May 2008 Archives by author

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Starting: Thu May 1 00:01:36 CEST 2008
Ending: Sat May 31 15:25:58 CEST 2008
Messages: 567

[gmx-users] hybrid or Hamiltonian REMD in gromacs Mu Yuguang (Dr)
[gmx-users] Atom names mismatch George Abadir
[gmx-users] Atom names mismatch George Abadir
[gmx-users] Atom names mismatch George Abadir
[gmx-users] Atom names mismatch George Abadir
[gmx-users] Re: Atom names mismatch George Abadir
[gmx-users] Atom names mismatch George Abadir
[gmx-users] Atom names mismatch - PyMol retain order George Abadir
[gmx-users] Building simple alcohol topologies Mark Abraham
[gmx-users] DCCM Mark Abraham
[gmx-users] adding missing hydrogen in PDB files Mark Abraham
[gmx-users] combining differently-generated force-fields Mark Abraham
[gmx-users] GROMACS parallel set up Questions. Mark Abraham
[gmx-users] timesteps don't match error Mark Abraham
[gmx-users] using xmp file Mark Abraham
[gmx-users] using xmp file Mark Abraham
[gmx-users] Error of g_rms Mark Abraham
[gmx-users] Calculating average of B-factor Mark Abraham
[gmx-users] Can not open file:md323.xtc Mark Abraham
[gmx-users] A question about DNA and normal mode analysis in gromacs Mark Abraham
[gmx-users] help with lipids and pdb2gmx Mark Abraham
[gmx-users] when I switch to ffG43a1, the problem occurs Mark Abraham
[gmx-users] Alternate to xmgrace Mark Abraham
[gmx-users] Equilibration Mark Abraham
[gmx-users] Parallel processing Mark Abraham
[gmx-users] problem with simulation of phosphatidic acid, possibly in my topology? Mark Abraham
[gmx-users] Angle definition in g_hbond ... Mark Abraham
[gmx-users] Box size Increase Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] Help needed urgently...!!! Mark Abraham
[gmx-users] REMD: average potential energy as a function of temperatue Mark Abraham
[gmx-users] Help for GNUPlot Mark Abraham
[gmx-users] Help for GNUPlot Mark Abraham
[gmx-users] position and distance restraining Mark Abraham
[gmx-users] acetyl Mark Abraham
[gmx-users] High pressure Mark Abraham
[gmx-users] msd and diffusion coefficient and getting unfolded trajectory Mark Abraham
[gmx-users] pdb2gmx Mark Abraham
[gmx-users] Fw: Electron Density Across the Lipid Bilayer Mark Abraham
[gmx-users] mpi.h is missing... Mark Abraham
[gmx-users] confusion regarding tpbconv Mark Abraham
[gmx-users] .itp file for polymer Mark Abraham
[gmx-users] bilayer DMPC Mark Abraham
[gmx-users] Re:confusion regarding tpbconv Mark Abraham
[gmx-users] problem with energy minimization Mark Abraham
[gmx-users] distance restrained energy minimisation Mark Abraham
[gmx-users] how to build the input files of an infinite system Mark Abraham
[gmx-users] Range checking error Mark Abraham
[gmx-users] Range checking error Mark Abraham
[gmx-users] atomname -> atomic number Mark Abraham
[gmx-users] Making PDB file Mark Abraham
[gmx-users] atomname -> atomic number Mark Abraham
[gmx-users] RMSD plot Mark Abraham
[gmx-users] trjorder problems Mark Abraham
[gmx-users] water distortion above bilayer Mark Abraham
[gmx-users] problem regarding energy minimization Mark Abraham
[gmx-users] Water molecule can not be settled Mark Abraham
[gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water) Mark Abraham
[gmx-users] how to remd analysi? Mark Abraham
[gmx-users] .trr file Mark Abraham
回复： Re: [gmx-users] how to remd analysi? Mark Abraham
[gmx-users] about DMSO c-c bond and c-o bond in ffg53a6 force field Mark Abraham
[gmx-users] generation of amorphous surface Mark Abraham
[gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water) Mark Abraham
[gmx-users] Error while running starting grompp and mdrun Mark Abraham
