March 2012 Archives by author

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Starting: Thu Mar 1 00:11:48 CET 2012
Ending: Sat Mar 31 21:16:29 CEST 2012
Messages: 1028

[gmx-users] Umbrella sampling to calculate binding energy under martini force field Du Jiangfeng (BIOCH)
[gmx-users] Amber99bsc0 Amir Abbasi
[gmx-users] on the dissociation of protein complex during MD Mark Abraham
[gmx-users] crashed run... Mark Abraham
[gmx-users] dihedral distributions Mark Abraham
[gmx-users] Random option - genion Mark Abraham
[gmx-users] Segmentation fault - Implicit solvent Mark Abraham
[gmx-users] mdrun -multi flag Mark Abraham
[gmx-users] MDrun append... Mark Abraham
[gmx-users] dssp and gromacs version Mark Abraham
[gmx-users] [ bondedtypes ] Mark Abraham
[gmx-users] Re: Re: Re: Re: mdrun -multi flag (Mark Abraham) (Justin A. Lemkul) Mark Abraham
[gmx-users] do_dssp segmentation fault Mark Abraham
[gmx-users] Anomalous temperature Mark Abraham
[gmx-users] do_dssp segmentation fault Mark Abraham
[gmx-users] problem in using OPLS forcefield parameter in lipid simulation Mark Abraham
[gmx-users] cannot determine precision of trn file Mark Abraham
[gmx-users] Distance between selected atoms during simulation Mark Abraham
[gmx-users] How to answer in this mailing list? Mark Abraham
[gmx-users] g_msd segmentation fault Mark Abraham
[gmx-users] segmentation fault err Mark Abraham
[gmx-users] folding of coordinates in trajectory files Mark Abraham
[gmx-users] cannot determine precision of trn file Mark Abraham
[gmx-users] g_bar bug with temperature Mark Abraham
[gmx-users] Coupling groups Mark Abraham
[gmx-users] Coupling groups Mark Abraham
[gmx-users] how to add custom potential function Mark Abraham
[gmx-users] LINCS problem with EM and Virtual sites Mark Abraham
[gmx-users] grompp - Group protein not found Mark Abraham
[gmx-users] HOW TO USE SILVER ATOMS IN AMBER99 FORCE FIELD Mark Abraham
[gmx-users] hydrophobic and hydrophilic in implicit solvent Mark Abraham
[gmx-users] grompp - Group protein not found Mark Abraham
[gmx-users] mdrun - topol.tpr Mark Abraham
[gmx-users] Periodic molecules and minimum bonded cut-off Mark Abraham
[gmx-users] g_select problem (Invalid command line argument:) Mark Abraham
[gmx-users] Residue 'NAG' not found in residue topology database Mark Abraham
[gmx-users] Gromacs 3.3.3 on Lion Xgrid Mark Abraham
[gmx-users] How to input multiple trr files? Mark Abraham
[gmx-users] How to input multiple trr files? Mark Abraham
[gmx-users] Read mdcrd from AMBER ---> Error Message Mark Abraham
[gmx-users] Re: Re: hydrophobic and hydrophilic in implicit solvent Mark Abraham
[gmx-users] g_helix not recognizing protein backbone Mark Abraham
[gmx-users] I need a tutorial for gromacs-4.0.5 Mark Abraham
[gmx-users] I need a tutorial for gromacs-4.0.5 Mark Abraham
[gmx-users] Recommended protocol for cooling down temperature in 50 K steps Mark Abraham
[gmx-users] Re: Atom O5 not found in residue seq.nr. 1 while adding atom Mark Abraham
[gmx-users] LINCS Fatal error Mark Abraham
[gmx-users] Segmentation fault Mark Abraham
[gmx-users] -p topol.top input/output error Mark Abraham
[gmx-users] Gromacs installation in Cygwin Mark Abraham
[gmx-users] Error Message when installing GROMACS. Mark Abraham
[gmx-users] grompp - Group protein not found Mark Abraham
[gmx-users] -p topol.top input/output error Mark Abraham
[gmx-users] uninstall gromacs Mark Abraham
[gmx-users] GROMACS stalls for NPT simulation when using -npme and -dd flags Mark Abraham
[gmx-users] Error Message in Make clean command for installation. Mark Abraham
[gmx-users] error message during make after gtomacs configuration Mark Abraham
[gmx-users] error message during make after gtomacs configuration Mark Abraham
[gmx-users] gromacs 4.5.5 cygwin installation error message Mark Abraham
[gmx-users] genconf, grompp Mark Abraham
[gmx-users] g_dist without output file Mark Abraham
Fw: [gmx-users] gromacs 4.5.5 cygwin installation error message Mark Abraham
[gmx-users] gromacs 4.5.5 cygwin installation error message Mark Abraham
[gmx-users] gromacs 4.5.5 cygwin installation error message Mark Abraham
[gmx-users] Generation of the Distance Restraints Mark Abraham
[gmx-users] Generation of the Distance Restraints Mark Abraham
[gmx-users] help on replica exchange dynamics with gromacs Mark Abraham
[gmx-users] Generation of the Distance Restraints Mark Abraham
[gmx-users] Generation of the Distance Restraints Mark Abraham
[gmx-users] pme note Mark Abraham
[gmx-users] Generation of the Distance Restraints Mark Abraham
[gmx-users] Generation of the Distance Restraints Mark Abraham
[gmx-users] Unreadable trajetory Mark Abraham
[gmx-users] Importance of -rcon and -dd options when using mdrun with mpi. Mark Abraham
[gmx-users] tpbconv and tpr file problem... Mark Abraham
[gmx-users] Where in the source code is the .edr file written? Mark Abraham
[gmx-users] gromacs 3.3.3 and gromacs 4.5.5 Mark Abraham
[gmx-users] on the RAM capacity needed for GROMACS Mark Abraham
[gmx-users] using MPI Mark Abraham
[gmx-users] Re.Importance of -rcon and -dd options when Mark Abraham
[gmx-users] Problems with simulation on multi-nodes cluster Mark Abraham
[gmx-users] Problems with simulation on multi-nodes cluster Mark Abraham
[gmx-users] Generation of the Distance Restraints Mark Abraham
[gmx-users] Structural features for LINCS application Mark Abraham
[gmx-users] Generation of the Distance Restraints Mark Abraham
[gmx-users] tpbconv and tpr file problem... Mark Abraham
[gmx-users] genion -pname no NA molecule (sodium) type Mark Abraham
[gmx-users] genion -pname no NA molecule (sodium) type Mark Abraham
[gmx-users] newest version of gromacs under cygwin Mark Abraham
[gmx-users] Energy minimization of crystal structure with water Mark Abraham
[gmx-users] nrexcl in topology Mark Abraham
[gmx-users] extending simulation Mark Abraham
[gmx-users] Editing potential parameters Mark Abraham
[gmx-users] Help regarding running DSSP in gmx Mark Abraham
[gmx-users] Trjconv PDB files define solvent as "ATOM"? Mark Abraham
[gmx-users] Problems with simulation on multi-nodes cluster Mark Abraham
[gmx-users] resolution of cygwin installation issues Mark Abraham
[gmx-users] resolution of cygwin installation issues Mark Abraham
[gmx-users] problem in oplsaa ffbonded.itp Mark Abraham
[gmx-users] regarding em potential energy positive Mark Abraham
[gmx-users] regarding em potential energy positive Mark Abraham
[gmx-users] on installation Xmgrace under cygwin Mark Abraham
[gmx-users] bond managment in grompp Mark Abraham
[gmx-users] on installation Xmgrace under cygwin Mark Abraham
[gmx-users] on xmgrace Mark Abraham
[gmx-users] Generating topology Mark Abraham
[gmx-users] bond managment in grompp Mark Abraham
[gmx-users] continue replica exchange MD Mark Abraham
[gmx-users] pdb2gmx input file error Mark Abraham
[gmx-users] Erroneous bond in average pdb Mark Abraham
[gmx-users] Generation of the Distance Restraints Mark Abraham
[gmx-users] Editing the functions of amber Mark Abraham
[gmx-users] Editing the functions of amber Mark Abraham
[gmx-users] Error: no domain decomposition, Source code file: domdec.c, line: 6436 Mark Abraham
[gmx-users] Editing the functions of amber Mark Abraham
[gmx-users] BUG: Free energy calculation Mark Abraham
[gmx-users] Equilibrate the water around my molecule Mark Abraham
[gmx-users] a question related to productioon MD Mark Abraham
[gmx-users] Problem in running Equilibration step Mark Abraham
[gmx-users] About center of mass removal Mark Abraham
