February 2008 Archives by thread

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Starting: Fri Feb 1 00:34:15 CET 2008
Ending: Fri Feb 29 19:29:25 CET 2008
Messages: 486

• [gmx-users] Weird structure after minimization (membrane proteinsimulation   Mark Abraham
  • [gmx-users] Weird structure after minimization (membrane protein simulation)   Alok
    • [gmx-users] Weird structure after minimization (membrane protein simulation)   Mark Abraham
• [gmx-users] NOE restraints and undefined hydrogen atoms, virtual interaction sites   Mark Abraham
• [gmx-users] Re: Weird behavior with Pull code   Ilya Chorny
• [gmx-users] torsion potential with 7 parameters   Xavier Periole
  • [gmx-users] torsion potential with 7 parameters   Ángel Piñeiro
    • [gmx-users] torsion potential with 7 parameters   Xavier Periole
• [gmx-users] Rugged dG/dlambda when turning off charges   Maik Goette
• [gmx-users] RE: RE : FEP : separating components of dgdl   Berk Hess
• [gmx-users] Methanethiosulfonate - amberff   dwunnick at uni-osnabrueck.de
• [gmx-users] What Parameters Can Be Analyzes Using Data of .edo File?   Anirban Ghosh
  • [gmx-users] What Parameters Can Be Analyzes Using Data of .edo File?   Justin A. Lemkul
• [gmx-users] concatenate tpr file   pragya chohan
  • [gmx-users] concatenate tpr file   Justin A. Lemkul
  • [gmx-users] concatenate tpr file   Xavier Periole
  • [gmx-users] concatenate tpr file   Mark Abraham
• [gmx-users] Re: help   Justin A. Lemkul
• [gmx-users] analysis of POPC   pragya chohan
  • [gmx-users] analysis of POPC   Justin A. Lemkul
    • [gmx-users] analysis of POPC   pragya chohan
      • [gmx-users] analysis of POPC   Justin A. Lemkul
• [gmx-users] analysis of POPC   Alan Dodd
  • [gmx-users] analysis of POPC   Eric Jakobsson
• [gmx-users] exchanged pairs in the log file of a remd simulation   OZGE ENGIN
  • [gmx-users] exchanged pairs in the log file of a remd simulation   David van der Spoel
    • [gmx-users] exchanged pairs in the log file of a remd simulation   Berk Hess
  • [gmx-users] exchanged pairs in the log file of a remd simulation   Mark Abraham
• [gmx-users] QM/MM cpmd   jacopo.sgrignani at unifi.it
  • [gmx-users] QM/MM cpmd   Marius Retegan
• [gmx-users] fatal error in g_order   pragya chohan
  • [gmx-users] fatal error in g_order   Justin A. Lemkul
    • [gmx-users] fatal error in g_order   pragya chohan
      • [gmx-users] fatal error in g_order   Justin A. Lemkul
• [gmx-users] exchanged pairs in the log file of a remd simulation   OZGE ENGIN
  • [gmx-users] exchanged pairs in the log file of a remd simulation   Mark Abraham
• [gmx-users] MD of DNA-protein complex AND non-protein inhibitor   jlenz
  • [gmx-users] MD of DNA-protein complex AND non-protein inhibitor   Justin A. Lemkul
  • [gmx-users] MD of DNA-protein complex AND non-protein inhibitor   Maik Goette
• [gmx-users] Weird structure after minimization (membrane protein simulation)   chris.neale at utoronto.ca
• [gmx-users] MD of DNA-protein complex AND non-protein inhibitor   Joern Lenz
  • [gmx-users] MD of DNA-protein complex AND non-protein inhibitor   Mark Abraham
• [gmx-users] Query   rohit gole
  • [gmx-users] Query   Mark Abraham
    • [gmx-users] Periodic Boundary condition   Rohit
      • [gmx-users] Periodic Boundary condition   Mark Abraham
      • [gmx-users] Periodic Boundary condition   Rohit
      • [gmx-users] Periodic Boundary condition   Mark Abraham
      • [gmx-users] Periodic Boundary condition   Yawar Qadri
• [gmx-users] Deviations in free energies with slow growth (single and 3-step process)   Maik Goette
  • [gmx-users] Deviations in free energies with slow growth (single and 3-step process)   David Mobley
    • [gmx-users] Deviations in free energies with slow growth (single and 3-step process)   Maik Goette
      • [gmx-users] Deviations in free energies with slow growth (single and 3-step process)   David Mobley
• [gmx-users] FEP : separating components of dgdl   BON Michael
  • [gmx-users] FEP : separating components of dgdl   Maik Goette
  • [gmx-users] RE: FEP : separating components of dgdl   Berk Hess
• [gmx-users] How to obtain the temperature from a given trajectory   hector Mtz-Seara
• [gmx-users] How to obtain the temperature from a given trajectory   hector Mtz-Seara
