November 2007 Archives by date

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Starting: Thu Nov 1 01:10:13 CET 2007
Ending: Fri Nov 30 21:11:15 CET 2007
Messages: 651

[gmx-users] How compare the simulated structure of the same peptide to the NMR strucutre? fufengliu at tju.edu.cn
[gmx-users] bug energy - continuity md Mark Abraham
[gmx-users] editconf -mead Mark Abraham
[gmx-users] How compare the simulated structure of the same peptide to the NMR strucutre? Mark Abraham
[gmx-users] how are you zhuliang at tju.edu.cn
[gmx-users] how are you james zhang
[gmx-users] itp for alamethicin pragya chohan
[gmx-users] itp for alamethicin Dallas B. Warren
[gmx-users] how are you Mark Abraham
[gmx-users] itp for alamethicin Mark Abraham
[gmx-users] itp for alamethicin chris.neale at utoronto.ca
[gmx-users] quasiharmonic eigenvalue units / Schlitter entropy David van der Spoel
[gmx-users] alamethicin error pragya chohan
[gmx-users] mdrun -rerun and box size bug not fixed? Michel Cuendet
[gmx-users] POPC simulation Moutusi Manna
[gmx-users] POPC simulation Marc F. Lensink
[gmx-users] mdrun -rerun and box size bug not fixed? David Mobley
[gmx-users] Regarding Box-X Box-Y values from g_energy Sona Aramyan
[gmx-users] Regarding Box-X Box-Y values from g_energy Alan Dodd
[gmx-users] Regarding Box-X Box-Y values from g_energy Sona Aramyan
[gmx-users] "Specified frame doesn't exist or file not seekable" when using .xtc Qiao Baofu
[gmx-users] "Specified frame doesn't exist or file not seekable" when using .xtc David van der Spoel
[gmx-users] *.gro output file being written to inverse Luciano Costa
[gmx-users] "Specified frame doesn't exist or file not seekable" when using .xtc Qiao Baofu
[gmx-users] "Specified frame doesn't exist or file not seekable" when using .xtc David van der Spoel
[gmx-users] mdrun 3.3.2 crash - gmx_sumi called in serial run with RF Michel Cuendet
[gmx-users] RE: gmx-users Digest, Vol 43, Issue 1 Ricardo Gobato
[gmx-users] mdrun 3.3.2 crash - gmx_sumi called in serial run with RF David van der Spoel
[gmx-users] POPC simulation chris.neale at utoronto.ca
[gmx-users] CSDs syawash Rezaei
[gmx-users] CSDs David van der Spoel
[gmx-users] Regarding Box-X Box-Y values from g_energy Tsjerk Wassenaar
[gmx-users] Simulating Infinite Nanotube Patrick Lafond
[gmx-users] *.gro output file being written to inverse Tsjerk Wassenaar
[gmx-users] Simulating Infinite Nanotube Robert Johnson
[gmx-users] alamethicin error Mark Abraham
[gmx-users] POPC simulation Mark Abraham
[gmx-users] POPC simulation Chris Neale
[gmx-users] mdrun -rerun and box size bug not fixed? Berk Hess
[gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS himanshu khandelia
[gmx-users] Energy profiles for 2 separate peptide chains in a simulation box. Huey Ling Tan
[gmx-users] Re: mdrun -rerun and box size bug not fixed? Michel Cuendet
[gmx-users] Energy profiles for 2 separate peptide chains in a simulation box. Mark Abraham
[gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS Mark Abraham
[gmx-users] Energy profiles for 2 separate peptide chains in a simulation box. Huey Ling Tan
[gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS himanshu khandelia
[gmx-users] Re: mdrun -rerun and box size bug not fixed? David van der Spoel
[gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS Mark Abraham
[gmx-users] Problems in energygrps and tc-grps Huey Ling Tan
[gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS himanshu khandelia
[gmx-users] Energy profiles for 2 separate peptide chains in a simulation box. Mark Abraham
[gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS Mark Abraham
[gmx-users] Problems in energygrps and tc-grps Mark Abraham
[gmx-users] Converting PDB to gromacs (Hydrogen problems) Craig Schwartz
[gmx-users] Converting PDB to gromacs (Hydrogen problems) Mark Abraham
[gmx-users] gramicidin A pragya chohan
[gmx-users] (no subject) sarbani chattopadhyay
[gmx-users] (no subject) Mark Abraham
[gmx-users] gramicidin A Mark Abraham
[gmx-users] gramicidin A pragya chohan
[gmx-users] gramicidin A Mark Abraham
[gmx-users] g_rdf problem avinash kumar
[gmx-users] g_rdf problem David van der Spoel
[gmx-users] Placing a peptide at the air/water interface OZGE ENGIN
[gmx-users] Placing a peptide at the air/water interface OZGE ENGIN
[gmx-users] Placing a peptide at the air/water interface Mark Abraham
[gmx-users] MSD analysis Jian Dai
[gmx-users] Placing a peptide at the air/water interface OZGE ENGIN
[gmx-users] Placing a peptide at the air/water interface David van der Spoel
[gmx-users] soft-core and coulomb transformation bharat v. adkar
[gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS himanshu khandelia
[gmx-users] How to calculate total enery of a protein csreddy at ncbs.res.in
[gmx-users] Fatal error:Atom index (1) in settles out of bounds (1-0) willting
[gmx-users] How to calculate total enery of a protein David van der Spoel
[gmx-users] How to calculate total enery of a protein Mark Abraham
[gmx-users] Fatal error:Atom index (1) in settles out of bounds (1-0) Yang Ye
[gmx-users] gcc problem 余翔
[gmx-users] problem with extended run using grompp sarbani chattopadhyay
[gmx-users] gcc problem David van der Spoel
[gmx-users] Problem of mdrun compiled by different gcc version YuXiang
