January 2015 Archives by author

Messages sorted by: [ thread ] [ subject ] [ date ]
More info on this list...

Starting: Thu Jan 1 01:22:46 CET 2015
Ending: Sat Jan 31 23:35:56 CET 2015
Messages: 456

[gmx-users] How to introduce Mg2+ ions to system that are necessary for nucleotide co-enzymes? Hassan Aaryapour
[gmx-users] How to do parallel simulation by OpenMP? Hassan Aaryapour
[gmx-users] Segmentation fault on HPC Mark Abraham
[gmx-users] regarding Ionic currents Mark Abraham
[gmx-users] Error on restart REMD simulations Mark Abraham
[gmx-users] How can i save all run processes ... Mark Abraham
[gmx-users] cpu gpu performance Mark Abraham
[gmx-users] How to calculate energy after production MD Mark Abraham
[gmx-users] trash error in linux Mark Abraham
[gmx-users] How to calculate energy after production MD Mark Abraham
[gmx-users] There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files Mark Abraham
[gmx-users] g_tune_pme_mpi on GPU cluster fails Mark Abraham
[gmx-users] Particle decomposition from GMX 5.X on Mark Abraham
[gmx-users] Gromacs Installation problem Mark Abraham
[gmx-users] compiling issue Mark Abraham
[gmx-users] compiling issue Mark Abraham
[gmx-users] PME question in GMX4.6.5 Mark Abraham
[gmx-users] Infinite cutoffs with periodic boundary condition Mark Abraham
[gmx-users] Infinite cutoffs with periodic boundary condition Mark Abraham
[gmx-users] double size a box Mark Abraham
[gmx-users] PME question in GMX4.6.5 Mark Abraham
[gmx-users] Applying restraints into 'secondary structure' of a Protein Mark Abraham
[gmx-users] Virial Calculation in Gromacs Source Code Mark Abraham
[gmx-users] trjconv mismatch Mark Abraham
[gmx-users] Using -all flag in g_angle command Mark Abraham
[gmx-users] Gromacs precision and the precision of values set in the mdp file Mark Abraham
[gmx-users] Re PME question in GMX4.6.5 Mark Abraham
[gmx-users] Using -all flag in g_angle command Mark Abraham
[gmx-users] TIP4P equilibration Mark Abraham
[gmx-users] tabulated non-bonded potentials with replica exchange (potentials that change with temperature) Mark Abraham
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Mark Abraham
[gmx-users] Simulations in triplicates. Mark Abraham
[gmx-users] segfault in g_clustsize Mark Abraham
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Mark Abraham
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Mark Abraham
[gmx-users] segfault in g_clustsize Mark Abraham
[gmx-users] recovering topology from tpr Mark Abraham
[gmx-users] how can we modify *.rtp file (again again) Mark Abraham
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Mark Abraham
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Mark Abraham
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Mark Abraham
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Mark Abraham
[gmx-users] Atoms in the .top are not numbered consecutively from 1 Mark Abraham
[gmx-users] Significant differences in Ewald Vs PME for clay sheet Mark Abraham
[gmx-users] Significant differences in Ewald Vs PME for clay sheet Mark Abraham
[gmx-users] Log output of GPU accelerated GROMACS Mark Abraham
[gmx-users] coordinates file format Mark Abraham
[gmx-users] coordinates file format Mark Abraham
[gmx-users] coordinates file format Mark Abraham
[gmx-users] coordinates file format Mark Abraham
[gmx-users] coordinates file format Mark Abraham
[gmx-users] A question regarding electrostatic and coulomb energies. Mark Abraham
[gmx-users] problem in centering of my protein in the box Mark Abraham
[gmx-users] How to do parallel simulation by OpenMP? Mark Abraham
