April 2008 Archives by author

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Starting: Tue Apr 1 00:33:08 CEST 2008
Ending: Wed Apr 30 17:21:19 CEST 2008
Messages: 569

[gmx-users] Talk slides from the Gromacs Stanford 2008 workshop Mu Yuguang (Dr)
[gmx-users] Warning message with 3.3.3 but not with 3.3.1 =?GB2312?B?1tyyqA==?=
[gmx-users] Entropy correction in PMF Ángel Piñeiro
[gmx-users] Entropy correction in PMF Ángel Piñeiro
[gmx-users] Entropy correction in PMF Ángel Piñeiro
[gmx-users] problem with g_order Ángel Piñeiro
[gmx-users] B factor and R factor Miguel Ortiz-Lombardía
[gmx-users] gromacs analysis performance on a dual core suse box. Stéphane Téletchéa
[gmx-users] call for help =?gb2312?B?stzV6Q==?=
[gmx-users] call for help =?gb2312?B?stzV6Q==?=
[gmx-users] Problem with ref_t and tau_t values Miguel Fernández Oliva
[gmx-users] converting scp to tip4p - pdb2gmx bug? Martin Höfling
[gmx-users] about nmr refinement Rogelio Hernández
[gmx-users] about NMR Refinement Rogelio Hernández
[gmx-users] g msd freeze Kateřina Hynštová
[gmx-users] g msd freeze Kateřina Hynštová
[gmx-users] g_msd freeze Kateřina Hynštová
[gmx-users] RE: g_angle Kateřina Hynštová
[gmx-users] Help, cannot compile with mpi Martin Höfling
[gmx-users] Blue Gene/P Mark Abraham
[gmx-users] Blue Gene/P Mark Abraham
[gmx-users] how to put two rmsd plot in one plot Mark Abraham
[gmx-users] atomtypes, parameters in file do not match parameters in manual Mark Abraham
[gmx-users] To the GMX developers-distance restraints Mark Abraham
[gmx-users] RMSD VS. parallel simulation Mark Abraham
[gmx-users] segmentation fault Mark Abraham
[gmx-users] Re: RMSD VS. parallel simulation Mark Abraham
[gmx-users] How to specify conection between 2 molecule in the top file? Mark Abraham
[gmx-users] How to specify conection between 2 molecule in the top file? Mark Abraham
[gmx-users] Double or single precision Mark Abraham
[gmx-users] Re: Re: RMSD VS. parallel simulation (Mark Abraham) Mark Abraham
[gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode Mark Abraham
[gmx-users] g_rmsf Mark Abraham
[gmx-users] Langevin Dynamic "bd-temp" parameter Mark Abraham
[gmx-users] trjconv chaged the chain names of multi-chain complex? Mark Abraham
[gmx-users] g msd freeze Mark Abraham
[gmx-users] g_msd freeze Mark Abraham
[gmx-users] query about diferent cutoffs Mark Abraham
[gmx-users] Help improving multi core processor's speed Mark Abraham
[gmx-users] error for runing second simulation using the topology file Mark Abraham
[gmx-users] How can I install Gromacs on Window XP? Mark Abraham
[gmx-users] Can GROMACS simulate the bond forming and breaking Mark Abraham
[gmx-users] call for help Mark Abraham
[gmx-users] mpi error Mark Abraham
[gmx-users] Help uninstall and recompiling Mark Abraham
[gmx-users] Bad .tpr or .xtc files? Mark Abraham
[gmx-users] MTH force field Mark Abraham
[gmx-users] a problem about the residence Mark Abraham
[gmx-users] How to heat a system and equilibrate it? Mark Abraham
[gmx-users] cholesterol distortion Mark Abraham
[gmx-users] How to heat a system and equilibrate it? Mark Abraham
[gmx-users] Problem running grompp Mark Abraham
[gmx-users] log file has converted into.log.swp file Mark Abraham
[gmx-users] density and CG MARTINI force field Mark Abraham
[gmx-users] calculating CD spectra Mark Abraham
[gmx-users] Why my system collapsed? Mark Abraham
[gmx-users] GTP in topology Mark Abraham
[gmx-users] reg hybrid dynamics Mark Abraham
[gmx-users] about fourier grid Mark Abraham
[gmx-users] dielectric constant Mark Abraham
[gmx-users] dielectric constant Mark Abraham
[gmx-users] Conformation search! Mark Abraham
[gmx-users] water in channel by "Dowser" Mark Abraham
[gmx-users] hydrogen bonds of peptide with lipids Mark Abraham
[gmx-users] acetone parameter Mark Abraham
[gmx-users] Conformation search! Mark Abraham
[gmx-users] trjconv error Mark Abraham
