February 2015 Archives by author

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Starting: Sun Feb 1 00:05:04 CET 2015
Ending: Sat Feb 28 21:16:11 CET 2015
Messages: 561

[gmx-users] Virtual sites and diffusion coefficients. sujithkakkat .
[gmx-users] Virtual sites and diffusion coefficients. sujithkakkat .
[gmx-users] Question on forcefields? sujithkakkat .
[gmx-users] insert-molecules module Mark Abraham
[gmx-users] residues in force fields Mark Abraham
[gmx-users] Compilation errors (5.0.4) Mark Abraham
[gmx-users] combine two solvent box to one large box. Mark Abraham
[gmx-users] Virtual sites and diffusion coefficients. Mark Abraham
[gmx-users] Problem with 5.0.4 build Mark Abraham
[gmx-users] gromacs.org_gmx-users Digest, Vol 130, Issue 12 Mark Abraham
[gmx-users] Unable to install gromacs Mark Abraham
[gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working) Mark Abraham
[gmx-users] no residue type with Amber99SB-ILDN ff Mark Abraham
[gmx-users] A question regarding electrostatic and coulomb energies. Mark Abraham
[gmx-users] Insufficient disk space error Mark Abraham
[gmx-users] counting dihedral transitions not working with gmx angle Mark Abraham
[gmx-users] Effect of time step size Mark Abraham
[gmx-users] trajectory tools don't work with large .xtc / .trr files Mark Abraham
[gmx-users] special coulombic interaction in 1-3 atoms (bonded atoms) Mark Abraham
[gmx-users] Gromacs's FTP site problems Mark Abraham
[gmx-users] check for bad contacts and/or reduce the time step if appropriate Mark Abraham
[gmx-users] Larger simulation times because of many [ pairs ]? Mark Abraham
[gmx-users] Fwd: Odd behavior in log files for two simulations with only different nstlog for Gromacs 5.0.4 Mark Abraham
[gmx-users] counting dihedral transitions not working with gmx angle (Mark Abraham) Mark Abraham
[gmx-users] GPU Installation Mark Abraham
[gmx-users] Regarding DSSP Mark Abraham
[gmx-users] Problem in new version of Gromacs 5.0 Mark Abraham
[gmx-users] Problem in new version of Gromacs 5.0 Mark Abraham
[gmx-users] mdrun -nsteps Mark Abraham
[gmx-users] check_bonds_timestep() only reports the first suspicious bond Mark Abraham
[gmx-users] Doubt about energies in a very simple system Mark Abraham
[gmx-users] several runs Mark Abraham
[gmx-users] GROMACS 4.6.7 not running on more than 16 MPI threads Mark Abraham
[gmx-users] Doubt about energies in a very simple system Mark Abraham
[gmx-users] Error in generated Replica Exchange statistics in log file Mark Abraham
[gmx-users] about source code of the old version of GROAMCS (1.0 to 2.0) Mark Abraham
[gmx-users] Error in generated Replica Exchange statistics in log file Abhi Acharya
[gmx-users] Finding Surface tension between two interface Bishnu Acharya
[gmx-users] Finding Surface tension between two interface Bishnu Acharya
[gmx-users] Creating box, Bishnu Acharya
[gmx-users] Creating box, Bishnu Acharya
[gmx-users] counting dihedral transitions not working with gmx angle Cristi Amariei
[gmx-users] counting dihedral transitions not working with gmx angle (Mark Abraham) Cristi Amariei
[gmx-users] counting dihedral transitions not working with gmx angle (Mark Abraham) Cristi Amariei
[gmx-users] Conversion of Harmonic potential parameters to Morse potential parameters Jashimuddin Ashraf
[gmx-users] Simulation of polarizable Carbon nanotubes Jashimuddin Ashraf
[gmx-users] Simulation of polarizable Carbon nanotubes Jashimuddin Ashraf
[gmx-users] combine two solvent box to one large box. BIRD
[gmx-users] merge group BIRD
[gmx-users] Can only find GPU'S on first node Barnett, James W
[gmx-users] [ constraints ] in .rtp database not recognized by pdb2gmx Barnett, James W
[gmx-users] Comb. Rule 2 LJ Params. Being Stored in .tpr as Rule 1 and Vice Versa? Barnett, James W
[gmx-users] Can only find GPU'S on first node Barnett, James W
[gmx-users] GPU low performance Barnett, James W
[gmx-users] Gromacs's FTP site problems Silvio a Beccara
[gmx-users] Computing Resource - Laptop VITALY VITALIEVICH CHABAN
[gmx-users] Covalent bond/crosslink formation with calcium Turgay Cakmak
[gmx-users] Covalent bond/crosslink formation with calcium Turgay Cakmak
[gmx-users] problem installing gromacs- libcurl Marcello Cammarata
[gmx-users] problem installing gromacs- libcurl Marcello Cammarata
[gmx-users] gromacs Abid Channa
[gmx-users] gromacs Abid Channa
[gmx-users] gromacs Abid Channa
[gmx-users] gromacs Abid Channa
[gmx-users] How I extend command Abid Channa
[gmx-users] How I extend command? Abid Channa
