July 2010 Archives by author

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Starting: Thu Jul 1 01:57:11 CEST 2010
Ending: Sat Jul 31 22:17:42 CEST 2010
Messages: 640

[gmx-users] mpi installation problems Ryan S Davis (rsdavis1)
[gmx-users] Gromacs to APBS Mark Abraham
[gmx-users] the job is not being distributed Mark Abraham
[gmx-users] Capping residues Mark Abraham
[gmx-users] amber/charmm force field and HB lifetime at low temperature Mark Abraham
[gmx-users] Re: Re: Re:Chain Terminus Mark Abraham
[gmx-users] Problem with Lennard Jones cross terms Mark Abraham
[gmx-users] Capping residues Mark Abraham
[gmx-users] B-factor Mark Abraham
[gmx-users] GBSA calculations Mark Abraham
[gmx-users] Re: Re: Fwd: missing atom Mark Abraham
[gmx-users] Units of the Amber99 parameters Mark Abraham
[gmx-users] problem with trjconv -pbc cluster Mark Abraham
[gmx-users] problem while simulating metal ions Mark Abraham
[gmx-users] No such moleculetype SOL Mark Abraham
[gmx-users] No such moleculetype SOL Mark Abraham
[gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96 Mark Abraham
[gmx-users] energy contributions Mark Abraham
[gmx-users] question about solvating Mark Abraham
[gmx-users] mpi run Mark Abraham
[gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory Mark Abraham
[gmx-users] how to determine the box size Mark Abraham
[gmx-users] Solvating protein Mark Abraham
[gmx-users] Frozen N2 in a very long tube Mark Abraham
[gmx-users] energygrp_excl and PME Mark Abraham
[gmx-users] g_msd Mark Abraham
[gmx-users] Compile-time errors with MKL Mark Abraham
[gmx-users] Stabilizing a heavy metal ion in solution Mark Abraham
[gmx-users] Compile-time errors with MKL Mark Abraham
[gmx-users] NPT for compression Mark Abraham
[gmx-users] NPT for compressing the system Mark Abraham
[gmx-users] Compile-time errors with MKL Mark Abraham
[gmx-users] Removing water from a trajectory Mark Abraham
[gmx-users] Rcut-off etc. Mark Abraham
[gmx-users] extracting coordinates Vishal Agarwal
[gmx-users] Re: amber parameters in gromacs Alan
[gmx-users] Re: amber parameters in gromacs Alan
[gmx-users] Re: Help needed with ACPYPI Alan
[gmx-users] energies in amber, namd and gromacs Alan
[gmx-users] gromacs energies very different from other MD engines for the very same system and conditions Alan
[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition Alan
[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition Alan
[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition Alan
[gmx-users] gmx 4.5 configure options confusing Alan
[gmx-users] error compiling gmx 4.5 on Mac 10.6.4 Alan
[gmx-users] Re: error compiling gmx 4.5 on Mac 10.6.4 Alan
[gmx-users] tests for gmx 4.5 Alan
[gmx-users] gmx 4.5 issue with grompp Alan
[gmx-users] installation: gromacs on Mac.10.5.8 leopard KACHMAR Ali
[gmx-users] installation: gromacs on Mac.10.5.8 leopard KACHMAR Ali
[gmx-users] installation: gromacs on Mac.10.5.8 leopard KACHMAR Ali
[gmx-users] installation: gromacs on Mac.10.5.8 leopard KACHMAR Ali
[gmx-users] installation: gromacs on Mac.10.5.8 leopard KACHMAR Ali
[gmx-users] installation: gromacs on Mac.10.5.8 leopard KACHMAR Ali
[gmx-users] installation: gromacs on Mac.10.5.8 leopard KACHMAR Ali
[gmx-users] installation: gromacs on Mac.10.5.8 leopard KACHMAR Ali
[gmx-users] installation: gromacs on Mac.10.5.8 leopard KACHMAR Ali
[gmx-users] (no subject) Anitha
[gmx-users] (no subject) Anitha
[gmx-users] (no subject) Anitha
[gmx-users] Problems with installing mpi-version of Gromacs Pinchas Aped
[gmx-users] potential git server downtime Rossen Apostolov
[gmx-users] GROMACS-4.5-beta1 is out! Rossen Apostolov
[gmx-users] Pullx file Aswathy
[gmx-users] Selecting a force field for dioxane Saikat Banerjee
[gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96 C. Batistakis
[gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96 C. Batistakis
[gmx-users] Avoid generation of angles, pairs and dihedrals from pdb2gmx C. Batistakis
[gmx-users] Coarse-Grain: GROMACS bond information to VMD C. Batistakis
[gmx-users] pdb2gmx doesn´t generate H Pascal Baumann
[gmx-users] Maximum table size for tabulated non-bonded potential Julie Bernauer
[gmx-users] Compile-time errors with MKL Elton Carvalho
[gmx-users] Compile-time errors with MKL Elton Carvalho
[gmx-users] Compile-time errors with MKL Elton Carvalho
[gmx-users] frezzing a bond Elton Carvalho
[gmx-users] Segmentation Fault with g_dielectric Jennifer Casey
[gmx-users] Errors with g_dielectric Jennifer Casey
[gmx-users] Re: the Pressure control in GROMACS 4.0.7 Vitaly Chaban
[gmx-users] Re: Frozen N2 in a very long tube Vitaly Chaban
