February 2005 Archives by thread

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Starting: Tue Feb 1 05:10:57 CET 2005
Ending: Mon Feb 28 22:28:51 CET 2005
Messages: 283

[gmx-users] mdrun discrepancy jaimin at iitb.ac.in
- [gmx-users] mdrun discrepancy Haberl Florian
[gmx-users] Re: Re: Re: Re: Glucose ring transition Patel Ronak Y
[gmx-users] Fatal error: Not enough ref_t and tau_t values! Markus O Kaukonen
- [gmx-users] Fatal error: Not enough ref_t and tau_t values! David van der Spoel
  - [gmx-users] how to detect jumping to periodic image ? Sandeep Somani
    - [gmx-users] how to detect jumping to periodic image ? David van der Spoel
    - [gmx-users] how to detect jumping to periodic image ? Anton Feenstra
- [gmx-users] Fatal error: Not enough ref_t and tau_t values! Choon Peng
- [gmx-users] Fatal error: Not enough ref_t and tau_t values! shavkat mamatkulov
[gmx-users] parallel problems... Arvid Soderhall
- [gmx-users] parallel problems... David van der Spoel
- [gmx-users] parallel problems... Florian Haberl
[gmx-users] thanks Jaimin Shah
- [gmx-users] thanks David van der Spoel
[gmx-users] computing tilt of helix Milan Melichercik
- [gmx-users] computing tilt of helix Marc F. Lensink
  - [gmx-users] md rerun Marc Bruning
    - [gmx-users] md rerun David van der Spoel
    - [gmx-users] md rerun Marc Bruning
    - [gmx-users] md rerun Marc Bruning
- [gmx-users] computing tilt of helix Berk Hess
[gmx-users] unusually long run required Jaimin Shah
- [gmx-users] unusually long run required Anton Feenstra
[gmx-users] free energy calculation Bamidele Adisa
[gmx-users] checkpoint gmx status Alan Wilter Sousa da Silva
- [gmx-users] checkpoint gmx status David van der Spoel
[gmx-users] unusually long run required David van der Spoel
[gmx-users] Compiling problem on IBM JS20 BladeCenter with Linux Suse 9 and Myrinet Pietro Lopriore
- [gmx-users] Compiling problem on IBM JS20 BladeCenter with Linux Suse 9 and Myrinet David van der Spoel
[gmx-users] GROMACS on double processor nodes Pietro Lopriore
- [gmx-users] GROMACS on double processor nodes David van der Spoel
[gmx-users] NVT or NPT ensemble? Hendrik Preuss
- [gmx-users] NVT or NPT ensemble? David van der Spoel
[gmx-users] ASP improper dihedral opls Ilya Chorny
[gmx-users] Free enrgy calculation in Dimers Nalantha Wanasundara
[gmx-users] How to do cluster analysis in the essential space after PCA? Anton Feenstra
[gmx-users] 4 processor system Anton Feenstra
[gmx-users] #ifdef in *.rtp - is it possible ? Anton Feenstra
[gmx-users] a few questions Anton Feenstra
[gmx-users] dppc.itp and ffg43a Anton Feenstra
[gmx-users] Re: GROMACS and Amber FF Anton Feenstra
[gmx-users] Re: Re: unusually long run required jaimin at iitb.ac.in
- [gmx-users] Re: Re: unusually long run required Anton Feenstra
- [gmx-users] constraining distance and minimum image convention Ester Chiessi
[gmx-users] fata error SLN Prasad Reddy
- [gmx-users] fata error Anton Feenstra
[gmx-users] ssh on parallel machine for mdrun: any way for background execution of the command? Luca Mollica
- [gmx-users] ssh on parallel machine for mdrun: any way for background execution of the command? Florian Haberl
- [gmx-users] ssh on parallel machine for mdrun: any way for background execution of the command? Tivadar Orban
  - [gmx-users] ssh on parallel machine for mdrun: any way for background execution of the command? Anton Feenstra
