March 2014 Archives by author

Messages sorted by: [ thread ] [ subject ] [ date ]
More info on this list...

Starting: Sat Mar 1 04:25:00 CET 2014
Ending: Mon Mar 31 23:49:54 CEST 2014
Messages: 633

[gmx-users] A question about "blowing up" sujithkakkat .
[gmx-users] A question about "blowing up" sujithkakkat .
[gmx-users] Dubious results with NPT sujithkakkat .
[gmx-users] Dubious results with NPT sujithkakkat .
[gmx-users] Dubious results with NPT sujithkakkat .
[gmx-users] Question about topology construction. sujithkakkat .
[gmx-users] Area of Mixed lipid Bilayer ABEL Stephane 175950
[gmx-users] Set the environment variables of "FFTW3_INCLUDE_DIR" and "FFTW3_LIBRARIES" Hassan Aaryapour
[gmx-users] Set the environment variables of "FFTW3_INCLUDE_DIR" and "FFTW3_LIBRARIES" Hassan Aaryapour
[gmx-users] Two-body Bonded Distance Mark Abraham
[gmx-users] dihedral doubt Mark Abraham
[gmx-users] Fwd: Regarding trjorder Mark Abraham
[gmx-users] Question about Improper Dihedral of Charmm in gmx & ParamChem Mark Abraham
[gmx-users] Fwd: Regarding trjorder Mark Abraham
[gmx-users] No default U-B types charmm Mark Abraham
[gmx-users] Apple cluster Mark Abraham
[gmx-users] Problems with periodic syatems Mark Abraham
[gmx-users] Launching MPI/OpenMP hybrid run Mark Abraham
[gmx-users] SImulation with urea Mark Abraham
[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995) Mark Abraham
[gmx-users] Parsing g_rms binary rmsd comparison matrix Mark Abraham
[gmx-users] Parsing g_rms binary rmsd comparison matrix Mark Abraham
[gmx-users] Generate many random configurations Mark Abraham
[gmx-users] how to split gromacs tpr file Mark Abraham
[gmx-users] Bug in gromacs-5.0-beta2 [Jan 29] Mark Abraham
[gmx-users] tip3p Mark Abraham
[gmx-users] CHARMM36 force field available for GROMACS Mark Abraham
[gmx-users] Performing protein-ligand GROMACS MD under pH 5 conditions Mark Abraham
[gmx-users] Problem in extending simulation with state.cpt while changing number of cores Mark Abraham
[gmx-users] parameters problem Mark Abraham
[gmx-users] Problem in extending simulation with state.cpt while changing number of cores Mark Abraham
[gmx-users] Simulation with Ligand Mark Abraham
[gmx-users] choosing Ensemble for production MD run Mark Abraham
[gmx-users] g_energy (energygrps) Mark Abraham
[gmx-users] g_energy (energygrps) Mark Abraham
[gmx-users] Single or Double precision? Mark Abraham
[gmx-users] Thread affinity error when Running Gromacs 4.6.3 on Bluegene/P Mark Abraham
[gmx-users] surprising: what's the reason? Mark Abraham
[gmx-users] FW: error after 1ns of md run during production Mark Abraham
[gmx-users] GPU problem Mark Abraham
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P Mark Abraham
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P Mark Abraham
[gmx-users] looping job: time not updating Mark Abraham
[gmx-users] h_bonds Mark Abraham
[gmx-users] multi threading on rocks cluster Mark Abraham
[gmx-users] Dubious results with NPT Mark Abraham
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P Mark Abraham
[gmx-users] surprising: what's the reason? Mark Abraham
[gmx-users] Rigid water model Mark Abraham
[gmx-users] ligand binding sampling Mark Abraham
[gmx-users] surprising: what's the reason? Mark Abraham
[gmx-users] How can I concatenate multiple g96 configurations into a single trajectory? Mark Abraham
[gmx-users] creation coordinate file with special distance between system components Mark Abraham
[gmx-users] Is cholesterol model available in Charmm36 ff? Mark Abraham
[gmx-users] plotting rmsf Mark Abraham
[gmx-users] Running a single job using 2 different GROMACS version Mark Abraham
[gmx-users] Multi-GPU calculation Mark Abraham
[gmx-users] Parameterisation of transition metal ions in gromacs Mark Abraham
[gmx-users] Question about topology construction. Mark Abraham
[gmx-users] Error: illegal instruction (core dumped) Mark Abraham
[gmx-users] User-defined potentials and meaning of table extension Mark Abraham
[gmx-users] Double parameters Mark Abraham
[gmx-users] Unable to generate file.gro with gromacs.4.6.3-1 Mark Abraham
[gmx-users] PME on GPU4.6.2) Mark Abraham
[gmx-users] Error: illegal instruction (core dumped) Mark Abraham
[gmx-users] free energy of removal of a molecule from the bulk Mark Abraham
[gmx-users] refcoord-scaling Mark Abraham
[gmx-users] Add atom to .itp file Mark Abraham
[gmx-users] amber ff gromacs Mark Abraham
[gmx-users] Error: illegal instruction (core dumped) Mark Abraham
[gmx-users] MPI error in gromacs 4.6 Mark Abraham
[gmx-users] MPI error in gromacs 4.6 Mark Abraham
[gmx-users] MPI error in gromacs 4.6 Mark Abraham
[gmx-users] MPI error in gromacs 4.6, more Errors Mark Abraham
[gmx-users] refcoord-scaling Mark Abraham
[gmx-users] Error: illegal instruction (core dumped) Mark Abraham
[gmx-users] Gromacs not writing checkpoint files with multidir/replex (v 4.6.4) Mark Abraham
[gmx-users] [gmx-developers] Problem in compiling Gromacs 4.6.1 with GPU on MAC OS X Mark Abraham
[gmx-users] [gmx-developers] Problem in compiling Gromacs 4.6.1 with GPU on MAC OS X Mark Abraham
[gmx-users] Problems when loading .trr and/or .trj GROMACS trajectory files in VMD? Mark Abraham
[gmx-users] Warning: pressure scaling more than 1%, mu: 58.1548 58.1548 58.1548 Received the TERM signal, stopping at the next NS step Mark Abraham
[gmx-users] Difficulty preparing a polymer (PEG) for simulation Mark Abraham
[gmx-users] Question for bdc = xy Mark Abraham
[gmx-users] restarting run on GPU Mark Abraham
[gmx-users] Saving velocities of one atom at every timestep Mark Abraham
[gmx-users] charmm forcefield patches in gromacs Mark Abraham
[gmx-users] Function type Fourier Dih. not implemented in ip_pert Mark Abraham
[gmx-users] Area of Mixed lipid Bilayer Nikhil Agrawal
[gmx-users] ParamChem CHARMM to GROMACS conversion Albert
[gmx-users] ligand binding sampling Albert
[gmx-users] Rigid water model Michelle Aranha
[gmx-users] Rigid water model Michelle Aranha
[gmx-users] topology file Michelle Aranha
[gmx-users] Fwd: sigma unit conversion Barnett, James W.
