February 2011 Archives by thread

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Starting: Tue Feb 1 01:33:11 CET 2011
Ending: Mon Feb 28 23:48:53 CET 2011
Messages: 806

• [gmx-users] Anil Kumar invited you to Dropbox   Dropbox
• [gmx-users] Re: Essential dynamics   bharat gupta
• [gmx-users] RE : essential dynamics   bharat gupta
• [gmx-users] How to calculate solvation energy?   Saikat Banerjee
• [gmx-users] Re: RE : essential dynamics   bharat gupta
  • [gmx-users] Re: RE : essential dynamics   Tsjerk Wassenaar
    • [gmx-users] Re: RE : essential dynamics   bharat gupta
      • [gmx-users] Re: RE : essential dynamics   bharat gupta
• [gmx-users] mdrun with append option   Mark Abraham
  • [gmx-users] mdrun with append option   Sai Pooja
    • [gmx-users] mdrun with append option   Sai Pooja
      • [gmx-users] mdrun with append option   Justin A. Lemkul
      • [gmx-users] mdrun with append option   Sai Pooja
      • [gmx-users] mdrun with append option   Justin A. Lemkul
      • [gmx-users] mdrun with append option   Sai Pooja
      • [gmx-users] mdrun with append option   Justin A. Lemkul
      • [gmx-users] mdrun with append option   Mark Abraham
      • [gmx-users] mdrun with append option   Justin A. Lemkul
      • [gmx-users] mdrun with append option   Sai Pooja
      • [gmx-users] mdrun with append option   Mark Abraham
      • [gmx-users] mdrun with append option   Sai Pooja
      • [gmx-users] mdrun with append option   Justin A. Lemkul
      • [gmx-users] mdrun with append option   Sai Pooja
      • [gmx-users] mdrun with append option   Sai Pooja
      • [gmx-users] mdrun with append option   Justin A. Lemkul
• [gmx-users] Source Code for Lennard Jones Interaction   Mark Abraham
• [gmx-users] General MD question   Carsten Kutzner
• [gmx-users] extending a simulation   Adwait Mevada
  • [gmx-users] extending a simulation   Mark Abraham
• [gmx-users] General MD question   Itamar Kass (Med)
• [gmx-users] Charge groups   mohsen ramezanpour
  • [gmx-users] Charge groups   Justin A. Lemkul
• [gmx-users] segmentation fault: g_velacc   Vigneshwar Ramakrishnan
  • [gmx-users] segmentation fault: g_velacc   Justin A. Lemkul
    • [gmx-users] segmentation fault: g_velacc   Carsten Kutzner
      • [gmx-users] segmentation fault: g_velacc   Carsten Kutzner
      • [gmx-users] segmentation fault: g_velacc   Vigneshwar Ramakrishnan
• [gmx-users] hbond constraint   Justin A. Lemkul
• [gmx-users] g_velacc   Nilesh Dhumal
  • [gmx-users] g_velacc   Florian Dommert
• [gmx-users] angle constrain, constrained PF6 anion   gyorgy.hantal at fc.up.pt
  • [gmx-users] angle constrain, constrained PF6 anion   Justin A. Lemkul
    • [gmx-users] angle constrain, constrained PF6 anion   gyorgy.hantal at fc.up.pt
      • [gmx-users] angle constrain, constrained PF6 anion   Justin A. Lemkul
• [gmx-users] luck   Mr Bernard Ramos
  • [gmx-users] luck   Justin A. Lemkul
    • [gmx-users] luck   Mr Bernard Ramos
      • [gmx-users] luck   Justin A. Lemkul
      • [gmx-users] luck   Mr Bernard Ramos
• [gmx-users] lactam bridge problems   Jerez Te
  • [gmx-users] lactam bridge problems   Justin A. Lemkul
    • [gmx-users] lactam bridge problems   Jerez Te
• [gmx-users] Re: angle constrain, constrained PF6 anion   Vitaly Chaban
• [gmx-users] Inaccurate pressure readings   Denny Frost
  • [gmx-users] Inaccurate pressure readings   Justin A. Lemkul
    • [gmx-users] Inaccurate pressure readings   Denny Frost
• [gmx-users] Re: g_velacc   Vitaly Chaban
• [gmx-users] Dynamics of non-protein molecules.   Yasen Atanasov
  • [gmx-users] Dynamics of non-protein molecules.   Justin A. Lemkul
• [gmx-users] Inaccurate pressure readings   Justin A. Lemkul
  • [gmx-users] Inaccurate pressure readings   Denny Frost
    • [gmx-users] Inaccurate pressure readings   Justin A. Lemkul
• [gmx-users] Protein in a solvated box   simon sham
  • [gmx-users] Protein in a solvated box   Justin A. Lemkul
• [gmx-users] RE : Essential dynamics   bharat gupta
• [gmx-users] Re: change in secondary structure   bharat gupta
  • [gmx-users] Re: change in secondary structure   Justin A. Lemkul
    • [gmx-users] Re: change in secondary structure   bharat gupta
      • [gmx-users] Re: change in secondary structure   Justin A. Lemkul
      • [gmx-users] Re: change in secondary structure   bharat gupta
      • [gmx-users] Re: change in secondary structure   Justin A. Lemkul
      • [gmx-users] Re: change in secondary structure   bharat gupta
      • [gmx-users] Re: change in secondary structure   Justin A. Lemkul
      • [gmx-users] Re: change in secondary structure   bharat gupta
      • [gmx-users] Re: change in secondary structure   Justin A. Lemkul
      • [gmx-users] Re: change in secondary structure   bharat gupta
• [gmx-users] Re:General MD question   lloyd riggs
  • [gmx-users] Re:General MD question   Carsten Kutzner
• [gmx-users] links warnangles   vferrario at units.it
  • [gmx-users] links warnangles   Justin A. Lemkul
    • [gmx-users] links warnangles   vferrario at units.it
      • [gmx-users] links warnangles   Justin A. Lemkul
      • [gmx-users] links warnangles   Justin A. Lemkul
      • [gmx-users] links warnangles   vferrario at units.it
      • [gmx-users] links warnangles   vferrario at units.it
      • [gmx-users] links warnangles   Justin A. Lemkul
      • [gmx-users] links warnangles   vferrario at units.it
      • [gmx-users] links warnangles   Justin A. Lemkul
      • [gmx-users] links warnangles   Justin A. Lemkul
      • [gmx-users] links warnangles   Justin A. Lemkul
      • [gmx-users] links warnangles   vferrario at units.it
      • [gmx-users] links warnangles   vferrario at units.it
      • [gmx-users] links warnangles   Justin A. Lemkul
      • [gmx-users] links warnangles   vferrario at units.it
      • [gmx-users] links warnangles   Justin A. Lemkul
      • [gmx-users] links warnangles   vferrario at units.it
      • [gmx-users] links warnangles   Dimitris Dellis
      • [gmx-users] links warnangles   Justin A. Lemkul
      • [gmx-users] links warnangles   Dimitris Dellis
      • [gmx-users] links warnangles   vferrario at units.it
• [gmx-users] error during installation of gromacs 4.5.3 on windows (cygwin platform)   bharat gupta
• [gmx-users] protein+ligand+membrane: which forcefield?   anna.marabotti at isa.cnr.it
  • [gmx-users] protein+ligand+membrane: which forcefield?   Justin A. Lemkul
  • [gmx-users] protein+ligand+membrane: which forcefield?   vferrario at units.it
• [gmx-users] energy minimization of a charged system in vacuum   devicerandom
• [gmx-users] energy minimization of a charged system in vacuum   devicerandom
• [gmx-users] Improper dihedral   Thomas Koller
• [gmx-users] how to add hydrogen ions   Olga Ivchenko
  • [gmx-users] how to add hydrogen ions   Mark Abraham
    • [gmx-users] how to add hydrogen ions   Erik Marklund
