August 2008 Archives by date
Starting: Fri Aug 1 00:56:59 CEST 2008
Ending: Sun Aug 31 23:37:47 CEST 2008
Messages: 620
- [gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X)
Roland Schulz
- [gmx-users] analysizing the sam.edo script?
xi zhao
- [gmx-users] Tyrosine problems again
chris.neale at utoronto.ca
- [gmx-users] Tyrosine problems again
chris.neale at utoronto.ca
- [gmx-users] how to fix a position in the single eigenvector in essential dynamics sampling?
xi zhao
- [gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X)
Carsten Kutzner
- [gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X)
Alan
- [gmx-users] Re: gmx-users Digest, Vol 51, Issue 116
Alan
- [gmx-users] amb2gmx for big systems
Alan
- [gmx-users] how to fix a position in the single eigenvector in essential dynamics sampling?
Bert de Groot
- [gmx-users] analysizing the sam.edo script?
Bert de Groot
- [gmx-users] Re: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue
Bert de Groot
- [gmx-users] dimerization problem
Tsjerk Wassenaar
- [gmx-users] Re: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue
Tsjerk Wassenaar
- [gmx-users] Testing (was: Tyrosine problems again)
David van der Spoel
- [gmx-users] Creating a new topology using OPLSAA
Mike Wykes
- [gmx-users] Re: Putting more than one peptide
alkasrivastava at iitb.ac.in
- [gmx-users] Re: Putting more than one peptide
Justin A. Lemkul
- [gmx-users] Testing
Justin A. Lemkul
- [gmx-users] Order parameters of lipid
Justin A. Lemkul
- [gmx-users] query about essential dynamics
sangeeta kundu
- [gmx-users] Order parameters of lipid
Alan Dodd
- [gmx-users] Order parameters of lipid
Justin A. Lemkul
- [gmx-users] Re: Putting more than one peptide
Vitaly Chaban
- [gmx-users] Testing
chris.neale at utoronto.ca
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 5
minnale
- [gmx-users] Testing
David Chan
- [gmx-users] Testing
David van der Spoel
- [gmx-users] Testing
chris.neale at utoronto.ca
- [gmx-users] Fwd: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue
Tsjerk Wassenaar
- [gmx-users] Testing (was: Tyrosine problems again)
Roland Schulz
- [gmx-users] Testing
David van der Spoel
- [gmx-users] Testing
Roland Schulz
- [gmx-users] Testing (was: Tyrosine problems again)
dichan at ucalgary.ca
- [gmx-users] dihedral potential OPLSAA force field
David Huang
- [gmx-users] dihedral potential OPLSAA force field (correction)
David Huang
- [gmx-users] Re: Putting more than one peptide
Sheyore Omovie
- [gmx-users] Testing (was: Tyrosine problems again)
David van der Spoel
- [gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed
Vitaly Chaban
- [gmx-users] Fwd: membrane simulations with gromacs
chris.neale at utoronto.ca
- [gmx-users] AMOEBA in gromacs
Grange Hermitage
- [gmx-users] Normal Mode Analysis in Double-Precision
Inon Sharony
- [gmx-users] segmentation fault in g_anaeig
Inon Sharony
- [gmx-users] how to extend 1ns Unfolding simulation to 6ns
ravi sharma
- [gmx-users] how to extend 1ns Unfolding simulation to 6ns
Justin A. Lemkul
- [gmx-users] segmentation fault in g_anaeig
Tsjerk Wassenaar
- [gmx-users] Normal Mode Analysis in Double-Precision
Ran Friedman
- [gmx-users] Umbrella Sampling
Alexandr Malafeev
- [gmx-users] RE: Umbrella Sampling
Vitaly Chaban
- [gmx-users] segmentation fault in g_anaeig
Inon Sharony
- [gmx-users] RE: how to extend 1ns Unfolding simulation to 6ns
Vitaly Chaban
- [gmx-users] Normal Mode Analysis in Double-Precision
Inon Sharony
- [gmx-users] Please help: POPC membrane simulation
mahesh kulharia
- [gmx-users] Normal Mode Analysis in Double-Precision
Ran Friedman
- [gmx-users] Please help: POPC membrane simulation
Justin A. Lemkul
- [gmx-users] Please help: POPC membrane simulation
Florian Haberl
- [gmx-users] Normal Mode Analysis in Double-Precision
Inon Sharony
- [gmx-users] Re: Umbrella Sampling
Alexandr Malafeev
- [gmx-users] Normal Mode Analysis in Double-Precision
Ran Friedman
- [gmx-users] Normal Mode Analysis in Double-Precision
Inon Sharony
- [gmx-users] Normal Mode Analysis in Double-Precision
Ran Friedman
- [gmx-users] Normal Mode Analysis in Double-Precision
Inon Sharony
- [gmx-users] Normal Mode Analysis in Double-Precision
Ran Friedman
- [gmx-users] Force Distance Curve from .trr .xtc
VENKATESH HARIHARAN
- [gmx-users] Question about octahedral boxes
Justin A. Lemkul
- [gmx-users] Re: Question about octahedral boxes (solved)
Justin A. Lemkul
- [gmx-users] how long simulation takes to get stable when constrains is none in mdp file?
wang kelvin
- [gmx-users] parameters for protonated nitrogen
Samuel Coulbourn Flores 花山
- [gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed
David van der Spoel
- [gmx-users] how long simulation takes to get stable when constrains is none in mdp file?
David van der Spoel
- [gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed
Vitaly Chaban
- [gmx-users] Define proper set of topology parameters for new molecule in different FF.
Andrey Frolov
- [gmx-users] how long simulation takes to get stable when constrains is none in mdp file?