[gmx-users] water can't freeze Mark Abraham
[gmx-users] confirm bdd22a55a5075c60cd9dc4382a75e0b7689a1d11 Mark Abraham
[gmx-users] Error of mdrun Mark Abraham
[gmx-users] Error of mdrun Mark Abraham
[gmx-users] a question Mark Abraham
[gmx-users] the number of water molecules Mark Abraham
[gmx-users] rtp file Mark Abraham
[gmx-users] Choose of force fields of ethanol and B-DNA with 15 base pairs Mark Abraham
[gmx-users] request for default word-wrap on the mailing list Mark Abraham
[gmx-users] Range checking error Mark Abraham
[gmx-users] Loop displacement calculation? Mark Abraham
[gmx-users] Fatal error: Could not write energies Mark Abraham
[gmx-users] Re: ice box contact water box Mark Abraham
[gmx-users] Loop displacement calculation? Mark Abraham
[gmx-users] grompp error, invalid line in .gro file Mark Abraham
[gmx-users] how to use GROMACS to model carbon nanotubes Mark Abraham
[gmx-users] trjconv error Mark Abraham
[gmx-users] A question Mark Abraham
[gmx-users] position restraints Mark Abraham
[gmx-users] position restraints Mark Abraham
[gmx-users] position restraints Mark Abraham
[gmx-users] Infinite system PBC and Bonded Interaction Mark Abraham
[gmx-users] Ion Parametrization in OPLS-AA forcefield Mark Abraham
[gmx-users] Defining charges: [atomtypes] vs [atoms] Mark Abraham
[gmx-users] about NMR Refinement Mark Abraham
[gmx-users] problem running parallel simulation regarding the md log file Mark Abraham
[gmx-users] Understanding about OPLS-aa for lipids Mark Abraham
[gmx-users] negative eigenvalues occured and not "nearly zero" Mark Abraham
[gmx-users] negative eigenvalues occured and not "nearly zero" Mark Abraham
[gmx-users] Unable to continue the simulation Mark Abraham
[gmx-users] question Mark Abraham
[gmx-users] Can any body suggest me how do I generate the initial structure with the pre-quil. membrane and the small molecules put on top of it and check the effect of UV on it? Mark Abraham
[gmx-users] Infinite system PBC and Bonded Interaction Mark Abraham
[gmx-users] Running simulations in different versions Mark Abraham
[gmx-users] Need help with installation on Itanium2 Mark Abraham
[gmx-users] Need help with installation on Itanium2 Mark Abraham
[gmx-users] Re: gmx-users Digest, Vol 48, Issue 97 Mark Abraham
[gmx-users] help with gromacs install in opensuse 64b Mark Abraham
[gmx-users] syntax for switching between multiple position restraint .itp in the .top file Mark Abraham
[gmx-users] help with gromacs install in opensuse 64b Mark Abraham
[gmx-users] force field parameters for hydronium Mark Abraham
[gmx-users] Help after gromacs installation Mark Abraham
[gmx-users] a huge topology parameter c1 (angles) Mark Abraham
[gmx-users] upgrade version - "make distclean"? Mark Abraham
[gmx-users] old patch for slow networks Jones de Andrade
[gmx-users] CPMD and gmx Vasilii Artyukhov
[gmx-users] water can't freeze Vasilii Artyukhov
[gmx-users] Lipid forcefield to use with TIP5P/OPLSaa Vasilii Artyukhov
[gmx-users] Lipid forcefield to use with TIP5P/OPLSaa Vasilii Artyukhov
[gmx-users] Need help with installation on Itanium2 Vasilii Artyukhov
[gmx-users] Need help with installation on Itanium2 Vasilii Artyukhov
[gmx-users] Need help with installation on Itanium2 Vasilii Artyukhov
[gmx-users] force field parameters for hydronium Vasilii Artyukhov
[gmx-users] force field parameters for hydronium Vasilii Artyukhov
[gmx-users] log file has converted into.log.swp file Anamika Awasthi
[gmx-users] about fourier grid Anamika Awasthi
[gmx-users] infinite molecule problem - Follow up info Computational Structural BIology
[gmx-users] angle analysis Zuzana Benkova
[gmx-users] g_angle Zuzana Benkova
[gmx-users] inconsistent shifts Bert
[gmx-users] Re: gmx-users Digest, Vol 48, Issue 24 Bert
[gmx-users] query about .xpm file Bert
[gmx-users] force field parameters for hydronium Bert
[gmx-users] Re: gmx-users Digest, Vol 48, Issue 82 Bonner, Carl E.