[gmx-users] Heating a wall adjacent to the fluid Rahul Chatterjee
[gmx-users] sampling techniques when calculating diffusion coefficients using Green-Kubo Ying Chen
[gmx-users] HOW TO CONVERT .XTC FILE TO DCD FORMAT Guillaume Chevrot
[gmx-users] How I extend command? Chandan Choudhury
[gmx-users] Double counting of h-bonds g_hbond:issue Udaya Dahal
[gmx-users] Double counting of h-bonds g_hbond:issue Udaya Dahal
[gmx-users] Double counting of h-bonds g_hbond:issue Udaya Dahal
[gmx-users] Compilation errors (5.0.4) Satyabrata Das
[gmx-users] Changing atom names from pdb to gro in editconf Rebeca García Fandiño
[gmx-users] GAFF and alkynes Rebeca García Fandiño
[gmx-users] GAFF and alkynes Rebeca García Fandiño
[gmx-users] GAFF and alkynes Rebeca García Fandiño
[gmx-users] GAFF and alkynes (Justin Lemkul) Rebeca García Fandiño
[gmx-users] Error during mdrun Rohit Farmer
[gmx-users] How I extend command Rohit Farmer
[gmx-users] g_MSD results for different sampling intervals Carlos SOTO GARZA
[gmx-users] adding polyatomic species in water #SUKRITI GUPTA#
[gmx-users] several runs Victor Rosas Garcia
[gmx-users] Question on forcefields? Yuri Garmay
[gmx-users] topolbuild error Zahra Ghanbari
[gmx-users] topolbuild error Zahra Ghanbari
[gmx-users] GPU Installation Carmen Di Giovanni
[gmx-users] GPU Installation Carmen Di Giovanni
[gmx-users] GPU low performance Carmen Di Giovanni
[gmx-users] GPU low performance Carmen Di Giovanni
[gmx-users] GPU low performance Carmen Di Giovanni
[gmx-users] GPU low performance Carmen Di Giovanni
[gmx-users] GPU low performance Carmen Di Giovanni
[gmx-users] GPU low performance Carmen Di Giovanni
[gmx-users] GPU low performance Carmen Di Giovanni
[gmx-users] GPU low performance Carmen Di Giovanni
[gmx-users] GPU low performance Carmen Di Giovanni
[gmx-users] GTX980 performance Carmen Di Giovanni
[gmx-users] GTX980 performance Carmen Di Giovanni
[gmx-users] GTX980 performance Carmen Di Giovanni
[gmx-users] GPU low performance Carmen Di Giovanni
[gmx-users] Significant differences in Ewald Vs PME for clay sheet Gaurav Goel
[gmx-users] Using g_mindist for calculating hydrophobic interaction between protein and ligand Agnivo Gosai
[gmx-users] A quick question regarding topology generation Agnivo Gosai
[gmx-users] pdb2gmx question - protonation Agnivo Gosai
[gmx-users] H-Bonding residues against specific frames Agnivo Gosai
[gmx-users] Salt bridge calculation using GROMACS analysis tools Agnivo Gosai
[gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg Agnivo Gosai
[gmx-users] Umbrella Sampling and histograms smoothness Agnivo Gosai
[gmx-users] Umbrella Sampling and histograms smoothness Agnivo Gosai
[gmx-users] Umbrella sampling restraining potential Agnivo Gosai
[gmx-users] Umbrella Sampling and Histogram Agnivo Gosai
[gmx-users] Umbrella Sampling and Histogram Agnivo Gosai
[gmx-users] Umbrella Sampling and Histogram Agnivo Gosai
[gmx-users] GROMACS 4.6.7 not running on more than 16 MPI threads Agnivo Gosai
[gmx-users] GROMACS 4.6.7 not running on more than 16 MPI threads Agnivo Gosai
[gmx-users] GROMACS 4.6.7 not running on more than 16 MPI threads Agnivo Gosai
[gmx-users] Re : GROMACS 4.6.7 not running on more than 16 MPI threads Agnivo Gosai
[gmx-users] Re : Re : GROMACS 4.6.7 not running on more than 16 MPI threads Agnivo Gosai
[gmx-users] Creating POSRES option for MDP file Agnivo Gosai
[gmx-users] Computing Resource - Laptop Douglas Grahame
[gmx-users] Computing Resource - Laptop Douglas Grahame
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? Harry Mark Greenblatt
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? Harry Mark Greenblatt
[gmx-users] modified residues and residual charge Harry Mark Greenblatt
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? Harry Mark Greenblatt
[gmx-users] New web server for setup of membrane simulation systems Jochen Hub
[gmx-users] breaking S-S bond using pdb2gmx Sahithya S Iyer
[gmx-users] breaking S-S bond using pdb2gmx Sahithya S Iyer
[gmx-users] User Defined walls and Potential Karnesh Jain
[gmx-users] MD run failed.. Kalyanashis Jana
[gmx-users] MD run failed.. Kalyanashis Jana
[gmx-users] g_rms with two trajectories Julian
[gmx-users] g_rms with two trajectories Julian
[gmx-users] g_rms with two trajectories Julian
[gmx-users] q-bio Summer School 2015 Christoph Junghans
[gmx-users] trajectory tools don't work with large .xtc / .trr files Wojciech Kopeć
[gmx-users] Position restraints and free energy calculations Kortzak, Daniel
