October 2007 Archives by author

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Starting: Mon Oct 1 00:08:33 CEST 2007
Ending: Wed Oct 31 22:50:50 CET 2007
Messages: 551

[gmx-users] Reading XTC files from fortran90 Mark Abraham
[gmx-users] Reading XTC files from fortran90 Mark Abraham
[gmx-users] MPIRUN problem when switched to 8 np (searched the list) Mark Abraham
[gmx-users] Help for simulating the metalcluster Mark Abraham
[gmx-users] Reading XTC files from fortran90 Mark Abraham
[gmx-users] g_lie problem Mark Abraham
[gmx-users] mdrun error after 2.6nS Mark Abraham
[gmx-users] g_rms Mark Abraham
[gmx-users] g_rms Mark Abraham
[gmx-users] g_rms Mark Abraham
[gmx-users] mdrun error after 2.6nS Mark Abraham
[gmx-users] g_rms Mark Abraham
[gmx-users] getting a good .gro file from a pdb file while the topology is ready Mark Abraham
[gmx-users] getting a good .gro file from a pdb file while the topology is ready Mark Abraham
[gmx-users] getting a good .gro file from a pdb file while the topology is ready Mark Abraham
[gmx-users] lot of pdb files written during minimization without asking for them ? Mark Abraham
[gmx-users] gmx continuation run Mark Abraham
[gmx-users] restart md from the point it had stopped Mark Abraham
[gmx-users] anisotropic pressure coupling for temperature annealing Mark Abraham
[gmx-users] Re: Problems prior to running lipid-protein simulation Mark Abraham
[gmx-users] HC atomtype Mark Abraham
[gmx-users] HC atomtype Mark Abraham
[gmx-users] 3.3.2 volume Mark Abraham
[gmx-users] 3.3.2 volume Mark Abraham
[gmx-users] non-existent angles found from trajectory g_angle Mark Abraham
[gmx-users] cut-offs in j. kerrigans drug/enzyme tutorial Mark Abraham
[gmx-users] t-couple warning Mark Abraham
[gmx-users] g_sas by 3.3.1 and 3.3.2 give different results Mark Abraham
[gmx-users] non-existent angles found from trajectory g_angle Mark Abraham
[gmx-users] stuck Mark Abraham
[gmx-users] Fatal error Mark Abraham
[gmx-users] Energy of each composition Mark Abraham
[gmx-users] errores during compilation of GROMACS 3.3.2 Mark Abraham
[gmx-users] errores during compilation of GROMACS 3.3.2 Mark Abraham
[gmx-users] problem with linear molecules and suggested fix Mark Abraham
[gmx-users] forcefield validation Mark Abraham
[gmx-users] g_hbond Mark Abraham
[gmx-users] Long range electrostatic potential Mark Abraham
[gmx-users] H- bond Mark Abraham
[gmx-users] install problem on IBM powerpc AIX 5.3 Mark Abraham
[gmx-users] install problem on IBM powerpc AIX 5.3 Mark Abraham
[gmx-users] Addition of ions in vacuum simulations Mark Abraham
[gmx-users] Addition of ions in vacuum simulations Mark Abraham
[gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel Mark Abraham
[gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel Mark Abraham
[gmx-users] install problem on IBM powerpc AIX 5.3 Mark Abraham
[gmx-users] install problem on IBM powerpc AIX 5.3 Mark Abraham
[gmx-users] uneven distribution of water across the bilayer Mark Abraham
[gmx-users] applying force and fixing atoms in gromacs Mark Abraham
[gmx-users] Pull code with runtype start Mark Abraham
[gmx-users] Pull code with runtype start Mark Abraham
[gmx-users] Concatenate .edr file Mark Abraham
[gmx-users] Qeury on freezing an atom with negatice co-ordinates Mark Abraham
[gmx-users] b-factor Mark Abraham
[gmx-users] Position restricted md Mark Abraham
[gmx-users] Problem in downloading source code Mark Abraham
[gmx-users] Position restricted md Mark Abraham
[gmx-users] problem in g_confrms Mark Abraham
[gmx-users] g_rmsf and pbc Mark Abraham
[gmx-users] alpha Carbon-Aromatic ring hydrogen bond Mark Abraham
[gmx-users] Source code through email Mark Abraham
[gmx-users] make_ndx Mark Abraham
[gmx-users] g_energy has no bond entry when MD analysis Mark Abraham
[gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ? Mark Abraham
[gmx-users] queue up simulations Mark Abraham
[gmx-users] problems with opls_ Mark Abraham
[gmx-users] Re: trjconv help Mark Abraham
[gmx-users] constraining two diff molecules removes LJ interaction? Mark Abraham
[gmx-users] Problem putting 2 identical peptide chains in a simulation box Mark Abraham
[gmx-users] Problem putting 2 identical peptide chains in a simulation box Mark Abraham
[gmx-users] PBC, lincs and bonds breaking Mark Abraham
[gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ???? Mark Abraham
[gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ???? Mark Abraham
[gmx-users] angle between helices Mark Abraham
[gmx-users] potential energy of only the protein Mark Abraham
[gmx-users] g_sas problem Mark Abraham
[gmx-users] langevin dynamics Mark Abraham
[gmx-users] langevin dynamics Mark Abraham
[gmx-users] grompp error for alamethicin Mark Abraham
[gmx-users] uneven distribution of water across the bilayer Alok
[gmx-users] uneven distribution of water across the bilayer Alok
[gmx-users] alpha Carbon-Aromatic ring hydrogen bond Alok
[gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ? Alok
[gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ? Alok
[gmx-users] solvate using genbox results in water in the >centerofthe bilayer. How to edit pdb file contents in gromacs ? Alok
[gmx-users] solvate using genbox results in water in thecenterofthe bilayer. How to edit pdb file contents in gromacs ? Alok
[gmx-users] Removal of unwanted water from lipid bilayer after solvating the structure from genbox: problem and solution Alok
[gmx-users] Reading XTC files from fortran90 Jones de Andrade
[gmx-users] Reading XTC files from fortran90 Jones de Andrade
[gmx-users] Reading XTC files from fortran90 Jones de Andrade
[gmx-users] Dummies usage doubts Jones de Andrade
[gmx-users] Dummies usage doubts Jones de Andrade
[gmx-users] Dummies usage doubts Jones de Andrade
[gmx-users] Dummies usage doubts Jones de Andrade
[gmx-users] Dummies usage doubts Jones de Andrade
[gmx-users] Dummies usage doubts Jones de Andrade
[gmx-users] constraining two diff molecules removes LJ interaction? Guilherme Menegon Arantes
[gmx-users] Help for simulating the metalcluster Vasilii Artyukhov
[gmx-users] Rerefence on Berendsen vs. Nose-Hoover Vasilii Artyukhov
[gmx-users] queue up simulations Vasilii Artyukhov
[gmx-users] Postdoc position available (virtual reality, interactive simulations) Marc Baaden
[gmx-users] ascii Covariance matrix Arneh Babakhani
[gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory van Bemmelen
[gmx-users] getting a good .gro file from a pdb file while the topology is ready van Bemmelen
[gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory van Bemmelen
[gmx-users] Tool for visualizing disulphide bonds van Bemmelen
[gmx-users] Long range electrostatic potential van Bemmelen
[gmx-users] No scale up beyond 4 processors for 240000 atom system Christian Burisch
[gmx-users] 3.3.2 volume Christian Burisch
[gmx-users] Large VCM error for a POPC bilayer simulation : 2nd attempt Rainer Böckmann
[gmx-users] GROMETA - Gromacs with Metadynamics, and more Carlo Camilloni
[gmx-users] g_rmsf Segmentation fault Tommy Carstensen
[gmx-users] g_wham Jose Javier Lopez Cascales
[gmx-users] Rerefence on Berendsen vs Nose-Hoover John D. Chodera
[gmx-users] MSD near specific molecules Jian Dai
[gmx-users] only one cpu "works" in my linux cluster Alan Dodd
[gmx-users] only one cpu "works" in my linux cluster Alan Dodd
[gmx-users] How to change the box size during simuation Alan Dodd
[gmx-users] anisotropic pressure coupling for temperature annealing Alan Dodd
[gmx-users] forcefield validation Alan Dodd
[gmx-users] angle between helices Alan Dodd
[gmx-users] Re: Viewing Dodecahedral Systems Sean Drummond
[gmx-users] How to calculate the average distance or energy between two residues? MoJie Duan
[gmx-users] g_order atom distance warning Stephen M. Dutz
[gmx-users] Re: g_order in GROMACS 3.3.2 and 3.3.1 Stephen M. Dutz
[gmx-users] the comm_mode OZGE ENGIN
[gmx-users] Tool for visualizing disulphide bonds OZGE ENGIN
[gmx-users] the comm_mode OZGE ENGIN
[gmx-users] Addition of ions in vacuum simulations OZGE ENGIN
[gmx-users] Addition of ions in vacuum simulations OZGE ENGIN
[gmx-users] GROMACS-3.3.2 on BG/L Ivano Eberini
[gmx-users] Compiling GROMACS with FORTRAN? Ivano Eberini
[gmx-users] Compiling GROMACS with FORTRAN? Ivano Eberini
[gmx-users] restart md from the point it had stopped Diego Enry
[gmx-users] restart md from the point it had stopped Diego Enry
[gmx-users] restart md from the point it had stopped Diego Enry
[gmx-users] grompp error Diego Enry
[gmx-users] No scale up beyond 4 processors for 240000 atom system Diego Enry
[gmx-users] tabulated potential - why table length is rc+1nm Nickle Fan
[gmx-users] genbox using tip5p water results in too few number of water molecules JW Feng
