force between two atoms SeungPyo Hong
[gmx-users] Implicit solvent simulation SeungPyo Hong
[gmx-users] Implicit solvent simulation SeungPyo Hong
[gmx-users] number of coordinates in coordinate file does not match topology SeungPyo Hong
[gmx-users] Topology builder Bruno Horta
[gmx-users] Topology builder Bruno Horta
[gmx-users] parameters of hydrogen peroxide H2O2 Jochen Hub
[gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet Kazem Jahanbakhsh
[gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet Kazem Jahanbakhsh
[gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet Kazem Jahanbakhsh
[gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet Kazem Jahanbakhsh
[gmx-users] Implicit solvent simulation Eric Jakobsson
[gmx-users] FW: rvdw Yin Jian
[gmx-users] FW: rvdw Yin Jian
[gmx-users] FW: rvdw Yin Jian
[gmx-users] FW: rvdw Yin Jian
[gmx-users] Carbon Nanotube Simulation Issues Robert Johnson
[gmx-users] Re: Carbon Nanotube Simulation Issues Robert Johnson
[gmx-users] Re: Carbon Nanotube Simulation Issues Robert Johnson
[gmx-users] Re: Carbon Nanotube Simulation Issues Robert Johnson
[gmx-users] Re: Carbon Nanotube Simulation Issues Robert Johnson
[gmx-users] Re: Carbon Nanotube Simulation Issues Robert Johnson
[gmx-users] g_wham and PMF problem Sudha Mani Karra
[gmx-users] g_wham and PMF problem Sudha Mani Karra
[gmx-users] g_wham and PMF problem Sudha Mani Karra
[gmx-users] g_wham and PMF problem Sudha Mani Karra
[gmx-users] g_wham and PMF problem Sudha Mani Karra
[gmx-users] Less than Graceful Jim Kress
[gmx-users] Is there a way to compile gromacs with MPICH instead of LAM? Jim Kress
[gmx-users] Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run Jim Kress
[gmx-users] Re: Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run (Jim Kress) Jim Kress
[gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet Carsten Kutzner
[gmx-users] g_wham and PMF problem Lu Lanyuan
[gmx-users] Problem regarding genbox Alif M Latif
[gmx-users] Xenon non-bonded parameterization Morgan Lawrenz
[gmx-users] Calculations of area per lipid using g_sas Hwankyu Lee
[gmx-users] Re: Calculations of area per lipid using g_sas Hwankyu Lee
[gmx-users] Re: Re: Calculations of area per lipid using g_sas Hwankyu Lee
[gmx-users] Analytic first derivatives with respect to parameters? Lee-Ping
[gmx-users] Wasting too much time recompiling Lee-Ping
[gmx-users] RE: gmx-users Digest, Vol 39, Issue 102 Lee-Ping
[gmx-users] Dismantling the methyl group Jussi Lehtola
[gmx-users] Dismantling the methyl group Jussi Lehtola
[gmx-users] Dismantling the methyl group Jussi Lehtola
[gmx-users] Segmentation fault after dt=2fs Justin Lemkul
[gmx-users] phosphated residue??? Justin Lemkul
[gmx-users] Minimizing a molecule not recognised by gromacs Justin Lemkul
[gmx-users] adding mixed solvent using genbox Justin Lemkul
[gmx-users] Atomtype:CB Justin Lemkul
[gmx-users] How to get ligand top file for oplsaa? Rui Li
[gmx-users] about truncated octahedral periodic box Rui Li
[gmx-users] about truncated octahedral periodic box Rui Li
[gmx-users] the atomic charges in ligand Rui Li
[gmx-users] the atomic charges in ligand Rui Li
[gmx-users] OpenMosix and Gromacs Erik Lindahl
[gmx-users] Normal Mode Analysis Erik Lindahl
[gmx-users] Topology builder Erik Lindahl
[gmx-users] free energy perturbations and B-parameter specifications Erik Lindahl
[gmx-users] Runtime need of cpp.exe Erik Lindahl
[gmx-users] Magic number error Erik Lindahl
[gmx-users] Implicit solvent simulation Erik Lindahl
[gmx-users] Re: Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run (Jim Kress) Erik Lindahl
[gmx-users] Implicit solvent simulation Erik Lindahl
