September 2011 Archives by author

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Starting: Thu Sep 1 02:12:40 CEST 2011
Ending: Fri Sep 30 19:30:46 CEST 2011
Messages: 685

[gmx-users] How to make a CG topology for a modified residue? Du Jiangfeng (BIOCH)
[gmx-users] Convert an unnormal residues contained protein from all-atoms model to coarse grained model. Du Jiangfeng (BIOCH)
[gmx-users] Problem when adding new residue in itp file Du Jiangfeng (BIOCH)
[gmx-users] Half double pair list method in GROMACS ABEL Stephane 175950
[gmx-users] Half double pair list method in GROMACS [update] ABEL Stephane 175950
[gmx-users] Calculation of the isothermal compressibility with g_energy for a box with different components. ABEL Stephane 175950
[gmx-users] Identifying representative structures from a g_sham generated 2d energy plot Bailey A.
[gmx-users] Identifying representative structures from a g_sham Bailey A.
[gmx-users] Re: which charge is used in gromacs program Mark Abraham
[gmx-users] GROMACS 4.5.4 keep crashing all the time Mark Abraham
[gmx-users] g_hbond Mark Abraham
[gmx-users] GROMACS 4.5.4 keep crashing all the time Mark Abraham
[gmx-users] GROMACS 4.5.4 keep crashing all the time Mark Abraham
[gmx-users] atom type not in rtp entry Mark Abraham
[gmx-users] REMD Error Mark Abraham
[gmx-users] position restraint Mark Abraham
[gmx-users] how to set domain decomposition for inhomogeneous systems? Mark Abraham
[gmx-users] Question about adding hydrogens to a newly constructed residue Mark Abraham
[gmx-users] how to set domain decomposition for inhomogeneous systems? Mark Abraham
[gmx-users] Error from residues added to rtp file Mark Abraham
[gmx-users] Question about adding hydrogens to a newly constructed residue Mark Abraham
[gmx-users] Counting number of non-bonded interactions ? Mark Abraham
[gmx-users] Question about adding hydrogens to a newly constructed residue Mark Abraham
[gmx-users] atom type OXT Mark Abraham
[gmx-users] Average no of hbonds Mark Abraham
[gmx-users] A question about simulating a box of ethane in GROMACS Mark Abraham
Antw: Re: Re: [gmx-users] constant PH simulations Mark Abraham
[gmx-users] energy terms vs. temperature Mark Abraham
[gmx-users] A question about simulating a box of ethane in GROMACS Mark Abraham
[gmx-users] No addition of ions Mark Abraham
[gmx-users] Installation gromacs in Scientific Linux Mark Abraham
[gmx-users] Trajectory viewing by freeing a part Mark Abraham
[gmx-users] conversion of gromacs topology format Mark Abraham
[gmx-users] How to make a CG topology for a modified residue? Mark Abraham
[gmx-users] dialanine using charmm27 ff Mark Abraham
[gmx-users] X and Y dimensions in nanometers Mark Abraham
[gmx-users] Re: no output in g_dist Mark Abraham
[gmx-users] amb2gmx.pl to convert GLYCAM topology Mark Abraham
[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE Mark Abraham
[gmx-users] gridcount Mark Abraham
[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE Mark Abraham
[gmx-users] dialanine using charmm27 ff Mark Abraham
[gmx-users] Groamacs for metal ion Mark Abraham
[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE Mark Abraham
[gmx-users] How do I examine the results didn't write issue Mark Abraham
[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology Mark Abraham
[gmx-users] Twin-range cut-off Mark Abraham
[gmx-users] adding Ca2+ ions to the solvent (either randomly or restrained) Mark Abraham
[gmx-users] V(R) around protein Mark Abraham
[gmx-users] V(R) around protein Mark Abraham
[gmx-users] dialanine using charmm27 ff Mark Abraham
[gmx-users] g_dist error Mark Abraham
[gmx-users] g_dist error Mark Abraham
[gmx-users] Strangeness in gro file Mark Abraham
[gmx-users] g_dist error Mark Abraham
[gmx-users] g_rms matrix between wt and mutant Mark Abraham
[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE Mark Abraham
[gmx-users] installation of FFTW Mark Abraham
[gmx-users] Potential energy problem Mark Abraham
[gmx-users] equilibration: run time or number of steps? Mark Abraham
[gmx-users] Fwd: Gromacs_trouble Mark Abraham
[gmx-users] Re: strangeness in gro file Mark Abraham
[gmx-users] residue numbering different Mark Abraham
[gmx-users] if PRODRG calculate incorrectly Mark Abraham
[gmx-users] different sets of fudgeQQ and fudgeLJ Mark Abraham
[gmx-users] positive Leonard Jones Energy Mark Abraham
[gmx-users] Questions regarding REMD simulation Mark Abraham
[gmx-users] RDF - first minimum of O-O Mark Abraham
[gmx-users] Membrane protein simulation Mark Abraham
[gmx-users] Fatal Error: Constraints present with Normal Mode Analysis, this combination is not supported Mark Abraham
[gmx-users] Temperature for different groups Mark Abraham
[gmx-users] sd integrator Mark Abraham
[gmx-users] sd integrator Mark Abraham
[gmx-users] particle decomp crashes while domain decomp does not Mark Abraham
[gmx-users] problem in compiling GMX with MPI Mark Abraham
[gmx-users] error while install GMX4.5.5 Mark Abraham