  • [gmx-users] How to obtain the temperature from a given trajectory   Mark Abraham
  • [gmx-users] How to obtain the temperature from a given trajectory   Berk Hess
• [gmx-users] analysis of POPC   chris.neale at utoronto.ca
• [gmx-users] Source code file: gmxfio.c, line: 784   vijay kumar hinge vijay
  • [gmx-users] Source code file: gmxfio.c, line: 784   Mark Abraham
    • [gmx-users] Source code file: gmxfio.c, line: 784   Martin Höfling
• [gmx-users] RE:Source code file: gmxfio.c, line: 784   vijay kumar hinge vijay
• [gmx-users] segmentation fault (wrong settings in mdp file)   Egidijus Kuprusevicius
  • [gmx-users] segmentation fault (wrong settings in mdp file)   Louic Vermeer
    • [gmx-users] segmentation fault (wrong settings in mdp file)   Justin A. Lemkul
      • [gmx-users] segmentation fault (wrong settings in mdp file)   Mark Abraham
• [gmx-users] Re: Warning: pressure scaling more than 1%   Wissensbund at gmx.net
• [gmx-users] Re: Warning: pressure scaling more than 1%   Wissensbund at gmx.net
• [gmx-users] Re: WARNING concerning lipid.itp   Wissensbund at gmx.net
• [gmx-users] RE : FEP : separating components of dgdl   BON Michael
  • [gmx-users] RE: RE : FEP : separating components of dgdl   Berk Hess
  • [gmx-users] RE : FEP : separating components of dgdl   Maik Goette
• [gmx-users] Total energy of protein only   Yoshiko Santoso
• [gmx-users] Re: WARNING concerning lipid.itp   chris.neale at utoronto.ca
• [gmx-users] Total energy of protein only   chris.neale at utoronto.ca
• [gmx-users] Change in .gro in grompp   Caleb Carlin
  • [gmx-users] Change in .gro in grompp   Justin A. Lemkul
  • [gmx-users] Change in .gro in grompp   Mark Abraham
    • [gmx-users] Change in .gro in grompp   Tsjerk Wassenaar
      • [gmx-users] Change in .gro in grompp   Caleb Carlin
      • [gmx-users] Change in .gro in grompp   Mark Abraham
• [gmx-users] Gro file with more than 99999 atoms   Tandia, Adama
  • [gmx-users] Gro file with more than 99999 atoms   Tsjerk Wassenaar
• [gmx-users] pdb2gmx: Adding non standard residues and molecular moieties   Eddie Mende
  • [gmx-users] pdb2gmx: Adding non standard residues and molecular moieties   Maik Goette
  • [gmx-users] pdb2gmx: Adding non standard residues and molecular moieties   Mark Abraham
    • [gmx-users] pdb2gmx: Adding non standard residues and molecular moieties   David van der Spoel
• [gmx-users] itp file for phosphate ion   Eddie Mende
  • [gmx-users] itp file for phosphate ion   Justin A. Lemkul
• [gmx-users] g_dist producing inconsistent values   Alan Dodd
• [gmx-users] gmx-cpmd   jacopo.sgrignani at unifi.it
  • [gmx-users] gmx-cpmd   Marius Retegan
• [gmx-users] Re: installation problem for MAC OS   Warner Yuen
  • [gmx-users] Re: installation problem for MAC OS   Mark Abraham
• [gmx-users] grompp error "Not enough space" on IBM AIX   Chris Neale
  • [gmx-users] grompp error "Not enough space" on IBM AIX   David van der Spoel
    • [gmx-users] grompp error "Not enough space" on IBM AIX   Marius Retegan
• [gmx-users] (no subject)   mahendra awale
  • [gmx-users] (no subject)   Tsjerk Wassenaar
• [gmx-users] Phosphohistidine parameters   Eddie Mende
  • [gmx-users] Phosphohistidine parameters   Justin A. Lemkul
    • [gmx-users] Phosphohistidine parameters   Satyan Sharma
    • [gmx-users] Phosphohistidine parameters   Satyan Sharma
  • [gmx-users] Phosphohistidine parameters   Mark Abraham
• [gmx-users] g_dist producing inconsistent values   Alan Dodd
  • [gmx-users] g_dist producing inconsistent values   Mark Abraham
• [gmx-users] Problem with amidation in pdb2gmx   s4026869 at student.uq.edu.au
  • [gmx-users] Problem with amidation in pdb2gmx   Justin A. Lemkul
  • [gmx-users] Problem with amidation in pdb2gmx   Justin A. Lemkul
    • [gmx-users] Problem with amidation in pdb2gmx   Justin A. Lemkul
      • [gmx-users] Problem with amidation in pdb2gmx   Mitchell Stanton-Cook
• [gmx-users] g_dist producing inconsistent values   chris.neale at utoronto.ca
  • [gmx-users] g_dist producing inconsistent values   David van der Spoel
• [gmx-users] do-dssp   David Mobley
  • [gmx-users] do-dssp   David van der Spoel
• [gmx-users] g_dist producing inconsistent values   chris.neale at utoronto.ca
• [gmx-users] Re: installation problem for MAC OS   Warner Yuen
  • [gmx-users] Re: installation problem for MAC OS   Erik Lindahl