Tsjerk Wassenaar
- [gmx-users] table force-field
Alexandr Malafeev
- [gmx-users] table force-field
Justin A. Lemkul
- [gmx-users] how long simulation takes to get stable when constrains is none in mdp file?
wang kelvin
- [gmx-users] table force-field
Alexandr Malafeev
- [gmx-users] table force-field
Justin A. Lemkul
- [gmx-users] table force-field
Alexandr Malafeev
- [gmx-users] table force-field
Justin A. Lemkul
- [gmx-users] table force-field
Alexandr Malafeev
- [gmx-users] membrane with OPLS force field
Rebeca García Fandiño
- [gmx-users] membrane with OPLS force field
Justin A. Lemkul
- [gmx-users] some questions about gmx_density.c
beibei
- [gmx-users] RE: Define proper set of topology parameters for new molecule in different FF.
Vitaly Chaban
- [gmx-users] RE: how long simulation takes to get stable when constrains is none in mdp file?
Vitaly Chaban
- [gmx-users] membrane with OPLS force field
Chris Neale
- [gmx-users] membrane with OPLS force field
Rebeca García Fandiño
- [gmx-users] some questions about gmx_density.c
Yang Ye
- [gmx-users] membrane with OPLS force field
Chris Neale
- [gmx-users] force feield paremeters for magnesium
Mahnam
- [gmx-users] charge density
Sunjoo Lee
- [gmx-users] force feield paremeters for magnesium
Justin A. Lemkul
- [gmx-users] RE: Define proper set of topology parameters for new molecule in different FF.
Andrey Frolov
- [gmx-users] RE: Define proper set of topology parameters for new molecule in different FF.
Justin A. Lemkul
- [gmx-users] how to fix the COM of group in the pull.
xi zhao
- [gmx-users] A fix to eigio.c ?
eladp at elaine.tau.ac.il
- [gmx-users] membrane with OPLS force field
Volker Wirth
- [gmx-users] RE: how to fix the COM of group in the pull.
Vitaly Chaban
- [gmx-users] how to fix the center of mass of the protein in the pull simulation
xi zhao
- [gmx-users] RE[4]: Define proper set of topology parameters for new molecule in different FF.
Vitaly Chaban
- [gmx-users] membrane with OPLS force field
Justin A. Lemkul
- [gmx-users] Some Issues on Substrates/PBC
Michael Hirtz
- [gmx-users] membrane with OPLS force field
Volker Wirth
- [gmx-users] Some Issues on Substrates/PBC
André Farias de Moura
- [gmx-users] Some Issues on Substrates/PBC
Justin A. Lemkul
- [gmx-users] membrane with OPLS force field
Justin A. Lemkul
- [gmx-users] peptide translation
priyanka srivastava
- [gmx-users] Determining temperature from velocities
Andy Shelley
- [gmx-users] remove center of mass motion
M. Emal Alekozai
- [gmx-users] top file definitions_1
rosip at qb.ffyb.uba.ar
- [gmx-users] top file definitions_1
Justin A. Lemkul
- [gmx-users] gromos function type assigned by grompp
Romelia Salomon
- [gmx-users] remove center of mass motion
Justin A. Lemkul
- [gmx-users] Run test in parallel
ikedaike
- [gmx-users] nature of gromacs / gcc-4.x problem
chris.neale at utoronto.ca
- [gmx-users] Run test in parallel
Yang Ye
- [gmx-users] Run test in parallel
ikedaike
- [gmx-users] Run test in parallel
Yang Ye
- [gmx-users] Run test in parallel
ikedaike
- [gmx-users] nature of gromacs / gcc-4.x problem
David van der Spoel
- [gmx-users] single-precision *.tpr data after a double-precision run
Inon Sharony
- [gmx-users] single-precision *.tpr data after a double-precision run
Ran Friedman
- [gmx-users] g_covar with correlation matrix
Ran Friedman
- [gmx-users] Some Issues on Substrates/PBC
Michael Hirtz
- [gmx-users] Some Issues on Substrates/PBC
Michael Hirtz
- [gmx-users] single-precision *.tpr data after a double-precision run
Inon Sharony
- [gmx-users] Some Issues on Substrates/PBC
Justin A. Lemkul
- [gmx-users] ACE patch in FFG43a1
priyanka srivastava
- [gmx-users] single-precision *.tpr data after a double-precision run
Ran Friedman
- [gmx-users] single-precision *.tpr data after a double-precision run
Inon Sharony
- [gmx-users] single-precision *.tpr data after a double-precision run
Ran Friedman
- [gmx-users] single-precision *.tpr data after a double-precision run
David Osguthorpe
- [gmx-users] nature of gromacs / gcc-4.x problem
chris.neale at utoronto.ca
- [gmx-users] error comm-grps=Protein SOL
M. Emal Alekozai
- [gmx-users] error comm-grps=Protein SOL
Justin A. Lemkul
- [gmx-users] gromos function type assigned by grompp
Justin A. Lemkul
- [gmx-users] simulating with air
Andy Shelley
- [gmx-users] simulating with air
Justin A. Lemkul
- [gmx-users] error comm-grps=Protein SOL
M. Emal Alekozai
- [gmx-users] gromos function type assigned by grompp
Romelia Salomon
- [gmx-users] error comm-grps=Protein SOL
Justin A. Lemkul
- [gmx-users] gromos function type assigned by grompp
Justin A. Lemkul
- [gmx-users] gromos function type assigned by grompp
Romelia Salomon
- [gmx-users] gromos function type assigned by grompp
Justin A. Lemkul
- [gmx-users] gromos function type assigned by grompp
Romelia Salomon
- [gmx-users] regarding grompp warning
prasun kumar
- [gmx-users] ACE patch in FFG43a1