[gmx-users] Force field parameters in water or in vacuum? Mark Abraham
[gmx-users] Error while running starting grompp and mdrun Mark Abraham
[gmx-users] Unable to minimize energy Mark Abraham
[gmx-users] Simulate the organic molecule => input / output error Mark Abraham
[gmx-users] Re: Force field parameters in water or in vacuum? Mark Abraham
[gmx-users] about DMSO c-c bond and c-o bond in ffg53a6 force field Mark Abraham
[gmx-users] coordinates of the mass center Mark Abraham
[gmx-users] can we regenerate *.trr by *.log?? Mark Abraham
[gmx-users] Max #atoms in a charge group: 68 > 64 Mark Abraham
[gmx-users] Max #atoms in a charge group: 68 > 64 Mark Abraham
[gmx-users] pdb file error Mark Abraham
[gmx-users] coordinates of the mass center Mark Abraham
[gmx-users] a problem about the minimization Mark Abraham
[gmx-users] Question about binding free energy calculation Mark Abraham
[gmx-users] dihedral parameters in oplsaa Mark Abraham
[gmx-users] Killing mdrun based on execution time Mark Abraham
[gmx-users] Protein out of box Mark Abraham
[gmx-users] Calculating bond energy Mark Abraham
[gmx-users] no of interacting water molecules with solvated protein atoms Mark Abraham
[gmx-users] Problem of lipid-protein simulation Mark Abraham
[gmx-users] Understanding of production run with same parameters in md.mdp file Mark Abraham
[gmx-users] Calculating bond energy Mark Abraham
[gmx-users] inconsistency in .pdb files Mark Abraham
[gmx-users] simulating chemical reactions Mark Abraham
[gmx-users] Atom names mismatch Mark Abraham
[gmx-users] Atom names mismatch Mark Abraham
[gmx-users] Atom names mismatch - PyMol retain order Mark Abraham
[gmx-users] crash nsgrid.c Fabio Affinito
[gmx-users] crash nsgrid.c Fabio Affinito
[gmx-users] g_rdf: normalization issues? Vasilii Artyukhov
[gmx-users] Re: g_rdf: normalization issues? Vasilii Artyukhov
[gmx-users] Re: g_rdf: normalization issues? Vasilii Artyukhov
[gmx-users] confusion regarding tpbconv Anamika Awasthi
[gmx-users] confusion regarding tpbconv Anamika Awasthi
[gmx-users] Re:confusion regarding tpbconv Anamika Awasthi
[gmx-users] can we regenerate *.trr by *.log?? Anamika Awasthi
[gmx-users] atomname -> atomic number Daniel Baum
[gmx-users] atomname -> atomic number Daniel Baum
[gmx-users] Free energy calculations and speed problems van Bemmelen
[gmx-users] problem with genion (gromacs 3.3.99) Julie Bernauer
[gmx-users] Implicit Solvent Simulations Una Bjarnadottir
[gmx-users] modify the distance constraints force constant during the simulation Andrea Bortolato
[gmx-users] GroMeta v.2.0 Carlo Camilloni
[gmx-users] User Contributions Vitaly Chaban
[gmx-users] Green-Cubo relation Vitaly Chaban
[gmx-users] QM/MM between Gromacs and Gamess-US Hanning Chen
[gmx-users] QM/MM compilation Ramon Crehuet
[gmx-users] msd and diffusion coefficient and getting unfolded trajectory Ananya Debnath
[gmx-users] msd and diffusion coefficient and getting unfolded trajectory Ananya Debnath
[gmx-users] Pressure and All-bonds Dimitris Dellis
[gmx-users] Re: Pressure and All-bonds Dimitris Dellis
[gmx-users] Unable to neutralize my system Alan Dodd
[gmx-users] cutting the trajectory in small subtrajectories Alan Dodd
[gmx-users] Re: Re: water distortion above bilayer Alan Dodd
[gmx-users] how to edit pdb file Alan Dodd
[gmx-users] All tests failed Florian Dommert
[gmx-users] using xmp file Florian Dommert
[gmx-users] cutting the trajectory in small subtrajectories Florian Dommert
[gmx-users] cutting the trajectory in small subtrajectories Florian Dommert
[gmx-users] mpi.h is missing... Dmitri Dubov
[gmx-users] Ordering with trjorder Dmitri Dubov
[gmx-users] oxaloacetate and atp E.M.