    • [gmx-users] Re: installation problem for MAC OS   Yiannis
• [gmx-users] g_dist producing inconsistent values   Alan Dodd
  • [gmx-users] g_dist producing inconsistent values   Patrick Fuchs
• [gmx-users] To know about constant stress ensemble   shankari hariharan
• [gmx-users] Pre-announcement: advanced Gromacs workshop at Stanford April 7-8   Erik Lindahl
• [gmx-users] Proline on OPLSSaa   Mauro Puppett
  • [gmx-users] Proline on OPLSSaa   Mark Abraham
    • [gmx-users] Proline on OPLSSaa   Tsjerk Wassenaar
      • [gmx-users] Proline on OPLSSaa   Mauro Puppett
      • [gmx-users] Proline on OPLSSaa   Mark Abraham
• [gmx-users] Re: Total Energy protein only   chris.neale at utoronto.ca
• [gmx-users] non bonded interactions   Sheyore Omovie
  • [gmx-users] non bonded interactions   Xavier Periole
    • [gmx-users] non bonded interactions   Sheyore Omovie
      • [gmx-users] non bonded interactions   Sheyore Omovie
      • [gmx-users] non bonded interactions   mark.abraham at anu.edu.au
• [gmx-users] non bonded interactions   chris.neale at utoronto.ca
• [gmx-users] GMX compilation with "--enable-threads"   yren at home.ipe.ac.cn
  • [gmx-users] GMX compilation with "--enable-threads"   mark.abraham at anu.edu.au
• [gmx-users] GMX compilation with "--enable-threads"   yren at home.ipe.ac.cn
  • [gmx-users] GMX compilation with "--enable-threads"   mark.abraham at anu.edu.au
• [gmx-users] selecting multiple groups while using analysis routines like trjconv   himanshu khandelia
  • [gmx-users] selecting multiple groups while using analysis routines like trjconv   Marcus Kubitzki
• [gmx-users] Re: free energy calculation   David Mobley
• [gmx-users] Wheter the drift velocity has been removed from calculating the temperature?   Hu Zhongqiao
  • [gmx-users] Wheter the drift velocity has been removed from calculating the temperature?   David van der Spoel
• [gmx-users] Hello   Anamika Awasthi
  • [gmx-users] Hello   Tsjerk Wassenaar
  • [gmx-users] Hello   Justin A. Lemkul
• [gmx-users] Re: Wheter the drift velocity has been removed from calculating the temperature?   Hu Zhongqiao
  • [gmx-users] Re: Wheter the drift velocity has been removed from calculating the temperature?   David van der Spoel
• [gmx-users] adding a polar Hydrogen atom to pdb file   kinshuk at chem.iitb.ac.in
  • [gmx-users] adding a polar Hydrogen atom to pdb file   Justin A. Lemkul
• [gmx-users] RSS feed for gromacs.org?   Moore, Jonathan (J)
  • [gmx-users] RSS feed for gromacs.org?   David van der Spoel
• [gmx-users] Generate topology file for Gromacs a from Accelrys or pdb file   Tandia, Adama
  • [gmx-users] Generate topology file for Gromacs a from Accelrys or pdb file   Mark Abraham
• [gmx-users] Temperature of the system when using stochastic dynamics in vacuum   钩深致远
  • [gmx-users] Temperature of the system when using stochastic dynamics in vacuum   Berk Hess
• [gmx-users] g_rms , getting rmsd matrix and the histogram of this matrix   OZGE ENGIN
  • [gmx-users] g_rms , getting rmsd matrix and the histogram of this matrix   Xavier Periole
• [gmx-users] RAM memory   zazeri
  • [gmx-users] RAM memory   Mark Abraham
    • [gmx-users] RAM memory   zazeri
• [gmx-users] the 2 nd column of the output of g_cluster with -dist option   OZGE ENGIN
  • [gmx-users] the 2 nd column of the output of g_cluster with -dist option   Xavier Periole
• [gmx-users] the 2 nd column of the output of g_cluster with -dist option   OZGE ENGIN
  • [gmx-users] the 2 nd column of the output of g_cluster with -dist option   Xavier Periole
• [gmx-users] adding atoms in PDB file   s lal badshah
  • [gmx-users] adding atoms in PDB file   mark.abraham at anu.edu.au
• [gmx-users] "Lam" is not required for running parallel job   sunita at chem.iitb.ac.in
  • [gmx-users] "Lam" is not required for running parallel job   mark.abraham at anu.edu.au
    • [gmx-users] "Lam" is not required for running parallel job   sunita at chem.iitb.ac.in
      • [gmx-users] "Lam" is not required for running parallel job   Carsten Kutzner
      • [gmx-users] "Lam" is not required for running parallel job   Jochen Hub
      • [gmx-users] "Lam" is not required for running parallel job   Martin Höfling
      • [gmx-users] "Lam" is not required for running parallel job   mark.abraham at anu.edu.au