[gmx-users] Replex in REMD Mark Abraham
[gmx-users] g_mindist doubt Mark Abraham
[gmx-users] problem in compiling GMX with MPI Mark Abraham
[gmx-users] diferent version of gcc Mark Abraham
[gmx-users] Runtime on 8 processors Mark Abraham
[gmx-users] if PRODRG calculate incorrectly Mark Abraham
[gmx-users] Error mesage Mark Abraham
[gmx-users] About MD Mark Abraham
[gmx-users] g_analyze doubt Mark Abraham
[gmx-users] g_analyze doubt Mark Abraham
[gmx-users] About MD Mark Abraham
[gmx-users] About MD Mark Abraham
[gmx-users] -shell option of g_hbond Mark Abraham
[gmx-users] VACF Mark Abraham
[gmx-users] Re: PCA depends of the number of frames? Mark Abraham
[gmx-users] atomic concentration in x and y axis Mark Abraham
[gmx-users] Dimer simulation problem Mark Abraham
[gmx-users] BD with Hydrodynamic interactions? Mark Abraham
[gmx-users] Pressure estimation from NVT Mark Abraham
[gmx-users] simulation with position constraint by a harmonic potential Mark Abraham
[gmx-users] Error in analyzing traj.trr file using g_clustsize, etc. Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] Combining energy files Mark Abraham
[gmx-users] ApoA1 benchmark or reading CHARMM topologies in gromacs Mark Abraham
[gmx-users] REMD problem Mark Abraham
[gmx-users] Re: simulation of protein/water and phosphate ion Mark Abraham
[gmx-users] Runs OK on small CPS but fails on large number of CPUs... Mark Abraham
[gmx-users] gromacs tools and namd Mark Abraham
[gmx-users] REMD problem Mark Abraham
[gmx-users] -shell option of g_hbond Sajad Ahrari
[gmx-users] applied electric field on the pure water Saeid Akbarshahi
[gmx-users] Re: applied electric field on the pure water Saeid Akbarshahi
[gmx-users] Applied electric field on the pure water Saeid Akbarshahi
[gmx-users] Applied electric field on the pure water Saeid Akbarshahi
[gmx-users] Applied electric field on the pure water Saeid Akbarshahi
[gmx-users] amb2gmx.pl to convert GLYCAM topology Alan
[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology Alan
[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology Alan
[gmx-users] acpype generated different tip3p water paramters Alan
[gmx-users] particle decomp crashes while domain decomp das not Florian Altvater
[gmx-users] particle decomp crashes while domain decomp does not Florian Altvater
[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE Rossen Apostolov
[gmx-users] New maintenance release: 4.5.5 Rossen Apostolov
[gmx-users] VACF Prema Awati
[gmx-users] Fw: VACF Prema Awati
[gmx-users] (no subject) Prema Awati
[gmx-users] diferent version of gcc Víctor Bahamonde
[gmx-users] TI/FEP, BAR, and topologies Michael Brunsteiner
[gmx-users] Structure of the input Lara Bunte
[gmx-users] Free energy sampling using G_bar Fabian Casteblanco
[gmx-users] Temperature for different groups Marcelino Arciniega Castro
[gmx-users] Re: which charge is used in gromacs program Dr. Vitaly V. Chaban
[gmx-users] Re: which charge is used in gromacs program Dr. Vitaly V. Chaban
[gmx-users] Re: Non-zero total charge Dr. Vitaly V. Chaban
[gmx-users] Re: energy terms vs. temperature Dr. Vitaly V. Chaban
[gmx-users] Re: energy terms vs. temperature Dr. Vitaly V. Chaban
[gmx-users] Re: GROMACS @ Facebook Dr. Vitaly V. Chaban
[gmx-users] Manual Counterion Placement Marc Charendoff
[gmx-users] tpbconv question Marc Charendoff
[gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps) Shilpi Chaurasia
[gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps) Shilpi Chaurasia
[gmx-users] pull code problem: between protofilaments Shilpi Chaurasia
[gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27 Jackson Chief
[gmx-users] 3D pressure profile of a bilayer Amit Choubey
[gmx-users] 3D pressure profile of a bilayer Amit Choubey
[gmx-users] Membrane protein simulation Michael Daily
[gmx-users] opls parameters fir gramicidin terminal groups Michael Daily
[gmx-users] constant PH simulations João M. Damas
[gmx-users] constant PH simulations João M. Damas
[gmx-users] Dimer simulation problem Sarath Chandra Dantu
[gmx-users] Error from residues added to rtp file Delmotte, Antoine
[gmx-users] Error from residues added to rtp file Delmotte, Antoine
[gmx-users] Deformation of monomer in pulling simulation Robert Dole
[gmx-users] Fatal Error: Constraints present with Normal Mode Analysis, this combination is not supported Andrey Dyachenko
[gmx-users] phase transition in MD simulation Elisabeth
[gmx-users] Nucleic Acid in vacuo Matthias Ernst
[gmx-users] Nucleic Acid in vacuo Matthias Ernst
[gmx-users] Re: cannot inactivate fitting in g_rmsf - incomplete coordinates are written Thomas Evangelidis
[gmx-users] Doubt about HSD and HSE conformation on Charmm27 Rodrigo Faccioli
[gmx-users] Doubt about HSD and HSE conformation on Charmm27 Rodrigo Faccioli
[gmx-users] analysis of PMF calculations Rebeca García Fandiño
[gmx-users] analysis of PMF calculations Rebeca García Fandiño
[gmx-users] analysis of PMF calculations Rebeca García Fandiño
