January 2005 Archives by thread

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Starting: Sat Jan 1 11:22:21 CET 2005
Ending: Mon Jan 31 18:31:08 CET 2005
Messages: 298

[gmx-users] Position restraint doesn't work David van der Spoel
- [gmx-users] Position restraint doesn't work asaraujo at if.sc.usp.br
  - [gmx-users] Position restraint doesn't work David van der Spoel
[gmx-users] Relaxation of protein molecules xieyh at hkusua.hku.hk
- [gmx-users] Relaxation of protein molecules Anton Feenstra
[gmx-users] g_rms Itamar Kass
[gmx-users] g_rms Itamar Kass
[gmx-users] g_rms Itamar Kass
- [gmx-users] g_rms Anton Feenstra
  - [gmx-users] g_rms Itamar Kass
[gmx-users] g_rms Itamar Kass
[gmx-users] position restraint herbst at fhi-berlin.mpg.de
- [gmx-users] position restraint Anton Feenstra
[gmx-users] Re:Re:trr file Anton Feenstra
[gmx-users] couple of questions about H-bonds and constraints Anton Feenstra
[gmx-users] g_dipoles VISWANADHA SRIDHARA
- [gmx-users] g_dipoles David van der Spoel
[gmx-users] PBC question Osmany Guirola Cruz
[gmx-users] edr after several continuation. xieyh at hkusua.hku.hk
- [gmx-users] edr after several continuation. Dallas Warren
[gmx-users] No. of solvent molecules around Solute Fabian Boes
[gmx-users] How to compute covariance??? Semen Esilevsky
[gmx-users] Compiling Error with icce Florian Haberl
- [gmx-users] Compiling Error with icce Florian Haberl
  - [gmx-users] Compiling Error with icce Erik Lindahl
    - [gmx-users] Compiling Error with icce Florian Haberl
    - [gmx-users] problem with myrinet Nguyen Hoang Phuong
    - [gmx-users] problem with myrinet David van der Spoel
[gmx-users] peptide in Acetonitrile and water Osmany Guirola Cruz
- [gmx-users] peptide in Acetonitrile and water Dallas Warren
[gmx-users] ffgmx for lipids strony_w_w_w at op.pl
[gmx-users] PR EM Alberto Malvezzi
- [gmx-users] PR EM Itamar Kass
[gmx-users] Re: Minimization Gia Maisuradze
[gmx-users] d.lzm ond 32 cpus Florian Haberl
[gmx-users] Can't put the protein in the box using genbox M.Naser
- [gmx-users] Can't put the protein in the box using genbox Dallas Warren
[gmx-users] genion Alberto Malvezzi
- [gmx-users] genion Dallas Warren
- [gmx-users] genion Ran Friedman
[gmx-users] PRODRG available for download / release of PRODRG2.5 server Daan van Aalten
[gmx-users] solvation free energie calculations Ivica Res
[gmx-users] error in preparing .tpr file vema aparna
- [gmx-users] error in preparing .tpr file Ran Friedman
  - [gmx-users] problem with g_mindist output Sandeep Somani
    - [gmx-users] problem with g_mindist output Ran Friedman
[gmx-users] Data and Knowledge Management Tools for Computational Chemists Marc Baaden
[gmx-users] Data and Knowledge Management Tools for Computational Chemists Peter C. Lai
[gmx-users] g_mindist, truncated octahedron and amber trajectory cailliez
- [gmx-users] g_mindist, truncated octahedron and amber trajectory Berk Hess
  - [gmx-users] RNA problem Ken Rotondi
[gmx-users] importing RNA Ken Rotondi
[gmx-users] LJ simulation Manoj
- [gmx-users] LJ simulation Berk Hess
[gmx-users] importing RNA Alessandra Villa
- [gmx-users] importing RNA Ken Rotondi
  - [gmx-users] importing RNA Berk Hess
    - [gmx-users] importing RNA Ken Rotondi
[gmx-users] "Missing" water hydrogens Alan Dodd
[gmx-users] g_filter question Marc Baaden
- [gmx-users] g_filter question Berk Hess
[gmx-users] Enforced rotation of a subunit Kay Gottschalk
[gmx-users] Lipari-Szabo analysis Yegor Smurnyy