[gmx-users] dynamic of a peptide in a mixture TFE/H2O ( 30/70 %) Luisa Calvanese
[gmx-users] FW: dynamic of a peptide in a mixture TFE/H2O ( 30/70 %) Luisa Calvanese
[gmx-users] about pull code Yunierkis Perez Castillo
[gmx-users] x2top, error generating topology Vitaly Chaban
[gmx-users] Re: x2top, error generating topology Vitaly Chaban
[gmx-users] How to heat a system and equilibrate it? Vitaly Chaban
[gmx-users] How to heat a system and equilibrate it? Vitaly Chaban
[gmx-users] epsilon in mdp Vitaly Chaban
[gmx-users] DCCM Ramya Cherukupalli
[gmx-users] DCCM Ramya Cherukupalli
[gmx-users] How to center my trimer in my simulation box. Ilya Chorny
[gmx-users] How to center my trimer in my simulation box. Ilya Chorny
[gmx-users] How to center my trimer in my simulation box. Ilya Chorny
[gmx-users] How to center my trimer in my simulation box. Ilya Chorny
[gmx-users] Converting OPLS parameters Ramon Crehuet
[gmx-users] How constraint structure not conformation Anthony Cruz
[gmx-users] Conformation search! Anthony Cruz
[gmx-users] Conformation search! Anthony Cruz
[gmx-users] Conformation search! Anthony Cruz
[gmx-users] cholesterol distortion Jian Dai
[gmx-users] continuation run in parallel with shuffle and sort option Ananya Debnath
[gmx-users] re:continuation run in parallel with shuffle and sort option Ananya Debnath
[gmx-users] make_ndx for separating all atoms in two monolayers in a bilayer Ananya Debnath
[gmx-users] How to center my trimer in my simulation box. Alan Dodd
[gmx-users] problem with g_order Alan Dodd
[gmx-users] Help, cannot compile with mpi Florian Dommert
[gmx-users] Help, cannot compile with mpi Florian Dommert
[gmx-users] help with gromacs install in opensuse 64b Florian Dommert
[gmx-users] Configure (beginner level question) Florian Dommert
[gmx-users] Polarizative models for water Dmitri Dubov
[gmx-users] Polarizative models for water Dmitri Dubov
[gmx-users] Polarizative models for water Dmitri Dubov
[gmx-users] error with pdb2gmx when using AMBER ff in GROMACS OZGE ENGIN
[gmx-users] how to put two rmsd plot in one plot Diego Enry
[gmx-users] Help, cannot compile with mpi Diego Enry
[gmx-users] help with gromacs install in opensuse 64b Diego Enry
[gmx-users] a problem about the residence L. Michel Espinoza-Fonseca
[gmx-users] Infinite system PBC and Bonded Interaction Eudes Fileti
[gmx-users] Infinite system PBC and Bonded Interaction Eudes Fileti
[gmx-users] Infinite system PBC and Bonded Interaction Eudes Fileti
[gmx-users] Conformation search! Ran Friedman
[gmx-users] residual negative charge? Ran Friedman
[gmx-users] water can't freeze Ran Friedman
[gmx-users] urgent question Ran Friedman
[gmx-users] Converting OPLS parameters Ran Friedman
[gmx-users] set up topology in free energy calculations Maik Goette
[gmx-users] GTP in topology Maik Goette
[gmx-users] free energy calculation Maik Goette
[gmx-users] CPMD and gmx Andrey V Golovin
[gmx-users] CPMD and gmx Andrey V Golovin
[gmx-users] Error gmxtest Nadia Gro
[gmx-users] Error gmxtest Nadia Gro
[gmx-users] Error gmxtest Nadia Gro
[gmx-users] gromacs analysis performance on a dual core suse box. Florian Haberl
[gmx-users] How can I install Gromacs on Window XP? Hero
[gmx-users] Water flow through Carbon Nanotube Hero
[gmx-users] structure files of water and CNT Hero
[gmx-users] water flow in CNT Hero
[gmx-users] water in channel by "Dowser" Hero
[gmx-users] Water in graphite plates Hero
[gmx-users] CNT Hero
[gmx-users] Re: CNT Hero
[gmx-users] x2top error in CNT simulation Hero
[gmx-users] Re: x2top error in CNT simulation (David van der Spoel) Hero
[gmx-users] x2top error in CNT simulation on Gromacs 3.3.3 Hero
[gmx-users] Blue Gene/P Berk Hess
[gmx-users] restraints or constraints over two molecules Berk Hess
[gmx-users] difference between pbc = full and pbc =xy Berk Hess
[gmx-users] VdW and Coulomb SR contribution to dVdl in thermodynamic integration Berk Hess
[gmx-users] DCCM Berk Hess
[gmx-users] 3.3.2 -b option not functioning as expected Berk Hess
[gmx-users] grompp error, invalid line in .gro file Berk Hess
FW: [gmx-users] couette flow Berk Hess
[gmx-users] couette flow Berk Hess
[gmx-users] couette flow Berk Hess
[gmx-users] Entropy correction in PMF Berk Hess
[gmx-users] problem running parallel simulation regarding the md log file Berk Hess
[gmx-users] negative eigenvalues occured and not "nearly zero" Berk Hess
[gmx-users] negative eigenvalues occured and not "nearly zero" Berk Hess
[gmx-users] Range checking error SeungPyo Hong
[gmx-users] Loop displacement calculation? SeungPyo Hong
[gmx-users] Loop displacement calculation? SeungPyo Hong
[gmx-users] Loop displacement calculation? SeungPyo Hong
[gmx-users] gmxtest, error during pdb2gmx step. SeungPyo Hong
[gmx-users] membrane stabilisation Jochen Hub
[gmx-users] NVT and NVE JMandumpal
[gmx-users] NVT and NVE JMandumpal
[gmx-users] NVT and NVE JMandumpal
[gmx-users] Unit of diffusion coefficient JMandumpal
[gmx-users] Epsilon in ffoplsaanb.itp JMandumpal
[gmx-users] acetone parameter JMandumpal
[gmx-users] restraints or constraints over two molecules Eric Jakobsson
[gmx-users] how to simulate 2 structures together Radhika Jaswal
[gmx-users] Water in graphite plates Raymond C. Fort Jr.
