October 2015 Archives by author

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Starting: Thu Oct 1 02:20:57 CEST 2015
Ending: Sat Oct 31 21:52:01 CET 2015
Messages: 601

[gmx-users] updates about ACPYPE yunshi11 .
[gmx-users] suspension of colloids in GROMACS CARDELLINI ANNALISA
[gmx-users] Gromacs and Gcc5.2 Mark Abraham
[gmx-users] vdw modifier and coulomb modifier Mark Abraham
[gmx-users] Hexagonal prisms box Mark Abraham
[gmx-users] Building gromacs on CRAY XC40 Mark Abraham
[gmx-users] Energy minimization error Mark Abraham
[gmx-users] PBC Mark Abraham
[gmx-users] Pull Code Error "unknown left hand" Mark Abraham
[gmx-users] Hydrogen virtual sites and AMBER FF Mark Abraham
[gmx-users] Hydrogen virtual sites and AMBER FF Mark Abraham
[gmx-users] PBC Mark Abraham
[gmx-users] Building gromacs on CRAY XC40 Mark Abraham
[gmx-users] Van der Waals force extraction in Gromacs 5.0 Mark Abraham
[gmx-users] Van der Waals force extraction in Gromacs 5.0 Mark Abraham
[gmx-users] GROMACS On GPU Mark Abraham
[gmx-users] GROMACS On GPU Mark Abraham
[gmx-users] GROMACS On GPU Mark Abraham
[gmx-users] GROMACS On GPU Mark Abraham
[gmx-users] pdb2gmx error Mark Abraham
[gmx-users] PBC Mark Abraham
[gmx-users] PBC Mark Abraham
[gmx-users] A problem with potential energy values and openMP Mark Abraham
[gmx-users] output control Mark Abraham
[gmx-users] output control Mark Abraham
[gmx-users] bond lenght distribution? Mark Abraham
[gmx-users] Message-ID: <CANnYEw4dDD9YKA=MaMQaNAeU5dKdaPGBKJHSxM2_O7Uc3pBzvQ at mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Mark Abraham
[gmx-users] problem with restarting from cpt and _prev.cpt file in REMD simulation Mark Abraham
[gmx-users] -gpu_id option with more than 10 GPUs Mark Abraham
[gmx-users] -gpu_id option with more than 10 GPUs Mark Abraham
[gmx-users] GROMACS 5.0.7 released Mark Abraham
[gmx-users] when will q4md-forcefieldtools.org be back Mark Abraham
[gmx-users] Artificial Restraint/Wall/Potential at box top Mark Abraham
[gmx-users] Position Restraints problem Mark Abraham
[gmx-users] Position Restraints problem Mark Abraham
[gmx-users] What is Mnbf/s? Mark Abraham
[gmx-users] Unified topology Mark Abraham
[gmx-users] Gromacs 4.6.7 plumed /segmentation error with imput files Mark Abraham
[gmx-users] Gromacs 4.6.7 plumed /segmentation error with imput files Mark Abraham
[gmx-users] Energy minimization error Mark Abraham
[gmx-users] energy minimization error Mark Abraham
[gmx-users] walp lipids around protein in membrane protein simulation Mark Abraham
[gmx-users] walp lipids around protein in membrane protein simulation Mark Abraham
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Mark Abraham
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Mark Abraham
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Mark Abraham
[gmx-users] energy minimization error Mark Abraham
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Mark Abraham
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Mark Abraham
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Mark Abraham
[gmx-users] problem compiling gromacs 5.1 Mark Abraham
[gmx-users] problem compiling gromacs 5.1 Mark Abraham
[gmx-users] compressed tng file Mark Abraham
[gmx-users] compressed tng file Mark Abraham
[gmx-users] compressed tng file Mark Abraham
[gmx-users] compressed tng file Mark Abraham
[gmx-users] problem compiling gromacs 5.1 Mark Abraham
[gmx-users] Dihedral Coeffecient Conversion Mark Abraham
[gmx-users] Dihedral Coeffecient Conversion Mark Abraham
[gmx-users] A simple em.mdp and md.mdp file for GMX 5.0 Mark Abraham
[gmx-users] multiple processes of a gromacs tool requiring user action at runtime on one Cray XC30 node using aprun Mark Abraham
[gmx-users] multiple processes of a gromacs tool requiring user action at runtime on one Cray XC30 node using aprun Mark Abraham
[gmx-users] multiple processes of a gromacs tool requiring user action at runtime on one Cray XC30 node using aprun Mark Abraham
[gmx-users] multiple processes of a gromacs tool requiring user action at runtime on one Cray XC30 node using aprun Mark Abraham
[gmx-users] Multi-node Replica Exchange Segfault Mark Abraham
[gmx-users] Multi-node Replica Exchange Segfault Mark Abraham
[gmx-users] Multi-node Replica Exchange Segfault Mark Abraham
[gmx-users] Multi-node Replica Exchange Segfault Mark Abraham
[gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype) Alan
[gmx-users] The simplest em.mdp file for GMX 5 (and perhaps for 4.5) Alan
[gmx-users] The simplest em.mdp file for GMX 5 (and perhaps for 4.5) Alan
[gmx-users] A simple em.mdp and md.mdp file for GMX 5.0 Alan