      • [gmx-users] "Lam" is not required for running parallel job   sunita at chem.iitb.ac.in
• [gmx-users] Strange output with Genbox   Jens Pohl
  • [gmx-users] Strange output with Genbox   David van der Spoel
  • [gmx-users] Strange output with Genbox   mark.abraham at anu.edu.au
• [gmx-users] Strange output with Genbox   Jens Pohl
  • [gmx-users] Strange output with Genbox   David van der Spoel
• [gmx-users] (no subject)   cilpa at users.csc.fi
  • [gmx-users] (no subject)   Maik Goette
    • [gmx-users] toluene tutorial sc-power value   cilpa at users.csc.fi
      • [gmx-users] toluene tutorial sc-power value   Maik Goette
      • [gmx-users] toluene tutorial sc-power value   cilpa at users.csc.fi
      • [gmx-users] toluene tutorial sc-power value   Maik Goette
      • [gmx-users] toluene tutorial sc-power value   cilpa at users.csc.fi
      • [gmx-users] toluene tutorial sc-power value   Maik Goette
      • [gmx-users] toluene tutorial sc-power value   cilpa at users.csc.fi
      • [gmx-users] toluene tutorial sc-power value   Maik Goette
• [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   reich at mpikg.mpg.de
  • [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   Berk Hess
    • [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   Stéphane Téletchéa
      • [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   Berk Hess
      • [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   Stéphane Téletchéa
• [gmx-users] problem regarding protein in water simulation   sudheer babu
  • [gmx-users] problem regarding protein in water simulation   Jochen Hub
    • [gmx-users] problem regarding protein in water simulation   David van der Spoel
  • [gmx-users] problem regarding protein in water simulation   Mark Abraham
• [gmx-users] Problem of running double precision with constraint forces by pull code   wendung at umich.edu
  • [gmx-users] Problem of running double precision with constraint forces by pull code   Mark Abraham
• [gmx-users] Problem in constraint force pulling   wendung at umich.edu
• [gmx-users] eigenvalues as a function of time   L. Michel Espinoza-Fonseca
  • [gmx-users] eigenvalues as a function of time   Marcus Kubitzki
    • [gmx-users] eigenvalues as a function of time   L. Michel Espinoza-Fonseca
    • [gmx-users] eigenvalues as a function of time   L. Michel Espinoza-Fonseca
      • [gmx-users] eigenvalues as a function of time   Tsjerk Wassenaar
      • [gmx-users] eigenvalues as a function of time   L. Michel Espinoza-Fonseca
      • [gmx-users] eigenvalues as a function of time   Tsjerk Wassenaar
      • [gmx-users] eigenvalues as a function of time   L. Michel Espinoza-Fonseca
• [gmx-users] Strange output with Genbox   Jens Pohl
• [gmx-users] Strange output with Genbox   Jens Pohl
  • [gmx-users] Strange output with Genbox   mark.abraham at anu.edu.au
• [gmx-users] Strange output with Genbox   Jens Pohl
• [gmx-users] Does One need to set comm_mode = none for an equilibrium MD to get exact MSD?   Hu Zhongqiao
  • [gmx-users] Does One need to set comm_mode = none for an equilibrium MD to get exact MSD?   David van der Spoel
• [gmx-users] subscription   Anamika Awasthi
• [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   reich at mpikg.mpg.de
  • [gmx-users] Skewed box using Parrinello-Rahman pressure coupling   Berk Hess
• [gmx-users] Strange dgdl-value together with lincs   Maik Goette
  • [gmx-users] Strange dgdl-value together with lincs   Berk Hess
    • [gmx-users] Strange dgdl-value together with lincs   Maik Goette
      • [gmx-users] Strange dgdl-value together with lincs   Berk Hess
      • [gmx-users] Strange dgdl-value together with lincs   Berk Hess
      • [gmx-users] Strange dgdl-value together with lincs   Maik Goette
      • [gmx-users] Strange dgdl-value together with lincs   Berk Hess
      • [gmx-users] Strange dgdl-value together with lincs   David Mobley
      • [gmx-users] Strange dgdl-value together with lincs   Maik Goette
• [gmx-users] still got the problem with the output of g_cluster   OZGE ENGIN
  • [gmx-users] still got the problem with the output of g_cluster   Mark Abraham
• [gmx-users] still got the problem with the output of g_cluster   OZGE ENGIN
  • [gmx-users] still got the problem with the output of g_cluster   mark.abraham at anu.edu.au