[gmx-users] Re: Install problem Erik Lindahl
[gmx-users] Implicit solvent simulation Erik Lindahl
[gmx-users] FW: rvdw Erik Lindahl
[gmx-users] CVS code needed Erik Lindahl
[gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet Erik Lindahl
[gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet Erik Lindahl
[gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet Erik Lindahl
[gmx-users] g_energy doubt Eduardo Martins Lopes
[gmx-users] N-glycosylation of a protein Eric Lorent
[gmx-users] get_index Pedro Alexandre de Araújo Gomes Lapido Loureiro
[gmx-users] get_index Pedro Alexandre de Araújo Gomes Lapido Loureiro
[gmx-users] get_index Pedro Alexandre de Araújo Gomes Lapido Loureiro
[gmx-users] get_index Pedro Alexandre de Araújo Gomes Lapido Loureiro
[gmx-users] uniform dielectric constant Mikael Lund
[gmx-users] Implicit solvent simulation Edgar Luttmann
[gmx-users] C500 Configuration and parameters help ROHIT MALSHE
[gmx-users] restarting a run using tpbconv N-J.M. Macaluso
[gmx-users] restarting a run using tpbconv N-J.M. Macaluso
[gmx-users] restarting a run using tpbconv N-J.M. Macaluso
[gmx-users] Segmentation fault after dt=2fs Mahnam
[gmx-users] Segmentation fault after dt=2fs Mahnam
[gmx-users] S-S Bonds Roberto Marchese
[gmx-users] ARGN Roberto Marchese
[gmx-users] Dismantling the methyl group Erik Marklund
[gmx-users] Dismantling the methyl group Erik Marklund
[gmx-users] problem regarding freezegrps Erik Marklund
[gmx-users] dissociative water models Erik Marklund
[gmx-users] simulations using structureless surface-2 Erik Marklund
[gmx-users] simulations using structureless surface-2 Erik Marklund
[gmx-users] Problem regarding genbox Erik Marklund
[gmx-users] segmentation fault John Mercer
[gmx-users] install problem John Mercer
[gmx-users] pb with temperature in bd (2) BON Michael
[gmx-users] OPLSaa+Lipid.itp question Oliver Mirus
[gmx-users] Regarding POPE " H " atom type modification Oliver Mirus
[gmx-users] Re: Regarding POPE " H " atom type modification Oliver Mirus
[gmx-users] dummy atom definition in FEP David Mobley
[gmx-users] FEP and soft-core potentials David Mobley
[gmx-users] FEP and soft-core potentials David Mobley
[gmx-users] charge_calculation David Mobley
[gmx-users] FEP method in protein-ligand systems David Mobley
[gmx-users] (no subject) Frankie Montenegro
[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units Frankie Montenegro
[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units Frankie Montenegro
[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units Frankie Montenegro
[gmx-users] Implicit solvent simulation Moore, Jonathan (J)
[gmx-users] number of coordinates in coordinate file does not match topology Moore, Jonathan (J)
[gmx-users] number of coordinates in coordinate file does not match topology Moore, Jonathan (J)
[gmx-users] number of coordinates in coordinate file does not match topology Moore, Jonathan (J)
[gmx-users] Re: Install problem Ibrahim M. Moustafa
[gmx-users] Error_message Chris Neale
[gmx-users] Magic number error Chris Neale
[gmx-users] shortage of shared memory Chris Neale
[gmx-users] Magic number error Chris Neale
[gmx-users] which tpr? Terry Nelson
[gmx-users] FEP method in protein-ligand systems Diego Nolasco
[gmx-users] FEP method in protein-ligand systems Diego Nolasco
[gmx-users] Regarding Na ions Osmair Vital de Oliveira
[gmx-users] g_rdf dual core Osmair Vital de Oliveira
[gmx-users] g_rdf dual core Osmair Vital de Oliveira
[gmx-users] FEP and soft-core potentials Georgios Patargias
[gmx-users] FEP and soft-core potentials Georgios Patargias
[gmx-users] Parellel Gromacs Xavier Periole
[gmx-users] which tool to use a measure a user-defined angle in a traj TJ Piggot