David van der Spoel
- [gmx-users] grompp and box size
prasun kumar
- [gmx-users] regarding grompp warning
Justin A. Lemkul
- [gmx-users] grompp and box size
Justin A. Lemkul
- [gmx-users] RE: simulating with air
Vitaly Chaban
- [gmx-users] RE: grompp and box size
Vitaly Chaban
- [gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X)
Steffen Wolf
- [gmx-users] Re: CHARMM FF
Roland Schulz
- [gmx-users] RE: grompp and box size
Tsjerk Wassenaar
- [gmx-users] RE: grompp and box size
Vitaly Chaban
- [gmx-users] RMSD between
jayant james
- [gmx-users] RMSD between
David van der Spoel
- [gmx-users] AMBER and gromacs atoms renaming
Ragnarok sdf
- [gmx-users] AMBER and gromacs atoms renaming
Shay Amram
- [gmx-users] AMBER and gromacs atoms renaming
Justin A. Lemkul
- [gmx-users] AMBER and gromacs atoms renaming
Tsjerk Wassenaar
- [gmx-users] PROBLEM : rdf O-H of water from tutorial
niharendu choudhury
- [gmx-users] PROBLEM : rdf O-H of water from tutorial
David van der Spoel
- [gmx-users] rdf O-H of water from tutorial
Vitaly Chaban
- [gmx-users] Residue specific secondary structure analysis
Biswaranjan Meher
- [gmx-users] Residue specific secondary structure analysis
Justin A. Lemkul
- [gmx-users] Pressure coupling
Matteus Lindgren
- [gmx-users] AFM pulling: after bond-breakage force does not drop to zero
Thomas Schlesier
- [gmx-users] AFM pulling: after bond-breakage force does not drop to zero
Thomas Schlesier
- [gmx-users] pdb2gmx -inter automatised ?
Christian Fufezan
- [gmx-users] translation
priyanka srivastava
- [gmx-users] pdb2gmx -inter automatised ?
Justin A. Lemkul
- [gmx-users] translation
Justin A. Lemkul
- [gmx-users] translation
priyanka srivastava
- [gmx-users] translation
Justin A. Lemkul
- [gmx-users] translation
priyanka srivastava
- [gmx-users] ensuring that compilation used gcc 3.x
Chris Neale
- [gmx-users] re: ensuring that compilation used gcc 3.x
David Chan
- [gmx-users] ensuring that compilation used gcc 3.x
Chris Neale
- [gmx-users] Error in pdb2gmx
vivek sharma
- [gmx-users] Error in pdb2gmx
David van der Spoel
- [gmx-users] requested for GROMACS package
shiny chandy
- [gmx-users] requested for GROMACS package
Justin A. Lemkul
- [gmx-users] Error in pdb2gmx
vivek sharma
- [gmx-users] Error in pdb2gmx
David van der Spoel
- [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
vivek sharma
- [gmx-users] ASP-LIG Interaction Energy : MDRUN
nahren manuel
- [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
David van der Spoel
- [gmx-users] Error in pdb2gmx
vivek sharma
- [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
Justin A. Lemkul
- [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
vivek sharma
- [gmx-users] Error in pdb2gmx
Justin A. Lemkul
- [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
Per Larsson
- [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
nahren manuel
- [gmx-users] ASP-LIG Interaction Energy : MDRUN
Justin A. Lemkul
- [gmx-users] pdb2gmx -inter automatised ?
Christian Fufezan
- [gmx-users] pdb2gmx -inter automatised ?
Tsjerk Wassenaar
- [gmx-users] Re: requested for GROMACS package
Vitaly Chaban
- [gmx-users] Error in pdb2gmx
Tsjerk Wassenaar
- [gmx-users] one component plasma simulations (OCP)
Argyrios Karatrantos
- [gmx-users] one component plasma simulations (OCP)
David van der Spoel
- [gmx-users] gmx does not recognize HIE as protein
Rebeca García Fandiño
- [gmx-users] gmx does not recognize HIE as protein
Tsjerk Wassenaar
- [gmx-users] debian packages from CVS versions
Martin Höfling
- [gmx-users] error: 1 particles communicated to PME node 3 (...)
Rebeca García Fandiño
- [gmx-users] error: 1 particles communicated to PME node 3 (...)
Justin A. Lemkul
- [gmx-users] Force Field Parameters Nitrogen and Oxygen
Andy Shelley
- [gmx-users] OCP simulations
Argyrios Karatrantos
- [gmx-users] Force Field Parameters Nitrogen and Oxygen
Justin A. Lemkul
- [gmx-users] Re: requested for GROMACS package
Justin A. Lemkul
- [gmx-users] A bug of trjconv for force output?
LuLanyuan
- [gmx-users] colour of the molecules
hhhh huan
- [gmx-users] Error in pdb2gmx
vivek sharma
- [gmx-users] Error in pdb2gmx
Tsjerk Wassenaar
- [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
vivek sharma
- [gmx-users] Error in pdb2gmx
Tsjerk Wassenaar
- [gmx-users] colour of the molecules
Florian Haberl
- [gmx-users] Re: Force Field Parameters Nitrogen and Oxygen
Vitaly Chaban
- [gmx-users] Re: simulating with air
Vitaly Chaban
- [gmx-users] A bug of trjconv for force output?
Berk Hess
- [gmx-users] Re: colour of the molecules
Vitaly Chaban
- [gmx-users] mistake!!
sarbani chattopadhyay
- [gmx-users] Problems extending a calculation (in steps and Benchmark)
Rebeca García Fandiño
- [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
vivek sharma
- [gmx-users] Re: categorization
Vitaly Chaban
- [gmx-users] Re: Energy minimization output
alkasrivastava at iitb.ac.in
- [gmx-users] mistake!!