• [gmx-users] still got the problem with the output of g_cluster   OZGE ENGIN
  • [gmx-users] still got the problem with the output of g_cluster   mark.abraham at anu.edu.au
• [gmx-users] still got the problem with the output of g_cluster   OZGE ENGIN
• [gmx-users] (no subject)   Luisa Calvanese
  • [gmx-users] (no subject)   Maik Goette
• [gmx-users] there is no enough information about the implementation of both diagonalization and Monte Carlo methods of g_cluster in the manual   OZGE ENGIN
  • [gmx-users] there is no enough information about the implementation of both diagonalization and Monte Carlo methods of g_cluster in the manual   David van der Spoel
• [gmx-users] problem regarding insertion of protein into lipidbilayer   sudheer babu
  • [gmx-users] problem regarding insertion of protein into lipidbilayer   Justin A. Lemkul
    • [gmx-users] problem regarding insertion of protein into lipidbilayer   Stéphane Téletchéa
• [gmx-users] Abnormal fluctuation in RMSD   Anamika Awasthi
  • [gmx-users] Abnormal fluctuation in RMSD   Florian Haberl
  • [gmx-users] Abnormal fluctuation in RMSD   Justin A. Lemkul
• [gmx-users] abnormal RMSD   Anamika Awasthi
  • [gmx-users] abnormal RMSD   Justin A. Lemkul
    • [gmx-users] abnormal RMSD   Tsjerk Wassenaar
  • [gmx-users] abnormal RMSD   Anamika Awasthi
    • [gmx-users] abnormal RMSD   Justin A. Lemkul
• [gmx-users] Abnormal RMSD   Anamika Awasthi
• [gmx-users] How to ask pdb2gmx to print all parameters in the itp file   LeeHui
• [gmx-users] "rmsd distance" and "rmsd deviation" option for the -dista option of g_cluster   OZGE ENGIN
• [gmx-users] How to ask pdb2gmx to print all parameters in the itp file   Alan Dodd
  • [gmx-users] How to ask pdb2gmx to print all parameters in the itp file   Tsjerk Wassenaar
    • [gmx-users] How to ask pdb2gmx to print all parameters in the itp file   Mark James Abraham
• [gmx-users] Stanford workshop april 7-8   Erik Lindahl
• [gmx-users] Stanford workshop april 7-8   OZGE ENGIN
  • [gmx-users] Stanford workshop april 7-8   Erik Lindahl
    • [gmx-users] Pressure Coupling for DPPC Bilayers   Sona Aramyan
• [gmx-users] about using amb2gmx.pl   xi zhao
  • [gmx-users] about using amb2gmx.pl   Mark Abraham
    • 回复： Re: [gmx-users] about using amb2gmx.pl   xi zhao
      • »Ø¸´£º Re: [gmx-users] about using amb2gmx.pl   Justin A. Lemkul
      • 回复： Re: [gmx-users] about using amb2gmx.pl   Mark Abraham
      • 回复： Re: 回复： Re: [gmx-users] about using amb2gmx.pl   xi zhao
      • 回复： Re: 回复： Re: [gmx-users] about using amb2gmx.pl   Mark Abraham
      • 回复： Re: 回复： Re: 回复： Re: [gmx-users] about using amb2gmx.pl   xi zhao
      • 回复： Re: 回复： Re: 回复： Re: [gmx-users] about using amb2gmx.pl   Mark Abraham
      • 回复： Re: 回复： Re: 回复： Re: 回复： Re: [gmx-users] about using amb2gmx.pl   xi zhao
      • »Ø¸´£º Re: »Ø¸´£º Re: »Ø¸´£º Re: »Ø¸´£º Re: [gmx-users] about using amb2gmx.pl   Justin A. Lemkul
      • 回复： Re: 回复： Re: 回复： Re: 回复： Re: 回复： Re: [gmx-users] about using amb2gmx.pl   xi zhao
      • =?GB2312?B?u9i4tKO6IFJlOiC72Li0o7ogUmU6ILvYuLSjuiBSZTogu9i4tA==?= =?GB2312?B?o7ogUmU6ILvYuLSBfyBSZTogW2dteC11c2Vyc10gYWJvdXQgdXNpbmcgYW1iMg==?= =?GB2312?B?Z214LnBs?=   Mark Abraham
      • 回复： Re: 回复： Re: 回复： Re: 回复： Re: [gmx-users] about using amb2gmx.pl   Mark Abraham
      • Re: 回复： Re: 回复： Re: 回复： Re: 回复： Re: [gmx-users] about using amb2gmx.pl   David Mobley
      • 回复： Re: 回复： Re: 回复： Re: 回复： Re: 回复： Re: [gmx-users] about using amb2gmx.pl   xi zhao
• [gmx-users] How to ask pdb2gmx to print all parameters in the itp file   LeeHui
• [gmx-users] Free Energy Calculations   Justin A. Lemkul
  • [gmx-users] Free Energy Calculations   David Mobley
    • [gmx-users] Free Energy Calculations   David Mobley
    • [gmx-users] Free Energy Calculations   Justin A. Lemkul
• [gmx-users] distance options for g_cluster   OZGE ENGIN
  • [gmx-users] distance options for g_cluster   Mark Abraham
• [gmx-users] problem with structure factor in g_rdf   jagannath mondal
• [gmx-users] distance options for g_cluster   OZGE ENGIN
• [gmx-users] Patch for PME in Free Energy?   Justin A. Lemkul
• [gmx-users] Polyethylene   Zuzana Benkova
• [gmx-users] RE: Patch for PME in Free Energy?   van Bemmelen
  • [gmx-users] RE: Patch for PME in Free Energy?   Justin A. Lemkul
• [gmx-users] Loss of GTP in topology file.   s lal badshah