      • [gmx-users] how to add hydrogen ions   Olga Ivchenko
• [gmx-users] protein+ligand+membrane: which forcefield?   Anna Marabotti
• [gmx-users] water segment in the z-direction   chris.neale at utoronto.ca
• [gmx-users] solvent change-reg.   chandran karunakaran
  • [gmx-users] solvent change-reg.   Justin A. Lemkul
• [gmx-users] Energy calculation problem with molecule leaving the box   Gordan Horvat
  • [gmx-users] Energy calculation problem with molecule leaving the box   Mark Abraham
• [gmx-users] Normal modes are not orthogonal???   Kumaran Baskaran
  • [gmx-users] Normal modes are not orthogonal???   David van der Spoel
    • [gmx-users] Normal modes are not orthogonal???   Kumaran Baskaran
• [gmx-users] Nonequilibrium MD- implementing a temperature gradient simulation   Gaurav Goel
• [gmx-users] Adding modified nucleotide to a forcefield   william Stebbeds
  • [gmx-users] Adding modified nucleotide to a forcefield   Justin A. Lemkul
    • [gmx-users] Adding modified nucleotide to a forcefield   william Stebbeds
      • [gmx-users] Adding modified nucleotide to a forcefield   Justin A. Lemkul
      • [gmx-users] Adding modified nucleotide to a forcefield   william Stebbeds
      • [gmx-users] Adding modified nucleotide to a forcefield   Justin A. Lemkul
      • [gmx-users] Adding modified nucleotide to a forcefield   william Stebbeds
      • [gmx-users] Adding modified nucleotide to a forcefield   Mark Abraham
• [gmx-users] High Temperature simulations   simon sham
  • [gmx-users] High Temperature simulations   Justin A. Lemkul
• [gmx-users] view the vibrational modes   Ramachandran G
  • [gmx-users] view the vibrational modes   Mark Abraham
• [gmx-users] problem with force fields while running membrane protein simulation   Mohana lakshmi
  • [gmx-users] problem with force fields while running membrane protein simulation   Mark Abraham
    • [gmx-users] problem with force fields while running membrane protein simulation   Mohana lakshmi
      • [gmx-users] problem with force fields while running membrane protein simulation   Mark Abraham
      • [gmx-users] problem with force fields while running membrane protein simulation   Mohana lakshmi
      • [gmx-users] problem with force fields while running membrane protein simulation   Justin A. Lemkul
• [gmx-users] what standard is successful when doing EM   gromacs
  • [gmx-users] what standard is successful when doing EM   Mark Abraham
• [gmx-users] Re: Energy calculation problem with molecule leaving the box   Gordan Horvat
• [gmx-users] Error Messages   simon sham
  • [gmx-users] Error Messages   Justin A. Lemkul
• [gmx-users] harmonic restraint with OpenMM   Jochen Hub
• [gmx-users] Re: Starting two threads   bharat gupta
  • [gmx-users] Re: Starting two threads   william Stebbeds
• [gmx-users] Porting Amber parmbsc0 force field to Gromacs   william Stebbeds
  • [gmx-users] Porting Amber parmbsc0 force field to Gromacs   Justin A. Lemkul
    • [gmx-users] gnuplot   delara aghaie
      • [gmx-users] gnuplot   Tim Harder
    • [gmx-users] Porting Amber parmbsc0 force field to Gromacs   william Stebbeds
• [gmx-users] Charge groups   mohsen ramezanpour
  • [gmx-users] Re: Charge groups   mohsen ramezanpour
  • [gmx-users] Charge groups   Justin A. Lemkul
• [gmx-users] topology with all hydrogens   mohsen ramezanpour
  • [gmx-users] topology with all hydrogens   Tsjerk Wassenaar
    • [gmx-users] topology with all hydrogens   mohsen ramezanpour
      • [gmx-users] topology with all hydrogens   Tsjerk Wassenaar
• [gmx-users] How to include specific atom in force field ffG43a1   Rini Gupta
  • [gmx-users] How to include specific atom in force field ffG43a1   Justin A. Lemkul
• [gmx-users] How to include specific atom in force field ffG43a1   Rini Gupta
• [gmx-users] Warning: atom names in CG topology file and CG pdb file do not match   Faezeh Kargar
  • [gmx-users] Warning: atom names in CG topology file and CG pdb file do not match   Justin A. Lemkul
• [gmx-users] include a few .itp files   Алексей Раевский
  • [gmx-users] include a few .itp files   Justin A. Lemkul
• [gmx-users] Why REMD simulation becomes so slow when the number of replicas becomes large?   Qiong Zhang
  • [gmx-users] Why REMD simulation becomes so slow when the number of replicas becomes large?   Mark Abraham
• [gmx-users] interface_enrgy   shahid nayeem
  • [gmx-users] interface_enrgy   Justin A. Lemkul
    • [gmx-users] interface_enrgy   shahid nayeem
      • [gmx-users] interface_enrgy   Justin A. Lemkul
• [gmx-users] configure: error: cannot compute sizeof (off_t)   vferrario at units.it
  • [gmx-users] configure: error: cannot compute sizeof (off_t)   Mark Abraham
• [gmx-users] Why REMD simulation becomes so slow when the number of replicas becomes large?   Qiong Zhang
  • [gmx-users] Why REMD simulation becomes so slow when the number of replicas becomes large?   Mark Abraham
• [gmx-users] free energy calculation , grompp crash   Da-Wei Li
  • [gmx-users] Re: free energy calculation , grompp crash   Da-Wei Li
    • [gmx-users] Re: free energy calculation , grompp crash   Da-Wei Li
      • [gmx-users] Re: free energy calculation , grompp crash   TJ Mustard
      • [gmx-users] Re: free energy calculation , grompp crash   Da-Wei Li
      • [gmx-users] Re: free energy calculation , grompp crash   Justin A. Lemkul
      • [gmx-users] Re: free energy calculation , grompp crash   TJ Mustard
      • [gmx-users] Re: free energy calculation , grompp crash   Da-Wei Li
      • [gmx-users] Re: free energy calculation , grompp crash   Da-Wei Li
      • [gmx-users] Re: free energy calculation , grompp crash   TJ Mustard
      • [gmx-users] Re: free energy calculation , grompp crash   Da-Wei Li
      • [gmx-users] Re: free energy calculation , grompp crash   Justin A. Lemkul
      • [gmx-users] Anealling   TJ Mustard
      • [gmx-users] Anealling   Justin A. Lemkul
      • [gmx-users] Re: free energy calculation , grompp crash   Da-Wei Li
      • [gmx-users] Re: free energy calculation , grompp crash   Justin A. Lemkul
• [gmx-users] Minimization and torsion angles   abdullah ahmed
  • [gmx-users] Minimization and torsion angles   Mark Abraham
• [gmx-users] about heating protocol   Osmany Guirola Cruz
  • [gmx-users] about heating protocol   Justin A. Lemkul
• [gmx-users] pdb2gmx conversion loss of significant figures   Matthew Chan
  • [gmx-users] pdb2gmx conversion loss of significant figures   Justin A. Lemkul
• [gmx-users] about pressure coupling   Osmany Guirola Cruz
  • [gmx-users] about pressure coupling   Justin A. Lemkul
• [gmx-users] Increasing machine precision   abdullah ahmed
  • [gmx-users] Increasing machine precision   Erik Marklund
• [gmx-users] Re:Re:Why REMD simulation becomes so slow when the number of replicas becomes large?   Qiong Zhang