[gmx-users] Launching MPI/OpenMP hybrid run Alexander Björling
[gmx-users] genion Andrew Bostick
[gmx-users] genion Andrew Bostick
[gmx-users] enthalpy of ion + protein interaction Andrew Bostick
[gmx-users] binding delta G, H and S for ion-protein Andrew Bostick
[gmx-users] binding delta G, H and S for ion-protein Andrew Bostick
[gmx-users] binding delta G, H and S for ion-protein Andrew Bostick
[gmx-users] binding delta G, H and S for ion-protein Andrew Bostick
[gmx-users] Out of Disk Space Dr. Vitaly Chaban
[gmx-users] Free energy calculation of a charged system Dr. Vitaly Chaban
[gmx-users] Function type Fourier Dih. not implemented in ip_pert Dr. Vitaly Chaban
[gmx-users] Function type Fourier Dih. not implemented in ip_pert Dr. Vitaly Chaban
[gmx-users] Function type Fourier Dih. not implemented in ip_pert Dr. Vitaly Chaban
[gmx-users] g_traj time unit Chandan Choudhury
[gmx-users] Single or Double precision? Dario Corrada
[gmx-users] Using pull code to keep two monomers near each other Sébastien Côté
[gmx-users] Using pull code to keep two monomers near each other Michael Daily
[gmx-users] Gromacs not writing checkpoint files with multidir/replex (v 4.6.4) Michael Daily
[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995) João M. Damas
[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995) João M. Damas
[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995) João M. Damas
[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995) João M. Damas
[gmx-users] How can I concatenate multiple g96 configurations into a single trajectory? Andrew DeYoung
[gmx-users] How can I concatenate multiple g96 configurations into a single trajectory? Andrew DeYoung
[gmx-users] Saving velocities of one atom at every timestep Andrew DeYoung
[gmx-users] FW: error after 1ns of md run during production Sucharita Dey
[gmx-users] asking for N and C termini for DNA and giving error Sucharita Dey
[gmx-users] asking for N and C termini for DNA and giving error Sucharita Dey
[gmx-users] asking for N and C termini for DNA and giving error Sucharita Dey
[gmx-users] asking for N and C termini for DNA and giving error Sucharita Dey
[gmx-users] No default Angle types Mayank Dixit
[gmx-users] No default Angle types Mayank Dixit
[gmx-users] Gromos DPPC bilayer: different results for 4.0.7 and 4.6.5 Patrick Fuchs
[gmx-users] Spatial distribution Norbert GARNIER
[gmx-users] Fwd: Need Help in Gromacs Balasubramani GL
[gmx-users] Assistance required for ligand parameterization Balasubramani GL
[gmx-users] [gmx-developers] Problem in compiling Gromacs 4.6.1 with GPU on MAC OS X Anders Gabrielsson
[gmx-users] g_potential Neha Gandhi
[gmx-users] help regarding building topology of Lanitibiotics (small natural peptides) Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU)
[gmx-users] Bug in gromacs-5.0-beta2 [Jan 29] Pavan Ghatty
[gmx-users] Problem in extending simulation with state.cpt while changing number of cores Bappa Ghosh
[gmx-users] Problem in extending simulation with state.cpt while changing number of cores Bappa Ghosh
[gmx-users] Option:Coupled to heme Gmail2
[gmx-users] Option:Coupled to heme Gmail2
[gmx-users] CHARMM36 force field available for GROMACS Gmail2
[gmx-users] Dispersion correction for protein interfaces Jason Grosch
[gmx-users] False Atommass and charge? GtrAngus
[gmx-users] probability density map GtrAngus
[gmx-users] False Atommass and charge? GtrAngus
[gmx-users] False Atommass and charge? GtrAngus
[gmx-users] Water out of box? Negative Z-Coordinates GtrAngus
[gmx-users] dihedral doubt Andres Ortega Guerrero
[gmx-users] dihedral doubt Andres Ortega Guerrero
[gmx-users] dihedral doubt Andres Ortega Guerrero
[gmx-users] NVT problem Andres Ortega Guerrero
[gmx-users] NVT problem Andres Ortega Guerrero
[gmx-users] NVT problem Andres Ortega Guerrero
[gmx-users] NVT problem Andres Ortega Guerrero
[gmx-users] missing residues in PDB file Andres Ortega Guerrero
[gmx-users] Umbrella pulling Drug + Ion channel Andres Ortega Guerrero
[gmx-users] Umbrella pulling Drug + Ion channel Andres Ortega Guerrero
[gmx-users] Umbrella pulling Drug + Ion channel Andres Ortega Guerrero
[gmx-users] Umbrella pulling Drug + Ion channel Andres Ortega Guerrero
[gmx-users] missing residues in PDB file Guo, Yanan
[gmx-users] swm4-ndp water with anisotropic polarizibility Peter Hamm
[gmx-users] swm4-ndp water with anisotropic polarizibility Peter Hamm
[gmx-users] Golshan Hejazi Golshan Hejazi
[gmx-users] Parsing g_rms binary rmsd comparison matrix João Henriques
[gmx-users] Parsing g_rms binary rmsd comparison matrix João Henriques