[gmx-users] Calculating bond energy Yulia Einav
[gmx-users] Calculating bond energy Yulia Einav
[gmx-users] Calculating bond energy Yulia Einav
[gmx-users] Calculating bond energy Yulia Einav
[gmx-users] Force constant defined in flexible TIP3P water model Changsun Eun
[gmx-users] Energy minimization of a simple model without PBC Ivan Fedyanin
[gmx-users] Water molecule can not be settled Robert Fenwick
[gmx-users] Free energy - Hydrogen bond solute-solvent - Ethanol as an example. Eudes Fileti
[gmx-users] Re: Free energy - Hydrogen bond solute-solvent - Ethanol as an example. Eudes Fileti
[gmx-users] Plotting B-factor Ran Friedman
[gmx-users] multiple time step algorithm Ran Friedman
[gmx-users] multiple time step algorithm Ran Friedman
[gmx-users] QM/MM compilation Ran Friedman
[gmx-users] Fw: Electron Density Across the Lipid Bilayer ANINDITA GAYEN
[gmx-users] bilayer DMPC ANINDITA GAYEN
[gmx-users] Re: gmx-users Digest, Vol 49, Issue 53 bilayer area problem ANINDITA GAYEN
[gmx-users] water distortion above bilayer ANINDITA GAYEN
[gmx-users] Re: Re: water distortion above bilayer ANINDITA GAYEN
[gmx-users] 1-4 Scaling Problem? ANINDITA GAYEN
[gmx-users] Re:Re: 1-4 scaling problem? ANINDITA GAYEN
[gmx-users] Fw: Re: 1-4 scaling problem? ANINDITA GAYEN
[gmx-users] bilayer area gradually increasing!!!!! ANINDITA GAYEN
[gmx-users] multiple time step algorithm Cristina GRECO
[gmx-users] multiple time step algorithm Cristina GRECO
[gmx-users] multiple time step algorithm Cristina GRECO
[gmx-users] Re: combining differently-generated force-fields Maik Goette
[gmx-users] Free energy - Hydrogen bond solute-solvent - Ethanol as an example. Maik Goette
[gmx-users] Free energy of discharging and then recharging not zero Maik Goette
[gmx-users] Free energy of discharging and then recharging not zero Maik Goette
[gmx-users] atomname -> atomic number Gerrit Groenhof
[gmx-users] QM/MM compilation Gerrit Groenhof
[gmx-users] Making PDB file User Gromacs
[gmx-users] (no subject) Florian Haberl
[gmx-users] Help for GNUPlot Florian Haberl
[gmx-users] Making PDB file Florian Haberl
[gmx-users] RMSD plot Florian Haberl
[gmx-users] Understanding of production run with same parameters in md.mdp file Florian Haberl
[gmx-users] problems to get gromacs running on cluster Florian Haberl
[gmx-users] benchmark: buying a new cluster Berk Hess
[gmx-users] Re: g_rdf: normalization issues? Berk Hess
[gmx-users] Unable to neutralize my system Berk Hess
[gmx-users] Re: g_rdf: normalization issues? Berk Hess
[gmx-users] crash nsgrid.c Berk Hess
[gmx-users] multiple time step algorithm Berk Hess
[gmx-users] multiple time step algorithm Berk Hess
[gmx-users] Semi-isotropic pressure coupling Berk Hess
[gmx-users] Ordering with trjorder Berk Hess
[gmx-users] dipole momentum calculation in Gromacs/CPMD Berk Hess
[gmx-users] [ angle_restraints_z ] Berk Hess
[gmx-users] [ angle_restraints_z ] Berk Hess
[gmx-users] Free energy calculations and speed problems Berk Hess
[gmx-users] coordinates of the mass center Berk Hess
[gmx-users] Max #atoms in a charge group: 68 > 64 Berk Hess
[gmx-users] How to use tabulated potentials to do coarse grained simulation? Berk Hess
[gmx-users] How to use tabulated potentials to do coarse grained simulation?("Segmentation fault Berk Hess
[gmx-users] Mdrun kills all other(single CPU)mdrun processes started by same father process? Berk Hess
[gmx-users] .itp file for polymer David Huang
[gmx-users] Script: Loading .ndx files into PyMol Martin Höfling
[gmx-users] Atom names mismatch - PyMol retain order Martin Höfling
[gmx-users] Atom names mismatch - PyMol retain order Martin Höfling
[gmx-users] Crashing NPT run, 1.5 ns JMandumpal
[gmx-users] Semi-isotropic pressure coupling Sumanth Jamadagni
[gmx-users] no of interacting water molecules with solvated protein atoms Anupam Nath Jha
[gmx-users] REMD: average potential energy as a function of temperatue Robert Johnson
[gmx-users] Free energy of discharging and then recharging not zero Robert Johnson
[gmx-users] Free energy of discharging and then recharging not zero Robert Johnson
[gmx-users] Free energy of discharging and then recharging not zero Robert Johnson
[gmx-users] Free energy of discharging and then recharging not zero Robert Johnson
[gmx-users] Capped CNT Robert Johnson
[gmx-users] 3rd Annual CMM 'Users Meet Developers' Workshop on QM/MM Simulations Robert Johnson
[gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water) CIHAN NADIR KAPLAN
[gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water) Nadir Kaplan
[gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water) Nadir Kaplan
[gmx-users] stochastic dynamics and barostat in Gromacs Argyrios Karatrantos
[gmx-users] RDF values lower than 1 Argyrios Karatrantos
[gmx-users] lipid paraemeters Syma Khalid
[gmx-users] acetyl Bernhard Knapp
[gmx-users] gromacs 4.0 release Bernhard Knapp
[gmx-users] problems to get gromacs running on cluster Bernhard Knapp
[gmx-users] Plotting B-factor Kukol, Andreas
[gmx-users] Fatal error: No such moleculetype Cl Kukol, Andreas
[gmx-users] Re: combining differently-generated force-fields Kukol, Andreas
[gmx-users] gromos96 forcefield Kukol, Andreas
[gmx-users] pdb2gmx Kukol, Andreas
[gmx-users] cutting the trajectory in small subtrajectories Kukol, Andreas
[gmx-users] Energy minimisation problem Kukol, Andreas
[gmx-users] Energy minimisation problem Kukol, Andreas
[gmx-users] Angle definition in g_hbond ... Anil Kumar
[gmx-users] Fatal error: No such moleculetype Cl Anil Kumar
[gmx-users] NVT simulation Daniel Larsson
[gmx-users] ngmx crash Daniel Larsson
[gmx-users] how to neutralise: Non-integer charges Daniel Larsson
[gmx-users] chirality check Daniel Larsson
[gmx-users] Help for GNUPlot Per Larsson
[gmx-users] Implicit Solvent Simulations Per Larsson
[gmx-users] Plotting B-factor Alif M Latif
[gmx-users] Calculating average of B-factor Alif M Latif
[gmx-users] Protein out of box Alif M Latif
[gmx-users] Building simple alcohol topologies Jussi Lehtola
[gmx-users] Building simple alcohol topologies Jussi Lehtola
[gmx-users] Question about x2top Jussi Lehtola
[gmx-users] mpi.h is missing... Jussi Lehtola
[gmx-users] mpi.h is missing... Jussi Lehtola
[gmx-users] Energy minimisation problem Jussi Lehtola
[gmx-users] Energy minimisation problem Jussi Lehtola
[gmx-users] Energy minimisation problem Jussi Lehtola
[gmx-users] oxaloacetate and atp Justin A. Lemkul
[gmx-users] adding missing hydrogen in PDB files Justin A. Lemkul
[gmx-users] adding missing hydrogen in PDB files Justin A. Lemkul
[gmx-users] using xmp file Justin A. Lemkul
[gmx-users] help with lipids and pdb2gmx Justin A. Lemkul
[gmx-users] cannot determin precesion of .trn file Justin A. Lemkul
[gmx-users] Unable to neutralize my system Justin A. Lemkul
[gmx-users] How to create S-S bond Justin A. Lemkul
[gmx-users] Unable to neutralize my system Justin A. Lemkul
[gmx-users] Question about x2top Justin A. Lemkul
[gmx-users] Free energy of discharging and then recharging not zero Justin A. Lemkul
[gmx-users] SWCNT Topology Justin A. Lemkul
[gmx-users] gromos96 forcefield Justin A. Lemkul
[gmx-users] problem with energy minimization Justin A. Lemkul
[gmx-users] Simulation of ordered molecular structures Justin A. Lemkul
[gmx-users] gromos96 forcefield Justin A. Lemkul
[gmx-users] Ramachandran plots in GRACE Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] RMSD plot Justin A. Lemkul
[gmx-users] How to build a custom protein (PDB file) Justin A. Lemkul
[gmx-users] Free energy calculations and speed problems Justin A. Lemkul
[gmx-users] Free energy calculations and speed problems Justin A. Lemkul
[gmx-users] Free energy calculations and speed problems Justin A. Lemkul
[gmx-users] how to edit pdb file Justin A. Lemkul
[gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water) Justin A. Lemkul
[gmx-users] Force field parameters in water or in vacuum? Justin A. Lemkul
[gmx-users] Max #atoms in a charge group: 68 > 64 Justin A. Lemkul
[gmx-users] pdb file error Justin A. Lemkul
[gmx-users] the pdb file => input / output error Justin A. Lemkul
[gmx-users] input/output error when running Hessian matrix in double precision Justin A. Lemkul
[gmx-users] Constraints only on Backbone Justin A. Lemkul
Fwd: Re: [gmx-users] Constraints only on Backbone Justin A. Lemkul
[gmx-users] Generate velocity frame Justin A. Lemkul
[gmx-users] lipid gel phase simulation model building Justin A. Lemkul
[gmx-users] inconsistency in .pdb files Justin A. Lemkul
[gmx-users] Re: Thanks a lot / information Justin A. Lemkul
[gmx-users] 1-4 Scaling Problem? Marc F. Lensink
[gmx-users] bilayer area gradually increasing!!!!! Marc F. Lensink
[gmx-users] lipid gel phase simulation model building Marc F. Lensink
[gmx-users] g_hbond distance distribution problem Dechang Li
[gmx-users] g_hbond distance distribution problem Dechang Li
[gmx-users] mutation FE calculation with oplsaa Qiang Li
[gmx-users] Force field parameters in water or in vacuum? Chih-Ying Lin