[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units TJ Piggot
[gmx-users] Implicit solvent simulation TJ Piggot
[gmx-users] Implicit solvent simulation TJ Piggot
[gmx-users] Gromacs Performance mesurement Utkal Ranjan Pradhan
[gmx-users] error running position restraints Utkal Ranjan Pradhan
[gmx-users] Runtime need of cpp.exe Utkal Ranjan Pradhan
[gmx-users] Runtime need of cpp.exe Utkal Ranjan Pradhan
[gmx-users] Runtime need of cpp.exe Utkal Ranjan Pradhan
[gmx-users] dummy atom definition prob in FEP Wang Qin
[gmx-users] dummy atom definition prob in FEP Wang Qin
[gmx-users] dummy atom definition in FEP Wang Qin
[gmx-users] dummy atom definition in FEP Wang Qin
[gmx-users] genion - hangs up Rigden, LucianeVMello
[gmx-users] genion - hangs up Rigden, LucianeVMello
[gmx-users] mdp files gromacs 3.3 Rigden, LucianeVMello
[gmx-users] Do you need to have the parameters numbered in order? Arthur Roberts
[gmx-users] grompp failure on BG/L YOLANDA SMALL
[gmx-users] HETATM records of crystallized water SWAPNA
[gmx-users] HETATM records of crystallized water SWAPNA
[gmx-users] OpenMosix and Gromacs Nicolas Sapay
[gmx-users] Wasting too much time recompiling Lars Schaefer
[gmx-users] Wasting too much time recompiling Lars Schaefer
[gmx-users] Problems with SA: temp not changing Monika Sharma
[gmx-users] Another problem with Stimulated Annealing Monika Sharma
[gmx-users] Another problem with Stimulated Annealing Monika Sharma
[gmx-users] ACE parameter error in ffG53a5/6? Mauricio Pablo Sica
[gmx-users] ACE group parameter error un ffG53a5-6? Mauricio Pablo Sica
[gmx-users] ACE parameter error in ffG53a5-6? Mauricio Pablo Sica
[gmx-users] pdb2gmx not recognizing disulfides David van der Spoel
[gmx-users] pdb2gmx not recognizing disulfides David van der Spoel
[gmx-users] translate David van der Spoel
[gmx-users] pdb2gmx not recognizing disulfides David van der Spoel
[gmx-users] Dismantling the methyl group David van der Spoel
[gmx-users] pdb2gmx not recognizing disulfides David van der Spoel
[gmx-users] which tpr? David van der Spoel
[gmx-users] Flexible Water David van der Spoel
[gmx-users] GROMACS Summer of Code... David van der Spoel
[gmx-users] [Fwd: How simulate two peptides in a box?] David van der Spoel
[gmx-users] [Fwd: How simulate two peptides in a box?] David van der Spoel
[gmx-users] [Fwd: How simulate two peptides in a box?] David van der Spoel
[gmx-users] Topology builder David van der Spoel
[gmx-users] ARGN David van der Spoel
[gmx-users] get_index David van der Spoel
[gmx-users] get_index David van der Spoel
[gmx-users] get_index David van der Spoel
[gmx-users] Error_message David van der Spoel
[gmx-users] Nanotubes with Tubegen David van der Spoel
[gmx-users] Problems with SA: temp not changing David van der Spoel
[gmx-users] HETATM records of crystallized water David van der Spoel
[gmx-users] Another problem with Stimulated Annealing David van der Spoel
[gmx-users] Another problem with Stimulated Annealing David van der Spoel
[gmx-users] Re: Nanotubes with Tubegen David van der Spoel
[gmx-users] a recruit's quention David van der Spoel
[gmx-users] How to create correct .gro file? David van der Spoel
[gmx-users] Some problems with tools David van der Spoel
[gmx-users] Re: Nanotubes with Tubegen David van der Spoel
[gmx-users] Re: Gromacs and mpirun David van der Spoel
[gmx-users] shortage of shared memory David van der Spoel
[gmx-users] Less than Graceful David van der Spoel
[gmx-users] Calculations of area per lipid using g_sas David van der Spoel
[gmx-users] Where is the origin of the coordinate system? David van der Spoel