[gmx-users] residues in force fields Mark Abraham
[gmx-users] Obtaining PMF for change in domain position Abhi Acharya
[gmx-users] Using COM pulling and Enforced Rotations together Abhi Acharya
[gmx-users] Using COM pulling and Enforced Rotations together Abhi Acharya
[gmx-users] Regarding g_cluster output. Abhi Acharya
[gmx-users] Transition matrix generation Adelman, Joshua Lev
[gmx-users] g_sas problem? Albert
[gmx-users] g_sas problem? Albert
[gmx-users] g_sas problem? Albert
[gmx-users] using pull_geometry=cylinder for asymmetric pull-molecule Alexandra Antipina
[gmx-users] Topology file Aranha, Michelle
[gmx-users] TIP4P equilibration Aranha, Michelle
[gmx-users] implicit_genborn_params for Na+ Mana Asq
[gmx-users] double size a box BIRD
[gmx-users] about CG MD Position Constraint BIRD
[gmx-users] constant pH simulations in GROMACS 4.5 Antonio Baptista
[gmx-users] PCA projections using g_anaeig Antonio Baptista
[gmx-users] Reg: topology and parameter files for dichlormethane Akshay Bhatnagar
[gmx-users] Distance restraint file error Deep Bhattacharya
[gmx-users] Is the PMF from "gmx wham" a free energy curve? Alexander Björling
[gmx-users] Is the PMF from "gmx wham" a free energy curve? Alexander Björling
[gmx-users] Covalent bond/crosslink formation with calcium Turgay Cakmak
[gmx-users] Segmentation fault in g_sas with bigger probe Francesco Carbone
[gmx-users] Segmentation fault in g_sas with bigger probe Francesco Carbone
[gmx-users] segfault in g_clustsize Dr. Vitaly Chaban
[gmx-users] segfault in g_clustsize Dr. Vitaly Chaban
[gmx-users] segfault in g_clustsize Dr. Vitaly Chaban
[gmx-users] How to calculate energy after production MD Navneet Chaturvedi
[gmx-users] How to calculate energy after production MD Navneet Chaturvedi
[gmx-users] Doubt regarding nrexcl parameter in topology Chandan Choudhury
[gmx-users] Pressure coupling error Riccardo Concu
[gmx-users] Pressure coupling error Riccardo Concu
[gmx-users] potential energy Bogdan Costescu
[gmx-users] potential energy Bogdan Costescu
[gmx-users] AMBER99 topology for ADP Somlata Das
[gmx-users] fe2s2 simulation Somlata Das
[gmx-users] Energy minimization problem in Choline Chloride+Urea mixture in Gromacs Suman Das
[gmx-users] Urea Topology Sagar De'Biomimic
[gmx-users] How to compute persistence length in gromacs Christian Bope Domilongo
[gmx-users] How to compute persistence length in gromacs Christian Bope Domilongo
[gmx-users] recovering topology from tpr M.Cristina Donnamaria
[gmx-users] recovering topology from tpr Rebeca García Fandiño
[gmx-users] fe2s2 simulation Rohit Farmer
[gmx-users] Implicit solvent in Gromacs 5.0.3 Stephen Fried
[gmx-users] Wrong profile obtained in umbrella sampling tutorial Victor Rosas Garcia
[gmx-users] Wrong profile obtained in umbrella sampling tutorial Victor Rosas Garcia
[gmx-users] clustering using gromos method Adriana Garro
[gmx-users] clustering using gromos method Adriana Garro
[gmx-users] clustering using gromos method Adriana Garro
[gmx-users] backmapping protein + dppc Adriana Garro
[gmx-users] backmapping protein + dppc Adriana Garro
[gmx-users] backmapping protein + dppc Adriana Garro
[gmx-users] backmapping protein + dppc Adriana Garro
[gmx-users] backmapping protein + dppc Adriana Garro
[gmx-users] compiling issue Éric Germaneau
[gmx-users] compiling issue Éric Germaneau
[gmx-users] compiling issue Éric Germaneau
[gmx-users] compiling issue Éric Germaneau
[gmx-users] Significant differences in Ewald Vs PME for clay sheet Gaurav Goel
[gmx-users] Significant differences in Ewald Vs PME for clay sheet Gaurav Goel