[gmx-users] re-sort frames by RMSD João Henriques
[gmx-users] re-sort frames by RMSD João Henriques
[gmx-users] re-sort frames by RMSD João Henriques
[gmx-users] g_covar warnings João Henriques
[gmx-users] g_covar warnings João Henriques
[gmx-users] g_covar warnings João Henriques
[gmx-users] re-sort frames by RMSD João Henriques
[gmx-users] G_bundle for PN vector orientation Wood Irene
[gmx-users] access to gmx Mostafa Javaheri
[gmx-users] Docking validation Mostafa Javaheri
[gmx-users] CHARMM36 force field available for GROMACS Jim
[gmx-users] CHARMM36 force field available for GROMACS Jim
[gmx-users] berger lipid parameters in amber99sb-ildn ff Monoj Mon Kalita
[gmx-users] berger lipid parameters in amber99sb-ildn ff Monoj Mon Kalita
[gmx-users] charmm forcefield patches in gromacs Gurunath Katagi
[gmx-users] antiparallel beta sheet Nidhi Katyal
[gmx-users] parameters problem Nidhi Katyal
[gmx-users] parameters problem Nidhi Katyal
[gmx-users] parameters problem Nidhi Katyal
[gmx-users] parameters problem Nidhi Katyal
[gmx-users] Effect of a single mutation in a protein Pappu Kumar
[gmx-users] Effect of a single mutation in a protein Pappu Kumar
[gmx-users] Checking the possibility of one complex out of possible two Pappu Kumar
[gmx-users] Effect of a single mutation in a protein Pappu Kumar
[gmx-users] simulation of a trimer Pappu Kumar
[gmx-users] Checking the possibility of one complex out of possible two Pappu Kumar
[gmx-users] Adding TPO and SEP to G53a6 Forcefield Pavan Kumar
[gmx-users] Out of Disk Space Pavan Kumar
[gmx-users] Out of Disk Space Pavan Kumar
[gmx-users] MPI error in gromacs 4.6 Pavan Kumar
[gmx-users] MPI error in gromacs 4.6 Pavan Kumar
[gmx-users] Cavity size calculation Praveen Kumar
[gmx-users] Regarding structure analysis of DNA Sathish Kumar
[gmx-users] Regarding calculation of torsion angles in DNA Sathish Kumar
[gmx-users] Launching MPI/OpenMP hybrid run Carsten Kutzner
[gmx-users] Launching MPI/OpenMP hybrid run Carsten Kutzner
[gmx-users] g_tune_pme scalevdw option not working? Carsten Kutzner
[gmx-users] g_tune_pme scalevdw option not working? Carsten Kutzner
[gmx-users] g_tune_pme scalevdw option not working? Carsten Kutzner
[gmx-users] compilation error with gcc in non-standard location Carsten Kutzner
[gmx-users] Warning: pressure scaling more than 1%, mu: 58.1548 58.1548 58.1548 Received the TERM signal, stopping at the next NS step Lakshmi
[gmx-users] Two-body Bonded Distance Justin Lemkul
[gmx-users] A question about "blowing up" Justin Lemkul
[gmx-users] A question about "blowing up" Justin Lemkul
[gmx-users] A question about "blowing up" Justin Lemkul
[gmx-users] dihedral doubt Justin Lemkul
[gmx-users] dihedral doubt Justin Lemkul
[gmx-users] .top file after using amber2gromacs Justin Lemkul
[gmx-users] .top file after using amber2gromacs Justin Lemkul
[gmx-users] md_pull code in umbrella sampling Justin Lemkul
[gmx-users] Regarding structure analysis of DNA Justin Lemkul
[gmx-users] Set the environment variables of "FFTW3_INCLUDE_DIR" and "FFTW3_LIBRARIES" Justin Lemkul
[gmx-users] Question about Improper Dihedral of Charmm in gmx & ParamChem Justin Lemkul
[gmx-users] Two-body Bonded Distance Justin Lemkul
[gmx-users] No default U-B types charmm Justin Lemkul
[gmx-users] Error Mdrun Justin Lemkul
[gmx-users] No default U-B types charmm Justin Lemkul
[gmx-users] No default U-B types charmm Justin Lemkul
[gmx-users] Option:Coupled to heme Justin Lemkul
[gmx-users] Option:Coupled to heme Justin Lemkul
[gmx-users] Two-body Bonded Distance Justin Lemkul
[gmx-users] antiparallel beta sheet Justin Lemkul
[gmx-users] No default U-B types charmm Justin Lemkul
[gmx-users] dna with charmm36 Justin Lemkul
[gmx-users] tip5p and charmm Justin Lemkul
[gmx-users] dna with charmm36 Justin Lemkul
[gmx-users] Question about Improper Dihedral of Charmm in gmx &, ParamChem Justin Lemkul
[gmx-users] REMD Melting Curve Justin Lemkul
[gmx-users] access to gmx Justin Lemkul
[gmx-users] SImulation with urea Justin Lemkul
[gmx-users] pbc problems Justin Lemkul
[gmx-users] REMD Melting Curve Justin Lemkul
[gmx-users] pbc problems Justin Lemkul
[gmx-users] inclusion of water in gromacs input files Justin Lemkul
[gmx-users] charge group number Justin Lemkul
[gmx-users] Adding Urea in simulation Justin Lemkul
[gmx-users] Fwd: Need Help in Gromacs Justin Lemkul
[gmx-users] entropy calculation Justin Lemkul
[gmx-users] help with g_puckering Justin Lemkul
[gmx-users] inclusion of water in gromacs input files Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] Generate many random configurations Justin Lemkul