[gmx-users] problem with extended run using grompp Justin A. Lemkul
[gmx-users] soft-core and coulomb transformation David Mobley
[gmx-users] Simulating Infinite Nanotube Patrick Lafond
[gmx-users] Performing simulation at air/water interface OZGE ENGIN
[gmx-users] soft-core and coulomb transformation bharat v. adkar
[gmx-users] Performing simulation at air/water interface Pedro Alexandre de Araújo Gomes Lapido Loureiro
[gmx-users] Performing simulation at air/water interface OZGE ENGIN
[gmx-users] soft-core and coulomb transformation David Mobley
[gmx-users] regarding continuation of a simulation raghava alapati
[gmx-users] soft-core and coulomb transformation bharat v. adkar
[gmx-users] soft-core and coulomb transformation David Mobley
[gmx-users] problem with extended run using grompp Mark Abraham
[gmx-users] regarding continuation of a simulation Mark Abraham
[gmx-users] Performing simulation at air/water interface Mark Abraham
[gmx-users] alamethicin error pragya chohan
[gmx-users] Re: mdrun -rerun and box size bug not fixed? Michel Cuendet
[gmx-users] alamethicin error Mark Abraham
[gmx-users] Re: mdrun -rerun and box size bug not fixed? Michel Cuendet
[gmx-users] Re: mdrun -rerun and box size bug not fixed? Berk Hess
[gmx-users] protein residue numbering not retained in GROMACS ? himanshu khandelia
[gmx-users] problem with waters in protein/membrane simulation N-J.M. Macaluso
[gmx-users] Re: mdrun -rerun and box size bug not fixed? Michel Cuendet
[gmx-users] problem with waters in protein/membrane simulation Alan Dodd
[gmx-users] Re: mdrun -rerun and box size bug not fixed? Berk Hess
[gmx-users] protein/membrane simulation parameters N-J.M. Macaluso
[gmx-users] How can I add hydrogen? Eudes Fileti
[gmx-users] How can I add hydrogen? Florian Haberl
[gmx-users] CSDs jahanshah ashkani
[gmx-users] grompp error jahanshah ashkani
[gmx-users] CSDs David van der Spoel
[gmx-users] CSDs jahanshah ashkani
[gmx-users] CSDs David van der Spoel
[gmx-users] Help: A ligand covalently bond to protein Tanping Li
[gmx-users] Genion: specify minimum distance between counter-ion and solute Narayanan Veeraraghavan
[gmx-users] Help: A ligand covalently bond to protein Yang Ye
[gmx-users] Help: A ligand covalently bond to protein Tanping Li
[gmx-users] Help: A ligand covalently bond to protein Yang Ye
[gmx-users] Re: gmx-users Digest, Vol 43, Issue 21 Eudes Fileti
[gmx-users] grompp error Mark Abraham
[gmx-users] Help: A ligand covalently bond to protein Mark Abraham
[gmx-users] protein residue numbering not retained in GROMACS ? Mark Abraham
[gmx-users] protein/membrane simulation parameters Mark Abraham
[gmx-users] Genion: specify minimum distance between counter-ion and solute Mark Abraham
[gmx-users] can not pass gmxtest Li Qiang
[gmx-users] can not pass gmxtest Mark Abraham
[gmx-users] Installation problem:gcc-g77 Panichakorn Jaiyong
[gmx-users] Installation problem:gcc-g77 David van der Spoel
[gmx-users] Installation problem:gcc-g77 Mark Abraham
[gmx-users] can not pass gmxtest Yang Ye
[gmx-users] can not pass gmxtest Li Qiang
[gmx-users] Force tolarence ss aa
[gmx-users] can not pass gmxtest Yang Ye
[gmx-users] protein/membrane simulation parameters Stéphane Téletchéa
[gmx-users] Protonate and OPLS Eudes Fileti
[gmx-users] can not pass gmxtest Li Qiang
[gmx-users] Doubt Reg. Selection of force field and pdb2gmx program csreddy at ncbs.res.in
[gmx-users] Protonate and OPLS Mark Abraham
[gmx-users] can not pass gmxtest Mark Abraham
[gmx-users] Doubt Reg. Selection of force field and pdb2gmx program Mark Abraham
[gmx-users] Force tolarence Mark Abraham
[gmx-users] gmx 3.3.2 explodes with libc.so.6 Dmytro Kovalskyy
[gmx-users] "cannot compute sizeof (int), 77" on AIX 5.3 PPC p575 (searched the list) liu xin
[gmx-users] gmx 3.3.2 explodes with libc.so.6 David van der Spoel
[gmx-users] Where is the GROMOS87 force field when using pdb2gmx maria goranovic
[gmx-users] Where is the GROMOS87 force field when using pdb2gmx David van der Spoel
[gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx maria goranovic
[gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx David van der Spoel
[gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx maria goranovic
[gmx-users] installation error pragya chohan
[gmx-users] Re: mdrun -rerun and box size bug not fixed? Michel Cuendet
[gmx-users] Re: mdrun -rerun and box size bug not fixed? David Mobley
[gmx-users] combining gromos96 (43a2) and berger lipid force field maria goranovic
[gmx-users] Sulfate parameters anyone ? maria goranovic
[gmx-users] combining gromos96 (43a2) and berger lipid force field Alan Dodd
[gmx-users] Sulfate parameters anyone ? Justin A. Lemkul
[gmx-users] gmx 3.3.2 explodes with libc.so.6 Dmytro Kovalskyy
[gmx-users] box explodes after 13ns Belquis Mothana
[gmx-users] Periodic Boundary conditions Paul Whitford
[gmx-users] combining gromos96 (43a2) and berger lipid force field Mark Abraham
[gmx-users] installation error Mark Abraham
[gmx-users] "cannot compute sizeof (int), 77" on AIX 5.3 PPC p575 (searched the list) Mark Abraham
[gmx-users] soft-core and coulomb transformation bharat v. adkar
[gmx-users] segmentation fault vinod kumar
[gmx-users] segmentation fault David van der Spoel
[gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx Erik Lindahl
[gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx himanshu khandelia
[gmx-users] Periodic Boundary conditions Berk Hess
[gmx-users] fatal error using grompp karan syal
[gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx Mark Abraham
[gmx-users] fatal error using grompp Mark Abraham
[gmx-users] gmx 3.3.2 explodes with libc.so.6 Yang Ye
[gmx-users] Re: mdrun -rerun and box size bug not fixed? Michel Cuendet
[gmx-users] "cannot compute sizeof (int), 77" on AIX 5.3 PPC p575 (searched the list) Christian Burisch
[gmx-users] gmx 3.3.2 explodes with libc.so.6 David van der Spoel
[gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx Patrick Fuchs
[gmx-users] gmx 3.3.2 explodes with libc.so.6 Yang Ye
[gmx-users] How is the particle density of type B computed in g_rdf ? Grace Li
[gmx-users] How is the particle density of type B computed in g_rdf ? David van der Spoel
[gmx-users] gmx 3.3.2 explodes with libc.so.6 Li Qiang
[gmx-users] bonded Buckingham interaction Frankie Montenegro
[gmx-users] bonded Buckingham interaction David van der Spoel
[gmx-users] bonded Buckingham interaction Frankie Montenegro
[gmx-users] bonded Buckingham interaction David van der Spoel
[gmx-users] bonded Buckingham interaction Berk Hess
[gmx-users] gmx 3.3.2 explodes with libc.so.6 Bruce Milne
[gmx-users] How to set N-terminal lysine carry only +1 unit charge? Hu Zhongqiao
[gmx-users] gmx 3.3.2 explodes with libc.so.6 Li Qiang
[gmx-users] gmx 3.3.2 explodes with libc.so.6 Li Qiang
[gmx-users] gmx 3.3.2 explodes with libc.so.6 Dmytro Kovalskyy
[gmx-users] How to set N-terminal lysine carry only +1 unit charge? Yang Ye
[gmx-users] gmx 3.3.2 explodes with libc.so.6 Yang Ye
[gmx-users] gmx 3.3.2 explodes with libc.so.6 Yang Ye
[gmx-users] coordinate files for molecules consisting of new (non-standard) residues Teresa Silva
[gmx-users] installation error pragya chohan
[gmx-users] installation error David van der Spoel
[gmx-users] gmx 3.3.2 explodes with libc.so.6 David van der Spoel
[gmx-users] gmx 3.3.2 explodes with libc.so.6 Yang Ye
[gmx-users] gmx 3.3.2 explodes with libc.so.6 David van der Spoel
[gmx-users] mdrun error pragya chohan
[gmx-users] Re: How to set N-terminal lysine carry only +1 unit charge? Hu Zhongqiao
[gmx-users] genernal problem in simulation Kitty Ji
[gmx-users] mdrun error Justin A. Lemkul
[gmx-users] Re: How to set N-terminal lysine carry only +1 unit charge? Yang Ye
[gmx-users] gmx 3.3.2 explodes with libc.so.6 Yang Ye
[gmx-users] genernal problem in simulation Yang Ye
[gmx-users] How to set N-terminal lysine carry only +1 unit charge? Henry O Ify
[gmx-users] (no subject) OZGE ENGIN
[gmx-users] How to set N-terminal lysine carry only +1 unit charge? Yang Ye
[gmx-users] (no subject) Mark Abraham
[gmx-users] mdrun error Mark Abraham
[gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs jantonioms J. A. Mondragon S
[gmx-users] coordinate files for molecules consisting of new (non-standard) residues Mark Abraham
[gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs Mark Abraham
[gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs jantonioms J. A. Mondragon S
[gmx-users] soft-core and coulomb transformation bharat v. adkar
[gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs David van der Spoel
[gmx-users] mdrun error pragya chohan
[gmx-users] mdrun error Justin A. Lemkul
[gmx-users] mdrun error pragya chohan
[gmx-users] mdrun error Justin A. Lemkul
[gmx-users] soft-core and coulomb transformation David Mobley
[gmx-users] Ace-Ala-Nac to Ace-Gly-Nac David Mobley
[gmx-users] trjorder does not write trajectory file Dmytro Kovalskyy
[gmx-users] trjorder does not write trajectory file Justin A. Lemkul
[gmx-users] mdrun error pragya chohan
[gmx-users] mdrun error Justin A. Lemkul
[gmx-users] mdrun error Justin A. Lemkul
[gmx-users] mdrun error Mark Abraham
[gmx-users] Incomplete header: nr 3078 time 9408 Dechang Li
[gmx-users] Incomplete header: nr 3078 time 9408 David van der Spoel
[gmx-users] trjorder does not write trajectory file Dmytro Kovalskyy
[gmx-users] Re:Re: Incomplete header: nr 3078 time 9408 Dechang Li
[gmx-users] trjorder does not write trajectory file Justin A. Lemkul
[gmx-users] trjorder does not write trajectory file Mark Abraham
[gmx-users] (no subject) dongsheng zhang
[gmx-users] Re:Re: Incomplete header: nr 3078 time 9408 Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] force=nan in frame 0 dongsheng zhang
[gmx-users] force=nan in frame 0 Mark Abraham
[gmx-users] Parallel run on IBM p575 "poe mpi" liu xin
[gmx-users] "cannot compute sizeof (int), 77" on AIX 5.3 PPC p575 (searched the list) liu xin
[gmx-users] Parallel run on IBM p575 "poe mpi" David van der Spoel
[gmx-users] soft-core and coulomb transformation bharat v. adkar
[gmx-users] soft-core and coulomb transformation David van der Spoel
[gmx-users] widom in Gromacs Argyrios Karatrantos
[gmx-users] widom in Gromacs Berk Hess
[gmx-users] Tools for axial symmetry Eudes Fileti
[gmx-users] Tools for axial symmetry Berk Hess
[gmx-users] Tools for axial symmetry Henry O Ify
[gmx-users] (no subject) pragya chohan
[gmx-users] soft-core and coulomb transformation David Mobley
[gmx-users] force=nan in frame 0 dongsheng zhang
[gmx-users] soft-core and coulomb transformation Berk Hess