• [gmx-users] Re: No residue type for 'ARG' as a starting terminus   bipin singh
  • [gmx-users] Re: No residue type for 'ARG' as a starting terminus   Mark Abraham
    • [gmx-users] Re: No residue type for 'ARG' as a starting terminus   bipin singh
      • [gmx-users] Re: No residue type for 'ARG' as a starting terminus   Mark Abraham
      • [gmx-users] Re: No residue type for 'ARG' as a starting terminus   bipin singh
• [gmx-users] OPLS and RB parameters in GROMACS   sulatha M. S
  • [gmx-users] OPLS and RB parameters in GROMACS   Andrew Paluch
    • [gmx-users] OPLS and RB parameters in GROMACS   sulatha M. S
      • [gmx-users] OPLS and RB parameters in GROMACS   Mark Abraham
      • [gmx-users] OPLS and RB parameters in GROMACS   sulatha M. S
      • [gmx-users] OPLS and RB parameters in GROMACS   Rainer Boeckmann
      • [gmx-users] OPLS and RB parameters in GROMACS   Rainer Boeckmann
      • [gmx-users] OPLS and RB parameters in GROMACS   sulatha M. S
• [gmx-users] Re:gmx-users Digest, Vol 82, Issue 56   gromacs
• [gmx-users] sufrace tension RMSD too big   gromacs
• [gmx-users] Reduced Units   Tomy van Batis
• [gmx-users] Nice Present   boaz kan-tor
• [gmx-users] ask for help on MARTINI SIMULATION OF POPC lipids with polarisable water   wezhao at ucalgary.ca
  • [gmx-users] ask for help on MARTINI SIMULATION OF POPC lipids with polarisable water   XAvier Periole
    • [gmx-users] ask for help on MARTINI SIMULATION OF POPC lipids with polarisable water   wezhao at ucalgary.ca
• [gmx-users] Help with B2AR within the POPC membrane   Aldo Segura
  • [gmx-users] Help with B2AR within the POPC membrane   Justin A. Lemkul
    • [gmx-users] Help with B2AR within the POPC membrane   Aldo Segura
      • [gmx-users] Help with B2AR within the POPC membrane   Justin A. Lemkul
      • [gmx-users] Help with B2AR within the POPC membrane   Aldo Segura
• [gmx-users] Re: g_rmsf   bharat gupta
  • [gmx-users] Re: g_rmsf   Justin A. Lemkul
    • [gmx-users] Re: g_rmsf   bharat gupta
      • [gmx-users] Re: g_rmsf   Justin A. Lemkul
      • [gmx-users] Re: g_rmsf   bipin singh
      • [gmx-users] Re: g_rmsf   bharat gupta
      • [gmx-users] Re: g_rmsf   Tsjerk Wassenaar
      • [gmx-users] Re: g_rmsf   bharat gupta
      • [gmx-users] Re: g_rmsf   Tsjerk Wassenaar
      • [gmx-users] Re: g_rmsf   bharat gupta
      • [gmx-users] Re: g_rmsf   Mark Abraham
      • [gmx-users] Re: g_rmsf   bipin singh
• [gmx-users] solvation_box_preparation   shahid nayeem
• [gmx-users] add force field   lina zhao
  • [gmx-users] add force field   David van der Spoel
    • [gmx-users] add force field   lina zhao
      • [gmx-users] add force field   Mark Abraham
      • [gmx-users] add force field   lina zhao
• [gmx-users] gen_vel during gradual NVT equilibration   bipin singh
  • [gmx-users] gen_vel during gradual NVT equilibration   Justin A. Lemkul
  • [gmx-users] gen_vel during gradual NVT equilibration   Erik Marklund
• [gmx-users] solvation_box_preparation   Justin A. Lemkul
• [gmx-users] error in equilibration   shiva birgani
  • [gmx-users] error in equilibration   Mark Abraham
    • [gmx-users] error in equilibration   Justin A. Lemkul
• [gmx-users] solvation_box_preparation   Justin A. Lemkul
• [gmx-users] pull code   Poojari, Chetan
  • [gmx-users] pull code   Justin A. Lemkul
    • [gmx-users] pull code   Poojari, Chetan
      • [gmx-users] pull code   Justin A. Lemkul
      • [gmx-users] pull code   Poojari, Chetan
      • [gmx-users] pull code   Justin A. Lemkul
• [gmx-users] PRODRG   mohsen ramezanpour
  • [gmx-users] PRODRG   Mark Abraham
    • [gmx-users] PRODRG   jorge_quintero at ciencias.uis.edu.co
      • [gmx-users] PRODRG   TJ Mustard
      • [gmx-users] PRODRG   Justin A. Lemkul
      • [gmx-users] PRODRG   jorge_quintero at ciencias.uis.edu.co
      • [gmx-users] PRODRG   mohsen ramezanpour
      • [gmx-users] PRODRG   Justin A. Lemkul
      • [gmx-users] PRODRG   mohsen ramezanpour
      • [gmx-users] PRODRG   Justin A. Lemkul
      • [gmx-users] PRODRG   Mark Abraham
• [gmx-users] Dangling phospholipids   "Dr. Ramón Garduño-Juárez"
  • [gmx-users] Dangling phospholipids   Justin A. Lemkul
    • [gmx-users] Dangling phospholipids   "Dr. Ramón Garduño-Juárez"
      • [gmx-users] Dangling phospholipids   Justin A. Lemkul
• [gmx-users] Annealing--Fatal Error message can't be right.   William Welch
  • [gmx-users] Annealing--Fatal Error message can't be right.   Justin A. Lemkul
• [gmx-users] Comparing ff in Topology file by PRODRG and gromos G45a3   XUEMING TANG
  • [gmx-users] Comparing ff in Topology file by PRODRG and gromos G45a3   Justin A. Lemkul
• [gmx-users] Domain decomposition configuration   Denny Frost
  • [gmx-users] Domain decomposition configuration   Justin A. Lemkul
    • [gmx-users] Domain decomposition configuration   Denny Frost
      • [gmx-users] Domain decomposition configuration   Justin A. Lemkul
      • [gmx-users] Domain decomposition configuration   Denny Frost
      • [gmx-users] Domain decomposition configuration   Justin A. Lemkul
      • [gmx-users] Domain decomposition configuration   Denny Frost
      • [gmx-users] Domain decomposition configuration   Justin A. Lemkul
      • [gmx-users] Domain decomposition configuration   Mark Abraham
      • [gmx-users] Domain decomposition configuration   Justin A. Lemkul
      • [gmx-users] Domain decomposition configuration   Mark Abraham
      • [gmx-users] Domain decomposition configuration   Justin A. Lemkul
• [gmx-users] g_hbond and 4.5.2 version   Zuzana Benkova
  • [gmx-users] g_hbond and 4.5.2 version   Justin A. Lemkul
    • [gmx-users] g_hbond and 4.5.2 version   Erik Marklund
      • [gmx-users] g_hbond and 4.5.2 version   Zuzana Benkova
      • [gmx-users] g_hbond and 4.5.2 version   Zuzana Benkova
      • [gmx-users] g_hbond and 4.5.2 version   Erik Marklund
• [gmx-users] how to switch from NPT to NVT ensemble during equilibration   Rini Gupta
  • [gmx-users] how to switch from NPT to NVT ensemble during equilibration   Mark Abraham
• [gmx-users] localpressure.dat file not created   maxcw at physics.ucsb.edu
  • [gmx-users] localpressure.dat file not created   Mark Abraham
    • [gmx-users] localpressure.dat file not created   maxcw at physics.ucsb.edu
      • [gmx-users] localpressure.dat file not created   Justin A. Lemkul
• [gmx-users] server_for_Gaussian   shahid nayeem
  • [gmx-users] server_for_Gaussian   Justin A. Lemkul
• [gmx-users] Error: No such moleculetype Protein   Anirban Ghosh
  • [gmx-users] Error: No such moleculetype Protein   Tsjerk Wassenaar
    • [gmx-users] Error: No such moleculetype Protein   Anirban Ghosh
      • [gmx-users] Error: No such moleculetype Protein   Anirban Ghosh
• [gmx-users] Re: server_for_Gaussian   Thomas Schlesier
  • [gmx-users] Re: server_for_Gaussian   Diego Enry
• [gmx-users] WHAM with multiple force constants   jkhao at ifr88.cnrs-mrs.fr