- [gmx-users] Lipari-Szabo analysis David van der Spoel
[gmx-users] A question about OPLS force field zjim
- [gmx-users] A question about OPLS force field Erik Lindahl
[gmx-users] Energy minimization Andrea Bacconi
- [gmx-users] Energy minimization Florian Haberl
- [gmx-users] Energy minimization Itamar Kass
[gmx-users] protein local density Dmitry Kovalsky
Re: Re: [gmx-users] A question about OPLS force field zjim
[gmx-users] ambconv: Segmentation fault Sichun Yang
- [gmx-users] ambconv: Segmentation fault david.evans at ulsop.ac.uk
[gmx-users] coulombtype and cutoff selection selection Jian Zou
- [gmx-users] coulombtype and cutoff selection selection David van der Spoel
[gmx-users] g_dielectric VISWANADHA SRIDHARA
[gmx-users] Re: coulombtype and cutoff selection selection Jian Zou
[gmx-users] Plotting .xvg files VISWANADHA SRIDHARA
- [gmx-users] Plotting .xvg files Kay Gottschalk
- [gmx-users] Plotting .xvg files Florian Haberl
[gmx-users] crash due to huge files using reaction field hverli at cbiot.ufrgs.br
- [gmx-users] crash due to huge files using reaction field David van der Spoel
  - [gmx-users] crash due to huge files using reaction field hverli at cbiot.ufrgs.br
    - [gmx-users] crash due to huge files using reaction field David van der Spoel
    - [gmx-users] crash due to huge files using reaction field hverli at cbiot.ufrgs.br
    - [gmx-users] crash due to huge files using reaction field Robert d'Rozario
    - [gmx-users] crash due to huge files using reaction field Steffen Haerterich
[gmx-users] performance Cesar Lopez
[gmx-users] Plotting .xvg files VISWANADHA SRIDHARA
- [gmx-users] Plotting .xvg files Nuno R. L. Ferreira
- [gmx-users] Plotting .xvg files Kay Gottschalk
- [gmx-users] Plotting .xvg files Haberl Florian
[gmx-users] segmentation fault message with g_hbond Lei Zhou
- [gmx-users] segmentation fault message with g_hbond David
[gmx-users] segmentation fault message with g_hbond (fwd) Lei Zhou
- [gmx-users] segmentation fault message with g_hbond (fwd) David van der Spoel
[gmx-users] Re: Energy Minimization Gia Maisuradze
- [gmx-users] Re: Energy Minimization David van der Spoel
  - [gmx-users] Re: Energy Minimization Gia Maisuradze
    - [gmx-users] Re: Energy Minimization David
    - [gmx-users] Re: Energy Minimization Gia Maisuradze
[gmx-users] How to built a protein model basing on the X-ray diffraction structure at different pH environment zjim
- [gmx-users] How to built a protein model basing on the X-ray diffraction structure at different pH environment Xavier Periole
  - [gmx-users] How to built a protein model basing on the X-ray diffraction structure at different pH environment david.evans at ulsop.ac.uk
- [gmx-users] How to built a protein model basing on the X-ray diffraction structure at different pH environment Ran Friedman
[gmx-users] simulation of the protein in vacuum Nikolai Smolin
- [gmx-users] simulation of the protein in vacuum David van der Spoel
[gmx-users] Plotting .xvg files VISWANADHA SRIDHARA
[gmx-users] simulation of the protein in vacuum Alan Wilter Sousa da Silva
- [gmx-users] simulation of the protein in vacuum David van der Spoel
  - [gmx-users] pairwise rmsd Kay Gottschalk
    - [gmx-users] pairwise rmsd Xavier Periole
- [gmx-users] simulation of the protein in vacuum Alan Wilter Sousa da Silva
  - [gmx-users] simulation of the protein in vacuum Kay Gottschalk
[gmx-users] VMD trajectory view Luciane V. Mello
- [gmx-users] VMD trajectory view Nuno R. L. Ferreira
- [gmx-users] VMD trajectory view Florian Haberl