[gmx-users] Xenon non-bonded parameterization David van der Spoel
[gmx-users] Xenon non-bonded parameterization David van der Spoel
[gmx-users] Re: The Lennard-Jones parameter of Na+? (Mark Abraham) David van der Spoel
[gmx-users] Re: gmx-users Digest, Vol 39, Issue 37 David van der Spoel
[gmx-users] Re: gmx-users Digest, Vol 39, Issue 37 David van der Spoel
[gmx-users] [Fwd: conjugate gradients with constraints] David van der Spoel
[gmx-users] Regarding D-Alanine paramters David van der Spoel
[gmx-users] Re:Regarding D-Alanine paramters David van der Spoel
[gmx-users] Analytic first derivatives with respect to parameters? David van der Spoel
[gmx-users] Is there a way to compile gromacs with MPICH instead of LAM? David van der Spoel
[gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion David van der Spoel
[gmx-users] Segmentation fault after dt=2fs David van der Spoel
[gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion David van der Spoel
[gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion David van der Spoel
[gmx-users] Segmentation fault after dt=2fs David van der Spoel
[gmx-users] Some Questions David van der Spoel
[gmx-users] Regarding polymer equillibration (pressure changes) David van der Spoel
[gmx-users] Error during grompp David van der Spoel
[gmx-users] Re: gmx-users Digest, Vol 39, Issue 56 David van der Spoel
[gmx-users] Runtime need of cpp.exe David van der Spoel
[gmx-users] Runtime need of cpp.exe David van der Spoel
[gmx-users] Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run David van der Spoel
[gmx-users] Magic number error David van der Spoel
[gmx-users] Implicit solvent simulation David van der Spoel
[gmx-users] Implicit solvent simulation David van der Spoel
[gmx-users] uniform dielectric constant David van der Spoel
[gmx-users] Implicit solvent simulation David van der Spoel
[gmx-users] install problem David van der Spoel
[gmx-users] How to include Mg in the input file? David van der Spoel
[gmx-users] g_rdf dual core David van der Spoel
[gmx-users] number of coordinates in coordinate file does not match topology David van der Spoel
[gmx-users] question regarding restraints David van der Spoel
[gmx-users] restarting a run using tpbconv David van der Spoel
[gmx-users] wat is the way to solve this prob David van der Spoel
[gmx-users] wat is the way to solve this prob David van der Spoel
[gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet David van der Spoel
[gmx-users] HEME simulation David van der Spoel
[gmx-users] adding mixed solvent using genbox David van der Spoel
[gmx-users] [Fwd: Problem with Position restrained dynamics] David van der Spoel
[gmx-users] GAMESS-US for Hybrid QM/MM Srivastava, Dhiraj (UMC-Student)
[gmx-users] Nanotubes with Tubegen Christopher Stiles
[gmx-users] Re: Nanotubes with Tubegen Christopher Stiles
[gmx-users] Re: Nanotubes with Tubegen Christopher Stiles
[gmx-users] Re: Nanotubes with Tubegen Christopher Stiles
[gmx-users] mdp file help Christopher Stiles
[gmx-users] number of coordinates in coordinate file does not match topology Christopher Stiles
[gmx-users] number of coordinates in coordinate file does not match topology Christopher Stiles
[gmx-users] number of coordinates in coordinate file does not match topology Christopher Stiles
[gmx-users] Carbon Nanotube Simulation Issues Christopher Stiles
[gmx-users] Re: Carbon Nanotube Simulation Issues Christopher Stiles
[gmx-users] Re: Carbon Nanotube Simulation Issues Christopher Stiles
[gmx-users] Re: Carbon Nanotube Simulation Issues Christopher Stiles
[gmx-users] Re: Carbon Nanotube Simulation Issues Christopher Stiles
[gmx-users] Re: Carbon Nanotube Simulation Issues Christopher Stiles
