January 2009 Archives by author

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Starting: Thu Jan 1 11:17:13 CEST 2009
Ending: Sat Jan 31 13:46:53 CEST 2009
Messages: 565

[gmx-users] environment variable GMX_MAXCONSTRWARN to -1, Martin Höfling
[gmx-users] Problem with 4.0.3 Martin Höfling
[gmx-users] Software Raid and low GROMACS performance Martin Höfling
[gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2 João M. Damas
[gmx-users] help with REMD Rebeca García Fandiño
[gmx-users] diffusion of oxygen in water Mark Abraham
[gmx-users] Adding water to a lipid bilayer Mark Abraham
[gmx-users] about xterm window in gromacs demo Mark Abraham
[gmx-users] calculation of the order parameter S2 Mark Abraham
[gmx-users] problem with mdrun in parallel Mark Abraham
[gmx-users] force evaluation Mark Abraham
[gmx-users] Re:problem with mdrun in parallel Mark Abraham
[gmx-users] Removing water from sides of bilayer Mark Abraham
[gmx-users] chloroform box Mark Abraham
[gmx-users] force evaluation Mark Abraham
[gmx-users] Opinion requested regarding NVIDIA® Tesla™ Personal Supercomputer Mark Abraham
[gmx-users] restraining Ca2+ ion Mark Abraham
[gmx-users] restraining Ca2+ ion Mark Abraham
[gmx-users] chcl3 box Mark Abraham
[gmx-users] REMD protein-ligand separation Mark Abraham
[gmx-users] intermittent crashes running on multiple nodes Mark Abraham
[gmx-users] Strange grompp error: System has non-zero total charge Mark Abraham
[gmx-users] minimization problem Mark Abraham
[gmx-users] Onw question about rlist rvdw rcoulomb and nstlist Mark Abraham
[gmx-users] Best performace with 0 core for PME calcuation Mark Abraham
[gmx-users] Box Exploding Error Mark Abraham
[gmx-users] about complexing protein and ligand Mark Abraham
[gmx-users] Box Exploding Error Mark Abraham
[gmx-users] help with REMD Mark Abraham
[gmx-users] using rerun to extract energies for protein from trr file Mark Abraham
[gmx-users] using rerun to extract energies for protein fromtrr file Mark Abraham
[gmx-users] Qestion about how to define groups by chain id in a protein ? Mark Abraham
[gmx-users] Thank you Mark Abraham
[gmx-users] Light-controlled MD Mark Abraham
[gmx-users] After MD simulation => put the sample under Scattering Mark Abraham
[gmx-users] why the trajectory file is not output Mark Abraham
[gmx-users] why the trajectory file is not output Mark Abraham
[gmx-users] freez group Mark Abraham
[gmx-users] To run in gromacs 4.0.3 in cluster Mark Abraham
[gmx-users] freez group Mark Abraham
[gmx-users] new atom type and force field Mark Abraham
[gmx-users] ligand-protein distance restraint Mark Abraham
[gmx-users] ligand-protein distance restraint Mark Abraham
[gmx-users] ligand-protein distance restraint Mark Abraham
[gmx-users] the wanging: atom names don't match in top and gro file Mark Abraham
Fwd: [gmx-users] Invalid atom number 6415 in indexfile Mark Abraham
[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS Mark Abraham
[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS Mark Abraham
[gmx-users] How to run postion restraining step in gromacs Mark Abraham
[gmx-users] Grompp error in 4.x regarding dihedral multiplicity Mark Abraham
[gmx-users] How to get topol.top files from DRGGMX.ITP files? Mark Abraham
[gmx-users] restarting a replica exchange simulations Mark Abraham
SV: [gmx-users] Grompp error in 4.x regarding dihedral multiplicity Mark Abraham
[gmx-users] How to treat an isolated iron (Fe 2+) Alexandre Suman de Araujo
[gmx-users] Software Raid and low GROMACS performance Alexandre Suman de Araujo
[gmx-users] Software Raid and low GROMACS performance Alexandre Suman de Araujo
[gmx-users] Calculating acyl chain order parameter profile on phospholipid vesicles Cesar Luis Avila
[gmx-users] about xterm window in gromacs demo Shirin Awasthi
[gmx-users] about converting output Shirin Awasthi
[gmx-users] about complexing protein and ligand Shirin Awasthi
[gmx-users] Software inconsistency error. Homa Azizian
[gmx-users] query about random velocity generation Nuno Azoia
[gmx-users] RMSF and temperature factors Una Bjarnadottir
[gmx-users] ResNumber in PDB2GMX Alessandro Casoni
[gmx-users] units... Vitaly Chaban
[gmx-users] units... Vitaly Chaban
[gmx-users] units... Vitaly Chaban
[gmx-users] RE: Where can I get .gro and .itp files for different models of water? Vitaly Chaban
[gmx-users] g_clustsize Vitaly Chaban
[gmx-users] g_clustsize Vitaly Chaban