[gmx-users] analysis of PMF calculations Rebeca García Fandiño
[gmx-users] Force a gromacs tool to write step-by-step a result in a xvg file Dommert Florian
[gmx-users] Running two versions of GMX at a time Dommert Florian
[gmx-users] opls-aa, implicit solvent and GPUs Dommert Florian
[gmx-users] BD with Hydrodynamic interactions? Dommert Florian
[Fwd: Re: [gmx-users] BD with Hydrodynamic interactions?] Dommert Florian
[gmx-users] Error mesage Tanos Franca
[gmx-users] Error mesage Tanos Franca
[gmx-users] Problem building a polymer using pdb2gmx .... Alberto Sergio Garay
[gmx-users] Installation gromacs in Scientific Linux Nathalia Garces
[gmx-users] CfP: 2nd Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim), in Symposium on Theory of Modeling and Simulation, SCS Spring Sim 2012 Daniele Gianni
[gmx-users] CfP: 2nd Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim), in Symposium on Theory of Modeling and Simulation, SCS Spring Sim 2012 Daniele Gianni
[gmx-users] ApoA1 benchmark or reading CHARMM topologies in gromacs Pedro Gonnet
[gmx-users] Re: different sets of fudgeQQ and fudgeLJ Oliver Grant
Antw: Re: Re: [gmx-users] constant PH simulations (Emanuel Peter) Gerrit Groenhof
[gmx-users] constant PH simulations Gerrit Groenhof
[gmx-users] PCA depends of the number of frames? Ricardo Cuya Guizado
[gmx-users] Re: PCA depends of the number of frames? Ricardo Cuya Guizado
Antw: Re: Re: [gmx-users] constant PH simulations João Henriques
Antw: Re: Re: [gmx-users] constant PH simulations João Henriques
Antw: Re: Re: [gmx-users] constant PH simulations João Henriques
[gmx-users] position restraint Kun Huang
[gmx-users] installation of FFTW ITHAYARAJA
[gmx-users] Re: gmx-users Digest, Vol 89, Issue 104 ITHAYARAJA
[gmx-users] atom type not in rtp entry Sweta Iyer
[gmx-users] atom type OXT Sweta Iyer
[gmx-users] Re: atom type OXT Sweta Iyer
[gmx-users] Strangeness in gro file Sweta Iyer
[gmx-users] Re: strangeness in gro file Sweta Iyer
[gmx-users] Membrane protein simulation Sweta Iyer
[gmx-users] can i get the amber94 topology file for so4 molecule? Asha J
[gmx-users] Combining energy files Martin Kamp Jensen
[gmx-users] Combining energy files Martin Kamp Jensen
[gmx-users] Combining energy files Martin Kamp Jensen
[gmx-users] Non-zero total charge Munishika Kalia
[gmx-users] Non zero total charge Munishika Kalia
[gmx-users] GROMACS 4.5.4 keep crashing all the time Itamar Kass
[gmx-users] GROMACS 4.5.4 keep crashing all the time Itamar Kass
[gmx-users] GROMACS 4.5.4 keep crashing all the time Itamar Kass
[gmx-users] GROMACS 4.5.4 keep crashing all the time Itamar Kass
[gmx-users] GROMACS 4.5.4 keep crashing all the time Itamar Kass
[gmx-users] V(R) around protein E. Nihal Korkmaz
[gmx-users] V(R) around protein E. Nihal Korkmaz
[gmx-users] V(R) around protein E. Nihal Korkmaz
[gmx-users] Re: Constraints not working in pull code (sometimes, sometimes not) Krapnik
[gmx-users] Runtime on 8 processors Sumanth M. Kumar
[gmx-users] g_msd: Not enough points for fitting (0). Can not determine the diffusion constant Lalit
[gmx-users] g_msd: Not enough points for fitting (0). Can not determine the diffusion constant Lalit
[gmx-users] positive Leonard Jones Energy Gideon Lapidoth
[gmx-users] Re: positive Leonard Jones Energy (Mark Abraham) Gideon Lapidoth
[gmx-users] Gromacs 4.6? Matthew Lardy
[gmx-users] About MD Jussi Lehtola
[gmx-users] Re: which charge is used in gromacs program Justin A. Lemkul
[gmx-users] GROMACS 4.5.4 keep crashing all the time Justin A. Lemkul
[gmx-users] Non-zero total charge Justin A. Lemkul
[gmx-users] Problem building a polymer using pdb2gmx .... Justin A. Lemkul
[gmx-users] order parameter Justin A. Lemkul
[gmx-users] order parameter Justin A. Lemkul
[gmx-users] pdb2gmx response time Justin A. Lemkul
[gmx-users] order parameter Justin A. Lemkul
[gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27 Justin A. Lemkul
[gmx-users] problem in topology with AMBER99SB Justin A. Lemkul
[gmx-users] Deuterium order parametr Justin A. Lemkul
[gmx-users] constant PH simulations Justin A. Lemkul
[gmx-users] analysis tools Justin A. Lemkul
Antw: Re: [gmx-users] constant PH simulations Justin A. Lemkul
Yan: [gmx-users] analysis tools Justin A. Lemkul
[gmx-users] Average no of hbonds Justin A. Lemkul
Antw: Re: Re: [gmx-users] constant PH simulations Justin A. Lemkul
[gmx-users] Average no of hbonds Justin A. Lemkul
[gmx-users] Average no of hbonds Justin A. Lemkul
[gmx-users] A question about simulating a box of ethane in GROMACS Justin A. Lemkul
[gmx-users] Freezing secondary structure Justin A. Lemkul
[gmx-users] missing parameters in auto-generated topology file? Justin A. Lemkul
[gmx-users] energy terms vs. temperature Justin A. Lemkul
[gmx-users] energy terms vs. temperature Justin A. Lemkul
[gmx-users] gbsa.itp problem Justin A. Lemkul
[gmx-users] gbsa.itp problem Justin A. Lemkul
[gmx-users] gbsa.itp problem Justin A. Lemkul
[gmx-users] Re: energy terms vs. temperature Justin A. Lemkul
