December 2006 Archives by thread

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Starting: Fri Dec 1 00:01:05 CET 2006
Ending: Sun Dec 31 21:54:41 CET 2006
Messages: 288

• [gmx-users] indexing atoms *Altering code   toma0052
  • [gmx-users] indexing atoms *Altering code   David van der Spoel
• [gmx-users] AMBER atom type for Hydroxamate moeity   raja
  • [gmx-users] AMBER atom type for Hydroxamate moeity   Mark Abraham
    • [gmx-users] AMBER atom type for Hydroxamate moeity   raja
• [gmx-users] AMBER atom type for Hydroxamate moeity   raja
• [gmx-users] AMBER atom type for Hydroxamate moeity   raja
• [gmx-users] I got error in gromacs-3.2.1 installation time   ankit ashwinbhai patel
  • [gmx-users] I got error in gromacs-3.2.1 installation time   Mark Abraham
• [gmx-users] About g_cluster   Cesar Araujo
• [gmx-users] strange NTP trajectory   Qiao Baofu
  • [gmx-users] strange NTP trajectory   Yang Ye
• [gmx-users] Re: Official charmm support   Pär Bjelkmar
• [gmx-users] I need 256 lipids ...   David van der Spoel
• [gmx-users] editing HDB file ???   Karthikeyan Pasupathy
  • [gmx-users] editing HDB file ???   Yang Ye
  • [gmx-users] editing HDB file ???   Tsjerk Wassenaar
• [gmx-users] Surface Tension of a lipid bilayer   toma0052
  • [gmx-users] Surface Tension of a lipid bilayer   David van der Spoel
  • [gmx-users] Surface Tension of a lipid bilayer   Eric Jakobsson
• [gmx-users] opls parameters   Komath Damodaran
  • [gmx-users] opls parameters   Mark Abraham
    • [gmx-users] opls parameters   TJ Piggot
      • [gmx-users] opls parameters   Mark Abraham
      • [gmx-users] opls parameters   TJ Piggot
      • [gmx-users] opls parameters   Mark Abraham
      • [gmx-users] opls parameters   Dongsheng Zhang
      • [gmx-users] opls parameters   Erik Lindahl
• [gmx-users] Segmentaion fault error- installing gromacs-3.3.1 on MacOSX   Ibrahim M. Moustafa
  • [gmx-users] Segmentaion fault error- installing gromacs-3.3.1 on MacOSX   David van der Spoel
• [gmx-users] Question about NVT   Justin Lemkul
  • [gmx-users] Question about NVT   Mark Abraham
• [gmx-users] References for globular protein simulation using PME   Dilraj Lama
• [gmx-users] swapping the co-ordinates   Dinesh Pinisetty
  • [gmx-users] swapping the co-ordinates   David van der Spoel
  • [gmx-users] swapping the co-ordinates   Mark Abraham
  • [gmx-users] swapping the co-ordinates   Mark Abraham
• [gmx-users] Group-specific differences in RMS fluctuation results via g_rmsf   Keith Ball
• [gmx-users] COM motion removal after simulation   Martin Höfling
• [gmx-users] ATP/ADP topology for OPLS   Thorsten Kampmann
• [gmx-users] Re: Segmentation falt error - installing gromacs-3.3.1 on Mac-OSX   Ibrahim M. Moustafa
• [gmx-users] request   hadi behzadi
  • [gmx-users] request   Dallas B. Warren
  • [gmx-users] request   Mark Abraham
• [gmx-users] pulling force   Giacomo Bastianelli
  • [gmx-users] pulling force   Mark Abraham
• [gmx-users] Re:request   Kia Balali-Mood
• [gmx-users] gromacs local pressure version   msuk2 at uiuc.edu
• [gmx-users] (no subject)   Bio
  • [gmx-users] (no subject)   Mark Abraham
• [gmx-users] range checking error   Giacomo Bastianelli
• [gmx-users] range checking error   Naser, Md Abu
• [gmx-users] relative weight of direct and reciprocal sum   Argyrios Karatrantos
  • [gmx-users] relative weight of direct and reciprocal sum   Mark Abraham
• [gmx-users] (no subject)   hadi behzadi
  • [gmx-users] (no subject)   Mark Abraham
    • [gmx-users] (no subject)   Tsjerk Wassenaar
• [gmx-users] TFE-water minimization   Owen, Michael
  • [gmx-users] TFE-water minimization   Mark Abraham
• [gmx-users] fudgeQQ (again ...)   Lianqing Zheng
• [gmx-users] simulation of two peptides   Owen, Michael
  • [gmx-users] simulation of two peptides   Mark Abraham