[gmx-users] Calculating hydrogen bonds between specific residues Agnivo Gosai
[gmx-users] Using do_dssp with GROMACS 4.6.7. Agnivo Gosai
[gmx-users] Using do_dssp with GROMACS 4.6.7. Agnivo Gosai
[gmx-users] gromacs QMMM gaussian 09 (g09) input format Gerrit Groenhof
[gmx-users] QM/MM excited state optimization Gerrit Groenhof
[gmx-users] QM/MM excited state optimization (xiao) Gerrit Groenhof
[gmx-users] constant pH simulations in GROMACS 4.5 Gerrit Groenhof
[gmx-users] Virial Calculation in Gromacs Source Code Hardy, Adam
[gmx-users] Pressure coupling error Hardy, Adam
[gmx-users] All-atom vs United-atom force fields and hydrogen bonds Jason Hill
[gmx-users] AMBER99 topology for ADP Marc Hoemberger
[gmx-users] AMBER99 topology for ADP Marc Hoemberger
[gmx-users] constant pH simulations in GROMACS 4.5 Sahithya S Iyer
[gmx-users] Net charge error Siddhesh Kamat
[gmx-users] Fwd: Net charge error Siddhesh Kamat
[gmx-users] Fwd: Net charge error Siddhesh Kamat
[gmx-users] insert-molecules module Siddhesh Kamat
[gmx-users] Gromacs Installation problem Shankar Prasad Kanaujia
[gmx-users] Gromacs Installation problem Shankar Prasad Kanaujia
[gmx-users] restraint the CM of a molecules in any one of the directions. Sridhar Kumar Kannam
[gmx-users] restraint the CM of a molecules in any one of the directions. Sridhar Kumar Kannam
[gmx-users] restraint the CM of a molecules in any one of the directions. Sridhar Kumar Kannam
[gmx-users] Working on a GPU cluster with GROMACS 5 Jiri Kraus
[gmx-users] load imbalance: putting more load on GPU than CPU Pappu Kumar
[gmx-users] Error in Topology file Rajan Kumar
[gmx-users] regarding Ionic currents Sathish Kumar
[gmx-users] Calculating h-bonds frequency along the simulation Vered Kunik
[gmx-users] Calculating h-bonds frequency along the simulation Vered Kunik
[gmx-users] Using COM pulling and Enforced Rotations together Carsten Kutzner
[gmx-users] Working on a GPU cluster with GROMACS 5 Carsten Kutzner
[gmx-users] g_tune_pme_mpi on GPU cluster fails Carsten Kutzner
[gmx-users] Log output of GPU accelerated GROMACS Carsten Kutzner
[gmx-users] Performance difference between MPI ranks and OpenMP Carsten Kutzner
[gmx-users] g_tune_pme_mpi on GPU cluster fails Carsten Kutzner
[gmx-users] g_tune_pme_mpi on GPU cluster fails Carsten Kutzner
[gmx-users] Performance difference between MPI ranks and OpenMP Carsten Kutzner
[gmx-users] Cluster recommendations Carsten Kutzner
[gmx-users] Cluster recommendations Carsten Kutzner
[gmx-users] PME update Carsten Kutzner
[gmx-users] [MGMS-DS]: Molecular Modelling Workshop March 9-11, 2015 in Erlangen, Germany Harald Lanig
[gmx-users] Continuing umbrella sampling after crash Alexander Law
[gmx-users] Infinite cutoffs with periodic boundary condition 이종화(Jong Wha Lee)
[gmx-users] Jump in temperature each time a new simulation is started. Justin Lemkul
[gmx-users] Define box size Justin Lemkul
[gmx-users] choosing appropriate force field Justin Lemkul
[gmx-users] atom freezing Justin Lemkul
[gmx-users] atom freezing Justin Lemkul
[gmx-users] Greetings+Which computer? Justin Lemkul
[gmx-users] Energy minimization problem in Choline Chloride+Urea mixture in Gromacs Justin Lemkul
[gmx-users] Segmentation fault on HPC Justin Lemkul
[gmx-users] How to calculate energy after production MD Justin Lemkul
[gmx-users] Is the PMF from "gmx wham" a free energy curve? Justin Lemkul
[gmx-users] restraint the CM of a molecules in any one of the directions. Justin Lemkul
[gmx-users] g_sas problem? Justin Lemkul
[gmx-users] After solvation and before adding ions, number of molecules does not agree even though number of H2O molecules does Justin Lemkul