[gmx-users] Re: energy terms vs. temperature Justin A. Lemkul
[gmx-users] Re: gromacs doubts Justin A. Lemkul
[gmx-users] Permeability coefficient Justin A. Lemkul
[gmx-users] Bad water removal Justin A. Lemkul
[gmx-users] Trajectory viewing by freeing a part Justin A. Lemkul
[gmx-users] no output in g_dist Justin A. Lemkul
[gmx-users] compressing waterbox Justin A. Lemkul
[gmx-users] md.mdp file GPU one Justin A. Lemkul
[gmx-users] Re: g_sas of ligands Justin A. Lemkul
[gmx-users] Density Justin A. Lemkul
[gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps) Justin A. Lemkul
[gmx-users] radial distribution function Justin A. Lemkul
[gmx-users] radial distribution function Justin A. Lemkul
[gmx-users] gromacs 4.5 tools for trajectory analysis Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] radial distribution function Justin A. Lemkul
[gmx-users] radial distribution function Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 89, Issue 52 Justin A. Lemkul
[gmx-users] how to modify the md. log Justin A. Lemkul
[gmx-users] doing restarts Justin A. Lemkul
[gmx-users] doing restarts Justin A. Lemkul
[gmx-users] analysis of PMF calculations Justin A. Lemkul
[gmx-users] analysis of PMF calculations Justin A. Lemkul
[gmx-users] analysis of PMF calculations Justin A. Lemkul
[gmx-users] analysis of PMF calculations Justin A. Lemkul
[gmx-users] analysis of PMF calculations Justin A. Lemkul
[gmx-users] problem of lipid molecules entering voids of solvent during equilibration Justin A. Lemkul
[gmx-users] Re: no output in g_dist Justin A. Lemkul
[gmx-users] g_dist error Justin A. Lemkul
[gmx-users] g_dist output error Justin A. Lemkul
[gmx-users] g_dist error Justin A. Lemkul
[gmx-users] g_dist error Justin A. Lemkul
[gmx-users] How do I examine the results didn't write issue Justin A. Lemkul
[gmx-users] Nucleic Acid in vacuo Justin A. Lemkul
[gmx-users] g_rms matrix between wt and mutant Justin A. Lemkul
[gmx-users] g_rms matrix between wt and mutant Justin A. Lemkul
[gmx-users] Problem when adding new residue in itp file Justin A. Lemkul
[gmx-users] Twin-range cut-off Justin A. Lemkul
[gmx-users] g_dist error Justin A. Lemkul
[gmx-users] gmx output in VMD Justin A. Lemkul
[gmx-users] Unsubscribe me Please Justin A. Lemkul
[gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps) Justin A. Lemkul
[gmx-users] Nucleic Acid in vacuo Justin A. Lemkul
[gmx-users] simulation with amber10 and gromacs 4.5.1 Justin A. Lemkul
[gmx-users] Re: Gromacs_trouble Justin A. Lemkul
[gmx-users] equilibration: run time or number of steps? Justin A. Lemkul
[gmx-users] Re: strangeness in gro file Justin A. Lemkul
[gmx-users] Free energy sampling using G_bar Justin A. Lemkul
[gmx-users] Counting non-bonding interaction Justin A. Lemkul
[gmx-users] if PRODRG calculate incorrectly Justin A. Lemkul
[gmx-users] RDF - first minimum of O-O Justin A. Lemkul
[gmx-users] different sets of fudgeQQ and fudgeLJ Justin A. Lemkul
[gmx-users] RDF - first minimum of O-O Justin A. Lemkul
[gmx-users] Deformation of monomer in pulling simulation Justin A. Lemkul
[gmx-users] Manual Counterion Placement Justin A. Lemkul
[gmx-users] Membrane protein simulation Justin A. Lemkul
[gmx-users] problem with lipid membrane Justin A. Lemkul
[gmx-users] Re: positive Leonard Jones Energy (Mark Abraham) Justin A. Lemkul
[gmx-users] grompp errors Justin A. Lemkul
[gmx-users] problem with lipid membrane Justin A. Lemkul
[gmx-users] about periodic image minimum distance Justin A. Lemkul
[gmx-users] check point file corrupted - umbrella sampling Justin A. Lemkul
[gmx-users] check point file corrupted - umbrella sampling Justin A. Lemkul
[gmx-users] check point file corrupted - umbrella sampling Justin A. Lemkul
[gmx-users] reg box dimension Justin A. Lemkul
[gmx-users] reg box dimension Justin A. Lemkul
[gmx-users] Structure of the input Justin A. Lemkul
[gmx-users] problem with lipid membrane Justin A. Lemkul
[gmx-users] problem with pdb2gmx Justin A. Lemkul
[gmx-users] Dimer simulation problem Justin A. Lemkul
[gmx-users] Error mesage Justin A. Lemkul
[gmx-users] what difference between RMSF and RMDEV Justin A. Lemkul
[gmx-users] meaning of minus potential and buried surface area Justin A. Lemkul
[gmx-users] what difference between RMSF and RMDEV Justin A. Lemkul
[gmx-users] grompp error with distance restraints Justin A. Lemkul
[gmx-users] opls-aa, implicit solvent and GPUs Justin A. Lemkul
[gmx-users] meaning of minus potential and buried surface area Justin A. Lemkul
[gmx-users] Running the batch command Justin A. Lemkul
[gmx-users] concentration distribution Justin A. Lemkul
[gmx-users] Center of mass: distance restrain for groups Justin A. Lemkul
[gmx-users] Center of mass: distance restrain for groups Justin A. Lemkul
[gmx-users] Center of mass: distance restrain for groups Justin A. Lemkul
[gmx-users] simulation with position constraint by a harmonic potential Justin A. Lemkul
[gmx-users] simulation with position constraint by a harmonic potential Justin A. Lemkul