[gmx-users] Simulate the organic molecule => input / output error Chih-Ying Lin
[gmx-users] Re: Force field parameters in water or in vacuum? Chih-Ying Lin
[gmx-users] the pdb file => input / output error Chih-Ying Lin
[gmx-users] amber ports in gromas - bond length warning N-J.M. Macaluso
[gmx-users] amber ports in gromas - bond length warning N-J.M. Macaluso
[gmx-users] noe restraints and g_disre problems N-J.M. Macaluso
[gmx-users] adding missing hydrogen in PDB files Arijit Maitra
[gmx-users] adding missing hydrogen in PDB files Arijit Maitra
[gmx-users] multiple time step algorithm Erik Marklund
[gmx-users] how to neutralise: Non-integer charges Erik Marklund
[gmx-users] How to build a custom protein (PDB file) Erik Marklund
[gmx-users] bootrstrap complains about serial nr Erik Marklund
[gmx-users] no of interacting water molecules with solvated protein atoms Erik Marklund
[gmx-users] Calculating bond energy Erik Marklund
[gmx-users] Atom names mismatch - PyMol retain order Erik Marklund
[gmx-users] Re: combining differently-generated force-fields Low Soo Mei
[gmx-users] grompp -np -shuffle with position restraints Low Soo Mei
[gmx-users] .trr file Low Soo Mei
[gmx-users] Re: Atom names mismatch Low Soo Mei
[gmx-users] double sids error ? what ?! BON Michael
[gmx-users] RE : double sids error ? what ?! BON Michael
[gmx-users] Question about binding free energy calculation Ming
[gmx-users] Free energy of discharging and then recharging not zero David Mobley
[gmx-users] Free energy of discharging and then recharging not zero David Mobley
[gmx-users] Free energy calculations and speed problems David Mobley
[gmx-users] Free energy calculations and speed problems David Mobley
[gmx-users] mutation FE calculation with oplsaa David Mobley
[gmx-users] FEP doubts David Mobley
[gmx-users] Mdrun kills all other（single CPU）mdrun processes started by same father process? Peter Mueller
[gmx-users] pressure problems Marcelo Müller
[gmx-users] benchmark: buying a new cluster Chris Neale
[gmx-users] small typo in ions.itp: LI+ atom is NA Chris Neale
[gmx-users] Force field parameters in water or in vacuum? Chris Neale
[gmx-users] 1-4 Scaling Problem? Chris Neale
[gmx-users] 1-4 scaling problem? Chris Neale
[gmx-users] 1-4 Scaling Problem? Chris Neale
[gmx-users] Problem of lipid-protein simulation Chris Neale
[gmx-users] [ angle_restraints_z ] Terry Nelson
[gmx-users] [ angle_restraints_z ] Terry Nelson
[gmx-users] Hessian matrix calculation Collins Nganou
[gmx-users] Fatal error receive by running Hessian matrix Collins Nganou
[gmx-users] Hessian matrix calculation Collins Nganou
[gmx-users] input/output error when running Hessian matrix in double precision Collins Nganou
[gmx-users] calculation of eigenfrequency Collins Nganou
[gmx-users] Generate velocity frame Collins Nganou
[gmx-users] FEP doubts Diego Nolasco
[gmx-users] constraint pulling code Brian Novak
[gmx-users] Constraints only on Backbone Bjoern Olausson
[gmx-users] Non integer charge for ARG and CYX? Georgios Patargias
[gmx-users] Non integer charge for ARG and CYX? Georgios Patargias
[gmx-users] timesteps don't match error Xavier Periole
[gmx-users] timesteps don't match error Xavier Periole
[gmx-users] timesteps don't match error Xavier Periole
[gmx-users] timesteps don't match error Xavier Periole
[gmx-users] Help needed urgently...!!! Xavier Periole
[gmx-users] Fatal error: No such moleculetype Cl Xavier Periole
[gmx-users] make_ndx problem Xavier Periole
[gmx-users] Melting temperature of the potato, a bug in grompp? Xavier Periole
[gmx-users] confusion regarding tpbconv Xavier Periole
[gmx-users] Re:confusion regarding tpbconv Xavier Periole
[gmx-users] tip3p.gro Xavier Periole
[gmx-users] tip3p.gro Xavier Periole
[gmx-users] g_hbond distance distribution problem Xavier Periole
[gmx-users] 1-4 Scaling Problem? Xavier Periole
[gmx-users] Fwd: Problem of lipid-protein Simulation Xavier Periole
[gmx-users] Pdb2gmx and tip4p dummy atom position TJ Piggot
[gmx-users] Pdb2gmx and tip4p dummy atom position TJ Piggot
[gmx-users] lipid paraemeters Ángel Piñeiro
[gmx-users] All tests failed Ramadas Sunil Pophale
[gmx-users] simple and complex test failure Ramadas Sunil Pophale
[gmx-users] Re: gmx-users Digest, Vol 49, Issue 11 Ramadas Sunil Pophale
[gmx-users] pdb2gmx RAJAVARMAN.K
[gmx-users] adding missing hydrogen in PDB files Vigneshwar Ramakrishnan
[gmx-users] topolbuild 1.1.1, minor revisions to an all-atoms model gromacs topology generator Bruce D. Ray
[gmx-users] How to use tabulated potentials to do coarse grained simulation? Catfish SUN