[gmx-users] ParamChem CHARMM to GROMACS conversion Justin Lemkul
[gmx-users] Generate many random configurations Justin Lemkul
[gmx-users] Generate many random configurations Justin Lemkul
[gmx-users] impropers in Gromacs and acepype tool Justin Lemkul
[gmx-users] impropers in Gromacs and acepype tool Justin Lemkul
[gmx-users] impropers in Gromacs and acepype tool Justin Lemkul
[gmx-users] angle between benzene rings Justin Lemkul
[gmx-users] Generate many random configurations Justin Lemkul
[gmx-users] Assistance required for ligand parameterization Justin Lemkul
[gmx-users] Generate many random configurations Justin Lemkul
[gmx-users] Area of Mixed lipid Bilayer Justin Lemkul
[gmx-users] Using pull code to keep two monomers near each other Justin Lemkul
[gmx-users] Neutralize or add an Ions Concentration for a Membrane Simulation? Justin Lemkul
[gmx-users] SETTLE and LINCS Justin Lemkul
[gmx-users] CHARMM36 force field available for GROMACS Justin Lemkul
[gmx-users] Docking validation Justin Lemkul
[gmx-users] tip3p Justin Lemkul
[gmx-users] CHARMM36 force field available for GROMACS Justin Lemkul
[gmx-users] CHARMM36 force field available for GROMACS Justin Lemkul
[gmx-users] parameters problem Justin Lemkul
[gmx-users] Performing protein-ligand GROMACS MD under pH 5 conditions Justin Lemkul
[gmx-users] Spatial distribution Justin Lemkul
[gmx-users] parameters problem Justin Lemkul
[gmx-users] swm4-ndp water with anisotropic polarizibility Justin Lemkul
[gmx-users] parameters problem Justin Lemkul
[gmx-users] g_energy (energygrps) Justin Lemkul
[gmx-users] No default Angle types Justin Lemkul
[gmx-users] Problem with small number of water molecules Justin Lemkul
[gmx-users] Problem with small number of water molecules Justin Lemkul
[gmx-users] why not coordinates from cpt file Justin Lemkul
[gmx-users] Regarding calculation of torsion angles in DNA Justin Lemkul
[gmx-users] Dubious results with NPT Justin Lemkul
[gmx-users] No equilibration, annealing Justin Lemkul
[gmx-users] looping job: time not updating Justin Lemkul
[gmx-users] h_bonds Justin Lemkul
[gmx-users] h_bonds Justin Lemkul
[gmx-users] Bond length not finite error Justin Lemkul
[gmx-users] asking for N and C termini for DNA and giving error Justin Lemkul
[gmx-users] Position restraints Justin Lemkul
[gmx-users] Interaction energy graph Justin Lemkul
[gmx-users] NVT problem Justin Lemkul
[gmx-users] Swiss pdb viewer Justin Lemkul
[gmx-users] NVT problem Justin Lemkul
[gmx-users] NVT problem Justin Lemkul
[gmx-users] NVT problem Justin Lemkul
[gmx-users] problem of running multiple cores Justin Lemkul
[gmx-users] NVT problem Justin Lemkul
[gmx-users] problem of running multiple cores (Tom) Justin Lemkul
[gmx-users] genion Justin Lemkul
[gmx-users] Interaction energy graph Justin Lemkul
[gmx-users] binding delta G, H and S for ion-protein Justin Lemkul
[gmx-users] binding delta G, H and S for ion-protein Justin Lemkul
[gmx-users] asking for N and C termini for DNA and giving error Justin Lemkul
[gmx-users] constraint pulling Justin Lemkul
[gmx-users] How can I concatenate multiple g96 configurations into a single trajectory? Justin Lemkul
[gmx-users] PEG residue Justin Lemkul
[gmx-users] Is cholesterol model available in Charmm36 ff? Justin Lemkul
[gmx-users] CHARMM36 force field available for GROMACS Justin Lemkul
[gmx-users] CHARMM36 force field available for GROMACS Justin Lemkul
[gmx-users] Is cholesterol model available in Charmm36 ff? Justin Lemkul
[gmx-users] constraint pulling Justin Lemkul
[gmx-users] topology file Justin Lemkul
[gmx-users] editconf -box a b c Justin Lemkul
[gmx-users] editconf -box a b c Justin Lemkul
[gmx-users] Question about topology construction. Justin Lemkul
[gmx-users] User-defined potentials and meaning of table extension Justin Lemkul
[gmx-users] Question for bdc = xy Justin Lemkul
[gmx-users] Question for bdc = xy Justin Lemkul
[gmx-users] index file group names: Case sensitive Justin Lemkul
[gmx-users] False Atommass and charge? Justin Lemkul
[gmx-users] Unable to generate file.gro with gromacs.4.6.3-1 Justin Lemkul
[gmx-users] free energy of removal of a molecule from the bulk Justin Lemkul
[gmx-users] Error: illegal instruction (core dumped) Justin Lemkul
[gmx-users] Error: illegal instruction (core dumped) Justin Lemkul
[gmx-users] Add atom to .itp file Justin Lemkul
[gmx-users] MPI error in gromacs 4.6 Justin Lemkul
[gmx-users] MPI error in gromacs 4.6 Justin Lemkul
[gmx-users] MPI error in gromacs 4.6, more Errors Justin Lemkul
[gmx-users] Protein-Ligand MS simulation Justin Lemkul
[gmx-users] refcoord-scaling Justin Lemkul
