January 2011 Archives by author

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Starting: Sat Jan 1 00:57:48 CET 2011
Ending: Mon Jan 31 23:52:36 CET 2011
Messages: 1007

[gmx-users] problem when calculating the solvation free energy of ARG in water using PME. Itamar Kass (Med)
[gmx-users] RE : gmx-users Digest, Vol 81, Issue 58 ABEL Stephane 175950
[gmx-users] perfluorohexane pdb ABEL Stephane 175950
[gmx-users] perfluorohexane pdb... again ABEL Stephane 175950
[gmx-users] solvation box for say 50mM chaps solution ABEL Stephane 175950
[gmx-users] amber96 RB dihedrals in GMX 4.0 and 4.5 Badi' Abdul-Wahid
[gmx-users] Thiazolidinedione Tautomers Mark Abraham
[gmx-users] Thiazolidinedione Tautomers Mark Abraham
[gmx-users] The sum of the O-H distancesof the backbone hydrogen bonds ROH Mark Abraham
[gmx-users] Trifluoroethanol-Ethanol mixtures study Mark Abraham
[gmx-users] Email bounce message Mark Abraham
[gmx-users] How to get sufactant.gro, sufactant.top, Mark Abraham
[gmx-users] Trifluoroethanol-Ethanol mixtures study Mark Abraham
[gmx-users] percentage of secondary structure Mark Abraham
[gmx-users] percentage of secondary structure Mark Abraham
[gmx-users] percentage of secondary structure Mark Abraham
[gmx-users] Constraints and efficency Mark Abraham
[gmx-users] CNT Mark Abraham
[gmx-users] query for protein-igand binding energy calculation using LIE and Gromacs simulation Mark Abraham
[gmx-users] Re:Re: How to get sufactant.gro, sufactant.top, (Mark Abraham) Mark Abraham
[gmx-users] Questions concerning Gromacs Mark Abraham
[gmx-users] nanoparticles Mark Abraham
[gmx-users] Library file in.m2p not found Mark Abraham
[gmx-users] Library file in.m2p not found Mark Abraham
[gmx-users] Questions concerning Gromacs Mark Abraham
[gmx-users] Query about use of coulombtype for LIE in gromacs Mark Abraham
[gmx-users] Re: Average box size Mark Abraham
[gmx-users] methanol simulation Mark Abraham
[gmx-users] Question Mark Abraham
[gmx-users] Question Mark Abraham
[gmx-users] methanol simulation error Mark Abraham
[gmx-users] number of index elements not multiple of 3, these can not be angle triplet Mark Abraham
[gmx-users] Re: Re: methanol simulation error Mark Abraham
[gmx-users] inconsistent energies Mark Abraham
[gmx-users] Ion-Clustering? Mark Abraham
[gmx-users] g_msd Utility - (Unexpected) Different Results Depending on Output Flag Mark Abraham
[gmx-users] Re: inconsistent energies Mark Abraham
[gmx-users] error in ffgmxbon.itp Mark Abraham
[gmx-users] Atomtpe HW not found-2 Mark Abraham
[gmx-users] Pioglitazone Tautomers Mark Abraham
[gmx-users] the calculation time Mark Abraham
[gmx-users] Re: trjconv with multiple chains Mark Abraham
[gmx-users] Density of the box Mark Abraham
[gmx-users] ion jumping out of water box Mark Abraham
[gmx-users] Tautomer Prediction Mark Abraham
[gmx-users] RB Dihedrals with ffamber96 in Gromacs 4.5.3? Mark Abraham
[gmx-users] Simulations in vacuo Mark Abraham
[gmx-users] so difficult problem Mark Abraham
[gmx-users] pdb2gmx: segmentation fault Mark Abraham
[gmx-users] Installing multiple versions of GROMACS together? - program suffix Mark Abraham
[gmx-users] extending the simulation with modified mdp option Mark Abraham
[gmx-users] Error when execute g_energy - the message: not recognized, maybe different CPU? Mark Abraham
[gmx-users] number of cores with a large prime factor Mark Abraham
[gmx-users] Re: pdb2gmx: segmentation fault Mark Abraham
[gmx-users] Re: pdb2gmx: segmentation fault Mark Abraham
[gmx-users] Doubts regarding Simulation box - Thanks Mark Abraham
[gmx-users] segmentation fault Mark Abraham
[gmx-users] Installing Gromacs with Cygwin Mark Abraham
[gmx-users] segmentation error Mark Abraham
[gmx-users] grompp error Mark Abraham
[gmx-users] Position restraint problem Mark Abraham
[gmx-users] ACPYPE download Mark Abraham
[gmx-users] Re : genion Mark Abraham
[gmx-users] Problem with GB and coarse-grain forcefield Mark Abraham
[gmx-users] Position restraint problem Mark Abraham
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. Mark Abraham
[gmx-users] CNT Mark Abraham
[gmx-users] eNERGY mINIMIZATION Mark Abraham
[gmx-users] eNERGY mINIMIZATION Mark Abraham
[gmx-users] potential energy value Mark Abraham
[gmx-users] preparation_solvation_box Mark Abraham
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. Mark Abraham
[gmx-users] Fourier transformation of dipole autocorrelation function Mark Abraham
[gmx-users] Fourier transformation of dipole autocorrelation function Mark Abraham
[gmx-users] Gromacs 4 cannot reach Fmax in energy minimisation when version 3 did Mark Abraham
[gmx-users] Convert residue coordinates to dihedral angles Mark Abraham
[gmx-users] the final structure Mark Abraham
[gmx-users] Dell PowerEdge M710 with Intel Xeon 5667 processor Mark Abraham
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. Mark Abraham
[gmx-users] CNT Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] running a crashed run Mark Abraham
[gmx-users] running a crashed run Mark Abraham
[gmx-users] Re: Problem in Disulfide Bond Mark Abraham
[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3 Mark Abraham
[gmx-users] Re: Problem in Disulfide Bond Mark Abraham
[gmx-users] avoiding bad contact in continutation run Mark Abraham
[gmx-users] Inaccurate pressure readings Mark Abraham
[gmx-users] How to install a new Forcefield in Gromacs 4.5.3 Mark Abraham
[gmx-users] Re: avoiding bad contact in continutation run (Mark Abraham) Mark Abraham
[gmx-users] Box size and potential energy calculation Mark Abraham
[gmx-users] Box size and potential energy calculation Mark Abraham
[gmx-users] Query for RMSD Mark Abraham
[gmx-users] PRODRG server Mark Abraham
[gmx-users] adding of a new force field in gromacs 4.5.1 Mark Abraham
[gmx-users] pdb2gmx error_ resall.c, line: 321 Mark Abraham
[gmx-users] GPU gets faster with more molecules in system Mark Abraham
[gmx-users] amber96 RB dihedrals in GMX 4.0 and 4.5 Mark Abraham
[gmx-users] total charge of the system Mark Abraham
[gmx-users] total charge of the system Mark Abraham
[gmx-users] total charge of the system Mark Abraham
[gmx-users] total charge of the system Mark Abraham
[gmx-users] nstcomm nstcalcenergy defeats the purpose of nstcalcenergy Mark Abraham
[gmx-users] mdrun_mpi executable not found Mark Abraham
[gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97 Mark Abraham
[gmx-users] Two machines, same job, one fails Mark Abraham
[gmx-users] Two machines, same job, one fails Mark Abraham
[gmx-users] More than one settle type Mark Abraham
[gmx-users] RE: stopping a simulation in between without crashing any trajectories Mark Abraham
[gmx-users] validation of ligand parametrization Mark Abraham
[gmx-users] solvation_box Mark Abraham
[gmx-users] Re: change in the secondary structure after simulation Mark Abraham
[gmx-users] ZN2+ qtot 1.233e-06 ? Mark Abraham
[gmx-users] Re: change in the secondary structure after simulation Mark Abraham
[gmx-users] ZN2+ qtot 1.233e-06 ? Mark Abraham
[gmx-users] proton proton exchange and constant pH simulations. Mark Abraham
[gmx-users] Re: change in the secondary structure after simulation Mark Abraham
[gmx-users] Center of mass motion removal for partial filled PBC box Mark Abraham
[gmx-users] truncated LJ potential Mark Abraham
[gmx-users] truncated LJ potential Mark Abraham
[gmx-users] solvation_box_preparation Mark Abraham
[gmx-users] Simulation time losses with REMD Mark Abraham
[gmx-users] invacuo simulation Mark Abraham
[gmx-users] mdrun with append option Mark Abraham