[gmx-users] mdrun error pragya chohan
[gmx-users] REMD As A Function of Distance Between 2 Chains Huey Ling Tan
[gmx-users] soft-core and coulomb transformation David Mobley
[gmx-users] QMMM for element with "unknown" forcefield Tandia, Adama
[gmx-users] force=nan in frame 0 Yang Ye
[gmx-users] trjorder does not write trajectory file Dmytro Kovalskyy
[gmx-users] soft-core and coulomb transformation Berk Hess
[gmx-users] force=nan in frame 0 Dongsheng Zhang
[Bulk] Re: [gmx-users] force=nan in frame 0 Yang Ye
[gmx-users] REMD As A Function of Distance Between 2 Chains Mu Yuguang (Dr)
[gmx-users] soft-core and coulomb transformation David Mobley
[gmx-users] REMD As A Function of Distance Between 2 Chains Marcus Kubitzki
[gmx-users] stop mailing me Henry O Ify
[gmx-users] stop mailing me Justin A. Lemkul
[gmx-users] stop mailing me Mark Abraham
[gmx-users] histidine charges in ffopls.rtp Marius Retegan
[gmx-users] histidine charges in ffopls.rtp Ran Friedman
[gmx-users] histidine charges in ffopls.rtp Mark Abraham
[gmx-users] stop mailing me Henry O Ify
[gmx-users] G_hbond's hydrogen bond ordering? Danny Neil
[gmx-users] g-hbond and N acceptors Michel Cuendet
[gmx-users] g-hbond and N acceptors David van der Spoel
[gmx-users] histidine charges in ffopls.rtp Marius Retegan
[gmx-users] histidine charges in ffopls.rtp David van der Spoel
[gmx-users] Creating .top, .gro, .ndx, .itp files for TIP5Pwater JMandumpal
[gmx-users] Creating .top, .gro, .ndx, .itp files for TIP5Pwater David van der Spoel
[gmx-users] Re: gmx-users Digest, Vol 43, Issue 49 Gerrit Groenhof
[gmx-users] g-hbond and N acceptors Michel Cuendet
[gmx-users] soft-core and coulomb transformation Berk Hess
[gmx-users] problems about energy minimization renying
[gmx-users] stop mailing me Erik Lindahl
[gmx-users] soft-core and coulomb transformation bharat v. adkar
[gmx-users] g-hbond and N acceptors David van der Spoel
[gmx-users] g_order in a micelle Jonathan Khao
[gmx-users] g_order in a micelle David van der Spoel
[gmx-users] REMD As A Function of Distance Between 2 Chains Huey Ling Tan
[gmx-users] tabulated bonded interactions Ran Friedman
[gmx-users] g_order in a micelle Jonathan Khao
[gmx-users] SGI Altix - mdrun_mpi Nuno Loureiro Ferreira
[gmx-users] SGI Altix - mdrun_mpi Chris Neale
[gmx-users] Re: SGI Altix - mdrun_mpi Nuno Loureiro Ferreira
[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1 Chris Neale
[gmx-users] Re: SGI Altix - mdrun_mpi Chris Neale
[gmx-users] REMD As A Function of Distance Between 2 Chains Mark Abraham
[gmx-users] problems about energy minimization Mark Abraham
[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1 chris.neale at utoronto.ca
[gmx-users] soft-core and coulomb transformation bharat v. adkar
[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1 David van der Spoel
[gmx-users] REMD As A Function of Distance Between 2 Chains David van der Spoel
[gmx-users] tabulated bonded interactions Berk Hess
[gmx-users] REMD As A Function of Distance Between 2 Chains chiradip chatterjee
[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1 Yang Ye
[gmx-users] compilation fails on MAC OSX - Leopard Hadas Leonov
[gmx-users] compilation fails on MAC OSX - Leopard Hadas Leonov
[gmx-users] compilation fails on MAC OSX - Leopard Carsten Kutzner
[gmx-users] Minor Bug in latest stable release update Maik Goette
[gmx-users] high pressure simulations mateusz sikora
[gmx-users] high pressure simulations Mark Abraham
[gmx-users] high pressure simulations Ran Friedman
[gmx-users] high pressure simulations Andrés N. McCarthy
[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1 Yang Ye
[gmx-users] Minor Bug in latest stable release update Berk Hess
[gmx-users] high pressure simulations Andrés N. McCarthy
[gmx-users] position restrain pragya chohan
[gmx-users] position restrain Justin A. Lemkul
[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1 ccc-6.5.6.002-1 chris.neale at utoronto.ca
[gmx-users] How to delete bad water molecules renying
[gmx-users] How to delete bad water molecules chris.neale at utoronto.ca
[gmx-users] floating point exception for grompp -e ener.edr on some clusters chris.neale at utoronto.ca
[gmx-users] floating point exception for grompp -e ener.edr on some clusters David van der Spoel
[gmx-users] position restrain pragya chohan
[gmx-users] pressure coupling for bilayers pragya chohan
[gmx-users] pressure coupling for bilayers Xavier Periole
[gmx-users] G_sas reside area tangxuan
[gmx-users] How to delete bad water molecules David Mobley
[gmx-users] Differences in the bonded potentials in 3.3.2 vs. 3.3.1 Amadeu
[gmx-users] Differences in the bonded potentials in 3.3.2 vs. 3.3.1 David van der Spoel
[gmx-users] Differences in the bonded potentials in 3.3.2 vs. 3.3.1 Yang Ye
[gmx-users] How to delete bad water molecules Chris Neale
[gmx-users] G_sas reside area Mark Abraham
[gmx-users] out from the simulation box hhhh huan
[gmx-users] out from the simulation box Mark Abraham
[gmx-users] interaction energy of bulk TIP3P sandeep somani
[gmx-users] make hole question Andrei Neamtu
[gmx-users] make hole question Alok
[gmx-users] interaction energy of bulk TIP3P Mark Abraham
[gmx-users] Creating .top, .gro, .ndx, .itp files for TIP5Pwater JMandumpal