[gmx-users] RE: How to output a single index group Vitaly Chaban
[gmx-users] g_clustsize Vitaly Chaban
[gmx-users] g_clustsize Vitaly Chaban
[gmx-users] g_clustsize Vitaly Chaban
[gmx-users] g_clustsize Vitaly Chaban
[gmx-users] g_clustsize Vitaly Chaban
[gmx-users] g_clussize. strange error Vitaly Chaban
[gmx-users] RE: Tcl script Vitaly Chaban
[gmx-users] Numbering in xtc and in conf.gro. Does it coincide? Vitaly Chaban
[gmx-users] RE: Numbering in xtc and in conf.gro. Does it coincide? Vitaly Chaban
[gmx-users] RE: Constant Velocity Vitaly Chaban
[gmx-users] RE: Is there any option to output interaction energy based on energy groups? Vitaly Chaban
[gmx-users] Re: Constant Velocity Vitaly Chaban
[gmx-users] xtc groups. order of atoms Vitaly Chaban
[gmx-users] g_energy non-interactive Vitaly Chaban
[gmx-users] g_energy non-interactive Vitaly Chaban
[gmx-users] Re: why the trajectory file is not output Vitaly Chaban
[gmx-users] Re[2]: why the trajectory file is not output Vitaly Chaban
[gmx-users] Re[4]: why the trajectory file is not output Vitaly Chaban
[gmx-users] Opinion requested regarding NVIDIA® Tesla™ Personal Supercomputer Suman Chakrabarty
[gmx-users] Question regarding trjorder Suman Chakrabarty
[gmx-users] Question regarding trjorder Suman Chakrabarty
[gmx-users] force evaluation Suman Chakrabarty
[gmx-users] Problem with DMSO as solvent Suman Chakrabarty
[gmx-users] Problem with DMSO as solvent Suman Chakrabarty
[gmx-users] Problem with DMSO as solvent Suman Chakrabarty
[gmx-users] Strange grompp error: System has non-zero total charge Suman Chakrabarty
[gmx-users] force evaluation Silvia Crivelli
[gmx-users] new atom type and force field Shuangxing Dai
[gmx-users] using rerun to extract energies for protein from trr file Siavoush Dastmalchi
[gmx-users] using rerun to extract energies for protein fromtrr file Siavoush Dastmalchi
[gmx-users] using rerun to extract energies for protein fromtrrfile Siavoush Dastmalchi
[gmx-users] Equilibrating systems of rigid molecules Dimitris Dellis
[gmx-users] gromacs 3.3.3 vs 4.0.3 performance Dimitris Dellis
[gmx-users] gromacs 3.3.3 vs 4.0.3 performance Dimitris Dellis
[gmx-users] gromacs 3.3.3 vs 4.0.3 performance Dimitris Dellis
[gmx-users] Pull Code problems DimitryASuplatov
[gmx-users] Pull Code problems DimitryASuplatov
[gmx-users] Pull Code problems DimitryASuplatov
[gmx-users] Pull Code problems DimitryASuplatov
[gmx-users] Pull code - 2 DimitryASuplatov
[gmx-users] Analysis of Pull-code results DimitryASuplatov
[gmx-users] force evaluation Florian Dommert
[gmx-users] force evaluation Florian Dommert
[gmx-users] force evaluation Florian Dommert
[gmx-users] force evaluation Florian Dommert
[gmx-users] force evaluation Florian Dommert
[gmx-users] units... Florian Dommert
[gmx-users] g_mindist -pi gives segfault in 3.3.3 and 4.0.2 but not 3.3.1 Florian Dommert
[gmx-users] Gromacs 4.0.2 hangs? Yves Dubief
[gmx-users] deform option in parallel with Gromacs 4.0.2 Yves Dubief
[gmx-users] Adding water to a lipid bilayer Semen Esilevsky
[gmx-users] Generalized Born Semen Esilevsky
[gmx-users] Generalized Born Semen Esilevsky
[gmx-users] Re: Calculating electric field vector at snapshots Aaron Fafarman
[gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder Steve Fiedler
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Steve Fiedler
[gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder Steve Fiedler
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Steve Fiedler
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Steve Fiedler
[gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder Steve Fiedler
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Steve Fiedler
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Steve Fiedler
[gmx-users] CO2 Linear triatomic - topology problem Eudes Fileti
[gmx-users] compiling gromacs Pedro Alberto Valiente Flores
[gmx-users] g_clustsize Ran Friedman
[gmx-users] g_clustsize Ran Friedman
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Ran Friedman
[gmx-users] Release of the R.E.D.-III.1 tools FyD
[gmx-users] Unstable model : need suggesstion Sukesh Chandra Gain
[gmx-users] PhD position in Computational Structural Biology at Cambridge, UK Swanand Gore
[gmx-users] Box Exploding Error VENKATESH HARIHARAN
[gmx-users] Box Exploding Error VENKATESH HARIHARAN
[gmx-users] How to output a single index group VENKATESH HARIHARAN