[gmx-users] Position restraints and free energy calculations Kortzak, Daniel
[gmx-users] Free energy calculations with pull code and umbrella sampling Kortzak, Daniel
[gmx-users] Variable force constant in umbrella sampling Kortzak, Daniel
[gmx-users] Variable force constant in umbrella sampling Kortzak, Daniel
[gmx-users] how to calculate angles (molecules directions) Maryam Kowsar
[gmx-users] Fwd: how to calculate angles (molecules directions) Maryam Kowsar
[gmx-users] Fwd: how to calculate angles (molecules directions) Maryam Kowsar
[gmx-users] Fwd: how to calculate angles (molecules directions) Maryam Kowsar
[gmx-users] Fwd: how to calculate angles (molecules directions) Maryam Kowsar
[gmx-users] Simulation of polarizable Carbon nanotubes Peter Kroon
[gmx-users] Cluster recommendations Carsten Kutzner
[gmx-users] Problem with Lysozyme in Water Tutorial HANNIBAL LECTER
[gmx-users] Problem with Lysozyme in Water Tutorial HANNIBAL LECTER
[gmx-users] Regarding DSSP HANNIBAL LECTER
[gmx-users] Regarding DSSP HANNIBAL LECTER
[gmx-users] Regarding DSSP HANNIBAL LECTER
[gmx-users] Regarding DSSP HANNIBAL LECTER
[gmx-users] Regarding DSSP HANNIBAL LECTER
[gmx-users] Regarding DSSP HANNIBAL LECTER
[gmx-users] Regarding DSSP HANNIBAL LECTER
[gmx-users] MD run failed.. HANNIBAL LECTER
[gmx-users] MD run failed.. HANNIBAL LECTER
[gmx-users] [MGMS-DS]: Molecular Modelling Workshop March 9-11, 2015 in Erlangen, Germany Harald Lanig
[gmx-users] Umbrella Samling Alteration Alexander Law
[gmx-users] Umbrella Samling Alteration Alexander Law
[gmx-users] Umbrella Samling Alteration Alexander Law
[gmx-users] gromacs Alexander Law
[gmx-users] Umbrella Sampling Dissociation Constant Alexander Law
[gmx-users] Umbrella Sampling Dissociation Constant Alexander Law
[gmx-users] Umbrella Samling Alteration Justin Lemkul
[gmx-users] Force field For Protein-Ligand Complex Justin Lemkul
[gmx-users] topology and parameter set up Justin Lemkul
[gmx-users] Covalent bond/crosslink formation with calcium Justin Lemkul
[gmx-users] ngmx tools Justin Lemkul
[gmx-users] topology and parameter set up Justin Lemkul
[gmx-users] Problem with Lysozyme in Water Tutorial Justin Lemkul
[gmx-users] pressure simulation along the z-axis Justin Lemkul
[gmx-users] Using g_mindist for calculating hydrophobic interaction between protein and ligand Justin Lemkul
[gmx-users] Virtual sites and diffusion coefficients. Justin Lemkul
[gmx-users] Problem with Lysozyme in Water Tutorial Justin Lemkul
[gmx-users] Creating box, Justin Lemkul
[gmx-users] adding polyatomic species in water Justin Lemkul
[gmx-users] Peptide-membrane simulation force field parameters Justin Lemkul
[gmx-users] How to recover the .xtc from wrong operation 'dos2unix' Justin Lemkul
[gmx-users] Umbrella Samling Alteration Justin Lemkul
[gmx-users] Distance restraint between two chains' com Justin Lemkul
[gmx-users] Position restraints and free energy calculations Justin Lemkul
[gmx-users] no residue type with Amber99SB-ILDN ff Justin Lemkul
[gmx-users] no residue type with Amber99SB-ILDN ff Justin Lemkul
[gmx-users] no residue type with Amber99SB-ILDN ff Justin Lemkul
[gmx-users] Helicity Justin Lemkul
[gmx-users] A quick question regarding topology generation Justin Lemkul
[gmx-users] Covalent bond/crosslink formation with calcium Justin Lemkul
[gmx-users] Distance restraint between two chains' com Justin Lemkul
[gmx-users] pdb2gmx question - protonation Justin Lemkul
[gmx-users] Changing atom names from pdb to gro in editconf Justin Lemkul
[gmx-users] Umbrella Samling Alteration Justin Lemkul
[gmx-users] H-Bonding residues against specific frames Justin Lemkul
[gmx-users] Query regarding generation of gaps between lipid molecules after minimisation even after using position restraints Justin Lemkul
[gmx-users] ERROR OBTAINED FOR NVT OF DOPC AND PROTEIN SIMULATIONS Justin Lemkul
[gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg Justin Lemkul
[gmx-users] pH during free energy calculation Justin Lemkul
[gmx-users] Umbrella Sampling and histograms smoothness Justin Lemkul
[gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg Justin Lemkul
[gmx-users] Umbrella Sampling and histograms smoothness Justin Lemkul
[gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working) Justin Lemkul
[gmx-users] Effect of time step size Justin Lemkul
[gmx-users] Effect of time step size Justin Lemkul
[gmx-users] How to reply a message? Justin Lemkul
[gmx-users] Insertion of a carbon nanotube in a system Justin Lemkul