[gmx-users] GTP topology generation in OPLS-AA force field Shankar Prasad Kanaujia
[gmx-users] atomtypes, parameters in file do not match parameters in manual Andreas Kring
[gmx-users] Wrong heat capacity (water) Andreas Kring
[gmx-users] Re: Wrong heat capacity (water) Andreas Kring
[gmx-users] grompp error, invalid line in .gro file Andreas Kring
[gmx-users] grompp error, invalid line in .gro file Andreas Kring
[gmx-users] grompp error, invalid line in .gro file [SOLVED] Andreas Kring
[gmx-users] AA not present in the ffG43a1.rtp Kukol, Andreas
[gmx-users] carbon double bond parameters Kukol, Andreas
[gmx-users] Error in topology file Kukol, Andreas
[gmx-users] area per lipid Kukol, Andreas
[gmx-users] Lincs error and explosion of the system Egidijus Kuprusevicius
[gmx-users] a huge topology parameter c1 (angles) Egidijus Kuprusevicius
[gmx-users] old patch for slow networks Carsten Kutzner
[gmx-users] about fourier grid Carsten Kutzner
[gmx-users] how to make choices of COM in the system with freeze group? Daniel Larsson
[gmx-users] problem running parallel simulation regarding the md log file Alif M Latif
[gmx-users] crash with LINCS WARNING LeeHwan-kyu
[gmx-users] how to simulate 2 structures together Justin A. Lemkul
[gmx-users] how to calculate the RMSD of the peptide conformation relative to the NMR structure? Justin A. Lemkul
[gmx-users] oxygen gas parameters for simulation Justin A. Lemkul
[gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode Justin A. Lemkul
[gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode Justin A. Lemkul
[gmx-users] Re: gmx-users Digest, Vol 48, Issue 9 Justin A. Lemkul
[gmx-users] about tip3p water model Justin A. Lemkul
[gmx-users] (no subject) Justin A. Lemkul
[gmx-users] Error gmxtest Justin A. Lemkul
[gmx-users] trjconv chaged the chain names of multi-chain complex? Justin A. Lemkul
[gmx-users] g msd freeze Justin A. Lemkul
[gmx-users] AA not present in the ffG43a1.rtp Justin A. Lemkul
[gmx-users] mix solvent Justin A. Lemkul
[gmx-users] recognising phos group Justin A. Lemkul
[gmx-users] gromacs trajctory mmpbsa Justin A. Lemkul
[gmx-users] crash with LINCS WARNING Justin A. Lemkul
[gmx-users] xpm2ps help Justin A. Lemkul
[gmx-users] Minimize error Justin A. Lemkul
[gmx-users] structure files of water and CNT Justin A. Lemkul
[gmx-users] Re: Where can I find structure files of water and CNT? Justin A. Lemkul
[gmx-users] GTP in topology Justin A. Lemkul
[gmx-users] hydrogen bonds of peptide with lipids Justin A. Lemkul
[gmx-users] FW: dynamic of a peptide in a mixture TFE/H2O ( 30/70 %) Justin A. Lemkul
[gmx-users] hydrogen bonds of peptide with lipids Justin A. Lemkul
[gmx-users] Concatenate TPR files after restart Justin A. Lemkul
[gmx-users] Free energy calculation Justin A. Lemkul
[gmx-users] position restraints Justin A. Lemkul
[gmx-users] CNT Justin A. Lemkul
[gmx-users] grompp error, invalid line in .gro file Justin A. Lemkul
[gmx-users] urgent question Justin A. Lemkul
[gmx-users] position restraints Justin A. Lemkul
[gmx-users] position restraints Justin A. Lemkul
[gmx-users] position restraints Justin A. Lemkul
[gmx-users] position restraints Justin A. Lemkul
[gmx-users] position restraints Justin A. Lemkul
[gmx-users] Problem with ref_t and tau_t values Justin A. Lemkul
[gmx-users] Re:Understanding about OPLS-aa lipids Justin A. Lemkul
[gmx-users] Re:Understanding about OPLS-aa lipids Justin A. Lemkul
[gmx-users] converting scp to tip4p - pdb2gmx bug? Justin A. Lemkul
[gmx-users] help with mpirun and system exploding during heating Justin A. Lemkul
[gmx-users] help with gromacs install in opensuse 64b Justin A. Lemkul
[gmx-users] Question about gcc version Justin A. Lemkul
[gmx-users] Lincs error and explosion of the system Justin A. Lemkul
[gmx-users] area per lipid Justin A. Lemkul
[gmx-users] Question about gcc version Justin A. Lemkul
[gmx-users] restart run problem Justin A. Lemkul
[gmx-users] Question about gcc version Justin A. Lemkul
[gmx-users] Re:restart run problem Justin A. Lemkul
[gmx-users] Help after gromacs installation Justin A. Lemkul
[gmx-users] GTP topology generation in OPLS-AA force field Justin A. Lemkul
[gmx-users] Lipid forcefield to use with TIP5P/OPLSaa Marc F. Lensink