[gmx-users] genbox using tip5p water results in too few number of water molecules JW Feng
[gmx-users] solubility of PVME in TIP5P JW Feng
[gmx-users] Re: 3.3.2 trjconv -ur compact -pbc whole problem JW Feng
[gmx-users] Re: 3.3.2 trjconv -ur compact -pbc whole problem JW Feng
[gmx-users] t-couple warning JW Feng
[gmx-users] t-couple warning JW Feng
[gmx-users] Exploding box after 55.5ns of simulation JW Feng
[gmx-users] simulating Hexadecane in water Adam Fraser
[gmx-users] simulating hydrocarbons in water Adam Fraser
[gmx-users] simulating hydrocarbons in water Adam Fraser
[gmx-users] simulating hydrocarbons in water Adam Fraser
[gmx-users] simulating hydrocarbons in water Adam Fraser
[gmx-users] stuck Adam Fraser
[gmx-users] applying force and fixing atoms in gromacs Adam Fraser
[gmx-users] applying force and fixing atoms in gromacs Adam Fraser
[gmx-users] editconf -mead Ran Friedman
[gmx-users] Visualizing non-rectangular boxes Ignacio Fernández Galván
[gmx-users] Visualizing non-rectangular boxes Ignacio Fernández Galván
[gmx-users] Visualizing non-rectangular boxes Ignacio Fernández Galván
[gmx-users] Visualizing non-rectangular boxes Ignacio Fernández Galván
[gmx-users] Visualizing non-rectangular boxes Ignacio Fernández Galván
[gmx-users] bug energy - continuity md Ricardo Gobato
[gmx-users] mopac gcc g77 and x86_64 Andrey V. Golovin
[gmx-users] Re: mopac gcc g77 and x86_64 Andrey V. Golovin
[gmx-users] Fwd: project 4 Russell Green
[gmx-users] ascii Covariance matrix Russell Green
[gmx-users] Re: mopac gcc g77 and x86_64 Gerrit Groenhof
[gmx-users] x2top problem Patricia Gómez
[gmx-users] MPIRUN problem when switched to 8 np (searched the list) Florian Haberl
[gmx-users] MPIRUN problem when switched to 8 np (searched the list) Florian Haberl
[gmx-users] Problem in downloading source code Florian Haberl
[gmx-users] H- bond emra Heshmati
[gmx-users] fix for range checking errors in parallel double precision mdrun Berk Hess
[gmx-users] No scale up beyond 4 processors for 240000 atom system Berk Hess
[gmx-users] limit on energygrp_table Berk Hess
[gmx-users] How to change the box size during simuation Berk Hess
[gmx-users] 1-4 table size of 0 nm Berk Hess
[gmx-users] frequence from PCA eigenvalue Berk Hess
[gmx-users] missing Ryckaert-Bell in 3.3.2 is now considered asERROR? Berk Hess
[gmx-users] angle between helices Berk Hess
[gmx-users] langevin dynamics Berk Hess
[gmx-users] GROMACS/G03 QM/MM Bryan Op't Holt
[gmx-users] Rerefence on Berendsen vs Nose-Hoover Jochen Hub
[gmx-users] Rerefence on Berendsen vs. Nose-Hoover Jochen Hub
[gmx-users] Rerefence on Berendsen vs Nose-Hoover Jochen Hub
[gmx-users] Development of .ITP or .TOP file for non-standard molecules Michelle Hyers
[gmx-users] Constraining to fixed position "Martin Höfling"
*** GMX Spamverdacht *** [gmx-users] Constraining to fixed position "Martin Höfling"
[gmx-users] missing Ryckaert-Bell in 3.3.2 is now considered as ERROR? Martin Höfling
[gmx-users] GLYCAM (sugars) with TIP5P in GROMACS JMandumpal
[gmx-users] is there any size limit for simulation in gromacs Anupam Nath Jha
[gmx-users] angle between helices Anupam Nath Jha
[gmx-users] angle between helices Anupam Nath Jha
[gmx-users] 3.3.2 volume Yin Jian
[gmx-users] 3.3.2 volume Yin Jian
[gmx-users] 3.3.2 volume Yin Jian
[gmx-users] g_sas by 3.3.1 and 3.3.2 give different results Yin Jian
[gmx-users] g_sas by 3.3.1 and 3.3.2 give different results Yin Jian
[gmx-users] g_sas by 3.3.1 and 3.3.2 give different results Yin Jian
[gmx-users] g_sas by 3.3.1 and 3.3.2 give different results Yin Jian
[gmx-users] Calculating the energy of one molecule in themulti-molecule system Yin Jian
[gmx-users] thermodynamic integration Argyrios Karatrantos
[gmx-users] non-existent angles found from trajectory g_angle Sampo Karkola
[gmx-users] non-existent angles found from trajectory g_angle Sampo Karkola
[gmx-users] non-existent angles found from trajectory g_angle Sampo Karkola
[gmx-users] non-existent angles found from trajectory g_angle Sampo Karkola
[gmx-users] protein in membrane Itamar Kass
[gmx-users] simulation popc Itamar Kass
[gmx-users] errores during compilation of GROMACS 3.3.2 Itamar Kass
[gmx-users] errores during compilation of GROMACS 3.3.2 Itamar Kass
[gmx-users] errores during compilation of GROMACS 3.3.2 Itamar Kass
[gmx-users] langevin dynamics Syma Khalid