[gmx-users] why the trajectory file is not output He, Yang
[gmx-users] why the trajectory file is not output He, Yang
[gmx-users] why the trajectory file is not output He, Yang
[gmx-users] why the trajectory file is not output He, Yang
[gmx-users] why the trajectory file is not output He, Yang
[gmx-users] the wanging: atom names don't match in top and gro file He, Yang
[gmx-users] the wanging: atom names don't match in top and gro file He, Yang
[gmx-users] Gromacs 4.0.2 hangs? Berk Hess
[gmx-users] force evaluation Berk Hess
Subject: Re: Re: [gmx-users] Gromacs 4 bug? Berk Hess
[gmx-users] force evaluation Berk Hess
Subject: Re: Re: [gmx-users] Gromacs 4 bug? Berk Hess
[gmx-users] force evaluation Berk Hess
Subject: Re: Re: [gmx-users] Gromacs 4 bug? Berk Hess
[gmx-users] Best performace with 0 core for PME calcuation Berk Hess
[gmx-users] eigenvalues Berk Hess
[gmx-users] Best performace with 0 core for PME calcuation Berk Hess
Subject: Re: Re: [gmx-users] Gromacs 4 bug? Berk Hess
[gmx-users] Pull Code problems Berk Hess
[gmx-users] Pull Code problems Berk Hess
[gmx-users] Pull Code problems Berk Hess
[gmx-users] Pull Code problems Berk Hess
Subject: Re: Re: [gmx-users] Gromacs 4 bug? Berk Hess
[gmx-users] g_rotacf, order parameter S2 problem Berk Hess
[gmx-users] How does MDrun number atoms? Berk Hess
[gmx-users] mdrun 4.0 hangs (please report back) Berk Hess
[gmx-users] Inconsistent shifts Problem when using g_rdf Berk Hess
[gmx-users] g_mindist -pi gives segfault in 3.3.3 and 4.0.2 but not 3.3.1 Berk Hess
[gmx-users] mdrun output conformation file loses chain identifier Berk Hess
[gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2 Berk Hess
[gmx-users] deform option in parallel with Gromacs 4.0.2 Berk Hess
[gmx-users] temperature too high with reaction field Berk Hess
[gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder Berk Hess
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Berk Hess
[gmx-users] Domain Decomposision and Frozen Groups Berk Hess
[gmx-users] Domain Decomposision and Frozen Groups Berk Hess
[gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder Berk Hess
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Berk Hess
[gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder Berk Hess
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Berk Hess
[gmx-users] about the run program in gromacs 4.0.3 Berk Hess
[gmx-users] error using generic kernel Berk Hess
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Berk Hess
[gmx-users] Software inconsistency error. Berk Hess
[gmx-users] Segmentation fault with genbox -nmol (version 4.0.3) Berk Hess
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Berk Hess
[gmx-users] "nstlist=-1" and performance problem Berk Hess
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Berk Hess
[gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no. Berk Hess
[gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no. Berk Hess
[gmx-users] Re: decoupling charge while maintaining intramolecular potentials Berk Hess
[gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no. Berk Hess
[gmx-users] "nstlist=-1" and performance problem Berk Hess
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Berk Hess
[gmx-users] free energy with TIP4P bug fixed Berk Hess
[gmx-users] Re: free energy with TIP4P bug fixed Berk Hess
[gmx-users] Re: free energy with TIP4P bug fixed Berk Hess
[gmx-users] free energy with TIP4P bug fixed Berk Hess
[gmx-users] "nstlist=-1" dosen't work for parallel runs Berk Hess
[gmx-users] restarting a replica exchange simulations Berk Hess
[gmx-users] intermittent crashes running on multiple nodes Ron Hills
[gmx-users] Rugged dgdl curve in turning off/on the charge for Leu Jochen Hub
[gmx-users] ligand-protein distance restraint Pathumwadee Intharathep
[gmx-users] ligand-protein distance restraint Pathumwadee Intharathep
[gmx-users] ligand-protein distance restraint Pathumwadee Intharathep
[gmx-users] ligand-protein distance restraint Pathumwadee Intharathep
[gmx-users] About frozen groups Mohammed Kamal
[gmx-users] About frozen groups Mohammed Kamal
[gmx-users] (no subject) Morteza Khabiri
[gmx-users] freez group Morteza Khabiri
[gmx-users] freez group Morteza Khabiri
[gmx-users] Re: GROMACS 4.0.2 error Value of 'multiplicity' in Proper Dih. is 0 Himanshu Khandelia
[gmx-users] GIMLi user-contributed code for lipid mixture simulations Kindt, James