[gmx-users] g_sas problem? Justin Lemkul
[gmx-users] How to plot a droplet radius profile as a function of z-directio Justin Lemkul
[gmx-users] g_sas problem? Justin Lemkul
[gmx-users] How to introduce Mg2+ ions to system that are necessary for nucleotide co-enzymes? Justin Lemkul
[gmx-users] Wrong profile obtained in umbrella sampling tutorial Justin Lemkul
[gmx-users] After solvation and before adding ions, number of molecules does not agree even though number of H2O molecules Justin Lemkul
[gmx-users] restraint the CM of a molecules in any one of the directions. Justin Lemkul
[gmx-users] Error : Atomtype not found Justin Lemkul
[gmx-users] Calculating h-bonds frequency along the simulation Justin Lemkul
[gmx-users] Calculating h-bonds frequency along the simulation Justin Lemkul
[gmx-users] "invalid order for directive atomtypes", but only one ligand Justin Lemkul
[gmx-users] restraint the CM of a molecules in any one of the directions. Justin Lemkul
[gmx-users] RDF plot with large g(r) values Justin Lemkul
[gmx-users] "invalid order for directive atomtypes", but only one ligand Justin Lemkul
[gmx-users] Error : Atomtype not found Justin Lemkul
[gmx-users] gmxcheck killed Justin Lemkul
[gmx-users] GridMAT-MD Justin Lemkul
[gmx-users] Changing number of processors after a job restart Justin Lemkul
[gmx-users] Changing number of processors after a job restart Justin Lemkul
[gmx-users] Question Justin Lemkul
[gmx-users] potential energy Justin Lemkul
[gmx-users] potential energy Justin Lemkul
[gmx-users] potential energy Justin Lemkul
[gmx-users] potential energy Justin Lemkul
[gmx-users] How can i save all run processes ... Justin Lemkul
[gmx-users] potential energy Justin Lemkul
[gmx-users] During minimization "A charge group moved too far between two domain decomposition steps" Justin Lemkul
[gmx-users] Net charge error Justin Lemkul
[gmx-users] Fwd: Net charge error Justin Lemkul
[gmx-users] Fwd: Net charge error Justin Lemkul
[gmx-users] Box volume during dynamics Justin Lemkul
[gmx-users] Continuing umbrella sampling after crash Justin Lemkul
[gmx-users] trjconv mismatch in number of atoms Justin Lemkul
[gmx-users] analysing charmm trajectories Justin Lemkul
[gmx-users] Debugging 'inconsistent shifts' Justin Lemkul
[gmx-users] Water mediated hydrogen bonding Justin Lemkul
[gmx-users] Regarding g_cluster output. Justin Lemkul
[gmx-users] Water mediated hydrogen bonding Justin Lemkul
[gmx-users] AMBER99 topology for ADP Justin Lemkul
[gmx-users] Debugging 'inconsistent shifts' Justin Lemkul
[gmx-users] Atomtype P,SI not found from grompp Justin Lemkul
[gmx-users] Atomtype P,SI not found from grompp Justin Lemkul
[gmx-users] Atomtype P,SI not found from grompp Justin Lemkul
[gmx-users] Atomtype P,SI not found from grompp Justin Lemkul
[gmx-users] potential energy Justin Lemkul
[gmx-users] Too many LINCS warnings Justin Lemkul
[gmx-users] Error in Topology file Justin Lemkul
[gmx-users] how can we modify *.rtp file? Justin Lemkul
[gmx-users] using charmm rtf and parameter files in gromacs Justin Lemkul
[gmx-users] Atomtype P,SI not found from grompp Justin Lemkul
[gmx-users] Atomtype P,SI not found from grompp Justin Lemkul
[gmx-users] How to g_select water and ions? Justin Lemkul
[gmx-users] using pull_geometry=cylinder for asymmetric pull-molecule Justin Lemkul
[gmx-users] coordinates file format Justin Lemkul
[gmx-users] Ligand Topology file Justin Lemkul
[gmx-users] backmapping protein + dppc Justin Lemkul