[gmx-users] Re: Re: Re: [gmx-usersCreating .top, .gro, .ndx, .itp files for TIP5Pwater JMandumpal
[gmx-users] Re: Unable to install Mac OS X package David van der Spoel
[gmx-users] compilation fails on MAC OSX - Leopard Hadas Leonov
[gmx-users] compilation fails on MAC OSX - Leopard David van der Spoel
[gmx-users] Differences in the bonded potentials in 3.3.2 vs. 3.3.1 Amadeu
[gmx-users] (no subject) Christopher Stiles
[gmx-users] Differences in the bonded potentials in 3.3.2 vs. 3.3.1 David van der Spoel
[gmx-users] CNT Simulation with GROMOS96 43a1 force field Christopher Stiles
[gmx-users] CNT Simulation with GROMOS96 43a1 force field David van der Spoel
[gmx-users] How to add calcium ions at desired position? Peggy Yao
[gmx-users] How to add calcium ions at desired position? Justin A. Lemkul
[gmx-users] How to add calcium ions at desired position? Yang Ye
[gmx-users] Extending MD run Itamar Kass
[gmx-users] floating point exception for grompp -e ener.edr on some clusters chris.neale at utoronto.ca
[gmx-users] Extending MD run Justin A. Lemkul
[gmx-users] Extending MD run Itamar Kass
[gmx-users] Extending MD run Justin A. Lemkul
[gmx-users] Extending MD run Mark Abraham
[gmx-users] Extending MD run Justin A. Lemkul
[gmx-users] How to add calcium ions at desired position? Mark Abraham
[gmx-users] Extending MD run Mark Abraham
[gmx-users] Extending MD run Justin A. Lemkul
[gmx-users] Extending MD run Mark Abraham
[gmx-users] How to add calcium ions at desired position? liang
[gmx-users] floating point exception for grompp -e ener.edr on some clusters David van der Spoel
[gmx-users] Quasiharmonic entropies Ran Friedman
[gmx-users] water in lipid bilayer N-J.M. Macaluso
[gmx-users] water in lipid bilayer Mark Abraham
[gmx-users] water in lipid bilayer N-J.M. Macaluso
[gmx-users] water in lipid bilayer himanshu khandelia
[gmx-users] How to add calcium ions at desired position? Justin A. Lemkul
[gmx-users] water in lipid bilayer N-J.M. Macaluso
[gmx-users] water in lipid bilayer himanshu khandelia
[gmx-users] trjconv does not work! OZGE ENGIN
[gmx-users] trjconv does not work OZGE ENGIN
[gmx-users] trjconv does not work Ran Friedman
[gmx-users] trjconv does not work Xavier Periole
[gmx-users] trjconv does not work OZGE ENGIN
[gmx-users] trjconv does not work OZGE ENGIN
[gmx-users] trjconv does not work Ran Friedman
[gmx-users] trjconv does not work OZGE ENGIN
[gmx-users] trjconv does not work Ran Friedman
[gmx-users] trjconv does not work Alan Dodd
[gmx-users] water in lipid bilayer Chris Neale
[gmx-users] MPI configure "cannot compute sizeof (int)" Chris Borchert
[gmx-users] MPI configure "cannot compute sizeof (int)" Mark Abraham
[gmx-users] Adding polarizability Eric Shamay
[gmx-users] interaction energy of bulk TIP3P sandeep somani
[gmx-users] Adding polarizability Mark Abraham
[gmx-users] How to add calcium ions at desired position? Peggy Yao
[gmx-users] Creating .ndx for TIP5Pwater JMandumpal
[gmx-users] Why so many energy minimization and position restrained simulation steps? Peggy Yao
[gmx-users] How to specify .mdp file for position restrained simulation? Peggy Yao
[gmx-users] Adding polarizability David van der Spoel
[gmx-users] Creating .ndx for TIP5Pwater David van der Spoel
[gmx-users] Creating .ndx for TIP5Pwater Mark Abraham
[gmx-users] interaction energy of bulk TIP3P Mark Abraham
[gmx-users] Why so many energy minimization and position restrained simulation steps? Mark Abraham
[gmx-users] How to specify .mdp file for position restrained simulation? Mark Abraham
[gmx-users] How to specify .mdp file for position restrained simulation? Maik Goette
[gmx-users] Why so many energy minimization and position restrained simulation steps? Tsjerk Wassenaar
[gmx-users] How to specify .mdp file for position restrained simulation? Yang Ye
[gmx-users] problem using makehole grompp nur avneet
[gmx-users] Laptop switches off when running GROMACS Sergio de Alencar
[gmx-users] g_sas with 3.3 and 3.3.2 gives different results Isabella Daidone
[gmx-users] Laptop switches off when running GROMACS David van der Spoel
[gmx-users] g_sas with 3.3 and 3.3.2 gives different results David van der Spoel
[gmx-users] problem using makehole grompp Xavier Periole
[gmx-users] Laptop switches off when running GROMACS Mark Abraham
[gmx-users] How to specify .mdp file for position restrained simulation? jantonioms J. A. Mondragon S
[gmx-users] problem using makehole grompp Mark Abraham
[gmx-users] How to specify .mdp file for position restrained simulation? Mark Abraham
[gmx-users] MPI configure "cannot compute sizeof (int)" Chris Borchert
[gmx-users] Compiling GROMACS with FORTRAN? Mike Hanby
[gmx-users] free energy calculations in charged systems Argyrios Karatrantos
[gmx-users] Re: Problems with the file 2J3Q.pdb and residue 'TFL' David van der Spoel
[gmx-users] Help with energy minimizing protein in water box with CA2+ Peggy Yao
[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1 Li Qiang
[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1 David van der Spoel
[gmx-users] Help with energy minimizing protein in water box with CA2+ David van der Spoel
[gmx-users] free energy calculations in charged systems Maik Goette
[gmx-users] Help with energy minimizing protein in water box with CA2+ Tsjerk Wassenaar