[gmx-users] Lipid forcefield to use with TIP5P/OPLSaa Marc F. Lensink
[gmx-users] RMSD VS. parallel simulation DeChang Li
[gmx-users] Re: RMSD VS. parallel simulation Dechang Li
[gmx-users] Re: Re: RMSD VS. parallel simulation (Mark Abraham) Dechang Li
[gmx-users] the number of water molecules Dechang Li
[gmx-users] Re: the number of water molecules (Jian Zou) Dechang Li
[gmx-users] how to put two rmsd plot in one plot Rui Li
[gmx-users] Re: how to put two rmsd plot in one plot Rui Li
[gmx-users] about tip3p water model Rui Li
[gmx-users] how to control temperature Rui Li
[gmx-users] about specbond Rui Li
[gmx-users] Talk slides from the Gromacs Stanford 2008 workshop Erik Lindahl
[gmx-users] Talk slides from the Gromacs Stanford 2008 workshop Erik Lindahl
[gmx-users] Blue Gene/P Hannes Loeffler
[gmx-users] crash with LINCS WARNING Hannes Loeffler
[gmx-users] genbox memory problem LuLanyuan
[gmx-users] Unable to compile Gromacs-CVS because calcpot.c Daniel Adriano Silva M
[gmx-users] Unable to compile Gromacs-CVS because calcpot.c Daniel Adriano Silva M
[gmx-users] Problem running grompp Edward M
[gmx-users] (no subject) Mahnam
[gmx-users] mix solvent Mahnam
[gmx-users] call for help about the hydration number Erik Marklund
[gmx-users] Re: the number of water molecules (Jian Zou) Erik Marklund
[gmx-users] water can't freeze Erik Marklund
[gmx-users] A question Erik Marklund
[gmx-users] syntax for switching between multiple position restraint .itp in the .top file Low Soo Mei
[gmx-users] Re: syntax for switching between multiple position restraint .itp in the .top file Low Soo Mei
[gmx-users] gmx_sumi src/mdlib/rf_util.c fix Low Soo Mei
[gmx-users] upgrade version - "make distclean"? Low Soo Mei
[gmx-users] Re: upgrade version - "make distclean"? Low Soo Mei
[gmx-users] NVT and NVE Markus Miettinen
[gmx-users] NVT and NVE Markus Miettinen
[gmx-users] Re: Free energy David Mobley
[gmx-users] Entropy correction in PMF David Mobley
[gmx-users] How to specify conection between 2 molecule in the top file? Frankie Montenegro
[gmx-users] How to specify conection between 2 molecule in the top file? Frankie Montenegro
[gmx-users] AFMM parameter refinement Abu Naser
[gmx-users] continuation run in parallel with shuffle and, sort option Chris Neale
[gmx-users] 3.3.2 -b option not functioning as expected Chris Neale
[gmx-users] Lipid forcefield to use with TIP5P/OPLSaa Chris Neale
[gmx-users] 3.3.2 -b option not functioning as expected Chris Neale
[gmx-users] mdrun exectutable Marilisa Neri
[gmx-users] Re: gmx-users Digest, Vol 48, Issue 9 Collins Nganou
[gmx-users] CO2.pdb Collins Nganou
[gmx-users] MTH force field Collins Nganou
[gmx-users] Choose of force fields of ethanol and B-DNA with 15 base pairs Collins Nganou
[gmx-users] mdrun exectutable Xavier Periole
[gmx-users] How to center my trimer in my simulation box. Xavier Periole
[gmx-users] GTP topology generation in OPLS-AA force field TJ Piggot
[gmx-users] Configure (beginner level question) Ramadas Sunil Pophale
[gmx-users] Configure (Beginner level question) Ramadas Sunil Pophale
[gmx-users] topolbuild 1.1, update to an all-atoms model gromacs topology generator Bruce Ray
[gmx-users] xpm2ps help Rigden, LucianeVMello
[gmx-users] residual negative charge? Victor Manuel Rosas-Garcia
[gmx-users] g_rmsf SWAPNA
[gmx-users] water can't freeze Sagittarius
[gmx-users] restraints or constraints over two molecules Thomas Schlesier
[gmx-users] Re: restraints or constraints over two molecules Thomas Schlesier
[gmx-users] couette flow Matthew Schneemilch
[gmx-users] couette flow Matthew Schneemilch
[gmx-users] calculating CD spectra Marieke Schor
[gmx-users] Talk slides from the Gromacs Stanford 2008 workshop Satyan Sharma
[gmx-users] question Satyan Sharma
[gmx-users] trjconv chaged the chain names of multi-chain complex? Liu Shiyong
[gmx-users] Co2.pdb Ricardo Soares
[gmx-users] Concatenate TPR files after restart Ricardo Soares
[gmx-users] Concatenate TPR files after restart Ricardo Soares
[gmx-users] Minimize error Ana Carolina Sodero
[gmx-users] Error gmxtest David van der Spoel
[gmx-users] Error gmxtest David van der Spoel
[gmx-users] genion problem: is replacing 84 water molecules instead of 200 David van der Spoel