[gmx-users] Umbrella pulling Drug + Ion channel Justin Lemkul
[gmx-users] refcoord-scaling Justin Lemkul
[gmx-users] Umbrella pulling Drug + Ion channel Justin Lemkul
[gmx-users] g_select Justin Lemkul
[gmx-users] Umbrella pulling Drug + Ion channel Justin Lemkul
[gmx-users] Reg Gromacs in cluster problem Justin Lemkul
[gmx-users] g_select Justin Lemkul
[gmx-users] g_select Justin Lemkul
[gmx-users] Effect of a single mutation in a protein Justin Lemkul
[gmx-users] Ryckaert-Bellemans Dihedral with AMBER Justin Lemkul
[gmx-users] Umbrella pulling Drug + Ion channel Justin Lemkul
[gmx-users] Effect of a single mutation in a protein Justin Lemkul
[gmx-users] Umbrella pulling Drug + Ion channel Justin Lemkul
[gmx-users] Coulomb and Lennnard-Jones parameters Justin Lemkul
[gmx-users] Ryckaert-Bellemans Dihedral with AMBER Justin Lemkul
[gmx-users] Difficulty preparing a polymer (PEG) for simulation. Justin Lemkul
[gmx-users] g_covar warnings Justin Lemkul
[gmx-users] Problem with trjconv to keep molecule whole for multi-chain protein Justin Lemkul
[gmx-users] g_covar warnings Justin Lemkul
[gmx-users] Question for bdc = xy Justin Lemkul
[gmx-users] Effect of a single mutation in a protein Justin Lemkul
[gmx-users] Checking the possibility of one complex out of possible two Justin Lemkul
[gmx-users] help regarding building topology of Lanitibiotics (small natural peptides) Justin Lemkul
[gmx-users] g_traj time unit Justin Lemkul
[gmx-users] umbrella sampling with force clamping unfolding of ubiquitin Justin Lemkul
[gmx-users] charmm forcefield patches in gromacs Justin Lemkul
[gmx-users] interaction energy Justin Lemkul
[gmx-users] interaction energy Justin Lemkul
[gmx-users] How to provide the FFTW3 install directory Justin Lemkul
[gmx-users] Saving velocities of one atom at every timestep Justin Lemkul
[gmx-users] How to provide the FFTW3 install directory Justin Lemkul
[gmx-users] How to provide the FFTW3 install directory Justin Lemkul
[gmx-users] Function type Fourier Dih. not implemented in ip_pert Justin Lemkul
[gmx-users] How to provide the FFTW3 install directory Justin Lemkul
[gmx-users] Function type Fourier Dih. not implemented in ip_pert Justin Lemkul
[gmx-users] interaction energy Justin Lemkul
[gmx-users] Water out of box? Negative Z-Coordinates Justin Lemkul
[gmx-users] How to provide the FFTW3 install directory Justin Lemkul
[gmx-users] protein water contacts Justin Lemkul
[gmx-users] Double parameters Josip Lovrić
[gmx-users] Double parameters Josip Lovrić
[gmx-users] g_select Josip Lovrić
[gmx-users] g_select Josip Lovrić
[gmx-users] g_select Josip Lovrić
[gmx-users] g_select Josip Lovrić
[gmx-users] Simulation with Ligand Kavyashree M
[gmx-users] angle between benzene rings Sanku M
[gmx-users] .top file after using amber2gromacs Chetan Mahajan
[gmx-users] .top file after using amber2gromacs Chetan Mahajan
[gmx-users] .top file after using amber2gromacs Chetan Mahajan
[gmx-users] inclusion of water in gromacs input files Chetan Mahajan
[gmx-users] charge group number Chetan Mahajan
[gmx-users] inclusion of water in gromacs input files Chetan Mahajan
[gmx-users] sigma unit conversion Chetan Mahajan
[gmx-users] impropers in Gromacs and acepype tool Chetan Mahajan
[gmx-users] impropers in Gromacs and acepype tool Chetan Mahajan
[gmx-users] impropers in Gromacs and acepype tool Chetan Mahajan
[gmx-users] tip3p Chetan Mahajan
[gmx-users] tip3p Chetan Mahajan
[gmx-users] surprising: what's the reason? Chetan Mahajan
[gmx-users] surprising: what's the reason? Chetan Mahajan
[gmx-users] surprising: what's the reason? Chetan Mahajan
[gmx-users] surprising: what's the reason? Chetan Mahajan
[gmx-users] surprising: what's the reason? Chetan Mahajan
[gmx-users] refcoord-scaling Chetan Mahajan
[gmx-users] refcoord-scaling Chetan Mahajan
[gmx-users] refcoord-scaling Chetan Mahajan
[gmx-users] refcoord-scaling Chetan Mahajan
[gmx-users] refcoord-scaling Chetan Mahajan
[gmx-users] refcoord-scaling Chetan Mahajan
[gmx-users] probability density map Erik Marklund
[gmx-users] probability density map Erik Marklund
[gmx-users] Position restraints Nimmy McNimmerson
[gmx-users] User-defined potentials and meaning of table extension Davide Mercadante
[gmx-users] Problems when loading .trr and/or .trj GROMACS trajectory files in VMD? Juan Munoz-Garcia
[gmx-users] gmx gangle in the development version of gromacs Teemu Murtola
[gmx-users] gmx gangle in the development version of gromacs Teemu Murtola
[gmx-users] MPI error in gromacs 4.6 Ankita Naithani
[gmx-users] MPI error in gromacs 4.6 Ankita Naithani
[gmx-users] MPI error in gromacs 4.6, more Errors Ankita Naithani