• [gmx-users] relative weight between the direct space sum and reciprocal space sum   Argyrios Karatrantos
  • [gmx-users] relative weight between the direct space sum and reciprocal space sum   Mark Abraham
• [gmx-users] pdb2gmx... cys-cys bonds....   sharada
  • [gmx-users] pdb2gmx... cys-cys bonds....   Mark Abraham
    • [gmx-users] pdb2gmx... cys-cys bonds....   sharada
      • [gmx-users] pdb2gmx... cys-cys bonds....   Mark Abraham
• [gmx-users] Re: relative weight between the direct space sum and reciprocal space sum   Janne Hirvi
• [gmx-users] Re: fudgeQQ (again ...)   Janne Hirvi
  • [gmx-users] Re: fudgeQQ (again ...)   Lianqing Zheng
• [gmx-users] GROMACS with MPI/GAMMA   Tony Ladd
• [gmx-users] How to construct PMF from the result of AFM pulling?   clark
  • [gmx-users] How to construct PMF from the result of AFM pulling?   Mark Abraham
• [gmx-users] GROMACS with MPI/GAMMA   Tony Ladd
• [gmx-users] Re: fudgeQQ (again ...)   Janne Hirvi
  • [gmx-users] Re: fudgeQQ (again ...)   Lianqing Zheng
• [gmx-users] GROMACS exit codes; error in LAM installation?   Alan Dodd
  • [gmx-users] GROMACS exit codes; error in LAM installation?   Ansgar Esztermann
  • [gmx-users] GROMACS exit codes; error in LAM installation?   Mark Abraham
• [gmx-users] How to simulate a protein that contains two cuban cluster   "Stefan Schöbel"
  • [gmx-users] How to simulate a protein that contains two cuban cluster   Mark Abraham
• [gmx-users] charges for non-natural residues with gromos 53a6   Carsten Baldauf
  • [gmx-users] charges for non-natural residues with gromos 53a6   Mark Abraham
• [gmx-users] charges for non-natural residues with gromos 53a6   Carsten Baldauf
• [gmx-users] Re: fudgeQQ (again ...)   chris.neale at utoronto.ca
  • [gmx-users] Re: fudgeQQ (again ...)   Qiao Baofu
  • [gmx-users] Re: fudgeQQ (again ...)   Lianqing Zheng
• [gmx-users] Re: fudgeQQ (again ...)   chris.neale at utoronto.ca
• [gmx-users] error in pdb2gmx   Dmitriy Golubobsky
  • [gmx-users] error in pdb2gmx   Mark Abraham
• [gmx-users] Can I use different force field functions for a molecule   intelandamd
  • [gmx-users] Can I use different force field functions for a molecule   Mark Abraham
• [gmx-users] Simulation of two peptides   nur avneet
  • [gmx-users] Simulation of two peptides   Mark Abraham
• [gmx-users] NVT with lipid bilayer   Justin Lemkul
  • [gmx-users] print out energy values with more decimals   Nicolas SAPAY
    • [gmx-users] print out energy values with more decimals   Mark Abraham
    • [gmx-users] print out energy values with more decimals   David van der Spoel
    • [gmx-users] print out energy values with more decimals   Berk Hess
  • [gmx-users] NVT with lipid bilayer   Mark Abraham
    • [gmx-users] NVT with lipid bilayer   Justin Lemkul
• [gmx-users] NVT with lipid bilayer   Dr Itamar Kass
• [gmx-users] Re: fudgeQQ (again ...) and fudgeLJ   Qiao Baofu
• [gmx-users] setup for lipid force field   swamy kakumani
  • [gmx-users] setup for lipid force field   Mark Abraham
    • [gmx-users] Re: [suggest tutorials   swamy kakumani
      • [gmx-users] Re: [suggest tutorials   Mark Abraham
      • [gmx-users] Dipolar correlation function   chiradip chatterjee
      • [gmx-users] Dipolar correlation function   David van der Spoel
      • [gmx-users] Dipolar correlation function   chiradip chatterjee
• [gmx-users] RMSD   Michal Walczak
• [gmx-users] FENE potential-bond interaction   Argyrios Karatrantos
  • [gmx-users] FENE potential-bond interaction   Mark Abraham
    • [gmx-users] FENE potential-bond interaction   Tsjerk Wassenaar
      • [gmx-users] FENE potential-bond interaction   Mark Abraham
• [gmx-users] difficulties in creating octahedral boxes   Astrid Maaß
  • [gmx-users] difficulties in creating octahedral boxes   David van der Spoel