[gmx-users] the RMSD of Bond lengths, Bond angles, Dihedrals and Impropers Mark Abraham
[gmx-users] How to automate genion completely? Mark Abraham
[gmx-users] grompp is adding a bond in my model that should not be there Mark Abraham
[gmx-users] error in oscillation period Mark Abraham
[gmx-users] grompp is adding a bond in my model that should not be there Mark Abraham
[gmx-users] Equilibrate the water around my molecule Mark Abraham
[gmx-users] Equilibrate the water around my molecule Mark Abraham
[gmx-users] temperature Mark Abraham
[gmx-users] Problem: pdb2gmx with a more complex system Mark Abraham
[gmx-users] Problem: pdb2gmx with a more complex system Mark Abraham
[gmx-users] amber99sb_virtual site lipids dopc MCH3_N constraint types Mark Abraham
[gmx-users] dssp error Mark Abraham
[gmx-users] Calculating the electrostatic potential at a point over time Mark Abraham
[gmx-users] Segmentation Fault using g_cluster Mark Abraham
[gmx-users] Segmentation Fault using g_cluster Mark Abraham
[gmx-users] Position restraints problem Mark Abraham
[gmx-users] Position restraints problem Mark Abraham
[gmx-users] on MD at constant pH Mark Abraham
[gmx-users] Generation of the Distance Restraints Mark Abraham
[gmx-users] Generation of the Distance Restraints Mark Abraham
[gmx-users] crazy temperatures Mark Abraham
[gmx-users] using MPI Mark Abraham
[gmx-users] Re:200 CPU, 3ns/day for 80,000 atoms Mark Abraham
[gmx-users] About movie in GROMACS Mark Abraham
[gmx-users] Pressure coupling doubt Mark Abraham
[gmx-users] Shima Arasteh wants to share a link | Gromacs Mark Abraham
[gmx-users] about g_mindist.... Mark Abraham
[gmx-users] mpirun Mark Abraham
[gmx-users] Not able to continue with Equilibration Mark Abraham
[gmx-users] about g_mindist.... Mark Abraham
[gmx-users] Velocity autocorrelation Mark Abraham
[gmx-users] Not able to continue with Equilibration Mark Abraham
[gmx-users] protein melting experiment by GROMACS Mark Abraham
[gmx-users] Re: do_dssp error Mark Abraham
[gmx-users] Editing of the existing system Mark Abraham
[gmx-users] Editing of the existing system Mark Abraham
[gmx-users] large scale simulation? Mark Abraham
[gmx-users] index.ndx files Mark Abraham
[gmx-users] Re: large scale simulation? Mark Abraham
[gmx-users] help needed Mark Abraham
[gmx-users] Acpype Parameter Error? Alan
[gmx-users] dssp error Albert
[gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!! Albert
[gmx-users] how to optimize hydrogen bonds before simulation? Albert
[gmx-users] Re: do_dssp error Albert
[gmx-users] Re: gmx-users Digest, Vol 95, Issue 208 Albert
[gmx-users] Re: gmx-users Digest, Vol 95, Issue 208 Albert
[gmx-users] large scale simulation? Albert
[gmx-users] Re: large scale simulation? Albert
[gmx-users] g_tune_pme error in blue gene Albert
[gmx-users] Shima Arasteh wants to share a link | Gromacs Shima Arasteh
[gmx-users] Simple LJ system Jeff Armstrong
[gmx-users] folding of coordinates in trajectory files Jeff Armstrong
[gmx-users] tpbconv and tpr file problem... Anthony Cruz Balberdi
[gmx-users] tpbconv and tpr file problem... Anthony Cruz Balberdi
[gmx-users] tpbconv and tpr file problem... Anthony Cruz Balberdi
[gmx-users] g_msd with input by trjconv -pbc nojump:a concern Ioannis Beis
[gmx-users] Re: g_msd with input by trjconv -pbc nojump:a concern Ioannis Beis
[gmx-users] how modify the forcefield amino acid definitions for non-naturally occuring amino acids? Kirill Bessonov
[gmx-users] Is TRO defined correctly in the ffG43a1p forcefield file? Kirill Bessonov
[gmx-users] Re: how modify the forcefield amino acid definitions for non-naturally occuring amino acids? Kirill Bessonov
[gmx-users] Shima Arasteh wants to share a link | Gromacs Emanuel Birru
[gmx-users] number of coordinates in coordinate file does not match topology Acoot Brett
Fw: [gmx-users] number of coordinates in coordinate file does not match topology Acoot Brett
[gmx-users] on "tcoupl= V-rescale" Acoot Brett
[gmx-users] on -t nvt.cpt in the Justine Lemkul tutorial Acoot Brett
[gmx-users] on installation of gromacs 455 Acoot Brett
[gmx-users] resolution of cygwin installation issues Acoot Brett
[gmx-users] on installation Xmgrace under cygwin Acoot Brett
[gmx-users] on installation Xmgrace under cygwin Acoot Brett
[gmx-users] on xmgrace Acoot Brett
[gmx-users] on gromacs force field Acoot Brett
[gmx-users] pdb2gmx input file error Acoot Brett
[gmx-users] a question related to energy minimization "mdrun -v -deffnm em" Acoot Brett
[gmx-users] pdb2gmx input file error Acoot Brett
[gmx-users] a question related to trjconv and pdb file extraction Acoot Brett
[gmx-users] refcoord_scaling Acoot Brett
[gmx-users] a question related to productioon MD Acoot Brett
[gmx-users] RMSD analysis during production MD Acoot Brett
[gmx-users] on MD at constant pH Acoot Brett
[gmx-users] calculation Tm of the protein by GROMACS Acoot Brett
[gmx-users] a question related to REMD Acoot Brett
[gmx-users] on the force field Acoot Brett
[gmx-users] non-equilibrium MD Acoot Brett
[gmx-users] About the function of "-v' in mdrun Acoot Brett
[gmx-users] protein melting experiment by GROMACS Acoot Brett
[gmx-users] How to read in mdcrd files to gromacs? Broadbent, Richard
[gmx-users] impropers and residue number Lara Bunte
[gmx-users] Lennard-Jones Interactions in Gromacs Lara Bunte
[gmx-users] [ bondedtypes ] Lara Bunte
[gmx-users] Re: Lennard-Jones Interactions in Gromacs Lara Bunte
[gmx-users] [ bondedtypes ] Lara Bunte
[gmx-users] How to answer in this mailing list? Lara Bunte
[gmx-users] How to answer in this mailing list? Lara Bunte
[gmx-users] em.mdp file Lara Bunte
[gmx-users] grompp error - bondedtypes Lara Bunte
[gmx-users] grompp - Invalid command line argument Lara Bunte
[gmx-users] [ pairs ] section in topology Lara Bunte
[gmx-users] Two [ dihedrals ] Sections in Topology Lara Bunte
[gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte
[gmx-users] mdrun - topol.tpr Lara Bunte
[gmx-users] grompp - Group protein not found Lara Bunte
[gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte
[gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte
[gmx-users] grompp - Group protein not found Lara Bunte
[gmx-users] Information on .mdp files Lara Bunte
[gmx-users] nrexcl in topology Lara Bunte
[gmx-users] grompp - Group protein not found Lara Bunte
[gmx-users] Group protein not found in index file Lara Bunte
[gmx-users] Box Size in MD Lara Bunte
[gmx-users] Equilibrate the water around my molecule Lara Bunte
[gmx-users] Equilibrate the water around my molecule Lara Bunte
[gmx-users] Equilibrate the water around my molecule Lara Bunte
[gmx-users] Equilibrate the water around my molecule Lara Bunte
[gmx-users] System exploding Lara Bunte
[gmx-users] Radial distribution function by COM Fabian Casteblanco
[gmx-users] Re: Resources on simulation walls Dr. Vitaly V. Chaban
[gmx-users] Re: on the RAM capacity needed for GROMACS Dr. Vitaly V. Chaban
[gmx-users] Re: Simulated Annealing Protocol Dr. Vitaly V. Chaban
[gmx-users] electrostatics in liquid/vapor interface Dr. Vitaly V. Chaban
[gmx-users] Re:200 CPU, 3ns/day for 80,000 atoms Dr. Vitaly V. Chaban
[gmx-users] Re: crazy temperatures Dr. Vitaly V. Chaban
[gmx-users] Re: how to optimize hydrogen bonds before simulation? Dr. Vitaly V. Chaban
[gmx-users] Re: large scale simulations Dr. Vitaly V. Chaban
[gmx-users] Re: hkl harker sections Dr. Vitaly V. Chaban
[gmx-users] Gromacs 4.5.5 GPU Error TH Chew
[gmx-users] mpirun TH Chew
[gmx-users] grompp is adding a bond in my model that should not be there Jackson Chief