[gmx-users] A simple em.mdp and md.mdp file for GMX 5.0 Alan
[gmx-users] A simple em.mdp and md.mdp file for GMX 5.0 Alan
[gmx-users] Virtual Sites in protein-ligand systems Alan
[gmx-users] ligand contact map Albert
[gmx-users] domain decomposition error Musharaf Ali
[gmx-users] Selecting two groups in trjconv Irem Altan
[gmx-users] Adding ion to force field Irem Altan
[gmx-users] Adding ion to force field Irem Altan
[gmx-users] Adding ion to force field Irem Altan
[gmx-users] Adding ion to force field Irem Altan
[gmx-users] MD simulation with tip5p (with amber99sb) Irem Altan
[gmx-users] Gromacs and Namd workshop during SC15 Rossen Apostolov
[gmx-users] Construction of silver nanoparticles SAPNA BORAH
[gmx-users] Construction of silver nanoparticles SAPNA BORAH
[gmx-users] Construction of silver nanoparticles SAPNA BORAH
[gmx-users] Simulation of post translationally modified peptide SAPNA BORAH
[gmx-users] Enthalpy of Vaporization Pallavi Banerjee
[gmx-users] Enthalpy of Vaporization Pallavi Banerjee
[gmx-users] Enthalpy of Vaporization Pallavi Banerjee
[gmx-users] Is diffusion coefficient dependent on box size? Pallavi Banerjee
[gmx-users] Solubility check Pallavi Banerjee
[gmx-users] g_rdf with exclusions Pallavi Banerjee
[gmx-users] Viscosity calculation by g_tcaf Pallavi Banerjee
[gmx-users] GMXLIB does not induce residuetype.dat Barnett, James W
[gmx-users] Gromacs and Gcc5.2 Barnett, James W
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Barnett, James W
[gmx-users] Multi-node Replica Exchange Segfault Barnett, James W
[gmx-users] Multi-node Replica Exchange Segfault Barnett, James W
[gmx-users] Multi-node Replica Exchange Segfault Barnett, James W
[gmx-users] Multi-node Replica Exchange Segfault Barnett, James W
[gmx-users] Position Restraints problem Chiara Bello
[gmx-users] Do not consider the previous email, it was a mistake, I'm sorry. Chiara Bello
[gmx-users] FW: Position Restraints problem Chiara Bello
[gmx-users] FW: Position Restraints problem Chiara Bello
[gmx-users] PROBLEM WITH GROMOS96ff Chiara Bello
[gmx-users] question Andrew Bostick
[gmx-users] Normal Mode Analysis Vitaly V. Chaban
[gmx-users] Artificial Restraint/Wall/Potential at box top Vitaly V. Chaban
[gmx-users] acceptable errors in density and melting point Vitaly V. Chaban
[gmx-users] Temperature output file Vitaly V. Chaban
[gmx-users] suspension of colloids in GROMACS Vitaly V. Chaban
[gmx-users] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical? Vitaly V. Chaban
[gmx-users] Viscosity calculation by g_tcaf Vitaly V. Chaban
[gmx-users] combining OPLS Protein and Berger Lipids Vitaly V. Chaban
[gmx-users] Dihedral Coeffecient Conversion Vitaly V. Chaban
[gmx-users] implicit solvent with periodic molecules Vitaly V. Chaban
[gmx-users] Regarding non-bonded parameter of Zn-His for gromos96 53a6 ff Navneet Chaturvedi
[gmx-users] Gromacs and Gcc5.2 Nicolas Cheron
[gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype) Nicolas Cheron
[gmx-users] Unified topology Nicolas Cheron
[gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype) Nicolas Cheron
[gmx-users] GMXLIB does not induce residuetype.dat João M. Damas
[gmx-users] GMXLIB does not induce residuetype.dat João M. Damas
[gmx-users] GMXLIB does not induce residuetype.dat João M. Damas
[gmx-users] Query regarding exclusions and Coulomb-SR energies Siva Dasetty
[gmx-users] Query regarding exclusions and Coulomb-SR energies Siva Dasetty
[gmx-users] Exclusions section in topology. Siva Dasetty
[gmx-users] What is Mnbf/s? Andrew DeYoung
[gmx-users] Dynamic Cross Correlation ANAND AMITKUMAR Dharia
[gmx-users] Reminder: Farideh Khamseh wants to share "FF" with you Farideh via Dropbox
[gmx-users] multiple processes of a gromacs tool requiring user action at runtime on one Cray XC30 node using aprun Vedat Durmaz
[gmx-users] multiple processes of a gromacs tool requiring user action at runtime on one Cray XC30 node using aprun Vedat Durmaz
[gmx-users] multiple processes of a gromacs tool requiring user action at runtime on one Cray XC30 node using aprun Vedat Durmaz
[gmx-users] multiple processes of a gromacs tool requiring user action at runtime on one Cray XC30 node using aprun Vedat Durmaz
[gmx-users] multiple processes of a gromacs tool requiring user action at runtime on one Cray XC30 node using aprun Vedat Durmaz
[gmx-users] Install Gromacs on VirtualBox Simon Dürr
[gmx-users] Install Gromacs on VirtualBox Simon Dürr
[gmx-users] Install Gromacs on VirtualBox Simon Dürr
[gmx-users] Install Gromacs on VirtualBox Simon Dürr
[gmx-users] Install Gromacs on VirtualBox Simon Dürr
[gmx-users] NMA run problem KARAKAS Esra