[gmx-users] MPI error in gromacs 4.6, more Errors Ankita Naithani
[gmx-users] Swiss pdb viewer Nazanin
[gmx-users] md_pull code in umbrella sampling Christopher Neale
[gmx-users] Out of Disk Space Christopher Neale
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P Christopher Neale
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P Christopher Neale
[gmx-users] PEG residue Christopher Neale
[gmx-users] Unable to generate file.gro with gromacs.4.6.3-1 Christopher Neale
[gmx-users] Unable to generate file.gro with gromacs.4.6.3-1 Christopher Neale
[gmx-users] berger lipid parameters in amber99sb-ildn ff Christopher Neale
[gmx-users] berger lipid parameters in amber99sb-ildn ff Christopher Neale
[gmx-users] refcoord-scaling Christopher Neale
[gmx-users] Unable to generate file.gro with gromacs.4.6.3-1 Collins Nganou
[gmx-users] Error: illegal instruction (core dumped) Ly Minh Nhat
[gmx-users] Error: illegal instruction (core dumped) Ly Minh Nhat
[gmx-users] How to provide the FFTW3 install directory Ly Minh Nhat
[gmx-users] How to provide the FFTW3 install directory Ly Minh Nhat
[gmx-users] How to provide the FFTW3 install directory Ly Minh Nhat
[gmx-users] How to provide the FFTW3 install directory Ly Minh Nhat
[gmx-users] How to provide the FFTW3 install directory Ly Minh Nhat
[gmx-users] dihedral doubt Andres Ortega
[gmx-users] Error Mdrun Andres Ortega
[gmx-users] Neutralize or add an Ions Concentration for a Membrane Simulation? Andres Ortega
[gmx-users] SETTLE and LINCS Andres Ortega
[gmx-users] NVT problem Andres Ortega
[gmx-users] Pulling code Andres Ortega
[gmx-users] Umbrella pulling Drug + Ion channel Andres Ortega
[gmx-users] Dispersion correction for protein interfaces CHEN Pan
[gmx-users] Swiss pdb viewer Negar Parvizi
[gmx-users] Velocity Verlet integrator Mario Fernández Pendás
[gmx-users] g_energy (energygrps) Atila Petrosian
[gmx-users] g_energy (energygrps) Atila Petrosian
[gmx-users] g_energy (energygrps) Atila Petrosian
[gmx-users] g_energy (energygrps) Atila Petrosian
[gmx-users] creation coordinate file with special distance between system components Atila Petrosian
[gmx-users] Single or Double precision? Szilárd Páll
[gmx-users] Thread affinity error when Running Gromacs 4.6.3 on Bluegene/P Szilárd Páll
[gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI: version 1.7.4-2 for OpenMPI is compatibel Szilárd Páll
[gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI: version 1.7.4-2 for OpenMPI is compatibel Szilárd Páll
[gmx-users] Multi-GPU calculation Szilárd Páll
[gmx-users] [gmx-developers] Problem in compiling Gromacs 4.6.1 with GPU on MAC OS X Szilárd Páll
[gmx-users] genion Kalyan Reddy
[gmx-users] Fwd: Regarding trjorder Venkat Reddy
[gmx-users] Fwd: Regarding trjorder Venkat Reddy
[gmx-users] Add atom to .itp file Satyadeep Roat
[gmx-users] g_tune_pme scalevdw option not working? João Rodrigues
[gmx-users] g_tune_pme scalevdw option not working? João Rodrigues
[gmx-users] g_tune_pme scalevdw option not working? João Rodrigues
[gmx-users] g_tune_pme scalevdw option not working? João Rodrigues
[gmx-users] PME on GPU4.6.2) Albert Romano
[gmx-users] A converter for lammps to gromacs X Rules
[gmx-users] g_traj time unit X Rules
[gmx-users] A converter for lammps to gromacs X Rules
[gmx-users] Interaction energy graph Kannan S
[gmx-users] Interaction energy Kannan S
[gmx-users] REST2 with gromacs-4.5.5 plumed2.2.0 -hrex Saravanan
[gmx-users] Regarding the change in number of processors of simulation job Sujit Sarkar
[gmx-users] constraint pulling Thomas Schlesier
[gmx-users] Compilation issues with GROMACS 5 beta 2 Roland Schulz
[gmx-users] Coulomb and Lennnard-Jones parameters Maria Astón Serrano
[gmx-users] md_pull code in umbrella sampling Arunima Shilpi
[gmx-users] md_pull code in umbrella sampling Arunima Shilpi
[gmx-users] Rigid water model Michael Shirts
[gmx-users] Velocity Verlet integrator Michael Shirts
[gmx-users] gmx gangle in the development version of gromacs Eric Smoll
[gmx-users] gromacs.org_gmx-users Digest, Vol 119, Issue 23 Eric Smoll
[gmx-users] Area of Mixed lipid Bilayer Björn Sommer
[gmx-users] CELLmicrocosmos 2.2.2_1 MembraneEditor Minor Release Björn Sommer
[gmx-users] choosing Ensemble for production MD run Archana Sonawani-Jagtap
[gmx-users] g_bar crash David van der Spoel
[gmx-users] REMD Melting Curve David van der Spoel
[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995) David van der Spoel
[gmx-users] excuse me, I want to ask you some question about bond energy David van der Spoel
[gmx-users] binding delta G, H and S for ion-protein David van der Spoel