[gmx-users] Re: Pressure control in GROMACS 4.0.7 Vitaly Chaban
[gmx-users] Re: high repulsion in packed system Vitaly Chaban
[gmx-users] Re: Frozen N2 in a very long tube Vitaly Chaban
Fwd: [gmx-users] Re: Frozen N2 in a very long tube Vitaly Chaban
[gmx-users] Re: high repulsion in packed system Vitaly Chaban
[gmx-users] Re: g_cluster settings Vitaly Chaban
[gmx-users] Re: MD run for octanol system Vitaly Chaban
[gmx-users] Re: ffamber99sb error Vitaly Chaban
[gmx-users] Re: number of degrees of frredom Vitaly Chaban
[gmx-users] dissolution of gases in liquid Vitaly Chaban
[gmx-users] Fwd: dissolution of gases in liquid Vitaly Chaban
[gmx-users] Re: grommp_md error Vitaly Chaban
[gmx-users] Re: Stabilizing a heavy metal ion in solution Vitaly Chaban
[gmx-users] strain-stress, Young modulus, etc Vitaly Chaban
[gmx-users] Re: Selecting a force field for dioxane Vitaly Chaban
[gmx-users] no-pbc simulation in parallel Vitaly Chaban
[gmx-users] pull code example Vitaly Chaban
[gmx-users] bond potential selection Vitaly Chaban
[gmx-users] Re: switching off electrostatics Vitaly Chaban
[gmx-users] Re: Lincs warning but reasonable energy Vitaly Chaban
[gmx-users] Fwd: PE compressing - for reference only Vitaly Chaban
[gmx-users] Re: PE compressing Vitaly Chaban
[gmx-users] Re: NPT and NVT simulations Vitaly Chaban
[gmx-users] periodicity and correct output Vitaly Chaban
[gmx-users] Re: NPT and NVT simulations Vitaly Chaban
[gmx-users] periodicity and correct output Vitaly Chaban
[gmx-users] Re: compressing the system Vitaly Chaban
[gmx-users] Re: compressing the system Vitaly Chaban
[gmx-users] Re: parallel mdrun (mpimdrun) is slower than Vitaly Chaban
[gmx-users] g_cluster settings Marc Charendoff
[gmx-users] g_cluster Jarvis-Patrick Marc Charendoff
[gmx-users] Re: g_saltbr Ilya Chorny
[gmx-users] g_saltbr Ilya Chorny
[gmx-users] Re: g_saltbr Ilya Chorny
[gmx-users] Re: g_saltbr Ilya Chorny
[gmx-users] GROMACS-4.5-beta1 is out! Amit Choubey
[gmx-users] mean square displacement frequency Yongchul Chung
[gmx-users] mean square displacement frequency Yongchul Chung
[gmx-users] ffamber99sb error Arik Cohen
[gmx-users] pressure coupling Shuangxing Dai
[gmx-users] pressure coupling Shuangxing Dai
[gmx-users] question about dynamics Shuangxing Dai
[gmx-users] question about dynamics Shuangxing Dai
[gmx-users] translation Shuangxing Dai
[gmx-users] periodicity and correct output Shuangxing Dai
[gmx-users] periodicity and correct output Shuangxing Dai
[gmx-users] Fatal error: Nilesh Dhumal
[gmx-users] frezzing a bond Nilesh Dhumal
[gmx-users] frezzing a bond : NPT and NVT simulations Nilesh Dhumal
[gmx-users] Re: NPT and NVT simulations Nilesh Dhumal
[gmx-users] Re: NPT and NVT simulations Nilesh Dhumal
[gmx-users] Re: NPT and NVT simulations Nilesh Dhumal
[gmx-users] Re: NPT and NVT simulations Nilesh Dhumal
[gmx-users] Re: NPT and NVT simulations Nilesh Dhumal
[gmx-users] Re: NPT and NVT simulations Nilesh Dhumal
[gmx-users] installation: gromacs on Mac.10.5.8 leopard Florian Dommert
[gmx-users] installation: gromacs on Mac.10.5.8 leopard Florian Dommert
[gmx-users] installation: gromacs on Mac.10.5.8 leopard Florian Dommert
[gmx-users] installation: gromacs on Mac.10.5.8 leopard Florian Dommert
[gmx-users] installation: gromacs on Mac.10.5.8 leopard Florian Dommert
[gmx-users] Errors with g_dielectric Florian Dommert
[gmx-users] RE: [nonbond_params] section , choice of parameters Florian Dommert
[gmx-users] information regarding the bootstrap method implemented with the g_wham Ozge Engin
[gmx-users] version 4 pdb2gmx with ffamber broken on Mac? Daniel Ensign
[gmx-users] version 4 pdb2gmx with ffamber broken on Mac? Daniel Ensign
[gmx-users] installation: gromacs on Mac.10.5.8 leopard Esztermann, Ansgar
[gmx-users] installation: gromacs on Mac.10.5.8 leopard Esztermann, Ansgar
[gmx-users] charmmff Rodrigo Faccioli
[gmx-users] charmmff Rodrigo Faccioli
[gmx-users] charmmff Rodrigo Faccioli
[gmx-users] topology for a cyclic peptide Rebeca García Fandiño
[gmx-users] Re: g_cluster settings Ran Friedman
[gmx-users] g_cluster Jarvis-Patrick Ran Friedman
[gmx-users] NPH Simulations Ran Friedman
[gmx-users] Entropy from NMA Ran Friedman
[gmx-users] Entropy from NMA Ran Friedman
[gmx-users] Entropy from NMA Ran Friedman
[gmx-users] Entropy from NMA Ran Friedman
[gmx-users] Release of the R.E.D.-III.4 tools FyD
[gmx-users] amber/charmm force field and HB lifetime at low temperature Ramachandran G
[gmx-users] amber/charmm force field and HB lifetime at low temperature Ramachandran G
[gmx-users] tip5p in ffcharmm Ramachandran G
[gmx-users] genion Neha Gandhi