[gmx-users] 5ns simulation in 2 hours Jorge Fernandez-de-Cossio-Diaz
[gmx-users] polymer in octahedron box pbc problem Victor Rosas Garcia
[gmx-users] please help in analysis of picture attached Victor Rosas Garcia
[gmx-users] acceptable errors in density and melting point Victor Rosas Garcia
[gmx-users] acceptable errors in density and melting point Victor Rosas Garcia
[gmx-users] acceptable errors in density and melting point Victor Rosas Garcia
[gmx-users] how to let gromacs NOT calculate intra-molecular electrostatics in a molecule Victor Rosas Garcia
[gmx-users] A simple em.mdp and md.mdp file for GMX 5.0 Victor Rosas Garcia
[gmx-users] output control Pierre Ghesquiere
[gmx-users] output control Pierre Ghesquiere
[gmx-users] Dihedral Coeffecient Conversion Edwin Fernando Gomez
[gmx-users] Dftb as qmmm method with gromacs Groenhof, Gerrit
[gmx-users] PME on a non-neutral system Groenhof, Gerrit
[gmx-users] Amber03 parameters for PTR Amali Guruge
[gmx-users] Amber03 parameters for PTR Amali Guruge
[gmx-users] Testing mpi version of Gromacs 5.1 Joachim Hein
[gmx-users] PBC in membrane protein system Yasser Almeida Hernández
[gmx-users] Free Energy of Liquid Water Nathan K Houtz
[gmx-users] Free Energy of Liquid Water Nathan K Houtz
[gmx-users] Free Energy of Liquid Water Nathan K Houtz
[gmx-users] Free Energy of Liquid Water Nathan K Houtz
[gmx-users] Turning off nonbonded interactions in protein-DNA Kartheek
[gmx-users] Turning off nonbonded interactions in protein-DNA Kartheek
[gmx-users] error analysis in gmx wham Sepideh Kavousi
[gmx-users] Too many LINCS warning Anahita Khammari
[gmx-users] output control Maryam Kowsar
[gmx-users] output control Maryam Kowsar
[gmx-users] output control Maryam Kowsar
[gmx-users] output control Maryam Kowsar
[gmx-users] GPU installation of gromacs:Tesla K20c Peter Kroon
[gmx-users] "The sum of the two largest charge group radii is larger than rlist" Peter Kroon
[gmx-users] Turning off nonbonded interactions in protein-DNA Peter Kroon
[gmx-users] h-bonds by g_hbond and VMD and ptraj Ondrej Kroutil
[gmx-users] h-bonds by g_hbond and VMD and ptraj Ondrej Kroutil
[gmx-users] Pull Code Error "unknown left hand" Kutzner, Carsten
[gmx-users] Insert molecules in system with minimum distance between them Justin Lemkul
[gmx-users] Atom OXT in PHE Justin Lemkul
[gmx-users] colleague subscribed to gromacs mailing list but unable to get replies Justin Lemkul
[gmx-users] Peptide, lipid simulation Justin Lemkul
[gmx-users] Fw: JUSTIN kalp in dppc tutorial Justin Lemkul
[gmx-users] Fw: problem with Justine tutorial Justin Lemkul
[gmx-users] question Justin Lemkul
[gmx-users] Fw: InflateGRO script in KALP in DPPC tutorial Justin Lemkul
[gmx-users] genion problem Justin Lemkul
[gmx-users] Enthalpy of Vaporization Justin Lemkul
[gmx-users] Enthalpy of Vaporization Justin Lemkul
[gmx-users] Enthalpy of Vaporization Justin Lemkul
[gmx-users] Enthalpy of Vaporization Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] LINCS WARNING Justin Lemkul
[gmx-users] pdb2gmx error Justin Lemkul
[gmx-users] pdb2gmx error Justin Lemkul
[gmx-users] pdb2gmx error Justin Lemkul
[gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype) Justin Lemkul
[gmx-users] dihedral calculation Justin Lemkul
[gmx-users] Error Justin Lemkul
[gmx-users] Extending simulation Justin Lemkul
[gmx-users] bond lenght distribution? Justin Lemkul
[gmx-users] Construction of silver nanoparticles Justin Lemkul
[gmx-users] Is diffusion coefficient dependent on box size? Justin Lemkul
[gmx-users] velocity in trjconv Justin Lemkul
[gmx-users] Problems introducing TP2 phosphorylated tyrosine in charmm36 Start terminus GLY-565: GLY-NH3+ End terminus ASN-822: COO- Opening force field file /home/hkhandel/bin/gmx/gromacs5.1/share/gromacs/top/charmm36-jun2015.ff/merged.arn ------------------------------------------------------- Program gmx pdb2gmx, VERSION 5.1 Source code file: /home/hkhandel/DOWNLOADS/gromacs-5.1/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 746 Fatal error: Atom OXT in residue ILE 935 was not found in rtp entry etc. Justin Lemkul
[gmx-users] "The sum of the two largest charge group radii is larger than rlist" Justin Lemkul
[gmx-users] "The sum of the two largest charge group radii is larger than rlist" Justin Lemkul
[gmx-users] "The sum of the two largest charge group radii is larger than rlist" Justin Lemkul
[gmx-users] Construction of silver nanoparticles Justin Lemkul
[gmx-users] Extending simulation Justin Lemkul
[gmx-users] can not open em.tpr file Justin Lemkul
[gmx-users] Extending simulation Justin Lemkul
[gmx-users] Amber03 parameters for PTR Justin Lemkul