  • [gmx-users] difficulties in creating octahedral boxes   Ran Friedman
  • [gmx-users] difficulties in creating octahedral boxes   Hanna, Joanne
    • [gmx-users] genion question   Samuel C Flores
      • [gmx-users] genion question   Mark Abraham
    • [gmx-users] difficulties in creating octahedral boxes   Tsjerk Wassenaar
• [gmx-users] FENE potential   Argyrios Karatrantos
  • [gmx-users] FENE potential   Mark Abraham
    • [gmx-users] FENE potential   Tsjerk Wassenaar
• [gmx-users] fugeQQ in buckingham   wurl
  • [gmx-users] fugeQQ in buckingham   David van der Spoel
• [gmx-users] RE RE:fugeQQ in buckingham   Rongliang Wu
• [gmx-users] rdf / sdf around a specific point   Martin Höfling
  • [gmx-users] rdf / sdf around a specific point   Tsjerk Wassenaar
    • [gmx-users] rdf / sdf around a specific point   Martin Höfling
• [gmx-users] protein + a single lipid   sebastien santini
  • [gmx-users] protein + a single lipid   Mark Abraham
• [gmx-users] restricted clustering   Giacomo Bastianelli
  • [gmx-users] restricted clustering   Mark Abraham
• [gmx-users] monoclinic systems and pbc   Claus Valka
  • [gmx-users] monoclinic systems and pbc   Tsjerk Wassenaar
• [gmx-users] mcdonna at lpsat.com   donna at iflysib.unlp.edu.ar
• [gmx-users] tersoff potential   Cherry Y. Yates
  • [gmx-users] tersoff potential   Mark Abraham
• [gmx-users] TYR residue in OPLS-AA   Adam Mazur
  • [gmx-users] TYR residue in OPLS-AA   David van der Spoel
• [gmx-users] new mailing list user   anna artese
• [gmx-users] g_energy info   anna artese
  • [gmx-users] g_energy info   Erik Marklund
• [gmx-users] lately reading sequential unformatted external IO   Mahnam
• [gmx-users] localized molecular dynamics   Giacomo Bastianelli
  • [gmx-users] localized molecular dynamics   Mark Abraham
  • [gmx-users] localized molecular dynamics   David van der Spoel
• [gmx-users] dihedral   Prasad Gajula
• [gmx-users] rdf / sdf around a specific point   chris.neale at utoronto.ca
• [gmx-users] Free energy calculation, parallel or sequential lambda runs ?   Stéphane Téletchéa
  • [gmx-users] Free energy calculation, parallel or sequential lambda runs ?   David Mobley
    • [gmx-users] Free energy calculation, parallel or sequential lambda runs ?   Ignacio Fernández Galván
      • [gmx-users] Free energy calculation, parallel or sequential lambda runs ?   Stéphane Téletchéa
      • [gmx-users] Free energy calculation, parallel or sequential lambda runs ?   David Mobley
      • [gmx-users] Free energy calculation, parallel or sequential lambda runs ?   Ignacio Fernández Galván
    • [gmx-users] Free energy calculation, parallel or sequential lambda runs ?   Stéphane Téletchéa
• [gmx-users] How to implement dihedral restraints   chris.neale at utoronto.ca
  • [gmx-users] How to implement dihedral restraints   Mark Abraham
• [gmx-users] Pressure variation in NPT ensemble   nur avneet
  • [gmx-users] Pressure variation in NPT ensemble   Mark Abraham
• [gmx-users] error after genion   Carsten Baldauf
  • [gmx-users] error after genion   Tsjerk Wassenaar
• [gmx-users] How to implement dihedral restraints   chris.neale at utoronto.ca
• [gmx-users] Re: free energy calculation & TI   David Mobley
• [gmx-users] PME error in gromacs-3.3.1   Yuhui Li
  • [gmx-users] PME error in gromacs-3.3.1   Mark Abraham
  • [gmx-users] PME error in gromacs-3.3.1   Mark Abraham
• [gmx-users] problem with genbox   Li, Yun
  • [gmx-users] problem with genbox   Mark Abraham
• [gmx-users] problem with genbox   Li, Yun
  • [gmx-users] problem with genbox   David van der Spoel
• [gmx-users] XRAMA\environment variable\   Bio
  • [gmx-users] XRAMA\environment variable\   David van der Spoel
• [gmx-users] A problem with grompp   Александр Журавлев