[gmx-users] energy minimization of a charged system in vacuum Mark Abraham
[gmx-users] Re: gmx-users Digest, Vol 81, Issue 204 Mark Abraham
[gmx-users] Simulation time losses with REMD Mark Abraham
[gmx-users] mdrun with append option Mark Abraham
[gmx-users] Simulation time losses with REMD Mark Abraham
[gmx-users] ngmx doesnot work; CH3-CH2-OH Mark Abraham
[gmx-users] ngmx doesnot work; CH3-CH2-OH Mark Abraham
[gmx-users] Monitoring the water movement during simulation Mark Abraham
[gmx-users] 4.5.3 Installation under Cygwin Mark Abraham
Fwd: [gmx-users] Monitoring the water movement during simulation Mark Abraham
[gmx-users] Fwd: GROMACS user: error with pdb2gmx Mark Abraham
Fwd: [gmx-users] Monitoring the water movement during simulation Mark Abraham
Fwd: [gmx-users] Monitoring the water movement during simulation Mark Abraham
[gmx-users] Average box size Navjeet Ahalawat
[gmx-users] Re: gmx-users Digest, Vol 81, Issue 14 Navjeet Ahalawat
[gmx-users] Re: Average box size Navjeet Ahalawat
[gmx-users] Re: Average box size Navjeet Ahalawat
[gmx-users] Re: Average box size Navjeet Ahalawat
[gmx-users] Re:Re: Re: Average box size Navjeet Ahalawat
[gmx-users] Simulations on GPU Rossen Apostolov
[gmx-users] Simulations on GPU Rossen Apostolov
[gmx-users] gromacs on Lynnfield processors Guilherme Menegon Arantes
[gmx-users] order parameters of partially unsaturated chains JAVIER CEREZO BASTIDA
[gmx-users] Problem with COM movement Tomy van Batis
[gmx-users] all_force.xvg Solomon Berman
[gmx-users] g_msd Utility - (Unexpected) Different Results Depending on Output Flag Solomon Berman
[gmx-users] Need help troubleshooting an mdrun-gpu error message! Solomon Berman
[gmx-users] Problem with GB and coarse-grain forcefield Benjamin Bouvier
[gmx-users] Simulations on GPU Keith Callenberg
[gmx-users] Simulations on GPU Keith Callenberg
[gmx-users] Constraints and efficency Elton Carvalho
[gmx-users] Constraints and efficency Elton Carvalho
[gmx-users] temperature of different atom groups in the system Vitaly Chaban
[gmx-users] Re: Non integral charges Vitaly Chaban
[gmx-users] Re: Non integral charges Vitaly Chaban
[gmx-users] energy minimization of a charged system in vacuum Matt Chan
[gmx-users] divergent energy minimization results from identical starting system Matt Chan
[gmx-users] energy minimization of a charged system in vacuum Matthew Chan
[gmx-users] divergent energy minimization results from identical starting system Matthew Chan
[gmx-users] GROMOS96 topology for small molecule C.Y. Chang
[gmx-users] GROMOS96 topology for small molecule C.Y. Chang
[gmx-users] Signal: Segmentation faul Amit Choubey
[gmx-users] so difficult problem Amit Choubey
[gmx-users] so difficult problem Amit Choubey
[gmx-users] so difficult problem Amit Choubey
[gmx-users] number of index elements not multiple of 3, these can not be angle triplet Amit Choubey
[gmx-users] number of index elements not multiple of 3, these can not be angle triplet Amit Choubey
[gmx-users] trjconv with multiple chains Amit Choubey
[gmx-users] Energy minimization Amit Choubey
[gmx-users] Energy minimization Amit Choubey
[gmx-users] Energy minimization Amit Choubey
[gmx-users] spurious forces while doing pulling simulation Amit Choubey
[gmx-users] spurious forces while doing pulling simulation Amit Choubey
[gmx-users] spurious forces while doing pulling simulation Amit Choubey
[gmx-users] spurious forces while doing pulling simulation Amit Choubey
[gmx-users] spurious forces while doing pulling simulation Amit Choubey
[gmx-users] g_mindist clarification Chandan Choudhury
[gmx-users] gromacs 4.5.3 with threads instead of MPI Arnau Cordomi
[gmx-users] Ubuntu Installation Bogdan Costescu
[gmx-users] trjconv -fit rot+trans before a pbc? safe way to rotate a trajectory? Camilo Andrés Jimenez Cruz
[gmx-users] Gromacs + GPU: Problems running dppc example in ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz Camilo Andrés Jimenez Cruz
[gmx-users] Re: Gromacs + GPU: Problems running dppc example in ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz Camilo Andrés Jimenez Cruz
[gmx-users] Umbrella sampling Nilesh Dhumal
[gmx-users] Umbrella sampling Nilesh Dhumal
[gmx-users] g_sdf Nilesh Dhumal
[gmx-users] g_sdf Nilesh Dhumal
[gmx-users] histograms Nilesh Dhumal
[gmx-users] histograms Nilesh Dhumal
[gmx-users] histograms Nilesh Dhumal
[gmx-users] Fourier transformation of dipole autocorrelation function Nilesh Dhumal
[gmx-users] Fourier transformation of dipole autocorrelation function Nilesh Dhumal
[gmx-users] Fourier transformation of dipole autocorrelation function in matlab Nilesh Dhumal
[gmx-users] Fourier transformation of dipole autocorrelation function Florian Dommert
[gmx-users] PME parameter in GROMACS Florian Dommert
[gmx-users] error calculation via bootstrapping method in umbrella sampling simulation Ozge Engin
[gmx-users] XTC file not being created, while TRR file is Diego Enry
[gmx-users] Add bridging residue Edvin Erdtman
Sv: Re: [gmx-users] Add bridging residue Edvin Erdtman
[gmx-users] percentage of secondary structure Thomas Evangelidis
[gmx-users] Error when execute g_energy - the message: not recognized, maybe different CPU? Rodrigo Faccioli
[gmx-users] Error when execute g_energy - the message: not recognized, maybe different CPU? Rodrigo Faccioli
[gmx-users] the final structure Rodrigo Faccioli
[gmx-users] g_analyze with multiple sets Rebeca García Fandiño
[gmx-users] g_analyze with multiple sets Rebeca García Fandiño
[gmx-users] How to include FE2+ in ions.itp ? Tanos Franca
[gmx-users] file heme.rtp Tanos Franca
[gmx-users] Help with the heme group in forcefield gromos53a6 Tanos Franca
[gmx-users] Heme group in the forcefield gromos53a6 Tanos Celmar Costa Franca
[gmx-users] N-acetyl-d-glucosamine parameters Renato Freitas
[gmx-users] Inaccurate pressure readings Denny Frost
[gmx-users] Inaccurate pressure readings Denny Frost
[gmx-users] Inaccurate pressure readings Denny Frost
[gmx-users] Inaccurate pressure readings Denny Frost
[gmx-users] Inaccurate pressure readings Denny Frost
[gmx-users] Slow Runs Denny Frost
[gmx-users] Slow Runs Denny Frost
[gmx-users] Slow Runs Denny Frost
[gmx-users] Slow Runs Denny Frost
[gmx-users] Slow Runs Denny Frost
[gmx-users] Slow Runs Denny Frost
[gmx-users] Slow Runs Denny Frost
[gmx-users] Slow Runs Denny Frost
[gmx-users] Slow Runs Denny Frost
[gmx-users] Slow Runs Denny Frost
[gmx-users] hbond constraint Denny Frost
[gmx-users] g_mindist Ramachandran G
[gmx-users] extending the simulation with modified mdp option Ramachandran G
[gmx-users] extending the simulation with modified mdp option Ramachandran G
[gmx-users] extending the simulation with modified mdp option Ramachandran G
[gmx-users] Inaccurate pressure readings Warren Gallin
[gmx-users] How to create an rtp file for a lipid? "Dr. Ramón Garduño-Juárez"
[gmx-users] grompp charge group radii larger than rlist "Dr. Ramón Garduño-Juárez"
[gmx-users] DSPC all atom .itp file Anirban Ghosh
[gmx-users] CG to FG transformation error Anirban Ghosh
[gmx-users] DSPC all atom .itp file Anirban Ghosh
[gmx-users] COMETS 2011 - 2nd International Track on Collaborative Modeling and Simulation - Call for Papers Daniele Gianni
[gmx-users] glycam amber in gromacs mixed 1-4 scaling glycam06 fudgeQQ pairs coulomb amberports Oliver Grant
[gmx-users] Re: Problem in Disulfide Bond Oliver Grant
[gmx-users] Re: Problem in Disulfide Bond Oliver Grant
[gmx-users] 4. Requesting advice on pressure scaling in a protein-in-membrane system. (Daniel Adriano Silva M) Gerrit Groenhof
[gmx-users] Re: QMMM with ORCA Gerrit Groenhof