[gmx-users] langevin dynamics Syma Khalid
[gmx-users] quasiharmonic eigenvalue units / Schlitter entropy Marcin Krol
[gmx-users] (no) superlinear Scaling on Opterons Jens Krueger
[gmx-users] (no) superlinear Scaling on Opterons Jens Krueger
[gmx-users] running gromacs in parallel, and with nice levels Carsten Kutzner
[gmx-users] (no subject) Carsten Kutzner
[gmx-users] No improvement in scaling on introducing flow control Carsten Kutzner
[gmx-users] No improvement in scaling on introducing flow control Carsten Kutzner
[gmx-users] No improvement in scaling on introducing flow control Carsten Kutzner
[gmx-users] Energy of each composition chiloo Laohpongspaisan
[gmx-users] Re: gmx-users Digest, Vol 42, Issue 50 chiloo Laohpongspaisan
[gmx-users] b-factor Daniel Larsson
[gmx-users] time constants for the Parrinello-Rahman/nose-hoover coupling Hwankyu Lee
[gmx-users] g_order in GROMACS 3.3.2 and 3.3.1 Justin A. Lemkul
[gmx-users] Re: getting a good .gro file from a pdb file while thetopology is ready Justin A. Lemkul
[gmx-users] Re:Re: g_order in GROMACS 3.3.2 and 3.3.1 Justin A. Lemkul
[gmx-users] t-couple warning Justin A. Lemkul
[gmx-users] ngmx error messages Justin A. Lemkul
[gmx-users] pdb2gmx error - version 3.3.1 Justin A. Lemkul
[gmx-users] Large VCM error for a POPC bilayer simulation : 2ndattempt Justin A. Lemkul
[gmx-users] Problem putting 2 identical peptide chains in a simulation box Justin A. Lemkul
[gmx-users] Exploding box after 55.5ns of simulation Justin A. Lemkul
[gmx-users] angle between helices Marc F. Lensink
[gmx-users] angle between helices Marc F. Lensink
[gmx-users] limit on energygrp_table Adrien Leygue
[gmx-users] limit on energygrp_table Adrien Leygue
[gmx-users] 1-4 table size of 0 nm Adrien Leygue
[gmx-users] Amber to Gromacs Dechang Li
[gmx-users] the comm_mode Dechang Li
[gmx-users] g_hbond Dechang Li
[gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory Tanping Li
[gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory Tanping Li
[gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory Tanping Li
[gmx-users] IO problem on Cray XT3 MPP Erik Lindahl
[gmx-users] 3.3.2 Error when using the mpi option Erik Lindahl
[gmx-users] tabulated potential - why table length is rc+1nm Erik Lindahl
[gmx-users] ngmx error messages Erik Lindahl
[gmx-users] Tool for visualizing disulphide bonds Erik Lindahl
[gmx-users] errores during compilation of GROMACS 3.3.2 Erik Lindahl
[gmx-users] errores during compilation of GROMACS 3.3.2 Erik Lindahl
[gmx-users] errores during compilation of GROMACS 3.3.2 Erik Lindahl
[gmx-users] Postdoc position available (docking, free energy, drug design) Erik Lindahl
[gmx-users] install problem on IBM powerpc AIX 5.3 Erik Lindahl
[gmx-users] install problem on IBM powerpc AIX 5.3 Erik Lindahl
[gmx-users] time constants for the Parrinello-Rahman/nose-hoover coupling Erik Lindahl
[gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens Haining Liu
[gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens Haining Liu
[gmx-users] Surface Tension units Pedro Alexandre de Araújo Gomes Lapido Loureiro
[gmx-users] qasi-harmonic entropy calculation Pedro Alexandre de Araújo Gomes Lapido Loureiro
[gmx-users] qasi-harmonic entropy calculation Pedro Alexandre de Araújo Gomes Lapido Loureiro
[gmx-users] Fwd: FEP calculations problem and posible BUG on GROMACS-3.3.2 Daniel Adriano Silva M
[gmx-users] g_cluster questions Erik Marklund
[gmx-users] Concatenate .edr file Marcelo Fabricio Masman
[gmx-users] g_lie problem Blaise Mathias-Costa
[gmx-users] mdrun error after 2.6nS Blaise Mathias-Costa
[gmx-users] mdrun error after 2.6nS Blaise Mathias-Costa
[gmx-users] Re: Problems prior to running lipid-protein simulation Bruce Milne
[gmx-users] Re: Problems prior to running lipid-protein simulation Bruce Milne
[gmx-users] Re: ANTECHAMBER & GAFF David Mobley
[gmx-users] Re: FEP problem David Mobley
[gmx-users] weird problem on small molecules with triple bonds David Mobley
[gmx-users] forcefield validation David Mobley
[gmx-users] weird problem on small molecules with triple bonds David Mobley
[gmx-users] weird problem on small molecules with triple bonds David Mobley
[gmx-users] problem with linear molecules and suggested fix David Mobley
[gmx-users] forcefield validation David Mobley
[gmx-users] forcefield validation David Mobley
[gmx-users] thermodynamic integration David Mobley