  • [gmx-users] Loss of GTP in topology file.   Mark Abraham
    • [gmx-users] Loss of GTP in topology file.   Daniel Adriano Silva M
• [gmx-users] Registration open for Stanford workshop April 7 & 8   Erik Lindahl
• [gmx-users] calculating B-factor   pragya chohan
  • [gmx-users] calculating B-factor   Bjoern Windshuegel
    • [gmx-users] calculating B-factor   pragya chohan
• [gmx-users] angle and dihedral as a function of time   SWAPNA
  • [gmx-users] angle and dihedral as a function of time   Alok
• [gmx-users] Polyethylene   Zuzana Benkova
• [gmx-users] problem regarding .top file generated by genbox   sudheer babu
  • [gmx-users] problem regarding .top file generated by genbox   Justin A. Lemkul
    • [gmx-users] problem regarding .top file generated by genbox   Mark Abraham
• [gmx-users] Lennard Jones spheres   Chiara Parravicini
  • [gmx-users] Lennard Jones spheres   Mark Abraham
    • [gmx-users] Lennard Jones spheres   Chiara Parravicini
      • [gmx-users] Lennard Jones spheres   Mark Abraham
      • [gmx-users] Lennard Jones spheres   Chiara Parravicini
      • [gmx-users] Lennard Jones spheres   Mark Abraham
• [gmx-users] RE:problem regarding .top file generated by genbox   sudheer babu
  • [gmx-users] RE:problem regarding .top file generated by genbox   Mark Abraham
• [gmx-users] Re: gmx-users Digest, Vol 46, Issue 56   sudheer babu
  • [gmx-users] Re: gmx-users Digest, Vol 46, Issue 56   Mark Abraham
  • [gmx-users] Re: gmx-users Digest, Vol 46, Issue 56   Justin A. Lemkul
• [gmx-users] problem in hdb file   Zuzana Benkova
  • [gmx-users] problem in hdb file   Mark Abraham
• [gmx-users] Strange dgdl-value together with lincs   van Bemmelen
  • [gmx-users] Strange dgdl-value together with lincs   Berk Hess
  • [gmx-users] Strange dgdl-value together with lincs   Maik Goette
    • [gmx-users] Strange dgdl-value together with lincs   Berk Hess
• [gmx-users] Strange dgdl-value together with lincs   van Bemmelen
• [gmx-users] unfolding a protein   Siavoush Dastmalchi
  • [gmx-users] unfolding a protein   Justin A. Lemkul
    • [gmx-users] unfolding a protein   Siavoush Dastmalchi
      • [gmx-users] unfolding a protein   Justin A. Lemkul
      • [gmx-users] unfolding a protein   Siavoush Dastmalchi
      • [gmx-users] problem with Shake block crossing node boundaries   Siavoush Dastmalchi
      • [gmx-users] problem with Shake block crossing node boundaries   David van der Spoel
      • [gmx-users] problem with genion   Siavoush Dastmalchi
  • [gmx-users] unfolding a protein   mon_sharma at research.iiit.ac.in
    • [gmx-users] unfolding a protein   Xavier Periole
• [gmx-users] DNA adduct simulation: grompp error   Nathalie Geneste
  • [gmx-users] DNA adduct simulation: grompp error   TJ Piggot
  • [gmx-users] DNA adduct simulation: grompp error   Mark Abraham
• [gmx-users] Dose the GROMOS FF favour beta-sheets?   pascal.baillod at epfl.ch
  • [gmx-users] Dose the GROMOS FF favour beta-sheets?   Tsjerk Wassenaar
• [gmx-users] T-Coupling and COM removal   Ilya Chorny
• [gmx-users] twin range and switched cutoffs energy differences   David Osguthorpe
  • [gmx-users] memory requirements   Syma Khalid
    • [gmx-users] memory requirements   Erik Lindahl
      • [gmx-users] memory requirements   Syma Khalid
  • [gmx-users] twin range and switched cutoffs energy differences   Mark Abraham
    • [gmx-users] twin range and switched cutoffs energy differences   David Osguthorpe
• [gmx-users] Problem regarding tc_grps   sudheer babu
  • [gmx-users] Problem regarding tc_grps   Justin A. Lemkul
• [gmx-users] How to take snapshots every 1 nano-sec of a 30 nano-se simulation?   Anirban Ghosh
  • [gmx-users] How to take snapshots every 1 nano-sec of a 30 nano-se simulation?   David van der Spoel
• [gmx-users] problem about position restrain   sudheer babu
  • [gmx-users] problem about position restrain   Justin A. Lemkul
    • [gmx-users] problem about position restrain   Daniel Larsson
• [gmx-users] Building Topology with all hydrogens   Subhrangshu Supakar
  • [gmx-users] Building Topology with all hydrogens   Justin A. Lemkul
• [gmx-users] Re: T-Coupling and COM removal   Markus Miettinen
• [gmx-users] CHARMM nonbonded parameters and grompp output   Justin A. Lemkul
  • [gmx-users] CHARMM nonbonded parameters and grompp output   David van der Spoel