[gmx-users] g_sas, what should be "a group for output" xieyh at hkusua.hku.hk
[gmx-users] gmx FF with hydrogens for NMR stuff Alan Wilter Sousa da Silva
- [gmx-users] gmx FF with hydrogens for NMR stuff Xavier Periole
- [gmx-users] Re: gmx FF with hydrogens for NMR stuff Alan Wilter Sousa da Silva
[gmx-users] You probably have an atom called K (potassium ???) not defined in the FF Alan Wilter Sousa da Silva
- [gmx-users] You probably have an atom called K (potassium ???) not defined in the FF David
[gmx-users] Energy minimization Andrea Bacconi
- [gmx-users] Energy minimization David
[gmx-users] convert TINKER .arc trajectory file? Weihua Guo
Re: [gmx-users] g_sas, what should be "a group for output" zjim
- [gmx-users] g_sas, what should be "a group for output" Berk Hess
[gmx-users] autocorrelation function Jozef Hritz
- [gmx-users] autocorrelation function David van der Spoel
  - [gmx-users] shift cutoffs Marc Bruning
    - [gmx-users] shift cutoffs Berk Hess
[gmx-users] Energy minimization Markus O Kaukonen
[gmx-users] Question about "ffG43b1.rtp" zjim
[gmx-users] Question about "ffG43b1.rtp" zjim
[gmx-users] Lipid tilts Qing Zhu
- [gmx-users] Lipid tilts X.Periole
[gmx-users] question about mpi run 孔韧
[gmx-users] You probably have an atom called K (potassium ???) not defined in the FF VISWANADHA SRIDHARA
[gmx-users] AMBCONV tip3p problem Berk Hess
- [gmx-users] AMBCONV tip3p problem david.evans at ulsop.ac.uk
  - [gmx-users] AMBCONV tip3p problem Berk Hess
    - [gmx-users] AMBCONV tip3p problem david.evans at ulsop.ac.uk
  - [gmx-users] g_cluster Kay Gottschalk
[gmx-users] Overriding atomtypes Nuno R. L. Ferreira
- [gmx-users] Overriding atomtypes David
[gmx-users] opls-aa/L force field parameter modify zjim
- [gmx-users] opls-aa/L force field parameter modify David
- [gmx-users] lipid monolayer isotherm Hector Mtz-Seara
  - [gmx-users] lipid monolayer isotherm Andre Farias de Moura
    - [gmx-users] buried surface Osmany Guirola Cruz
    - [gmx-users] buried surface David van der Spoel
    - [gmx-users] lipid monolayer isotherm Hector Mtz-Seara Monne
    - [gmx-users] lipid monolayer isotherm Andre Farias de Moura
    - [gmx-users] lipid monolayer isotherm Hector Mtz-Seara
    - [gmx-users] lipid monolayer isotherm Andre Farias de Moura
    - [gmx-users] lipid monolayer isotherm Hector Mtz-Seara
[gmx-users] error:multiple T-coupling groups vema aparna
- [gmx-users] error:multiple T-coupling groups David van der Spoel
[gmx-users] gmx FF with hydrogens for NMR stuff vema aparna
[gmx-users] monitoring trans-cis transition of proline residue Shang-Te Danny Hsu
[gmx-users] hexagonal box Michal Kolinski
- [gmx-users] hexagonal box Abil Aliev
- [gmx-users] hexagonal box David van der Spoel
[gmx-users] Re zjim
[gmx-users] computing contacts Luca Mollica
- [gmx-users] computing contacts David van der Spoel
[gmx-users] DMSO w/ GROMOS96 Attila Borics
- [gmx-users] DMSO w/ GROMOS96 David van der Spoel
[gmx-users] timestep for brownian dynamics herbst at fhi-berlin.mpg.de
[gmx-users] paralleling problems Cesar Lopez
- [gmx-users] paralleling problems Dallas Warren
[gmx-users] Surface tension Coupling gromacs user
[gmx-users] Surface tension Coupling gromacs user
- [gmx-users] Surface tension Coupling Hector Mtz-Seara
  - [gmx-users] Surface tension Coupling Andre Farias de Moura
[gmx-users] temperature coupling in NVT Peter Friedel
[gmx-users] capped residue Luciane V. Mello
- [gmx-users] capped residue Xavier Periole