[gmx-users] Stabilizing a heavy metal ion in solution Francisco Garcia
[gmx-users] hydrogen bonds Vasilis Georgilas
[gmx-users] Re: hydrogen bonds Vasilis Georgilas
[gmx-users] Re: hydrogen bonds Vasilis Georgilas
[gmx-users] Re: hydrogen bonds Vasilis Georgilas
[gmx-users] Removing water from a trajectory Anirban Ghosh
[gmx-users] g_lie query Anirban Ghosh
[gmx-users] g_lie query Anirban Ghosh
[gmx-users] g_lie query Anirban Ghosh
[gmx-users] Problem with Lennard Jones cross terms Gaurav Goel
[gmx-users] Problem with Lennard Jones cross terms Gaurav Goel
[gmx-users] g_msd Gaurav Goel
[gmx-users] extracting coordinates Gaurav Goel
[gmx-users] does generating velocity keep centre of mass motion zero? Gaurav Goel
[gmx-users] Fwd: missing atom Oliver Grant
[gmx-users] RE: gmx-users Digest, Vol 75, Issue 23 Oliver Grant
[gmx-users] to visualise protein conformation after every 1ns Oliver Grant
Re: [gmx-users] pdb2gmx doesn´t generate H Oliver Grant
[gmx-users] g_msd Ricardo Cuya Guizado
[gmx-users] 1. Re: g_msd (Gaurav Goel) Ricardo Cuya Guizado
[gmx-users] question about non-bonded parameters for CHARMM in GROMACS Michael Francis Hagan
[gmx-users] gromacs energies very different from other MD engine for the very same system and conditions Berk Hess
[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition Berk Hess
[gmx-users] Location of a molecule in a dodecahedron Birgit Hischenhuber
[gmx-users] MD run for octanol system Esteban Gabriel Vega Hissi
[gmx-users] problem while simulating metal ions Kwee Hong
[gmx-users] how gromacs calculate center of mass for broken molecules? Kun Huang
[gmx-users] amber parameters in gromacs Rolf Erwin Isele-Holder
[gmx-users] Re: amber parameters in gromacs Rolf Erwin Isele-Holder
[gmx-users] energy contributions / question about solvating jojo J
[gmx-users] how to determine the box size jojo J
[gmx-users] top file jojo J
[gmx-users] top file jojo J
[gmx-users] Ewald setting for hydrocarbon system? jojo J
[gmx-users] mdp file settings for PME jojo J
[gmx-users] Treating nonbondend interactions in GROMACS jojo J
[gmx-users] Free Energy Calculation Using Tabulated Potentials Nimesh Jain
[gmx-users] g_anaeig & pymol Carla Jamous
[gmx-users] selenomethionine parameters for ffG53a6 Deniz KARASU
[gmx-users] Phonon calculations in periodic crystals Anne Kelley
[gmx-users] Phonon calculations in periodic crystals Anne Kelley
[gmx-users] alchemical free energy changes upon change in sc_alpha and sc_power Ilja Khavrutskii
[gmx-users] gromacs energies very different from other MD engine for the very same system and conditions Ilja Khavrutskii
[gmx-users] Re: alchemical free energy changes upon change in sc_alpha and sc_power Ilja Khavrutskii
[gmx-users] OPLS-2005 forcefield parameters for carbohydrates in Gromacs 4.0.7? Steven R. Kirk
[gmx-users] Ewald summation Thanasis Koukoulas
[gmx-users] Re: gmx-users Digest, Vol 75, Issue 107 Thanasis Koukoulas
[gmx-users] Re: gmx-users Digest, Vol 75, Issue 107 Thanasis Koukoulas
[gmx-users] "simulated long enough" message from tpbconv Krzysztof Kuczera
[gmx-users] Fwd: missing atom Carsten Kutzner
[gmx-users] mpi run Carsten Kutzner
[gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory Carsten Kutzner
[gmx-users] P4_error for extending coarse grained MD simulations Carsten Kutzner
[gmx-users] P4_error for extending coarse grained MD simulations Carsten Kutzner
[gmx-users] Installing gromacs from git Carsten Kutzner
[gmx-users] decomposition Carsten Kutzner
[gmx-users] mpi installation problems Carsten Kutzner
[gmx-users] mpi run #ZHAO LINA#
[gmx-users] Capping residues Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 189 Justin A. Lemkul
[gmx-users] protein stability as a dimer Justin A. Lemkul
[gmx-users] amber parameters in gromacs Justin A. Lemkul
[gmx-users] protein stability as a dimer Justin A. Lemkul
[gmx-users] another pull-code question Justin A. Lemkul
[gmx-users] Capping residues Justin A. Lemkul
[gmx-users] hdb file Justin A. Lemkul
[gmx-users] Re: g_wham Justin A. Lemkul
[gmx-users] Re: another pull-code question Justin A. Lemkul
[gmx-users] another pull-code question Justin A. Lemkul
[gmx-users] Capping residues Justin A. Lemkul
[gmx-users] Is there a way to protonate small molecules with gromacs without editing ffgmx2.hdb file? Justin A. Lemkul
[gmx-users] Capping residues Justin A. Lemkul
[gmx-users] contact map Justin A. Lemkul
[gmx-users] pressure coupling Justin A. Lemkul
[gmx-users] Implicit solvent Justin A. Lemkul
[gmx-users] pressure coupling Justin A. Lemkul
[gmx-users] RE: gmx-users Digest, Vol 75, Issue 23 Justin A. Lemkul
[gmx-users] visual program Justin A. Lemkul