[gmx-users] GAFF and alkynes Justin Lemkul
[gmx-users] Effect of time step size Justin Lemkul
[gmx-users] Effect of time step size Justin Lemkul
[gmx-users] GAFF and alkynes Justin Lemkul
[gmx-users] Semiisotropic pressure coupling Justin Lemkul
[gmx-users] Semiisotropic pressure coupling Justin Lemkul
[gmx-users] Semiisotropic pressure coupling Justin Lemkul
[gmx-users] ffnonbonded.itp and ffbonded.itp files are missing DPPC somehow Justin Lemkul
[gmx-users] Difference between dihedral and torsional angles. Justin Lemkul
[gmx-users] Problem executing do_dssp in gromacs Justin Lemkul
[gmx-users] multiple ligands topology Justin Lemkul
[gmx-users] calculating interaction energies of dimers and ligand Justin Lemkul
[gmx-users] multiple ligands topology Justin Lemkul
[gmx-users] merge group Justin Lemkul
[gmx-users] [ constraints ] in .rtp database not recognized by pdb2gmx Justin Lemkul
[gmx-users] Comb. Rule 2 LJ Params. Being Stored in .tpr as Rule 1 and Vice Versa? Justin Lemkul
[gmx-users] multiple ligands topology Justin Lemkul
[gmx-users] GAFF and alkynes (Justin Lemkul) Justin Lemkul
[gmx-users] Semiisotropic pressure coupling Justin Lemkul
[gmx-users] Semiisotropic pressure coupling Justin Lemkul
[gmx-users] Semiisotropic pressure coupling Justin Lemkul
[gmx-users] Fwd: Odd behavior in log files for two simulations with only different nstlog for Gromacs 5.0.4 Justin Lemkul
[gmx-users] lower Area per lipid for DPPC with CHARMM36 Justin Lemkul
[gmx-users] Semiisotropic pressure coupling Justin Lemkul
[gmx-users] Umbrella sampling restraining potential Justin Lemkul
[gmx-users] How to examine our created topology Justin Lemkul
[gmx-users] error: Atom 1 in multiple Energy Mon. groups Justin Lemkul
[gmx-users] error: Atom 1 in multiple Energy Mon. groups Justin Lemkul
[gmx-users] error: Atom 1 in multiple Energy Mon. groups Justin Lemkul
[gmx-users] How to examine our created topology Justin Lemkul
[gmx-users] Semiisotropic pressure coupling Justin Lemkul
[gmx-users] Semiisotropic pressure coupling Justin Lemkul
[gmx-users] electric fields Justin Lemkul
[gmx-users] Semiisotropic pressure coupling Justin Lemkul
[gmx-users] electric fields Justin Lemkul
[gmx-users] NVT step Justin Lemkul
[gmx-users] Re; calculating interaction energies of dimers and ligand Justin Lemkul
[gmx-users] breaking S-S bond using pdb2gmx Justin Lemkul
[gmx-users] multiple ligands topology Justin Lemkul
[gmx-users] Problem executing do_dssp in gromacs Justin Lemkul
[gmx-users] Regarding DSSP Justin Lemkul
[gmx-users] Problem executing do_dssp in gromacs Justin Lemkul
[gmx-users] Regarding DSSP Justin Lemkul
[gmx-users] Regarding DSSP Justin Lemkul
[gmx-users] Problem in new version of Gromacs 5.0 Justin Lemkul
[gmx-users] Regarding DSSP Justin Lemkul
[gmx-users] Regarding DSSP Justin Lemkul
[gmx-users] Regarding DSSP Justin Lemkul
[gmx-users] Double counting of h-bonds g_hbond:issue Justin Lemkul
[gmx-users] Problem executing do_dssp in gromacs Justin Lemkul
[gmx-users] Semiisotropic pressure coupling Justin Lemkul
[gmx-users] Semiisotropic pressure coupling Justin Lemkul
[gmx-users] ffbond.itp Justin Lemkul
[gmx-users] Double counting of h-bonds g_hbond:issue Justin Lemkul
[gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT Justin Lemkul
[gmx-users] simulation of heme along with h2o2 Justin Lemkul
[gmx-users] GPU low performance Justin Lemkul
[gmx-users] GPU low performance Justin Lemkul
[gmx-users] GPU low performance Justin Lemkul
[gmx-users] Need of mdp files Justin Lemkul
[gmx-users] Imidazolium ring opening during energy minimization Justin Lemkul
[gmx-users] simulation of heme along with h2o2 Justin Lemkul
[gmx-users] simulation of heme along with h2o2 Justin Lemkul
[gmx-users] DNA-Protein complex MD failing Justin Lemkul
[gmx-users] Umbrella Sampling and Histogram Justin Lemkul
[gmx-users] Heating a wall adjacent to the fluid Justin Lemkul
[gmx-users] MD run failed.. Justin Lemkul
[gmx-users] DNA-Protein complex MD failing Justin Lemkul
[gmx-users] How to examine our created topology Justin Lemkul
[gmx-users] Various errors in pulling simulations Justin Lemkul
[gmx-users] HOW TO CONVERT .XTC FILE TO DCD FORMAT Justin Lemkul
[gmx-users] MD run failed.. Justin Lemkul
[gmx-users] Simulation of polarizable Carbon nanotubes Justin Lemkul
[gmx-users] analysis of the secondary structure diagram Justin Lemkul
[gmx-users] mdrun crash Justin Lemkul
[gmx-users] ffbond.itp Justin Lemkul