- [gmx-users] AFM pulling of two groups Ester Chiessi
  - [gmx-users] AFM pulling of two groups Berk Hess
    - [gmx-users] AFM pulling of two groups Ester Chiessi
    - [gmx-users] AFM pulling of two groups Berk Hess
    - [gmx-users] AFM pulling of two groups Ester Chiessi
[gmx-users] nonbonded LJ parameters Sabrina Costa
- [gmx-users] nonbonded LJ parameters Nuno R. L. Ferreira
[gmx-users] timestep for brownian dynamics herbst at fhi-berlin.mpg.de
[gmx-users] Hydrogen duplication mkrzemin at nmr.chem.uu.nl
- [gmx-users] tc-grps problem!! Hector Mtz-Seara
  - [gmx-users] tc-grps problem!! David van der Spoel
- [gmx-users] Hydrogen duplication David van der Spoel
[gmx-users] constraints vs bonds Nuno R. L. Ferreira
[gmx-users] RNA ffG43a2.hdb problems Ken Rotondi
[gmx-users] RNA ffG43a2.hdb problems Ken Rotondi
- [gmx-users] RNA ffG43a2.hdb problems Ken Rotondi
  - [gmx-users] g_cluster Kay Gottschalk
[gmx-users] 'GROMOS96 manual and user guide' zjim
[gmx-users] CCl4 solvent xieyh at hkusua.hku.hk
[gmx-users] AFM pulling of two groups Justin MacCallum
[gmx-users] how to calculate mass density in a cylinder? Jian Zou
[gmx-users] errors during installation Jaimin Shah
- [gmx-users] errors during installation Florian Haberl
[gmx-users] error: T-coupling groups vema aparna
- [gmx-users] error: T-coupling groups Florian Haberl
[gmx-users] Re: error: T-coupling groups Zhenting Gao
[gmx-users] Fmax Andrea Bacconi
[gmx-users] LINCS error deepa rajamani
[gmx-users] a qusition of pdb file zjim
- [gmx-users] a qusition of pdb file David van der Spoel
[gmx-users] the qusition about the AFM zjim
[gmx-users] charge on protein 4tejender
- [gmx-users] charge on protein Heikki Käsnänen
- [gmx-users] charge on protein David van der Spoel
  - [gmx-users] charge on protein Gia Maisuradze
    - [gmx-users] charge on protein David
    - [gmx-users] charge on protein Gia Maisuradze
    - [gmx-users] charge on protein David van der Spoel
    - [gmx-users] charge on protein Gia Maisuradze
    - [gmx-users] charge on protein David van der Spoel
[gmx-users] Segmentation fault in g_rms eladp at hemi.tau.ac.il
[gmx-users] Re: "Fmax (Andrea Bacconi)" 4tejender
[gmx-users] 4 processor system shouliang dong
- [gmx-users] 4 processor system Florian Haberl
  - [gmx-users] 4 processor system David van der Spoel
- [gmx-users] 4 processor system leafyoung81-group at yahoo.com
  - [gmx-users] #ifdef in *.rtp - is it possible ? Arturas
    - [gmx-users] #ifdef in *.rtp - is it possible ? David van der Spoel
    - [gmx-users] #ifdef in *.rtp - is it possible ? Arturas
    - [gmx-users] #ifdef in *.rtp - is it possible ? Nuno R. L. Ferreira
    - [gmx-users] #ifdef in *.rtp - is it possible ? David van der Spoel
[gmx-users] Re: GROMACS and Amber FF David van der Spoel
- [gmx-users] constraint pulling Ester Chiessi
  - [gmx-users] constraint pulling Berk Hess
[gmx-users] Number of native contact llshen
- [gmx-users] Number of native contact Sandeep Somani
[gmx-users] how to determine the 'afm_dir' vecter and initial spring coordinate 'afm_init' zjim
[gmx-users] Problem running in parallel GROMACS quanta at chem.unipune.ernet.in
[gmx-users] Who ever used CCl4 solvent? xieyh at hkusua.hku.hk
[gmx-users] parallel GROMACS question: more the nodes, slower Gromacs ... :-( Luca Mollica
[gmx-users] parallel GROMACS question: more the nodes, slower Gromacs ... :-( Luca Mollica
- [gmx-users] parallel GROMACS question: more the nodes, slower Gromacs ... :-( David