Justin A. Lemkul
- [gmx-users] colour of the molecules
Justin A. Lemkul
- [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
Justin A. Lemkul
- [gmx-users] Re: Energy minimization output
Kukol, Andreas
- [gmx-users] Re: Energy minimization output
Justin A. Lemkul
- [gmx-users] Problems extending a calculation (in steps and Benchmark)
Justin A. Lemkul
- [gmx-users] Re: categorization
Justin A. Lemkul
- [gmx-users] invalid number of nodes
Rebeca García Fandiño
- [gmx-users] invalid number of nodes
Carsten Kutzner
- [gmx-users] invalid number of nodes
Berk Hess
- [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
vivek sharma
- [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
Justin A. Lemkul
- [gmx-users] error: 1 particles communicated to PME node 3 (...)
Berk Hess
- [gmx-users] invalid number of nodes
Rebeca García Fandiño
- [gmx-users] CHARMM FF
Roland Schulz
- [gmx-users] invalid number of nodes
Berk Hess
- [gmx-users] invalid number of nodes
Carsten Kutzner
- [gmx-users] invalid number of nodes
Berk Hess
- [gmx-users] colour of the molecules
hhhh huan
- [gmx-users] colour of the molecules
Justin A. Lemkul
- [gmx-users] more than one drug in lipid?
serdar durdagi
- [gmx-users] more than one drug in lipid?
Justin A. Lemkul
- [gmx-users] Dielectric constant
avinash kumar
- [gmx-users] about size of group of monomers vs time
Rogelio Hernández
- [gmx-users] Re: simulating with air
Andy Shelley
- [gmx-users] Re: Re: colour of the molecules
Vitaly Chaban
- [gmx-users] Re: simulating with air
Vitaly Chaban
- [gmx-users] Re: simulating with air
Andy Shelley
- [gmx-users] Re: simulating with air
Vitaly Chaban
- [gmx-users] Re: about size of group of monomers vs time
Vitaly Chaban
- [gmx-users] tfe
shahrbanoo karbalaee
- [gmx-users] AFM pulling rate
Malin Bergenstråhle
- [gmx-users] not running on higher no of nodes
Anupam Nath Jha
- [gmx-users] about size of group of monomers vs time
Ran Friedman
- [gmx-users] Cluster Size Distribution
Alif M Latif
- [gmx-users] Cluster Size Distribution
Ran Friedman
- [gmx-users] AFM pulling rate
Berk Hess
- [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
Justin A. Lemkul
- [gmx-users] tfe
Justin A. Lemkul
- [gmx-users] tfe
shahrbanoo karbalaee
- [gmx-users] Dielectric constant
Berk Hess
- [gmx-users] water tip3p
Alan
- [gmx-users] tfe
Justin A. Lemkul
- [gmx-users] flexible organic solvents
Sascha Rehm
- [gmx-users] [ atomtypes ] are not case sensitive?
Alan
- [gmx-users] flexible organic solvents
Kukol, Andreas
- [gmx-users] problems with PBC in editconf
Rebeca García Fandiño
- [gmx-users] problems with PBC in editconf
Justin A. Lemkul
- [gmx-users] LINCS warning
serdar durdagi
- [gmx-users] addition of all hydrogens in pdb2gmx
sridhar acharya
- [gmx-users] about size of group of monomers vs time
Rogelio Hernández
- [gmx-users] LINCS warning
Justin A. Lemkul
- [gmx-users] addition of all hydrogens in pdb2gmx
Tsjerk Wassenaar
- [gmx-users] Dielectric constant
avinash kumar
- [gmx-users] Empty trr file !!??
ranqi zhu
- [gmx-users] Empty trr file !!??
Justin A. Lemkul
- [gmx-users] Re: Empty trr file
Vitaly Chaban
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 61
Vitaly Chaban
- [gmx-users] problem with parallelization on a dual quad-core machine
Hongxian He
- [gmx-users] Imposing distance restraints between two residues
plmallip at mail.uh.edu
- [gmx-users] Imposing distance restraints between two residues
plmallip at mail.uh.edu
- [gmx-users] Imposing distance restraints between two residues
Justin A. Lemkul
- [gmx-users] New Gromacs-CPMD QMMM webpage
Pradip Biswas
- [gmx-users] Imposing distance restraints between two
plmallip at mail.uh.edu
- [gmx-users] Imposing distance restraints between two
Grange Hermitage
- [gmx-users] Dielectric constant
Berk Hess
- [gmx-users] tfe
shahrbanoo karbalaee
- [gmx-users] Out of office AutoReply
charloteaux.b
- [gmx-users] tfe
Justin A. Lemkul
- [gmx-users] Out of office AutoReply
charloteaux.b
- [gmx-users] do_dssp
minnale
- [gmx-users] do_dssp
Justin A. Lemkul
- [gmx-users] do_dssp
Justin A. Lemkul
- [gmx-users] do_dssp
minnale
- [gmx-users] do_dssp
Justin A. Lemkul
- [gmx-users] Out of office AutoReply
charloteaux.b
- [gmx-users] do_dssp
Nuno Azoia
- [gmx-users] all-bonds option
serdar durdagi
- [gmx-users] Position restraints on a pentamer
plmallip at mail.uh.edu
- [gmx-users] Position restraints on a pentamer
plmallip at mail.uh.edu
- [gmx-users] Position restraints on a pentamer
Justin A. Lemkul
- [gmx-users] Out of office AutoReply
charloteaux.b
- [gmx-users] topology for Amyloid beta peptide
ffavela at fis.cinvestav.mx
- [gmx-users] G_RMS for different simulations
Ricardo Soares
- [gmx-users] G_RMS for different simulations
Ricardo Soares
- [gmx-users] AW: all-bonds option
serdar durdagi
- [gmx-users] Out of office AutoReply
charloteaux.b
- [gmx-users] tfe
shahrbanoo karbalaee
- [gmx-users] problem with protein secondary structure analysis
minnale
- [gmx-users] problem with protein secondary structure analysis
Justin A. Lemkul
- [gmx-users] tfe
Justin A. Lemkul
- [gmx-users] about how to set the environment variable
beibei
- [gmx-users] about how to set the environment variable