[gmx-users] simulation with position constraint by a harmonic potential Justin A. Lemkul
[gmx-users] Pressure estimation from NVT Justin A. Lemkul
[gmx-users] Re: simulation of protein/water and phosphate ion Justin A. Lemkul
[gmx-users] Combining energy files Justin A. Lemkul
[gmx-users] simulation with position constraint by a harmonic potential Justin A. Lemkul
[gmx-users] simulation with position constraint by a harmonic potential Justin A. Lemkul
[gmx-users] Pressure estimation from NVT Justin A. Lemkul
[gmx-users] Doubt about HSD and HSE conformation on Charmm27 Justin A. Lemkul
[gmx-users] Re: problem in binding free energy calculation and setting Lambda Justin A. Lemkul
[gmx-users] Center of mass: distance restrain for groups Justin A. Lemkul
[gmx-users] xpm2ps Justin A. Lemkul
[gmx-users] Re: problem in binding free energy calculation and setting Lambda Justin A. Lemkul
[gmx-users] non interactive command Justin A. Lemkul
[gmx-users] non interactive command Justin A. Lemkul
[gmx-users] non interactive command Justin A. Lemkul
[gmx-users] REMD problem Justin A. Lemkul
[gmx-users] REMD problem Justin A. Lemkul
[gmx-users] REMD problem Justin A. Lemkul
[gmx-users] REMD problem Justin A. Lemkul
[gmx-users] REMD problem Justin A. Lemkul
[gmx-users] REMD problem Justin A. Lemkul
[gmx-users] REMD problem Justin A. Lemkul
[gmx-users] REMD problem Justin A. Lemkul
[gmx-users] Fwd: pdb2gmx converting coordinates incorrectly. Justin A. Lemkul
[gmx-users] Regarding OPLSAA Justin A. Lemkul
[gmx-users] how to plot the difference between two contact maps Justin A. Lemkul
[gmx-users] Error - please help Justin A. Lemkul
[gmx-users] REMD problem Justin A. Lemkul
[gmx-users] Negative Pressure After Energy Minimization Justin A. Lemkul
[gmx-users] make_ndx unable to save Justin A. Lemkul
[gmx-users] Time-varying Ion Charges Zach Levine
[gmx-users] Center of mass: distance restrain for groups Li, Hualin
[gmx-users] Center of mass: distance restrain for groups Li, Hualin
[gmx-users] Center of mass: distance restrain for groups Li, Hualin
[gmx-users] Center of mass: distance restrain for groups Li, Hualin
[gmx-users] Center of mass: distance restrain for groups Li, Hualin
[gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27 Jianguo Li
[gmx-users] how to handle different atom names between pdb and rtp files. Jianguo Li
[gmx-users] residue numbering different Jianguo Li
[gmx-users] Re: about non-writing issue Jianguo Li
[gmx-users] Counting number of non-bonded interactions ? Chih-Ying Lin
[gmx-users] Counting non-bonding interaction Chih-Ying Lin
[gmx-users] Invitation to connect on LinkedIn ekalabya bissoyi via LinkedIn
[gmx-users] Invitation to connect on LinkedIn Hideya Nakamura via LinkedIn
[gmx-users] simulation with position constraint by a harmonic potential Liu, Liang
[gmx-users] simulation with position constraint by a harmonic potential Liu, Liang
[gmx-users] simulation with position constraint by a harmonic potential Liu, Liang
[gmx-users] simulation with position constraint by a harmonic potential Liu, Liang
[gmx-users] simulation with position constraint by a harmonic potential Liu, Liang
[gmx-users] simulation with position constraint by a harmonic potential Liu, Liang
[gmx-users] REMD problem Liu, Liang
[gmx-users] REMD problem Liu, Liang
[gmx-users] REMD problem Liu, Liang
[gmx-users] REMD problem Liu, Liang
[gmx-users] REMD problem Liu, Liang
[gmx-users] REMD problem Liu, Liang
[gmx-users] REMD problem Liu, Liang
[gmx-users] REMD problem Liu, Liang
[gmx-users] REMD problem Liu, Liang
[gmx-users] REMD problem Liu, Liang
[gmx-users] REMD problem Liu, Liang
[gmx-users] REMD problem Liu, Liang
[gmx-users] Dimer simulation Kavyashree M
[gmx-users] Dimer simulation problem Kavyashree M
[gmx-users] Dimer simulation problem Kavyashree M
[gmx-users] Dimer simulation problem Kavyashree M
[gmx-users] Dimer simulation problem Kavyashree M
[gmx-users] BD with Hydrodynamic interactions? Sanku M
[gmx-users] BD with Hydrodynamic interactions? Sanku M
[gmx-users] problem in topology with AMBER99SB Anna Marabotti
[gmx-users] about periodic image minimum distance Anna Marabotti
[gmx-users] Pressure estimation from NVT Sikandar Mashayak
[gmx-users] Pressure estimation from NVT Sikandar Mashayak
[gmx-users] problem in binding free energy calculation and setting Lambda Marcelo Fabricio Masman
[gmx-users] radial distribution function Moeed
[gmx-users] radial distribution function Moeed
[gmx-users] radial distribution function Moeed
[gmx-users] radial distribution function Moeed
[gmx-users] radial distribution function Moeed
[gmx-users] radial distribution function Moeed
[gmx-users] energy terms vs. temperature Juliette N.
[gmx-users] energy terms vs. temperature Juliette N.
[gmx-users] Re: energy terms vs. temperature Juliette N.
[gmx-users] doing restarts Juliette N.
[gmx-users] doing restarts Juliette N.
[gmx-users] equilibration: run time or number of steps? Juliette N.