[gmx-users] Test-set problem with Gromacs 3.3.3 David van der Spoel
[gmx-users] atomtypes, parameters in file do not match parameters in manual David van der Spoel
[gmx-users] using dummy atoms David van der Spoel
[gmx-users] hydrogen simulation and topology file David van der Spoel
[gmx-users] mdrun exectutable David van der Spoel
[gmx-users] inconsistent shifts David van der Spoel
[gmx-users] x2top, error generating topology David van der Spoel
[gmx-users] a problem about the residence David van der Spoel
[gmx-users] Unit of diffusion coefficient David van der Spoel
[gmx-users] Wrong heat capacity (water) David van der Spoel
[gmx-users] Epsilon in ffoplsaanb.itp David van der Spoel
[gmx-users] [Fwd: a problem about the residence] David van der Spoel
[gmx-users] xpm2ps help David van der Spoel
[gmx-users] Unable to compile Gromacs-CVS because calcpot.c David van der Spoel
[gmx-users] about specbond David van der Spoel
[gmx-users] Conformation Search with Gromacs David van der Spoel
[gmx-users] Warning message with 3.3.3 but not with 3.3.1 David van der Spoel
[gmx-users] Warning message with 3.3.3 but not with 3.3.1 David van der Spoel
[gmx-users] Warning message with 3.3.3 but not with 3.3.1 David van der Spoel
[gmx-users] GDB Debugging - GROMACS(v-3.3.3) Application with OpenMPI(v-1.2.5/v-1.2.6) David van der Spoel
[gmx-users] epsilon in mdp David van der Spoel
[gmx-users] query about .xpm file David van der Spoel
[gmx-users] acetone parameter David van der Spoel
[gmx-users] dielectric constant David van der Spoel
[gmx-users] a question David van der Spoel
[gmx-users] Black hole / Galactic dynamics David van der Spoel
[gmx-users] 3.3.2 -b option not functioning as expected David van der Spoel
[gmx-users] x2top error in CNT simulation David van der Spoel
[gmx-users] Re: x2top error in CNT simulation (David van der Spoel) David van der Spoel
[gmx-users] Re: Fatal error:couldnt write energies David van der Spoel
[gmx-users] negative eigenvalues occured and not "nearly zero" David van der Spoel
[gmx-users] question David van der Spoel
[gmx-users] question David van der Spoel
[gmx-users] Polarizative models for water David van der Spoel
[gmx-users] Question about gcc version David van der Spoel
[gmx-users] force field parameters for hydronium David van der Spoel
[gmx-users] Question about gcc version David van der Spoel
[gmx-users] Polarizative models for water David van der Spoel
[gmx-users] Question about gcc version David van der Spoel
[gmx-users] upgrade version - "make distclean"? David van der Spoel
[gmx-users] a huge topology parameter c1 (angles) David van der Spoel
[gmx-users] Polarizative models for water David van der Spoel
[gmx-users] solvent insertion analysis David van der Spoel
[gmx-users] GDB Debugging - GROMACS(v-3.3.3) Application with OpenMPI(v-1.2.5/v-1.2.6) Mukesh K Srivastava
[gmx-users] Re: gmx-users Digest, Vol 48, Issue 54 Mukesh K Srivastava
[gmx-users] how to control temperature Mitchell Stanton-Cook
[gmx-users] how to use GROMACS to model carbon nanotubes Christopher Stiles
[gmx-users] x2top error in CNT simulation on Gromacs 3.3.3 Christopher Stiles
[gmx-users] RE: x2top error in CNT simulation on Gromacs 3.3.3 (Christopher Stiles) Christopher Stiles
[gmx-users] structure files of water and CNT Stiles, Christopher Dale
[gmx-users] AA not present in the ffG43a1.rtp Mattia Sturlese
[gmx-users] genion problem: is replacing 84 water molecules instead of 200 Subhrangshu Supakar
[gmx-users] Can any body suggest me how do I generate the initial structure with the pre-quil. membrane and the small molecules put on top of it and check the effect of UV on it? Subhrangshu Supakar
[gmx-users] Conformation Search with Gromacs Tandia, Adama
[gmx-users] Blue Gene/P Peter Tieleman
[gmx-users] Blue Gene/P Peter Tieleman
[gmx-users] Installation problem on Mac OS-X Zuowei Wang
[gmx-users] Installation problem on Mac OS X Zuowei Wang
[gmx-users] recognising phos group Tsjerk Wassenaar
[gmx-users] recognising phos group Tsjerk Wassenaar
[gmx-users] Bad .tpr or .xtc files? Tsjerk Wassenaar
[gmx-users] Bad .tpr or .xtc files? Tsjerk Wassenaar
[gmx-users] Bad .tpr or .xtc files? Tsjerk Wassenaar
[gmx-users] rtp files Tsjerk Wassenaar