[gmx-users] After solvation and before adding ions, number of molecules does not agree even though number of H2O molecules Justin Lemkul
[gmx-users] Implicit solvent in Gromacs 5.0.3 Justin Lemkul
[gmx-users] Energy minimization for Inositol pyrophosphate Justin Lemkul
[gmx-users] Execution of EM step:5 failed Justin Lemkul
[gmx-users] Calculating hydrogen bonds between specific residues Justin Lemkul
[gmx-users] Using do_dssp with GROMACS 4.6.7. Justin Lemkul
[gmx-users] How to compute persistence length in gromacs Justin Lemkul
[gmx-users] Energy minimization for Inositol pyrophosphate Justin Lemkul
[gmx-users] After solvation and before adding ions, number of molecules does not agree even though number of H2O molecules Justin Lemkul
[gmx-users] Error during NVT Justin Lemkul
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Jiaqi Lin
[gmx-users] how does PME auto-tuning work Jiaqi Lin
[gmx-users] how does PME auto-tuning work Jiaqi Lin
[gmx-users] how does PME auto-tuning work Jiaqi Lin
[gmx-users] how does PME auto-tuning work Jiaqi Lin
[gmx-users] how does PME auto-tuning work Jiaqi Lin
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Jiaqi Lin
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Jiaqi Lin
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Jiaqi Lin
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Jiaqi Lin
[gmx-users] After solvation and before adding ions, number of molecules does not agree even though number of H2O molecules does Thomas Lipscomb
[gmx-users] After solvation and before adding ions, number of molecules does not agree even though number of H2O molecules Thomas Lipscomb
[gmx-users] Test if Trajectories are Independent Johnny Lu
[gmx-users] regarding Contact Existence Map Erik Marklund
[gmx-users] g_hbond not running Erik Marklund
[gmx-users] Calculating h-bonds frequency along the simulation Erik Marklund
[gmx-users] coordinates file format Erik Marklund
[gmx-users] can't generate pdb file in g_cluster Nizar Masbukhin
[gmx-users] regarding Contact Existence Map Nizar Masbukhin
[gmx-users] REST2 tutorial Shyno Mathew
[gmx-users] Working on a GPU cluster with GROMACS 5 Ebert Maximilian
[gmx-users] Working on a GPU cluster with GROMACS 5 Ebert Maximilian
[gmx-users] Working on a GPU cluster with GROMACS 5 Ebert Maximilian
[gmx-users] Working on a GPU cluster with GROMACS 5 Ebert Maximilian
[gmx-users] g_tune_pme_mpi on GPU cluster fails Ebert Maximilian
[gmx-users] Log output of GPU accelerated GROMACS Ebert Maximilian
[gmx-users] g_tune_pme_mpi on GPU cluster fails Ebert Maximilian
[gmx-users] Performance difference between MPI ranks and OpenMP Ebert Maximilian
[gmx-users] Performance difference between MPI ranks and OpenMP Ebert Maximilian
[gmx-users] g_tune_pme_mpi on GPU cluster fails Ebert Maximilian
[gmx-users] g_rotacf lag time Ebert Maximilian
[gmx-users] Cosine content of an eigenvector in PCA after 100ns still 0.9 Ebert Maximilian
[gmx-users] Cosine content of an eigenvector in PCA after 100ns still 0.9 Ebert Maximilian
[gmx-users] Cluster recommendations David McGiven
[gmx-users] Cluster recommendations David McGiven
[gmx-users] Cluster recommendations David McGiven
[gmx-users] Cluster recommendations David McGiven
[gmx-users] Cluster recommendations David McGiven
[gmx-users] Particle decomposition from GMX 5.X on Ilaria Mereu
[gmx-users] Fixed orientation Felipe Merino
[gmx-users] Execution of EM step:5 failed Stephen P. Molnar
[gmx-users] RDF plot with large g(r) values André Farias de Moura
[gmx-users] RDF plot with large g(r) values André Farias de Moura
[gmx-users] g_select syntax unavailable in GROMACS 5.0 and 5.0.1 Teemu Murtola