[gmx-users] Amber03 parameters for PTR Justin Lemkul
[gmx-users] Regarding non-bonded parameter of Zn-His for gromos96 53a6 ff Justin Lemkul
[gmx-users] grompp Justin Lemkul
[gmx-users] pdb2gmx error Justin Lemkul
[gmx-users] FW: Position Restraints problem Justin Lemkul
[gmx-users] membed error Justin Lemkul
[gmx-users] acceptable errors in density and melting point Justin Lemkul
[gmx-users] RDF com Justin Lemkul
[gmx-users] grompp error Justin Lemkul
[gmx-users] protein complex Justin Lemkul
[gmx-users] g_rdf with exclusions Justin Lemkul
[gmx-users] Too many LINCS warning Justin Lemkul
[gmx-users] protein complex Justin Lemkul
[gmx-users] Radius of gyration Justin Lemkul
[gmx-users] pbc Justin Lemkul
[gmx-users] Radius of gyration Justin Lemkul
[gmx-users] moved atoms Justin Lemkul
[gmx-users] Adding ion to force field Justin Lemkul
[gmx-users] how to let gromacs NOT calculate intra-molecular electrostatics in a molecule Justin Lemkul
[gmx-users] Adding ion to force field Justin Lemkul
[gmx-users] PME on a non-neutral system Justin Lemkul
[gmx-users] Adding ion to force field Justin Lemkul
[gmx-users] Turning off nonbonded interactions in protein-DNA Justin Lemkul
[gmx-users] GROMACS compatible Charmm36 Phospho residues Justin Lemkul
[gmx-users] Temperature output file Justin Lemkul
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Justin Lemkul
[gmx-users] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical? Justin Lemkul
[gmx-users] suspension of colloids in GROMACS Justin Lemkul
[gmx-users] Virtual Sites + Capped Termini Justin Lemkul
[gmx-users] MD of two structure together-receptor+ligand Justin Lemkul
[gmx-users] PROBLEM WITH GROMOS96ff Justin Lemkul
[gmx-users] Segmentation fault in some windows of umbrella sampling Justin Lemkul
[gmx-users] GROMACS compatible Charmm36 Phospho residues Justin Lemkul
[gmx-users] Segmentation fault in some windows of umbrella sampling Justin Lemkul
[gmx-users] ***UNCHECKED*** Insert into a box Justin Lemkul
[gmx-users] Verify if position restrain was applied Justin Lemkul
[gmx-users] GMX polarizable water model Justin Lemkul
[gmx-users] The simplest em.mdp file for GMX 5 (and perhaps for 4.5) Justin Lemkul
[gmx-users] The simplest em.mdp file for GMX 5 (and perhaps for 4.5) Justin Lemkul
[gmx-users] protein topology Justin Lemkul
[gmx-users] protein topology Justin Lemkul
[gmx-users] Group Protein_LIG referenced in the .mdp file was not found in the index file.:Protein-Ligand MD Justin Lemkul
[gmx-users] Domain decomposition error Justin Lemkul
[gmx-users] Incomplete compiling Gromacs 5.1 Justin Lemkul
[gmx-users] MD simulation with tip5p (with amber99sb) Justin Lemkul
[gmx-users] Virtual Sites in protein-ligand systems Justin Lemkul
[gmx-users] There is no error message but the dynamic don´t show the correct number of frames Justin Lemkul
[gmx-users] There is no error message but the dynamic don´t show the correct number of frames Justin Lemkul
[gmx-users] There is no error message but the dynamic don´t show the correct number of frames Justin Lemkul
[gmx-users] There is no error message but the dynamic don´t show the correct number of frames Justin Lemkul
[gmx-users] Domain decomposition error Justin Lemkul
[gmx-users] Virtual Sites in protein-ligand systems Justin Lemkul
[gmx-users] Heat Capacity Justin Lemkul
[gmx-users] biphasic simulation and surface-surface tension calculation James Lord
[gmx-users] MD on cyclooxygenase 2 Stella Maganhi
[gmx-users] Gromacs 4.6.7 plumed /segmentation error with imput files Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Ana Marija
[gmx-users] problem compiling gromacs 5.1 Ana Marija
[gmx-users] problem compiling gromacs 5.1 Ana Marija
[gmx-users] problem compiling gromacs 5.1 Ana Marija
[gmx-users] problem compiling gromacs 5.1 Ana Marija
[gmx-users] h-bonds by g_hbond and VMD and ptraj Erik Marklund
[gmx-users] Virtual sites error Erik Marklund
[gmx-users] Virtual sites error Erik Marklund
[gmx-users] [gmx-developers] DNA is one moltype or two moltype? Erik Marklund
[gmx-users] protein complex Erik Marklund
[gmx-users] frequency of contact between all residue pairs Erik Marklund
[gmx-users] GROMACS On GPU Nikhil Maroli
[gmx-users] GPU installation of gromacs:Tesla K20c Nikhil Maroli
[gmx-users] MD of two structure together-receptor+ligand Nikhil Maroli
[gmx-users] GPU Accelerated MD in Gromacs Nikhil Maroli
[gmx-users] protein topology Nikhil Maroli
[gmx-users] Group Protein_LIG referenced in the .mdp file was not found in the index file.:Protein-Ligand MD Nikhil Maroli
[gmx-users] dssp on results of HREX simulation Shyno Mathew
[gmx-users] dssp on results of HREX simulation Shyno Mathew