[gmx-users] How can we have better performances on an IBM JS20- Myrinet-Linux cluster? Pietro Lopriore
[gmx-users] using atom id to specify the position_restraints Binbin Liu
- [gmx-users] using atom id to specify the position_restraints David van der Spoel
  - [gmx-users] using atom id to specify the position_restraints Anton Feenstra
[gmx-users] Metalloproteins-creation of topology files chandran karunakaran
[gmx-users] opls parameters for organic molecules Uwe Richter
[gmx-users] Re: gmx-users Digest, Vol 10, Issue 9 Binbin Liu
- [gmx-users] Re: gmx-users Digest, Vol 10, Issue 9 David van der Spoel
[gmx-users] PRODRG2.5 server Osmany Guirola Cruz
[gmx-users] Metalloproteins-creation of topology files bruno.rizzuti at email.it
[gmx-users] bounded water molecules Raghunadha Reddy Burri
- [gmx-users] bounded water molecules David van der Spoel
[gmx-users] The trajectory and energy in by different nodes Tanping Li
- [gmx-users] The fftw and mpi Tanping Li
[gmx-users] (no subject) Aina Quintilla
- [gmx-users] (no subject) David van der Spoel
- [gmx-users] (no subject) Daan van Aalten
[gmx-users] Proteins on a solid surface Jon
- [gmx-users] Proteins on a solid surface David van der Spoel
- [gmx-users] Proteins on a solid surface Yu Sun (Denis)
[gmx-users] Trouble creating topology file Bill Evans
- [gmx-users] Trouble creating topology file David van der Spoel
[gmx-users] Umbrella Sampling question Adrian Gustavo Turjanski
- [gmx-users] Umbrella Sampling question Ilya Chorny
[gmx-users] best structure UCT Staff Member - Jackson
- [gmx-users] best structure David van der Spoel
[gmx-users] Implicit Solvation in Gromacs Gaurav Porwal
[gmx-users] pdb file for muscle caldesmon herbst at fhi-berlin.mpg.de
- [gmx-users] pdb file for muscle caldesmon David van der Spoel
[gmx-users] Harmonic potential mn2 at hw.ac.uk
- [gmx-users] Harmonic potential David van der Spoel
[gmx-users] water molecule not settled, is due to the change in the form of the box? Attilio
- [gmx-users] water molecule not settled, is due to the change in the form of the box? Attilio
[gmx-users] water molecule not settled, is due to the change in the form of the box? Attilio
- [gmx-users] water molecule not settled, is due to the change in the form of the box? David van der Spoel
  - [gmx-users] water molecule not settled, is due to the change in the form of the box? Attilio
- [gmx-users] DNA/RNA records for OPLS force field in GROMACS format. Andrey V Golovin
  - [gmx-users] DNA/RNA records for OPLS force field in GROMACS format. Marc Kreissler
    - [gmx-users] DNA/RNA records for OPLS force field in GROMACS format. david.evans at ulsop.ac.uk
    - [gmx-users] DNA/RNA records for OPLS force field in GROMACS format. Andrey V. Golovin
    - [gmx-users] DNA/RNA records for OPLS force field in GROMACS format. Maik Goette
- [gmx-users] water molecule not settled, is due to the change in the form of the box? Florian Haberl
  - [gmx-users] water molecule not settled, is due to the change in the form of the box? Andrey V Golovin
  - [gmx-users] distance between atoms of system and periodic image Ester Chiessi
    - [gmx-users] distance between atoms of system and periodic image David van der Spoel
    - [gmx-users] distance between atoms of system and periodic image Ester Chiessi
  - [gmx-users] water molecule not settled, is due to the change in the form of the box? parinald at unsl.edu.ar