Tsjerk Wassenaar
- [gmx-users] problem with protein secondary structure analysis
minnale
- [gmx-users] Out of office AutoReply
charloteaux.b
- [gmx-users] problem with protein secondary structure analysis
Tsjerk Wassenaar
- [gmx-users] problem with protein secondary structure analysis
minnale
- [gmx-users] problem with protein secondary structure analysis
minnale
- [gmx-users] Out of office AutoReply
charloteaux.b
- [gmx-users] problem with protein secondary structure analysis
Shay Amram
- [gmx-users] tfe
shahrbanoo karbalaee
- [gmx-users] Out of office AutoReply
charloteaux.b
- [gmx-users] tfe
Justin A. Lemkul
- [gmx-users] problem with protein secondary structure analysis
Justin A. Lemkul
- [gmx-users] problem with protein secondary structure analysis
minnale
- [gmx-users] Out of office AutoReply
charloteaux.b
- [gmx-users] XTC error
hhhh huan
- [gmx-users] Error in trjconv
M.Parthiban
- [gmx-users] XTC error
David van der Spoel
- [gmx-users] quantum chemistry to gromacs topology approaches
Grange Hermitage
- [gmx-users] generating conf.gro
Vitaly Chaban
- [gmx-users] Error in trjconv
Tsjerk Wassenaar
- [gmx-users] generating conf.gro
Tsjerk Wassenaar
- [gmx-users] Out of office AutoReply
charloteaux.b
- [gmx-users] temperature coupling for complex+ligand+water+ions
Alan
- [gmx-users] Out of office AutoReply
charloteaux.b
- [gmx-users] catastrophic error: "timer not defined"
DimitryASuplatov
- [gmx-users] temperature coupling for complex+ligand+water+ions
Justin A. Lemkul
- [gmx-users] catastrophic error: "timer not defined"
Berk Hess
- [gmx-users] tfe
shahrbanoo karbalaee
- [gmx-users] tfe
Justin A. Lemkul
- [gmx-users] Out of office AutoReply
charloteaux.b
- [gmx-users] [ atomtypes ] are not case sensitive?
Berk Hess
- [gmx-users] CHARMM FF
Nicolas Sapay
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 66
minnale
- [gmx-users] protein/dmso simulation
prasun kumar
- [gmx-users] generating conf.gro
Vitaly Chaban
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 66
Justin A. Lemkul
- [gmx-users] protein/dmso simulation
Justin A. Lemkul
- [gmx-users] charge density
Sunjoo Lee
- [gmx-users] Re:Error in trjconv
M.Parthiban
- [gmx-users] protein/dmso simulation
Bhanu
- [gmx-users] dmso/peptide simulation
prasun kumar
- [gmx-users] Re:Error in trjconv
Tsjerk Wassenaar
- [gmx-users] Re: protein/dmso simulation
Vitaly Chaban
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 66
Tsjerk Wassenaar
- [gmx-users] charmm and oplsaa simulation results don't match
sarbani chattopadhyay
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 77
M.Parthiban
- [gmx-users] Error in trjconv
M.Parthiban
- [gmx-users] dmso/peptide simulation
prasun kumar
- [gmx-users] dmso/peptide simulation
Justin A. Lemkul
- [gmx-users] Re: temperature coupling for complex+ligand+water+ions
Alan
- [Fwd: Re: [gmx-users]build topology file for a molecule define with new residues]
cilpa at users.csc.fi
- [gmx-users] Error in trjconv
Tsjerk Wassenaar
- [Fwd: Re: [gmx-users]build topology file for a molecule define with new residues]
Justin A. Lemkul
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 78
Vitaly Chaban
- [gmx-users] RE: [ atomtypes ] are not case sensitive?
Alan
- [gmx-users] dmso/peptide simulation
Anil Kumar
- [gmx-users] Re: temperature coupling for complex+ligand+water+ions
Justin A. Lemkul
- [gmx-users] RE: [ atomtypes ] are not case sensitive?
Berk Hess
- [Fwd: Re: [gmx-users]build topology file for a molecule define with new residues]
cilpa at users.csc.fi
- [gmx-users] charmm and oplsaa simulation results don't match
Chris Neale
- FW: [gmx-users] charmm and oplsaa simulation results don't match
Berk Hess
- FW: [gmx-users] charmm and oplsaa simulation results don't match
sarbani chattopadhyay
- [gmx-users] Questions about brownian/langevin dynamics of bead-spring polymers
Suman Chakrabarty
- [gmx-users] Help with grompp with amber99 forcefield
Ragnarok sdf
- [gmx-users] charmm and oplsaa simulation results don't match
Chris Neale
- [gmx-users] Help with grompp with amber99 forcefield
Justin A. Lemkul
- [gmx-users] Using Morse potentials with ENCAD force field
Andy Shelley
- [gmx-users] REMD trjcat -demux problem
Di Pan
- [gmx-users] tfe.itp
shahrbanoo karbalaee
- [gmx-users] REMD trjcat -demux problem
David van der Spoel
- [gmx-users] Using Morse potentials with ENCAD force field
David van der Spoel
- [gmx-users] flexible organic solvents
patrick fuchs
- [gmx-users] tfe.itp
Justin A. Lemkul
- [gmx-users] FFTW & Gromacs installation on AIX 5.3
Senthil Kumar M
- [gmx-users] FFTW & Gromacs installation on AIX 5.3
Justin A. Lemkul
- [gmx-users] MDRUN with MPIRUN
vivek sharma
- [gmx-users] New Gromacs-CPMD QMMM webpage
vidhya sankar
- [gmx-users] FFTW & Gromacs installation on AIX 5.3
Dimitris Dellis
- [gmx-users] FFTW & Gromacs installation on AIX 5.3
chris.neale at utoronto.ca
- [gmx-users] MDRUN with MPIRUN
Kukol, Andreas
- [gmx-users] MDRUN with MPIRUN
vivek sharma
- [gmx-users] rb1 test failed after recompiling gromacs 3.3.2
Nicolas Sapay
- [gmx-users] Using Morse potentials with ENCAD force field
Andy Shelley
- [gmx-users] AFM and g_wham
xi zhao
- [gmx-users] Simulations backward in time.