- [gmx-users] parallel GROMACS question: more the nodes, slower Gromacs ... :-( Choon Peng
[gmx-users] TIP5P and Free Energy Ronen Zangi
- [gmx-users] TIP5P and Free Energy Berk Hess
  - [gmx-users] TIP5P and Free Energy Ronen Zangi
[gmx-users] libgm.so error running benchmark-gmxbench-3.0 Rajiv
[gmx-users] grompp not running - please advise Jaimin Shah
[gmx-users] first example (demo) not working Jaimin Shah
- [gmx-users] first example (demo) not working David van der Spoel
[gmx-users] Re: GROMACS and Amber FF Michel Cuendet
[gmx-users] Re: How to enable fortran inner loops in Itanium 2 Michel Cuendet
[gmx-users] Scaling on superclusters Florian Haberl
- [gmx-users] Scaling on superclusters David van der Spoel
  - [gmx-users] Scaling on superclusters Florian Haberl
[gmx-users] lipid parameters and ffG43 Chris Shaw
[gmx-users] surface tension units Ashish Gupta
[gmx-users] lipid parameters and ffG43 Chris Shaw
[gmx-users] dppc.itp and ffg43a Chris Shaw
[gmx-users] Help regarding Force fields file Atul Kumar
- [gmx-users] Help regarding Force fields file David van der Spoel
[gmx-users] output file of mk_angndx Yan Li
- [gmx-users] output file of mk_angndx David van der Spoel
[gmx-users] K+ atom type is not found in GROMOS96 Binbin Liu
- [gmx-users] K+ atom type is not found in GROMOS96 Xavier Periole
- [gmx-users] K+ atom type is not found in GROMOS96 Florian Haberl
- [gmx-users] K+ atom type is not found in GROMOS96 Xavier Periole
- [gmx-users] K+ atom type and KCl crystals Marc Baaden
  - [gmx-users] K+ atom type and KCl crystals Erik Lindahl
[gmx-users] unable to run energy minimization on short peptide Jaimin Shah
[gmx-users] Wrong Nose-Hoover integrator Michel Cuendet
[gmx-users] K+ atom type is not found in GROMOS96 Binbin Liu
- [gmx-users] K+ atom type is not found in GROMOS96 Xavier Periole
[gmx-users] unable to run energy minimization on short peptide Luca Mollica
[gmx-users] Forec field equation Atul Kumar
- [gmx-users] Forec field equation David
[gmx-users] a few questions Robert Soliva
[gmx-users] Building all atom topology Ilya Chorny
[gmx-users] atom index (1) in settles out of bounds (1-0) infante at few.vu.nl
- [gmx-users] atom index (1) in settles out of bounds (1-0) Berk Hess
[gmx-users] Problem with Glucose ring Patel Ronak Y
- [gmx-users] Problem with Glucose ring David
[gmx-users] Re: gmx-users Digest, Vol 9, Issue 51 Patel Ronak Y
- [gmx-users] Re: gmx-users Digest, Vol 9, Issue 51 David van der Spoel
[gmx-users] Simulation in Vacuum xieyh at hkusua.hku.hk
- [gmx-users] Simulation in Vacuum Dallas Warren
[gmx-users] Error in running parallel GROMACS quanta at chem.unipune.ernet.in
- [gmx-users] Error in running parallel GROMACS David van der Spoel
[gmx-users] energy units Ashish Gupta
- [gmx-users] energy units David van der Spoel
[gmx-users] A wired fatal error in grompp about ions Binbin Liu
- [gmx-users] A wired fatal error in grompp about ions David van der Spoel
[gmx-users] Re: Re: Re: Glucose Ring transition Patel Ronak Y
- [gmx-users] Re: Re: Re: Glucose Ring transition David van der Spoel
[gmx-users] trajectory not seen Jaimin Shah
- [gmx-users] trajectory not seen David van der Spoel
[gmx-users] How to do cluster analysis in the essential space after PCA? Zhenting Gao
[gmx-users] Flying ice cube lpgomes at fiocruz.br
- [gmx-users] Flying ice cube David van der Spoel

Last message date: Mon Jan 31 18:31:08 CET 2005
Archived on: Thu Nov 14 12:01:22 CET 2013

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