[gmx-users] analysis tools Namd Namd
[gmx-users] check point file corrupted - umbrella sampling Chris Neale
[gmx-users] g_hbond Steven Neumann
[gmx-users] Average no of hbonds Steven Neumann
[gmx-users] Average no of hbonds Steven Neumann
[gmx-users] Average no of hbonds Steven Neumann
[gmx-users] g_sas of ligands Steven Neumann
[gmx-users] g_sas of ligands Steven Neumann
[gmx-users] Re: g_sas of ligands Steven Neumann
[gmx-users] RDF - first minimum of O-O Steven Neumann
[gmx-users] RDF - first minimum of O-O Steven Neumann
[gmx-users] RDF - first minimum of O-O Steven Neumann
[gmx-users] RDF - first minimum of O-O Steven Neumann
[gmx-users] problem in compiling GMX with MPI Jinan Niu
[gmx-users] problem in compiling GMX with MPI Jinan Niu
[gmx-users] problem in compiling GMX with MPI Jinan Niu
[gmx-users] g_cluster -dm option Francesco Oteri
[gmx-users] Non zero total charge Andrew Paluch
[gmx-users] anisotripic polarization in water model Park, Jae Hyun nmn
[gmx-users] turn-off Lennard-Jone interaction for a particular pair. Park, Jae Hyun nmn
[gmx-users] order parameter Parthasarathi, Ramya
[gmx-users] order parameter Parthasarathi, Ramya
[gmx-users] Deuterium order parametr Parthasarathi, Ramya
[gmx-users] Deuterium order parametr Parthasarathi, Ramya
[gmx-users] X and Y dimensions in nanometers Conrado Pedebos
Antw: [gmx-users] constant PH simulations Emanuel Peter
Antw: Re: [gmx-users] constant PH simulations Emanuel Peter
Antw: Re: Re: [gmx-users] constant PH simulations Emanuel Peter
Antw: Re: Re: [gmx-users] constant PH simulations (Emanuel Peter) Emanuel Peter
Antw: Re: Antw: Re: Re: [gmx-users] constant PH simulations Emanuel Peter
Antw: Re: Re: Antw: Re: Re: [gmx-users] constant PH simulations Emanuel Peter
[gmx-users] Constant-pH simulation Emanuel Peter
[gmx-users] sd integrator Sai Pooja
[gmx-users] sd integrator Sai Pooja
[gmx-users] check point file corrupted - umbrella sampling Poojari, Chetan
[gmx-users] check point file corrupted - umbrella sampling Poojari, Chetan
[gmx-users] check point file corrupted - umbrella sampling Poojari, Chetan
[gmx-users] check point file corrupted - umbrella sampling Poojari, Chetan
[gmx-users] check point file corrupted - umbrella sampling Poojari, Chetan
[gmx-users] REMD problem Manuel Prinz
[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE Szilárd Páll
[gmx-users] problem with pdb2gmx Saurav Saha
[gmx-users] Error - please help Sarina
[gmx-users] Negative Pressure After Energy Minimization Saumya
[gmx-users] g_dist error Thomas Schlesier
[gmx-users] opls-aa, implicit solvent and GPUs Ehud Schreiber
[gmx-users] opls-aa, implicit solvent and GPUs Ehud Schreiber
[gmx-users] error while install GMX4.5.5 Roland Schulz
[gmx-users] Question about adding hydrogens to a newly constructed residue J. Nathan Scott
[gmx-users] Question about adding hydrogens to a newly constructed residue J. Nathan Scott
[gmx-users] Question about adding hydrogens to a newly constructed residue J. Nathan Scott
[gmx-users] Questions regarding REMD simulation SebastianWaltz
[gmx-users] missing parameters in auto-generated topology file? Yun Shi
[gmx-users] amb2gmx.pl to convert GLYCAM topology Yun Shi
[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology Yun Shi
[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology Yun Shi
[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology Yun Shi
[gmx-users] different sets of fudgeQQ and fudgeLJ Yun Shi
[gmx-users] different sets of fudgeQQ and fudgeLJ Yun Shi
[gmx-users] Re: different sets of fudgeQQ and fudgeLJ Yun Shi
[gmx-users] acpype generated different tip3p water paramters Yun Shi
[gmx-users] g_sas Smolin, Nikolai
[gmx-users] xpm2ps Smolin, Nikolai
[gmx-users] dialanine using charmm27 ff Sandeep Somani
[gmx-users] dialanine using charmm27 ff Sandeep Somani
[gmx-users] dialanine using charmm27 ff Sandeep Somani
[gmx-users] A question about simulating a box of ethane in GROMACS Phil (Yang) Song
[gmx-users] A question about simulating a box of ethane in GROMACS Phil (Yang) Song
[gmx-users] GROMACS @ Facebook David van der Spoel
[gmx-users] Runs OK on small CPS but fails on large number of CPUs... Tandia, Adama
[gmx-users] Error in analyzing traj.trr file using g_clustsize, etc. A Taqia
[gmx-users] g_rms matrix between wt and mutant Shay Teaching
[gmx-users] g_rms matrix between wt and mutant Shay Teaching
[gmx-users] g_rms matrix between wt and mutant Shay Teaching
[gmx-users] g_rms matrix between wt and mutant Shay Teaching
[gmx-users] g_rms matrix between wt and mutant Shay Teaching
[gmx-users] Membrane protein simulation Shay Teaching
[gmx-users] Twin-range cut-off Rabab Toubar
[gmx-users] REMD Error Jose Tusell
[gmx-users] REMD Error Jose Tusell
[gmx-users] REMD Error Jose Tusell
[gmx-users] Re: gmx-users Digest, Vol 89, Issue 166 Ravi Kumar Venkatraman
[gmx-users] Regarding OPLSAA Ravi Kumar Venkatraman
[gmx-users] Re: gmx-users Digest, Vol 89, Issue 167 Ravi Kumar Venkatraman
Antw: Re: Re: [gmx-users] constant PH simulations Diogo Vila Viçosa
[gmx-users] X and Y dimensions in nanometers Dallas Warren
[gmx-users] phase transition in MD simulation Dallas Warren
[gmx-users] radial distribution function Dallas Warren
[gmx-users] radial distribution function Dallas Warren
[gmx-users] g_msd: Not enough points for fitting (0). Can not determine the diffusion constant Dallas Warren
[gmx-users] g_analyze doubt Dallas Warren
[gmx-users] VACF Dallas Warren
[gmx-users] Pressure estimation from NVT Dallas Warren