[gmx-users] grompp is adding a bond in my model that should not be there Jackson Chief
[gmx-users] new OPLS-AA dihedral parameters for hydrocarbons ? Ester Chiessi
[gmx-users] g_rotacf autocorrelation function Yongchul Chung
[gmx-users] Re: g_rotacf autocorrelation function Yongchul Chung
[gmx-users] GROMACS stalls for NPT simulation when using -npme and -dd flags Stephen Cox
[gmx-users] Re: gmx-users Digest, Vol 95, Issue 60 Stephen Cox
[gmx-users] Re: gmx-users Digest, Vol 95, Issue 60 Stephen Cox
[gmx-users] GROMACS stalls for NPT simulation when using -npme and -dd flags Stephen Cox
[gmx-users] grompp warning with SHAKE, but ok with LINCS D_Roy
[gmx-users] Re: Test particle insertion extra coordinate João M. Damas
[gmx-users] Re: Test particle insertion extra coordinate João M. Damas
[gmx-users] Charge groups for particle insertion João M. Damas
[gmx-users] Advice on High Precision Structure File Formats Andrew DeYoung
[gmx-users] Periodic molecules and minimum bonded cut-off Andrew DeYoung
[gmx-users] Periodic molecules and minimum bonded cut-off Andrew DeYoung
[gmx-users] Recommended protocol for cooling down temperature in 50 K steps Andrew DeYoung
[gmx-users] Resources on simulation walls Andrew DeYoung
[gmx-users] Calculating the center of mass of a molecule Andrew DeYoung
[gmx-users] Literature reading on DispCorr for energy and pressure Andrew DeYoung
[gmx-users] How the pressure is computed Andrew DeYoung
[gmx-users] Re: How the pressure is computed Andrew DeYoung
[gmx-users] Where in the source code is the .edr file written? Andrew DeYoung
[gmx-users] Energy exclusions for freeze groups, and the pressure Andrew DeYoung
[gmx-users] Re: Energy exclusions for freeze groups, and the pressure Andrew DeYoung
[gmx-users] Creating an atomtype where all nonbonded interactions are enumerated Andrew DeYoung
[gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated Andrew DeYoung
[gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated Andrew DeYoung
[gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated Andrew DeYoung
[gmx-users] Do checkpoint files contain energies? Andrew DeYoung
[gmx-users] Calculating the electrostatic potential at a point over time Andrew DeYoung
[gmx-users] Using CHARMM27 with TIP4PEW Karl Debiec
[gmx-users] Amber99bsc0 Matthias Ernst
[gmx-users] Gromacs 3.3.3 on Lion Xgrid Esztermann, Ansgar
[gmx-users] questions about Principal Component Analysis Thomas Evangelidis
[gmx-users] Re: questions about Principal Component Analysis Thomas Evangelidis
[gmx-users] cluster analysis of flexible peptide trajectory Thomas Evangelidis
[gmx-users] Principal Components Analysis in Gromacs Thomas Evangelidis
[gmx-users] Re: Gromacs-GPU benchmark test killed after exhausting the memory Efrat Exlrod
[gmx-users] deformations aplying an electric field Rebeca García Fandiño
[gmx-users] question about replica exchange Asaf Farhi
[gmx-users] Editing potential parameters Asaf Farhi
[gmx-users] Editing the functions of amber Asaf Farhi
[gmx-users] Editing the functions of amber Asaf Farhi
[gmx-users] Editing the functions of amber Asaf Farhi
[gmx-users] Editing the functions of amber Asaf Farhi
[gmx-users] Editing the functions of amber Asaf Farhi
[gmx-users] Editing the functions of amber Asaf Farhi
[gmx-users] x,y and z components of rmsf? Asaf Farhi
[gmx-users] g_msd segmentation fault Dommert Florian
[gmx-users] mdrun - topol.tpr Dommert Florian
[gmx-users] g_msd with input by trjconv -pbc nojump:a concern Dommert Florian
[gmx-users] Re: g_msd with input by trjconv -pbc nojump:a concern Dommert Florian
[gmx-users] Ion parameters in OPLS AA force field Dommert Florian
[gmx-users] Ion parameters in OPLS AA force field Dommert Florian
[gmx-users] Re: Re: Ion parameters in OPLS AA force field Dommert Florian
[gmx-users] Re: large scale simulation? Dommert Florian
[gmx-users] Re: large scale simulation? Dommert Florian
[gmx-users] RE: quasi-harmonic entropy calculation Ran Friedman
[gmx-users] radial distribution normal in g_order Denny Frost
[gmx-users] crazy temperatures Warren Gallin
[gmx-users] Reading starting velocities Ignacio Fernández Galván
[gmx-users] Velocity autocorrelation Ignacio Fernández Galván
[gmx-users] Velocity autocorrelation Ignacio Fernández Galván
[gmx-users] Velocity autocorrelation Ignacio Fernández Galván
[gmx-users] Velocity autocorrelation Ignacio Fernández Galván
[gmx-users] Charge delocalization fullerene R.Perez Garcia
[gmx-users] Charge delocalization fullerene R.Perez Garcia
[gmx-users] center the system on specific atoms type R.Perez Garcia
[gmx-users] center the system on specific atoms type R.Perez Garcia
[gmx-users] nrexcl in topology R.Perez Garcia
[gmx-users] ***Extended deadline: March 26*** COMETS 2012 - 3rd International Track on Collaborative Modeling and Simulation - Call for Papers Daniele Gianni
[gmx-users] Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q Biswajit Gorai
[gmx-users] Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q Biswajit Gorai
[gmx-users] Re: How to add dihedral information from the GAFF topology Biswajit Gorai
[gmx-users] Where would I find the 45A4 GROMOS force field? Marc Gordon
[gmx-users] Where would I find the 45A4 GROMOS force field? Marc Gordon
[gmx-users] Where would I find the 45A4 GROMOS force field? Marc Gordon
[gmx-users] g_energy Kinetic Energy Hovakim Grabski
[gmx-users] HBonds between molecules Hovakim Grabski
[gmx-users] DNA podophyllotoxin Hovakim Grabski
[gmx-users] Re: on MD at constant pH (Acoot Brett) Gerrit Groenhof
[gmx-users] Gromacs 3.3.3 on Lion Xgrid Benjamin Hall
[gmx-users] Not able to continue with Equilibration Hendry
[gmx-users] Not able to continue with Equilibration Hendry
[gmx-users] dssp and gromacs version João Henriques
[gmx-users] problem with g_bar Berk Hess
[gmx-users] Re: RE: problem with g_bar Berk Hess
[gmx-users] g_wham position 0 Jochen Hub
[gmx-users] Statistical error of Umbrella Sampling Jochen Hub
[gmx-users] Installing g_mdmat from Gromacs analysis package Suhaila Haji Mohd Hussin
[gmx-users] Problem Installing Gromacs Suhaila Haji Mohd Hussin
[gmx-users] Problem Installing Gromacs Suhaila Haji Mohd Hussin
[gmx-users] Problem installing Gromacs: What next? Suhaila Haji Mohd Hussin
[gmx-users] FW: Problem installing Gromacs: What next? Suhaila Haji Mohd Hussin
[gmx-users] FW: Problem installing Gromacs: What next? Suhaila Haji Mohd Hussin
FW: [gmx-users] FW: Problem installing Gromacs: What next? Suhaila Haji Mohd Hussin
[gmx-users] Cluster analysis IISER_Minal
[gmx-users] cannot determine precision of trn file Nidhi Katyal
[gmx-users] cannot determine precision of trn file Nidhi Katyal
[gmx-users] addition of two solvents Nidhi Katyal
[gmx-users] HB lifetime Nidhi Katyal
[gmx-users] HB lifetime Nidhi Katyal
[gmx-users] HB lifetime Nidhi Katyal
[gmx-users] amber99sb_virtual site lipids dopc MCH3_N constraint types Song Ke
[gmx-users] Re: gmx-users Digest, Vol 95, Issue 175 Song Ke
[gmx-users] Re: Re: Ion parameters in OPLS AA force field Kathleen Kirchner
[gmx-users] g_bar bug with temperature Tom Kirchner
[gmx-users] problem with g_bar Tom Kirchner
[gmx-users] Re: RE: problem with g_bar Tom Kirchner
[gmx-users] Re: RE: RE: problem with g_bar Tom Kirchner
[gmx-users] CHARMM27 topology for DOPC Krzysztof Kuczera
[gmx-users] Velocity autocorrelation Krzysztof Kuczera
[gmx-users] grompp error - bondedtypes Kukol, Andreas
[gmx-users] grompp - Group protein not found Kukol, Andreas
[gmx-users] continue replica exchange MD Kukol, Andreas
[gmx-users] fatal error Kukol, Andreas