[gmx-users] dssp on results of HREX simulation Shyno Mathew
[gmx-users] cluster analysis on HREX results Shyno Mathew
[gmx-users] GMXLIB does not induce residuetype.dat Ebert Maximilian
[gmx-users] GMXLIB does not induce residuetype.dat Ebert Maximilian
[gmx-users] Free oxygen in water AMBER FF definition to use in GROMACS Ebert Maximilian
[gmx-users] Possibility to keep molecules during MD at a certain distance Ebert Maximilian
[gmx-users] RMSF calculation of carbon alpha Ebert Maximilian
[gmx-users] RMSF calculation of carbon alpha Ebert Maximilian
[gmx-users] RMSF calculation of carbon alpha Ebert Maximilian
[gmx-users] RMSF calculation of carbon alpha Ebert Maximilian
[gmx-users] RMSF calculation of carbon alpha Ebert Maximilian
[gmx-users] Gromacs Ebert Maximilian
[gmx-users] GMXLIB does not induce residuetype.dat Ebert Maximilian
[gmx-users] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical? Ebert Maximilian
[gmx-users] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical? Ebert Maximilian
[gmx-users] Verify if position restrain was applied Ebert Maximilian
[gmx-users] Verify if position restrain was applied Ebert Maximilian
[gmx-users] Verify if position restrain was applied Ebert Maximilian
[gmx-users] Verify if position restrain was applied Ebert Maximilian
[gmx-users] -gpu_id option with more than 10 GPUs Robert McGibbon
[gmx-users] vdw modifier and coulomb modifier Parvez Mh
[gmx-users] dihedral calculation Parvez Mh
[gmx-users] dihedral calculation Parvez Mh
[gmx-users] velocity in trjconv Parvez Mh
[gmx-users] Hang Parvez Mh
[gmx-users] Radius of gyration Parvez Mh
[gmx-users] Radius of gyration Parvez Mh
[gmx-users] frequency of contact between all residue pairs Dina Mirijanian
[gmx-users] frequency of contact between all residue pairs Dina Mirijanian
[gmx-users] frequency of contact between all residue pairs Dina Mirijanian
[gmx-users] Temperature output file Ali Mohyeddin
[gmx-users] How to generate a model beta sheet Jagannath Mondal
[gmx-users] Free Energy of Liquid Water André Farias de Moura
[gmx-users] Free Energy of Liquid Water André Farias de Moura
[gmx-users] How to generate a model beta sheet André Farias de Moura
[gmx-users] Analysis of old xtc file using gromacs-5 tools Teemu Murtola
[gmx-users] Analysis of old xtc file using gromacs-5 tools Teemu Murtola
[gmx-users] Insert molecules in system with minimum distance between them Teemu Murtola
[gmx-users] automate gmx sasa Teemu Murtola
[gmx-users] Analysis of old xtc file using gromacs-5 tools Teemu Murtola
[gmx-users] Analysis of old xtc file using gromacs-5 tools Teemu Murtola
[gmx-users] ligand contact map Teemu Murtola
[gmx-users] gmx distance Teemu Murtola
[gmx-users] gmx distance Teemu Murtola
[gmx-users] Dynamic Cross Correlation Naba
[gmx-users] Enthalpy of Vaporization Rasoul Nasiri
[gmx-users] Enthalpy of Vaporization Rasoul Nasiri
[gmx-users] Enthalpy of Vaporization Rasoul Nasiri
[gmx-users] automate gmx sasa Andrei Neamtu
[gmx-users] automate gmx sasa Andrei Neamtu
[gmx-users] distance dependent energy Cuong Nguyen
[gmx-users] Pull Code Error "unknown left hand" Stella Nickerson
[gmx-users] Virtual Sites + Capped Termini Joan Clark Nicolas
[gmx-users] Virtual Sites + Capped Termini Joan Clark Nicolas
[gmx-users] Virtual Sites in protein-ligand systems Joan Clark Nicolas
[gmx-users] Virtual Sites in protein-ligand systems Joan Clark Nicolas
[gmx-users] GROMACS On GPU Nikhil
[gmx-users] installing gromacs-5.0.5 Nikhil
[gmx-users] protein topology Nikhil
[gmx-users] protein topology Nikhil
[gmx-users] how to install and run gromacs on gpu Nikhil
[gmx-users] installation of gromacs Kim Jessica Novacek
[gmx-users] Message-ID: <CANnYEw4dDD9YKA=MaMQaNAeU5dKdaPGBKJHSxM2_O7Uc3pBzvQ at mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Kim Jessica Novacek
[gmx-users] Message-ID: <CANnYEw4dDD9YKA=MaMQaNAeU5dKdaPGBKJHSxM2_O7Uc3pBzvQ at mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Kim Jessica Novacek
[gmx-users] Welcome to the "gromacs.org_gmx-users" mailing list Mishelle Oña
[gmx-users] There is no error message but the dynamic don´t show the correct number of frames Mishelle Oña
[gmx-users] There is no error message but the dynamic don´t show the correct number of frames Mishelle Oña
[gmx-users] There is no error message but the dynamic don´t show the correct number of frames Mishelle Oña
[gmx-users] There is no error message but the dynamic don´t show the correct number of frames Mishelle Oña
[gmx-users] There is no error message but the dynamic don´t show the correct number of frames Mishelle Oña
[gmx-users] regarding on g_rotacf CHEN Pan