    - [gmx-users] water molecule not settled, is due to the change in the form of the box? Florian Haberl
    - [gmx-users] PME vs. default electrostatics Arturas
    - [gmx-users] PME vs. default electrostatics David van der Spoel
[gmx-users] Demo not work Yunhong Hotta
- [gmx-users] Demo not work Florian Haberl
[gmx-users] problem regarding incomplete frame during gmxcheck jaimin at iitb.ac.in
[gmx-users] shift to the side Alberto Malvezzi
- [gmx-users] shift to the side David van der Spoel
[gmx-users] charge groups Marc Kreissler
- [gmx-users] charge groups Dallas Warren
  - [gmx-users] charge groups Erik Lindahl
[Fwd: Re: [gmx-users] best structure] David van der Spoel
[gmx-users] error in running MD vema aparna
[gmx-users] best structure Pim Schravendijk
[gmx-users] h-bonds in gromacs Attilio
- [gmx-users] h-bonds in gromacs Giacomo De Mori
  - [gmx-users] h-bonds in gromacs Giacomo De Mori
[gmx-users] (no subject) P Sturzenegger
- [gmx-users] (no subject) David van der Spoel
[gmx-users] Reading xtc Files Gunjan Mohan
- [gmx-users] Reading xtc Files T.A.Wassenaar
[gmx-users] Molecular Dynamics Litterature gar at pbgweb.no-ip.org
- [gmx-users] Molecular Dynamics Litterature diego vallejo
- [gmx-users] Molecular Dynamics Litterature Yang Ye
  - [gmx-users] Molecular Dynamics Litterature Peter C. Lai
    - [gmx-users] Molecular Dynamics Litterature mario orsi
[gmx-users] topology files generated with PRODRG and ffG43a1bon.itp coding Aina Quintilla
[gmx-users] About NME group construction ygao at phase1.unl.edu
- [gmx-users] About NME group construction David van der Spoel
  - [gmx-users] About NME group construction ygao at phase1.unl.edu
    - [gmx-users] About NME group construction ygao at phase1.unl.edu
    - [gmx-users] About NME group construction David van der Spoel
    - [gmx-users] About NME group construction ygao at phase1.unl.edu
    - [gmx-users] About NME group construction David van der Spoel
    - [gmx-users] About NME group construction ygao at phase1.unl.edu
    - [gmx-users] About NME group construction David van der Spoel
    - [gmx-users] About NME group construction David van der Spoel
- [gmx-users] If you use g_sdf ... Dallas Warren
[gmx-users] Molecular Dynamics Litterature gar at pbgweb.no-ip.org
- [gmx-users] Molecular Dynamics Litterature Peter C. Lai
  - [gmx-users] pull code with pbc=full Ester Chiessi
[gmx-users] strange error jaimin at iitb.ac.in
[gmx-users] including missing atoms Alan Wilter Sousa da Silva
- [gmx-users] including missing atoms ran at hemi.tau.ac.il
[gmx-users] ngmx not installed Jason de Joannis
- [gmx-users] ngmx not installed David van der Spoel
- [gmx-users] ngmx not installed Erik Lindahl
  - [gmx-users] ngmx not installed David van der Spoel
[gmx-users] Cationic Dummy Atom Method Maik Goette
- [gmx-users] Cationic Dummy Atom Method David van der Spoel
  - [gmx-users] Cationic Dummy Atom Method Maik Goette
    - [gmx-users] Cationic Dummy Atom Method David van der Spoel
[gmx-users] Re: including missing atoms Alan Wilter Sousa da Silva
[gmx-users] pull code with pbc=full Berk Hess
[gmx-users] Debugging Kirill Titievsky
- [gmx-users] Debugging David van der Spoel
  - [gmx-users] Assembly codes Manoj
    - [gmx-users] Assembly codes David van der Spoel
  - [gmx-users] Debugging Kirill Titievsky
  - [gmx-users] Debugging Kirill Titievsky
- [gmx-users] Debugging Erik Lindahl
  - [gmx-users] Debugging Kirill Titievsky