[gmx-users] REMD equilibration Kukol, Andreas
[gmx-users] Trjconv PDB files define solvent as "ATOM"? John Ladasky
[gmx-users] Trjconv PDB files define solvent as "ATOM"? John Ladasky
[gmx-users] How to automate genion completely? John Ladasky
[gmx-users] how to use charmm ff in gmx and carbohydrate forcefield Peter C. Lai
[gmx-users] Extending simulation with -pd Peter C. Lai
[gmx-users] Gromacs 3.3.3 on Lion Xgrid Peter C. Lai
[gmx-users] grompp - Group protein not found Peter C. Lai
[gmx-users] Missing Interactions in [ angles ] Section in Topology Peter C. Lai
[gmx-users] HOW TO USE SILVER ATOMS IN AMBER99 FORCE FIELD Peter C. Lai
[gmx-users] grompp - Group protein not found Peter C. Lai
[gmx-users] Missing Interactions in [ angles ] Section in Topology Peter C. Lai
[gmx-users] gromacs 4.5.5 cygwin installation error message Peter C. Lai
[gmx-users] gromacs 4.5.5 cygwin installation error message Peter C. Lai
[gmx-users] gromacs 4.5.5 cygwin installation error message Peter C. Lai
[gmx-users] gromacs 4.5.5 cygwin installation error message Peter C. Lai
[gmx-users] gromacs 4.5.5 cygwin installation error message Peter C. Lai
[gmx-users] hydrogen hydrogen interaction Peter C. Lai
[gmx-users] Problems with simulation on multi-nodes cluster Peter C. Lai
[gmx-users] a question related to energy minimization "mdrun -v -deffnm em" Peter C. Lai
[gmx-users] CHARMM27 topology for DOPC Peter C. Lai
[gmx-users] Fatal error: Atom CG is used in the topology database... Peter C. Lai
[gmx-users] Adjust time intervals Peter C. Lai
[gmx-users] About the function of "-v' in mdrun Peter C. Lai
[gmx-users] large scale simulation? Peter C. Lai
[gmx-users] index.ndx files Peter C. Lai
[gmx-users] Re: Umbrella Sampling - ligand Justin A. Lemkul
[gmx-users] Segmentation fault - Implicit solvent Justin A. Lemkul
[gmx-users] Random option - genion Justin A. Lemkul
[gmx-users] Segmentation fault - Implicit solvent Justin A. Lemkul
[gmx-users] genconf -renumber merges atom number and ID columns Justin A. Lemkul
[gmx-users] Segmentation fault - Implicit solvent Justin A. Lemkul
[gmx-users] impropers and residue number Justin A. Lemkul
[gmx-users] Re: Re: mdrun -multi flag (Mark Abraham) Justin A. Lemkul
[gmx-users] Re: Lennard-Jones Interactions in Gromacs Justin A. Lemkul
[gmx-users] [ bondedtypes ] Justin A. Lemkul
[gmx-users] Re: Re: Re: Re: mdrun -multi flag (Mark Abraham) (Justin A. Lemkul) Justin A. Lemkul
[gmx-users] Is TRO defined correctly in the ffG43a1p forcefield file? Justin A. Lemkul
[gmx-users] how modify the forcefield amino acid definitions for non-naturally occuring amino acids? Justin A. Lemkul
[gmx-users] a warning in grompp Justin A. Lemkul
[gmx-users] Simple LJ system Justin A. Lemkul
[gmx-users] Re: how modify the forcefield amino acid definitions for non-naturally occuring amino acids? Justin A. Lemkul
[gmx-users] Umbrella Sampling - NPT Justin A. Lemkul
[gmx-users] Re: Lennard-Jones Interactions in Gromacs Justin A. Lemkul
[gmx-users] Imitation of the protein part Justin A. Lemkul
[gmx-users] em.mdp file Justin A. Lemkul
[gmx-users] em.mdp file Justin A. Lemkul
[gmx-users] grompp error - bondedtypes Justin A. Lemkul
[gmx-users] grompp error - bondedtypes Justin A. Lemkul
[gmx-users] a question related to MD by gromacs Justin A. Lemkul
[gmx-users] tpbconv to extend a simulation Justin A. Lemkul
[gmx-users] grompp - Invalid command line argument Justin A. Lemkul
[gmx-users] [ pairs ] section in topology Justin A. Lemkul
[gmx-users] Two [ dihedrals ] Sections in Topology Justin A. Lemkul
[gmx-users] Missing Interactions in [ angles ] Section in Topology Justin A. Lemkul
[gmx-users] Missing Interactions in [ angles ] Section in Topology Justin A. Lemkul
[gmx-users] Inconsistent shifts - is it something wrong with pbc Justin A. Lemkul
[gmx-users] g_sdf -> and g_spatial Justin A. Lemkul
[gmx-users] Umbrella_pull_simulation Justin A. Lemkul
[gmx-users] Missing Interactions in [ angles ] Section in Topology Justin A. Lemkul
[gmx-users] g_select problem (Invalid command line argument:) Justin A. Lemkul
[gmx-users] hydrophobic and hydrophilic in implicit solvent Justin A. Lemkul
[gmx-users] Periodic molecules and minimum bonded cut-off Justin A. Lemkul
[gmx-users] g_energy Kinetic Energy Justin A. Lemkul
[gmx-users] g_select vs trjorder Justin A. Lemkul
[gmx-users] Umbrella Sampling - Ligand Protein Justin A. Lemkul
[gmx-users] g_select vs trjorder Justin A. Lemkul
[gmx-users] g_select vs trjorder Justin A. Lemkul
[gmx-users] Radial distribution function by COM Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] g_helix not recognizing protein backbone Justin A. Lemkul
[gmx-users] 'not allocate memory' Justin A. Lemkul
[gmx-users] Recommended protocol for cooling down temperature in 50 K steps Justin A. Lemkul
[gmx-users] Missing Interactions in [ angles ] Section in Topology Justin A. Lemkul
[gmx-users] Force field Justin A. Lemkul
[gmx-users] genconf Justin A. Lemkul
[gmx-users] genconf Justin A. Lemkul
[gmx-users] genconf, grompp Justin A. Lemkul
[gmx-users] genconf,grompp Justin A. Lemkul
[gmx-users] Calculating the center of mass of a molecule Justin A. Lemkul
[gmx-users] Installing g_mdmat from Gromacs analysis package Justin A. Lemkul
[gmx-users] genbox,genconf Justin A. Lemkul
[gmx-users] Umbrella Sampling - Ligand Protein Justin A. Lemkul
[gmx-users] protein-ligand tutorial problem Justin A. Lemkul
[gmx-users] Segmentation fault Justin A. Lemkul
[gmx-users] Umbrella Sampling - Ligand Protein Justin A. Lemkul
[gmx-users] Generation of the Distance Restraints Justin A. Lemkul
[gmx-users] Umbrella Sampling - Ligand Protein Justin A. Lemkul
[gmx-users] pdb file Justin A. Lemkul
[gmx-users] Generation of the Distance Restraints Justin A. Lemkul
[gmx-users] Reg final error Justin A. Lemkul
[gmx-users] addition of two solvents Justin A. Lemkul
[gmx-users] How the pressure is computed Justin A. Lemkul
[gmx-users] clashes Justin A. Lemkul
[gmx-users] Re: How the pressure is computed Justin A. Lemkul
[gmx-users] clashes Justin A. Lemkul
Fwd: [gmx-users] Generation of the Distance Restraints Justin A. Lemkul
Fwd: [gmx-users] Generation of the Distance Restraints Justin A. Lemkul
[gmx-users] hydrogen hydrogen interaction Justin A. Lemkul
[gmx-users] Umbrella_pull_simulation Justin A. Lemkul
[gmx-users] Information on .mdp files Justin A. Lemkul
[gmx-users] g_sas Justin A. Lemkul
[gmx-users] bug in g_msd Justin A. Lemkul
[gmx-users] g_sas Justin A. Lemkul
[gmx-users] Simulated Annealing Protocol... Justin A. Lemkul
[gmx-users] Gromacs installation question: Where is my Gromacs? Justin A. Lemkul
[gmx-users] Gromacs installation question: Where is my Gromacs? Justin A. Lemkul
[gmx-users] Gromacs installation question: Where is my Gromacs? Justin A. Lemkul
[gmx-users] Simulated Annealing Protocol... Justin A. Lemkul
[gmx-users] g_sas; could not find a Van der Waals radius Justin A. Lemkul
[gmx-users] How to do Normal Modes Analysis with Gromacs4.5.5? Justin A. Lemkul
[gmx-users] Simulated Annealing Protocol... Justin A. Lemkul
[gmx-users] opls topology for butanol, hexanol, heptanol Justin A. Lemkul
[gmx-users] HBonds between molecules Justin A. Lemkul
[gmx-users] Problem Installing Gromacs Justin A. Lemkul
[gmx-users] Problem installing Gromacs: What next? Justin A. Lemkul
[gmx-users] FW: Problem installing Gromacs: What next? Justin A. Lemkul
[gmx-users] FW: Problem installing Gromacs: What next? Justin A. Lemkul
[gmx-users] number of coordinates in coordinate file does not match topology Justin A. Lemkul