[gmx-users] g_select syntax unavailable in GROMACS 5.0 and 5.0.1 Teemu Murtola
[gmx-users] Changing number of processors after a job restart Nash, Anthony
[gmx-users] Changing number of processors after a job restart Nash, Anthony
[gmx-users] Changing number of processors after a job restart Nash, Anthony
[gmx-users] g_sas values of zero and Warning Nash, Anthony
[gmx-users] Energy minimization problem in Choline Chloride+Urea mixture in Gromacs Christopher Neale
[gmx-users] tabulated non-bonded potentials with replica exchange (potentials that change with temperature) Christopher Neale
[gmx-users] tabulated non-bonded potentials with replica exchange (potentials that change with temperature) Christopher Neale
[gmx-users] tabulated non-bonded potentials with replica exchange (potentials that change with temperature) Christopher Neale
[gmx-users] Simulations in triplicates. B P
[gmx-users] Simulations in triplicates. B P
[gmx-users] analysing charmm trajectories Chiara Parravicini
[gmx-users] analysing charmm trajectories Chiara Parravicini
[gmx-users] During minimization "A charge group moved too far between two domain decomposition steps" XAvier Periole
[gmx-users] During minimization "A charge group moved too far between two domain decomposition steps" XAvier Periole
[gmx-users] clustering using gromos method XAvier Periole
[gmx-users] clustering using gromos method XAvier Periole
[gmx-users] Particle decomposition from GMX 5.X on Szilárd Páll
[gmx-users] Particle decomposition from GMX 5.X on Szilárd Páll
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Szilárd Páll
[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing Szilárd Páll
[gmx-users] Applying restraints into 'secondary structure' of a Protein Carlos Navarro Retamal
[gmx-users] Applying restraints into 'secondary structure' of a Protein Carlos Navarro Retamal
[gmx-users] Using -all flag in g_angle command GAYATHRI S
[gmx-users] Using -all flag in g_angle command GAYATHRI S
[gmx-users] Using -all flag in g_angle command GAYATHRI S
[gmx-users] A question regarding electrostatic and coulomb energies. IÑIGO SAENZ
[gmx-users] "invalid order for directive atomtypes", but only one ligand Jonathan Saboury
[gmx-users] "invalid order for directive atomtypes", but only one ligand Jonathan Saboury
[gmx-users] During minimization "A charge group moved too far between two domain decomposition steps" Jonathan Saboury
[gmx-users] During minimization "A charge group moved too far between two domain decomposition steps" Jonathan Saboury
[gmx-users] Problem in energy minimization of Protein-ligand complex in Lipid membrane Padmani Sandhu
[gmx-users] Interface/buried erea Saman Shahriyari
[gmx-users] Interface/buried erea Saman Shahriyari
[gmx-users] Fwd: Frequency dependent dielectric of water Bharat Sharma
[gmx-users] Fwd: Frequency dependent dielectric of water Bharat Sharma
[gmx-users] Question Igor Shchechkin
[gmx-users] The problem is fixed Igor Shchechkin
[gmx-users] Cluster studies of ions Meena Singh
[gmx-users] Reg: topology and parameter files for dichlormethane Eric Smoll
[gmx-users] Gromacs precision and the precision of values set in the mdp file Eric Smoll
[gmx-users] g_sas question Eric Smoll
[gmx-users] Importing a trajectory into MOE Sandeep Somani
[gmx-users] Fwd: Frequency dependent dielectric of water David van der Spoel
[gmx-users] GridMAT-MD David van der Spoel
[gmx-users] Error message in GROMACS David van der Spoel
[gmx-users] dipole derivative David van der Spoel
[gmx-users] Decomposing the long range term of interaction energy David van der Spoel