[gmx-users] Excessive memory usage of mdrun Sotirios Dionysios I. Papadatos
[gmx-users] maestro cms file to gromacs Sotirios Dionysios I. Papadatos
[gmx-users] how to install and run gromacs on gpu Atila Petrosian
[gmx-users] LINCS WARNING Vy Phan
[gmx-users] LINCS WARNING Vy Phan
[gmx-users] combining OPLS Protein and Berger Lipids Nihit Pokhrel
[gmx-users] combining OPLS Protein and Berger Lipids Nihit Pokhrel
[gmx-users] RDF com Deva Priya
[gmx-users] radial density profiles gmx Deva Priya
[gmx-users] RDF com Deva Priya
[gmx-users] gmx distance Deva Priya
[gmx-users] gmx distance Deva Priya
[gmx-users] gmx distance Deva Priya
[gmx-users] Hang Deva Priya
[gmx-users] gmx distance Deva Priya
[gmx-users] gmx density origin Deva Priya
[gmx-users] Selecting two groups in trjconv Deva Priya
[gmx-users] GPU Accelerated MD in Gromacs Deva Priya
[gmx-users] How to generate a model beta sheet Deva Priya
[gmx-users] How OpenMP works with CUDA/GPU in Gromacs Szilárd Páll
[gmx-users] Gromacs GPU got hang Szilárd Páll
[gmx-users] Gromacs GPU got hang Szilárd Páll
[gmx-users] Error in gromacs-5.1 installation Szilárd Páll
[gmx-users] Install Gromacs on VirtualBox Szilárd Páll
[gmx-users] Analysis of old xtc file using gromacs-5 tools Szilárd Páll
[gmx-users] GPU+CPU Szilárd Páll
[gmx-users] GPU+CPU Szilárd Páll
[gmx-users] Martini domain decomposition problem Szilárd Páll
[gmx-users] frequent stop of GPU jobs at specific simulation steps. Szilárd Páll
[gmx-users] Install Gromacs on VirtualBox Szilárd Páll
[gmx-users] installation of gromacs Szilárd Páll
[gmx-users] Install Gromacs on VirtualBox Szilárd Páll
[gmx-users] Install Gromacs on VirtualBox Szilárd Páll
[gmx-users] Building gromacs on CRAY XC40 Szilárd Páll
[gmx-users] Building gromacs on CRAY XC40 Szilárd Páll
[gmx-users] Install Gromacs on VirtualBox Szilárd Páll
[gmx-users] Testing mpi version of Gromacs 5.1 Szilárd Páll
[gmx-users] Testing mpi version of Gromacs 5.1 Szilárd Páll
[gmx-users] Gromacs GPU got hang Szilárd Páll
[gmx-users] -gpu_id option with more than 10 GPUs Szilárd Páll
[gmx-users] -gpu_id option with more than 10 GPUs Szilárd Páll
[gmx-users] -gpu_id option with more than 10 GPUs Szilárd Páll
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Szilárd Páll
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Szilárd Páll
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Szilárd Páll
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Szilárd Páll
[gmx-users] gromacs 4.6.7 plumed -Segmentation fault Szilárd Páll
[gmx-users] Incomplete compiling Gromacs 5.1 Szilárd Páll
[gmx-users] Differences between gmx bar and pymbar free energy Gmx QA
[gmx-users] Differences between gmx bar and pymbar free energy Gmx QA
[gmx-users] multiple processes of a gromacs tool requiring user action at runtime on one Cray XC30 node using aprun Rashmi
[gmx-users] Analysis of old xtc file using gromacs-5 tools Venkat Reddy
[gmx-users] Analysis of old xtc file using gromacs-5 tools Venkat Reddy
[gmx-users] Analysis of old xtc file using gromacs-5 tools Venkat Reddy
[gmx-users] Analysis of old xtc file using gromacs-5 tools Venkat Reddy
[gmx-users] Analysis of old xtc file using gromacs-5 tools Venkat Reddy
[gmx-users] velocity in trjconv Venkat Reddy
[gmx-users] pdb2gmx error Dries Van Rompaey
[gmx-users] pdb2gmx error Dries Van Rompaey
[gmx-users] pdb2gmx error Dries Van Rompaey
[gmx-users] pdb2gmx error Dries Van Rompaey
[gmx-users] pdb2gmx error Dries Van Rompaey
[gmx-users] pdb2gmx error Dries Van Rompaey
[gmx-users] genion problem Golnaz Roudsari
[gmx-users] protein complex Sana Saeed
[gmx-users] pbc Sana Saeed
[gmx-users] protein complex Sana Saeed
[gmx-users] moved atoms Sana Saeed
[gmx-users] remove water Sana Saeed
[gmx-users] 5ns simulation in 2 hours Sana Saeed
[gmx-users] colleague subscribed to gromacs mailing list but unable to get replies Raag Saluja
[gmx-users] free energy of mutated protein Raag Saluja
[gmx-users] Dftb as qmmm method with gromacs Padmani Sandhu
[gmx-users] Dftb as qmmm method with gromacs Padmani Sandhu
[gmx-users] Simulations of proteins in membrane bilayer Catarina A. Carvalheda dos Santos
[gmx-users] Gromacs GPU got hang M Teguh Satria
[gmx-users] How OpenMP works with CUDA/GPU in Gromacs M Teguh Satria
[gmx-users] Gromacs GPU got hang M Teguh Satria
[gmx-users] pbc=xy with 2 walls and verlet scheme Joerg Sauter
[gmx-users] maestro cms file to gromacs Michael Shirts
[gmx-users] Free Energy of Liquid Water Michael Shirts
[gmx-users] Free Energy of Liquid Water Michael Shirts
[gmx-users] error unknown bond_atomtype CH1 Aishwary Shivgan
[gmx-users] forcefield parameter for bromide ion Smith, Micholas D.