[gmx-users] Re: Gromacs 4 bug? Bernhard Knapp
[gmx-users] Extract diagonal from xpm matrix Kukol, Andreas
[gmx-users] Tcl script Kukol, Andreas
[gmx-users] polyalanine melt Kukol, Andreas
[gmx-users] index file for DPPC Kukol, Andreas
[gmx-users] dear KUTZNER (flow control) Carsten Kutzner
[gmx-users] dear KUTZNER (flow control) Carsten Kutzner
[gmx-users] Best performace with 0 core for PME calcuation Carsten Kutzner
[gmx-users] low latency Carsten Kutzner
[gmx-users] Equilibrating systems of rigid molecules Jussi Lehtola
Subject: Re: Re: [gmx-users] Gromacs 4 bug? Jussi Lehtola
[gmx-users] about the run program in gromacs 4.0.3 Jussi Lehtola
[gmx-users] Unstable model : need suggesstion Justin A. Lemkul
[gmx-users] about converting output Justin A. Lemkul
[gmx-users] Question regarding trjorder Justin A. Lemkul
[gmx-users] Question regarding trjorder Justin A. Lemkul
[gmx-users] chloroform box Justin A. Lemkul
[gmx-users] Removing water from sides of bilayer Justin A. Lemkul
[gmx-users] putting extra molecules in the box with genbox Justin A. Lemkul
[gmx-users] phi/psi Justin A. Lemkul
[gmx-users] restraining Ca2+ ion Justin A. Lemkul
[gmx-users] Problem with DMSO as solvent Justin A. Lemkul
[gmx-users] restraining Ca2+ ion Justin A. Lemkul
[gmx-users] Problem with DMSO as solvent Justin A. Lemkul
[gmx-users] restraining Ca2+ ion Justin A. Lemkul
[gmx-users] restraining Ca2+ ion Justin A. Lemkul
[gmx-users] minimization problem Justin A. Lemkul
[gmx-users] unit of the opls-aa force field in Gromacs package Justin A. Lemkul
[gmx-users] Box Exploding Error Justin A. Lemkul
[gmx-users] Best performace with 0 core for PME calcuation Justin A. Lemkul
[gmx-users] smd_forces Justin A. Lemkul
[gmx-users] atom H is missing in the first residue in a chain Justin A. Lemkul
[gmx-users] atom H is missing in the first residue in a chain Justin A. Lemkul
[gmx-users] atom H is missing in the first residue in a chain Justin A. Lemkul
[gmx-users] atom H is missing in the first residue in a chain Justin A. Lemkul
[gmx-users] atom H is missing in the first residue in a chain Justin A. Lemkul
[gmx-users] How does MDrun number atoms? Justin A. Lemkul
[gmx-users] How to treat an isolated iron (Fe 2+) Justin A. Lemkul
[gmx-users] Creating top-file for molecules not included in the forcefield Justin A. Lemkul
[gmx-users] MD simulating cyclic peptides including D-aminoacids Justin A. Lemkul
[gmx-users] units... Justin A. Lemkul
[gmx-users] units... Justin A. Lemkul
[gmx-users] environment variable GMX_MAXCONSTRWARN to -1, Justin A. Lemkul
[gmx-users] wrong format in input file ffamber03.hdb on line Justin A. Lemkul
[gmx-users] Where can I get .gro and .itp files for different models of water? Justin A. Lemkul
[gmx-users] How to determine if it is the pi-pi stacking interaction? Justin A. Lemkul
[gmx-users] Gromacs 4.0.3 released Justin A. Lemkul
[gmx-users] Qestion about how to define groups by chain id in a protein ? Justin A. Lemkul
[gmx-users] About frozen groups Justin A. Lemkul
[gmx-users] Qestion about how to define groups by chain id in a protein ? Justin A. Lemkul
[gmx-users] Qestion about how to define groups by chain id in a protein ? Justin A. Lemkul
[gmx-users] Qestion about how to define groups by chain id in a protein ? Justin A. Lemkul
[gmx-users] MD vs Scattering Justin A. Lemkul
[gmx-users] About frozen groups Justin A. Lemkul
[gmx-users] pull code Justin A. Lemkul
[gmx-users] Invalid atom number 6415 in indexfile Justin A. Lemkul
[gmx-users] index file for DPPC Justin A. Lemkul
[gmx-users] getting started-protein folding Justin A. Lemkul
[gmx-users] g_energy non-interactive Justin A. Lemkul
[gmx-users] why the trajectory file is not output Justin A. Lemkul
[gmx-users] why the trajectory file is not output Justin A. Lemkul
[gmx-users] why the trajectory file is not output Justin A. Lemkul
[gmx-users] Re: gormacs files for CG DNA Justin A. Lemkul
[gmx-users] Carbon tetrachloride Justin A. Lemkul
[gmx-users] Segmentation fault with genbox -nmol (version 4.0.3) Justin A. Lemkul
[gmx-users] the wanging: atom names don't match in top and gro file Justin A. Lemkul
[gmx-users] Invalid atom number 6415 in indexfile Justin A. Lemkul
[gmx-users] charge groups Justin A. Lemkul
Fwd: [gmx-users] Invalid atom number 6415 in indexfile Justin A. Lemkul
[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS Justin A. Lemkul