[gmx-users] potential energy of only the protein David Mobley
[gmx-users] langevin dynamics David Mobley
[gmx-users] Designing a topology file: bonded/non-bonded mess Frankie Montenegro
[gmx-users] Designing a topology file: bonded/non-bonded mess Frankie Montenegro
[gmx-users] qasi-harmonic entropy calculation Naser, Md Abu
[gmx-users] qasi-harmonic entropy calculation Naser, Md Abu
[gmx-users] qasi-harmonic entropy calculation Naser, Md Abu
[gmx-users] qasi-harmonic entropy calculation Naser, Md Abu
[gmx-users] Problems prior to running lipid-protein simulation adak Nasiripour
[gmx-users] what do negative eigenvalues imply? Chris Neale
[gmx-users] what do negative eigenvalues imply? Chris Neale
[gmx-users] Long range electrostatic potential Georgios Patargias
[gmx-users] Long range electrostatic potential Georgios Patargias
[gmx-users] langevin dynamics Georgios Patargias
[gmx-users] getting a good .gro file from a pdb file while the topology is ready Xavier Periole
[gmx-users] Calculating the energy of one molecule in the multi-molecule system Xavier Periole
[gmx-users] Addition of ions in vacuum simulations Xavier Periole
[gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel Xavier Periole
[gmx-users] simulating hydrocarbons in water TJ Piggot
[gmx-users] problems with opls_ TJ Piggot
[gmx-users] Fatal error Mauro Puppett
[gmx-users] anisotropic pressure coupling for temperature annealing Q733
[gmx-users] quasiharmonic eigenvalue units / Schlitter entropy Ran Friedman, Biochemisches Inst.
[gmx-users] gmxtest results: improper call in complex/acetonitrileRF Bruce Ray
[gmx-users] topolbuild: attempt at a Gromacs topology builder added to Gromacs user contributed software Bruce Ray
[gmx-users] Gromacs on IBM cluster Marius Retegan
[gmx-users] Gromacs on IBM cluster Marius Retegan
[gmx-users] Gromacs on IBM cluster Marius Retegan
[gmx-users] Nucleic Acid Simulations with Gromacs Anna Reymer
[gmx-users] ngmx error messages Sagittarius
[gmx-users] ngmx error messages Sagittarius
[gmx-users] ngmx error messages Sagittarius
[gmx-users] Help for simulating the metalcluster Utpal Sarkar
[gmx-users] forcefield validation Qin Shanshan
[gmx-users] forcefield validation Qin Shanshan
[gmx-users] forcefield validation Qin Shanshan
[gmx-users] forcefield validation Qin Shanshan
[gmx-users] Nucleic Acid Simulations with Gromacs Monika Sharma
[gmx-users] Nucleic Acid Simulations with Gromacs Monika Sharma
[gmx-users] Running Gromacs on the Grid Workshop 14.-15.11. Atte Sillanpää
Patchfile? Re: [gmx-users] gromacs 3.3.2 Allen Smith
[gmx-users] getting a good .gro file from a pdb file while the topology is ready Allen Smith
[gmx-users] getting a good .gro file from a pdb file while the topology is ready Allen Smith
[gmx-users] Re: getting a good .gro file from a pdb file while thetopology is ready Allen Smith
[gmx-users] getting a good .gro file from a pdb file while the topology is ready Allen Smith
[gmx-users] Re: Amber to Gromacs Vojtěch Spiwok
Patchfile? Re: [gmx-users] gromacs 3.3.2 David van der Spoel
[gmx-users] Is there a test set for GROMACS 3.3.1 ? David van der Spoel
[gmx-users] Re: Re: Is there a test set for GROMACS 3.3.1 ? (David van der Spoel) David van der Spoel
[gmx-users] Re: Is there a test set for GROMACS 3.3.1 ? David van der Spoel
[gmx-users] grompp not recognizing mdp file parameters David van der Spoel
[gmx-users] (no) superlinear Scaling on Opterons David van der Spoel
[gmx-users] Development of .ITP or .TOP file for non-standard molecules David van der Spoel
[gmx-users] IO problem on Cray XT3 MPP David van der Spoel
[gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory David van der Spoel
[gmx-users] genbox using tip5p water results in too few number of water molecules David van der Spoel
[gmx-users] genbox using tip5p water results in too few number of water molecules David van der Spoel
[gmx-users] xtc error David van der Spoel
[gmx-users] Criteria and Energy Conservation David van der Spoel
[gmx-users] simulating hydrocarbons in water David van der Spoel
[gmx-users] simulating hydrocarbons in water David van der Spoel
[gmx-users] Criteria and Energy Conservation David van der Spoel
[gmx-users] xtc error David van der Spoel
[gmx-users] Dummies usage doubts David van der Spoel
[gmx-users] Dummies usage doubts David van der Spoel