[gmx-users] g_density CHARMM Ramon Guixà
[gmx-users] g_density CHARMM Ramon Guixà
[gmx-users] g_density CHARMM Ramon Guixà
[gmx-users] Simulations in vacuo Zoe Hall
[gmx-users] Dell PowerEdge M710 with Intel Xeon 5667 processor Maryam Hamzehee
[gmx-users] Dell PowerEdge M710 with Intel Xeon 5667 processor Maryam Hamzehee
[gmx-users] Box size and potential energy calculation Tim Harder
[gmx-users] Re: [ atomtypes ] are not case sensitive? Berk Hess
[gmx-users] truncated LJ potential Berk Hess
[gmx-users] truncated LJ potential Berk Hess
[gmx-users] truncated LJ potential Berk Hess
[gmx-users] Important: Bugs in NEMD calculation Berk Hess
[gmx-users] Important: Bugs in NEMD calculation Berk Hess
[gmx-users] RE: Important: Bugs in NEMD calculation Berk Hess
[gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ? Berk Hess
[gmx-users] pdb2gmx: segmentation fault Kwee Hong
[gmx-users] pdb2gmx: segmentation fault Kwee Hong
[gmx-users] pdb2gmx: segmentation fault Kwee Hong
[gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong
[gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong
[gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong
[gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong
[gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong
[gmx-users] doubts on g_confrms output Kwee Hong
[gmx-users] doubts on running em in vacuo Kwee Hong
[gmx-users] invacuo simulation Kwee Hong
[gmx-users] invacuo simulation Kwee Hong
[gmx-users] RNA with small molecule Muslum Ilgu
[gmx-users] RNA with small molecule Muslum Ilgu
[gmx-users] inconsistent energies Vlad Isaev
[gmx-users] Re: inconsistent energies Vlad Isaev
[gmx-users] dipole moment Olga Ivchenko
[gmx-users] dipole moment Olga Ivchenko
[gmx-users] dipole moment Olga Ivchenko
[gmx-users] proton proton exchange and constant pH simulations. Olga Ivchenko
[gmx-users] proton proton exchange and constant pH simulations. Olga Ivchenko
[gmx-users] Problem with using topolbuild1_3.tgz Sweta Iyer
[gmx-users] Re: Problem with using topolbuild1_3.tgz Sweta Iyer
[gmx-users] table-extension in mdp ?! jojo J
[gmx-users] different versions- different output! jojo J
[gmx-users] number of index elements not multiple of 3, these can not be angle triplet Carla Jamous
[gmx-users] number of index elements not multiple of 3, these can not be angle triplet Carla Jamous
[gmx-users] Re: Calculating lattice enegies for molecular crystals Adam Bin Idu Jion
[gmx-users] Convert residue coordinates to dihedral angles Adam Bin Idu Jion
[gmx-users] Source Code for Lennard Jones Interaction Apoorv Kalyankar
[gmx-users] transmembrane protein simulation Itamar Kass
[gmx-users] mdrun_mpi executable not found Justin Kat
[gmx-users] mdrun_mpi executable not found Justin Kat
[gmx-users] mdrun_mpi executable not found Justin Kat
[gmx-users] mdrun_mpi executable not found Justin Kat
[gmx-users] mdrun_mpi executable not found Justin Kat
[gmx-users] Output error mpirun/mdrun_mpi Justin Kat
[gmx-users] ACPYPE Kerrigan, John
[gmx-users] Questions concerning Gromacs Thomas Koller
[gmx-users] Questions concerning Gromacs Thomas Koller
[gmx-users] Question Thomas Koller
[gmx-users] problem with LINCS Thomas Koller
[gmx-users] decorrelation function Thomas Koller
[gmx-users] decorrelation function Thomas Koller
[gmx-users] Re: gmx-users Digest, Vol 81, Issue 204 Thomas Koller
[gmx-users] rdf range Thomas Koller
[gmx-users] Questions concerning autocorrealtion function Thomas Koller
[gmx-users] Gromacs 4 cannot reach Fmax in energy minimisation when version 3 did Cara Kreck
[gmx-users] g_tune_pme big standard deviation in perf.out output Carsten Kutzner
[gmx-users] gromacs 4.5.3 with threads instead of MPI Carsten Kutzner
[gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ? Carsten Kutzner
[gmx-users] Re: Gromacs + GPU: Problems running dppc example in ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz Carsten Kutzner
[gmx-users] van der Walls radius and implicit solvation Per Larsson
[gmx-users] OPLS implicit solvent problems Per Larsson
[gmx-users] Ubuntu Installation Jussi Lehtola
[gmx-users] Slow Runs Jussi Lehtola
[gmx-users] electron density Justin A. Lemkul
[gmx-users] electron density Justin A. Lemkul
[gmx-users] Umbrella sampling Justin A. Lemkul
[gmx-users] Interaction_between_protein_small_molecule Justin A. Lemkul
[gmx-users] distance between two atoms of diff protein residue Justin A. Lemkul
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file Justin A. Lemkul
[gmx-users] all_force.xvg Justin A. Lemkul
[gmx-users] Signal: Segmentation faul Justin A. Lemkul
[gmx-users] NPT Justin A. Lemkul
[gmx-users] NPT Justin A. Lemkul
[gmx-users] g_sas values for peptide in water and in DPC micelle Justin A. Lemkul
[gmx-users] g_mindist Justin A. Lemkul
[gmx-users] percentage of secondary structure Justin A. Lemkul
[gmx-users] help regarding simulation Justin A. Lemkul
[gmx-users] percentage of secondary structure Justin A. Lemkul
[gmx-users] percentage of secondary structure Justin A. Lemkul
[gmx-users] CNT Justin A. Lemkul
[gmx-users] g_sdf Justin A. Lemkul
[gmx-users] Library file in.m2p not found Justin A. Lemkul
[gmx-users] HFIP solvent box... Justin A. Lemkul
[gmx-users] How to include FE2+ in ions.itp ? Justin A. Lemkul
[gmx-users] md simulation for ternary complex Justin A. Lemkul
[gmx-users] problem running the demo Justin A. Lemkul
[gmx-users] Question Justin A. Lemkul
[gmx-users] methanol simulation Justin A. Lemkul
[gmx-users] methanol simulation error Justin A. Lemkul
[gmx-users] trjconv with multiple chains problem Justin A. Lemkul
[gmx-users] Re: methanol simulation error Justin A. Lemkul
[gmx-users] number of index elements not multiple of 3, these can not be angle triplet Justin A. Lemkul
[gmx-users] trjconv with multiple chains Justin A. Lemkul
[gmx-users] To make continuous trj in REMD Justin A. Lemkul
[gmx-users] To make continuous trj in REMD Justin A. Lemkul
[gmx-users] Re: Re: methanol simulation error Justin A. Lemkul
[gmx-users] To make continuous trj in REMD Justin A. Lemkul
[gmx-users] Requesting advice on pressure scaling in a protein-in-membrane system. Justin A. Lemkul
[gmx-users] justin Justin A. Lemkul
[gmx-users] Ubuntu Installation Justin A. Lemkul
[gmx-users] Ubuntu Installation Justin A. Lemkul
[gmx-users] Ubuntu Installation Justin A. Lemkul
[gmx-users] problem running the demo Justin A. Lemkul
[gmx-users] temperature of different atom groups in the system Justin A. Lemkul
[gmx-users] g_density CHARMM Justin A. Lemkul
[gmx-users] g_density CHARMM Justin A. Lemkul
[gmx-users] file heme.rtp Justin A. Lemkul
[gmx-users] query for binding energy Justin A. Lemkul
[gmx-users] Add bridging residue Justin A. Lemkul
Sv: Re: [gmx-users] Add bridging residue Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] extending the simulation with modified mdp option Justin A. Lemkul
[gmx-users] topoloy for CNT Justin A. Lemkul
[gmx-users] creating mdrun_mpi with cmake Justin A. Lemkul
[gmx-users] galactose Justin A. Lemkul
[gmx-users] galactose Justin A. Lemkul
[gmx-users] Installing multiple versions of GROMACS together? - program suffix Justin A. Lemkul
[gmx-users] Installing multiple versions of GROMACS together? - program suffix Justin A. Lemkul
[gmx-users] Installing multiple versions of GROMACS together? - program suffix Justin A. Lemkul
[gmx-users] extending the simulation with modified mdp option Justin A. Lemkul
[gmx-users] Error when execute g_energy - the message: not recognized, maybe different CPU? Justin A. Lemkul
[gmx-users] Error when execute g_energy - the message: not recognized, maybe different CPU? Justin A. Lemkul