[gmx-users] Group protein not found in index file Justin A. Lemkul
[gmx-users] Group protein not found in index file Justin A. Lemkul
[gmx-users] FW: Problem installing Gromacs: What next? Justin A. Lemkul
[gmx-users] Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q Justin A. Lemkul
[gmx-users] Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] problem in oplsaa ffbonded.itp Justin A. Lemkul
[gmx-users] regarding em potential energy positive Justin A. Lemkul
[gmx-users] regarding em potential energy positive Justin A. Lemkul
[gmx-users] Creating an atomtype where all nonbonded interactions are enumerated Justin A. Lemkul
[gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated Justin A. Lemkul
[gmx-users] Box Size in MD Justin A. Lemkul
[gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated Justin A. Lemkul
[gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated Justin A. Lemkul
[gmx-users] a question related to trjconv and pdb file extraction Justin A. Lemkul
[gmx-users] Structure averaging problem using g_rmsf Justin A. Lemkul
[gmx-users] REMD equilibration Justin A. Lemkul
[gmx-users] Re: Neigborsearching, Electrostatics and vdw options Justin A. Lemkul
[gmx-users] BUG: Free energy calculation Justin A. Lemkul
[gmx-users] genbox Justin A. Lemkul
[gmx-users] refcoord_scaling Justin A. Lemkul
[gmx-users] parameters of em.mdp Justin A. Lemkul
[gmx-users] parameters of em.mdp Justin A. Lemkul
[gmx-users] Do checkpoint files contain energies? Justin A. Lemkul
[gmx-users] Fatal error: Atom CG is used in the topology database... Justin A. Lemkul
[gmx-users] renumber charge group Justin A. Lemkul
[gmx-users] RMSD analysis during production MD Justin A. Lemkul
[gmx-users] How to automate genion completely? Justin A. Lemkul
[gmx-users] Adjust time intervals Justin A. Lemkul
[gmx-users] Adjust time intervals Justin A. Lemkul
[gmx-users] Adjust time intervals Justin A. Lemkul
[gmx-users] Fatal error: Atom CG is used in the topology database... Justin A. Lemkul
[gmx-users] Re: How to add dihedral information from the GAFF topology Justin A. Lemkul
[gmx-users] About center of mass removal Justin A. Lemkul
[gmx-users] Equilibrate the water around my molecule Justin A. Lemkul
[gmx-users] Re: How to add dihedral information from the GAFF topology Justin A. Lemkul
[gmx-users] Problem: pdb2gmx with a more complex system Justin A. Lemkul
[gmx-users] Re: How to add dihedral information from the GAFF topology Justin A. Lemkul
[gmx-users] Re: How to add dihedral information from the GAFF topology Justin A. Lemkul
[gmx-users] Re: How to add dihedral information from the GAFF topology Justin A. Lemkul
[gmx-users] on MD at constant pH Justin A. Lemkul
[gmx-users] Re: How to add dihedral information from the GAFF topology Justin A. Lemkul
[gmx-users] Where would I find the 45A4 GROMOS force field? Justin A. Lemkul
[gmx-users] a question related to REMD Justin A. Lemkul
[gmx-users] Where would I find the 45A4 GROMOS force field? Justin A. Lemkul
[gmx-users] Re: How to add dihedral information from the GAFF topology Justin A. Lemkul
[gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!! Justin A. Lemkul
[gmx-users] construction of homopolymer from non-standard monomers in gromacs Justin A. Lemkul
[gmx-users] About cutt-off scheme .. Justin A. Lemkul
[gmx-users] About cutt-off scheme .. Justin A. Lemkul
[gmx-users] About cutt-off scheme .. Justin A. Lemkul
[gmx-users] How to fix Water during simulation ? Justin A. Lemkul
[gmx-users] Not able to continue with Equilibration Justin A. Lemkul
[gmx-users] Not able to continue with Equilibration Justin A. Lemkul
[gmx-users] About Distance.pl script Justin A. Lemkul
[gmx-users] About Distance.pl script Justin A. Lemkul
[gmx-users] About desired Spacing in Distance.pl script Justin A. Lemkul
[gmx-users] how to optimize hydrogen bonds before simulation? Justin A. Lemkul
[gmx-users] System exploding Justin A. Lemkul
[gmx-users] protein melting experiment by GROMACS Justin A. Lemkul
[gmx-users] Not able to continue with Equilibration Justin A. Lemkul
[gmx-users] HB lifetime Justin A. Lemkul
[gmx-users] About Umbrella spacing Justin A. Lemkul
[gmx-users] DNA podophyllotoxin Justin A. Lemkul
[gmx-users] index.ndx files Justin A. Lemkul
[gmx-users] Editing of the existing system Justin A. Lemkul
[gmx-users] Regarding to relaxation time Justin A. Lemkul
[gmx-users] Editing of the existing system Justin A. Lemkul
[gmx-users] genion Justin A. Lemkul
[gmx-users] genion Justin A. Lemkul
[gmx-users] Editing of the existing system Justin A. Lemkul
[gmx-users] Cutoff settings for CHARMM36 Siew Wen Leong
[gmx-users] mdrun - topol.tpr Siew Wen Leong
[gmx-users] Re: Dielectric constant calculation with Gromacs-3.3.1 Liang
[gmx-users] Help us steer future GROMACS development, with a chance to win a $2000+ Tesla C2075 GPU Erik Lindahl
[gmx-users] IMPORTANT REMINDER: Gromacs survey (with a chance to win a $2000 GPU) Erik Lindahl
[gmx-users] Announcement: Large biomolecule benchmark report Hannes Loeffler
[gmx-users] Announcement: Large biomolecule benchmark report Hannes Loeffler
[gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!! Hannes Loeffler
[gmx-users] Umbrella sampling along Radius of gyration Sanku M
[gmx-users] Test particle insertion extra coordinate MPID
[gmx-users] Re: Test particle insertion extra coordinate MPID
[gmx-users] Re: Test particle insertion extra coordinate MPID
[gmx-users] Re: Test particle insertion extra coordinate MPID
[gmx-users] g_helix not recognizing protein backbone MPID
[gmx-users] Re: g_helix not recognizing protein backbone MPID
[gmx-users] Looking for a GROMACS expert for summer'2012 intern/co-op MQ
[gmx-users] Bus error Erik Marklund
[gmx-users] using MPI Erik Marklund
[gmx-users] continue replica exchange MD Erik Marklund
[gmx-users] REMD equilibration Erik Marklund
[gmx-users] dssp error Erik Marklund
[gmx-users] amber99sb_virtual site lipids dopc MCH3_N constraint types Erik Marklund
[gmx-users] x,y and z components of rmsf? Erik Marklund
[gmx-users] Calculate Bulk Pressure Tensor? Erik Marklund
[gmx-users] HB lifetime Erik Marklund
[gmx-users] HB lifetime Erik Marklund
[gmx-users] Re: do_dssp error Erik Marklund
[gmx-users] Re: gmx-users Digest, Vol 95, Issue 208 Erik Marklund
[gmx-users] Scale down/ up velocities when coupling temperature and pressure? Erik Marklund
[gmx-users] em.mdp file Marzinek, Jan
[gmx-users] on -t nvt.cpt in the Justine Lemkul tutorial Marzinek, Jan
[gmx-users] a warning in grompp Banafsheh Mehrazma
[gmx-users] g_msd segmentation fault Gavin Melaugh
[gmx-users] folding of coordinates in trajectory files Gavin Melaugh
[gmx-users] bug in g_msd Gavin Melaugh
[gmx-users] [Fwd: bug in g_msd] Gavin Melaugh
[gmx-users] fatal error Gavin Melaugh
[gmx-users] genbox Gavin Melaugh
[gmx-users] RMSD sudden jump Davide Mercadante
[gmx-users] RMSD sudden jump Davide Mercadante
[gmx-users] RMSD sudden jump Davide Mercadante
[gmx-users] Segmentation Fault using g_cluster Davide Mercadante
[gmx-users] Segmentation Fault using g_cluster Davide Mercadante
[gmx-users] Martini Dariush Mohammadyani
[gmx-users] Martini Dariush Mohammadyani
[gmx-users] clashes Dariush Mohammadyani
[gmx-users] clashes Dariush Mohammadyani
[gmx-users] Box Size in MD Dariush Mohammadyani
[gmx-users] About Distance.pl script Dariush Mohammadyani
[gmx-users] GROMACS roadmap? GROMACS - OpenMM collaboration? Marco Moller
[gmx-users] dihedral distributions Juliette N.
[gmx-users] dihedral distributions Juliette N.
[gmx-users] tpbconv to extend a simulation Juliette N.