Sumanth Jamadagni
- [gmx-users] tfe.itp
shahrbanoo karbalaee
- [gmx-users] pdb file ???
Chih-Ying Lin
- [gmx-users] The WARNING
Chih-Ying Lin
- [gmx-users] The WARNING
David van der Spoel
- [gmx-users] Simulations backward in time.
David van der Spoel
- [gmx-users] call for help
曹臻
- [gmx-users] Re: tfe.itp
Vitaly Chaban
- [gmx-users] RE: [ atomtypes ] are not case sensitive?
Alan
- [gmx-users] Re: The WARNING
Vitaly Chaban
- [gmx-users] pdb file ???
Tsjerk Wassenaar
- [gmx-users] Re: The WARNING
Tsjerk Wassenaar
- [gmx-users] Re: Simulations backward in time
Vitaly Chaban
- [gmx-users] Re: The WARNING
Vitaly Chaban
- [gmx-users] Re: Simulations backward in time
David van der Spoel
- [gmx-users] tfe
shahrbanoo karbalaee
- [gmx-users] tfe
Justin A. Lemkul
- [gmx-users] simulation problems
baloilgiullare
- [gmx-users] HELP::Running Gromacs in parellel
vivek sharma
- [gmx-users] Re: Using Morse potentials with ENCAD force field
Vitaly Chaban
- [gmx-users] Re: Simulations backward in time
Jochen Hub
- [gmx-users] Re: New Gromacs-CPMD QMMM webpage
Vitaly Chaban
- [gmx-users] HELP::Running Gromacs in parellel
Justin A. Lemkul
- [gmx-users] Visualizing gromacs result
vivek sharma
- [gmx-users] Re: Simulations backward in time
Vitaly Chaban
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 89
Vitaly Chaban
- [gmx-users] Re: Simulations backward in time
Vitaly Chaban
- FW: [gmx-users] Re: Simulations backward in time
Berk Hess
- [gmx-users] Re: Simulations backward in time
Vitaly Chaban
- [gmx-users] simulations backward in time
Sumanth Jamadagni
- [gmx-users] New Gromacs-CPMD QMMM webpage
Pradip Biswas
- [gmx-users] [Fwd: WARNING: Found more than 12 triclinic correction vectors, ignoring some.]
Justin A. Lemkul
- [gmx-users] Visualizing gromacs result
Jochen Hub
- [gmx-users] simulations backward in time
Jussi Lehtola
- [gmx-users] regarding 2002 post showing protein unfolding with long timesteps
chris.neale at utoronto.ca
- [gmx-users] Re: Using Morse potentials with ENCAD force field
Vitaly Chaban
- [gmx-users] tfe and gromos9653a
shahrbanoo karbalaee
- [gmx-users] cgnr
Chih-Ying Lin
- [gmx-users] cgnr
LuLanyuan
- [gmx-users] Salt molecule - ion bond
Chih-Ying Lin
- [gmx-users] regarding 2002 post showing protein unfolding with long timesteps
David van der Spoel
- [gmx-users] tfe and gromos9653a
Justin A. Lemkul
- [gmx-users] Re: Salt molecule - ion bond
Vitaly Chaban
- [gmx-users] Salt molecule - ion bond
Justin A. Lemkul
- [gmx-users] rb1 test failed after recompiling gromacs 3.3.2
Nicolas Sapay
- [gmx-users] rb1 test failed after recompiling gromacs 3.3.2
Justin A. Lemkul
- [gmx-users] The WARNING
Chih-Ying Lin
- [gmx-users] Re: The WARNING
Tsjerk Wassenaar
- [gmx-users] rb1 test failed after recompiling gromacs 3.3.2
Nicolas Sapay
- [gmx-users] How to display simulation box in VMD?
Suman Chakrabarty
- [gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"
M. Emal Alekozai
- [gmx-users] Re: The WARNING
Vitaly Chaban
- [gmx-users] How to display simulation box in VMD?