[gmx-users] Re: pdb2gmx: segmentation fault Justin A. Lemkul
[gmx-users] Re: pdb2gmx: segmentation fault Justin A. Lemkul
[gmx-users] Re: pdb2gmx: segmentation fault Justin A. Lemkul
[gmx-users] g_analyze with multiple sets Justin A. Lemkul
[gmx-users] so difficult problem Justin A. Lemkul
[gmx-users] CNT Justin A. Lemkul
[gmx-users] problem with LINCS Justin A. Lemkul
[gmx-users] Position restraint problem Justin A. Lemkul
[gmx-users] Energy minimization Justin A. Lemkul
[gmx-users] so difficult problem Justin A. Lemkul
[gmx-users] Non integral charges Justin A. Lemkul
[gmx-users] Viscosity calculations Justin A. Lemkul
[gmx-users] Re: Non integral charges Justin A. Lemkul
[gmx-users] galactose bond stretch Justin A. Lemkul
[gmx-users] galactose bond stretch Justin A. Lemkul
[gmx-users] ACPYPE download Justin A. Lemkul
[gmx-users] Re:Viscosity calculations Justin A. Lemkul
[gmx-users] spurious forces while doing pulling simulation Justin A. Lemkul
[gmx-users] problem running the demo Justin A. Lemkul
[gmx-users] Segmentation Fault in EM Justin A. Lemkul
[gmx-users] Segmentation Fault in EM Justin A. Lemkul
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. Justin A. Lemkul
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. Justin A. Lemkul
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. Justin A. Lemkul
[gmx-users] spurious forces while doing pulling simulation Justin A. Lemkul
[gmx-users] spurious forces while doing pulling simulation Justin A. Lemkul
[gmx-users] spurious forces while doing pulling simulation Justin A. Lemkul
[gmx-users] potential energy value Justin A. Lemkul
[gmx-users] Equilibration Justin A. Lemkul
[gmx-users] GROMOS96 topology for small molecule Justin A. Lemkul
[gmx-users] Re:Re: CNT Justin A. Lemkul
[gmx-users] Heme group in the forcefield gromos53a6 Justin A. Lemkul
[gmx-users] CNT Justin A. Lemkul
[gmx-users] grompp error Justin A. Lemkul
[gmx-users] PRODRG server Justin A. Lemkul
[gmx-users] the final structure Justin A. Lemkul
[gmx-users] Help with the heme group in forcefield gromos53a6 Justin A. Lemkul
[gmx-users] Re: Problem in Disulfide Bond Justin A. Lemkul
[gmx-users] CNT Justin A. Lemkul
[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3 Justin A. Lemkul
[gmx-users] Re: Problem in Disulfide Bond Justin A. Lemkul
[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3 Justin A. Lemkul
[gmx-users] QM/MM viewer (was: CNT) Justin A. Lemkul
[gmx-users] Re: avoiding bad contact in continutation run (Mark Abraham) Justin A. Lemkul
[gmx-users] How to install a new Forcefield in Gromacs 4.5.3 Justin A. Lemkul
[gmx-users] avoiding bad contact in continutation run Justin A. Lemkul
[gmx-users] How to install a new Forcefield in Gromacs 4.5.3 Justin A. Lemkul
[gmx-users] How to install a new Forcefield in Gromacs 4.5.3 Justin A. Lemkul
[gmx-users] How to create an rtp file for a lipid? Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] Inaccurate pressure readings Justin A. Lemkul
[gmx-users] Inaccurate pressure readings Justin A. Lemkul
[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3 Justin A. Lemkul
[gmx-users] Inaccurate pressure readings Justin A. Lemkul
[gmx-users] Running a crashed run Justin A. Lemkul
[gmx-users] How to install a new Forcefield in Gromacs 4.5.3 Justin A. Lemkul
[gmx-users] How to install a new Forcefield in Gromacs 4.5.3 Justin A. Lemkul
[gmx-users] How to install a new Forcefield in Gromacs 4.5.3 Justin A. Lemkul
[gmx-users] Regarding g_analyze Justin A. Lemkul
[gmx-users] Regarding g_analyze Justin A. Lemkul
[gmx-users] Visualizing the simulation in VMD Justin A. Lemkul
[gmx-users] Regarding g_analyze Justin A. Lemkul
[gmx-users] Visualizing the simulation in VMD Justin A. Lemkul
[gmx-users] Fwd: RMSD calculation of a specific region Justin A. Lemkul
[gmx-users] charge group radii larger that rlist-rvdw Justin A. Lemkul
[gmx-users] fatal error Justin A. Lemkul
[gmx-users] Error in generating DPPC using grompp Justin A. Lemkul
[gmx-users] Gromacs 4 cannot reach Fmax in energy minimisation when version 3 did Justin A. Lemkul
[gmx-users] charge group radii larger that rlist-rvdw Justin A. Lemkul
[gmx-users] RNA with small molecule Justin A. Lemkul
[gmx-users] RNA with small molecule Justin A. Lemkul
[gmx-users] fatal error Justin A. Lemkul
[gmx-users] fatal error Justin A. Lemkul
[gmx-users] Fwd: RMSD calculation of a specific region Justin A. Lemkul
[gmx-users] charge group radii larger that rlist-rvdw Justin A. Lemkul
[gmx-users] charge group radii larger that rlist-rvdw Justin A. Lemkul
[gmx-users] PRODRG server Justin A. Lemkul
[gmx-users] PRODRG server Justin A. Lemkul
[gmx-users] charge group radii larger that rlist-rvdw Justin A. Lemkul
[gmx-users] fatal error Justin A. Lemkul
[gmx-users] fatal error Justin A. Lemkul
[gmx-users] Swiss pdb viewer Justin A. Lemkul
[gmx-users] using Berger Lipids in gromacs 4.5.3 Justin A. Lemkul
[gmx-users] adding of a new force field in gromacs 4.5.1 Justin A. Lemkul
[gmx-users] charge group radii larger that rlist-rvdw Justin A. Lemkul
[gmx-users] Re: Secondary structure loss in implicit solvent simulations Justin A. Lemkul
[gmx-users] Gromos96 manual and user guid Justin A. Lemkul
[gmx-users] PRODRG server Justin A. Lemkul
[gmx-users] Error in generating DPPC using grompp Justin A. Lemkul
[gmx-users] Atomtype HW not found when using grompp for energy minimization Justin A. Lemkul
[gmx-users] using Berger Lipids in gromacs 4.5.3 Justin A. Lemkul
[gmx-users] PRODRG server Justin A. Lemkul
[gmx-users] using Berger Lipids in gromacs 4.5.3 Justin A. Lemkul
[gmx-users] cannot rename checkpoint file Justin A. Lemkul
[gmx-users] mdrun_mpi executable not found Justin A. Lemkul
[gmx-users] using Berger Lipids in gromacs 4.5.3 Justin A. Lemkul
[gmx-users] mdrun_mpi executable not found Justin A. Lemkul
[gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97 Justin A. Lemkul
[gmx-users] compiling error in tools Justin A. Lemkul
[gmx-users] segmentation fault while running eneconv Justin A. Lemkul
[gmx-users] Umbrella Sampling for a single molecule Justin A. Lemkul
[gmx-users] Re: segmentation fault while running eneconv Justin A. Lemkul
[gmx-users] Two machines, same job, one fails Justin A. Lemkul
[gmx-users] Two machines, same job, one fails Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97 Justin A. Lemkul
[gmx-users] validation of ligand parametrization Justin A. Lemkul
[gmx-users] Re: Re: segmentation fault while running eneconv Justin A. Lemkul
[gmx-users] grompp charge group radii larger than rlist Justin A. Lemkul
[gmx-users] mdrun_mpi executable not found Justin A. Lemkul
[gmx-users] Re: change in the secondary structure after simulation Justin A. Lemkul
[gmx-users] gro to itp Justin A. Lemkul
[gmx-users] Re: change in the secondary structure after simulation Justin A. Lemkul
[gmx-users] proton proton exchange and constant pH simulations. Justin A. Lemkul
[gmx-users] Re: change in the secondary structure after simulation Justin A. Lemkul
[gmx-users] remove all waters from the pdb file Justin A. Lemkul
[gmx-users] Re: change in the secondary structure after simulation Justin A. Lemkul
[gmx-users] solvation_box_preparation Justin A. Lemkul
[gmx-users] protein movement in lipid bilayer during simulation Justin A. Lemkul
[gmx-users] Slow Runs Justin A. Lemkul
[gmx-users] Output error mpirun/mdrun_mpi Justin A. Lemkul
[gmx-users] g_mindist clarification Justin A. Lemkul
[gmx-users] how to define the box when protein protruding out of the lipid bi layer membrane Justin A. Lemkul