  • [gmx-users] CHARMM nonbonded parameters and grompp output   Mark Abraham
    • [gmx-users] CHARMM nonbonded parameters and grompp output   Justin A. Lemkul
      • [gmx-users] CHARMM nonbonded parameters and grompp output   Mark Abraham
      • [gmx-users] CHARMM nonbonded parameters and grompp output   Justin A. Lemkul
      • [gmx-users] CHARMM nonbonded parameters and grompp output   Mark Abraham
      • [gmx-users] CHARMM nonbonded parameters and grompp output   Justin A. Lemkul
      • [gmx-users] CHARMM nonbonded parameters and grompp output   Mark Abraham
• [gmx-users]build topology file for a molecule define with new residues   cilpa at users.csc.fi
  • [gmx-users]build topology file for a molecule define with new residues   Justin A. Lemkul
    • [gmx-users]build topology file for a molecule define with new residues   Tsjerk Wassenaar
      • [gmx-users]build topology file for a molecule define with new residues   cilpa at users.csc.fi
• [gmx-users] Free energy for charged molecules with PME   Anirban Mudi
  • [gmx-users] Free energy for charged molecules with PME   Berk Hess
• [gmx-users] Color in wheel   Hwankyu Lee
  • [gmx-users] Color in wheel   Mark Abraham
• [gmx-users] Re: gmx-users Digest, Vol 46, Issue 67   sudheer babu
• [gmx-users] Selection of multiple residues   maria goranovic
  • [gmx-users] Selection of multiple residues   Bjoern Windshuegel
    • [gmx-users] Selection of multiple residues   maria goranovic
      • [gmx-users] Selection of multiple residues   Bjoern Windshuegel
  • [gmx-users] Selection of multiple residues   Berk Hess
    • [gmx-users] Selection of multiple residues   Mark Abraham
• [gmx-users] gmx_alltoall   Anna Marabotti
  • [gmx-users] gmx_alltoall   Carsten Kutzner
• [gmx-users] problem regarding pr.mdp file of protein embedded in popc   sudheer babu
  • [gmx-users] problem regarding pr.mdp file of protein embedded in popc   Mark Abraham
• [gmx-users] Re: Dose the GROMOS FF favour beta-sheets?   pascal.baillod at epfl.ch
  • [gmx-users] Re: Dose the GROMOS FF favour beta-sheets?   Florian Haberl
• [gmx-users] Temparature and density   csreddy at ncbs.res.in
  • [gmx-users] Temparature and density   Tsjerk Wassenaar
    • [gmx-users] TFE in molecular dynamic   Luisa Calvanese
    • [gmx-users] TFE in molecular dynamic   Luisa Calvanese
      • [gmx-users] TFE in molecular dynamic   Mark Abraham
• [gmx-users] GTPgammaS topology   Sekar Ramachandran
• [gmx-users] error in coordinate file   s lal badshah
  • [gmx-users] error in coordinate file   Venky Krishna
  • [gmx-users] error in coordinate file   Mark Abraham
• [gmx-users] which type of cysteine residue?   OZGE ENGIN
  • [gmx-users] which type of cysteine residue?   Justin A. Lemkul
• [gmx-users] Strange PDO output during umbrella sampling   Ilya Chorny
• [gmx-users] Re: Strange PDO output during umbrella sampling   Ilya Chorny
• [gmx-users] problem with exchange probabilities in remd   OZGE ENGIN
  • [gmx-users] creating trajectory with ligand close to the protein   David Osguthorpe
    • [gmx-users] creating trajectory with ligand close to the protein   Mark Abraham
      • [gmx-users] creating trajectory with ligand close to the protein   David Osguthorpe
      • [gmx-users] creating trajectory with ligand close to the protein   Tsjerk Wassenaar
  • [gmx-users] problem with exchange probabilities in remd   Mark Abraham
  • [gmx-users] problem with exchange probabilities in remd   David van der Spoel
• [gmx-users] problem with exchange probabilities in remd   OZGE ENGIN
• [gmx-users] demixing REMD trajectories   madeleine.kittner at mpikg.mpg.de
  • [gmx-users] demixing REMD trajectories   David van der Spoel
  • [gmx-users] AGAIN: demixing REMD trajectories   madeleine.kittner at mpikg.mpg.de
    • [gmx-users] AGAIN: demixing REMD trajectories   David van der Spoel
• [gmx-users] AGAIN: demixing REMD trajectories   madeleine.kittner at mpikg.mpg.de
  • [gmx-users] AGAIN: demixing REMD trajectories   David van der Spoel
• [gmx-users] problem about Pr.mdp   sudheer babu
  • [gmx-users] problem about Pr.mdp   Justin A. Lemkul
• [gmx-users] Harmonic dihedral restraints   Robert Johnson
  • [gmx-users] Harmonic dihedral restraints   David Mobley
    • [gmx-users] Harmonic dihedral restraints   Robert Johnson