[gmx-users] Simulation of polarizable Carbon nanotubes Justin Lemkul
[gmx-users] g_rdf Justin Lemkul
[gmx-users] Error during mdrun Justin Lemkul
[gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS Justin Lemkul
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? Justin Lemkul
[gmx-users] GROMOS vs. CHARMM dihedrals Justin Lemkul
[gmx-users] Doubt about energies in a very simple system Justin Lemkul
[gmx-users] several runs Justin Lemkul
[gmx-users] Doubt about energies in a very simple system Justin Lemkul
[gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS Justin Lemkul
[gmx-users] Energy minimization for Inositol pyrophosphate Justin Lemkul
[gmx-users] Application of electric field on membrane Justin Lemkul
[gmx-users] g_MSD results for different sampling intervals Justin Lemkul
[gmx-users] Problem executing do_dssp in gromacs Justin Lemkul
[gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS Justin Lemkul
[gmx-users] Problem executing do_dssp in gromacs Justin Lemkul
[gmx-users] Regarding RDF calculations Justin Lemkul
[gmx-users] Problems Running Gromacs v-5.0.4 Justin Lemkul
[gmx-users] Fwd: Umbrella sampling Tutorial Fatal Error Justin Lemkul
[gmx-users] Creating POSRES option for MDP file Justin Lemkul
[gmx-users] Questions regarding usage of the covariance analysis Justin Lemkul
[gmx-users] Fwd: Odd behavior in log files for two simulations with only different nstlog for Gromacs 5.0.4 Shuxiang Li
[gmx-users] After solvation and before adding ions, number of molecules does not agree Thomas Lipscomb
[gmx-users] After solvation and before adding ions, number of molecules does not agree Thomas Lipscomb
[gmx-users] ffnonbonded.itp and ffbonded.itp files are missing DPPC somehow Thomas Lipscomb
[gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS Thomas Lipscomb
[gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS Thomas Lipscomb
[gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS Thomas Lipscomb
[gmx-users] Announcement: release of FESetup 1.1 Hannes Loeffler
[gmx-users] help to select a faster system for gromacs MD runs SAKO MIRZAIE
[gmx-users] DNA-protein complex - which force field to use? Erik Marklund
[gmx-users] g_rms with two trajectories Erik Marklund
[gmx-users] g_rms with two trajectories Erik Marklund
[gmx-users] single strand DNA in hairpin conformation Erik Marklund
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? David McGiven
[gmx-users] Cluster recommendations David McGiven
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? David McGiven
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? David McGiven
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? David McGiven
[gmx-users] GMX 5.0 compilation across different platforms David McGiven
[gmx-users] GMX 5.0 compilation across different platforms David McGiven
[gmx-users] DNA-protein complex - which force field to use? Felipe Merino
[gmx-users] Problem with Lysozyme in Water Tutorial Stephen P. Molnar
[gmx-users] Problem with Lysozyme in Water Tutorial Stephen P. Molnar
[gmx-users] Problem with Lysozyme in Water Tutorial Stephen P. Molnar
[gmx-users] Problems Running Gromacs v-5.0.4 Stephen P. Molnar
[gmx-users] Problems Running Gromacs v-5.0.4 Stephen P. Molnar
[gmx-users] Problems Running Gromacs v-5.0.4 Stephen P. Molnar
[gmx-users] analysis of the secondary structure diagram Nazli
[gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff to the cluster "middle" Christopher Neale
[gmx-users] Fwd: how to calculate angles (molecules directions) Christopher Neale
[gmx-users] Variable force constant in umbrella sampling Christopher Neale
[gmx-users] Fwd: how to calculate angles (molecules directions) Christopher Neale
[gmx-users] Fwd: how to calculate angles (molecules directions) Christopher Neale
[gmx-users] make_ndx selection of backbone residues Christopher Neale
[gmx-users] gromacs Christopher Neale
[gmx-users] Semiisotropic pressure coupling Christopher Neale
[gmx-users] Semiisotropic pressure coupling Christopher Neale
[gmx-users] Fwd: Odd behavior in log files for two simulations with only different nstlog for Gromacs 5.0.4 Christopher Neale
[gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff to the cluster "middle" Christopher Neale
[gmx-users] DNA-protein complex - which force field to use? Paulo Netz
[gmx-users] Difference between dihedral and torsional angles. B P
[gmx-users] trajectory tools don't work with large .xtc / .trr files Rafael R. Pappalardo
[gmx-users] check_bonds_timestep() only reports the first suspicious bond Mario Fernández Pendás