[gmx-users] sum of largest charge group radii Justin A. Lemkul
[gmx-users] sum of largest charge group radii Justin A. Lemkul
[gmx-users] change in secondary structure after npt equilibration Justin A. Lemkul
[gmx-users] sum of largest charge group radii Justin A. Lemkul
[gmx-users] change in secondary structure after npt equilibration Justin A. Lemkul
[gmx-users] sum of largest charge group radii Justin A. Lemkul
[gmx-users] change in secondary structure after npt equilibration Justin A. Lemkul
[gmx-users] change in secondary structure after npt equilibration Justin A. Lemkul
[gmx-users] Slow Runs Justin A. Lemkul
[gmx-users] Slow Runs Justin A. Lemkul
[gmx-users] Slow Runs Justin A. Lemkul
[gmx-users] Slow Runs Justin A. Lemkul
[gmx-users] Slow Runs Justin A. Lemkul
[gmx-users] Slow Runs Justin A. Lemkul
[gmx-users] Slow Runs Justin A. Lemkul
[gmx-users] Slow Runs Justin A. Lemkul
[gmx-users] Slow Runs Justin A. Lemkul
[gmx-users] Slow Runs Justin A. Lemkul
[gmx-users] Missing Amino Acids Justin A. Lemkul
[gmx-users] mdrun with append option Justin A. Lemkul
[gmx-users] mdrun with append option Justin A. Lemkul
[gmx-users] ngmx doesnot work; CH3-CH2-OH Justin A. Lemkul
[gmx-users] luck Justin A. Lemkul
[gmx-users] solvation_box_preparation Justin A. Lemkul
[gmx-users] luck Justin A. Lemkul
[gmx-users] luck Justin A. Lemkul
[gmx-users] local pressure calcuation for Gromacs-4.5 Jianguo Li
[gmx-users] Viscosity calculations Xiaohu Li
[gmx-users] Re:Viscosity calculations Xiaohu Li
[gmx-users] Important: Bugs in NEMD calculation Xiaohu Li
[gmx-users] RE: Important: Bugs in NEMD calculation Xiaohu Li
[gmx-users] Re: gmx-users Digest, Vol 81, Issue 130 Xiaohu Li
[gmx-users] RE: Important: Bugs in NEMD calculation Xiaohu Li
[gmx-users] QMMM with ORCA Xiaohu Li
[gmx-users] Re: mdrun_mpi executable not found Xiaohu Li
[gmx-users] Re: QMMM with ORCA Xiaohu Li
[gmx-users] QMMM with ORCA Xiaohu Li
[gmx-users] Re: QMMM with ORCA Xiaohu Li
[gmx-users] ZN2+ qtot 1.233e-06 ? Chih-Ying Lin
[gmx-users] ZN2+ qtot 1.233e-06 ? Chih-Ying Lin
[gmx-users] Warning about (short) potential interruption - moving DNS servers for gromacs.org Erik Lindahl
[gmx-users] CG to FG transformation error Martti Louhivuori
[gmx-users] Requesting advice on pressure scaling in a protein-in-membrane system. Daniel Adriano Silva M
[gmx-users] Energy minimization - single/double precision Kavyashree M
[gmx-users] Doubts regarding Simulation box Kavyashree M
[gmx-users] Doubts regarding Simulation box - Thanks Kavyashree M
[gmx-users] Density of the box Kavyashree M
[gmx-users] Doubts regarding Simulation box - Thanks Kavyashree M
[gmx-users] Non integral charges Kavyashree M
[gmx-users] Non integral charges Kavyashree M
[gmx-users] charge group radii larger that rlist-rvdw Kavyashree M
[gmx-users] charge group radii larger that rlist-rvdw Kavyashree M
[gmx-users] charge group radii larger that rlist-rvdw Kavyashree M
[gmx-users] charge group radii larger that rlist-rvdw Kavyashree M
[gmx-users] charge group radii larger that rlist-rvdw Kavyashree M
[gmx-users] charge group radii larger that rlist-rvdw Kavyashree M
[gmx-users] charge group radii larger that rlist-rvdw Kavyashree M
[gmx-users] how to simulate linear rigid rod Sanku M
[gmx-users] proton proton exchange and constant pH simulations. Miguel Machuqueiro
[gmx-users] adding of a new force field in gromacs 4.5.1 mina Madah
[gmx-users] adding of a new force field in gromacs 4.5.1 mina Madah
[gmx-users] Ubuntu Installation Sergio Manzetti
[gmx-users] Ubuntu Installation Sergio Manzetti
[gmx-users] Ubuntu Installation Sergio Manzetti
[gmx-users] Mesa GLproto stuff UBUNTU Sergio Manzetti
[gmx-users] QM/MM viewer Sergio Manzetti
[gmx-users] Fwd: Viewing results from Groamcs QM/MM sims Sergio Manzetti
[gmx-users] Radial distribution function in gromacs Sergio Manzetti
[gmx-users] problem running the demo Mao Mao
[gmx-users] problem running the demo Mao Mao
[gmx-users] problem running the demo Mao Mao
[gmx-users] segmentation fault while running eneconv Anna Marabotti
[gmx-users] Re: Re: segmentation fault while running eneconv Anna Marabotti
[gmx-users] Ion-Clustering? Erik Marklund
[gmx-users] ion jumping out of water box Erik Marklund
[gmx-users] Simulations in vacuo Erik Marklund
[gmx-users] Re : genion Erik Marklund
[gmx-users] Non integral charges Erik Marklund
[gmx-users] Slow Runs Erik Marklund
[gmx-users] Slow Runs Erik Marklund
[gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ? David McGiven
[gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ? David McGiven
[gmx-users] Sampling windows Gavin Melaugh
[gmx-users] Sampling windows Gavin Melaugh
[gmx-users] Sampling windows Gavin Melaugh
[gmx-users] Sampling windows Gavin Melaugh
[gmx-users] PMF using constraints Gavin Melaugh
[gmx-users] Constraint pulling Gavin Melaugh
[gmx-users] Gromacs 4 cannot reach Fmax in energy minimisation when version 3 did Gavin Melaugh
[gmx-users] Pull code Gavin Melaugh
[gmx-users] sum of largest charge group radii Gavin Melaugh
[gmx-users] sum of largest charge group radii Gavin Melaugh
[gmx-users] sum of largest charge group radii Gavin Melaugh
[gmx-users] sum of largest charge group radii Gavin Melaugh
[gmx-users] Using g_select to detect water pores in a bilayer Manuel Nuno Melo
[gmx-users] avoiding bad contact in continutation run Adwait Mevada
[gmx-users] Re: avoiding bad contact in continutation run (Mark Abraham) Adwait Mevada
[gmx-users] Re: gmx-users Digest, Vol 81, Issue 140 Adwait Mevada
[gmx-users] Re: avoiding bad contact in continutation run (Mark Abraham) Adwait Mevada
[gmx-users] transmembrane protein simulation Krzysztof Mlynarczyk
[gmx-users] Using g_select to detect water pores in a bilayer Teemu Murtola
[gmx-users] Segmentation Fault in EM TJ Mustard
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. TJ Mustard
[gmx-users] Segmentation Fault in EM TJ Mustard
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. TJ Mustard
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. TJ Mustard
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. TJ Mustard
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. TJ Mustard
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. TJ Mustard
[gmx-users] table-extension in mdp ?! TJ Mustard
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. TJ Mustard
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. TJ Mustard
[gmx-users] Two machines, same job, one fails TJ Mustard
[gmx-users] Two machines, same job, one fails TJ Mustard
[gmx-users] Two machines, same job, one fails TJ Mustard
[gmx-users] Two machines, same job, one fails TJ Mustard
[gmx-users] Two machines, same job, one fails TJ Mustard
[gmx-users] Waterbox simulation on GPU Christian Mötzing
[gmx-users] Waterbox simulation on GPU Christian Mötzing
[gmx-users] Waterbox simulation on GPU Christian Mötzing
[gmx-users] Box size and potential energy calculation Christian Mötzing
[gmx-users] Box size and potential energy calculation Christian Mötzing
[gmx-users] Box size and potential energy calculation Christian Mötzing
[gmx-users] GPU gets faster with more molecules in system Christian Mötzing
[gmx-users] Thiazolidinedione Tautomers Nancy
[gmx-users] Thiazolidinedione Tautomers Nancy
[gmx-users] Pioglitazone Tautomers Nancy
[gmx-users] Tautomer Prediction Nancy
[gmx-users] TZD Tautomers Nancy
[gmx-users] TZD Tautomer Distribution Nancy
[gmx-users] Slow Runs Chris Neale
[gmx-users] RB Dihedrals with ffamber96 in Gromacs 4.5.3? RJ Nowling
[gmx-users] Simulations on GPU Francesco Oteri
[gmx-users] Simulations on GPU Francesco Oteri