    - [gmx-users] Debugging Erik Lindahl
    - [gmx-users] Debugging Kirill Titievsky
    - [gmx-users] Debugging Erik Lindahl
    - [gmx-users] Debugging Andrey V Golovin
[gmx-users] Forcefields VISWANADHA SRIDHARA
- [gmx-users] Forcefields David van der Spoel
[gmx-users] molecular oxygen Cesar Lopez
- [gmx-users] molecular oxygen David van der Spoel
  - [gmx-users] molecular oxygen Cesar Lopez
    - [gmx-users] molecular oxygen David van der Spoel
[gmx-users] TIP5P box density ygao at phase1.unl.edu
- [gmx-users] TIP5P box density David van der Spoel
[gmx-users] ngmx not installed Jason de Joannis
[gmx-users] How to constraint protein + lipid, to move water into the pore channel Chittima Laohpongspaisan
- [gmx-users] How to constraint protein + lipid, to move water into the pore channel Maik Goette
[gmx-users] ngmx not installed Jason de Joannis
[gmx-users] About g_dih analyze ygao at phase1.unl.edu
- [gmx-users] About g_dih analyze David van der Spoel
  - [gmx-users] About g_dih analyze ygao at phase1.unl.edu
    - [gmx-users] About g_dih analyze David
    - [gmx-users] About g_dih analyze ygao at phase1.unl.edu
    - [gmx-users] About g_dih analyze David
    - [gmx-users] About g_dih analyze ygao at phase1.unl.edu
    - [gmx-users] About g_dih analyze David
    - [gmx-users] About g_dih analyze ygao at phase1.unl.edu
    - [gmx-users] About g_dih analyze Dallas Warren
[gmx-users] rerun problem neda mirsamadi
- [gmx-users] rerun problem David van der Spoel
  - [gmx-users] rerun problem Tanping Li
[gmx-users] LIE interaction Cesar Lopez
- [gmx-users] LIE interaction Anton Feenstra
  - [gmx-users] LIE interaction Cesar Lopez
[gmx-users] starting structure of DLPC lipid bilayer Qing Zhu
- [gmx-users] starting structure of DLPC lipid bilayer Marcos Villarreal
- [gmx-users] starting structure of DLPC lipid bilayer David L. Bostick
[gmx-users] error during energy minimization shailza singh
- [gmx-users] error during energy minimization Itamar Kass
  - [gmx-users] error during energy minimization shailza singh
    - [gmx-users] error during energy minimization Itamar Kass
    - [gmx-users] error during energy minimization shailza singh
    - [gmx-users] error during energy minimization Itamar Kass
    - [gmx-users] error during energy minimization shailza singh
    - [gmx-users] error during energy minimization Itamar Kass
- [gmx-users] error during energy minimization David
[gmx-users] (no subject) Dongsheng Zhang
- [gmx-users] (no subject) David
[gmx-users] Questions about opls-aa force field for gromacs zjim
- [gmx-users] Questions about opls-aa force field for gromacs David
[gmx-users] Adding a new molecule Ramachandra Rao Gullapalli
- [gmx-users] Adding a new molecule David
[gmx-users] Adding a new molecule Ramachandra Rao Gullapalli
- [gmx-users] Adding a new molecule David
[gmx-users] multple T-coupling errors Yunhong Hotta
- [gmx-users] multple T-coupling errors Haberl Florian
[gmx-users] problem in energy minimization shailza singh
[gmx-users] Topology for hetroatom (PRODRG) Alok
- [gmx-users] Topology for hetroatom (PRODRG) David
  - [gmx-users] Principal Component Analysis Gia Maisuradze
  - [gmx-users] Topology for hetroatom (PRODRG) Alok
    - [gmx-users] Topology for hetroatom (PRODRG) David
    - [gmx-users] Topology for hetroatom (PRODRG) Alok
    - [gmx-users] Topology for hetroatom (PRODRG) David