  • [gmx-users] WHAM with multiple force constants   XAvier Periole
  • [gmx-users] WHAM with multiple force constants   Jochen Hub
• [gmx-users] ref_temp and gen_temp during simulated annealing   bipin singh
  • [gmx-users] ref_temp and gen_temp during simulated annealing   Justin A. Lemkul
• [gmx-users] rotamers during minimization   abdullah ahmed
  • [gmx-users] rotamers during minimization   Justin A. Lemkul
• [gmx-users] Dangling phospholipids   Dallas Warren
• [gmx-users] Problem with Gromacs Installation   majid hasan
• [gmx-users] More than one settle type.   Sikandar Mashayak
  • [gmx-users] More than one settle type.   Mark Abraham
• [gmx-users] crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning   Sanjay Kumar Upadhyay
  • [gmx-users] crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning   Mark Abraham
• [gmx-users] re: extending the simulation   bharat gupta
• [gmx-users] Fwd: Question on Gromacs: rlist, rvdw, rcoulomb   David van der Spoel
• [gmx-users] Re: Extending the simulation   bharat gupta
  • [gmx-users] Re: Extending the simulation   Mark Abraham
    • [gmx-users] Re: Extending the simulation   bharat gupta
      • [gmx-users] Re: Extending the simulation   Justin A. Lemkul
• [gmx-users] Re: crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning (Mark Abraham)   Sanjay Kumar Upadhyay
  • [gmx-users] Re: crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning (Mark Abraham)   Mark Abraham
    • [gmx-users] Re: crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning (Mark Abraham)   Justin A. Lemkul
• [gmx-users] Performance in ia64 and x86_64   Ignacio Fernández Galván
  • [gmx-users] Performance in ia64 and x86_64   Mark Abraham
    • [gmx-users] Performance in ia64 and x86_64   Ignacio Fernández Galván
      • [gmx-users] Performance in ia64 and x86_64   Mark Abraham
      • [gmx-users] Performance in ia64 and x86_64   Ignacio Fernández Galván
      • [gmx-users] Performance in ia64 and x86_64   Carsten Kutzner
      • [gmx-users] Performance in ia64 and x86_64   Ignacio Fernández Galván
      • [gmx-users] Performance in ia64 and x86_64   Mark Abraham
  • [gmx-users] Performance in ia64 and x86_64   Carsten Kutzner
• [gmx-users] Charges   Tanos Franca
  • [gmx-users] Charges   Justin A. Lemkul
• [gmx-users] NVT run   Thomas Koller
  • [gmx-users] NVT run   Mark Abraham
  • [gmx-users] NVT run   Justin A. Lemkul
• [gmx-users] Fwd: Question on Gromacs: rlist, rvdw, rcoulomb   Mark Abraham
  • [gmx-users] Fwd: Question on Gromacs: rlist, rvdw, rcoulomb   Erik Marklund
• [gmx-users] extracting a structure from confout.gro file   najwa drici
  • [gmx-users] extracting a structure from confout.gro file   Justin A. Lemkul
    • [gmx-users] extracting a structure from confout.gro file   Mark Abraham
• [gmx-users] rotamers and rings   abdullah ahmed
  • [gmx-users] rotamers and rings   Justin A. Lemkul
• [gmx-users] only one model is displayed   Kwee Hong
• [gmx-users] Re: only one model is displayed   Kwee Hong
  • [gmx-users] Re: only one model is displayed   Justin A. Lemkul
• [gmx-users] doubts on g_confrms output   Kwee Hong
  • [gmx-users] doubts on g_confrms output   Mark Abraham
    • [gmx-users] doubts on g_confrms output   Kwee Hong
      • [gmx-users] doubts on g_confrms output   Mark Abraham
      • [gmx-users] doubts on g_confrms output   Tsjerk Wassenaar
      • [gmx-users] doubts on g_confrms output   Mark Abraham
      • [gmx-users] doubts on g_confrms output   David van der Spoel
      • [gmx-users] doubts on g_confrms output   Tsjerk Wassenaar
• [gmx-users] Add custom residue to DNA index group   william Stebbeds
  • [gmx-users] Add custom residue to DNA index group   Mark Abraham
    • [gmx-users] Add custom residue to DNA index group   william Stebbeds
      • [gmx-users] Add custom residue to DNA index group   Sarath Chandra Dantu
      • [gmx-users] Add custom residue to DNA index group   william Stebbeds
      • [gmx-users] Add custom residue to DNA index group   Justin A. Lemkul
      • [gmx-users] Add custom residue to DNA index group   william Stebbeds
      • [gmx-users] Terminus Atoms genrestr?   TJ Mustard
      • [gmx-users] Terminus Atoms genrestr?   Justin A. Lemkul
      • [gmx-users] Terminus Atoms genrestr?   TJ Mustard
      • [gmx-users] Terminus Atoms genrestr?   Justin A. Lemkul
      • [gmx-users] Terminus Atoms genrestr?   TJ Mustard
      • [gmx-users] Terminus Atoms genrestr?   Teemu Murtola
      • [gmx-users] Terminus Atoms genrestr?   Justin A. Lemkul
      • [gmx-users] Terminus Atoms genrestr?   Mark Abraham
      • [gmx-users] Add custom residue to DNA index group   Justin A. Lemkul
      • [gmx-users] Add custom residue to DNA index group   william Stebbeds
• [gmx-users] genbox error   Rini Gupta
  • [gmx-users] genbox error   Justin A. Lemkul
    • [gmx-users] genbox error   Mark Abraham
  • [gmx-users] genbox error   Mark Abraham
    • Re:[gmx-users] genbox error   Rini Gupta
      • [gmx-users] genbox error   Mark Abraham
      • Re: Re: [gmx-users] genbox error   Rini Gupta
• [gmx-users] gromos96 charges   najwa drici
  • [gmx-users] gromos96 charges   Justin A. Lemkul
• [gmx-users] Active site   mohsen ramezanpour
  • [gmx-users] Active site   Justin A. Lemkul
    • [gmx-users] Active site   mohsen ramezanpour
      • [gmx-users] Active site   Justin A. Lemkul
      • [gmx-users] Active site   mohsen ramezanpour
      • [gmx-users] Active site   Justin A. Lemkul
• [gmx-users] how to fixe distance   najwa drici
  • [gmx-users] how to fixe distance   Mark Abraham
  • [gmx-users] how to fixe distance   Justin A. Lemkul
  • [gmx-users] FEP energy errors with positional restraints?   TJ Mustard
    • [gmx-users] FEP energy errors with positional restraints?   Mark Abraham
      • [gmx-users] FEP energy errors with positional restraints?   TJ Mustard
      • [gmx-users] FEP energy errors with positional restraints?   Mark Abraham
      • [gmx-users] FEP energy errors with positional restraints?   TJ Mustard
      • [gmx-users] FEP energy errors with positional restraints?   Mark Abraham
      • [gmx-users] FEP energy errors with positional restraints?   TJ Mustard
      • [gmx-users] FEP energy errors with positional restraints?   Mark Abraham
• [gmx-users] leapfrog does not yet support Nose-Hoover chains   英雄不再寂寞
• [gmx-users] Output of Gromacs Demo   majid hasan
  • [gmx-users] Output of Gromacs Demo   TJ Mustard
    • [gmx-users] Output of Gromacs Demo   Tsjerk Wassenaar
    • [gmx-users] Output of Gromacs Demo   majid hasan
      • [gmx-users] Output of Gromacs Demo   Justin A. Lemkul
      • [gmx-users] Output of Gromacs Demo   majid hasan
      • [gmx-users] Output of Gromacs Demo   Justin A. Lemkul
      • [gmx-users] Output of Gromacs Demo   majid hasan
• [gmx-users] Re: gmx-users Digest, Vol 82, Issue 103   Adwait Mevada