[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS Justin A. Lemkul
[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS Justin A. Lemkul
[gmx-users] Melittin in Methanol....... Justin A. Lemkul
[gmx-users] grompp error: Incorrect number of parameters - found 1, expected 2 or 4 Justin A. Lemkul
Fwd: [gmx-users] Invalid atom number 6415 in indexfile Justin A. Lemkul
Fwd: [gmx-users] Invalid atom number 6415 in indexfile Justin A. Lemkul
[gmx-users] question about ligand Justin A. Lemkul
[gmx-users] calculating surface tension Justin A. Lemkul
[gmx-users] compiling gromacs Justin A. Lemkul
[gmx-users] IN4 molecule type error Justin A. Lemkul
[gmx-users] gromacs 3.3.3 vs 4.0.3 performance Justin A. Lemkul
[gmx-users] energy groups Justin A. Lemkul
[gmx-users] Melittin in methanol... Justin A. Lemkul
[gmx-users] Melittin in methanol... Justin A. Lemkul
[gmx-users] COM motion removal Justin A. Lemkul
[gmx-users] "No default proper Dih.type Justin A. Lemkul
[gmx-users] restraining Ca2+ ion Marc F. Lensink
[gmx-users] MD simulating cyclic peptides including D-aminoacids Joern Lenz
[gmx-users] MD simulating cyclic peptides including D-aminoacids Joern Lenz
[gmx-users] S2Min and S2Max Dechang Li
[gmx-users] calculation of the order parameter S2 Dechang Li
[gmx-users] Re: Re: calculation of the order parameter S2 (Xavier Periole) Dechang Li
[gmx-users] Re: Re: calculation of the order parameter S2 (Xavier Periole) Dechang Li
[gmx-users] g_rotacf, order parameter S2 problem Dechang Li
[gmx-users] How to determine if it is the pi-pi stacking interaction? Chih-Ying Lin
[gmx-users] Light-controlled MD Chih-Ying Lin
[gmx-users] After MD simulation => put the sample under Scattering Chih-Ying Lin
[gmx-users] After MD simulation => put the sample under Chih-Ying Lin
[gmx-users] Simulation Techniques Chih-Ying Lin
[gmx-users] MD vs Scattering Chih-Ying Lin
[gmx-users] MD vs Scattering Chih-Ying Lin
[gmx-users] Inconsistent shifts Problem when using g_rdf Lin, Pohan
[gmx-users] Inconsistent shifts Problem when using g_rdf Lin, Pohan
[gmx-users] Gromacs 4.0.3 released Erik Lindahl
[gmx-users] Rosetta Academic Training Workshop Nir London
[gmx-users] "nstlist=-1" and performance problem LuLanyuan
[gmx-users] "nstlist=-1" and performance problem LuLanyuan
[gmx-users] "nstlist=-1" and performance problem LuLanyuan
[gmx-users] "nstlist=-1" and performance problem LuLanyuan
[gmx-users] "nstlist=-1" dosen't work for parallel runs LuLanyuan
[gmx-users] "nstlist=-1" dosen't work for parallel runs LuLanyuan
[gmx-users] g_clustsize bug ( (fwd) Alessandro Magliano
[gmx-users] Re: Re: g_clustsize bug Alessandro Magliano
[gmx-users] question about ligand Xiang Mao
[gmx-users] RE: How to output a single index group Omer Markovitch
[gmx-users] putting extra molecules in the box with genbox Oliver Masur
[gmx-users] grompp error: Incorrect number of parameters - found 1, expected 2 or 4 Oliver Masur
[gmx-users] rcoulomb, rlist David Mobley
[gmx-users] Re: free energy with TIP4P bug fixed David Mobley
[gmx-users] TIP4P/TIP4P-Ew bug potentially affecting all calculations done with TIP4P with some (few?) exceptions David Mobley
[gmx-users] free energy with TIP4P bug fixed David Mobley
[gmx-users] Problem with 4.0.3 Stephen P. Molnar
[gmx-users] Problem with 4.0.3 Stephen P. Molnar
[gmx-users] Problem with 4.0.3 Stephen P. Molnar
[gmx-users] Abu added you as a friend on Reunion.com! Abu Naser
[gmx-users] Abu added you as a friend on Reunion.com! Abu Naser
[gmx-users] phi/psi Chris Neale
[gmx-users] g_mindist -pi gives segfault in 3.3.3 and 4.0.2 but not 3.3.1 Chris Neale
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Chris Neale
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Chris Neale
[gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no. Chris Neale
[gmx-users] range of magnitude for force constant Terry Nelson
[gmx-users] Best performace with 0 core for PME calcuation Nicolas
[gmx-users] Best performace with 0 core for PME calcuation Nicolas
[gmx-users] Best performace with 0 core for PME calcuation Nicolas
[gmx-users] Best performace with 0 core for PME calcuation Nicolas
[gmx-users] Best performace with 0 core for PME calcuation Nicolas
[gmx-users] REMD protein-ligand separation David Osguthorpe
[gmx-users] polyalanine melt XAvier Periole
[gmx-users] restore pbc after a rotation XAvier Periole
[gmx-users] about the run program in gromacs 4.0.3 XAvier Periole