[gmx-users] Reg final error RAMYA NAGA
[gmx-users] Dimethyl Sulfoxide Electromagnetic Absorbance Nancy
[gmx-users] Dimethyl Sulfoxide Electromagnetic Absorbance Nancy
[gmx-users] Dimethyl Sulfoxide EM Absorbance Nancy
[gmx-users] DNA podophyllotoxin Paulo Netz
[gmx-users] PBC - Protein and Ligands Steven Neumann
[gmx-users] Segmentation fault - Implicit solvent Steven Neumann
[gmx-users] Segmentation fault - Implicit solvent Steven Neumann
[gmx-users] Segmentation fault - Implicit solvent Steven Neumann
[gmx-users] Segmentation fault - Implicit solvent Steven Neumann
[gmx-users] Segmentation fault - Implicit solvent Steven Neumann
[gmx-users] Segmentation fault - Implicit solvent Steven Neumann
[gmx-users] Segmentation fault - Implicit solvent Steven Neumann
[gmx-users] Extending simulation with -pd Steven Neumann
[gmx-users] Umbrella Sampling - NPT Steven Neumann
[gmx-users] Imitation of the protein part Steven Neumann
[gmx-users] Coupling groups Steven Neumann
[gmx-users] Coupling groups Steven Neumann
[gmx-users] Coupling groups Steven Neumann
[gmx-users] Helix - Ligand binding - mimic stability Steven Neumann
[gmx-users] Umbrella Sampling - Ligand Protein Steven Neumann
[gmx-users] Umbrella Sampling - Protein Ligand Steven Neumann
[gmx-users] Umbrella Sampling - Ligand Protein Steven Neumann
[gmx-users] Umbrella Sampling - Ligand Protein Steven Neumann
[gmx-users] Umbrella Sampling - Ligand Protein Steven Neumann
[gmx-users] Umbrella Sampling - Ligand Protein Steven Neumann
[gmx-users] entropic contribution from Umbrella Sampling Steven Neumann
[gmx-users] Force constant - Umbrella Sampling Steven Neumann
[gmx-users] Statistical error of Umbrella Sampling Steven Neumann
[gmx-users] index.ndx files Eduardo Oliveira
[gmx-users] index.ndx files Eduardo Oliveira
[gmx-users] index.ndx files Eduardo Oliveira
[gmx-users] genion Eduardo Oliveira
[gmx-users] Resources on simulation walls Francesco Oteri
[gmx-users] Structural features for LINCS application Francesco Oteri
[gmx-users] Structural features for LINCS application Francesco Oteri
[gmx-users] Importance of -rcon and -dd options when using mdrun with mpi. PAVAN PAYGHAN
[gmx-users] Re.Importance of -rcon and -dd options when PAVAN PAYGHAN
[gmx-users] Re: Importance of -rcon and -dd options PAVAN PAYGHAN
[gmx-users] gromacs 4.5.5 cygwin installation error message Wholly Peach
[gmx-users] gromacs 4.5.5 cygwin installation error message Wholly Peach
Fw: [gmx-users] gromacs 4.5.5 cygwin installation error message Wholly Peach
[gmx-users] gromacs 4.5.5 cygwin installation error message Wholly Peach
[gmx-users] gromacs 4.5.5 cygwin installation error message Wholly Peach
[gmx-users] gromacs 4.5.5 cygwin installation error message Wholly Peach
[gmx-users] gromacs 3.3.3 and gromacs 4.5.5 Wholly Peach
[gmx-users] on the RAM capacity needed for GROMACS Wholly Peach
[gmx-users] pdb2gmx error message Wholly Peach
[gmx-users] genion -pname no NA molecule (sodium) type Wholly Peach
[gmx-users] genion -pname no NA molecule (sodium) type Wholly Peach
[gmx-users] Equilibriation nvt.mdp error Wholly Peach
[gmx-users] newest version of gromacs under cygwin Wholly Peach
[gmx-users] g_fg2cg XAvier Periole
[gmx-users] About martini XAvier Periole
[gmx-users] Exploding Protein with 4.6 and 4.5.5 XAvier Periole
[gmx-users] g_dist without output file Atila Petrosian
[gmx-users] g_spatial (gromacs 4.5 manual) Atila Petrosian
[gmx-users] g_dist without output file Atila Petrosian
[gmx-users] g_dist without output file Atila Petrosian
[gmx-users] g_dist without output file Atila Petrosian
[gmx-users] Literature reading on DispCorr for energy and pressure Thomas Piggot
[gmx-users] Ion parameters in OPLS AA force field Thomas Piggot
[gmx-users] g_energy Payman Pirzadeh
[gmx-users] g_energy surf*surftens Payman Pirzadeh
[gmx-users] help on replica exchange dynamics with gromacs Raghuvir Pissurlenkar
[gmx-users] SUGAR-PIE: Scripted Utility to Get Atomic Resolution by Positional Interpolation/Extrapolation Ángel Piñeiro
[gmx-users] on the dissociation of protein complex during MD Dialing Pretty
[gmx-users] a question related to MD by gromacs Dialing Pretty
[gmx-users] I need a tutorial for gromacs-4.0.5 Dialing Pretty
[gmx-users] I need a tutorial for gromacs-4.0.5 Dialing Pretty
[gmx-users] Force field Dialing Pretty
[gmx-users] Gromacs installation in Cygwin Dialing Pretty
[gmx-users] -p topol.top input/output error Dialing Pretty
[gmx-users] -p topol.top input/output error Dialing Pretty
[gmx-users] uninstall gromacs Dialing Pretty
[gmx-users] -p topol.top input/output error Dialing Pretty
[gmx-users] error message during make after gtomacs configuration Dialing Pretty
[gmx-users] error message during make after gtomacs configuration Dialing Pretty
[gmx-users] Gromacs-GPU benchmark test killed after exhausting the memory Szilárd Páll
[gmx-users] Re: Gromacs-GPU benchmark test killed after exhausting the memory Szilárd Páll
[gmx-users] GROMACS stalls for NPT simulation when using -npme and -dd flags Szilárd Páll
[gmx-users] Gromacs 4.5.5 GPU Error Szilárd Páll
[gmx-users] Announcement: Large biomolecule benchmark report Szilárd Páll
[gmx-users] Scaling/performance on Gromacs 4 Szilárd Páll
[gmx-users] 4.6 development version Szilárd Páll
[gmx-users] Vi plugin for Gromacs files Szilárd Páll
[gmx-users] About the function of "-v' in mdrun Szilárd Páll
[gmx-users] large scale simulation? Szilárd Páll
[gmx-users] pull code - i-motif constant velocity pull Raghav
AW: [gmx-users] Information on .mdp files Rausch, Felix
AW: [gmx-users] About movie in GROMACS Rausch, Felix
AW: [gmx-users] Not able to continue with Equilibration Rausch, Felix
AW: [gmx-users] Not able to continue with Equilibration Rausch, Felix
[gmx-users] Umbrella sampling multiple pull groups Sabine Reisser
[gmx-users] Umbrella sampling multiple pull groups Sabine Reisser
[gmx-users] BUG: Free energy calculation Sabine Reisser
[gmx-users] BUG: Free energy calculation Sabine Reisser
[gmx-users] Random option - genion Maurício Menegatti Rigo
[gmx-users] Random option - genion Maurício Menegatti Rigo
[gmx-users] temperature Roy Roshko
[gmx-users] a request regarding pdb2gmx and specbond.dat Ehud Schreiber
[gmx-users] 4.6 development version SebastianWaltz
[gmx-users] AZH (AZIDOHOMOALANINE) or C4 H8 N4 O2 SebastianWaltz
[gmx-users] REMD equilibration SebastianWaltz
[gmx-users] Exploding Protein with 4.6 and 4.5.5 SebastianWaltz
[gmx-users] (no subject) Anik Sen
[gmx-users] Dielectric constant calculation with Gromacs-3.3.1 Liang Shi
[gmx-users] Scale down/ up velocities when coupling temperature and pressure? Yun Shi
[gmx-users] BUG: Free energy calculation Michael Shirts
[gmx-users] BUG: Free energy calculation Michael Shirts
[gmx-users] genconf -renumber merges atom number and ID columns Ricardo O. S. Soares
[gmx-users] genconf -renumber merges atom number and ID columns Ricardo O. S. Soares
[gmx-users] Charmm Cholesterol parameters - str to itp Ricardo O. S. Soares
[gmx-users] Charmm Cholesterol parameters - str to itp Ricardo O. S. Soares
[gmx-users] Fatal error: Atom CG is used in the topology database... Andy Somogyi
[gmx-users] Fatal error: Atom CG is used in the topology database... Andy Somogyi
[gmx-users] Advice on High Precision Structure File Formats David van der Spoel
[gmx-users] genconf David van der Spoel
[gmx-users] Dielectric constant calculation with Gromacs-3.3.1 David van der Spoel
[gmx-users] Re: Dielectric constant calculation with Gromacs-3.3.1 David van der Spoel
[gmx-users] There was 1 error in input file(s) David van der Spoel
[gmx-users] Announcement: Large biomolecule benchmark report David van der Spoel
[gmx-users] Gromacs installation question: Where is my Gromacs? David van der Spoel
[gmx-users] Gromacs installation question: Where is my Gromacs? David van der Spoel
[gmx-users] Gromacs installation question: Where is my Gromacs? David van der Spoel
[gmx-users] How to do Normal Modes Analysis with Gromacs4.5.5? David van der Spoel
[gmx-users] How to do Normal Modes Analysis with Gromacs4.5.5? David van der Spoel
[gmx-users] Dimethyl Sulfoxide Electromagnetic Absorbance David van der Spoel
[gmx-users] Re: quasi-harmonic entropy calculation David van der Spoel
[gmx-users] Charmm Cholesterol parameters - str to itp David van der Spoel
[gmx-users] Re: How to add dihedral information from the GAFF topology David van der Spoel
[gmx-users] on the force field David van der Spoel
[gmx-users] Velocity autocorrelation David van der Spoel