[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1 chris.neale at utoronto.ca
[gmx-users] free energy calculations in charged systems Berk Hess
[gmx-users] Help with energy minimizing protein in water box with CA2+ Mark Abraham
[gmx-users] how to get basic trajectory information out trjcat maria goranovic
[gmx-users] commanf for wrapping pragya chohan
[gmx-users] commanf for wrapping karan syal
[gmx-users] Simulations on Leopard - slow and crashing, cannot compile with lam-mpi Hadas Leonov
[gmx-users] how to get basic trajectory information out trjcat Tsjerk Wassenaar
[gmx-users] Simulations on Leopard - slow and crashing, cannot compile with lam-mpi Hadas Leonov
[gmx-users] commanf for wrapping Mark Abraham
[gmx-users] GROMACS in parallel on a multicore PC? Vasilii Artyukhov
[gmx-users] GROMACS in parallel on a multicore PC? Carsten Kutzner
[gmx-users] GROMACS in parallel on a multicore PC? Vasilii Artyukhov
[gmx-users] GROMACS in parallel on a multicore PC? David van der Spoel
[gmx-users] GROMACS in parallel on a multicore PC? Yang Ye
[gmx-users] Question about embedding a force field with no torsion term Bo Zhou
[gmx-users] molecule of metane Foh
[gmx-users] molecule of metane Justin A. Lemkul
[gmx-users] restart an amber run in gromacs servaas michielssens
[gmx-users] gromacs preformance versus amber servaas michielssens
[gmx-users] restart amber run in gromacs servaas michielssens
[gmx-users] Adding polarizability David Mobley
[gmx-users] Adding polarizability David van der Spoel
[gmx-users] Question about embedding a force field with no torsion term Mark Abraham
[gmx-users] gromacs preformance versus amber David van der Spoel
[gmx-users] gromacs preformance versus amber Mark Abraham
[gmx-users] restart an amber run in gromacs Mark Abraham
[gmx-users] Adding polarizability David Mobley
[gmx-users] restart an amber run in gromacs David Mobley
[gmx-users] Re: Question about embedding a force field with no torsion term Bo Zhou
[gmx-users] Re: Question about embedding a force field with no torsion term Mark Abraham
[gmx-users] floating point exception for grompp -e ener.edr on some clusters chris.neale at utoronto.ca
[gmx-users] molecule of metane foh
[gmx-users] Re: Question about embedding a force field with no torsion term Yang Ye
[gmx-users] molecule of metane Mark Abraham
[gmx-users] What is the relationship between simulation time and real time Q733
[gmx-users] What is the relationship between simulation time and real time Mark Abraham
[gmx-users] What is the relationship between simulation time and real time David van der Spoel
[gmx-users] floating point exception for grompp -e ener.edr on some clusters David van der Spoel
[gmx-users] What is the relationship between simulation time Q733
[gmx-users] What is the relationship between simulation time David van der Spoel
[gmx-users] restart an amber run in gromacs Tsjerk Wassenaar
[gmx-users] Re:Re: gromacs preformance versus amber (David van der Spoel) servaas michielssens
[gmx-users] NOE distance restraints Chiara Parravicini
[gmx-users] Re: gmx-users Digest, Vol 43, Issue 81 servaas michielssens
[gmx-users] Problem in starting make hole nur avneet
[gmx-users] Problem in starting make hole Mark Abraham
[gmx-users] Re: gmx-users Digest, Vol 43, Issue 81 Mark Abraham
[gmx-users] problems about trjconv Di Pan
[gmx-users] problems about trjconv Justin A. Lemkul
[gmx-users] problem with mdrun performing replica exchange MD OZGE ENGIN
[gmx-users] problem with mdrun performing replica exchange MD Berk Hess
[gmx-users] problem with mdrun performing replica exchange MD OZGE ENGIN
[gmx-users] problem with mdrun performing replica exchange MD Berk Hess
[gmx-users] energy minimization of a bilayer Ananya Debnath
[gmx-users] problem with mdrun performing replica exchange MD OZGE ENGIN
[gmx-users] problem with mdrun performing replica exchange MD David van der Spoel
[gmx-users] problem with mdrun performing replica exchange MD OZGE ENGIN
[gmx-users] problem with mdrun performing replicaexchange MD Berk Hess
[gmx-users] problem with mdrun performing replica exchange MD Xavier Periole
[gmx-users] problem with mdrun performing replica exchange MD Xavier Periole
[gmx-users] regarding .gro file Ananya Debnath
[gmx-users] regarding .gro file Mu Yuguang (Dr)
[gmx-users] regarding .gro file Mark Abraham
[gmx-users] energy minimization of a bilayer Mark Abraham
[gmx-users] problems with gromacs tools under certain compilations Grace Li
[gmx-users] asymmetric distribution of water pragya chohan
[gmx-users] asymmetric distribution of water David van der Spoel
[gmx-users] problems with gromacs tools under certain compilations Mark Abraham
[gmx-users] Q's about adding bonded interaction Frankie Montenegro
[gmx-users] Q's about adding bonded interaction Mark Abraham
[gmx-users] regarding .gro file Ananya Debnath
[gmx-users] intel or gcc for opteron Myunggi Yi
[gmx-users] Re: intel or gcc for opteron Myunggi Yi
[gmx-users] Re: intel or gcc for opteron David van der Spoel
[gmx-users] Re: intel or gcc for opteron Myunggi Yi
[gmx-users] Re: intel or gcc for opteron David van der Spoel
[gmx-users] Neutralizing the total charge of the system in vacuum OZGE ENGIN
[gmx-users] Neutralizing the total charge of the system in vacuum Ran Friedman, Biochemisches Inst.