[gmx-users] Simulations in triplicates. David van der Spoel
[gmx-users] Dihedral angle autocorrelation function David van der Spoel
[gmx-users] Jump in temperature each time a new simulation is started. Dan Sponseller
[gmx-users] using charmm rtf and parameter files in gromacs Sudharsan Sridharan
[gmx-users] PCA projections using g_anaeig James Starlight
[gmx-users] PCA projections using g_anaeig James Starlight
[gmx-users] Define box size Seera Suryanarayana
[gmx-users] Decomposing the long range term of interaction energy Diogo Martins de Sá
[gmx-users] Debugging 'inconsistent shifts' Kalev Takkis
[gmx-users] Debugging 'inconsistent shifts' Kalev Takkis
[gmx-users] Debugging 'inconsistent shifts' Kalev Takkis
[gmx-users] PME question in GMX4.6.5 Tom
[gmx-users] PME question in GMX4.6.5 Tom
[gmx-users] Re PME question in GMX4.6.5 Tom
[gmx-users] gmxcheck killed Jennifer Vo
[gmx-users] trjconv mismatch in number of atoms Jennifer Vo
[gmx-users] trjconv mismatch Jennifer Vo
[gmx-users] trjconv mismatch Jennifer Vo
[gmx-users] Atomtype P,SI not found from grompp Jennifer Vo
[gmx-users] Atomtype P,SI not found from grompp Jennifer Vo
[gmx-users] Atomtype P,SI not found from grompp Jennifer Vo
[gmx-users] Atomtype P,SI not found from grompp Jennifer Vo
[gmx-users] Atomtype P,SI not found from grompp Jennifer Vo
[gmx-users] Too many LINCS warnings Jennifer Vo
[gmx-users] Atomtype P,SI not found from grompp Jennifer Vo
[gmx-users] Atoms in the .top are not numbered consecutively from 1 Jennifer Vo
[gmx-users] Atoms in the .top are not numbered consecutively from 1 Jennifer Vo
[gmx-users] Atomtype P,SI not found from grompp Jennifer Vo
[gmx-users] Atomtype P,SI not found from grompp Jennifer Vo
[gmx-users] Topology file Tsjerk Wassenaar
[gmx-users] Dihedral pca Tsjerk Wassenaar
[gmx-users] rotating triclinic box Tsjerk Wassenaar
[gmx-users] trjconv mismatch Tsjerk Wassenaar
[gmx-users] Cosine content of an eigenvector in PCA after 100ns still 0.9 Tsjerk Wassenaar
[gmx-users] Cosine content of an eigenvector in PCA after 100ns still 0.9 Tsjerk Wassenaar
[gmx-users] backmapping protein + dppc Tsjerk Wassenaar
[gmx-users] backmapping protein + dppc Tsjerk Wassenaar
[gmx-users] PCA projections using g_anaeig Tsjerk Wassenaar
[gmx-users] backmapping protein + dppc Tsjerk Wassenaar
[gmx-users] backmapping protein + dppc Tsjerk Wassenaar
[gmx-users] PCA projections using g_anaeig Tsjerk Wassenaar
[gmx-users] Doubt in Gromacs nsteps, ps and ns Tsjerk Wassenaar
[gmx-users] Segmentation fault on HPC Tomek Wlodarski
[gmx-users] Segmentation fault on HPC Tomek Wlodarski
[gmx-users] g_select syntax unavailable in GROMACS 5.0 and 5.0.1 Kester Wong
[gmx-users] g_select syntax unavailable in GROMACS 5.0 and 5.0.1 Kester Wong
[gmx-users] How to plot a droplet radius profile as a function of z-directio Kester Wong
[gmx-users] RDF plot with large g(r) values Kester Wong
[gmx-users] RDF plot with large g(r) values Kester Wong
[gmx-users] RDF plot with large g(r) values Kester Wong
[gmx-users] How to g_select water and ions? Kester Wong
[gmx-users] Importing a trajectory into MOE adam
[gmx-users] Ligand Topology file neha bharti
[gmx-users] Error during NVT neha bharti
[gmx-users] Energy minimization for Inositol pyrophosphate ashish bihani
[gmx-users] Energy minimization for Inositol pyrophosphate ashish bihani
[gmx-users] Error : Atomtype not found protim chakraborti
[gmx-users] Error : Atomtype not found protim chakraborti
[gmx-users] Dihedral angle autocorrelation function atanu das
[gmx-users] Dihedral angle autocorrelation function atanu das