      • [gmx-users] Harmonic dihedral restraints   Mark Abraham
      • [gmx-users] Harmonic dihedral restraints   Robert Johnson
      • [gmx-users] Harmonic dihedral restraints   David Mobley
      • [gmx-users] Harmonic dihedral restraints   Robert Johnson
      • [gmx-users] Harmonic dihedral restraints   Justin A. Lemkul
• [gmx-users] Re: AGAIN: demixing REMD trajectories   madeleine.kittner at mpikg.mpg.de
• [gmx-users] Re: gmx-users Digest, Vol 46, Issue 79   sudheer babu
• [gmx-users] g_enemat   msvijayabaskar at aol.in
  • [gmx-users] g_enemat   Mark Abraham
• [gmx-users] still problem of pr.mdp   sudheer babu
  • [gmx-users] still problem of pr.mdp   Justin A. Lemkul
  • [gmx-users] still problem of pr.mdp   Dallas B. Warren
• [gmx-users] Concerning DSSP   Ricardo Soares
  • [gmx-users] Concerning DSSP   David van der Spoel
    • [gmx-users] Concerning DSSP   Ricardo Soares
      • [gmx-users] Concerning DSSP   David van der Spoel
• [gmx-users] (no subject)   Jay McAliley
• [gmx-users] pbc=full in 3.3.2   Jay McAliley
• [gmx-users] Concerning DSSP   Ricardo Soares
  • [gmx-users] Concerning DSSP   Justin A. Lemkul
    • [gmx-users] Concerning DSSP   Ricardo Soares
• [gmx-users] problem of general velocities   sudheer babu
  • [gmx-users] problem of general velocities   mark.abraham at anu.edu.au
• [gmx-users] PME grid parameters in large system run in parallel in Gromacs 4 CVS   Daniel Larsson
  • [gmx-users] PME grid parameters in large system run in parallel in Gromacs 4 CVS   Berk Hess
• [gmx-users] peptide is going outside of box   kinshuk at chem.iitb.ac.in
  • [gmx-users] peptide is going outside of box   Mark Abraham
• [gmx-users] Time step and constraints   钩深致远
• [gmx-users] pbc=full in 3.3.2   Jay McAliley
• [gmx-users] simulation box   sudheer babu
  • [gmx-users] simulation box   Justin A. Lemkul
• [gmx-users] MPI compilation without shared FFTW libraries   Hans Martin Senn
  • [gmx-users] MPI compilation without shared FFTW libraries   David van der Spoel
    • [gmx-users] excluded volume   Yin Jian
• [gmx-users] Best Minimization Protocol for given protein   Russell Green
• [gmx-users] Free energy of turning on restraints   Robert Johnson
  • [gmx-users] Free energy of turning on restraints   David Mobley
    • [gmx-users] Free energy of turning on restraints   Robert Johnson
• [gmx-users] cannot do constraint force run in parallel?   Nickle Fan
  • [gmx-users] cannot do constraint force run in parallel?   David van der Spoel
    • [gmx-users] cannot do constraint force run in parallel?   Berk Hess
• [gmx-users] TIP5P/TIP4P and OPLS-AA   John R. Dowdle
  • [gmx-users] TIP5P/TIP4P and OPLS-AA   David van der Spoel
• [gmx-users] nrexcl 3 or 4 in combination with pairs 1-4   Claus Valka
  • [gmx-users] nrexcl 3 or 4 in combination with pairs 1-4   Berk Hess
• [gmx-users] Average area per lipid   Stephen Dutz
  • [gmx-users] Average area per lipid   Mark Abraham
• [gmx-users] Merge two trajectories   CHANDRIKA RAO
  • [gmx-users] Merge two trajectories   Ilya Chorny
  • [gmx-users] Merge two trajectories   Mark Abraham
• [gmx-users] Merge two trajectories   sharada
• [gmx-users] Merge two trajectories   sharada
• [gmx-users] MPICH 1.2 vs. GMX 4.0   yren at home.ipe.ac.cn
  • [gmx-users] MPICH 1.2 vs. GMX 4.0   Mark Abraham
  • [gmx-users] MPICH 1.2 vs. GMX 4.0   Florian Haberl
  • [gmx-users] MPICH 1.2 vs. GMX 4.0   Carsten Kutzner
• [gmx-users] Noe distance restraints   Chiara Parravicini
  • [gmx-users] Noe distance restraints   Mark Abraham
    • [gmx-users] Noe distance restraints   Chiara Parravicini
      • [gmx-users] Noe distance restraints   Mark Abraham
      • [gmx-users] Noe distance restraints   Chiara Parravicini
• [gmx-users] (no subject)   alkasrivastava at iitb.ac.in
  • [gmx-users] (no subject)   David van der Spoel
• [gmx-users] GROMACS 3.3.3 released   David van der Spoel
• [gmx-users] protein in water production run   sudheer babu
  • [gmx-users] protein in water production run   David van der Spoel
• [gmx-users] Re: merging two trajectory files   alkasrivastava at iitb.ac.in
  • [gmx-users] Re: merging two trajectory files   Mark Abraham

Last message date: Fri Feb 29 19:29:25 CET 2008
Archived on: Thu Nov 14 12:04:17 CET 2013

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