Nicolas Sapay
- [gmx-users] g_rotacf
rams rams
- [gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"
Chris Neale
- [gmx-users] Help - No default Bond types dna
Ragnarok sdf
- [gmx-users] pull.pdo and AFM force
xi zhao
- [gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"
M. Emal Alekozai
- [gmx-users] Vacuum Simulation of Alanine Dipeptide =>production run
M. Emal Alekozai
- [gmx-users] Error while running gromacs in parellel
vivek sharma
- [gmx-users] Help - No default Bond types dna
Justin A. Lemkul
- [gmx-users] groups to write to trr
Vitaly Chaban
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 96
Ragnarok sdf
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 96
Justin A. Lemkul
- [gmx-users] groups to write to trr
Shay Amram
- [gmx-users] groups to write to trr
Justin A. Lemkul
- [gmx-users] g_sgangle
Chih-Ying Lin
- [gmx-users] g_angle , g_bond distribution
Chih-Ying Lin
- [gmx-users] g_energy
Chih-Ying Lin
- [gmx-users] g_sgangle
Justin A. Lemkul
- [gmx-users] g_energy
Justin A. Lemkul
- [gmx-users] groups to write to trr
Vitaly Chaban
- [gmx-users] Re: groups to write to trr
Vitaly Chaban
- [gmx-users] g_rotacf
rams rams
- [gmx-users] Re: groups to write to trr
Justin A. Lemkul
- [gmx-users] Re: groups to write to trr
Tsjerk Wassenaar
- [gmx-users] #include "ffG45a3.itp"
Chih-Ying Lin
- [gmx-users] #include "ffG45a3.itp"
David van der Spoel
- [gmx-users] QMMM
ha salem
- [gmx-users] #include "ffG45a3.itp"
Chih-Ying Lin
- [gmx-users] #include "ffG45a3.itp"
Justin A. Lemkul
- [gmx-users] Mailman CGI error!!! The Mailman CGI wrapper encountered a fatal error. This entry is being stored in your syslog: Group mismatch error. Mailman expected the CGI wrapper script to be executed as group "nobody", but the system's web server executed the CGI script as group "apache". Try tweaking the web server to run the script as group "nobody", or re-run configure, providing the command line option `--with-cgi-gid=apache'.
Brian Wengerter
- [gmx-users] Re: Using Morse potentials with ENCAD force field
Andy Shelley
- [gmx-users] g_hbond output analysis
parthiban at ncbs.res.in
- [gmx-users] g_hbond output analysis
Florian Haberl
- [gmx-users] Re: Using Morse potentials with ENCAD force field
Vitaly Chaban
- [gmx-users] heat_capacity_&_viscosity
Sang-Min Park
- [gmx-users] Genion failing in parallel runs.
Bhanu
- [gmx-users] Choose groups for force output
Matteus Lindgren
- [gmx-users] Genion failing in parallel runs.
Justin A. Lemkul
- [gmx-users] Genion failing in parallel runs.
Florian Haberl
- [gmx-users] Re:g_mindist option
alkasrivastava at iitb.ac.in
- [gmx-users] Re:g_mindist option
Justin A. Lemkul
- [gmx-users] Re[2]: Using Morse potentials with ENCAD force field
Vitaly Chaban
- [gmx-users] Re[2]: Using Morse potentials with ENCAD force field
Justin A. Lemkul
- [gmx-users] Corrupt TRR file -- skipping a bad frame?
Matt Wyczalkowski
- [gmx-users] The molecular structure
Chih-Ying Lin
- [gmx-users] The molecular structure
Justin A. Lemkul
- [gmx-users] Corrupt TRR file -- skipping a bad frame?
Justin A. Lemkul
- [gmx-users] g_hbond output analysis
parthiban at ncbs.res.in
- [gmx-users] How to use g_energy after parellal mdrun
vivek sharma
- [gmx-users] ffg53a5
shahrbanoo karbalaee
- [gmx-users] trjconv error
parthiban at ncbs.res.in
- [gmx-users] g_hbond output analysis
David van der Spoel
- [gmx-users] Re: Re:Re:g_mindist option
alkasrivastava at iitb.ac.in
- [gmx-users] Re: Re:Re:g_mindist option
Tsjerk Wassenaar
- [gmx-users] trjconv error
Tsjerk Wassenaar
- [gmx-users] ffg53a5
Tsjerk Wassenaar
- [gmx-users] Corrupt TRR file -- skipping a bad frame?
Tsjerk Wassenaar
- [gmx-users] G_SDF if reference atoms are in different residues
Hawtin R.
- [gmx-users] when gen_vel should be "no"
sarbani chattopadhyay
- [gmx-users] Re: Help
Justin A. Lemkul
- [gmx-users] when gen_vel should be "no"
Justin A. Lemkul
- [gmx-users] Error with LINC warning
vivek sharma
- [gmx-users] ffg53a5
Justin A. Lemkul
- [gmx-users] Error with LINC warning
Justin A. Lemkul
- [gmx-users] trjconv error
parthiban at ncbs.res.in
- [gmx-users] Re: Help
Justin A. Lemkul
- [gmx-users] trjconv error
Tsjerk Wassenaar
- [gmx-users] when gen_vel should be "no"
Florian Dommert
- [gmx-users] error ffg53a5
shahrbanoo karbalaee
- [gmx-users] error ffg53a5
Justin A. Lemkul
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97
Ragnarok sdf
- [gmx-users] RE: g_mindist option
van Bemmelen
- [gmx-users] error ffg53a
shahrbanoo karbalaee
- [gmx-users] error ffg53a
Justin A. Lemkul
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97
Justin A. Lemkul
- [gmx-users] when gen_vel should be "no"
Jochen Hub
- [gmx-users] How to use g_energy after parellal mdrun
Jochen Hub
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97
Ragnarok sdf
- [gmx-users] error ffg53a and thanks
shahrbanoo karbalaee
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97
Justin A. Lemkul
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97 (Justin A. Lemkul)
Ragnarok sdf
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97 (Justin A. Lemkul)
Justin A. Lemkul
- [gmx-users] Keeping portions of a protein fixed during energy minimization and MD simulations
shyamala iyer
- [gmx-users] Keeping portions of a protein fixed during energy minimization and MD simulations
Justin A. Lemkul
- [gmx-users] Re: trjconv error
parthiban at ncbs.res.in
- [gmx-users] How to use g_energy after parellal mdrun
vivek sharma
- [gmx-users] Differences in version 3.0 and 3.3
Cheong Wee Loong, Daniel
- [gmx-users] Warnings while grompp_d
vivek sharma
- [gmx-users] Re: trjconv error
Tsjerk Wassenaar
- [gmx-users] Warnings while grompp_d
Jochen Hub
- [gmx-users] How to use g_energy after parellal mdrun
Jochen Hub
- [gmx-users] Corrupt TRR file -- skipping a bad frame?