[gmx-users] restore pbc after a rotation XAvier Periole
[gmx-users] restore pbc after a rotation XAvier Periole
[gmx-users] "nstlist=-1" and performance problem XAvier Periole
[gmx-users] calculation of the order parameter S2 Xavier Periole
[gmx-users] Re: Re: calculation of the order parameter S2 (Xavier Periole) Xavier Periole
[gmx-users] Re: Re: calculation of the order parameter S2 (Xavier Periole) Xavier Periole
[gmx-users] eigenvalues Xavier Periole
[gmx-users] g_rotacf, order parameter S2 problem Xavier Periole
[gmx-users] eigenvalues TJ Piggot
[gmx-users] REMD protein-ligand separation Iakov Polyak
[gmx-users] Creating top-file for molecules not included in the forcefield Sascha Rehm
[gmx-users] x2top Marius Retegan
[gmx-users] IN4 molecule type error Ms. Aswathy S
[gmx-users] Help Jason Holley - Untamed African Safaris
[gmx-users] Domain Decomposision and Frozen Groups Reza Salari
[gmx-users] Domain Decomposision and Frozen Groups Reza Salari
[gmx-users] Domain Decomposision and Frozen Groups Reza Salari
[gmx-users] Branched topology / Converting from psf Roland Schulz
[gmx-users] eigenvalues Monika Sharma
[gmx-users] eigenvalues Monika Sharma
[gmx-users] Re: decoupling charge while maintaining intramolecular potentials (chris.neale@utoronto.ca) Michael Shirts
[gmx-users] Re: decoupling charge while maintaining intramolecular potentials Michael Shirts
[gmx-users] Qestion about how to define groups by chain id in a protein ? Liu Shiyong
[gmx-users] Qestion about how to define groups by chain id in a protein ? Liu Shiyong
[gmx-users] Qestion about how to define groups by chain id in a protein ? Liu Shiyong
[gmx-users] Qestion about how to define groups by chain id in a protein ? Liu Shiyong
[gmx-users] Is there any option to output interaction energy based on energy groups? Liu Shiyong
[gmx-users] Invalid atom number 6415 in indexfile Liu Shiyong
[gmx-users] Invalid atom number 6415 in indexfile Liu Shiyong
[gmx-users] charge groups Liu Shiyong
Fwd: [gmx-users] Invalid atom number 6415 in indexfile Liu Shiyong
Fwd: [gmx-users] Invalid atom number 6415 in indexfile Liu Shiyong
Fwd: [gmx-users] Invalid atom number 6415 in indexfile Liu Shiyong
Fwd: [gmx-users] Invalid atom number 6415 in indexfile Liu Shiyong
[gmx-users] energy groups Liu Shiyong
[gmx-users] mdrun output conformation file loses chain identifier Lee Soin
[gmx-users] mdrun output conformation file loses chain identifier Lee Soin
[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS Yanmei Song
[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS Yanmei Song
[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS Yanmei Song
[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS Yanmei Song
[gmx-users] Question about the pairs parameters Yanmei Song
[gmx-users] S2Min and S2Max David van der Spoel
[gmx-users] Generalized Born David van der Spoel
[gmx-users] "symtab" error mesaage using gromacs402 David van der Spoel
[gmx-users] "symtab" error mesaage using gromacs402 David van der Spoel
[gmx-users] RMSF and temperature factors David van der Spoel
[gmx-users] minimization problems David van der Spoel
[gmx-users] minimization problem David van der Spoel
[gmx-users] Equilibrating systems of rigid molecules David van der Spoel
[gmx-users] Best performace with 0 core for PME calcuation David van der Spoel
[gmx-users] g_rotacf, order parameter S2 problem David van der Spoel
[gmx-users] Problem with X2top command David van der Spoel
[gmx-users] g_clustsize bug ( (fwd) David van der Spoel
[gmx-users] GROMACS 4.0.2 error Value of 'multiplicity' in Proper Dih. is 0, David van der Spoel
[gmx-users] Re: Re: g_clustsize bug David van der Spoel
[gmx-users] MD simulating cyclic peptides including D-aminoacids David van der Spoel
[gmx-users] Inconsistent shifts Problem when using g_rdf David van der Spoel
[gmx-users] Problem with 4.0.3 David van der Spoel
[gmx-users] Problem with 4.0.3 David van der Spoel
[gmx-users] g_clustsize David van der Spoel
[gmx-users] Simulation Techniques David van der Spoel
[gmx-users] g_clussize. strange error David van der Spoel
[gmx-users] Numbering in xtc and in conf.gro. Does it coincide? David van der Spoel
[gmx-users] Bug in g_energy for calculating heat capacity? David van der Spoel
[gmx-users] Is there any option to output interaction energy based on energy groups? David van der Spoel