[gmx-users] how can we modify *.rtp file? marzieh dehghan
[gmx-users] how can we modify *.rtp file? (again) marzieh dehghan
[gmx-users] GridMAT-MD m g
[gmx-users] Restarting crashed simulation bharat gupta
[gmx-users] problem in centering of my protein in the box nazli kashani javid
[gmx-users] Greetings+Which computer? amitabh jayaswal
[gmx-users] There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files sang eun jee
[gmx-users] Dihedral pca pratibha kapoor
[gmx-users] Dihedral pca pratibha kapoor
[gmx-users] Dihedral pca pratibha kapoor
[gmx-users] Dihedral pca pratibha kapoor
[gmx-users] Dihedral pca pratibha kapoor
[gmx-users] Transition matrix generation pratibha kapoor
[gmx-users] Dihedral pca ruchi lohia
[gmx-users] atom freezing mah maz
[gmx-users] atom freezing mah maz
[gmx-users] atom freezing mah maz
[gmx-users] trash error in linux mah maz
[gmx-users] trash error in linux mah maz
[gmx-users] potential energy mah maz
[gmx-users] potential energy mah maz
[gmx-users] potential energy mah maz
[gmx-users] potential energy mah maz
[gmx-users] potential energy mah maz
[gmx-users] potential energy mah maz
[gmx-users] potential energy mah maz
[gmx-users] potential energy mah maz
[gmx-users] coordinates file format mah maz
[gmx-users] coordinates file format mah maz
[gmx-users] coordinates file format mah maz
[gmx-users] coordinates file format mah maz
[gmx-users] coordinates file format mah maz
[gmx-users] coordinates file format mah maz
[gmx-users] Simulations in triplicates. ms
[gmx-users] Water mediated hydrogen bonding suhani nagpal
[gmx-users] Water mediated hydrogen bonding suhani nagpal
[gmx-users] Doubt in Gromacs nsteps, ps and ns salam pradeep
[gmx-users] Doubt in Gromacs nsteps, ps and ns salam pradeep
[gmx-users] gromacs.org_gmx-users Digest, Vol 129, Issue 4 asasa qsqs
[gmx-users] Electrostatic potential asasa qsqs
[gmx-users] Electrostatic potential asasa qsqs
[gmx-users] gromacs.org_gmx-users Digest, Vol 129, Issue 32 asasa qsqs
[gmx-users] GridMAT-MD asasa qsqs
[gmx-users] GridMAT-MD asasa qsqs
[gmx-users] PME update asasa qsqs
[gmx-users] adding new residue fatemeh ramezani
[gmx-users] Error on restart REMD simulations leila salimi
[gmx-users] residues in force fields shahab shariati
[gmx-users] residues in force fields shahab shariati
[gmx-users] Dihedral pca bipin singh
[gmx-users] Dihedral pca bipin singh
[gmx-users] Dihedral pca bipin singh
[gmx-users] AMBER99 topology for ADP bipin singh
[gmx-users] Doubt regarding nrexcl parameter in topology bipin singh
[gmx-users] Doubt regarding nrexcl parameter in topology bipin singh
[gmx-users] choosing appropriate force field elham tazikeh
[gmx-users] preparing pdb file elham tazikeh
[gmx-users] How can i save all run processes ... elham tazikeh
[gmx-users] How can i save all run processes ... elham tazikeh
[gmx-users] QM/MM excited state optimization xiao
[gmx-users] QM/MM excited state optimization xiao
[gmx-users] QM/MM excited state optimization (xiao) xiao
[gmx-users] dipole derivative xy21hb
[gmx-users] rotating triclinic box felipe zapata
[gmx-users] Box volume during dynamics felipe zapata
[gmx-users] cpu gpu performance h.alizadeh at znu.ac.ir
[gmx-users] Questions about implementing REST in GROMACS 4.6.5 周双艳
[gmx-users] How to calculate local pressure by using virial 张正财
[gmx-users] A question of Non-equilibrium MD in gromacs 陶璐

Last message date: Sat Jan 31 23:35:56 CET 2015
Archived on: Sat Jan 31 23:35:57 CET 2015

Messages sorted by: [ thread ] [ subject ] [ date ]
More info on this list...

This archive was generated by Pipermail 0.09 (Mailman edition).