[gmx-users] Velocity autocorrelation David van der Spoel
[gmx-users] large scale simulation? David van der Spoel
[gmx-users] g_energy surf*surftens David van der Spoel
[gmx-users] Velocity autocorrelation David van der Spoel
[gmx-users] Re: large scale simulations David van der Spoel
[gmx-users] (no subject) Ashalatha Sreshty
[gmx-users] Error: no domain decomposition, Source code file: domdec.c, line: 6436 Ashalatha Sreshty
[gmx-users] Distance between selected atoms during simulation James Starlight
[gmx-users] Generation of the Distance Restraints James Starlight
[gmx-users] Generation of the Distance Restraints James Starlight
[gmx-users] Generation of the Distance Restraints James Starlight
[gmx-users] Generation of the Distance Restraints James Starlight
[gmx-users] Generation of the Distance Restraints James Starlight
[gmx-users] Generation of the Distance Restraints James Starlight
[gmx-users] Generation of the Distance Restraints James Starlight
Fwd: [gmx-users] Generation of the Distance Restraints James Starlight
Fwd: [gmx-users] Generation of the Distance Restraints James Starlight
[gmx-users] Problems with simulation on multi-nodes cluster James Starlight
[gmx-users] Generation of the Distance Restraints James Starlight
[gmx-users] Problems with simulation on multi-nodes cluster James Starlight
[gmx-users] Generation of the Distance Restraints James Starlight
[gmx-users] Problems with simulation on multi-nodes cluster James Starlight
[gmx-users] Generation of the Distance Restraints James Starlight
[gmx-users] Principal Components Analysis in Gromacs James Starlight
[gmx-users] Generation of the Distance Restraints James Starlight
[gmx-users] Principal Components Analysis in Gromacs James Starlight
[gmx-users] Generation of the Distance Restraints James Starlight
[gmx-users] Editing of the existing system James Starlight
[gmx-users] Editing of the existing system James Starlight
[gmx-users] Editing of the existing system James Starlight
[gmx-users] Editing of the existing system James Starlight
[gmx-users] Editing of the existing system James Starlight
[gmx-users] Editing of the existing system James Starlight
[gmx-users] Re:g_energy Oliver Stueker
[gmx-users] pdb file Oliver Stueker
[gmx-users] Re: Neigborsearching, Electrostatics and vdw options Oliver Stueker
[gmx-users] Where would I find the 45A4 GROMOS force field? Oliver Stueker
[gmx-users] large scale simulation? Oliver Stueker
[gmx-users] how to use charmm ff in gmx and carbohydrate forcefield Tom
[gmx-users] problem in using OPLS forcefield parameter in lipid simulation Anushree Tripathi
[gmx-users] Energy minimization of crystal structure with water NG HUI WEN
[gmx-users] Energy minimization of crystal structure with water NG HUI WEN
[gmx-users] Charge groups for particle insertion Tina Wang
[gmx-users] Ques Xianwei Wang
[gmx-users] Ques Xianwei Wang
[gmx-users] dihedral distributions Dallas Warren
[gmx-users] g_sdf -> and g_spatial Dallas Warren
[gmx-users] Cluster analysis Dallas Warren
[gmx-users] on gromacs force field Dallas Warren
[gmx-users] About the function of "-v' in mdrun Dallas Warren
[gmx-users] one ligand in ATB Tsjerk Wassenaar
[gmx-users] g_select problem (Invalid command line argument:) Tsjerk Wassenaar
[gmx-users] Charge delocalization fullerene Tsjerk Wassenaar
[gmx-users] Re: questions about Principal Component Analysis Tsjerk Wassenaar
[gmx-users] Ques Tsjerk Wassenaar
[gmx-users] RMSD sudden jump Tsjerk Wassenaar
[gmx-users] center the system on specific atoms type Tsjerk Wassenaar
[gmx-users] center the system on specific atoms type Tsjerk Wassenaar
[gmx-users] Equilibriation nvt.mdp error Tsjerk Wassenaar
[gmx-users] grompp warning with SHAKE, but ok with LINCS Tsjerk Wassenaar
Fw: [gmx-users] number of coordinates in coordinate file does not match topology Tsjerk Wassenaar
[gmx-users] on "tcoupl= V-rescale" Tsjerk Wassenaar
[gmx-users] on "tcoupl= V-rescale" Tsjerk Wassenaar
[gmx-users] on "tcoupl= V-rescale" Tsjerk Wassenaar
[gmx-users] on -t nvt.cpt in the Justine Lemkul tutorial Tsjerk Wassenaar
[gmx-users] Help regarding running DSSP in gmx Tsjerk Wassenaar
[gmx-users] Trjconv PDB files define solvent as "ATOM"? Tsjerk Wassenaar
[gmx-users] Re: g_msd with input by trjconv -pbc nojump:a concern Tsjerk Wassenaar
[gmx-users] pdb2gmx input file error Tsjerk Wassenaar
[gmx-users] Box Size in MD Tsjerk Wassenaar
[gmx-users] grompp is adding a bond in my model that should not be there Tsjerk Wassenaar
[gmx-users] Principal Components Analysis in Gromacs Tsjerk Wassenaar
[gmx-users] Principal Components Analysis in Gromacs Tsjerk Wassenaar
[gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!! Tsjerk Wassenaar
[gmx-users] x,y and z components of rmsf? Tsjerk Wassenaar
[gmx-users] x,y and z components of rmsf? Tsjerk Wassenaar
[gmx-users] Re: crazy temperatures Tsjerk Wassenaar
[gmx-users] Position restraints problem Tsjerk Wassenaar
[gmx-users] opls topology for butanol, hexanol, heptanol Zhuyi Xue
[gmx-users] HOW TO USE SILVER ATOMS IN AMBER99 FORCE FIELD Kavosh Zandsalimi
[gmx-users] Calculate Bulk Pressure Tensor? Weilong Zhao
[gmx-users] Unreadable trajetory Jernej Zidar
[gmx-users] re: Unreadable trajectory [solved] Jernej Zidar
[gmx-users] Problem: pdb2gmx with a more complex system Jernej Zidar
[gmx-users] Re: Problem: pdb2gmx with a more complex system Jernej Zidar
[gmx-users] Position restraints problem Jernej Zidar
[gmx-users] Position restraints problem Jernej Zidar
[gmx-users] Position restraints problem Jernej Zidar
[gmx-users] Editing the functions of amber Matthew Zwier
[gmx-users] How to input multiple trr files? a a
[gmx-users] How to interpret the cosine content result? a a
[gmx-users] How to input multiple trr files? a a
[gmx-users] Read mdcrd from AMBER ---> Error Message a a
[gmx-users] Error Message when installing GROMACS. a a
[gmx-users] Error Message in Make clean command for installation. a a
[gmx-users] Can GROMACS read binpos trajectory files? a a
[gmx-users] How to read in mdcrd files to gromacs? a a
[gmx-users] How to set the VMD_PLUGIN_PATH for gromacs analysis? a a
[gmx-users] Gromacs installation question: Where is my Gromacs? bestenborstel
[gmx-users] Gromacs installation question: Where is my Gromacs? bestenborstel
[gmx-users] Gromacs installation question: Where is my Gromacs? bestenborstel
[gmx-users] Gromacs installation question: Where is my Gromacs? bestenborstel
[gmx-users] Gromacs installation question: Where is my Gromacs? bestenborstel
[gmx-users] how to add custom potential function smith bill
[gmx-users] mdrun -multi flag bo.shuang
[gmx-users] Re: Re: mdrun -multi flag (Mark Abraham) bo.shuang
[gmx-users] Re: Re: Re: Re: mdrun -multi flag (Mark Abraham) (Justin A. Lemkul) bo.shuang
[gmx-users] hydrophobic and hydrophilic in implicit solvent bo.shuang
[gmx-users] hydrophobic and hydrophilic in implicit solvent bo.shuang
[gmx-users] Re: Re: hydrophobic and hydrophilic in implicit solvent bo.shuang
[gmx-users] hydrogen hydrogen interaction bo.shuang
[gmx-users] Generating topology Spring buds
[gmx-users] Structure averaging problem using g_rmsf Spring buds
[gmx-users] Structure averaging problem using g_rmsf Spring buds
[gmx-users] Problem in running Equilibration step Spring buds
[gmx-users] help needed oindrila das
[gmx-users] crashed run... rama david
[gmx-users] MDrun append... rama david
[gmx-users] LINCS Fatal error rama david
[gmx-users] Segmentation fault rama david
[gmx-users] About martini rama david
[gmx-users] protein-ligand tutorial problem rama david
[gmx-users] Regarding PCA rama david
[gmx-users] Simulated Annealing Protocol... rama david
[gmx-users] Simulated Annealing Protocol... rama david
[gmx-users] Erroneous bond in average pdb rama david
[gmx-users] About center of mass removal rama david
[gmx-users] About center of mass removal rama david
[gmx-users] About movie in GROMACS rama david
[gmx-users] about g_mindist.... rama david
[gmx-users] Shima Arasteh wants to share a link | Gromacs rama david
[gmx-users] About cutt-off scheme .. rama david
[gmx-users] About cutt-off scheme .. rama david
[gmx-users] about g_mindist.... rama david
[gmx-users] About cutt-off scheme .. rama david
[gmx-users] Fwd: About g_energy analysis rama david
[gmx-users] Regarding to relaxation time rama david
[gmx-users] g_fg2cg dina dusti
[gmx-users] g_fg2cg dina dusti
[gmx-users] Martini dina dusti
[gmx-users] Martini dina dusti
[gmx-users] Martini dina dusti