[gmx-users] Re: Carbon Nanotube Simulation Issues Christopher Stiles
[gmx-users] Re: Carbon Nanotube Simulation Issues Christopher Stiles
[gmx-users] RE: gmx-users Digest, Vol 39, Issue 102 Christopher Stiles
[gmx-users] Re: Carbon Nanotube Simulation Issues Christopher Stiles
[gmx-users] x2top & GMXLIB Christopher Stiles
[gmx-users] Minimizing a molecule not recognised by gromacs Subhrangshu Supakar
[gmx-users] What is the box type of output files? Lam Nguyen Sy
[gmx-users] What is the box type of output files? Lam Nguyen Sy
[gmx-users] How to create correct .gro file? Lam Nguyen Sy
[gmx-users] How to create correct .gro file? Lam Nguyen Sy
[gmx-users] Re: Gromacs and mpirun Lam Nguyen Sy
[gmx-users] Where is the origin of the coordinate system? Lam Nguyen Sy
[gmx-users] get_index Stéphane Téletchéa
[gmx-users] Less than Graceful Stéphane Téletchéa
[gmx-users] Implicit solvent simulation Stéphane Téletchéa
[gmx-users] Segmentation fault after dt=2fs Stéphane Téletchéa
[gmx-users] Segmentation fault after dt=2fs Stéphane Téletchéa
[gmx-users] Implicit solvent simulation Stéphane Téletchéa
[gmx-users] dummy atom definition prob in FEP Stéphane Téletchéa
[gmx-users] CVS code needed Kumar V
[gmx-users] Error during grompp Dallas B. Warren
[gmx-users] Re: gmx-users Digest, Vol 39, Issue 56 Dallas B. Warren
[gmx-users] Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run Dallas B. Warren
[gmx-users] problem regarding total time elapsed Dallas B. Warren
[gmx-users] [Fwd: How simulate two peptides in a box?] Tsjerk Wassenaar
[gmx-users] pdb2gmx not recognizing disulfides Tsjerk Wassenaar
[gmx-users] Dismantling the methyl group Tsjerk Wassenaar
[gmx-users] S-S Bonds Tsjerk Wassenaar
[gmx-users] trajconv Tsjerk Wassenaar
[gmx-users] which tpr? Tsjerk Wassenaar
[gmx-users] How to get ligand top file for oplsaa? Tsjerk Wassenaar
[gmx-users] Fwd: Can you help me? (Problem with simulating two peptides -TAW-) Tsjerk Wassenaar
[gmx-users] protein-protein complex Tsjerk Wassenaar
[gmx-users] about truncated octahedral periodic box Tsjerk Wassenaar
[gmx-users] about truncated octahedral periodic box Tsjerk Wassenaar
[gmx-users] Re: Conversion of gromacs parameters to AMBER parameters Tsjerk Wassenaar
[gmx-users] get_index Tsjerk Wassenaar
[gmx-users] Solvent_box Tsjerk Wassenaar
[gmx-users] Fwd: GROMACS_solvent_box Tsjerk Wassenaar
[gmx-users] Solvent_box Tsjerk Wassenaar
[gmx-users] Sphingomyelin parameters Tsjerk Wassenaar
[gmx-users] which tool to use a measure a user-defined angle in a traj Tsjerk Wassenaar
[gmx-users] Magic number error Tsjerk Wassenaar
[gmx-users] Problem with genbox Tsjerk Wassenaar
[gmx-users] problem with genion Tsjerk Wassenaar
[gmx-users] problem with genion Tsjerk Wassenaar
[gmx-users] which tool to use a measure a user-defined angle in a traj Tsjerk Wassenaar
[gmx-users] problem with genion Tsjerk Wassenaar
[gmx-users] What if there are multi-definition of dihedrals? Tsjerk Wassenaar
[gmx-users] Runtime need of cpp.exe Tsjerk Wassenaar
[gmx-users] genion - hangs up Tsjerk Wassenaar
[gmx-users] ACE parameter error in ffG53a5-6? Tsjerk Wassenaar
[gmx-users] Error in pr Tsjerk Wassenaar
[gmx-users] N-glycosylation of a protein Steffen Wolf
[gmx-users] How Long to Equlibrate? Steffen Wolf
[gmx-users] What if there are multi-definition of dihedrals? WU Yanbin
[gmx-users] Some Questions Omid Yazdan
[gmx-users] pdb2gmx not recognizing disulfides Yang Ye
[gmx-users] Dismantling the methyl group Yang Ye
[gmx-users] What is the box type of output files? Yang Ye
[gmx-users] about truncated octahedral periodic box Yang Ye
[gmx-users] about truncated octahedral periodic box Yang Ye