[gmx-users] Neutralizing the total charge of the system in vacuum David van der Spoel
[gmx-users] Semiisotropic pressure coupling & comm_grps (VCM) Alok
[gmx-users] CNT Carbon Nanotube simulation with the GROMOS96 43a1 force field Christopher Stiles
[gmx-users] area by lipid maite lopez cabezas
[gmx-users] area by lipid Alan Dodd
[gmx-users] area by lipid maite lopez cabezas
[gmx-users] area by lipid Alan Dodd
[gmx-users] area by lipid Mark Abraham
[gmx-users] regarding .gro file Mark Abraham
[gmx-users] how to write the correct top file for membrane protein system? liang
[gmx-users] how to write the correct top file for membrane protein system? Justin A. Lemkul
[gmx-users] how to write the correct top file for membrane protein system? liang
[gmx-users] grompp JMandumpal
[gmx-users] Re: intel or gcc for opteron Myunggi Yi
[gmx-users] how to deduce charges for gromos forcefield? Q733
[gmx-users] how to write the correct top file for membraneprotein system? Hadas Leonov
[gmx-users] Re: intel or gcc for opteron David van der Spoel
[gmx-users] how to deduce charges for gromos forcefield? David van der Spoel
[gmx-users] regarding .gro file Tsjerk Wassenaar
[gmx-users] grompp Tsjerk Wassenaar
[gmx-users] area by lipid maite lopez cabezas
[gmx-users] how to write the correct top file for membraneprotein system? liang
[gmx-users] grompp Mark Abraham
[gmx-users] how to write the correct top file for membrane protein system? Mark Abraham
[gmx-users] how to write the correct top file for membraneprotein system? Mark Abraham
[gmx-users] how to write the correct top file for membraneprotein system? Hadas Leonov
[gmx-users] Problem with replica exchange in vacuum OZGE ENGIN
[gmx-users] Problem with replica exchange in vacuum OZGE ENGIN
[gmx-users] Problem with replica exchange in vacuum Xavier Periole
[gmx-users] area by lipid Alan Dodd
[gmx-users] Re: how to write the correct top file for membrane protein liang
[gmx-users] Re: how to write the correct top file for membrane protein Mark Abraham
[gmx-users] Chains blowing Apart csreddy at ncbs.res.in
[gmx-users] Re: About the parameters for REMD in vacuum Xavier Periole
[gmx-users] Chains blowing Apart Xavier Periole
[gmx-users] Re: Chain separation problem Xavier Periole
[gmx-users] Re: Chain separation problem csreddy at ncbs.res.in
[gmx-users] Re: Chain separation problem Xavier Periole
[gmx-users] [Fwd: Semiisotropic pressure coupling & comm_grps (VCM)] David van der Spoel
[gmx-users] [Fwd: Semiisotropic pressure coupling & comm_grps (VCM)] Xavier Periole
[gmx-users] Re: Chain separation problem Mark Abraham
[gmx-users] Confusion Regarding Vacuum csreddy at ncbs.res.in
[gmx-users] Coarse-graining and tabulated non-bonded potentials - will write up on the wiki Steven Kirk
[gmx-users] Coarse-graining and tabulated non-bonded potentials - will write Berk Hess
[gmx-users] Confusion Regarding Vacuum Xavier Periole
[gmx-users] how to deduce charges for gromos forcefield? David Mobley
[gmx-users] Can 1-4 interactions be excluded seperately? Bo Zhou
[gmx-users] WCA potential Argyrios Karatrantos
[gmx-users] WCA potential Berk Hess
[gmx-users] Problems compiling GROMACS on IBM Blue Gene/L Fiona Reid
[gmx-users] Range checking error Yanzi Zhou
[gmx-users] Range checking error David van der Spoel
[gmx-users] Range checking error Yanzi Zhou
[gmx-users] CNT Grompp errors and Force Field modifications Christopher Stiles
[gmx-users] how to solve this broken trjactory Belquis Mothana
[gmx-users] Range checking error Yanzi Zhou
[gmx-users] pdb2gmx error Tawhid Ezaz
[gmx-users] pdb2gmx error Justin A. Lemkul
[gmx-users] Confusion Regarding Vacuum Mark Abraham
[gmx-users] Range checking error Mark Abraham
[gmx-users] Moleculetype SOL contains no atoms JMandumpal
[gmx-users] Re:Moleculetype SOL contains no atoms JMandumpal
[gmx-users] pdb2gmx error Tawhid Ezaz
[gmx-users] how to solve this broken trjactory Mark Abraham
[gmx-users] pdb2gmx error Justin A. Lemkul
[gmx-users] [Fwd: Semiisotropic pressure coupling &comm_grps (VCM)] Alok
[gmx-users] creating .tpr file JMandumpal
[gmx-users] small organic molecules foh
[gmx-users] creating .tpr file David van der Spoel
[gmx-users] small organic molecules Xavier Periole
[gmx-users] Diffusion coefficients auryn_valemig
[gmx-users] Re: how to write the correct top file for membrane protein liang
[gmx-users] Gromacs slow and crashes on Leopard. Hadas Leonov
[gmx-users] Gromacs slow and crashes on Leopard. David van der Spoel
[gmx-users] Gromacs slow and crashes on Leopard. Hadas Leonov
[gmx-users] reading files vijaya subramanian