[gmx-users] sulfate in topology file with oplsaa forcefield Justin A. Lemkul
[gmx-users] No such moleculetype SOL Justin A. Lemkul
[gmx-users] Fatal error: Justin A. Lemkul
[gmx-users] problems with g_wham Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] Capping residues Justin A. Lemkul
[gmx-users] Capping residues Justin A. Lemkul
[gmx-users] Capping residues Justin A. Lemkul
[gmx-users] Capping residues Justin A. Lemkul
[gmx-users] problems with g_wham Justin A. Lemkul
[gmx-users] problems with g_wham Justin A. Lemkul
[gmx-users] Location of a molecule in a dodecahedron Justin A. Lemkul
[gmx-users] genbox and water model Justin A. Lemkul
[gmx-users] how to determine the box size Justin A. Lemkul
[gmx-users] top file Justin A. Lemkul
[gmx-users] top file Justin A. Lemkul
[gmx-users] fast rerun in order to get an energy Justin A. Lemkul
[gmx-users] Solvating protein Justin A. Lemkul
[gmx-users] Solvating protein Justin A. Lemkul
[gmx-users] Missing sugar atom in CHARMM dna.rtp Justin A. Lemkul
[gmx-users] pdb2gmx with DNA Justin A. Lemkul
[gmx-users] mdp file settings for PME Justin A. Lemkul
[gmx-users] the Pressure control in GROMACS 4.0.7 Justin A. Lemkul
[gmx-users] Re: Frozen N2 in a very long tube Justin A. Lemkul
[gmx-users] pdb2gmx with DNA Justin A. Lemkul
[gmx-users] Treating nonbondend interactions in GROMACS Justin A. Lemkul
[gmx-users] high repulsion in packed system Justin A. Lemkul
[gmx-users] -tu flag in g_hbond Justin A. Lemkul
[gmx-users] -tu flag in g_hbond Justin A. Lemkul
[gmx-users] -tu flag in g_hbond Justin A. Lemkul
[gmx-users] number of degrees of frredom Justin A. Lemkul
[gmx-users] question about dynamics Justin A. Lemkul
[gmx-users] question about dynamics Justin A. Lemkul
[gmx-users] grommp_md error Justin A. Lemkul
[gmx-users] grompp errors Justin A. Lemkul
[gmx-users] NPT for compression Justin A. Lemkul
[gmx-users] NPT for compressing the system Justin A. Lemkul
[gmx-users] version 4 pdb2gmx with ffamber broken on Mac? Justin A. Lemkul
[gmx-users] NPT for compressing the system Justin A. Lemkul
[gmx-users] position restrain file Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] DSSP and g_sas Justin A. Lemkul
[gmx-users] Grompp error: No default g96angle type Justin A. Lemkul
[gmx-users] Grompp error: No default g96angle type Justin A. Lemkul
[gmx-users] Semiisotropic Pressure coupling with PR Justin A. Lemkul
[gmx-users] Semiisotropic Pressure coupling with PR Justin A. Lemkul
[gmx-users] Pressure coupling Justin A. Lemkul
[gmx-users] Semiisotropic Pressure coupling with PR Justin A. Lemkul
[gmx-users] Semiisotropic Pressure coupling with PR Justin A. Lemkul
[gmx-users] how to write a frames.ndx for -fr option of trjconv Justin A. Lemkul
[gmx-users] inversion of lipid bilayer with water in the centre Justin A. Lemkul
[gmx-users] to visualise protein conformation after every 1ns Justin A. Lemkul
[gmx-users] Selecting a force field for dioxane Justin A. Lemkul
[gmx-users] Need For a Script Justin A. Lemkul
[gmx-users] frezzing a bond Justin A. Lemkul
[gmx-users] Charge grps and cut-off Justin A. Lemkul
[gmx-users] Charge grps and cut-off Justin A. Lemkul
[gmx-users] Charge grps and cut-off Justin A. Lemkul
[gmx-users] g_lie query Justin A. Lemkul
[gmx-users] Charge grps and cut-off Justin A. Lemkul
[gmx-users] Charge grps and cut-off Justin A. Lemkul
[gmx-users] Charge grps and cut-off Justin A. Lemkul
[gmx-users] Potential of mean force Justin A. Lemkul
[gmx-users] gromacs-localp-3.0.2 local pressure installation Justin A. Lemkul
[gmx-users] tip5p in ffcharmm Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] topology for a cyclic peptide Justin A. Lemkul
[gmx-users] Averege structure Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 75, Issue 117 (was: The grompp problem!!) Justin A. Lemkul
[gmx-users] trjcat : Magic Number Error in XTC file (read 0, should be 1995) Justin A. Lemkul
[gmx-users] pdb2gmx doesn´t generate H Justin A. Lemkul
[gmx-users] The iron-sulfur bond!! Justin A. Lemkul
[gmx-users] Ryckaert Bellemanm-dihedral in OPLS-AA Justin A. Lemkul
[gmx-users] Grompp error: No default g96angle type Justin A. Lemkul
[gmx-users] Problem in setup energy minimization step(grompp) Justin A. Lemkul
[gmx-users] Problem in setup energy minimization step(grompp) Justin A. Lemkul
[gmx-users] Problem in setup energy minimization step(grompp) Justin A. Lemkul
[gmx-users] nonbond_params Justin A. Lemkul
[gmx-users] nonbond_params Justin A. Lemkul
[gmx-users] Dear all Re: Topology file for phosphothreonine (TPO) for OPLS force field Justin A. Lemkul
[gmx-users] Re: NPT and NVT simulations Justin A. Lemkul