  • [gmx-users] lateral pressure analysis   Adwait Mevada
• [gmx-users] Re: Group LEU not found in index file   Adam Bin Idu Jion
  • [gmx-users] Re: Group LEU not found in index file   Justin A. Lemkul
• [gmx-users] specific heat   leila separdar
  • [gmx-users] Fwd: specific heat   leila separdar
    • [gmx-users] Fwd: specific heat   David van der Spoel
• Fw: [gmx-users] Output of Gromacs Demo   majid hasan
  • Fw: [gmx-users] Output of Gromacs Demo   Justin A. Lemkul
• Fw: [gmx-users] Output of Gromacs Demo   Tsjerk Wassenaar
• [gmx-users] TI problem: When Lambda is 0/1, Trun on/off soft core potential get different result   jia jia
• [gmx-users] CG to FG transformation error   Anirban Ghosh
  • [gmx-users] CG to FG transformation error   Justin A. Lemkul
• [gmx-users] different between g_hbond version   babu gokul
  • [gmx-users] different between g_hbond version   Erik Marklund
    • [gmx-users] different between g_hbond version   babu gokul
• [gmx-users] Simulation using Martini force field   politr at fh.huji.ac.il
  • [gmx-users] Simulation using Martini force field   XAvier Periole
    • [gmx-users] Simulation using Martini force field   devicerandom
      • [gmx-users] Simulation using Martini force field   XAvier Periole
      • [gmx-users] Simulation using Martini force field   devicerandom
    • [gmx-users] Simulation using Martini force field   politr at fh.huji.ac.il
      • [gmx-users] Simulation using Martini force field   XAvier Periole
• [gmx-users] how to use virtual sites?   Chuipeng Kong
• [gmx-users] visualizing more than 9999 residues....   Anna Marabotti
  • [gmx-users] visualizing more than 9999 residues....   Tsjerk Wassenaar
    • [gmx-users] visualizing more than 9999 residues....   Nicolas SAPAY
• [gmx-users] R: visualizing more than 9999 residues...   Anna Marabotti
  • [gmx-users] R: visualizing more than 9999 residues...   Tsjerk Wassenaar
• [gmx-users] question regarding friction coefficient in stochastic dynamics   Thomas Schlesier
• [gmx-users] Gromacs Installation   majid hasan
  • [gmx-users] Gromacs Installation   lina zhao
    • [gmx-users] Gromacs Installation   majid hasan
      • [gmx-users] Gromacs Installation   Justin A. Lemkul
      • [gmx-users] Gromacs Installation   majid hasan
      • [gmx-users] Gromacs Installation   ZHAO Lina
      • [gmx-users] Gromacs Installation   majid hasan
      • [gmx-users] Gromacs Installation   ZHAO Lina
      • [gmx-users] Gromacs Installation   majid hasan
      • [gmx-users] Gromacs Installation   Mark Abraham
      • [gmx-users] Gromacs Installation   majid hasan
• [gmx-users] free energy   Moeed
  • [gmx-users] free energy   TJ Mustard
  • [gmx-users] free energy   TJ Mustard
  • [gmx-users] free energy   Michael Shirts
• [gmx-users] Simulation using Martini force field   Ran Friedman
• [gmx-users] R: gmx-users Digest, Vol 82, Issue 113   Anna Marabotti
• [gmx-users] ffamber03 top file problem   gromacs564
  • [gmx-users] ffamber03 top file problem   X.Periole
• [gmx-users] number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology   Parul tew
  • [gmx-users] number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology   Terry
• [gmx-users] Whereabouts of NDLP???   ifat shub
  • [gmx-users] Whereabouts of NDLP???   Tsjerk Wassenaar
• [gmx-users] g_dipole   Nilesh Dhumal
  • [gmx-users] g_dipole   David van der Spoel
    • [gmx-users] g_dipole   Nilesh Dhumal
      • [gmx-users] g_dipole   Justin A. Lemkul
• [gmx-users] NVE simulation   Thomas Koller
  • [gmx-users] NVE simulation   Justin A. Lemkul
• [gmx-users] Umbrella sampling windows   Susana Tomasio
  • [gmx-users] Umbrella sampling windows   Justin A. Lemkul
    • [gmx-users] Umbrella sampling windows   Susana Tomasio
    • [gmx-users] Umbrella sampling windows   Susana Tomasio
  • [gmx-users] Umbrella sampling windows   Laura Kingsley
  • [gmx-users] Umbrella sampling windows   Laura Kingsley
• [gmx-users] top2psf.pl issue: trying to use vmd w/ MARTINI protein   John
  • [gmx-users] top2psf.pl issue: trying to use vmd w/ MARTINI protein   Justin A. Lemkul
• [gmx-users] Simulation using Martini force field   politr at fh.huji.ac.il
• [gmx-users] Advanced Simulation Analysis   simon sham
  • [gmx-users] Advanced Simulation Analysis   David van der Spoel
• [gmx-users] Re: free energy   TJ Mustard
• [gmx-users] Repulsion instead of adsorption   mina Madah
  • [gmx-users] Repulsion instead of adsorption   Justin A. Lemkul
• [gmx-users] on force fields   Mr Bernard Ramos
  • [gmx-users] on force fields   Mark Abraham
    • [gmx-users] on force fields   Mr Bernard Ramos
      • [gmx-users] on force fields   Justin A. Lemkul
      • [gmx-users] on force fields   Mr Bernard Ramos
      • [gmx-users] on force fields   Justin A. Lemkul
• [gmx-users] g_rmsf reference structure?   kulleperuma.kulleperuma at utoronto.ca
  • [gmx-users] g_rmsf reference structure?   Mark Abraham
    • [gmx-users] g_rmsf reference structure?   Tsjerk Wassenaar
• [gmx-users] Conatant pH simulation in GROMACS   bipin singh
  • [gmx-users] Conatant pH simulation in GROMACS   Mark Abraham
• [gmx-users] Periodic Boundary Conditions g_mindist -pi   ifat shub
  • [gmx-users] Periodic Boundary Conditions g_mindist -pi   Tsjerk Wassenaar
• [gmx-users] Re: gromacs QM/MM compilation with gaussian   Txema Mercero
• [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi   ifat shub
  • [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi   Mark Abraham
    • [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi   Tsjerk Wassenaar
• [gmx-users] initial structures for md simulations   oguz gurbulak
  • [gmx-users] initial structures for md simulations   Mark Abraham
    • [gmx-users] initial structures for md simulations   leila separdar
• [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)   Gerrit Groenhof
  • [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)   Txema Mercero
    • [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)   Gerrit Groenhof
      • [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)   Txema Mercero
• [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)   Xiaohu Li
• [gmx-users] Re: Re: g_rmsf reference structure? (Tsjerk Wassenaar)   kulleperuma.kulleperuma at utoronto.ca
• [gmx-users] Protein-membrane system   Aldo Segura
  • [gmx-users] Protein-membrane system   Justin A. Lemkul
    • [gmx-users] Protein-membrane system   Itamar Kass
      • [gmx-users] Protein-membrane system   Jianguo Li
      • [gmx-users] Protein-membrane system   Justin A. Lemkul
• [gmx-users] Re: angle constrain, constrained PF6 anion   Vitaly Chaban
• [gmx-users] mpirun error?   Justin Kat
  • [gmx-users] mpirun error?   Justin A. Lemkul
• [gmx-users] zero atoms for FE P   Moeed
  • [gmx-users] zero atoms for FE P   Justin A. Lemkul