[gmx-users] about truncated octahedral periodic box Yang Ye
[gmx-users] [Fwd: a question about your reply] Yang Ye
[gmx-users] Re:Error_message Yang Ye
[gmx-users] Error_message Yang Ye
[gmx-users] Regarding Na ions Yang Ye
[gmx-users] Less than Graceful Yang Ye
[gmx-users] Re: The Lennard-Jones parameter of Na+? (Mark Abraham) Yang Ye
[gmx-users] the atomic charges in ligand Yang Ye
[gmx-users] Solvent_box Yang Ye
[gmx-users] g_energy doubt Yang Ye
[gmx-users] the atomic charges in ligand Yang Ye
[gmx-users] Magic number error Yang Ye
[gmx-users] What if there are multi-definition of dihedrals? Yang Ye
[gmx-users] Error during grompp Yang Ye
[gmx-users] Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run Yang Ye
[gmx-users] Runtime need of cpp.exe Yang Ye
[gmx-users] restarting a run using tpbconv Yang Ye
[gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet Yang Ye
[gmx-users] regarding the positional restraints Yang Ye
[gmx-users] adding mixed solvent using genbox Yang Ye
[gmx-users] Carbon Nanotube Simulation Issues Yang Ye
[gmx-users] Re: Carbon Nanotube Simulation Issues Yang Ye
[gmx-users] Re: Carbon Nanotube Simulation Issues Yang Ye
[gmx-users] Re: Carbon Nanotube Simulation Issues Yang Ye
[gmx-users] mdp files gromacs 3.3 Yang Ye
[gmx-users] Re: Carbon Nanotube Simulation Issues Yang Ye
[gmx-users] Re: Carbon Nanotube Simulation Issues Yang Ye
[gmx-users] Chitosan topology Yang Ye
[gmx-users] Parellel Gromacs Yang Ye
[gmx-users] [Fwd: Problem with Position restrained dynamics] Ragothaman Yennamalli
[gmx-users] The Lennard-Jones parameter of Na+? Hu Zhongqiao
[gmx-users] Re: The Lennard-Jones parameter of Na+? (Mark Abraham) Hu Zhongqiao
[gmx-users] Problem with genbox Mark Zottola
[gmx-users] How Long to Equlibrate? Mark Zottola
[gmx-users] Re: Install problem bharat v. adkar
[gmx-users] How to include Mg in the input file? srinivas aripirala
[gmx-users] protein-protein complex fulya caglar
[gmx-users] protein-protein complex fulya caglar
[gmx-users] regarding the positional restraints aneesh chandran
[gmx-users] regarding the positional restraints aneesh chandran
[gmx-users] g_wham and PMF problem gportel at gwdg.de
[gmx-users] adding mixed solvent using genbox shankari hariharan
[gmx-users] Implicit solvent simulation steletch at jouy.inra.fr
[gmx-users] CVS code needed Arun kumar
[gmx-users] pdb file of a crystal lattice of epoxy resin vijay kumar
[gmx-users] wat is the way to solve this prob vijay kumar
[gmx-users] Error_message pkmukher
[gmx-users] Error_message pkmukher
[gmx-users] Error_message pkmukher
[gmx-users] Re:Error_message pkmukher
[gmx-users] Solvent_box pkmukher
[gmx-users] Solvent_box pkmukher
[gmx-users] Solvent_box pkmukher
[gmx-users] charge_calculation pkmukher
[gmx-users] Atomtype:CB pkmukher
[gmx-users] mdrun_problem pkmukher
[gmx-users] Re:mdrun_problem pkmukher
[gmx-users] error running position restraints priya priya
[gmx-users] Implementing WCA with OPLS-aa jtomlins at purdue.edu
[gmx-users] Regarding conversion of lipid parapeters to Amber format naga raju
[gmx-users] Re: Conversion of gromacs parameters to AMBER parameters naga raju
[gmx-users] Regarding neutralization of lipid bilayer naga raju
[gmx-users] Regarding Na ions naga raju
[gmx-users] Re: Regarding Na ions naga raju
[gmx-users] Regarding POPE " H " atom type modification naga raju
[gmx-users] Re: Regarding POPE " H " atom type modification naga raju
[gmx-users] Regarding D-Alanine paramters naga raju
[gmx-users] Re:Regarding D-Alanine paramters naga raju
[gmx-users] trajconv ann rose
[gmx-users] Regarding polymer equillibration (pressure changes ) ann rose
[gmx-users] Re: gmx-users Digest, Vol 39, Issue 56 ann rose