[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition Justin A. Lemkul
[gmx-users] energygrps and simulation run time Justin A. Lemkul
[gmx-users] Re: NPT and NVT simulations Justin A. Lemkul
[gmx-users] Re: NPT and NVT simulations Justin A. Lemkul
[gmx-users] Coarse-Grain: GROMACS bond information to VMD Justin A. Lemkul
[gmx-users] Re: g_saltbr Justin A. Lemkul
[gmx-users] Re: g_saltbr Justin A. Lemkul
[gmx-users] Re: NPT and NVT simulations Justin A. Lemkul
[gmx-users] trjcat skipping frames Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] Re: NPT and NVT simulations Justin A. Lemkul
[gmx-users] Re: NPT and NVT simulations Justin A. Lemkul
[gmx-users] hydrogen bonds Justin A. Lemkul
[gmx-users] no non bonded parameters from PRODRG Justin A. Lemkul
[gmx-users] Re: hydrogen bonds Justin A. Lemkul
[gmx-users] Using the Berendsen Barostat to Initialize and then switch to Parrinello-Rahman Justin A. Lemkul
[gmx-users] trjcat skipping frames Justin A. Lemkul
[gmx-users] Install error for gmx-4.5_beta1 Justin A. Lemkul
[gmx-users] Another install error: gmx-4.5 beta1 Justin A. Lemkul
[gmx-users] Re: hydrogen bonds Justin A. Lemkul
[gmx-users] Re: hydrogen bonds Justin A. Lemkul
[gmx-users] Pullx file Justin A. Lemkul
[gmx-users] Avoid generation of angles, pairs and dihedrals from pdb2gmx Da-Wei Li
[gmx-users] Tabulated potentials and performance Da-Wei Li
[gmx-users] Tabulated potentials and performance Da-Wei Li
[gmx-users] I wonder if anyone has a "gmx2lmp" tool Li, Shuo (liso)
[gmx-users] gromacs energies very different from other MD engine for the very same system and conditions Erik Lindahl
[gmx-users] Replica exhange - no. of processors Lanyuan Lu
[gmx-users] Tabulated potentials and performance Lanyuan Lu
[gmx-users] problem in cluster determination : g_clustsize and trjconv -pbc cluster problem Sanku M
[gmx-users] g_sas for martini coarse-grained particles Sanku M
[gmx-users] g_rdf Sanku M
[gmx-users] fast rerun in order to get an energy Magdalena
[gmx-users] Units of the Amber99 parameters Amir Marcovitz
[gmx-users] nonbond_params Amir Marcovitz
[gmx-users] nonbond_params Amir Marcovitz
[gmx-users] energygrps and simulation run time Amir Marcovitz
[gmx-users] [nonbond_params] section , choice of parameters Amir Marcovitz
[gmx-users] RE: [nonbond_params] section , choice of parameters Amir Marcovitz
[gmx-users] RE: RE: [nonbond_params] section , choice of parameters Amir Marcovitz
[gmx-users] Posting to list Andrew Mauro
[gmx-users] Using the Berendsen Barostat to Initialize and then switch to Parrinello-Rahman Andrew Mauro
[gmx-users] Pull code Gavin Melaugh
[gmx-users] pull code Gavin Melaugh
[gmx-users] Re: Pull code Gavin Melaugh
[gmx-users] another pull-code question Gavin Melaugh
[gmx-users] g_wham Gavin Melaugh
[gmx-users] Re: another pull-code question Gavin Melaugh
[gmx-users] Re: another pull-code question Gavin Melaugh
[gmx-users] another pull-code question Gavin Melaugh
[gmx-users] COM distances Gavin Melaugh
[gmx-users] COM distances Gavin Melaugh
[gmx-users] problems with g_wham Gavin Melaugh
[gmx-users] COM distances Gavin Melaugh
[gmx-users] problems with g_wham Gavin Melaugh
[gmx-users] problems with g_wham Gavin Melaugh
[gmx-users] problems with g_wham Gavin Melaugh
[gmx-users] problems with g_wham Gavin Melaugh
[gmx-users] problems with g_wham Gavin Melaugh
[gmx-users] The grompp problem!! (Urgently) Krzysztof Mlynarczyk
[gmx-users] hdb file Moeed
[gmx-users] high repulsion in packed system Moeed
[gmx-users] high repulsion in packed system Moeed
[gmx-users] number of degrees of frredom Moeed
[gmx-users] grommp_md error Moeed
[gmx-users] NPT for compression Moeed
[gmx-users] NPT for compressing the system Moeed
[gmx-users] NPT for compressing the system Moeed
[gmx-users] LINC warning but reasonable potential energy and force Moeed
[gmx-users] switching off electrostatics Moeed
[gmx-users] Lincs warning but reasonable energy! Moeed
[gmx-users] PE compressing Moeed
[gmx-users] compressing the system Moeed
[gmx-users] compressing the system Moeed
[gmx-users] the job is not being distributed Syed Tarique Moin
[gmx-users] how to strip velocities out of a .gro file Chris Neale
[gmx-users] mk_angndx Andrei Neamtu
[gmx-users] Need For a Script Samrat Pal
[gmx-users] Need For a Script Samrat Pal
[gmx-users] Need For a Script Samrat Pal
[gmx-users] Need For a Script Samrat Pal
[gmx-users] Need For a Script Samrat Pal
[gmx-users] implicit water model for protein folding simulation Samrat Pal
[gmx-users] Jarzynski equality in pulling simulation Samrat Pal
[gmx-users] Re: Jarzynski equality in pulling simulation Samrat Pal
[gmx-users] Compiling problems on MacOS X 10.6.4 Patargias, George