• [gmx-users] RE: simulation of a metal binding sites   bharat gupta
• [gmx-users] mismatch between energies of sequential minimization runs   Efrat Noy
  • [gmx-users] mismatch between energies of sequential minimization runs   Mark Abraham
• [gmx-users] RE: simulation of a metal binding sites   Ran Friedman
  • [gmx-users] RE: simulation of a metal binding sites   bharat gupta
    • [gmx-users] RE: simulation of a metal binding sites   Justin A. Lemkul
    • [gmx-users] RE: simulation of a metal binding sites   Marc Baaden
      • [gmx-users] RE: simulation of a metal binding sites   bharat gupta
• [gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)   Gerrit Groenhof
  • [gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)   Txema Mercero
    • [gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)   Gerrit Groenhof
      • [gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)   Txema Mercero
• [gmx-users] free energy blank dgdl   Moeed
  • [gmx-users] free energy blank dgdl   Justin A. Lemkul
  • [gmx-users] free energy blank dgdl   Da-Wei Li
• [gmx-users] Influence of rtpi on chemical potential   Pranay Doshi
• [gmx-users] domain decomposition error   Moeed
  • [gmx-users] domain decomposition error   Justin A. Lemkul
• [gmx-users] I need ligand topology file   ajaniharesh at gmail.com
  • [gmx-users] I need ligand topology file   Justin A. Lemkul
• [gmx-users] Re: angle constrain, constrained PF6 anion   Vitaly Chaban
• [gmx-users] Weeks Chandler Andersen potential   Rohit Malshe
  • [gmx-users] Weeks Chandler Andersen potential   Justin A. Lemkul
• [gmx-users] saving velocities and coordinates frequently   Amit Choubey
  • [gmx-users] saving velocities and coordinates frequently   Justin A. Lemkul
  • [gmx-users] saving velocities and coordinates frequently   Mark Abraham
• [gmx-users] about -CN triple bond   C.Y. Chang
  • [gmx-users] about -CN triple bond   Mark Abraham
    • [gmx-users] about -CN triple bond   C.Y. Chang
      • [gmx-users] about -CN triple bond   Mark Abraham
      • [gmx-users] about -CN triple bond   C.Y. Chang
      • [gmx-users] about -CN triple bond   Mark Abraham
      • [gmx-users] about -CN triple bond   C.Y. Chang
      • [gmx-users] about -CN triple bond   C.Y. Chang
• [gmx-users] backbone_few_sidechain_fixed   shahid nayeem
  • [gmx-users] backbone_few_sidechain_fixed   Mark Abraham
• [gmx-users] Re: Adding small molecule parameters to charmm force field   bharat gupta
  • [gmx-users] Fwd: Adding small molecule parameters to charmm force field   bharat gupta
    • [gmx-users] Fwd: Adding small molecule parameters to charmm force field   Justin A. Lemkul
      • [gmx-users] Fwd: Adding small molecule parameters to charmm force field   bharat gupta
• [gmx-users] Re: RE: simulation of a metal binding sites (bharat gupta)   Ran Friedman
• [gmx-users] where to insert a new include DPOSRES in topology file?   Anna Marabotti
  • [gmx-users] where to insert a new include DPOSRES in topology file?   Justin A. Lemkul
• [gmx-users] Target implementation date for gb_saltconc?   Matthew Zwier
  • [gmx-users] Target implementation date for gb_saltconc?   Per Larsson
• [gmx-users] configure: error: cannot compute sizeof (off_t)   Justin Kat
  • [gmx-users] configure: error: cannot compute sizeof (off_t)   Mark Abraham
• [gmx-users] SO4 ion   simon sham
  • [gmx-users] SO4 ion   Justin A. Lemkul
• [gmx-users] unable to display MARTINI system with VMD   John
  • [gmx-users] unable to display MARTINI system with VMD   Justin A. Lemkul
• [gmx-users] unable to display MARTINI system with VMD   Justin A. Lemkul
• [gmx-users] Umbrella sampling for protein-drug system   Aldo Segura
  • [gmx-users] Umbrella sampling for protein-drug system   Justin A. Lemkul
• [gmx-users] configure: error: cannot compute sizeof (off_t)   Justin Kat
  • [gmx-users] configure: error: cannot compute sizeof (off_t)   Carsten Kutzner
• [gmx-users] g_covar to calculate correlation of motion   bipin singh
  • [gmx-users] g_covar to calculate correlation of motion   Tsjerk Wassenaar
    • [gmx-users] g_covar to calculate correlation of motion   bipin singh
      • [gmx-users] g_covar to calculate correlation of motion   Tsjerk Wassenaar
      • [gmx-users] g_covar to calculate correlation of motion   bipin singh
• [gmx-users] removing pbc jumps from trajectory   Evelyne Deplazes
  • [gmx-users] removing pbc jumps from trajectory   XAvier Periole
• [gmx-users] Re: gmx-users Digest, Vol 82, Issue 150   Evelyne Deplazes
  • [gmx-users] Re: gmx-users Digest, Vol 82, Issue 150   XAvier Periole
  • [gmx-users] Re: gmx-users Digest, Vol 82, Issue 150   Tsjerk Wassenaar
• [gmx-users] how many contacts has a certain atom at MD   Olga Ivchenko
  • [gmx-users] how many contacts has a certain atom at MD   XAvier Periole
    • [gmx-users] how many contacts has a certain atom at MD   Erik Marklund
      • [gmx-users] how many contacts has a certain atom at MD   Justin A. Lemkul
      • [gmx-users] how many contacts has a certain atom at MD   Olga Ivchenko
      • [gmx-users] how many contacts has a certain atom at MD   Olga Ivchenko
      • [gmx-users] how many contacts has a certain atom at MD   Justin A. Lemkul
      • [gmx-users] how many contacts has a certain atom at MD   Olga Ivchenko
      • [gmx-users] how many contacts has a certain atom at MD   Justin A. Lemkul
      • [gmx-users] how many contacts has a certain atom at MD   Olga Ivchenko
      • [gmx-users] how many contacts has a certain atom at MD   Justin A. Lemkul
      • [gmx-users] how many contacts has a certain atom at MD   Olga Ivchenko
      • [gmx-users] how many contacts has a certain atom at MD   Justin A. Lemkul
      • [gmx-users] diffusion constant   Rebeca García Fandiño
• [gmx-users] free energy-couple-intramol options   Moeed
• [gmx-users] PMF from pull code, unexpected results   Michael Brunsteiner
• [gmx-users] An argument about long range electrostatics   Hassan Shallal
  • [gmx-users] An argument about long range electrostatics   Justin A. Lemkul
• [gmx-users] Can g_wham support using different temperature for different windows?   Jianguo Li
  • [gmx-users] Can g_wham support using different temperature for different windows?   Justin A. Lemkul
    • [gmx-users] Can g_wham support using different temperature for different windows?   Jianguo Li
      • [gmx-users] Can g_wham support using different temperature for different windows?   Justin A. Lemkul
      • [gmx-users] Can g_wham support using different temperature for different windows?   Jianguo Li
      • [gmx-users] Can g_wham support using different temperature for different windows?   Justin A. Lemkul
      • [gmx-users] Can g_wham support using different temperature for different windows?   Jianguo Li
      • [gmx-users] Can g_wham support using different temperature for different windows?   Jianguo Li