  • [gmx-users] A problem with grompp   David van der Spoel
    • [gmx-users] A problem with grompp   Ken Rotondi
      • [gmx-users] A problem with grompp   Mark Abraham
• [gmx-users] Query to display Gromacs compile time settings?   Michael John Hanby
  • [gmx-users] Query to display Gromacs compile time settings?   Stéphane Téletchéa
  • [gmx-users] Query to display Gromacs compile time settings?   Mark Abraham
    • [gmx-users] Query to display Gromacs compile time settings?   Erik Lindahl
• [gmx-users] PME error in gromacs-3.3.1   Yuhui Li
• [gmx-users] Query to display Gromacs compile time settings?   Michael John Hanby
• [gmx-users] how to add a force field or potential fu nction?   zzhwise1 at 163.com
  • [gmx-users] how to add a force field or potential fu nction?   Mark Abraham
• [gmx-users] mopac7 files at md.chem.rug.nl   Jeffrey Gardner
• [gmx-users] Excluding the frozen atoms from all the calculation with Pressure coupling?   shaoqingfly1981
• [gmx-users] (no subject)   Sivashangari Gnanasambandam
  • [gmx-users] (no subject)   Mark Abraham
• [gmx-users] Can we run a NPT simulation with fixed lengths in x and y direction?   Hu Zhongqiao
  • [gmx-users] Can we run a NPT simulation with fixed lengths in x and y direction?   David van der Spoel
    • [gmx-users] Can we run a NPT simulation with fixed lengths inx and y direction?   Sivashangari Gnanasambandam
      • [gmx-users] Can we run a NPT simulation with fixed lengths inx and y direction?   Tsjerk Wassenaar
      • [gmx-users] Can we run a NPT simulation with fixed lengths inxand y direction?   Sivashangari Gnanasambandam
      • [gmx-users] Can we run a NPT simulation with fixed lengths inxand y direction?   Tsjerk Wassenaar
      • [gmx-users] Can we run a NPT simulation with fixed lengths inxandy direction?   Dallas B. Warren
• [gmx-users] g_hbond   OZGE ENGIN
  • [gmx-users] g_hbond   Erik Marklund
    • [gmx-users] g_hbond   Diego Enry
  • [gmx-users] g_hbond   Florian Haberl
    • [gmx-users] g_hbond   Erik Marklund
• [gmx-users] Launching Replica Exchange MD   Bob Johnson
  • [gmx-users] Launching Replica Exchange MD   Mark Abraham
• [gmx-users] g_hbond   OZGE ENGIN
  • [gmx-users] g_hbond   Erik Marklund
• [gmx-users] mixing rules for LJ parameters?   Nicolas Winter
  • [gmx-users] mixing rules for LJ parameters?   Mark Abraham
  • [gmx-users] mixing rules for LJ parameters?   David van der Spoel
  • [gmx-users] mixing rules for LJ parameters?   Erik Lindahl
    • [gmx-users] mixing rules for LJ parameters?   Nicolas Winter
      • [gmx-users] mixing rules for LJ parameters?   Erik Lindahl
• [gmx-users] LJ question   Anthony Cruz Balberdi
• [gmx-users] Re: Launching Replica Exchange MD   Robert Johnson
• [gmx-users] mixing for new LJ parameters   Anthony Cruz Balberdi
• [gmx-users] merging several trr and edr files   Joern Lenz
  • [gmx-users] merging several trr and edr files   Caterina Arcangeli
    • [gmx-users] merging several trr and edr files   Mark Abraham
• [gmx-users] how to calculate the area of per lipid in membrane   linfu
• [gmx-users] how to calculate the area of per lipid in membrane   Alan Dodd
• [gmx-users] mdrun_mpi not exiting   sharath chandra
• [gmx-users] g_hbond in/output   OZGE ENGIN
  • [gmx-users] g_hbond in/output   Erik Marklund
• [gmx-users] TFE solvent box   correafe at iq.usp.br
  • [gmx-users] TFE solvent box   David van der Spoel
  • [gmx-users] TFE solvent box   chiradip chatterjee
• [gmx-users] Replica Exchange MD Errors   Robert Johnson
  • [gmx-users] Replica Exchange MD Errors   David van der Spoel
  • [gmx-users] Replica Exchange MD Errors   Mark Abraham
• [gmx-users] run gromacs on a single machine with mutiple CPUs   Seaclear Theory
  • [gmx-users] run gromacs on a single machine with mutiple CPUs   Mark Abraham