[gmx-users] Pressure estimation from NVT Dallas Warren
[gmx-users] Re: simulation of protein/water and phosphate ion Dallas Warren
[gmx-users] Re: simulation of protein/water and phosphate ion Dallas Warren
[gmx-users] GROMACS 4.5.4 keep crashing all the time Tsjerk Wassenaar
[gmx-users] GROMACS 4.5.4 keep crashing all the time Tsjerk Wassenaar
[gmx-users] GROMACS 4.5.4 keep crashing all the time Tsjerk Wassenaar
[gmx-users] Representative structure from MD trajectories Tsjerk Wassenaar
[gmx-users] Time-varying Ion Charges Tsjerk Wassenaar
[gmx-users] simulation with amber10 and gromacs 4.5.1 Tsjerk Wassenaar
[gmx-users] V(R) around protein Tsjerk Wassenaar
[gmx-users] Re: g_sas of ligands Tsjerk Wassenaar
[gmx-users] radial distribution function Tsjerk Wassenaar
[gmx-users] if PRODRG calculate incorrectly Tsjerk Wassenaar
[gmx-users] g_mindist doubt Tsjerk Wassenaar
[gmx-users] surface atoms Tsjerk Wassenaar
[gmx-users] PCA depends of the number of frames? Tsjerk Wassenaar
[gmx-users] PCA depends of the number of frames? Tsjerk Wassenaar
[gmx-users] tpbconv question Tsjerk Wassenaar
[gmx-users] Fwd: pdb2gmx converting coordinates incorrectly. William Welch
[gmx-users] how to handle different atom names between pdb and rtp files. KONG Xian
[gmx-users] comm_mode and accelerate Wang Xiaofeng
[gmx-users] How to use comm_mode and accelerate together? Wang Xiaofeng
[gmx-users] Surface tension calculation of a bilayer with bilayer normal in y-direction Shou-Chuang Yang
[gmx-users] 3D pressure profile of a bilayer Shou-Chuang Yang
[gmx-users] 3D pressure profile of a bilayer Shou-Chuang Yang
[gmx-users] pdb2gmx response time Yao Yao
[gmx-users] gbsa.itp problem Yao Yao
[gmx-users] gbsa.itp problem Yao Yao
[gmx-users] QM/MM/MD Semi-empirical Error Yao Yao
[gmx-users] QM/MM/MD Semi-empirical Error Yao Yao
[gmx-users] Trajectory viewing by freeing a part Ragothaman Yennamalli
[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE Marcin Zielinski
[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE Marcin Zielinski
[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE Marcin Zielinski
[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE Marcin Zielinski
[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE Marcin Zielinski
[gmx-users] Non zero total charge Matthew Zwier
[gmx-users] (no subject) mohammad agha
[gmx-users] question about martini coarse-grained mohammad agha
[gmx-users] question about martini coarse-grained mohammad agha
[gmx-users] question about position restraint in martini coarse-grained mohammad agha
Antw: Re: Re: Antw: Re: Re: [gmx-users] constant PH simulations baptista
[gmx-users] make_ndx unable to save ram bio
[gmx-users] Information baout DPCC by schiu elisa carli
[gmx-users] MD with membrane protein elisa carli
[gmx-users] Bad water removal madhumita das
[gmx-users] compressing waterbox madhumita das
[gmx-users] Potential energy problem madhumita das
[gmx-users] grompp error with distance restraints bob dole
[gmx-users] constant PH simulations fancy2012
[gmx-users] Permeability coefficient manoj gadhwal
[gmx-users] g_dist error aiswarya.pawar at gmail.com
[gmx-users] g_dist error aiswarya.pawar at gmail.com
[gmx-users] Running the batch command aiswarya.pawar at gmail.com
[gmx-users] g_analyze aiswarya.pawar at gmail.com
[gmx-users] About MD xiaojing gong
[gmx-users] About MD xiaojing gong
[gmx-users] About MD xiaojing gong
[gmx-users] Re: simulation of protein/water and phosphate ion bharat gupta
[gmx-users] Re: simulation of protein/water and phosphate ion bharat gupta
[gmx-users] Re: simulation of protein/water and phosphate ion bharat gupta
[gmx-users] Re: simulation of protein/water and phosphate ion bharat gupta
[gmx-users] gromacs tools and namd oguz gurbulak
[gmx-users] gromacs 4.5 tools for trajectory analysis Hasan haska
[gmx-users] half double pair list method in GROMACS intra\sa175950
[gmx-users] Half double pair list method in GROMACS intra\sa175950
[gmx-users] Force a gromacs tool to write step-by-step a result in a xvg file intra\sa175950
[gmx-users] Re: Force a gromacs tool to write step-by-step a result in a result in a xvg file intra\sa175950
[gmx-users] Running two versions of GMX at a time chandran karunakaran
[gmx-users] Problem in VMD meisam valizadeh kiamahalleh
[gmx-users] gmx output in VMD meisam valizadeh kiamahalleh
[gmx-users] problem in binding free energy calculation and setting Lambda meisam valizadeh kiamahalleh
[gmx-users] Re: problem in binding free energy calculation and setting Lambda meisam valizadeh kiamahalleh
[gmx-users] Re: problem in binding free energy calculation and setting Lambda meisam valizadeh kiamahalleh
[gmx-users] g_cluster -dm option santhu kumar
[gmx-users] Freezing secondary structure seunghwan lee
[gmx-users] no output in g_dist lina
[gmx-users] md.mdp file GPU one lina
[gmx-users] md.mdp file GPU one lina
[gmx-users] radial distribution function lina
[gmx-users] how to modify the md. log lina
[gmx-users] Re: how to modify the md. log lina
[gmx-users] radial distribution function lina
[gmx-users] how to modify the md. log lina
[gmx-users] How do I examine the results didn't write issue lina
[gmx-users] How do I examine the results didn't write issue lina
[gmx-users] How do I examine the results didn't write issue lina
[gmx-users] about non-writing issue lina
[gmx-users] Re: about non-writing issue lina
[gmx-users] Re: about non-writing issue lina
[gmx-users] MD with membrane protein lina