[gmx-users] t_fileio has initializer but incomplete type? (xtcio.h) T. Paramo
[gmx-users] Sampling windows XAvier Periole
[gmx-users] Sampling windows XAvier Periole
[gmx-users] Sampling windows XAvier Periole
Antw: Re: [gmx-users] total charge of the system Emanuel Peter
[gmx-users] galactose bond stretch Thomas Piggot
[gmx-users] galactose bond stretch Thomas Piggot
[gmx-users] N-acetyl-d-glucosamine parameters Thomas Piggot
[gmx-users] grompp charge group radii larger than rlist Thomas Piggot
[gmx-users] Re: change in the secondary structure after simulation Thomas Piggot
[gmx-users] order parameters of partially unsaturated chains Ángel Piñeiro
[gmx-users] order parameters of partially unsaturated chains Ángel Piñeiro
[gmx-users] Perfluorohexane Ángel Piñeiro
[gmx-users] perfluorohexane pdb... again Ángel Piñeiro
[gmx-users] perfluorohexane pdb... again Ángel Piñeiro
[gmx-users] perfluorohexane pdb... again Ángel Piñeiro
[gmx-users] perfluorohexane pdb... again Ángel Piñeiro
[gmx-users] Umbrella Sampling for a single molecule Sai Pooja
[gmx-users] mdrun with append option Sai Pooja
[gmx-users] mdrun with append option Sai Pooja
[gmx-users] mdrun with append option Sai Pooja
[gmx-users] mdrun with append option Sai Pooja
[gmx-users] mdrun with append option Sai Pooja
[gmx-users] Ubuntu Installationync-mailbox><next-undeleted><enter-command>set editor=vim Manuel Prinz
[gmx-users] When will FEP be on GPU? Szilárd Páll
[gmx-users] Dell PowerEdge M710 with Intel Xeon 5667 processor Szilárd Páll
[gmx-users] Dell PowerEdge M710 with Intel Xeon 5667 processor Szilárd Páll
[gmx-users] Need help troubleshooting an mdrun-gpu error message! Szilárd Páll
[gmx-users] To make continuous trj in REMD Qin Qiao
[gmx-users] To make continuous trj in REMD Qin Qiao
[gmx-users] To make continuous trj in REMD Qin Qiao
[gmx-users] Nose-hoover T-coupling in REMD Qin Qiao
[gmx-users] To make continuous trj in REMD Qin Qiao
[gmx-users] How to install a new Forcefield in Gromacs 4.5.3 Qin Qiao
[gmx-users] How to install a new Forcefield in Gromacs 4.5.3 Qin Qiao
[gmx-users] How to install a new Forcefield in Gromacs 4.5.3 Qin Qiao
[gmx-users] How to install a new Forcefield in Gromacs 4.5.3 Qin Qiao
[gmx-users] How to install a new Forcefield in Gromacs 4.5.3 Qin Qiao
[gmx-users] How to install a new Forcefield in Gromacs 4.5.3 Qin Qiao
[gmx-users] Installing Gromacs with Cygwin Mr Bernard Ramos
[gmx-users] luck Mr Bernard Ramos
[gmx-users] luck Mr Bernard Ramos
[gmx-users] luck Mr Bernard Ramos
[gmx-users] luck Mr Bernard Ramos
[gmx-users] Problem with using topolbuild1_3.tgz Bruce D. Ray
[gmx-users]Fwd: GROMACS and GBSA implicit water Bruce D. Ray
[gmx-users] Re: Problem with using topolbuild1_3.tgz Bruce D. Ray
[gmx-users] QMMM with ORCA Christoph Riplinger
[gmx-users] XTC file not being created, while TRR file is João Rodrigues
[gmx-users] Re: XTC file not being created, while TRR file is João Rodrigues
[gmx-users] trjconv -fit rot+trans before a pbc? safe way to rotate a trajectory? Roland Schulz
[gmx-users] can i run .tpr using Gromacs 4.5.3(has parallel) in cluster computer; the .tpr was created using gromacs 4.0.7 in my desktop (without parallel) Roland Schulz
[gmx-users] divergent energy minimization results from identical starting system Roland Schulz
[gmx-users] More than one settle type Shalabh
[gmx-users] Happy new year Hassan Shallal
[gmx-users] Secondary structure loss in implicit solvent simulations Michael Shirts
[gmx-users] Re: Secondary structure loss in implicit solvent simulations Michael Shirts
[gmx-users] Re: Secondary structure loss in implicit solvent simulations Michael Shirts
[gmx-users] Re: [ atomtypes ] are not case sensitive? Alan Wilter Sousa da Silva
[gmx-users] Trifluoroethanol-Ethanol mixtures study Marcelo Silva
[gmx-users] Trifluoroethanol-Ethanol mixtures study Marcelo Silva
[gmx-users] Perfluorohexane Marcelo Silva
[gmx-users] perfluorohexane pdb... again Marcelo Silva
[gmx-users] perfluorohexane pdb... again Marcelo Silva
[gmx-users] perfluorohexane pdb... again Marcelo Silva
[gmx-users] perfluorohexane pdb... again Marcelo Silva
[gmx-users] Position restraint problem Marcelo Silva
[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm. Marcelo Silva
[gmx-users] Position restraint problem Marcelo Silva
[gmx-users] Secondary structure loss in implicit solvent simulations K. Singhal
[gmx-users] Re: Secondary structure loss in implicit solvent simulations K. Singhal
[gmx-users] Re: Secondary structure loss in implicit solvent simulations K. Singhal
[gmx-users] Ion-Clustering? Micholas Smith
[gmx-users] Query for RMSD Archana Sonawani
[gmx-users] how to simulate linear rigid rod David van der Spoel
[gmx-users] Constraints and efficency David van der Spoel
[gmx-users] truncated LJ potential David van der Spoel
[gmx-users] Re: Calculating lattice enegies for molecular crystals David van der Spoel
[gmx-users] Re: question on implicit membrane in gromacs David van der Spoel
[gmx-users] Re: Contstraints = all-angles David van der Spoel
[gmx-users] Important: Bugs in NEMD calculation David van der Spoel
[gmx-users] Important: Bugs in NEMD calculation David van der Spoel
[gmx-users] dipole moment David van der Spoel
[gmx-users] dipole moment David van der Spoel
[gmx-users] specific heat David van der Spoel
[gmx-users] energy minimization of a charged system in vacuum David van der Spoel
[gmx-users] energy minimization of a charged system in vacuum David van der Spoel
[gmx-users] electron density Jianhui Tian
[gmx-users] electron density Jianhui Tian
[gmx-users] electron density Jianhui Tian
[gmx-users] ACPYPE download Jianhui Tian
[gmx-users] ACPYPE download Jianhui Tian
[gmx-users] ACPYPE download Jianhui Tian
[gmx-users] van der Walls radius and implicit solvation Diogo Vila Viçosa
[gmx-users] using Berger Lipids in gromacs 4.5.3 NG HUI WEN
[gmx-users] using Berger Lipids in gromacs 4.5.3 NG HUI WEN
[gmx-users] using Berger Lipids in gromacs 4.5.3 NG HUI WEN
[gmx-users] using Berger Lipids in gromacs 4.5.3 NG HUI WEN
[gmx-users] using Berger Lipids in gromacs 4.5.3 NG HUI WEN
[gmx-users] nstcomm set to 10 NG HUI WEN
[gmx-users] methanol simulation error Dallas Warren
[gmx-users] Pioglitazone Tautomers Dallas Warren
[gmx-users] CNT Dallas Warren
[gmx-users] Inaccurate pressure readings Dallas Warren
[gmx-users] Inaccurate pressure readings Dallas Warren
[gmx-users] Visualizing the simulation in VMD Dallas Warren
[gmx-users] Slow Runs Dallas Warren
[gmx-users] Major code reorganization in git coming up Tsjerk Wassenaar
[gmx-users] Optimization of the box size during an energy minimization? Tsjerk Wassenaar
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file Tsjerk Wassenaar
[gmx-users] Average box size Tsjerk Wassenaar
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file Tsjerk Wassenaar
[gmx-users] Re: Average box size Tsjerk Wassenaar
[gmx-users] Re: Average box size Tsjerk Wassenaar
[gmx-users] Re:Re: Re: Average box size Tsjerk Wassenaar
[gmx-users] so difficult problem Tsjerk Wassenaar
[gmx-users] Pioglitazone Tautomers Tsjerk Wassenaar
[gmx-users] ion jumping out of water box Tsjerk Wassenaar
[gmx-users] Density of the box Tsjerk Wassenaar
[gmx-users] trjconv -fit rot+trans before a pbc? safe way to rotate a trajectory? Tsjerk Wassenaar
[gmx-users] so difficult problem Tsjerk Wassenaar
[gmx-users] so difficult problem Tsjerk Wassenaar
[gmx-users] Doubts regarding Simulation box Tsjerk Wassenaar
[gmx-users] pdb2gmx: segmentation fault Tsjerk Wassenaar
[gmx-users] Doubts regarding Simulation box - Thanks Tsjerk Wassenaar