[gmx-users] g_energy non-interactive David van der Spoel
[gmx-users] g_rms: Too many iterations in routine JACOBI David van der Spoel
[gmx-users] g_rms: Too many iterations in routine JACOBI David van der Spoel
[gmx-users] g_rms: Too many iterations in routine JACOBI David van der Spoel
[gmx-users] reg: simulations in presence of electric fields David van der Spoel
[gmx-users] Segmentation fault with genbox -nmol (version 4.0.3) David van der Spoel
[gmx-users] Segmentation fault with genbox -nmol (version 4.0.3) David van der Spoel
[gmx-users] x2top David van der Spoel
[gmx-users] liquid vapour David van der Spoel
[gmx-users] gromacs 3.3.3 vs 4.0.3 performance David van der Spoel
[gmx-users] diffusion of oxygen in water Sunil Thapa
[gmx-users] Thank you Sunil Thapa
[gmx-users] CNS to Gromos87 Candice Viddal
[gmx-users] ftp Server Down? Dallas B. Warren
[gmx-users] Re FTP server down Dallas B. Warren
[gmx-users] eigenvalues Tsjerk Wassenaar
[gmx-users] eigenvalues Tsjerk Wassenaar
[gmx-users] re : heme group Tsjerk Wassenaar
[gmx-users] eigenvalues Tsjerk Wassenaar
[gmx-users] eigenvalues Tsjerk Wassenaar
[gmx-users] atom H is missing in the first residue in a chain Tsjerk Wassenaar
[gmx-users] is there any Problem in V. 3.3.3? Tsjerk Wassenaar
[gmx-users] how to identify the hydrophobic core residue to calcuate gyration Tsjerk Wassenaar
[gmx-users] MD vs Scattering Tsjerk Wassenaar
[gmx-users] problems with pdb2gmx command Tsjerk Wassenaar
[gmx-users] g_rms: Too many iterations in routine JACOBI Tsjerk Wassenaar
[gmx-users] restore pbc after a rotation Tsjerk Wassenaar
[gmx-users] restore pbc after a rotation Tsjerk Wassenaar
[gmx-users] Help Tsjerk Wassenaar
[gmx-users] query about random velocity generation Tsjerk Wassenaar
[gmx-users] Grompp error in 4.x regarding dihedral multiplicity Sarah Witzke
SV: [gmx-users] Grompp error in 4.x regarding dihedral multiplicity Sarah Witzke
[gmx-users] Forces are large - How to track down the culprit Steffen Wolf
[gmx-users] minimization problems Hongyan Xiao
[gmx-users] minimization problem Hongyan Xiao
[gmx-users] minimization problem Hongyan Xiao
[gmx-users] atom H is missing in the first residue in a chain Zhong Zheng
[gmx-users] atom H is missing in the first residue in a chain Zhong Zheng
[gmx-users] atom H is missing in the first residue in a chain Zhong Zheng
[gmx-users] atom H is missing in the first residue in a chain Zhong Zheng
[gmx-users] How to treat an isolated iron (Fe 2+) Zhong Zheng
[gmx-users] restarting a replica exchange simulations sarbani chattopadhyay
[gmx-users] Re: Onw question about rlist rvdw rcoulomb and nstlist chris.neale at utoronto.ca
[gmx-users] steered MD chris.neale at utoronto.ca
[gmx-users] steered MD chris.neale at utoronto.ca
[gmx-users] how to identify the hydrophobic core residue to calcuate gyration chris.neale at utoronto.ca
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance chris.neale at utoronto.ca
[gmx-users] decoupling charge while maintaining intramolecular potentials chris.neale at utoronto.ca
[gmx-users] why the trajectory file is not output chris.neale at utoronto.ca
[gmx-users] ligand-protein distance restraint chris.neale at utoronto.ca
[gmx-users] Re: decoupling charge while maintaining intramolecular potentials chris.neale at utoronto.ca
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance chris.neale at utoronto.ca
[gmx-users] decoupling charge while maintaining intramolecular potentials chris.neale at utoronto.ca
[gmx-users] range of magnitude for force constant chris.neale at utoronto.ca
[gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no. chris.neale at utoronto.ca
[gmx-users] free energy with TIP4P bug fixed chris.neale at utoronto.ca
[gmx-users] free energy with TIP4P bug fixed chris.neale at utoronto.ca
[gmx-users] free energy with TIP4P bug fixed chris.neale at utoronto.ca
[gmx-users] free energy with TIP4P bug fixed chris.neale at utoronto.ca
[gmx-users] How to run postion restraining step in gromacs dgayathri at ibab.ac.in
[gmx-users] getting started-protein folding dota
[gmx-users] environment variable GMX_MAXCONSTRWARN to -1, drugdesign
[gmx-users] Where can I get .gro and .itp files for different models of water? drugdesign
[gmx-users] wrong format in input file ffamber03.hdb on line drugdesign
[gmx-users] Rugged dgdl curve in turning off/on the charge for Leu friendli
[gmx-users] Rugged dgdl curve in turning off/on the charge for Leu friendli