[gmx-users] How to use tabulated potentials to do coarse grained simulation?("Segmentation fault" when running mdrun.) Catfish SUN
[gmx-users] tip3p.gro Nicolas Sapay
[gmx-users] gromos96 forcefield Thomas Schlesier
[gmx-users] gromos96 forcefield Thomas Schlesier
[gmx-users] lipid gel phase simulation model building Carsten Selle
[gmx-users] lipid gel phase simulation model building Carsten Selle
[gmx-users] LJ SIMULATION Arnab Senapati
[gmx-users] (no subject) Arnab Senapati
[gmx-users] Equilibration Arnab Senapati
[gmx-users] (no subject) Arnab Senapati
[Fwd: [gmx-users] (no subject)] Arnab Senapati
[gmx-users] Box size Increase Arnab Senapati
[gmx-users] (no subject) Arnab Senapati
[gmx-users] NVT simulation Arnab Senapati
[gmx-users] Tabulated potential Arnab Senapati
[gmx-users] High pressure Arnab Senapati
[gmx-users] tabulated potential Arnab Senapati
[gmx-users] Heat Flux on CNT Andy Shelley
[gmx-users] Free energy calculations and speed problems Michael Shirts
[gmx-users] LINCS and parallel simulation Philip Shushkov
[gmx-users] Local pressure profiles Philip Shushkov
[gmx-users] g_sas and PBC Gurpreet Singh
[gmx-users] g_sas and PBC Gurpreet Singh
[gmx-users] Ramachandran plots in GRACE Petr Sklenovsky
[gmx-users] How to build a custom protein (PDB file) Ricardo Soares
[gmx-users] How to build a custom protein (PDB file) Ricardo Soares
[gmx-users] Non integer charge for ARG and CYX? Eric J. Sorin
[gmx-users] Re: upgrade version - "make distclean"? David van der Spoel
[gmx-users] Building simple alcohol topologies David van der Spoel
[gmx-users] GROMACS parallel set up Questions. David van der Spoel
[gmx-users] Plotting B-factor David van der Spoel
[gmx-users] Building simple alcohol topologies David van der Spoel
[gmx-users] Solvent insertion analysis 2 David van der Spoel
[gmx-users] LJ SIMULATION David van der Spoel
[gmx-users] simple and complex test failure David van der Spoel
[gmx-users] Calculating average of B-factor David van der Spoel
[gmx-users] Re: gmx-users Digest, Vol 49, Issue 11 David van der Spoel
[gmx-users] Angle definition in g_hbond ... David van der Spoel
[gmx-users] double sids error ? what ?! David van der Spoel
[gmx-users] cannot determin precesion of .trn file David van der Spoel
[gmx-users] Angle definition in g_hbond ... David van der Spoel
[gmx-users] Heat Flux on CNT David van der Spoel
[gmx-users] how to obtain no. of aggregates vs time graph David van der Spoel
[gmx-users] box vectors entry in "gro" file David van der Spoel
[gmx-users] ngmx crash David van der Spoel
[gmx-users] High pressure David van der Spoel
[gmx-users] gromacs 4.0 release David van der Spoel
[gmx-users] RDF values lower than 1 David van der Spoel
[gmx-users] User Contributions David van der Spoel
[gmx-users] multiple time step algorithm David van der Spoel
[gmx-users] multiple time step algorithm David van der Spoel
[gmx-users] atomname -> atomic number David van der Spoel
[gmx-users] g_hbond distance distribution problem David van der Spoel
[gmx-users] g_hbond distance distribution problem David van der Spoel
[gmx-users] .trr file David van der Spoel
回复： Re: [gmx-users] how to remd analysi? David van der Spoel
[gmx-users] which code should I rewrite the function of "position restraints"? David van der Spoel
[gmx-users] Force field parameters in water or in vacuum? David van der Spoel
[gmx-users] Hessian matrix calculation David van der Spoel
[gmx-users] g_sas and PBC David van der Spoel
[gmx-users] g_sas and PBC David van der Spoel
[gmx-users] amber ports in gromas - bond length warning David van der Spoel
[gmx-users] Fatal error receive by running Hessian matrix David van der Spoel
[gmx-users] dihedral parameters in oplsaa David van der Spoel
[gmx-users] dihedral parameters in oplsaa David van der Spoel
[gmx-users] dihedral parameters in oplsaa David van der Spoel
[gmx-users] bootrstrap complains about serial nr David van der Spoel
[gmx-users] Killing mdrun based on execution time David van der Spoel
[gmx-users] dihedral parameters in oplsaa David van der Spoel
[gmx-users] Mdrun kills all other(single CPU)mdrun processes started by same father process? David van der Spoel
[gmx-users] Grid statement in md.log David van der Spoel
[gmx-users] how to fill water molecules only in required place David van der Spoel
[gmx-users] Re: Grid statement in md.log David van der Spoel
[gmx-users] Pdb2gmx and tip4p dummy atom position David van der Spoel
[gmx-users] Local pressure profiles David van der Spoel