[gmx-users] binding delta G, H and S for ion-protein David van der Spoel
[gmx-users] Cavity size calculation David van der Spoel
[gmx-users] A converter for lammps to gromacs David van der Spoel
[gmx-users] Difficulty preparing a polymer (PEG) for simulation. Dan Sponseller
[gmx-users] Difficulty preparing a polymer (PEG) for simulation Dan Sponseller
[gmx-users] Cross-correlation analysis in multidomain proteins James Starlight
[gmx-users] Detection of Internal water along MD trajectory James Starlight
[gmx-users] Apple cluster Steve
[gmx-users] (no subject) Prajisha Sujaya
[gmx-users] Out of Disk Space MUSYOKA THOMMAS
[gmx-users] Performing protein-ligand GROMACS MD under pH 5 conditions MUSYOKA THOMMAS
[gmx-users] Running a single job using 2 different GROMACS version MUSYOKA THOMMAS
[gmx-users] Protein-Ligand MS simulation MUSYOKA THOMMAS
[gmx-users] Detection of Internal water along MD trajectory Trayder Thomas
[gmx-users] Question about Improper Dihedral of Charmm in gmx & ParamChem Tom
[gmx-users] gromacs.org_gmx-users Digest, Vol 119, Issue 10 Tom
[gmx-users] problem of running multiple cores Tom
[gmx-users] NVT problem (Justin Lemkul) Tom
[gmx-users] Free energy calculation of a charged system Valentina
[gmx-users] Free energy calculation of a charged system Valentina
[gmx-users] free energy of removal of a molecule from the bulk Valentina
[gmx-users] free energy of removal of a molecule from the bulk Valentina
[gmx-users] tip5p and charmm Rafael I. Silverman y de la Vega
[gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI: version 1.7.4-2 for OpenMPI is compatibel Christian Wagner
[gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI: version 1.7.4-2 for OpenMPI is compatibel Christian Wagner
[gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI: version 1.7.4-2 for OpenMPI is compatibel Christian Wagner
[gmx-users] compilation error with gcc in non-standard location Christian Wagner
[gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI: version 1.7.4-2 for OpenMPI is compatibel Mirco Wahab
[gmx-users] Question about the electric field? Xianwei Wang
[gmx-users] Generate many random configurations Tsjerk Wassenaar
[gmx-users] CHARMM36 force field available for GROMACS Tsjerk Wassenaar
[gmx-users] about insane.py script on martini website. Tsjerk Wassenaar
[gmx-users] surprising: what's the reason? Tsjerk Wassenaar
[gmx-users] surprising: what's the reason? Tsjerk Wassenaar
[gmx-users] enthalpy of ion + protein interaction Tsjerk Wassenaar
[gmx-users] How can I concatenate multiple g96 configurations into a single trajectory? Tsjerk Wassenaar
[gmx-users] re-sort frames by RMSD Tsjerk Wassenaar
[gmx-users] g_traj time unit Tegar Nurwahyu Wijaya
[gmx-users] g_traj time unit Tegar Nurwahyu Wijaya
[gmx-users] g_traj time unit Tegar Nurwahyu Wijaya
[gmx-users] Question for bdc = xy ookami a
[gmx-users] Question for bdc = xy ookami a
[gmx-users] Question for bdc = xy ookami a
[gmx-users] Question for bdc = xy ookami a
[gmx-users] Launching MPI/OpenMP hybrid run alex.bjorling
[gmx-users] Launching MPI/OpenMP hybrid run alex.bjorling
[gmx-users] re-sort frames by RMSD andrea
[gmx-users] Thread affinity error when Running Gromacs 4.6.3 on Bluegene/P arrow50311
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P arrow50311
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P arrow50311
[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P arrow50311
[gmx-users] Multi-GPU calculation arrow50311
[gmx-users] Multi-GPU calculation arrow50311
[gmx-users] Problem with trjconv to keep molecule whole for multi-chain protein arrow50311
[gmx-users] REMD Melting Curve atanu_das
[gmx-users] PEG residue dan42
[gmx-users] REMD Melting Curve atanu das
[gmx-users] REMD Melting Curve atanu das
[gmx-users] Is cholesterol model available in Charmm36 ff? davhak
[gmx-users] Is cholesterol model available in Charmm36 ff? davhak
[gmx-users] Is cholesterol model available in Charmm36 ff? davhak
[gmx-users] Is cholesterol model available in Charmm36 ff? davhak
[gmx-users] Is cholesterol model available in Charmm36 ff? davhak
[gmx-users] Add atom to .itp file deep
[gmx-users] Problem with small number of water molecules ehs
[gmx-users] Problem with small number of water molecules ehs
[gmx-users] No equilibration, annealing ehs
[gmx-users] editconf -box a b c ehs
[gmx-users] editconf -box a b c ehs
[gmx-users] SImulation with urea bharat gupta
[gmx-users] SImulation with urea bharat gupta
[gmx-users] Adding Urea in simulation bharat gupta
[gmx-users] Adding Urea in simulation bharat gupta