Subject: Re: Re: [gmx-users] Gromacs 4 bug? patrick fuchs
Subject: Re: Re: [gmx-users] Gromacs 4 bug? patrick fuchs
Subject: Re: Re: [gmx-users] Gromacs 4 bug? patrick fuchs
Subject: Re: Re: [gmx-users] Gromacs 4 bug? patrick fuchs
Subject: Re: Re: [gmx-users] Gromacs 4 bug? patrick fuchs
Subject: Re: Re: [gmx-users] Gromacs 4 bug? patrick fuchs
[gmx-users] Tcl script varsha gautham
[gmx-users] How to get topol.top files from DRGGMX.ITP files? varsha gautham
[gmx-users] "No default proper Dih.type varsha gautham
[gmx-users] Re: Ligt-controlled MD - gmx-users Digest, Vol 57, Issue 58 ggroenh
[gmx-users] Quantitative output for g_mdmat ... a better way to list residue contacts maria goranovic
[gmx-users] problems with pdb2gmx command jaharvey at chem.umass.edu
[gmx-users] phi/psi jayant james
[gmx-users] restraining Ca2+ ion jayant james
[gmx-users] restraining Ca2+ ion jayant james
[gmx-users] restraining Ca2+ ion jayant james
[gmx-users] restraining Ca2+ ion jayant james
[gmx-users] restraining Ca2+ ion jayant james
[gmx-users] restraining Ca2+ ion jayant james
[gmx-users] LINCS warning jayant james
[gmx-users] polyalanine melt li jianguo
[gmx-users] GROMACS 4.0.2 error Value of 'multiplicity' in Proper Dih. is 0, himanshu khandelia
[gmx-users] index file for DPPC koukoulitsa at eie.gr
[gmx-users] Adding water to a lipid bilayer krithika krishnaswamy
[gmx-users] Removing water from sides of bilayer krithika krishnaswamy
[gmx-users] Problem with X2top command krithika krishnaswamy
[gmx-users] Constant Velocity avinash kumar
[gmx-users] pull code avinash kumar
[gmx-users] Carbon tetrachloride avinash kumar
[gmx-users] liquid vapour avinash kumar
[gmx-users] Pressure componets avinash kumar
[gmx-users] calculating surface tension avinash kumar
[gmx-users] pressure component avinash kumar
[gmx-users] query about random velocity generation sangeeta kundu
[gmx-users] chloroform box mohana lakshmi
[gmx-users] chcl3 box mohana lakshmi
[gmx-users] problem with mdrun in parallel huifang liu
[gmx-users] Re:problem with mdrun in parallel huifang liu
[gmx-users] "symtab" error mesaage using gromacs402 xin liu
[gmx-users] "symtab" error mesaage using gromacs402 xin liu
[gmx-users] problem with running mdrun in parallel map110+ at pitt.edu
[gmx-users] is there any Problem in V. 3.3.3? bala ms
[gmx-users] how to get charge group number (cgnr) naimah haron naimah
[gmx-users] g_rms: Too many iterations in routine JACOBI nishtha pandey
[gmx-users] g_rms: Too many iterations in routine JACOBI nishtha pandey
[gmx-users] g_rms: Too many iterations in routine JACOBI nishtha pandey
[gmx-users] g_rms: Too many iterations in routine JACOBI nishtha pandey
[gmx-users] about the run program in gromacs 4.0.3 anirban polley
[gmx-users] To run in gromacs 4.0.3 in cluster anirban polley
[gmx-users] steered MD rams rams
[gmx-users] smd_forces rams rams
[gmx-users] electric field effects rams rams
[gmx-users] reg: simulations in presence of electric fields rams rams
[gmx-users] reg: simulations in presence of electric fields rams rams
[gmx-users] dear KUTZNER (flow control) ha salem
[gmx-users] flow control ha salem
[gmx-users] low latency ha salem
[gmx-users] example lookup tables sam.moors at chem.kuleuven.be
[gmx-users] temperature too high with reaction field sam.moors at chem.kuleuven.be
[gmx-users] error using generic kernel sam.moors at chem.kuleuven.be
[gmx-users] re :about converting output sanjay23 at iitb.ac.in
[gmx-users] eigenvalues sanjay23 at iitb.ac.in
[gmx-users] re : heme group sanjay23 at iitb.ac.in
[gmx-users] eigenvalues sanjay23 at iitb.ac.in
[gmx-users] Melittin in Methanol....... sharada
[gmx-users] Melittin in Methanol....... sharada
[gmx-users] Melittin in methanol... sharada
[gmx-users] Melittin in methanol... sharada
[gmx-users] Melittin in methanol... sharada
[gmx-users] how to identify the hydrophobic core residue to calcuate gyration ravi sharma
[gmx-users] COM motion removal priyanka srivastava
[gmx-users] unit of the opls-aa force field in Gromacs package sunnytov at gmail.com
[gmx-users] How does MDrun number atoms? ttrudeau
[gmx-users] Re: How does MDrun number atoms? ttrudeau
[gmx-users] Onw question about rlist rvdw rcoulomb and nstlist xuji

Last message date: Sat Jan 31 13:46:53 CEST 2009
Archived on: Sat Jan 31 13:47:34 CEST 2009

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