[gmx-users] Dummies usage doubts David van der Spoel
[gmx-users] Dummies usage doubts David van der Spoel
[gmx-users] Dummies usage doubts David van der Spoel
[gmx-users] g_sas by 3.3.1 and 3.3.2 give different results David van der Spoel
[gmx-users] Compiling GROMACS with FORTRAN? David van der Spoel
[gmx-users] ngmx error messages David van der Spoel
[gmx-users] ngmx error messages David van der Spoel
[gmx-users] Designing a topology file: bonded/non-bonded mess David van der Spoel
[gmx-users] the comm_mode David van der Spoel
[gmx-users] Designing a topology file: bonded/non-bonded mess David van der Spoel
[gmx-users] Visualizing non-rectangular boxes David van der Spoel
[gmx-users] weird problem on small molecules with triple bonds David van der Spoel
[gmx-users] weird problem on small molecules with triple bonds David van der Spoel
[gmx-users] forcefield validation David van der Spoel
[gmx-users] install problem on IBM powerpc AIX 5.3 David van der Spoel
[gmx-users] Addition of ions in vacuum simulations David van der Spoel
[gmx-users] qasi-harmonic entropy calculation David van der Spoel
[gmx-users] Using h-angles taking to much time David van der Spoel
[gmx-users] 1 out of 14 complex tests FAILED in GROMACS 3.3.1 installation dec+water David van der Spoel
[gmx-users] g_rmsf and pbc David van der Spoel
[gmx-users] entropy calaculted script?? David van der Spoel
[gmx-users] surface tension calculation in g_energy David van der Spoel
[gmx-users] reference for urea.itp David van der Spoel
[gmx-users] reference for urea.itp David van der Spoel
[gmx-users] No improvement in scaling on introducing flow control David van der Spoel
[gmx-users] problems with opls_ David van der Spoel
[gmx-users] queue up simulations David van der Spoel
[gmx-users] PBC, lincs and bonds breaking David van der Spoel
[gmx-users] angle between helices David van der Spoel
[gmx-users] what do negative eigenvalues imply? David van der Spoel
[gmx-users] g_sas problem David van der Spoel
[gmx-users] Gromacs on IBM cluster David van der Spoel
[gmx-users] GNU compilers David van der Spoel
[gmx-users] Gromacs on IBM cluster David van der Spoel
[gmx-users] g_sas problem David van der Spoel
[gmx-users] g_rmsf Segmentation fault David van der Spoel
[gmx-users] 3.3.2 mdrun problems Mitchell Stanton-Cook
[gmx-users] Wall Potential Huey Ling Tan
[gmx-users] Umbrella Sampling on peptides Huey Ling Tan
[gmx-users] Problem putting 2 identical peptide chains in a simulation box Huey Ling Tan
[gmx-users] Problem putting 2 identical peptide chains in a simulation box Huey Ling Tan
[gmx-users] 3.3.2 Error when using the mpi option Triguero, Luciano O
[gmx-users] 3.3.2 Error when using the mpi option Triguero, Luciano O
[gmx-users] simulation popc Zoltan Varga
[gmx-users] density profile of bilayers Zoltan Varga
[gmx-users] lot of pdb files written during minimization withoutasking for them ? Dallas B. Warren
[gmx-users] Problems prior to running lipid-protein simulation Dallas B. Warren
[gmx-users] Fwd: FEP calculations problem and posible BUG onGROMACS-3.3.2 Dallas B. Warren
[gmx-users] Reading XTC files from fortran90 Tsjerk Wassenaar
[gmx-users] Reading XTC files from fortran90 Tsjerk Wassenaar
[gmx-users] mdrun error after 2.6nS Tsjerk Wassenaar
[gmx-users] mdrun error after 2.6nS Tsjerk Wassenaar
[gmx-users] human readable input for g_covar Tsjerk Wassenaar
[gmx-users] remove periodic boundary in tpr file Tsjerk Wassenaar
[gmx-users] remove periodic boundary in tpr file Tsjerk Wassenaar
[gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory Tsjerk Wassenaar
[gmx-users] getting a good .gro file from a pdb file while the topology is ready Tsjerk Wassenaar
[gmx-users] gmx continuation run Tsjerk Wassenaar
[gmx-users] restart md from the point it had stopped Tsjerk Wassenaar
[gmx-users] restart md from the point it had stopped Tsjerk Wassenaar
[gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens Tsjerk Wassenaar
[gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens Tsjerk Wassenaar
[gmx-users] is there any size limit for simulation in gromacs Tsjerk Wassenaar
[gmx-users] PBC, lincs and bonds breaking Paul Whitford
[gmx-users] PBC, lincs and bonds breaking Paul Whitford
[gmx-users] b-factor Steffen Wolf
[gmx-users] Concatenate .edr file Qi Yan
[gmx-users] How to change the box size during simuation WU Yanbin
[gmx-users] Nucleic Acid Simulations with Gromacs Yang Ye