[gmx-users] Is diffusion coefficient dependent on box size? Smith, Micholas D.
[gmx-users] PME on a non-neutral system Smith, Micholas D.
[gmx-users] PME on a non-neutral system Smith, Micholas D.
[gmx-users] 5ns simulation in 2 hours Smith, Micholas D.
[gmx-users] PME on a non-neutral system Albert Solernou
[gmx-users] PME on a non-neutral system Albert Solernou
[gmx-users] colleague subscribed to gromacs mailing list but unable to get replies David van der Spoel
[gmx-users] Van der Waals force extraction in Gromacs 5.0 David van der Spoel
[gmx-users] Van der Waals force extraction in Gromacs 5.0 David van der Spoel
[gmx-users] Hydrogen bonding energy calculation David van der Spoel
[gmx-users] Error in number og H-bond David van der Spoel
[gmx-users] Error of H-bond David van der Spoel
[gmx-users] compressed tng file David van der Spoel
[gmx-users] compressed tng file David van der Spoel
[gmx-users] Verify if position restrain was applied David van der Spoel
[gmx-users] Verify if position restrain was applied David van der Spoel
[gmx-users] Normal Mode Analysis Dan Sponseller
[gmx-users] Adding ion to force field Peter Stern
[gmx-users] Adding ion to force field Peter Stern
[gmx-users] Installation of GROMACS 5.1 Mikhail Stukan
[gmx-users] 5ns simulation in 2 hours Téletchéa Stéphane
[gmx-users] Simulations of proteins in membrane bilayer Terry
[gmx-users] Van der Waals force extraction in Gromacs 5.0 Naga Rajesh Tummala
[gmx-users] Hydrogen virtual sites and AMBER FF Timofey Tyugashev
[gmx-users] Virtual sites error Timofey Tyugashev
[gmx-users] Virtual sites error Timofey Tyugashev
[gmx-users] tutorial Urszula Uciechowska
[gmx-users] tutorial Urszula Uciechowska
[gmx-users] gmxpbsa -protein-DNA Urszula Uciechowska
[gmx-users] from rdf -com to number density Daskalakis Vangelis
[gmx-users] A problem with potential energy values and openMP Milko Vesterinen
[gmx-users] GROMACS compatible Charmm36 Phospho residues Parker de Waal
[gmx-users] GROMACS compatible Charmm36 Phospho residues Parker de Waal
[gmx-users] multinode GPU mpi Parker de Waal
[gmx-users] multinode GPU mpi Parker de Waal
[gmx-users] Installation of GROMACS 5.1 Mirco Wahab
[gmx-users] RMSF calculation of carbon alpha Tsjerk Wassenaar
[gmx-users] RMSF calculation of carbon alpha Tsjerk Wassenaar
[gmx-users] RMSF calculation of carbon alpha Tsjerk Wassenaar
[gmx-users] output control Tsjerk Wassenaar
[gmx-users] tutorial Tsjerk Wassenaar
[gmx-users] Building a box Tsjerk Wassenaar
[gmx-users] remove water Tsjerk Wassenaar
[gmx-users] domain decomposition error Tsjerk Wassenaar
[gmx-users] protein topology Tsjerk Wassenaar
[gmx-users] problem with restarting from cpt and _prev.cpt file in REMD simulation Tomek Wlodarski
[gmx-users] problem with restarting from cpt and _prev.cpt file in REMD simulation Tomek Wlodarski
[gmx-users] Solvent density around a Protein Hans Wurst
[gmx-users] compressed tng file Ahmet Yıldırım
[gmx-users] compressed tng file Ahmet Yıldırım
[gmx-users] compressed tng file Ahmet Yıldırım
[gmx-users] Cyclic peptide with ester linkage Chunlei ZHANG
[gmx-users] Incomplete compiling Gromacs 5.1 Chunlei ZHANG
[gmx-users] Incomplete compiling Gromacs 5.1 Chunlei ZHANG
[gmx-users] bond lenght distribution? Frank Zack
[gmx-users] bond lenght distribution? Frank Zack
[gmx-users] Hexagonal prisms box Juan David Orjuela Zuñiga
[gmx-users] bond, angles and dihedrals in the topology file faride badalkhani
[gmx-users] Energy minimization error faride badalkhani
[gmx-users] Energy minimization error faride badalkhani
[gmx-users] Energy minimization error faride badalkhani
[gmx-users] energy minimization error faride badalkhani
[gmx-users] energy minimization error faride badalkhani
[gmx-users] Building gromacs on CRAY XC40 kevin chen
[gmx-users] coordination atoms of ion marzieh dehghan
[gmx-users] "The sum of the two largest charge group radii is larger than rlist" Shima ebrahimi
[gmx-users] "The sum of the two largest charge group radii is larger than rlist" Shima ebrahimi
[gmx-users] Van der Waals force extraction in Gromacs 5.0 gozde ergin
[gmx-users] Van der Waals force extraction in Gromacs 5.0 gozde ergin
[gmx-users] Van der Waals force extraction in Gromacs 5.0 gozde ergin
[gmx-users] Segmentation fault in some windows of umbrella sampling gozde ergin