[gmx-users] g_fg2cg dina dusti
[gmx-users] pdb file dina dusti
[gmx-users] pdb file dina dusti
[gmx-users] pdb file dina dusti
[gmx-users] dssp error rarora at ens-cachan.fr
[gmx-users] Re: quasi-harmonic entropy calculation wmiranda at estudiantes.fbio.uh.cu
[gmx-users] submision wmiranda at estudiantes.fbio.uh.cu
[gmx-users] Re: Williams wmiranda at estudiantes.fbio.uh.cu
[gmx-users] Re: mass-weighted analysis wmiranda at estudiantes.fbio.uh.cu
[gmx-users] How to fix Water during simulation ? ajani haresh
[gmx-users] spatial distribution function prema.a at iiserpune.ac.in
[gmx-users] (no subject) saly jackson
[gmx-users] 'not allocate memory' saly jackson
[gmx-users] 'not allocate memory' saly jackson
[gmx-users] not allocate memory and genconf saly jackson
[gmx-users] genconf saly jackson
[gmx-users] genconf saly jackson
[gmx-users] (no subject) saly jackson
[gmx-users] 'genconf' saly jackson
[gmx-users] genconf, grompp saly jackson
[gmx-users] genconf,grompp saly jackson
[gmx-users] genconf, grompp saly jackson
[gmx-users] genconf, grompp saly jackson
[gmx-users] genbox,genconf saly jackson
[gmx-users] Segmentation fault saly jackson
[gmx-users] There was 1 error in input file(s) saly jackson
[gmx-users] g_select problem (Invalid command line argument:) leila karami
[gmx-users] g_select problem (Invalid command line argument:) leila karami
[gmx-users] g_select vs trjorder leila karami
[gmx-users] g_select vs trjorder leila karami
[gmx-users] g_select vs trjorder leila karami
[gmx-users] g_select vs trjorder leila karami
[gmx-users] g_select vs trjorder leila karami
[gmx-users] Help regarding running DSSP in gmx chandran karunakaran
[gmx-users] Running DSSP program chandran karunakaran
[gmx-users] Shima Arasteh wants to share a link | Gromacs rossen at kth.se
[gmx-users] do_dssp segmentation fault arun kumar
[gmx-users] do_dssp segmentation fault arun kumar
[gmx-users] Residue 'NAG' not found in residue topology database pragna lakshmi
[gmx-users] Atom O5 not found in residue seq.nr. 1 while adding atom pragna lakshmi
[gmx-users] Re: Atom O5 not found in residue seq.nr. 1 while adding atom pragna lakshmi
[gmx-users] Re: Atom O5 not found in residue seq.nr. 1 while adding atom pragna lakshmi
[gmx-users] dssp and gromacs version lina
[gmx-users] dssp and gromacs version lina
[gmx-users] g_dist without output file lina
[gmx-users] g_dist without output file lina
[gmx-users] g_dist without output file lina
[gmx-users] g_dist without output file lina
[gmx-users] Generating topology lina
[gmx-users] continue replica exchange MD lina
[gmx-users] Inconsistent shifts - is it something wrong with pbc ming ma
[gmx-users] Inconsistent shifts - is it something wrong with pbc ming ma
[gmx-users] g_sas afsaneh maleki
[gmx-users] g_dist without output file afsaneh maleki
[gmx-users] g_sas afsaneh maleki
[gmx-users] g_sas afsaneh maleki
[gmx-users] g_sas; could not find a Van der Waals radius afsaneh maleki
[gmx-users] Adjust time intervals afsaneh maleki
[gmx-users] Adjust time intervals afsaneh maleki
[gmx-users] Adjust time intervals afsaneh maleki
[gmx-users] RE: Cluster analysis minal
[gmx-users] Umbrella_pull_simulation shahid nayeem
[gmx-users] Umbrella_pull_simulation shahid nayeem
[gmx-users] Umbrella_pull_simulation shahid nayeem
[gmx-users] using MPI cuong nguyen
[gmx-users] using MPI cuong nguyen
[gmx-users] mpirun cuong nguyen
[gmx-users] LINCS problem with EM and Virtual sites francesco oteri
[gmx-users] charm to gromacs francesco oteri
[gmx-users] Fwd: charm to gromacs francesco oteri
[gmx-users] How to input multiple trr files? francesco oteri
[gmx-users] a request regarding pdb2gmx and specbond.dat francesco oteri
[gmx-users] Read mdcrd from AMBER ---> Error Message francesco oteri
[gmx-users] problem in oplsaa ffbonded.itp francesco oteri
[gmx-users] problem in oplsaa ffbonded.itp francesco oteri
[gmx-users] bond managment in grompp francesco oteri
[gmx-users] bond managment in grompp francesco oteri
[gmx-users] REMD equilibration francesco oteri
[gmx-users] REMD equilibration francesco oteri
[gmx-users] g_wham position 0 rainy908
[gmx-users] MDrun append... lloyd riggs
[gmx-users] Re: WHAM lloyd riggs
[gmx-users] Re:g_energy lloyd riggs
[gmx-users] Re:g_energy lloyd riggs
[gmx-users] Re:g_enemat lloyd riggs
[gmx-users] Re:g_energy g_enemat lloyd riggs
[gmx-users] 4.6 development version lloyd riggs
[gmx-users] Force constant - Umbrella Sampling lloyd riggs
[gmx-users] Re: WHAM question lloyd riggs
[gmx-users] Re: WHAM2 lloyd riggs
AW: [gmx-users] About movie in GROMACS lloyd riggs
[gmx-users] Re: hkl harker sections lloyd riggs
[gmx-users] About Distance.pl script vidhya sankar
[gmx-users] About desired Spacing in Distance.pl script vidhya sankar
[gmx-users] About Umbrella spacing vidhya sankar
[gmx-users] Vi plugin for Gromacs files hubert santuz
[gmx-users] error in oscillation period mohan maruthi sena
[gmx-users] How to do Normal Modes Analysis with Gromacs4.5.5? qiancheng shen
[gmx-users] How to do Normal Modes Analysis with Gromacs4.5.5? qiancheng shen
[gmx-users] How to do Normal Modes Analysis with Gromacs4.5.5? qiancheng shen
[gmx-users] How to do Normal Modes Analysis with Gromacs4.5.5? qiancheng shen
[gmx-users] Simulated Annealing Protocol... bipin singh
[gmx-users] How to add dihedral information from the GAFF topology bipin singh
[gmx-users] Re: How to add dihedral information from the GAFF topology bipin singh
[gmx-users] Re: How to add dihedral information from the GAFF topology bipin singh
[gmx-users] Re: How to add dihedral information from the GAFF topology bipin singh
[gmx-users] Re: How to add dihedral information from the GAFF topology bipin singh
[gmx-users] Re: How to add dihedral information from the GAFF topology bipin singh
[gmx-users] Re: How to add dihedral information from the GAFF topology bipin singh
[gmx-users] Pressure coupling doubt bipin singh
[gmx-users] Pressure coupling and Isothermal compressibility for a biphasic system bipin singh
[gmx-users] some questions about side chain dihedral angle sampling mircial at sjtu.edu.cn
[gmx-users] Re: some questions about side chain dihedral angle sampling mircial at sjtu.edu.cn
[gmx-users] extending simulation priya thiyagarajan
[gmx-users] regarding rmsd value priya thiyagarajan
[gmx-users] regarding em potential energy positive priya thiyagarajan
[gmx-users] regarding em potential energy positive priya thiyagarajan
[gmx-users] regarding potential energy positive priya thiyagarajan
[gmx-users] Umbrella sampling along Radius of gyration felmerino at uchile.cl
[gmx-users] Announcement: Large biomolecule benchmark report chris.neale at utoronto.ca
[gmx-users] crazy temperatures chris.neale at utoronto.ca
[gmx-users] Umbrella sampling along Radius of gyration chris.neale at utoronto.ca
[gmx-users] Not able to continue with Equilibration chris.neale at utoronto.ca
[gmx-users] using g_angle francesca vitalini
[gmx-users] reverse transformation with dihedral restraints francesca vitalini
[gmx-users] About martini francesca vitalini
[gmx-users] Generation of the Distance Restraints francesca vitalini
[gmx-users] Generation of the Distance Restraints francesca vitalini
[gmx-users] Not able to continue with Equilibration francesca vitalini
[gmx-users] Not able to continue with Equilibration francesca vitalini
[gmx-users] Not able to continue with Equilibration francesca vitalini
[gmx-users] Not able to continue with Equilibration francesca vitalini
[gmx-users] Not able to continue with Equilibration francesca vitalini
[gmx-users] x,y and z components of rmsf? patrick wintrode
[gmx-users] segmentation fault err shilpa yadahalli
[gmx-users] one ligand in ATB ahmet yıldırım
[gmx-users] pme note ahmet yıldırım
[gmx-users] Neigborsearching, Electrostatics and vdw options ahmet yıldırım
[gmx-users] Re: Neigborsearching, Electrostatics and vdw options ahmet yıldırım
[gmx-users] Re: Neigborsearching, Electrostatics and vdw options ahmet yıldırım
[gmx-users] parameters of em.mdp ahmet yıldırım
[gmx-users] parameters of em.mdp ahmet yıldırım
[gmx-users] renumber charge group ahmet yıldırım
[gmx-users] the RMSD of Bond lengths, Bond angles, Dihedrals and Impropers ahmet yıldırım
[gmx-users] Anomalous temperature zhongjin
[gmx-users] construction of homopolymer from non-standard monomers in gromacs Иимяа Фаамиилиияа

Last message date: Sat Mar 31 21:16:29 CEST 2012
Archived on: Thu Nov 14 12:12:32 CET 2013

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