    - [gmx-users] Topology for hetroatom (PRODRG) Alok
- [gmx-users] Topology for hetroatom (PRODRG) Maik Goette
  - [gmx-users] Topology for hetroatom (PRODRG) Alok
[gmx-users] improper dihedral and proper dihedral Dongsheng Zhang
- [gmx-users] improper dihedral and proper dihedral David
[gmx-users] monitor distance during simulation David L. Bostick
[gmx-users] Re: starting structure of DLPC lipid bilayer Zhu, Qing
[gmx-users] monitor distance during simulation Berk Hess
- [gmx-users] mdrun -rerun Shatadal Ghosh
  - [gmx-users] mdrun -rerun David
[gmx-users] ld_seed functioning? Björn Windshügel
- [gmx-users] ld_seed functioning? David
[gmx-users] total time for MDsimulation shailza singh
- [gmx-users] total time for MDsimulation Maik Goette
[gmx-users] gen_seed herbst at fhi-berlin.mpg.de
- [gmx-users] gen_seed David van der Spoel
[gmx-users] g_cluster Hendrik Preuss
[gmx-users] file truncated shailza singh
[gmx-users] Grace use problem ygao at phase1.unl.edu
- [gmx-users] Grace use problem David
[gmx-users] creating an rtp file Gireesh M Krishnan
- [gmx-users] creating an rtp file Maik Goette
[gmx-users] gmx ff all H again Alan Wilter Sousa da Silva
- [gmx-users] gmx ff all H again David
- [gmx-users] Re: gmx ff all H again Alan Wilter Sousa da Silva
[gmx-users] BUG: gromacs-REMD implementation Walter Ash
[gmx-users] BUG: gromacs-REMD implementation Walter Ash
- [gmx-users] BUG: gromacs-REMD implementation Berk Hess
[gmx-users] again the multiple T-coupling errors Yunhong Hotta
- [gmx-users] again the multiple T-coupling errors Haberl Florian
[gmx-users] Discussion about DNA naming Maik Goette
- [gmx-users] Discussion about DNA naming Andrey V. Golovin
  - [gmx-users] Discussion about DNA naming Maik Goette
[gmx-users] force field for long alkanes and membrane protein Binbin Liu
[gmx-users] force field for long alkanes and membrane protein Luca Mollica
[gmx-users] Position_restraints in .top vs freezegrps in .mdp Binbin Liu
[gmx-users] About .xvg file display ygao at phase1.unl.edu
- [gmx-users] About .xvg file display Andrey V. Golovin
  - [gmx-users] About .xvg file display ygao at phase1.unl.edu
    - [gmx-users] About .xvg file display Marc Vogt
[gmx-users] Topology for hetroatom (PRODRG) Alok
[gmx-users] Re :force field for long alkanes and membrane protein Binbin Liu
- [gmx-users] Gromacs and SHAKE Shatadal Ghosh
[gmx-users] Topology for hetroatom (PRODRG) Alok
[gmx-users] freeze atoms Cesar Lopez
[gmx-users] SPC/E, S-S bridge Kortvelyesi Tamas
[gmx-users] Compilation Error on OSX Amrapali Arshanapalli
- [gmx-users] Compilation Error on OSX Erik Lindahl
[gmx-users] fluctuation of protein coordinates shailza singh
- [gmx-users] fluctuation of protein coordinates Lars Schaefer
[gmx-users] pdb2gmx + rmsd from native structure Ivica Res
- [gmx-users] pdb2gmx + rmsd from native structure Rainer Böckmann
[gmx-users] program halted shailza singh
- [gmx-users] program halted Choon Peng
[gmx-users] running two proteinsMD in separate terminals shailza singh
[gmx-users] g_cluster problem Andrew Beevers
- [gmx-users] g_cluster problem Xavier Periole
Antw: [gmx-users] g_cluster problem Hendrik Preuss
[gmx-users] nucleic acid PDB input files Cameron Mura
[gmx-users] constraints Cesar Lopez
- [gmx-users] constraints David

Last message date: Mon Feb 28 22:28:51 CET 2005
Archived on: Thu Nov 14 12:01:26 CET 2013

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