[gmx-users] Segmentation fault in some windows of umbrella sampling gozde ergin
[gmx-users] Segmentation fault in some windows of umbrella sampling gozde ergin
[gmx-users] 5ns simulation in 2 hours gozde ergin
[gmx-users] Scd m g
[gmx-users] Error of H-bond m g
[gmx-users] Gromacs soumadwip ghosh
[gmx-users] when will q4md-forcefieldtools.org be back li he
[gmx-users] when will q4md-forcefieldtools.org be back li he
[gmx-users] how to let gromacs NOT calculate intra-molecular electrostatics in a molecule li he
[gmx-users] how to let gromacs NOT calculate intra-molecular electrostatics in a molecule li he
[gmx-users] how to let gromacs NOT calculate intra-molecular electrostatics in a molecule li he
[gmx-users] g_mmpbsa positive binding energy tasneem kausar
[gmx-users] Problems introducing TP2 phosphorylated tyrosine in charmm36 Start terminus GLY-565: GLY-NH3+ End terminus ASN-822: COO- Opening force field file /home/hkhandel/bin/gmx/gromacs5.1/share/gromacs/top/charmm36-jun2015.ff/merged.arn ------------------------------------------------------- Program gmx pdb2gmx, VERSION 5.1 Source code file: /home/hkhandel/DOWNLOADS/gromacs-5.1/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 746 Fatal error: Atom OXT in residue ILE 935 was not found in rtp entry etc. himanshu khandelia
[gmx-users] Extending simulation thomas knitter
[gmx-users] Extending simulation thomas knitter
[gmx-users] can not open em.tpr file thomas knitter
[gmx-users] Extending simulation thomas knitter
[gmx-users] Building a box thomas knitter
[gmx-users] ***UNCHECKED*** Insert into a box thomas knitter
[gmx-users] Heat Capacity thomas knitter
[gmx-users] g_mmpbsa time rajendra kumar
[gmx-users] g_mmpbsa positive binding energy rajendra kumar
[gmx-users] Hydrogen bonding energy calculation leoneverlasting
[gmx-users] Hydrogen bonding energy calculation (Ben) leoneverlasting
[gmx-users] please help in analysis of picture attached surbhi mahajan
[gmx-users] error unknown bond_atomtype CH1 surbhi mahajan
[gmx-users] coarse graining surbhi mahajan
[gmx-users] remove water surbhi mahajan
[gmx-users] PBC mah maz
[gmx-users] PBC mah maz
[gmx-users] PBC mah maz
[gmx-users] PBC mah maz
[gmx-users] forcefield parameter for bromide ion jagannath mondal
[gmx-users] Multi-node Replica Exchange Segfault jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] Artificial Restraint/Wall/Potential at box top shivangi nangia
[gmx-users] Error in number og H-bond asasa qsqs
[gmx-users] Error asasa qsqs
[gmx-users] polymer in octahedron box pbc problem gromacs query
[gmx-users] polymer in octahedron box pbc problem gromacs query
[gmx-users] polymer in octahedron box pbc problem gromacs query
[gmx-users] constraining charges gromacs query
[gmx-users] installing GROMACS mohammad r
[gmx-users] installing gromacs-5.0.5 mohammad r
[gmx-users] (no subject) saranya
[gmx-users] Gromacs saranya
[gmx-users] Gromacs saranya
[gmx-users] Gromacs saranya
[gmx-users] Fwd: Gromacs saranya
[gmx-users] MD of two structure together-receptor+ligand sun
[gmx-users] protein simulation elham tazikeh
[gmx-users] Peptide, lipid simulation badamkhatan togoldor
[gmx-users] grompp badamkhatan togoldor
[gmx-users] membed error badamkhatan togoldor
[gmx-users] Domain decomposition error badamkhatan togoldor
[gmx-users] Domain decomposition error badamkhatan togoldor
[gmx-users] Domain decomposition error badamkhatan togoldor
[gmx-users] Question of free energy calculation qian wang
[gmx-users] coarse grained multi-body cut-off distance error xiao
[gmx-users] GMX polarizable water model xy21hb
[gmx-users] GMX polarizable water model xy21hb
[gmx-users] implicit solvent with periodic molecules Анна Павловна Толстова
[gmx-users] grompp error محمد گره گشا
[gmx-users] grompp error محمد گره گشا
[gmx-users] grompp error محمد گره گشا
[gmx-users] Fw: JUSTIN kalp in dppc tutorial ‪neda razavi‬ ‪
[gmx-users] Fw: problem with Justine tutorial ‪neda razavi‬ ‪
[gmx-users] Fw: InflateGRO script in KALP in DPPC tutorial ‪neda razavi‬ ‪
[gmx-users] Fw: InflateGRO script in KALP in DPPC tutorial ‪neda razavi‬ ‪
[gmx-users] question about InflateGRO ‪neda razavi‬ ‪
[gmx-users] walp lipids around protein in membrane protein simulation 凌未风

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Archived on: Sat Oct 31 21:52:02 CET 2015

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