[gmx-users] reading files David van der Spoel
[gmx-users] The fifth column of the output file of g_sas command OZGE ENGIN
[gmx-users] how to solve this broken trjactory Belquis Mothana
[gmx-users] Barcelona vs Xeon Martin Höfling
[gmx-users] pdb2gmx error Tawhid Ezaz
[gmx-users] small organic molecules Dallas B. Warren
[gmx-users] pdb2gmx error Justin A. Lemkul
[gmx-users] gromacs installation in IBM BLUEGENE Anupam Nath Jha
[gmx-users] Gromacs slow and crashes on Leopard. Carsten Kutzner
[gmx-users] pdb2gmx error Tsjerk Wassenaar
[gmx-users] Barcelona vs Xeon Carsten Kutzner
[gmx-users] Barcelona vs Xeon Berk Hess
[gmx-users] Gromacs slow and crashes on Leopard. David van der Spoel
[gmx-users] Gromacs slow and crashes on Leopard. Hadas Leonov
[gmx-users] Gromacs slow and crashes on Leopard. David van der Spoel
[gmx-users] Gromacs slow and crashes on Leopard. Hadas Leonov
[gmx-users] parallel simulation crash on 6 processors servaas michielssens
[gmx-users] parallel simulation crash on 6 processors David van der Spoel
[gmx-users] Gromacs slow and crashes on Leopard. Carsten Kutzner
[gmx-users] opls bonded parameters singh
[gmx-users] gromacs installation in IBM BLUEGENE Fiona Reid
[gmx-users] Compile Gromacs-3.3.2 on HP xxxw9300 Workstation: AMD64 Opteron with Linux Tandia, Adama
[gmx-users] Setting up Carbon Nanotube Simulations Joshua D. Moore
[gmx-users] Compile Gromacs-3.3.2 on HP xxxw9300 Workstation: AMD64 Opteron with Linux David van der Spoel
[gmx-users] Gromacs slow and crashes on Leopard. Hadas Leonov
[gmx-users] Barcelona vs Xeon Martin Höfling
[gmx-users] ATP, GTP and REX Robert Fenwick
[gmx-users] ATP, GTP and REX Justin A. Lemkul
[gmx-users] rtp file özge kül
[gmx-users] rtp özge kül
[gmx-users] ATP, GTP and REX Maik Goette
[gmx-users] rtp file Justin A. Lemkul
[gmx-users] Double precision test failure Chris Snook
[gmx-users] gmxtest seems to have missing files Amin Astaneh
[gmx-users] Setting up Carbon Nanotube Simulations Robert Johnson
[gmx-users] Recover velocity from trr file and coordinates from xtc file Myunggi Yi
[gmx-users] Recover velocity from trr file and coordinates from xtc file Alan Dodd
[gmx-users] Re: parallel simulation crash on 6 processors servaas michielssens
[gmx-users] Chloroform Mauro Puppett
[gmx-users] osmotic pressure in Gromacs 杭军陆
[gmx-users] Re: parallel simulation crash on 6 processors Carsten Kutzner
[gmx-users] osmotic pressure in Gromacs David van der Spoel
[gmx-users] gmxtest seems to have missing files David van der Spoel
[gmx-users] osmotic pressure in Gromacs chris.neale at utoronto.ca
[gmx-users] Double precision test failure David van der Spoel
[gmx-users] rtp file özge kül
[gmx-users] rtp file Justin A. Lemkul
[gmx-users] Double precision test failure Chris Snook
[gmx-users] osmotic pressure in Gromacs Chris Neale
[gmx-users] Chloroform Dallas B. Warren
[gmx-users] Problem with S-S bond Blaise Costa
[gmx-users] Installation on IBM A.I.X.5.2.0.0 Li Zhenhai
[gmx-users] Compilation error: eNR_NBKERNEL_NR Tandia, Adama
[gmx-users] Problem with S-S bond Tsjerk Wassenaar
[gmx-users] Double precision test failure David van der Spoel
[gmx-users] Compilation error: eNR_NBKERNEL_NR David van der Spoel
[gmx-users] Replica Exchange MD using Gromacs Monika Sharma
[gmx-users] rtp file özge kül
[gmx-users] Replica Exchange MD using Gromacs OZGE ENGIN
[gmx-users] Double precision test failure Chris Snook
[gmx-users] Double precision test failure Berk Hess
[gmx-users] Problem in atom name correspondence between protein topology and coordinates after mutation grompp himanshu khandelia
[gmx-users] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp himanshu khandelia
[gmx-users] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp Justin A. Lemkul
[gmx-users] Writing initial coordinates to trajectory files Brian Helfrich
[gmx-users] Recover velocity from trr file and coordinates from xtc file Myunggi Yi
[gmx-users] Writing initial coordinates to trajectory files Berk Hess
[gmx-users] Problem with S-S bond Blaise Costa
[gmx-users] Writing initial coordinates to trajectory files Brian Helfrich
[gmx-users] GTP topology file for ffG43a1 Robert Fenwick
[gmx-users] Double precision test failure David van der Spoel
[gmx-users] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp David van der Spoel
[gmx-users] GTP topology file for ffG43a1 Justin A. Lemkul
[gmx-users] Recover velocity from trr file and coordinates from xtc file Alan Dodd

Last message date: Fri Nov 30 21:11:15 CET 2007
Archived on: Thu Nov 14 12:04:02 CET 2013

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