[gmx-users] Compiling problems on MacOS X 10.6.4 Patargias, George
[gmx-users] Compiling problems on MacOS X 10.6.4 Patargias, George
[gmx-users] Compiling problems on MacOS X 10.6.4 Patargias, George
[gmx-users] Missing sugar atom in CHARMM dna.rtp Patargias, George
[gmx-users] pdb2gmx with DNA Patargias, George
[gmx-users] pdb2gmx with DNA Patargias, George
[gmx-users] Re: Parameters for selenium Luis Paulo
[gmx-users] P4_error for extending coarse grained MD simulations XAvier Periole
[gmx-users] fast rerun in order to get an energy XAvier Periole
[gmx-users] g_sas for martini coarse-grained particles XAvier Periole
[gmx-users] g_sas for martini coarse-grained particles XAvier Periole
[gmx-users] fast rerun in order to get an energy Jeffery Perkins
[gmx-users] position restrain file Ping
[gmx-users] Capping residues Sai Pooja
[gmx-users] Capping residues Sai Pooja
[gmx-users] Capping residues Sai Pooja
[gmx-users] Capping residues Sai Pooja
[gmx-users] Capping residues Sai Pooja
[gmx-users] Capping residues Sai Pooja
[gmx-users] Capping residues Sai Pooja
[gmx-users] genbox and water model Sai Pooja
[gmx-users] Adding ions Sai Pooja
[gmx-users] Solvating protein Sai Pooja
[gmx-users] Solvating protein Sai Pooja
[gmx-users] Solvating protein Sai Pooja
[gmx-users] Solvating protein Sai Pooja
[gmx-users] Installing gromacs from git Sai Pooja
[gmx-users] Semiisotropic Pressure coupling with PR Sai Pooja
[gmx-users] Semiisotropic Pressure coupling with PR Sai Pooja
[gmx-users] Pressure coupling Sai Pooja
[gmx-users] Semiisotropic Pressure coupling with PR Sai Pooja
[gmx-users] Semiisotropic Pressure coupling with PR Sai Pooja
[gmx-users] Semiisotropic Pressure coupling with PR Sai Pooja
[gmx-users] Rcut-off etc. Sai Pooja
[gmx-users] Charge grps and cut-off Sai Pooja
[gmx-users] Charge grps and cut-off Sai Pooja
[gmx-users] Charge grps and cut-off Sai Pooja
[gmx-users] Charge grps and cut-off Sai Pooja
[gmx-users] Charge grps and cut-off Sai Pooja
[gmx-users] Charge grps and cut-off Sai Pooja
[gmx-users] Charge grps and cut-off Sai Pooja
[gmx-users] Charge grps and cut-off Sai Pooja
[gmx-users] g_rmsf Sai Pooja
[gmx-users] Replica exhange - no. of processors Sai Pooja
[gmx-users] Replica exhange - no. of processors Sai Pooja
[gmx-users] charmmff Sai Pooja
[gmx-users] Replica exhange - no. of processors Sai Pooja
[gmx-users] charmmff Sai Pooja
[gmx-users] charmmff Sai Pooja
[gmx-users] Backward compatibility of charmm-ff implementation Sai Pooja
[gmx-users] Re: QMMM cpmd Christoph Riplinger
[gmx-users] Is there a way to protonate small molecules with gromacs without editing ffgmx2.hdb file? Arthur Roberts
[gmx-users] parallel run with integrator=nm ? J. Rui Rodrigues
[gmx-users] Compiling problems on MacOS X 10.6.4 J. Rui Rodrigues
[gmx-users] Compiling problems on MacOS X 10.6.4 J. Rui Rodrigues
[gmx-users] scripting question J. Rui Rodrigues
[gmx-users] Entropy from NMA J. Rui Rodrigues
[gmx-users] Fatal error: No such moleculetype Cl X Rules
[gmx-users] Problem in setup energy minimization step(grompp) X Rules
[gmx-users] Problem in setup energy minimization step(grompp) X Rules
[gmx-users] The grompp problem!! (Urgently) Yuranat Saikatikorn
[gmx-users] Re: gmx-users Digest, Vol 75, Issue 117 Yuranat Saikatikorn
[gmx-users] The iron-sulfur bond!! Yuranat Saikatikorn
[gmx-users] DSSP and g_sas Bhanu Prakash Sandaka
[gmx-users] DSSP and g_sas Bhanu Prakash Sandaka
[gmx-users] Re: Pull code Thomas Schlesier
[gmx-users] Re: another pull-code question Thomas Schlesier
[gmx-users] Re: another pull-code question Thomas Schlesier
[gmx-users] Free Energy calculations of peptide-protein binding Ehud Schreiber
[gmx-users] HA1/HA2 chirality of GLY Ehud Schreiber
[gmx-users] RE: [nonbond_params] section , choice of parameters Ehud Schreiber
[gmx-users] RE: RE: [nonbond_params] section , choice of parameters Ehud Schreiber
[gmx-users] Free Energy calculations of peptide-protein binding Daniel Seeliger
[gmx-users] g_anaeig & pymol Daniel Seeliger
[gmx-users] decomposition Jacopo Sgrignani
[gmx-users] GBSA calculations Hassan Shallal
[gmx-users] how to write a frames.ndx for -fr option of trjconv Hassan Shallal
[gmx-users] scripting question Hassan Shallal
[gmx-users] scripting question Hassan Shallal
[gmx-users] cuda gmx template Timothy Sirk
[gmx-users] Re: amber parameters in gromacs David van der Spoel
[gmx-users] Is there a way to protonate small molecules with gromacs without editing ffgmx2.hdb file? David van der Spoel
[gmx-users] g_principal: memory corruption David van der Spoel
[gmx-users] Re: the Pressure control in GROMACS 4.0.7 David van der Spoel