[gmx-users] TZD Tautomers Tsjerk Wassenaar
[gmx-users] g_covar Tsjerk Wassenaar
[gmx-users] TZD Tautomer Distribution Tsjerk Wassenaar
[gmx-users] doubts on g_confrms output Tsjerk Wassenaar
[gmx-users] Can not open file: run.xtc Tsjerk Wassenaar
[gmx-users] remove all waters from the pdb file Tsjerk Wassenaar
[gmx-users] Eigenvectors Tsjerk Wassenaar
[gmx-users] Count the number of contacts between two proteins + pbc artifacts Tsjerk Wassenaar
[gmx-users] compiling error in tools Jennifer Williams
[gmx-users] Simulation time losses with REMD Martyn Winn
[gmx-users] Center of mass motion removal for partial filled PBC box WU Yanbin
[gmx-users] Eigenvectors Yao Yao
[gmx-users] Eigenvectors Yao Yao
[gmx-users] Eigenvectors Yao Yao
[gmx-users] truncated LJ potential Makoto Yoneya
[gmx-users] truncated LJ potential Makoto Yoneya
[gmx-users] truncated LJ potential Makoto Yoneya
[gmx-users] truncated LJ potential Makoto Yoneya
[gmx-users] truncated LJ potential Makoto Yoneya
[gmx-users] truncated LJ potential Makoto Yoneya
[gmx-users] Signal: Segmentation faul shikha agarwal
[gmx-users] error in ffgmxbon.itp delara aghaie
[gmx-users] GBSA implicit model and atom type anna
[gmx-users] PME parameter in GROMACS aldi asmadi
[gmx-users] CNT mustafa bilsel
[gmx-users] methanol simulation mustafa bilsel
[gmx-users] methanol simulation mustafa bilsel
[gmx-users] methanol simulation error mustafa bilsel
[gmx-users] Re: methanol simulation error mustafa bilsel
[gmx-users] Re: Re: methanol simulation error mustafa bilsel
[gmx-users] justin mustafa bilsel
[gmx-users] cannot rename checkpoint file ram bio
[gmx-users] protein movement in lipid bilayer during simulation ram bio
[gmx-users] protein movement in lipid bilayer during simulation ram bio
[gmx-users] Atomype HW not found trevor brown
[gmx-users] Atomtpe HW not found-2 trevor brown
[gmx-users] Water models usage info trevor brown
[gmx-users] topoloy for CNT trevor brown
[gmx-users] CNT trevor brown
[gmx-users] CNT trevor brown
[gmx-users] Re:Re: CNT trevor brown
[gmx-users] CNT trevor brown
[gmx-users] grompp error trevor brown
[gmx-users] CNT trevor brown
[gmx-users] CNT trevor brown
[gmx-users] (no subject) trevor brown
[gmx-users] (no subject) trevor brown
[gmx-users] gro to itp trevor brown
Re: [gmx-users] NPT wibke.sudholt at cloudbroker.com
Re: Re: [gmx-users] Trifluoroethanol-Ethanol mixtures study wibke.sudholt at cloudbroker.com
Re: [gmx-users] CNT wibke.sudholt at cloudbroker.com
Re: Re: [gmx-users] Questions concerning Gromacs wibke.sudholt at cloudbroker.com
Re: [gmx-users] methanol simulation error wibke.sudholt at cloudbroker.com
Re: Re: [gmx-users] g_msd Utility - (Unexpected) Different Results Depending on Output Flag wibke.sudholt at cloudbroker.com
Re: Re: [gmx-users] Nose-hoover T-coupling in REMD wibke.sudholt at cloudbroker.com
Re: [gmx-users] Pioglitazone Tautomers wibke.sudholt at cloudbroker.com
[gmx-users] Re: trjconv with multiple chains devicerandom
[gmx-users] Waterbox simulation on GPU devicerandom
[gmx-users] Installing multiple versions of GROMACS together? - program suffix devicerandom
[gmx-users] Installing multiple versions of GROMACS together? - program suffix devicerandom
[gmx-users] Installing multiple versions of GROMACS together? - program suffix devicerandom
[gmx-users] change in secondary structure after npt equilibration sonali dhindwal
[gmx-users] query for protein-igand binding energy calculation using LIE and Gromacs simulation devawati dutta
[gmx-users] Query about use of coulombtype for LIE in gromacs devawati dutta
[gmx-users] query for binding energy devawati dutta
[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3 maria goranovic
[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3 maria goranovic
[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3 maria goranovic
[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3 maria goranovic
[gmx-users] How to get sufactant.gro, sufactant.top, gromacs
[gmx-users] Re:Re: How to get sufactant.gro, sufactant.top, (Mark Abraham) gromacs
[gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97 gromacs
[gmx-users] Fw:Re:gmx-users Digest, Vol 81, Issue 192; PME, Estimate for the relative gromacs
[gmx-users] can i run .tpr using Gromacs 4.5.3(has parallel) in cluster computer; the .tpr was created using gromacs 4.0.7 in my desktop (without parallel) gromacs
[gmx-users] ngmx doesnot work; CH3-CH2-OH gromacs
[gmx-users] grompp error bharat gupta
[gmx-users] Energy minimization bharat gupta
[gmx-users] Energy minimization bharat gupta
[gmx-users] Energy minimization bharat gupta
[gmx-users] Re : genion bharat gupta
[gmx-users] eNERGY mINIMIZATION bharat gupta
[gmx-users] eNERGY mINIMIZATION bharat gupta
[gmx-users] Equilibration bharat gupta
[gmx-users] running a crashed run bharat gupta
[gmx-users] running a crashed run bharat gupta
[gmx-users] Running a crashed run bharat gupta
[gmx-users] Regarding g_analyze bharat gupta
[gmx-users] Visualizing the simulation in VMD bharat gupta
[gmx-users] Regarding g_analyze bharat gupta
[gmx-users] Visualizing the simulation in VMD bharat gupta
[gmx-users] RE: RMSD calculation of a specific region bharat gupta
[gmx-users] Fwd: RMSD calculation of a specific region bharat gupta
[gmx-users] Fwd: RMSD calculation of a specific region bharat gupta
[gmx-users] RE: stopping a simulation in between without crashing any trajectories bharat gupta
[gmx-users] Re: change in the secondary structure after simulation bharat gupta
[gmx-users] Re: change in the secondary structure after simulation bharat gupta
[gmx-users] Re: change in the secondary structure after simulation bharat gupta
[gmx-users] Re: change in the secondary structure after simulation bharat gupta
[gmx-users] Re: change in the secondary structure after simulation bharat gupta
[gmx-users] Re: change in the secondary structure after simulation bharat gupta
[gmx-users] Re : Change in secondary structure during the npt equilibration bharat gupta
[gmx-users] change in secondary structure after npt equilibration bharat gupta
[gmx-users] change in secondary structure after npt equilibration bharat gupta
[gmx-users] change in secondary structure after npt equilibration bharat gupta
[gmx-users] Monitoring the water movement during simulation bharat gupta
[gmx-users] Monitoring the water movement during simulation bharat gupta
Fwd: [gmx-users] Monitoring the water movement during simulation bharat gupta
Fwd: [gmx-users] Monitoring the water movement during simulation bharat gupta
Fwd: [gmx-users] Monitoring the water movement during simulation bharat gupta
Fwd: [gmx-users] Monitoring the water movement during simulation bharat gupta
Fwd: [gmx-users] Monitoring the water movement during simulation bharat gupta
Fwd: [gmx-users] Monitoring the water movement during simulation bharat gupta
Fwd: [gmx-users] Monitoring the water movement during simulation bharat gupta
[gmx-users] Re: segmentation fault while running eneconv anna.marabotti at isa.cnr.it
[gmx-users] md simulation for ternary complex kala
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file leila karami
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file leila karami
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc message leila karami
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file leila karami
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file leila karami
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file leila karami
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file leila karami