[gmx-users] modify the distance constraints force constant during the simulation Mitchell Stanton-Cook
[gmx-users] Capped CNT Christopher Stiles
[gmx-users] GROMACS parallel set up Questions. Subhrangshu Supakar
[gmx-users] Help for GNUPlot Zoltan Varga
[gmx-users] SWCNT Topology Mayank Verma
[gmx-users] Increase number of decimal places in force.xvg (g_traj) Lee-Ping Wang
[gmx-users] (no subject) Tsjerk Wassenaar
[gmx-users] box vectors entry in "gro" file Tsjerk Wassenaar
[gmx-users] g_rms: Too many iterations in routine JACOBI Tsjerk Wassenaar
[gmx-users] Re: g_rms: Too many iterations in routine JACOBI Tsjerk Wassenaar
[gmx-users] Melting temperature of the potato, a bug in grompp? Tsjerk Wassenaar
[gmx-users] creating a box from a single molecule Tsjerk Wassenaar
[gmx-users] the pdb file => input / output error Tsjerk Wassenaar
[gmx-users] how to edit pdb file Wei, Xiupeng
[gmx-users] how to edit pdb file Wei, Xiupeng
[gmx-users] Invitation to connect on LinkedIn Chandu_Cts Welcomes...All....Biotechies
[gmx-users] Unable to minimize energy Paul Whitford
[gmx-users] how to fill water molecules only in required place Santan William
[gmx-users] how to fill water molecules only in required place Santan William
[gmx-users] Simulation of ordered molecular structures Peyman Yamin
[gmx-users] creating a box from a single molecule Peyman Yamin
[gmx-users] benchmark: buying a new cluster Yang Ye
[gmx-users] NVT simulation Yang Ye
[gmx-users] Is such hardware suitable for gromacs Yang Ye
[gmx-users] how to edit pdb file Yang Ye
[gmx-users] amber ports in gromas - bond length warning Yang Ye
[gmx-users] Error while running starting grompp and mdrun Ragothaman Yennamalli
[gmx-users] Error while running starting grompp and mdrun Ragothaman Yennamalli
[gmx-users] problem with simulation of phosphatidic acid, possibly in my topology? Yiannis
[gmx-users] bilayer DMPC Yiannis
[gmx-users] box vectors entry in "gro" file Makoto Yoneya
[gmx-users] box vectors entry in "gro" file Makoto Yoneya
[gmx-users] which code should I rewrite the function of "position restraints"? Makoto Yoneya
[gmx-users] generation of amorphous surface h a
[gmx-users] inconsistency in .pdb files h a
[gmx-users] Re:confusion regarding tpbconv sudheer babu
[gmx-users] Error of g_rms s lal badshah
[gmx-users] Can not open file:md323.xtc s lal badshah
[gmx-users] Alternate to xmgrace s lal badshah
[gmx-users] Help for GNUPlot s lal badshah
[gmx-users] gcc 4.2.x baloilgiullare
[gmx-users] Re: modify the distance constraints force constant during the simulation chaban at univer.kharkov.ua
[gmx-users] tip3p.gro sarbani chattopadhyay
[gmx-users] tip3p.gro sarbani chattopadhyay
[gmx-users] cannot determin precesion of .trn file kinshuk at chem.iitb.ac.in
[gmx-users] How to create S-S bond kinshuk at chem.iitb.ac.in
[gmx-users] How to create S-S bond kinshuk at chem.iitb.ac.in
[gmx-users] dipole momentum calculation in Gromacs/CPMD yayan at chemie.fu-berlin.de
[gmx-users] using xmp file pragya chohan
[gmx-users] using xmp file pragya chohan
[gmx-users] cutting the trajectory in small subtrajectories serdar durdagi
[gmx-users] cutting the trajectory in small subtrajectories serdar durdagi
[gmx-users] REMD: average potential energy as a function of temperatue pascal.baillod at epfl.ch
[gmx-users] dihedral parameters in oplsaa friendli
[gmx-users] dihedral parameters in oplsaa friendli
[gmx-users] dihedral parameters in oplsaa friendli
[gmx-users] Re: gmx-users Digest, Vol 49, Issue 93 friendli
[gmx-users] dihedral parameters in oplsaa friendli
[gmx-users] mutation FE calculation with oplsaa friendli
[gmx-users] simulating chemical reactions gfunch
[gmx-users] QM/MM compilation ggroenh
[gmx-users] announcement: Advanced Gromacs workshop in Goettingen September 24-26 ggroenh
[gmx-users] Spice up your mobile chandrabhanseniya at gmail.com
[gmx-users] timesteps don't match error maria goranovic
[gmx-users] timesteps don't match error maria goranovic
[gmx-users] timesteps don't match error maria goranovic
[gmx-users] timesteps don't match error maria goranovic
[gmx-users] timesteps don't match error maria goranovic
[gmx-users] problem with simulation of phosphatidic acid, possibly in my topology? maria goranovic
[gmx-users] I am now on Refriendz! sunita gupta
[gmx-users] coordinates of the mass center yren at home.ipe.ac.cn
[gmx-users] (no subject) hhhh huan
[gmx-users] how to obtain no. of aggregates vs time graph hhhh huan
[gmx-users] pdb file error hhhh huan