[gmx-users] Re: Pressure control in GROMACS 4.0.7 David van der Spoel
[gmx-users] Re: the Pressure control in GROMACS 4.0.7 David van der Spoel
[gmx-users] grompp errors David van der Spoel
[gmx-users] (no subject) David van der Spoel
[gmx-users] Phonon calculations in periodic crystals David van der Spoel
[gmx-users] Pressure coupling David van der Spoel
[gmx-users] to visualise protein conformation after every 1ns David van der Spoel
[gmx-users] GROMACS-4.5-beta1 is out! David van der Spoel
[gmx-users] hydrogen-bonded complex Hao Sun
[gmx-users] Ewald summation Thanasis
[gmx-users] trjcat skipping frames Jared James Thompson
[gmx-users] trjcat skipping frames Jared James Thompson
[gmx-users] Simulation stops Jose Tusell
[gmx-users] Fatal error: No such moleculetype Cl Abhinav Verma
[gmx-users] hydrogen-bonded complex Dallas Warren
[gmx-users] Re: Re: Re:Chain Terminus Tsjerk Wassenaar
[gmx-users] B-factor Tsjerk Wassenaar
[gmx-users] how to strip velocities out of a .gro file Tsjerk Wassenaar
[gmx-users] how to strip velocities out of a .gro file Tsjerk Wassenaar
[gmx-users] wrong charge assignment(?) on ATP in rtp file Tsjerk Wassenaar
[gmx-users] to visualise protein conformation after every 1ns Tsjerk Wassenaar
[gmx-users] g_rmsf Tsjerk Wassenaar
[gmx-users] mean square displacement frequency Tsjerk Wassenaar
[gmx-users] grompp errors Amanda Watkins
[gmx-users] no non bonded parameters from PRODRG Jennifer Williams
[gmx-users] RE: trjcat -cat skips frames Mike Wykes
[gmx-users] why the pulling force between Graphite and CNT is repulsive force? Cun Zhang
Subject: [gmx-users] to visualise protein conformation after every 1ns Cun Zhang
[gmx-users] topology builiding pankhuri arora
[gmx-users] how to compile x2top separately? pankhuri arora
[gmx-users] inversion of lipid bilayer with water in the centre ram bio
[gmx-users] trjcat : Magic Number Error in XTC file (read 0, should be 1995) ram bio
[gmx-users] residue names in rtp file and their parameters chiba.s.ac
[gmx-users] wrong charge assignment(?) on ATP in rtp file chiba.s.ac
[gmx-users] wrong charge assignment(?) on ATP in rtp file chiba.s.ac
[gmx-users] protein stability as a dimer sonali dhindwal
[gmx-users] protein stability as a dimer sonali dhindwal
[gmx-users] to visualise protein conformation after every 1ns sonali dhindwal
[gmx-users] to visualise protein conformation after every 1ns sonali dhindwal
[gmx-users] to visualise protein conformation after every 1ns sonali dhindwal
[gmx-users] to visualise protein conformation after every 1ns sonali dhindwal
[gmx-users] water Mediated Hydrogen Bond babu gokul
[gmx-users] Help needed with ACPYPI sunita gupta
[gmx-users] Implicit solvent ithu
[gmx-users] energygrp_excl and PME jasmine
[gmx-users] g_energy output lists at jsx.dk
[gmx-users] visual program leila karami
[gmx-users] Where can I dowload DSSP program? chandran karunakaran
[gmx-users] Where can I dowload DSSP program? Ajeeta kaushiki
[gmx-users] Phosphorylated serine and threonine sumanth kumar
[gmx-users] Topology file for phosphoserine (SEP) for OPLS force field sumanth kumar
[gmx-users] Ryckaert Bellemanm-dihedral in OPLS-AA sumanth kumar
[gmx-users] Re: Ryckaert Bellemanm-dihedral in OPLS-AA sumanth kumar
[gmx-users] Dear all Re: Topology file for phosphothreonine (TPO) for OPLS force field sumanth kumar
[gmx-users] Entropy from NMA nahren manuel
[gmx-users] Entropy from NMA nahren manuel
[gmx-users] problem with trjconv -pbc cluster jagannath mondal
[gmx-users] problem with trjconv -pbc cluster jagannath mondal
[gmx-users] problem with trjconv -pbc cluster jagannath mondal
[gmx-users] problem with g_clustsize jagannath mondal
[gmx-users] Is there a way to protonate small molecules with gromacs without editing ffgmx2.hdb file? ms
[gmx-users] Implicit solvent ms
[gmx-users] Need For a Script ms
[gmx-users] scripting question ms
[gmx-users] Tabulated potentials and performance ms
[gmx-users] Tabulated potentials and performance ms
[gmx-users] Tabulated potentials and performance ms
[gmx-users] Tabulated potentials and performance ms
[gmx-users] Replica exhange - no. of processors ms
[gmx-users] implicit water model for protein folding simulation ms
[gmx-users] GROMACS-4.5-beta1 is out! ms
[gmx-users] energy corresponding to H-bond supti mukherjee
[gmx-users] No such moleculetype SOL nanogroup
[gmx-users] No such moleculetype SOL nanogroup
[gmx-users] mpi run nanogroup
[gmx-users] Grompp error: No default g96angle type shahid nayeem
[gmx-users] Grompp error: No default g96angle type shahid nayeem
[gmx-users] Grompp error: No default g96angle type shahid nayeem
[gmx-users] Heme_Grompp Error shahid nayeem