[gmx-users] umbrella sampling with force clamping unfolding of ubiquitin gwonchan
[gmx-users] Problems with periodic syatems susanta haldar
[gmx-users] about insane.py script on martini website. jhosamelly
[gmx-users] CHARMM36 force field available for GROMACS jim
[gmx-users] Compilation issues with GROMACS 5 beta 2 jk
[gmx-users] Compilation issues with GROMACS 5 beta 2 jk
[gmx-users] Two-body Bonded Distance jolayfield
[gmx-users] Two-body Bonded Distance jolayfield
[gmx-users] MM-GB/SA analysis in Gromacs kannan
[gmx-users] Interaction energy graph kannan
[gmx-users] Interaction energy graph kannan
[gmx-users] Interaction energy graph kannan
[gmx-users] GPU problem pratibha kapoor
[gmx-users] constraint pulling leila karami
[gmx-users] constraint pulling leila karami
[gmx-users] Ryckaert-Bellemans Dihedral with AMBER tarak karmakar
[gmx-users] Ryckaert-Bellemans Dihedral with AMBER tarak karmakar
[gmx-users] Ryckaert-Bellemans Dihedral with AMBER tarak karmakar
[gmx-users] A question about "blowing up" sujith ks
[gmx-users] Question about topology construction. sujith ks
[gmx-users] help regarding building topology of Lanitibiotics (small natural peptides) chetan kumar meena
[gmx-users] multi threading on rocks cluster michael.b
[gmx-users] free energy calculations michael.b
[gmx-users] segmentation fault in vanilla TI calculation, death without further noitice michael.b
[gmx-users] segmentation fault in vanilla TI calculation, death without further noitice michael.b
[gmx-users] compilation error with gcc in non-standard location michael.b
[gmx-users] compilation error with gcc in non-standard location michael.b
[gmx-users] index file group names: Case sensitive shivangi nangia
[gmx-users] Guidance on how to install Gromacs-5.0-beta2 ooker
[gmx-users] Error: illegal instruction (core dumped) ooker
[gmx-users] Error: illegal instruction (core dumped) ooker
[gmx-users] probability density map pratibha
[gmx-users] question about free energy pratibha
[gmx-users] restarting run on GPU pratibha
[gmx-users] restarting run on GPU pratibha
[gmx-users] interaction energy pratibha
[gmx-users] interaction energy pratibha
[gmx-users] interaction energy pratibha
[gmx-users] protein water contacts pratibha
[gmx-users] No default U-B types charmm gromacs query
[gmx-users] No default U-B types charmm gromacs query
[gmx-users] No default U-B types charmm gromacs query
[gmx-users] dna with charmm36 gromacs query
[gmx-users] dna with charmm36 gromacs query
[gmx-users] No default U-B types charmm gromacs query
[gmx-users] why not coordinates from cpt file gromacs query
[gmx-users] looping job: time not updating gromacs query
[gmx-users] looping job: time not updating gromacs query
[gmx-users] Bond length not finite error gromacs query
[gmx-users] Bond length not finite error gromacs query
[gmx-users] how to split gromacs tpr file sidra rafi
[gmx-users] how to split gromacs tpr file sidra rafi
[gmx-users] How to calculate RMSD between residues sidra rafi
[gmx-users] Generate many random configurations rankinb
[gmx-users] Generate many random configurations rankinb
[gmx-users] Generate many random configurations rankinb
[gmx-users] Generate many random configurations rankinb
[gmx-users] Generate many random configurations rankinb
[gmx-users] Generate many random configurations rankinb
[gmx-users] binding delta G, H and S for ion-protein lloyd riggs
[gmx-users] PEG residue lloyd riggs
[gmx-users] Reg Gromacs in cluster problem vidhya sankar
[gmx-users] gromacs.org_gmx-users Digest, Vol 119, Issue 8 sauravsaha
[gmx-users] help regarding building topology of Lanitibiotics (small natural peptides) bipin singh
[gmx-users] error after 1ns of md run during production sucharita
[gmx-users] Parameterisation of transition metal ions in gromacs sukriti002
[gmx-users] re-sort frames by RMSD unitALX
[gmx-users] re-sort frames by RMSD unitALX
[gmx-users] (no subject) cesteban at unsl.edu.ar
[gmx-users] help with g_puckering cesteban at unsl.edu.ar
[gmx-users] plotting rmsf vansh
[gmx-users] Out of Disk Space vansh
[gmx-users] h_bonds virk
[gmx-users] h_bonds virk
[gmx-users] h_bonds virk
[gmx-users] amber ff gromacs virk
[gmx-users] how to set pair list buffer when use cutoff scheme = group setup zhonghe xu
[gmx-users] Area of Mixed lipid Bilayer César Ávila
[gmx-users] pbc problems 申昊
[gmx-users] pbc problems 申昊
[gmx-users] entropy calculation 申昊

Last message date: Mon Mar 31 23:49:54 CEST 2014
Archived on: Mon Mar 31 23:49:55 CEST 2014

Messages sorted by: [ thread ] [ subject ] [ date ]
More info on this list...

This archive was generated by Pipermail 0.09 (Mailman edition).