[gmx-users] augustus 1, 2007: remediated pdb format pim schravendijk
[gmx-users] simulations using structureless surface singh
[gmx-users] simulations using structureless surface-2 singh
[gmx-users] [Fwd: How simulate two peptides in a box?] gurpreet singh
[gmx-users] [Fwd: How simulate two peptides in a box?] gurpreet singh
[gmx-users] [Fwd: How simulate two peptides in a box?] gurpreet singh
[gmx-users] problem regarding freezegrps gurpreet singh
[gmx-users] problem with genion gurpreet singh
[gmx-users] problem with genion gurpreet singh
[gmx-users] problem with genion gurpreet singh
[gmx-users] problem with genion gurpreet singh
[gmx-users] question regarding restraints gurpreet singh
[gmx-users] question regarding restraints gurpreet singh
[gmx-users] doubt in minimization gurpreet singh
[gmx-users] problem regarding total time elapsed gurpreet singh
[gmx-users] regarding g_energy harpreet singh
[gmx-users] Flexible Water gleb solomentsev
[gmx-users] dssp in gromacs taveechai taveecharoenkool
[gmx-users] Re: gmx-users Digest, Vol 39, Issue 37 taveechai taveecharoenkool
[gmx-users] Error durign Grompp fufengliu at tju.edu.cn
[gmx-users] Error running grompp fufengliu at tju.edu.cn
[gmx-users] How to simulate peptide capped with ACE? fufengliu at tju.edu.cn
[gmx-users] How to simulate peptide capped with ACE? fufengliu at tju.edu.cn
[gmx-users] GRomacs 3.3.1 parallel run fabio tombolato
[gmx-users] free energy calculation and constraint distance? bmmothan at ucalgary.ca
[gmx-users] free energy calculation and constraint distance? bmmothan at ucalgary.ca
[gmx-users] Constrains and TI bmmothan at ucalgary.ca
[gmx-users] Error in pr bmmothan at ucalgary.ca
[gmx-users] Parellel Gromacs bmmothan at ucalgary.ca
[gmx-users] HEME simulation gromacs user
[gmx-users] shortage of shared memory chris.neale at utoronto.ca
[gmx-users] Request for dihedral PMF test system or complete alanine dipeptide topology file chris.neale at utoronto.ca
[gmx-users] Lipid-protein force field problem. chris.neale at utoronto.ca
[gmx-users] g_desort available for download chris.neale at utoronto.ca
[gmx-users] which tool to use a measure a user-defined angle in a traj chris.neale at utoronto.ca
[gmx-users] request for enhanced options for force and coord output during mdrun chris.neale at utoronto.ca
[gmx-users] search page does not return mailing list posts after mid april 2007 chris.neale at utoronto.ca
[gmx-users] translate mahbubeh zarrabi
[gmx-users] Lipid-protein force field problem. zazeri
[gmx-users] Lipid-protein force field problem. zazeri
[gmx-users] Magic number error zazeri
[gmx-users] Magic number error zazeri
[gmx-users] Magic number error zazeri
[gmx-users] Magic number error zazeri
[gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion james zhang
[gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion james zhang
[gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion james zhang
[gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion james zhang
[gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion james zhang
[gmx-users] Problems about sigma & epsilon to C6 & C12 james zhang
[gmx-users] mdp file help james zhang
[gmx-users] About Temperature Gradient james zhang
[gmx-users] phosphated residue??? xi zhao
[gmx-users] Some problems with tools Дмитрий Егоров
Re: Re: [gmx-users] number of coordinates in coordinate file does notmatch topology Александр Журавлев
[gmx-users] a recruit's quention 樊
[gmx-users] a question about gromacs 里梦
[gmx-users] g_enemat 이선주

Last message date: Tue Jul 31 23:05:56 CEST 2007
Archived on: Thu Nov 14 12:03:46 CET 2013

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