[gmx-users] Can GROMACS simulate the bond forming and breaking Wei, Xiupeng
[gmx-users] water can't freeze Wei, Xiupeng
[gmx-users] water can't freeze Wei, Xiupeng
[gmx-users] cholesterol distortion Steffen Wolf
[gmx-users] Defining charges: [atomtypes] vs [atoms] Matt Wyczalkowski
[gmx-users] how to put two rmsd plot in one plot Kpiwara De X-nelo
[gmx-users] Bad .tpr or .xtc files? Peggy Yao
[gmx-users] Bad .tpr or .xtc files? Peggy Yao
[gmx-users] Bad .tpr or .xtc files? Peggy Yao
[gmx-users] Bad .tpr or .xtc files? Peggy Yao
[gmx-users] Why my system collapsed? Peggy Yao
[gmx-users] how to make choices of COM in the system with freeze group? Yang Ye
[gmx-users] Choose of force fields of ethanol and B-DNA with 15 base pairs Yang Ye
[gmx-users] syntax for switching between multiple position restraint .itp in the .top file Yang Ye
[gmx-users] query about diferent cutoffs Ragothaman Yennamalli
[gmx-users] mpi error Ragothaman Yennamalli
[gmx-users] trjconv error Ragothaman Yennamalli
[gmx-users] trjconv error Ragothaman Yennamalli
[gmx-users] trjconv error Ragothaman Yennamalli
[gmx-users] difference between pbc = full and pbc =xy Bo Zhou
[gmx-users] infinite molecule problem Bo Zhou
[gmx-users] infinite molecule problem - Follow up info Bo Zhou
[gmx-users] Re: infinite molecule problem - Follow up info Bo Zhou
[gmx-users] Warning message with 3.3.3 but not with 3.3.1 Bo Zhou
[gmx-users] Re: the number of water molecules Jian Zou
[gmx-users] Re: gmx-users Digest, Vol 48, Issue 67 Jian Zou
[gmx-users] Re: gmx-users Digest, Vol 48, Issue 97 Jian Zou
[gmx-users] urgent question Prettl Zsolt
[gmx-users] urgent question Prettl Zsolt
[gmx-users] A question samad ahadian
[gmx-users] A question samad ahadian
[gmx-users] Fatal error: Could not write energies sudheer babu
[gmx-users] Re: Fatal error:couldnt write energies sudheer babu
[gmx-users] Fatal error:couldn't write energies sudheer babu
[gmx-users] Fatalerror: Couldnt write energies sudheer babu
[gmx-users] Running simulations in different versions sudheer babu
[gmx-users] restart run problem sudheer babu
[gmx-users] Re:restart run problem sudheer babu
[gmx-users] error for runing second simulation using the topology file s lal badshah
[gmx-users] Error in topology file s lal badshah
[gmx-users] GTP in topology s lal badshah
[gmx-users] Error of mdrun s lal badshah
[gmx-users] Error of mdrun s lal badshah
[gmx-users] confirm bdd22a55a5075c60cd9dc4382a75e0b7689a1d11 munuswamy baskar
[gmx-users] Molecular dynamics of N-linked glycans in GROMACS bosis at post.tau.ac.il
[gmx-users] g_hbond -ins cfgauna at lab.cricyt.edu.ar
[gmx-users] solvent insertion analysis cfgauna at lab.cricyt.edu.ar
[gmx-users] area per lipid pragya chohan
[gmx-users] area per lipid pragya chohan
[gmx-users] help regarding analysis pragya chohan
[gmx-users] request pragya chohan
[gmx-users] area compressibility modulus pragya chohan
[gmx-users] problem with g_order pragya chohan
[gmx-users] Problem with lipid simulations chris.neale at utoronto.ca
[gmx-users] continuation run in parallel with shuffle and sort option chris.neale at utoronto.ca
[gmx-users] hydrogen bonds of peptide with lipids chris.neale at utoronto.ca
[gmx-users] request for default word-wrap on the mailing list chris.neale at utoronto.ca
[gmx-users] Entropy correction in PMF chris.neale at utoronto.ca
[gmx-users] area per lipid chris.neale at utoronto.ca
[gmx-users] Problem with lipid simulations csreddy at ncbs.res.in
[gmx-users] angle analysis serdar durdagi
[gmx-users] CNT serdar durdagi
[gmx-users] set up topology in free energy calculations friendli
[gmx-users] Problem with lipid simulations patrick fuchs
[gmx-users] how to calculate the RMSD of the peptide conformation relative to the NMR structure? fufengliu at tju.edu.cn
[gmx-users] oxygen gas parameters for simulation vips g
[gmx-users] using dummy atoms vips g
[gmx-users] using dummy atoms vips g
[gmx-users] hydrogen simulation and topology file vips g
[gmx-users] dielectric constant gadies at fh.huji.ac.il
[gmx-users] position restraints gadies at fh.huji.ac.il
[gmx-users] position restraints gadies at fh.huji.ac.il
[gmx-users] position restraints gadies at fh.huji.ac.il
[gmx-users] position restraints gadies at fh.huji.ac.il