[gmx-users] check_bonds_timestep() only reports the first suspicious bond Mario Fernández Pendás
[gmx-users] Semiisotropic pressure coupling Thomas Piggot
[gmx-users] Effect of time step size Faezeh Pousaneh
[gmx-users] Effect of time step size Faezeh Pousaneh
[gmx-users] Effect of time step size Faezeh Pousaneh
[gmx-users] Effect of time step size Faezeh Pousaneh
[gmx-users] Effect of time step size Faezeh Pousaneh
[gmx-users] Effect of time step size Faezeh Pousaneh
[gmx-users] How to examine our created topology Faezeh Pousaneh
[gmx-users] How to examine our created topology Faezeh Pousaneh
[gmx-users] How to examine our created topology Faezeh Pousaneh
[gmx-users] Problem in new version of Gromacs 5.0 Faezeh Pousaneh
[gmx-users] Problem in new version of Gromacs 5.0 Faezeh Pousaneh
[gmx-users] Problem in new version of Gromacs 5.0 Faezeh Pousaneh
[gmx-users] Problem in new version of Gromacs 5.0 Faezeh Pousaneh
[gmx-users] How to examine our created topology Faezeh Pousaneh
[gmx-users] How to examine our created topology Faezeh Pousaneh
[gmx-users] How to examine our created topology Faezeh Pousaneh
[gmx-users] Cluster recommendations Szilárd Páll
[gmx-users] Build-Gromacs installation error Szilárd Páll
[gmx-users] Heads up on Intel MPI 5.0.1.035 bug in mpigcc causing cmake problems Szilárd Páll
[gmx-users] GPU low performance Szilárd Páll
[gmx-users] GPU low performance Szilárd Páll
[gmx-users] GPU low performance Szilárd Páll
[gmx-users] GPU low performance Szilárd Páll
[gmx-users] GPU low performance Szilárd Páll
[gmx-users] GPU low performance Szilárd Páll
[gmx-users] GPU low performance Szilárd Páll
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? Szilárd Páll
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? Szilárd Páll
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? Szilárd Páll
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? Szilárd Páll
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? Szilárd Páll
[gmx-users] Computing Resource - Laptop Szilárd Páll
[gmx-users] several runs Szilárd Páll
[gmx-users] Computing Resource - Laptop Szilárd Páll
[gmx-users] several runs Szilárd Páll
[gmx-users] GTX980 performance Szilárd Páll
[gmx-users] GROMACS 4.6.7 not running on more than 16 MPI threads Szilárd Páll
[gmx-users] GMX 5.0 compilation across different platforms Szilárd Páll
[gmx-users] Re : GROMACS 4.6.7 not running on more than 16 MPI threads Szilárd Páll
[gmx-users] calculating interaction energies of dimers and ligand RJ
[gmx-users] Re;calculating interaction energies of dimers and ligand RJ
[gmx-users] simulation of heme along with h2o2 Sanchaita Rajkhowa
[gmx-users] simulation of heme along with h2o2 Sanchaita Rajkhowa
[gmx-users] simulation of heme along with h2o2 Sanchaita Rajkhowa
[gmx-users] Fwd: Umbrella sampling Tutorial Fatal Error Mohsen Ramezanpour
[gmx-users] topolbuild error Ray, Bruce D
[gmx-users] topolbuild error Ray, Bruce D
[gmx-users] Flat bottom position restraints Sabine Reisser
[gmx-users] Flat bottom position restraints Sabine Reisser
[gmx-users] Flat bottom position restraints Sabine Reisser
[gmx-users] mdrun -nsteps Sabine Reisser
[gmx-users] mdrun -nsteps Sabine Reisser
[gmx-users] Distance restraint between two chains' com WT Ren
[gmx-users] Distance restraint between two chains' com WT Ren
[gmx-users] Distance restraint between two chains' com WT Ren
[gmx-users] Distance restraint between two chains' com WT Ren
[gmx-users] Distance restraint between two chains' com WT Ren
[gmx-users] A question regarding electrostatic and coulomb energies. IÑIGO SAENZ
[gmx-users] Doubt about energies in a very simple system IÑIGO SAENZ
[gmx-users] Doubt about energies in a very simple system IÑIGO SAENZ
[gmx-users] Doubt about energies in a very simple system IÑIGO SAENZ
[gmx-users] Heads up on Intel MPI 5.0.1.035 bug in mpigcc causing cmake problems Åke Sandgren
[gmx-users] Heads up on Intel MPI 5.0.1.035 bug in mpigcc causing cmake problems Åke Sandgren
[gmx-users] Using "pairs" type 2 Liel Sapir
[gmx-users] building topology by ATB server Saman Shahriyari
[gmx-users] What is wrong with enthalpy? Igor Shchechkin
[gmx-users] How to reply a message? Igor Shchechkin
[gmx-users] What is wrong with enthalpy? Igor Shchechkin
[gmx-users] Imidazolium ring opening during energy minimization Meena Singh
[gmx-users] g_rms with two trajectories Smith, Micholas D.
[gmx-users] Can only find GPU'S on first node Smith, Micholas D.