      • [gmx-users] Can g_wham support using different temperature for different windows?   XAvier Periole
      • [gmx-users] Can g_wham support using different temperature for different windows?   Jianguo Li
      • [gmx-users] Can g_wham support using different temperature for different windows?   XAvier Periole
      • [gmx-users] Can g_wham support using different temperature for different windows?   Jianguo Li
      • [gmx-users] Can g_wham support using different temperature for different windows?   Justin A. Lemkul
      • [gmx-users] Can g_wham support using different temperature for different windows?   Justin A. Lemkul
      • [gmx-users] Can g_wham support using different temperature for different windows?   Jianguo Li
      • [gmx-users] Can g_wham support using different temperature for different windows?   Justin A. Lemkul
      • [gmx-users] Can g_wham support using different temperature for different windows?   Jianguo Li
      • [gmx-users] Can g_wham support using different temperature for different windows?   Patrick Fuchs
      • [gmx-users] Can g_wham support using different temperature for different windows?   Jianguo Li
• [gmx-users] ffamber03 RB dihedrals and amb2gmx.pl problem!   gromacs564
• [gmx-users] PMF from pull code, unexpected results   chris.neale at utoronto.ca
• [gmx-users] Can g_wham support using different temperature for different windows?   chris.neale at utoronto.ca
• [gmx-users] membrane bilayer simulation by OPLS FF   mircial at sjtu.edu.cn
• [gmx-users] %exist hydrogen bond   leila karami
  • [gmx-users] %exist hydrogen bond   Justin A. Lemkul
• [gmx-users] membrane bilayer simulation by OPLS FF   Dallas Warren
• [gmx-users] diffusion coefficients   Thomas Koller
• [gmx-users] ffamber03 RB dihedrals and amb2gmx.pl problem!   gromacs564
• [gmx-users] Dielectric constant for alkanes based on shell polarizable model   aldi asmadi
• [gmx-users] test on g_density   JAVIER CEREZO BASTIDA
• [gmx-users] problems with randoms seeds   Thomas Schlesier
  • [gmx-users] Re: problems with randoms seeds   Thomas Schlesier
• [gmx-users] index file for interaction energies   Nick
  • [gmx-users] index file for interaction energies   Justin A. Lemkul
    • [gmx-users] index file for interaction energies   Nick
      • [gmx-users] index file for interaction energies   Justin A. Lemkul
      • [gmx-users] index file for interaction energies   Nick
      • [gmx-users] index file for interaction energies   Justin A. Lemkul
• [gmx-users] Re: Differences in rmsd with different force field   bharat gupta
  • [gmx-users] Re: Differences in rmsd with different force field   Justin A. Lemkul
    • [gmx-users] Re: Differences in rmsd with different force field   bharat gupta
      • [gmx-users] Re: Differences in rmsd with different force field   Justin A. Lemkul
• [gmx-users] Re:gmx-users Digest, Vol 82, Issue 168   gromacs564
• [gmx-users] configure: error: cannot compute sizeof (off_t)   Justin Kat
  • [gmx-users] configure: error: cannot compute sizeof (off_t)   Mark Abraham
• [gmx-users] GROMACS installation query   Tom Dupree
  • [gmx-users] GROMACS installation query   Carsten Kutzner
• [gmx-users] Re: Adding chromophore parameters to the charmm force field   bharat gupta
  • [gmx-users] Re: Adding chromophore parameters to the charmm force field   Justin A. Lemkul
• [gmx-users] scaling of replica exchange   Valeria Losasso
  • [gmx-users] scaling of replica exchange   Luca Bellucci
  • [gmx-users] scaling of replica exchange   Luca
    • [gmx-users] scaling of replica exchange   Valeria Losasso
• [gmx-users] scaling of replica exchange   Mark Abraham
  • [gmx-users] scaling of replica exchange   Valeria Losasso
• [gmx-users] Van der waals interaction between nanotubes   sakthi kumaran
  • [gmx-users] Van der waals interaction between nanotubes   Justin A. Lemkul
    • [gmx-users] Van der waals interaction between nanotubes   sakthi kumaran
      • [gmx-users] Van der waals interaction between nanotubes   Justin A. Lemkul
• [gmx-users] %exist hydrogen bond   leila karami
  • [gmx-users] %exist hydrogen bond   Justin A. Lemkul
• [gmx-users] Library file ffamber_tip3p.gro not found in current directory   sunita gupta
  • [gmx-users] Library file ffamber_tip3p.gro not found in current directory   Justin A. Lemkul
• [gmx-users] scaling of replica exchange   Mark Abraham
  • [gmx-users] scaling of replica exchange   Fabio Affinito
• [gmx-users] scaling of replica exchange   Mark Abraham
• [gmx-users] %exist hydrogen bond   leila karami
  • [gmx-users] %exist hydrogen bond   Justin A. Lemkul
• [gmx-users] test on g_density   chris.neale at utoronto.ca
• [gmx-users] Residue 'DEF' not found in residue topology database   Emine Deniz Tekin
  • [gmx-users] Residue 'DEF' not found in residue topology database   Justin A. Lemkul
    • [gmx-users] Residue 'DEF' not found in residue topology database   Emine Deniz Tekin
      • [gmx-users] Residue 'DEF' not found in residue topology database   Justin A. Lemkul
• [gmx-users] %exist hydrogen bond   leila karami
• [gmx-users] Website search broken   Justin A. Lemkul
  • [gmx-users] Website search broken   Emine Deniz Tekin
    • [gmx-users] Website search broken   Olga Ivchenko
• [gmx-users] Interatomic distance matrices   J. Nathan Scott
  • [gmx-users] Interatomic distance matrices   Tsjerk Wassenaar
• [gmx-users] widom insertion   Thomas Koller
• [gmx-users] Re: PMF from pull code, unexpected results   Michael Brunsteiner
• [gmx-users] trr files transferability   Ravi Bhadauria
  • [gmx-users] trr files transferability   Mark Abraham
• [gmx-users] Minimisation restraints   Carla Jamous
  • [gmx-users] Minimisation restraints   Justin A. Lemkul
  • [gmx-users] Minimisation restraints   Thomas Evangelidis
• [gmx-users] 9 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.   ajani haresh
  • [gmx-users] 9 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.   Justin A. Lemkul
• [gmx-users] negative steps from tpbconv   Jesper Sørensen
  • [gmx-users] negative steps from tpbconv   XAvier Periole
    • [gmx-users] negative steps from tpbconv   Jesper Sørensen
      • [gmx-users] negative steps from tpbconv   Tsjerk Wassenaar
      • [gmx-users] negative steps from tpbconv   XAvier Periole
      • [gmx-users] negative steps from tpbconv   Jesper Sørensen
      • [gmx-users] negative steps from tpbconv   Tsjerk Wassenaar
• [gmx-users] topology files for ligands in MD Simulation under OPLS AA force field   mircial at sjtu.edu.cn
  • [gmx-users] topology files for ligands in MD Simulation under OPLS AA force field   Justin A. Lemkul
• [gmx-users] How to countting hydrogen bond lifetime and donor--acceptor residue's atom ?   gromacs564
  • [gmx-users] How to countting hydrogen bond lifetime and donor--acceptor residue's atom ?   Erik Marklund