[gmx-users] Heme_Grompp_error shahid nayeem
[gmx-users] Heme_Grompp_error shahid nayeem
[gmx-users] contact map atila petrosian
[gmx-users] how to strip velocities out of a .gro file shayamra at post.tau.ac.il
[gmx-users] Removing water from a trajectory shayamra at post.tau.ac.il
[gmx-users] Effects of reducing timestep braffert at purdue.edu
[gmx-users] Averege structure pawan raghav
[gmx-users] Problem in setup energy minimization step(grompp) bipin.singh at research.iiit.ac.in
[gmx-users] Problem in setup energy minimization step(grompp) bipin.singh at research.iiit.ac.in
[gmx-users] Re: Re: Re:Chain Terminus lloyd riggs
[gmx-users] Re: Re: Fwd: missing atom lloyd riggs
[gmx-users] NPH Simulations sapna sarupria
[gmx-users] Problem with Lennard Jones cross terms xrysostomos sfhsdfghsdfhsdgh
[gmx-users] Problem with Lennard Jones cross terms xrysostomos sfhsdfghsdfhsdgh
[gmx-users] Problem with Lennard Jones cross terms xrysostomos sfhsdfghsdfhsdgh
[gmx-users] -tu flag in g_hbond shahab shariati
[gmx-users] -tu flag in g_hbond shahab shariati
[gmx-users] -tu flag in g_hbond shahab shariati
[gmx-users] -tu flag in g_hbond shahab shariati
[gmx-users] MD run for octanol system vivek sharma
[gmx-users] Re: MD run for octanol system vivek sharma
[gmx-users] help: gromacs mistake shuai shuai
[gmx-users] Frozen N2 in a very long tube shuai shuai
[gmx-users] Re: Frozen N2 in a very long tube shuai shuai
[gmx-users] problem with angle restraints subarna thakur
[gmx-users] another pull-code question chris.neale at utoronto.ca
[gmx-users] another pull-code question chris.neale at utoronto.ca
[gmx-users] another pull-code question chris.neale at utoronto.ca
[gmx-users] how to strip velocities out of a .gro file chris.neale at utoronto.ca
[gmx-users] Free Energy calculations of peptide-protein binding chris.neale at utoronto.ca
[gmx-users] problem with trjconv -pbc cluster chris.neale at utoronto.ca
[gmx-users] problem with trjconv -pbc cluster chris.neale at utoronto.ca
[gmx-users] Frozen N2 in a very long tube; was "help: gromacs mistake" chris.neale at utoronto.ca
[gmx-users] wrong charge assignment(?) on ATP in rtp file chris.neale at utoronto.ca
[gmx-users] how gromacs calculate center of mass for broken molecules? chris.neale at utoronto.ca
[gmx-users] problem with trjconv -pbc cluster chris.neale at utoronto.ca
[gmx-users] COM distances chris.neale at utoronto.ca
[gmx-users] problem with g_clustsize chris.neale at utoronto.ca
[gmx-users] problems with g_wham chris.neale at utoronto.ca
[gmx-users] problems with g_wham chris.neale at utoronto.ca
[gmx-users] wrong charge assignment(?) on ATP in rtp file chris.neale at utoronto.ca
[gmx-users] problems with g_wham chris.neale at utoronto.ca
[gmx-users] Parameters for selenium chris.neale at utoronto.ca
[gmx-users] problems with g_wham chris.neale at utoronto.ca
[gmx-users] HA1/HA2 chirality of GLY chris.neale at utoronto.ca
[gmx-users] high repulsion in packed system chris.neale at utoronto.ca
[gmx-users] Re: selenium parameter chris.neale at utoronto.ca
[gmx-users] pull code example chris.neale at utoronto.ca
[gmx-users] gromacs energies very different from other MD engine for the very same system and conditions chris.neale at utoronto.ca
[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition chris.neale at utoronto.ca
[gmx-users] Pullx file chris.neale at utoronto.ca
[gmx-users] g_principal: memory corruption kulleperuma.kulleperuma at utoronto.ca
[gmx-users] Re: gmx-users Digest, Vol 75, Issue 18 kulleperuma.kulleperuma at utoronto.ca
[gmx-users] RE: gmx-users Digest, Vol 75, Issue 23 abdul wadood
[gmx-users] Potential of mean force abdul wadood
[gmx-users] Cohesive energies of Polymer Materials wuxiao
[gmx-users] parallel mdrun (mpimdrun) is slower than non-parallel mdrun? wuxiao
[gmx-users] gromacs-localp-3.0.2 installation problem kambiz yaghmaei
[gmx-users] gromacs-localp-3.0.2 local pressure installation kambiz yaghmaei
[gmx-users] (no subject) munubas at yahoo.com
[gmx-users] (no subject) munubas at yahoo.com
[gmx-users] (no subject) munubas at yahoo.com
[gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory zhongjin
[gmx-users] the Pressure control in GROMACS 4.0.7 zhongjin
[gmx-users] Re: the Pressure control in GROMACS 4.0.7 zhongjin
[gmx-users] sulfate in topology file with oplsaa forcefield you zou
[gmx-users] P4_error for extending coarse grained MD simulations 张春雷
[gmx-users] P4_error for extending coarse grained MD simulations 张春雷

Last message date: Sat Jul 31 22:17:42 CEST 2010
Archived on: Thu Nov 14 12:09:04 CET 2013

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