[gmx-users] Umbrella sampling Tutorial Fatal Error Nima Soltani
[gmx-users] Fwd: Umbrella sampling Tutorial Fatal Error Nima Soltani
[gmx-users] template.cpp compilation problem with Gromacs 5.0.4 Milton Sonoda
[gmx-users] template.cpp compilation problem with Gromacs 5.0.4 Milton Sonoda
[gmx-users] Finding Surface tension between two interface David van der Spoel
[gmx-users] What is wrong with enthalpy? David van der Spoel
[gmx-users] the issue of calculation of viscosity with NEMD David van der Spoel
[gmx-users] electric fields David van der Spoel
[gmx-users] electric fields David van der Spoel
[gmx-users] Application of electric field on membrane David van der Spoel
[gmx-users] Build-Gromacs installation error Dan Sponseller
[gmx-users] On the collective dynamics in terms of NMA and PCA James Starlight
[gmx-users] On the collective dynamics in terms of NMA and PCA James Starlight
[gmx-users] Questions regarding usage of the covariance analysis James Starlight
[gmx-users] Questions regarding usage of the covariance analysis James Starlight
[gmx-users] Various errors in pulling simulations Tim Stauch
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? Téletchéa Stéphane
[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ? Téletchéa Stéphane
[gmx-users] Unable to install gromacs Seera Suryanarayana
[gmx-users] How do we calculate free energy of simulated protein Seera Suryanarayana
[gmx-users] Semiisotropic pressure coupling Piggot T.
[gmx-users] Problem with 5.0.4 build Jim Tuccillo
[gmx-users] single strand DNA in hairpin conformation Urszula Uciechowska
[gmx-users] check for bad contacts and/or reduce the time step if appropriate Daniele Veclani
[gmx-users] HOW TO CONVERT .XTC FILE TO DCD FORMAT Spyridon Vicatos
[gmx-users] about source code of the old version of GROAMCS (1.0 to 2.0) Man Hoang Viet
[gmx-users] about source code of the old version of GROAMCS (1.0 to 2.0) Man Hoang Viet
[gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working) Felipe Villanelo
[gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working) Felipe Villanelo
[gmx-users] GROMOS vs. CHARMM dihedrals Bianca Villavicencio
[gmx-users] Helicity Diogo Vila Viçosa
[gmx-users] Helicity Diogo Vila Viçosa
[gmx-users] topology and parameter set up Jennifer Vo
[gmx-users] topology and parameter set up Jennifer Vo
[gmx-users] multiple ligands topology Jennifer Vo
[gmx-users] multiple ligands topology Jennifer Vo
[gmx-users] multiple ligands topology Jennifer Vo
[gmx-users] multiple ligands topology Jennifer Vo
[gmx-users] multiple ligands topology Jennifer Vo
[gmx-users] Gromacs in windows 7 with GPU Mirco Wahab
[gmx-users] mdrun -nsteps Tsjerk Wassenaar
[gmx-users] On the collective dynamics in terms of NMA and PCA Tsjerk Wassenaar
[gmx-users] On the collective dynamics in terms of NMA and PCA Tsjerk Wassenaar
[gmx-users] On the collective dynamics in terms of NMA and PCA Tsjerk Wassenaar
[gmx-users] adding polyatomic species in water Kester Wong
[gmx-users] How to recover the .xtc from wrong operation 'dos2unix' Xia, Xiaole
[gmx-users] gromacs.org_gmx-users Digest, Vol 130, Issue 12 Xia, Xiaole
[gmx-users] Larger simulation times because of many [ pairs ]? Fernando Yrazu
[gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT Jin Zhang
[gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT (Justin Lemkul) Jin Zhang
[gmx-users] special coulombic interaction in 1-3 atoms (bonded atoms) Ting Zheng
[gmx-users] DNA-protein complex - which force field to use? Jernej Zidar
[gmx-users] gromacs_win32.zip CPU version: All MS_Windows version: XP/NT/95 Libraries: Static Size: 17633280 FFTW version: 2.1.3 MPI support: no Installation prefix: customizable Comments: This is an unsupported native port of Gromacs to MS Windows. Start setup.exe after you have extracted all files. Note that you will have to specify the location of cpp in your mdp files - I\'ve included a free cpp in the gromacs binary directory. Contributed by: Erik Lindahl (lindahl at gromacs.org) Vasiliy Znamenskiy
[gmx-users] How to perform simulation between initial and final structures ananyachatterjee
[gmx-users] Force field For Protein-Ligand Complex neha bharti
[gmx-users] Energy minimization for Inositol pyrophosphate ashish bihani
[gmx-users] Format for nonbonded interactions (pairs) in a residue definition ashish bihani
[gmx-users] ffbond.itp marzieh dehghan
[gmx-users] ffbond.itp marzieh dehghan
[gmx-users] Build-Gromacs installation error rahul dhakne
[gmx-users] mdrun crash rahul dhakne
[gmx-users] Insertion of a carbon nanotube in a system soumadwip ghosh
[gmx-users] Error during mdrun soumadwip ghosh
[gmx-users] Regarding RDF calculations soumadwip ghosh
[gmx-users] error: Atom 1 in multiple Energy Mon. groups nazli kashani javid
[gmx-users] error: Atom 1 in multiple Energy Mon. groups nazli kashani javid