    • [gmx-users] How to countting hydrogen bond lifetime and donor--acceptor residue's atom ?   Erik Marklund
      • [gmx-users] How to countting hydrogen bond lifetime and donor--acceptor residue's atom ?   Justin A. Lemkul
• [gmx-users] CNT topology   sara
  • [gmx-users] CNT topology   Justin A. Lemkul
• [gmx-users] How to countting Hbonds lifetime   gromacs564
  • [gmx-users] How to countting Hbonds lifetime   Justin A. Lemkul
• [gmx-users] g_rms and g_cluster   shahid nayeem
  • [gmx-users] g_rms and g_cluster   Justin A. Lemkul
• [gmx-users] PMF from pull code, unexpected results   chris.neale at utoronto.ca
• [gmx-users] %exist hydrogen bond - difference between number of lines in input and output files   leila karami
  • [gmx-users] %exist hydrogen bond - difference between number of lines in input and output files   Justin A. Lemkul
• [gmx-users] Re: How to countting Hbonds lifetime   gromacs564
  • [gmx-users] Re: How to countting Hbonds lifetime   Justin A. Lemkul
• [gmx-users] water-medited hydrogen bonds - %exist hydrogen bonds   leila karami
  • [gmx-users] water-medited hydrogen bonds - %exist hydrogen bonds   Justin A. Lemkul
• [gmx-users] PMF from pull code, unexpected results   Michael Brunsteiner
• [gmx-users] topology files for ligands in MD Simulation under OPLS AA force field   Michael Brunsteiner
• [gmx-users] Stress/strain analysis   Tandia, Adama
• [gmx-users] GAUSSIAN Error message   Sergio Manzetti
  • [gmx-users] GAUSSIAN Error message   TJ Mustard
    • [gmx-users] GAUSSIAN Error message   Sergio Manzetti
      • [gmx-users] GAUSSIAN Error message   Txema Mercero
      • [gmx-users] GAUSSIAN Error message   TJ Mustard
• [gmx-users] g_dipole   Nilesh Dhumal
  • [gmx-users] g_dipole   Justin A. Lemkul
    • [gmx-users] g_dipole   Nilesh Dhumal
      • [gmx-users] g_dipole   Justin A. Lemkul
      • [gmx-users] g_dipole   André Farias de Moura
• [gmx-users] Re: gmx-users Digest, Vol 82, Issue 189   Gerrit Groenhof
• [gmx-users] henry constant   Thomas Koller
• [gmx-users] em mdrun   Nick
  • [gmx-users] em mdrun   Justin A. Lemkul
    • [gmx-users] em mdrun   Nick
    • [gmx-users] em mdrun   Nick
      • [gmx-users] em mdrun   Justin A. Lemkul
• [gmx-users] Help please.   Brody Bessire
• [gmx-users] Help please.   Dallas Warren
• [gmx-users] index file groups   Nick
  • [gmx-users] index file groups   Mark Abraham
    • [gmx-users] index file groups   Moeed
• [gmx-users] how many contacts has a certain atom at MD   Justin A. Lemkul
• [gmx-users] Questions on combination of Berger's united-atom force field for lipid and OPLS_AA force field for protein   mircial at sjtu.edu.cn
• [gmx-users] PBC   Carla Jamous
  • [gmx-users] PBC   Justin A. Lemkul
    • [gmx-users] PBC   Carla Jamous
• [gmx-users] Values of radial density profiles   sa
• [gmx-users] Questions on combination of Berger's united-atom force field for lipid and OPLS_AA force field for protein   chris.neale at utoronto.ca
• [gmx-users] g_velacc -mol option   Vigneshwar Ramakrishnan
• [gmx-users] Nitrogen box   sarah k
  • [gmx-users] Nitrogen box   Justin A. Lemkul
• [gmx-users] Fwd: Enquire about double strand DNA in gmx 4.5.3 charmm27 ff.Thank you.   David van der Spoel
  • [gmx-users] Fwd: Enquire about double strand DNA in gmx 4.5.3 charmm27 ff.Thank you.   David van der Spoel
• [gmx-users] query against box collapsed in case of tightly bound ligand   devawati dutta
  • [gmx-users] query against box collapsed in case of tightly bound ligand   Justin A. Lemkul
• [gmx-users] henry constant   Thomas Koller
• [gmx-users] problem with gromcas 4.5.3   leila separdar
  • [gmx-users] problem with gromcas 4.5.3   Justin A. Lemkul
• [gmx-users] PROCHEK-NMR instalation problem   najwa drici
  • [gmx-users] PROCHEK-NMR instalation problem   Justin A. Lemkul
• [gmx-users] excess chemical potential   Thomas Koller
• [gmx-users] ***Extended deadline: March 18*** COMETS 2011 - 2nd International Track on Collaborative Modeling and Simulation - Call for Papers   Daniele Gianni
• [gmx-users] Positive potential energy in simulation using polarizable model   aldi asmadi
  • [gmx-users] Positive potential energy in simulation using polarizable model   David van der Spoel
    • [gmx-users] Positive potential energy in simulation using polarizable model   aldi asmadi
      • [gmx-users] Positive potential energy in simulation using polarizable model   David van der Spoel
• [gmx-users] Re: Enquire about double strand DNA in gmx 4.5.3 charmm27 ff.Thank you.   Justin A. Lemkul
• [gmx-users] .tdr file not created   sakthi kumaran
  • [gmx-users] .tdr file not created   Justin A. Lemkul
• [gmx-users] AlF4 - producing LINCS errors   Matthew Cliff
• [gmx-users] AlF4 - producing LINCS errors   Mark Abraham
  • [gmx-users] AlF4 - producing LINCS errors   Matthew Cliff
• [gmx-users] about -CN triple bond   Mark Abraham
• [gmx-users] Regarding without solvent(water).   ajaniharesh at gmail.com
  • [gmx-users] Regarding without solvent(water).   Justin A. Lemkul
• [gmx-users] H-bond autocorrelation doubts   bipin singh
  • [gmx-users] H-bond autocorrelation doubts   André Farias de Moura
    • [gmx-users] H-bond autocorrelation doubts   bipin singh
      • [gmx-users] H-bond autocorrelation doubts   Erik Marklund
      • [gmx-users] H-bond autocorrelation doubts   bipin singh
      • [gmx-users] H-bond autocorrelation doubts   Erik Marklund
      • [gmx-users] H-bond autocorrelation doubts   André Farias de Moura
• [gmx-users] Regarding without solvent(water).   ajaniharesh at gmail.com
  • [gmx-users] Regarding without solvent(water).   Justin A. Lemkul
• [gmx-users] question about GBSA and opls-aa   Baoqiang Cao
  • [gmx-users] question about GBSA and opls-aa   Per Larsson
• [gmx-users] oplsaa galactose   nishap.patel at utoronto.ca
  • [gmx-users] oplsaa galactose   Justin A. Lemkul
    • [gmx-users] oplsaa galactose   nishap.patel at utoronto.ca
• [gmx-users] question about GBSA and opls-aa   Baoqiang Cao
• [gmx-users] Re: Regarding without solvent(water).   Justin A. Lemkul
• [gmx-users] Help regarding terinary complex simulation with ZN at active site   kala
  • [gmx-users] Help regarding terinary complex simulation with ZN at active site   Justin A. Lemkul
• [gmx-users] How to obtain the average radial density functions relative to the center of mass with g_rdf.   sa
• [gmx-users] How to obtain the average radial density functions relative to the center of mass with g_rdf.   Dallas Warren
• [gmx-users] charge group radii- use maxwarn or increase rlist?   Moeed
  • [gmx-users] charge group radii- use maxwarn or increase rlist?   Justin A. Lemkul
    • [gmx-users] charge group radii- use maxwarn or increase rlist?   Moeed

Last message date: Mon Feb 28 23:48:53 CET 2011
Archived on: Thu Nov 14 12:10:22 CET 2013

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