    • [gmx-users] run gromacs on a single machine with mutiple CPUs   Seaclear Theory
      • [gmx-users] run gromacs on a single machine with mutiple CPUs   Mark Abraham
      • [gmx-users] run gromacs on a single machine with mutiple CPUs   Seaclear Theory
      • [gmx-users] run gromacs on a single machine with mutiple CPUs   Yang Ye
      • [gmx-users] run gromacs on a single machine with mutiple CPUs   David van der Spoel
      • [gmx-users] run gromacs on a single machine with mutiple CPUs   Seaclear Theory
      • [gmx-users] run gromacs on a single machine with mutiple CPUs   David van der Spoel
      • [gmx-users] run gromacs on a single machine with mutiple CPUs   Seaclear Theory
      • [gmx-users] run gromacs on a single machine with mutiple CPUs   Seaclear Theory
      • [gmx-users] run gromacs on a single machine with mutiple CPUs   Mark Abraham
  • [gmx-users] run gromacs on a single machine with mutiple CPUs   Erik Lindahl
    • [gmx-users] run gromacs on a single machine with mutiple CPUs   Seaclear Theory
      • [gmx-users] run gromacs on a single machine with mutiple CPUs   Martin Höfling
• [gmx-users] a small bug?   Mu Yuguang (Dr)
  • [gmx-users] a small bug?   Mark Abraham
• [gmx-users] a small bug?   Mu Yuguang (Dr)
• [gmx-users] do_dssp   singh
  • [gmx-users] do_dssp   Tsjerk Wassenaar
    • [gmx-users] do_dssp   David van der Spoel
    • [gmx-users] do_dssp   singh
      • [gmx-users] do_dssp   David van der Spoel
• [gmx-users] limit of number of processors ??   이 선주
  • [gmx-users] limit of number of processors ??   David van der Spoel
• [gmx-users] segnentation fault in drug_enzyme_tutorial   Robert Kretschmer
  • [gmx-users] segnentation fault in drug_enzyme_tutorial   David van der Spoel
• [gmx-users] initial velocities   James Rustad
  • [gmx-users] configuration error   Cherry Y. Yates
    • [gmx-users] configuration error   David van der Spoel
  • [gmx-users] initial velocities   David van der Spoel
• [gmx-users] Can I use more memory to speed up computa tion?   intelandamd
  • [gmx-users] Can I use more memory to speed up computa tion?   David van der Spoel
• [gmx-users] -sel option / g_hbond   OZGE ENGIN
  • [gmx-users] -sel option / g_hbond   Erik Marklund
• [gmx-users] configuration error   Michael John Hanby
  • [gmx-users] configuration error   Cherry Y. Yates
    • [gmx-users] configuration error   Mark Abraham
• [gmx-users] starting conformation different   priya priya
  • [gmx-users] starting conformation different   Mark Abraham
    • [gmx-users] starting conformation different   Tsjerk Wassenaar
• [gmx-users] implicit solvent   Dmitriy Golubobsky
  • [gmx-users] implicit solvent   Mark Abraham
  • [gmx-users] implicit solvent   David van der Spoel
  • [gmx-users] g_wham and tol (tolerance) option   Arneh Babakhani
• [gmx-users] warning message while using eneconv   sunita at chem.iitb.ac.in
  • [gmx-users] warning message while using eneconv   David van der Spoel
    • [gmx-users] warning message while using eneconv   sunita at chem.iitb.ac.in
      • [gmx-users] warning message while using eneconv   sunita at chem.iitb.ac.in
      • [gmx-users] warning message while using eneconv   David van der Spoel
      • [gmx-users] warning message while using eneconv   sunita at chem.iitb.ac.in
      • [gmx-users] warning message while using eneconv   David van der Spoel
• [gmx-users] reactive flux   James Rustad
  • [gmx-users] reactive flux   David van der Spoel
• [gmx-users] Polymers: Shake Problem   acorrea at unisa.it
  • [gmx-users] Polymers: Shake Problem   David van der Spoel
• [gmx-users] problem with g_energy tool   Veera Krasnenko

Last message date: Sun Dec 31 21:54:41 CET 2006
Archived on: Thu Nov 14 12:03:22 CET 2013

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