[gmx-users] error: Atom 1 in multiple Energy Mon. groups nazli kashani javid
[gmx-users] error: Atom 1 in multiple Energy Mon. groups nazli kashani javid
[gmx-users] analysis of the secondary structure diagram nazli kashani javid
[gmx-users] Hope this can help someone using REMD in Gromacs jia jia
[gmx-users] Peptide-membrane simulation force field parameters tarak karmakar
[gmx-users] lower Area per lipid for DPPC with CHARMM36 tarak karmakar
[gmx-users] Peptide-membrane simulation force field parameters tarak karmakar
[gmx-users] lower Area per lipid for DPPC with CHARMM36 tarak karmakar
[gmx-users] lower Area per lipid for DPPC with CHARMM36 tarak karmakar
[gmx-users] Semiisotropic pressure coupling tarak karmakar
[gmx-users] Semiisotropic pressure coupling tarak karmakar
[gmx-users] chiara_marcolin wants to share a link | Gromacs rossen at kth.se
[gmx-users] hello every one rajan kumar
[gmx-users] HOW TO CONVERT .XTC FILE TO DCD FORMAT rajan kumar
[gmx-users] HOW TO CONVERT .XTC FILE TO DCD FORMAT rajan kumar
[gmx-users] GNM from .xtc file rajan kumar
[gmx-users] Force field For Protein-Ligand Complex rajendra kumar
[gmx-users] msd calculation mah maz
[gmx-users] electric fields mah maz
[gmx-users] electric fields mah maz
[gmx-users] electric fields mah maz
[gmx-users] electric fields mah maz
[gmx-users] several runs mah maz
[gmx-users] several runs mah maz
[gmx-users] several runs mah maz
[gmx-users] several runs mah maz
[gmx-users] Query regarding generation of gaps between lipid molecules after minimisation even after using position restraints Antara mazumdar
[gmx-users] ERROR OBTAINED FOR NVT OF DOPC AND PROTEIN SIMULATIONS Antara mazumdar
[gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg Antara mazumdar
[gmx-users] Need of mdp files Antara mazumdar
[gmx-users] DNA-Protein complex MD failing virginia miguel
[gmx-users] DNA-Protein complex MD failing virginia miguel
[gmx-users] gromacs_win32.zip CPU version: All MS_Windows version: XP/NT/95 Libraries: Static Size: 17633280 FFTW version: 2.1.3 MPI support: no Installation prefix: customizable Comments: This is an unsupported native port of Gromacs to MS Windows. Start setup.exe after you have extracted all files. Note that you will have to specify the location of cpp in your mdp files - I\'ve included a free cpp in the gromacs binary directory. Contributed by: Erik Lindahl (lindahl at gromacs.org) ms
[gmx-users] How do we calculate free energy of simulated protein ms
[gmx-users] Helicity shivangi nangia
[gmx-users] Helicity shivangi nangia
[gmx-users] Helicity shivangi nangia
[gmx-users] Semiisotropic pressure coupling shivangi nangia
[gmx-users] Semiisotropic pressure coupling shivangi nangia
[gmx-users] Semiisotropic pressure coupling shivangi nangia
[gmx-users] Semiisotropic pressure coupling shivangi nangia
[gmx-users] Semiisotropic pressure coupling shivangi nangia
[gmx-users] Semiisotropic pressure coupling shivangi nangia
[gmx-users] Semiisotropic pressure coupling shivangi nangia
[gmx-users] Semiisotropic pressure coupling shivangi nangia
[gmx-users] Semiisotropic pressure coupling shivangi nangia
[gmx-users] Semiisotropic pressure coupling shivangi nangia
[gmx-users] Application of electric field on membrane petrishia petrishia
[gmx-users] Application of electric field on membrane petrishia petrishia
[gmx-users] Insufficient disk space error salam pradeep
[gmx-users] Plz help File input/output error: Cannot write trajectory frame; salam pradeep
[gmx-users] ngmx tools asasa qsqs
[gmx-users] NVT step asasa qsqs
[gmx-users] Problem executing do_dssp in gromacs Aarti rana
[gmx-users] Problem executing do_dssp in gromacs Aarti rana
[gmx-users] Problem executing do_dssp in gromacs Aarti rana
[gmx-users] Problem executing do_dssp in gromacs Aarti rana
[gmx-users] Problem executing do_dssp in gromacs Aarti rana
[gmx-users] Umbrella Sampling and histograms smoothness lloyd riggs
[gmx-users] g_rdf leila salimi
[gmx-users] g_rdf leila salimi
[gmx-users] pH during free energy calculation vivek sharma
[gmx-users] no residue type with Amber99SB-ILDN ff Ahmet yıldırım
[gmx-users] no residue type with Amber99SB-ILDN ff Ahmet yıldırım
[gmx-users] no residue type with Amber99SB-ILDN ff Ahmet yıldırım
[gmx-users] no residue type with Amber99SB-ILDN ff Ahmet yıldırım
[gmx-users] no residue type with Amber99SB-ILDN ff Ahmet yıldırım
[gmx-users] screen output and total drift Ahmet yıldırım
[gmx-users] pressure simulation along the z-axis felipe zapata
[gmx-users] the issue of calculation of viscosity with NEMD 陈思言
[gmx-users] make_ndx selection of backbone residues 라지브간디
[gmx-users] Re;calculating interaction energies of dimers and ligand 라지브간디
[gmx-users] Gromacs in windows 7 with GPU 라지브간디

Last message date: Sat Feb 28 21:16:11 CET 2015
Archived on: Sat Feb 28 21:16:13 CET 2015

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