[gmx-users] problem with energy minimization sanjay23 at iitb.ac.in
[gmx-users] problem with energy minimization sanjay23 at iitb.ac.in
[gmx-users] chirality check sanjay23 at iitb.ac.in
[gmx-users] DCCM tuhin at iitk.ac.in
[gmx-users] position and distance restraining jayant james
[gmx-users] ngmx crash jayant james
[gmx-users] distance restrained energy minimisation jayant james
[gmx-users] about DMSO c-c bond and c-o bond in ffg53a6 force field wang kelvin
[gmx-users] about DMSO c-c bond and c-o bond in ffg53a6 force field wang kelvin
[gmx-users] problem with simulation of phosphatidic acid, possibly in my topology? himanshu khandelia
[gmx-users] Re: problem with simulation of phosphatidic acid, possibly in my topology? himanshu khandelia
[gmx-users] problem regarding energy minimization sangeeta kundu
[gmx-users] Solvent insertion analysis 2 cfgauna at lab.cricyt.edu.ar
[gmx-users] trjorder problems cfgauna at lab.cricyt.edu.ar
[gmx-users] Is Gay-Berne potential available in GROMACS? zhenlong li
[gmx-users] dssp or xpm2ps? andrea_guarnera at libero.it
[gmx-users] when I switch to ffG43a1, the problem occurs xin liu
[gmx-users] when I switch to ffG43a1, the problem occurs xin liu
[gmx-users] Re: tip3p.gro servaas michielssens
[gmx-users] make_ndx problem minnale
[gmx-users] g_rms: Too many iterations in routine JACOBI minnale
[gmx-users] Re: g_rms: Too many iterations in routine JACOBI minnale
[gmx-users] (no subject) minnale
[gmx-users] RMSD plot minnale
[gmx-users] Understanding of production run with same parameters in md.mdp file minnale
[gmx-users] Understanding of production run with same parameters in md.mdp file minnale
[gmx-users] Wrong potential energies in stochastic dynamics reich at mpikg.mpg.de
[gmx-users] Help needed urgently...!!! namita at ncbs.res.in
[gmx-users] Fatal error: No such moleculetype Cl namita at ncbs.res.in
[gmx-users] Unable to neutralize my system namita at ncbs.res.in
[gmx-users] Unable to neutralize my system namita at ncbs.res.in
[gmx-users] Range checking error namita at ncbs.res.in
[gmx-users] Range checking error namita at ncbs.res.in
[gmx-users] how to neutralise: Non-integer charges namita at ncbs.res.in
[gmx-users] Grid statement in md.log sapna sarupria
[gmx-users] Re: Grid statement in md.log sapna sarupria
[gmx-users] help with lipids and pdb2gmx fabracht sdf
[gmx-users] Angle definition in g_hbond ... sharada
[gmx-users] Angle definition in g_hbond ... sharada
[gmx-users] Angle definition in g_hbond ... sharada
[gmx-users] A question about DNA and normal mode analysis in gromacs silvester.thu
[gmx-users] Energy minimisation problem silvester.thu
[gmx-users] how to build the input files of an infinite system silvester.thu
[gmx-users] how to build the input files of an infinite system silvester.thu
[gmx-users] benchmark: buying a new cluster andrea spitaleri
[gmx-users] how to edit pdb file andrea spitaleri
[gmx-users] a problem about adding organic solvent with genbox zhuliang at tju.edu.cn
[gmx-users] a problem about the minimization zhuliang at tju.edu.cn
[gmx-users] Combining LJ & Buckingham? ttrudeau
[gmx-users] combining differently-generated force-fields chris.neale at utoronto.ca
[gmx-users] Re: combining differently-generated force-fields chris.neale at utoronto.ca
[gmx-users] bilayer DMPC chris.neale at utoronto.ca
[gmx-users] Re: gmx-users Digest, Vol 49, Issue 53 bilayer area problem chris.neale at utoronto.ca
[gmx-users] Force field parameters in water or in vacuum? chris.neale at utoronto.ca
[gmx-users] Re: 1-4 scaling problem? chris.neale at utoronto.ca
[gmx-users] Re: Problem of lipid-protein simulation chris.neale at utoronto.ca
[gmx-users] Re: bilayer area now gradually increasing!!!!!!!!!!!!!!!! chris.neale at utoronto.ca
[gmx-users] lipid gel phase simulation model building chris.neale at utoronto.ca
[gmx-users] Atom names mismatch chris.neale at utoronto.ca
[gmx-users] lipid gel phase simulation model building chris.neale at utoronto.ca
[gmx-users] Parallel processing mariognu-outside at yahoo.com.br
[gmx-users] how to remd analysi? xi zhao
回复： Re: [gmx-users] how to remd analysi? xi zhao
[gmx-users] Max #atoms in a charge group: 68 > 64 Samuel Coulbourn Flores 花山
[gmx-users] Max #atoms in a charge group: 68 > 64 Samuel Coulbourn Flores 花山
[gmx-users] Killing mdrun based on execution time Samuel Coulbourn Flores 花山
[gmx-users] Is such hardware suitable for gromacs 之光贾

Last message date: Sat May 31 15:25:58 CEST 2008
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