Alan Dodd
- [gmx-users] problems creating mixed solvent systems
Ted Fischer
- [gmx-users] M*tif installation
Ross KK Leung
- [gmx-users] M*tif installation
Justin A. Lemkul
- [gmx-users] problems creating mixed solvent systems
Justin A. Lemkul
- [gmx-users] M*tif installation
Ross KK Leung
- [gmx-users] M*tif installation
Justin A. Lemkul
- [gmx-users] M*tif installation
Florian Haberl
- [gmx-users] M*tif installation
Tsjerk Wassenaar
- [gmx-users] Re: M*tif installation
Vitaly Chaban
- [gmx-users] compare 3.3.3 vs 3.99.4 (bit long)
spitaleri.andrea at hsr.it
- [gmx-users] Disappear my solution
Morteza Khabiri
- [gmx-users] g_hbond + invalid command line argument -g
minnale
- [gmx-users] g_hbond + invalid command line argument -g
Justin A. Lemkul
- [gmx-users] Disappear my solution
Justin A. Lemkul
- [gmx-users] g_hbond + invalid command line argument -g
minnale
- [gmx-users] g_hbond + invalid command line argument -g
minnale
- [gmx-users] g_hbond + invalid command line argument -g
Justin A. Lemkul
- [gmx-users] Disappear my solution
Morteza Khabiri
- [gmx-users] M*tif installation
Suman Chakrabarty
- [gmx-users] Disappear my solution
Justin A. Lemkul
- [gmx-users] LJ question
Anthony Cruz
- [gmx-users] Disappear my solution
Morteza Khabiri
- [gmx-users] LJ question
David van der Spoel
- [gmx-users] (no subject)
Anjelika Gasilina
- [gmx-users] Disappear my solution
Justin A. Lemkul
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 109
Ragnarok sdf
- [gmx-users] LJ question
Anthony Cruz
- [gmx-users] mdrun failing with error message "reading tpx file (em.tpr) version 40 with version 31 program"
Anjelika Gasilina
- [gmx-users] LJ question
David van der Spoel
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 109
Justin A. Lemkul
- [gmx-users] Disappear my solution
Morteza Khabiri
- [gmx-users] Disappear my solution
Justin A. Lemkul
- [gmx-users] g_msd
ram ram
- [gmx-users] g_hbond + invalid command line argument -g
minnale
- [gmx-users] a question about the content in atm-pair.out file
Cao, Yang
- [gmx-users] about connections
ravi sharma
- [gmx-users] (no subject)
Tsjerk Wassenaar
- [gmx-users] g_hbond + invalid command line argument -g
David van der Spoel
- [gmx-users] problems creating mixed solvent systems
Ted Fischer
- [gmx-users] g_msd
Xavier Periole
- [gmx-users] FENE potential (Finitely extensible Nonlinear elastic model)
avinash kumar
- [gmx-users] FENE potential (Finitely extensible Nonlinear elastic model)
David van der Spoel
- [gmx-users] how to define small in RMSD
Ross KK Leung
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 118
minnale
- [gmx-users] a question about the content in atm-pair.out file
Shay Amram
- [gmx-users] Re: gmx-users Digest, Vol 52, Issue 118
Justin A. Lemkul
- [gmx-users] NPT restarts without .edr, can the simulations be used anyway?
Matteus Lindgren
- [gmx-users] Re: g_msd
Vitaly Chaban
- [gmx-users] Different results with and without constraints for pr coupling.
A.Rzepiela
- [gmx-users] genbox and triclinic boxes. Problem an workaround.
Jochen Hub
- [gmx-users] G_SDF if reference atoms are in different residues
chris.neale at utoronto.ca
- [gmx-users] Differences in version 3.0 and 3.3
chris.neale at utoronto.ca
- [gmx-users] Different results with and without constraints for pr coupling.
David van der Spoel
- [gmx-users] using gromacs for protein site-mutagenesis study
Ross KK Leung
- [gmx-users] using gromacs for protein site-mutagenesis study
Justin A. Lemkul
- [gmx-users] NPT restarts without .edr, can the simulations be used anyway?
Justin A. Lemkul
- [gmx-users] g_velacc
rams rams
- [gmx-users] g_velacc
David van der Spoel
- [gmx-users] Re: g_velacc
Vitaly Chaban
- [gmx-users] Re: g_velacc
rams rams
- [gmx-users] Re: g_hbond in version 3.4.1 vs rest (Especially higher one)
Justin A. Lemkul
- [gmx-users] Re: g_velacc
Florian Dommert
- [gmx-users] Re: g_velacc
David van der Spoel
- [gmx-users] Re: g_velacc
Vitaly Chaban
- [gmx-users] Multiple ppa files from a single parallel mdrun_mpi job
chris.neale at utoronto.ca
- [gmx-users] LINCS error
sarbani chattopadhyay
- [gmx-users] Re: g_velacc
rams rams
- [gmx-users] Re: g_velacc
Vitaly Chaban
- [gmx-users] LINCS error
Justin A. Lemkul
- [gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein?
Limei Zhang
- [gmx-users] QMMM
Pradip Biswas
- [gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein?
Justin A. Lemkul
Last message date:
Sun Aug 31 23:37:47 CEST 2008
Archived on: Thu Nov 14 12:05:01 CET 2013
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