[gmx-users] position restraints gadies at fh.huji.ac.il
[gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode maria goranovic
[gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode maria goranovic
[gmx-users] hydrogen bonds of peptide with lipids maria goranovic
[gmx-users] hydrogen bonds of peptide with lipids maria goranovic
[gmx-users] hydrogen bonds of peptide with lipids maria goranovic
[gmx-users] Double or single precision jacopo.sgrignani at unifi.it
[gmx-users] gromacs trajctory mmpbsa jacopo.sgrignani at unifi.it
[gmx-users] To the GMX developers-distance restraints jayant james
[gmx-users] recognising phos group jayant james
[gmx-users] recognising phos group jayant james
[gmx-users] Test-set problem with Gromacs 3.3.3 janne.hirvi at joensuu.fi
[gmx-users] a question shahrbanoo karbalaee
[gmx-users] rtp file shahrbanoo karbalaee
[gmx-users] rtp files shahrbanoo karbalaee
[gmx-users] question shahrbanoo karbalaee
[gmx-users] question shahrbanoo karbalaee
[gmx-users] Re: gmx-users Digest, Vol 48, Issue 95 shahrbanoo karbalaee
[gmx-users] gromacs analysis performance on a dual core suse box. himanshu khandelia
[gmx-users] B factor and R factor shuai lu
[gmx-users] How to heat a system and equilibrate it? shuai lu
[gmx-users] How to heat a system and equilibrate it? shuai lu
[gmx-users] Free energy calculation shuai lu
[gmx-users] Free energy calculation shuai lu
[gmx-users] free energy calculation shuai lu
[gmx-users] free energy calculation shuai lu
[gmx-users] density and CG MARTINI force field merc mertens
[gmx-users] Understanding about OPLS-aa for lipids minnale
[gmx-users] Re:Understanding about OPLS-aa lipids minnale
[gmx-users] Unable to continue the simulation minnale
[gmx-users] membrane stabilisation minnale
[gmx-users] Ion Parametrization in OPLS-AA forcefield srinivas ramachandran
[gmx-users] VdW and Coulomb SR contribution to dVdl in thermodynamic integration reich at mpikg.mpg.de
[gmx-users] VdW and Coulomb SR contribution to dVdl in thermodynamic integration reich at mpikg.mpg.de
[gmx-users] reg hybrid dynamics vidhya sankar
[gmx-users] DCCM vidhya sankar
[gmx-users] how to put two rmsd plot in one plot sebastien santini
[gmx-users] Help improving multi core processor's speed fabracht sdf
[gmx-users] Help uninstall and recompiling fabracht sdf
[gmx-users] Help, cannot compile with mpi fabracht sdf
[gmx-users] help with mpirun and system exploding during heating fabracht sdf
[gmx-users] help with gromacs install in opensuse 64b fabracht sdf
[gmx-users] help with gromacs install in opensuse 64b fabracht sdf
[gmx-users] help with gromacs install in opensuse 64b fabracht sdf
[gmx-users] Help after gromacs installation fabracht sdf
[gmx-users] position restraints chandrabhan seniya
[gmx-users] position restraints chandrabhan seniya
[gmx-users] Langevin Dynamic "bd-temp" parameter simon sham
[gmx-users] negative eigenvalues occured and not "nearly zero" silvester.thu
[gmx-users] negative eigenvalues occured and not "nearly zero" silvester.thu
[gmx-users] negative eigenvalues occured and not "nearly zero" silvester.thu
[gmx-users] negative eigenvalues occured and not "nearly zero" silvester.thu
[gmx-users] negative eigenvalues occured and not "nearly zero" silvester.thu
[gmx-users] segmentation fault Gitanjali tandon
[gmx-users] how to make choices of COM in the system with freeze group tuyusong
[gmx-users] how to make choices of COM in the system with freeze group? tuyusong
[gmx-users] Warning message with 3.3.3 but not with 3.3.1 tuyusong
[gmx-users] Warning message with 3.3.3 but not with 3.3.1 tuyusong
[gmx-users] how to make choices of COM in the system with freeze group? tuyusong
[gmx-users] Warning message with 3.3.3 but not with 3.3.1 tuyusong
[gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode weixin
[gmx-users] (no subject) weixin
[gmx-users] Discussion, weixin wants to chat weixin
[gmx-users] a problem about the residence zhuliang at tju.edu.cn
[gmx-users] call for help about the hydration number zhuliang at tju.edu.cn
[gmx-users] a problem about the residence zhuliang at tju.edu.cn

Last message date: Wed Apr 30 17:21:19 CEST 2008
Archived on: Wed Apr 30 17:23:02 CEST 2008

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