[gmx-users] g_covar shahrbanoo karbalaee
[gmx-users] g_covar shahrbanoo karbalaee
[gmx-users] pdb2gmx error_ resall.c, line: 321 udaya kiran
[gmx-users] pdb2gmx error_ resall.c, line: 321 udaya kiran
[gmx-users] transmembrane protein simulation Mohana lakshmi
[gmx-users] transmembrane protein simulation Mohana lakshmi
[gmx-users] transmembrane protein simulation Mohana lakshmi
[gmx-users] inconsistent energies CPU vs GPU zhaowh at mail.ustc.edu.cn
[gmx-users] trjconv with multiple chains ms
[gmx-users] justin ms
[gmx-users] Geometry-dependent (non-spherically symmetric) potentials ms
[gmx-users] energy minimization of a charged system in vacuum ms
[gmx-users] energy minimization of a charged system in vacuum ms
[gmx-users] Interaction_between_protein_small_molecule shahid nayeem
[gmx-users] preparation_solvation_box shahid nayeem
[gmx-users] solvation_box shahid nayeem
[gmx-users] solvation_box shahid nayeem
[gmx-users] solvation_box shahid nayeem
[gmx-users] solvation_box_preparation shahid nayeem
[gmx-users] solvation_box_preparation shahid nayeem
[gmx-users] solvation_box_preparation shahid nayeem
[gmx-users] Re: Problem in Disulfide Bond parthiban at ncbs.res.in
[gmx-users] Re: gmx-users Digest, Vol 81, Issue 126 parthiban at ncbs.res.in
[gmx-users] Re: Problem in Disulfide Bond parthiban at ncbs.res.in
[gmx-users] Re: Problem in Disulfide Bond parthiban at ncbs.res.in
[gmx-users] help regarding simulation onetwo
[gmx-users] The sum of the O-H distancesof the backbone hydrogen bonds ROH sreelakshmi ramesh
[gmx-users] distance between two atoms of diff protein residue sreelakshmi ramesh
[gmx-users] The sum of the O-H distancesof the backbone hydrogen bonds ROH sreelakshmi ramesh
[gmx-users] NPT mohsen ramezanpour
[gmx-users] NPT mohsen ramezanpour
[gmx-users] so difficult problem mohsen ramezanpour
[gmx-users] so difficult problem mohsen ramezanpour
[gmx-users] so difficult problem mohsen ramezanpour
[gmx-users] so difficult problem mohsen ramezanpour
[gmx-users] so difficult problem mohsen ramezanpour
[gmx-users] so difficult problem mohsen ramezanpour
[gmx-users] so difficult problem mohsen ramezanpour
[gmx-users] so difficult problem mohsen ramezanpour
[gmx-users] so difficult problem mohsen ramezanpour
[gmx-users] so difficult problem mohsen ramezanpour
[gmx-users] so difficult problem mohsen ramezanpour
[gmx-users] GROMOS96 topology for small molecule mohsen ramezanpour
[gmx-users] PRODRG server mohsen ramezanpour
[gmx-users] PRODRG server mohsen ramezanpour
[gmx-users] PRODRG server mohsen ramezanpour
[gmx-users] Gromos96 manual and user guid mohsen ramezanpour
[gmx-users] PRODRG server mohsen ramezanpour
[gmx-users] PRODRG server mohsen ramezanpour
[gmx-users] validation of ligand parametrization mohsen ramezanpour
[gmx-users] validation of ligand parametrization mohsen ramezanpour
[gmx-users] validation of ligand parametrization mohsen ramezanpour
[gmx-users] General MD question lloyd riggs
[gmx-users] Density of the box kavya at rishi.serc.iisc.ernet.in
[gmx-users] Density of the box kavya at rishi.serc.iisc.ernet.in
[gmx-users] Doubts regarding Simulation box kavya at rishi.serc.iisc.ernet.in
[gmx-users] Minimization-single or double precision kavya at rishi.serc.iisc.ernet.in
[gmx-users] (no subject) aish at rri.res.in
[gmx-users] g_sas values for peptide in water and in DPC micelle sa
[gmx-users] nanoparticles leila separdar
[gmx-users] segmentation fault leila separdar
[gmx-users] segmentation fault leila separdar
[gmx-users] segmentation error leila separdar
[gmx-users] specific heat leila separdar
[gmx-users] Missing Amino Acids simon sham
[gmx-users] HFIP solvent box... sharada
[gmx-users] Melting Temperatue ifat shub
[gmx-users] Count the number of contacts between two proteins + pbc artifacts ifat shub
[gmx-users] (no subject) harpreet singh
[gmx-users] Simulation time losses with REMD martyn.winn at stfc.ac.uk
[gmx-users] Atomtype HW not found when using grompp for energy minimization Parul tew
[gmx-users] how to define the box when protein protruding out of the lipid bi layer membrane Parul tew
[gmx-users] 4.5.3 Installation under Cygwin toma0052 at umn.edu
[gmx-users] 4.5.3 Installation under Cygwin toma0052 at umn.edu
[gmx-users] OPLS implicit solvent problems francesca.stanzione at unina.it
[gmx-users] (no subject) francesca.stanzione at unina.it
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc message chris.neale at utoronto.ca
[gmx-users] Umbrella sampling chris.neale at utoronto.ca
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc message chris.neale at utoronto.ca
[gmx-users] eordering of water molecules with Na+ ions coordinates in xtc file chris.neale at utoronto.ca
[gmx-users] creating mdrun_mpi with cmake chris.neale at utoronto.ca
[gmx-users] problem when calculating the solvation free energy of ARG in water using PME. chris.neale at utoronto.ca
[gmx-users] Melting Temperatue chris.neale at utoronto.ca
[gmx-users] creating mdrun_mpi with cmake chris.neale at utoronto.ca
[gmx-users] number of cores with a large prime factor chris.neale at utoronto.ca
[gmx-users] galactose nishap.patel at utoronto.ca
[gmx-users] galactose nishap.patel at utoronto.ca
[gmx-users] galactose nishap.patel at utoronto.ca
[gmx-users] galactose bond stretch nishap.patel at utoronto.ca
[gmx-users] galactose bond stretch nishap.patel at utoronto.ca
[gmx-users] Error in generating DPPC using grompp shobana visolingam
[gmx-users] histograms jalemkul at vt.edu
[gmx-users] ion jumping out of water box jalemkul at vt.edu
[gmx-users] histograms jalemkul at vt.edu
[gmx-users] histograms jalemkul at vt.edu
[gmx-users] perfluorohexane pdb jalemkul at vt.edu
[gmx-users] trjconv with multiple chains yuanyuan wang
[gmx-users] trjconv with multiple chains problem yuanyuan wang
[gmx-users] Re: trjconv with multiple chains yuanyuan wang
[gmx-users] percentage of secondary structure ahmet yıldırım
[gmx-users] percentage of secondary structure ahmet yıldırım
[gmx-users] percentage of secondary structure ahmet yıldırım
[gmx-users] percentage of secondary structure ahmet yıldırım
[gmx-users] percentage of secondary structure ahmet yıldırım
[gmx-users] percentage of secondary structure ahmet yıldırım
[gmx-users] Library file in.m2p not found ahmet yıldırım
[gmx-users] Library file in.m2p not found ahmet yıldırım
[gmx-users] Library file in.m2p not found ahmet yıldırım
[gmx-users] the calculation time ahmet yıldırım
[gmx-users] potential energy value ahmet yıldırım
[gmx-users] the final structure ahmet yıldırım
[gmx-users] fatal error ahmet yıldırım
[gmx-users] fatal error ahmet yıldırım
[gmx-users] fatal error ahmet yıldırım
[gmx-users] fatal error ahmet yıldırım
[gmx-users] fatal error ahmet yıldırım
[gmx-users] Swiss pdb viewer ahmet yıldırım
[gmx-users] total charge of the system ahmet yıldırım
[gmx-users] total charge of the system ahmet yıldırım
[gmx-users] total charge of the system ahmet yıldırım
[gmx-users] total charge of the system ahmet yıldırım
[gmx-users] Can not open file: run.xtc ahmet yıldırım
[gmx-users] Can not open file: run.xtc ahmet yıldırım
[gmx-users] nstcomm nstcalcenergy defeats the purpose of nstcalcenergy ahmet yıldırım
[gmx-users] remove all waters from the pdb file ahmet yıldırım
[gmx-users] remove all waters from the pdb file ahmet yıldırım
[gmx-users] ion jumping out of water box גדעון לפידות
[gmx-users] How to calculate rdf for some group respect to one reference axis 英雄不再寂寞

Last message date: Mon Jan 31 23:52:36 CET 2011
Archived on: Thu Nov 14 12:10:09 CET 2013

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