[gmx-users] Nucleic Acid Simulations with Gromacs Yang Ye
[gmx-users] How to calculate the average distance or energy between two residues? Yang Ye
[gmx-users] running gromacs in parallel, and with nice levels Yang Ye
[gmx-users] Tool for visualizing disulphide bonds Yang Ye
[gmx-users] the comm_mode Yang Ye
[gmx-users] the comm_mode Yang Ye
[gmx-users] the comm_mode Yang Ye
[gmx-users] pbc problem Yang Ye
[gmx-users] pdb2gmx error - version 3.3.1 Yang Ye
[gmx-users] Position restricted md Yang Ye
[gmx-users] entropy calaculted script?? Yang Ye
[gmx-users] Calculating the energy of one molecule in the Li Zhenhai
[gmx-users] Re: gmx-users Digest, Vol 42, Issue 47 Li Zhenhai
[gmx-users] Re: gmx-users Digest, Vol 42, Issue 50 Li Zhenhai
[gmx-users] surface tension calculation in g_energy Bo Zhou
[gmx-users] reference for urea.itp rzangi at att.net
[gmx-users] reference for urea.itp rzangi at att.net
[gmx-users] g_cluster questions andrea carotti
[gmx-users] g_rms andrea carotti
[gmx-users] g_rms andrea carotti
[gmx-users] g_rms andrea carotti
[gmx-users] g_rms andrea carotti
[gmx-users] xpm to ascii andrea carotti
[gmx-users] water molecules suffer from very long bond lengths sarbani chattopadhyay
[gmx-users] restart md from the point it had stopped sarbani chattopadhyay
[gmx-users] (no subject) sarbani chattopadhyay
[gmx-users] Position restricted md sarbani chattopadhyay
[gmx-users] Position restricted md sarbani chattopadhyay
[gmx-users] Position restricted md sarbani chattopadhyay
[gmx-users] alpha Carbon-Aromatic ring hydrogen bond sarbani chattopadhyay
[gmx-users] make_ndx sarbani chattopadhyay
[gmx-users] make_ndx sarbani chattopadhyay
[gmx-users] queue up simulations sarbani chattopadhyay
[gmx-users] Fwd: trjconv help sarbani chattopadhyay
[gmx-users] potential energy of only the protein sarbani chattopadhyay
[gmx-users] simulation popc pragya chohan
[gmx-users] grompp error pragya chohan
[gmx-users] grompp error for alamethicin pragya chohan
[gmx-users] Pull code with runtype start dtmirij
[gmx-users] Pull code with runtype start dtmirij
[gmx-users] Pull code with runtype start dtmirij
[gmx-users] frequence from PCA eigenvalue pascal.baillod at epfl.ch
[gmx-users] frequence from PCA eigenvalue pascal.baillod at epfl.ch
[gmx-users] Is there a test set for GROMACS 3.3.1 ? maria goranovic
[gmx-users] Re: Re: Is there a test set for GROMACS 3.3.1 ? (David van der Spoel) maria goranovic
[gmx-users] Re: Is there a test set for GROMACS 3.3.1 ? maria goranovic
[gmx-users] getting a good .gro file from a pdb file while the topology is ready maria goranovic
[gmx-users] Re: getting a good .gro file from a pdb file while the topology is ready maria goranovic
[gmx-users] lot of pdb files written during minimization without asking for them ? maria goranovic
[gmx-users] running gromacs in parallel, and with nice levels maria goranovic
[gmx-users] No scale up beyond 4 processors for 240000 atom system maria goranovic
[gmx-users] What is this warning on running grompp ? WARNING 1 [file md-new.mdp, line unknown] maria goranovic
[gmx-users] solvate using genbox results in water in the center of the bilayer. How to edit pdb file contents in gromacs ? maria goranovic
[gmx-users] problems with opls_ hhhh huan
[gmx-users] problems with opls_ hhhh huan
[gmx-users] Criteria and Energy Conservation gtroiano at if.usp.br
[gmx-users] Criteria and Energy Conservation gtroiano at if.usp.br
[gmx-users] Criteria and Energy Conservation gtroiano at if.usp.br
[gmx-users] Problem putting 2 identical peptide chains in a simulation box alokjain at iitk.ac.in
[gmx-users] Large VCM error for a POPC bilayer simulation himanshu khandelia
[gmx-users] Large VCM error for a POPC bilayer simulation : 2nd attempt himanshu khandelia
[gmx-users] Large VCM error for a POPC bilayer simulation : 2nd attempt himanshu khandelia
[gmx-users] Large VCM error for a POPC bilayer simulation : 2ndattempt himanshu khandelia
[gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel himanshu khandelia
[gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel himanshu khandelia
[gmx-users] 1 out of 14 complex tests FAILED in GROMACS 3.3.1 installation dec+water himanshu khandelia
[gmx-users] No improvement in scaling on introducing flow control himanshu khandelia
[gmx-users] No improvement in scaling on introducing flow control himanshu khandelia
[gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ???? himanshu khandelia
[gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ???? himanshu khandelia
[gmx-users] No improvement in scaling on introducing flow control himanshu khandelia
[gmx-users] Qeury on freezing an atom with negatice co-ordinates avinash kumar
[gmx-users] xtc error luciano.pgomes
[gmx-users] xtc error luciano.pgomes
[gmx-users] Re:gmx-users Digest, Vol 42, Issue 36 luciano.pgomes
[gmx-users] GNU compilers giordano mancini
[gmx-users] GNU compilers giordano mancini
[gmx-users] editconf -mead marcos
[gmx-users] editconf -mead marcos
[gmx-users] cut-offs in j. kerrigans drug/enzyme tutorial merc mertens
[gmx-users] Nucleic Acid Simulations with Gromacs gigo at poczta.ibb.waw.pl
[gmx-users] Problem in downloading source code raja
[gmx-users] Problem in downloading source code raja
[gmx-users] Problem in downloading source code raja
[gmx-users] Source code through email raja
[gmx-users] Visualizing non-rectangular boxes sebastien santini
[gmx-users] Calculating the energy of one molecule in the multi-molecule system shibalagu
[gmx-users] human readable input for g_covar mdaf at sina.com
[gmx-users] Using h-angles taking to much time harpreet singh
[gmx-users] Using h-angles taking to much time harpreet singh
[gmx-users] problem in g_confrms harpreet singh
[gmx-users] Surface Tension units priyanka srivastava
[gmx-users] density profile of bilayers priyanka srivastava
[gmx-users] gmx continuation run vijaya subramanian
[gmx-users] IO problem on Cray XT3 MPP vijaya subramanian
[gmx-users] remove periodic boundary in tpr file tangxuan
[gmx-users] remove periodic boundary in tpr file tangxuan
[gmx-users] pbc problem tangxuan
[gmx-users] b-factor tangxuan
[gmx-users] g_rmsf and pbc tangxuan
[gmx-users] g_rmsf and pbc tangxuan
[gmx-users] g_rmsf and pbc tangxuan
[gmx-users] g_sas problem tangxuan
[gmx-users] g_sas problem tangxuan
[gmx-users] g_sas problem tangxuan
[gmx-users] grompp not recognizing mdp file parameters toma0052
[gmx-users] Correcting for box jumps in pdo file bmmothan at ucalgary.ca
[gmx-users] Distance restraint jacopo.sgrignani at unifi.it
[gmx-users] grompp error chris.neale at utoronto.ca
[gmx-users] grompp error chris.neale at utoronto.ca
[gmx-users] Visualizing non-rectangular boxes chris.neale at utoronto.ca
[gmx-users] Visualizing non-rectangular boxes chris.neale at utoronto.ca
[gmx-users] Visualizing non-rectangular boxes chris.neale at utoronto.ca
[gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ? chris.neale at utoronto.ca
[gmx-users] solvate using genbox results in water in the > centerofthe bilayer. How to edit pdb file contents in gromacs ? chris.neale at utoronto.ca
[gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ? chris.neale at utoronto.ca
[gmx-users] solvate using genbox results in water in thecenterofthe bilayer. How to edit pdb file contents in gromacs ? chris.neale at utoronto.ca
[gmx-users] NVT to NPT. Works on a single processor, does VT to NPT. Works on a single processor, does not work on 4 ???? chris.neale at utoronto.ca
[gmx-users] MPIRUN problem when switched to 8 np (searched the list) liu xin
[gmx-users] MPIRUN problem when switched to 8 np (searched the list) liu xin
[gmx-users] only one cpu "works" in my linux cluster liu xin
[gmx-users] only one cpu "works" in my linux cluster liu xin
[gmx-users] only one cpu "works" in my linux cluster liu xin
[gmx-users] install problem on IBM powerpc AIX 5.3 liu xin
[gmx-users] install problem on IBM powerpc AIX 5.3 liu xin
[gmx-users] install problem on IBM powerpc AIX 5.3 liu xin
[gmx-users] install problem on IBM powerpc AIX 5.3 liu xin
[gmx-users] install problem on IBM powerpc AIX 5.3 liu xin
[gmx-users] protein in membrane mahbubeh zarrabi
[gmx-users] itp files mahbubeh zarrabi
[gmx-users] HC atomtype mahbubeh zarrabi
[gmx-users] HC atomtype mahbubeh zarrabi
[gmx-users] entropy calaculted script?? xi zhao
[gmx-users] g_energy has no bond entry when MD analysis xi zhao
回复： Re: [gmx-users] g_energy has no bond entry when MD analysis xi zhao
[gmx-users] g_order in GROMACS 3.3.2 and 3.3.1 林揚善
[gmx-users] Re:Re: g_order in GROMACS 3.3.2 and 3.3.1 林揚善

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Archived on: Thu Nov 14 12:03:58 CET 2013

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