[gmx-users] error while install GMX4.5.5 lina
[gmx-users] diferent version of gcc lina
[gmx-users] concentration distribution lina
[gmx-users] g_lie gal.fradin at live.biu.ac.il
[gmx-users] RE:g_lie gal.fradin at live.biu.ac.il
[gmx-users] how to handle different atom names between pdb and rtp files. gal.fradin at live.biu.ac.il
[gmx-users] Questions regarding REMD simulation gal.fradin at live.biu.ac.il
[gmx-users] Re:Aloha State, eyem noob
[gmx-users] No addition of ions aiswarya pawar
[gmx-users] conversion of gromacs topology format aiswarya pawar
[gmx-users] no output in g_dist aiswarya pawar
[gmx-users] Re: no output in g_dist aiswarya pawar
[gmx-users] gridcount aiswarya pawar
[gmx-users] Re: no output in g_dist aiswarya pawar
[gmx-users] g_dist error aiswarya pawar
[gmx-users] g_dist output error aiswarya pawar
[gmx-users] g_dist error aiswarya pawar
[gmx-users] g_dist error aiswarya pawar
[gmx-users] g_dist output error aiswarya pawar
[gmx-users] g_dist error aiswarya pawar
[gmx-users] g_dist error aiswarya pawar
[gmx-users] g_dist error aiswarya pawar
[gmx-users] residue numbering different aiswarya pawar
[gmx-users] g_mindist doubt aiswarya pawar
[gmx-users] g_mindist doubt aiswarya pawar
[gmx-users] surface atoms aiswarya pawar
[gmx-users] g_analyze doubt aiswarya pawar
[gmx-users] g_analyze doubt aiswarya pawar
[gmx-users] g_analyze doubt aiswarya pawar
[gmx-users] non interactive command aiswarya pawar
[gmx-users] non interactive command aiswarya pawar
[gmx-users] non interactive command aiswarya pawar
[gmx-users] Help OPLS-AA system explodes joselin peredo
[gmx-users] Groamacs for metal ion om prakash
[gmx-users] Unsubscribe me Please om prakash
[gmx-users] adding Ca2+ ions to the solvent (either randomly or restrained) m r
[gmx-users] MD Simulations pawan raghav
[gmx-users] concentration distribution raj
[gmx-users] atomic concentration in x and y axis raj
[gmx-users] simulation with amber10 and gromacs 4.5.1 vijayaraj ramadoss
[gmx-users] RE:g_lie lloyd riggs
[gmx-users] RE:g_lie lloyd riggs
[gmx-users] reg box dimension vidhya sankar
[gmx-users] reg box dimension vidhya sankar
[gmx-users] how to plot the difference between two contact maps ashutosh shandilya
[gmx-users] Representative structure from MD trajectories bipin singh
[gmx-users] Representative structure from MD trajectories bipin singh
[gmx-users] Representative structure from MD trajectories bipin singh
[gmx-users] Regarding clustering of MD data bipin singh
[gmx-users] Identifying representative structures from a g_sham generated 2d energy plot bipin singh
[gmx-users] Re: problem during Energy minimization Parul tew
[gmx-users] problem of lipid molecules entering voids of solvent during equilibration Parul tew
[gmx-users] problem with lipid membrane Parul tew
[gmx-users] problem with lipid membrane Parul tew
[gmx-users] Re: gmx-users Digest, Vol 89, Issue 107 Parul tew
[gmx-users] Density vferrario at units.it
[gmx-users] order parameter chris.neale at utoronto.ca
[gmx-users] GROMACS 4.5.4 keep crashing all the time chris.neale at utoronto.ca
[gmx-users] GROMACS 4.5.4 keep crashing all the time chris.neale at utoronto.ca
[gmx-users] Non-zero total charge chris.neale at utoronto.ca
[gmx-users] GROMACS 4.5.4 keep crashing all the time chris.neale at utoronto.ca
[gmx-users] half double pair list method in GROMACS chris.neale at utoronto.ca
[gmx-users] order parameter chris.neale at utoronto.ca
[gmx-users] Half double pair list method in GROMACS chris.neale at utoronto.ca
[gmx-users] GROMACS 4.5.4 keep crashing all the time chris.neale at utoronto.ca
[gmx-users] Half double pair list method in GROMACS chris.neale at utoronto.ca
[gmx-users] will united-atom POPC forcefield mater in pH 4 chris.neale at utoronto.ca
[gmx-users] Constraints not working in pull code (sometimes, sometimes not) chris.neale at utoronto.ca
[gmx-users] atom type OXT chris.neale at utoronto.ca
[gmx-users] Twin-range cut-off chris.neale at utoronto.ca
[gmx-users] check point file corrupted - umbrella sampling chris.neale at utoronto.ca
[gmx-users] About g_vanhove xiaowu759
[gmx-users] if PRODRG calculate incorrectly ahmet yıldırım
[gmx-users] if PRODRG calculate incorrectly ahmet yıldırım
[gmx-users] what difference between RMSF and RMDEV ahmet yıldırım
[gmx-users] meaning of minus potential and buried surface area ahmet yıldırım
[gmx-users] what difference between RMSF and RMDEV ahmet yıldırım
[gmx-users] meaning of minus potential and buried surface area ahmet yıldırım
[gmx-users] if PRODRG calculate incorrectly ahmet yıldırım
[gmx-users] proper dihedral scaling in free energy simulation lq z
[gmx-users] Questions regarding REMD simulation michael zhenin
[gmx-users] how to set domain decomposition for inhomogeneous systems? zhongjin
[gmx-users] how to set domain decomposition for inhomogeneous systems? zhongjin
[gmx-users] error while install GMX4.5.5 zhongjin
[gmx-users] error while install GMX4.5.5 zhongjin
[gmx-users] error while install GMX4.5.5 zhongjin
[gmx-users] Replex in REMD César Ávila
[gmx-users] (no subject) Алексей Раевский
[gmx-users] Re: gmx-users Digest, Vol 89, Issue 52 Алексей Раевский
[gmx-users] g_lie (again..) גדעון לפידות
[gmx-users] Re: gmx-users Digest, Vol 89, Issue 83 גדעון לפידות
[gmx-users] regarding energy run and g_lie גדעון לפידות

Last message date: Fri Sep 30 19:30:46 CEST 2011
Archived on: Thu Nov 14 12:11:40 CET 2013

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