May 2013 Archives by author

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Starting: Wed May 1 02:01:15 CEST 2013
Ending: Fri May 31 23:59:01 CEST 2013
Messages: 905

[gmx-users] probability from COM of micelle ABEL Stephane 175950
[gmx-users] doubt in mdrun Shine A
[gmx-users] including a new molecule to forcefield Amir Abbasi
[gmx-users] including a new molecule to forcefield Amir Abbasi
[gmx-users] epoxide group parameters Amir Abbasi
[gmx-users] stable branch using git Mark Abraham
[gmx-users] Re:Using virtual site Mark Abraham
[gmx-users] stable branch using git Mark Abraham
[gmx-users] Re: Using virtual site Mark Abraham
[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD Mark Abraham
[gmx-users] minimization of particular residue/atom Mark Abraham
[gmx-users] minimization of particular residue/atom Mark Abraham
[gmx-users] issue in replica exchange Mark Abraham
[gmx-users] issue in replica exchange Mark Abraham
[gmx-users] Error after trjconf processing Mark Abraham
[gmx-users] random seed in molecular dynamics Mark Abraham
[gmx-users] Error after trjconf processing Mark Abraham
[gmx-users] Error after trjconf processing Mark Abraham
[gmx-users] Error after trjconf processing Mark Abraham
[gmx-users] regression tests 4.6.1 with intel 13.0.1 Mark Abraham
[gmx-users] configuration/installation of gromacs-4.6.1 on heterogeneous cluster Mark Abraham
[gmx-users] configuration/installation of gromacs-4.6.1 on heterogeneous cluster Mark Abraham
[gmx-users] REMD Statistics Mark Abraham
[gmx-users] random seed in molecular dynamics Mark Abraham
[gmx-users] REMD Statistics Mark Abraham
[gmx-users] Problem with Installing Gromacs 4.6.1 with GPU Mark Abraham
[gmx-users] line wrapping on the gmx-users list Mark Abraham
[gmx-users] Conceptual question about the computational scaling of MD Mark Abraham
[gmx-users] Conceptual question about the computational scaling of MD Mark Abraham
[gmx-users] g_cluster warning Mark Abraham
[gmx-users] g_cluster warning Mark Abraham
[gmx-users] lincs errors late in simulation Mark Abraham
[gmx-users] numbering after 99999SOL Mark Abraham
[gmx-users] g_cluster warning Mark Abraham
[Spam:*****] [gmx-users] REMD analysis Mark Abraham
[gmx-users] Reduced Units Mark Abraham
[Spam:*****] [gmx-users] REMD analysis Mark Abraham
[gmx-users] About AMBER Force field SB 2012 (ff12SB), using ACPYPE Mark Abraham
[gmx-users] Performance (GMX4.6.1): MPI vs Threads Mark Abraham
[gmx-users] Reduced Units Mark Abraham
[gmx-users] 1-4 scaling factor Mark Abraham
[gmx-users] Comparing Gromacs versions Mark Abraham
[gmx-users] Inconsistent results in different clusters and cores Mark Abraham
[gmx-users] Comparing Gromacs versions Mark Abraham
[gmx-users] Re: REMD analysis Mark Abraham
[gmx-users] Expanding a .top file to have all connection information Mark Abraham
[gmx-users] Re: REMD analysis Mark Abraham
[gmx-users] Expanding a .top file to have all connection information Mark Abraham
[gmx-users] visualizing the system Mark Abraham
[gmx-users] compile Gromacs using Cray compilers Mark Abraham
[gmx-users] how to add angle_restraints and dihedral_restraints for atoms belonging to two different molecules Mark Abraham
[gmx-users] Re: REMD analysis Mark Abraham
[gmx-users] About Warnings and Note in Production MD Mark Abraham
[gmx-users] Notes from Production MD Mark Abraham
[gmx-users] Expanding a .top file to have all connection information Mark Abraham
[gmx-users] Re: DD fails Mark Abraham
[gmx-users] About CNT wrapped by Cyclic peptide Mark Abraham
[gmx-users] compile Gromacs using Cray compilers Mark Abraham
[gmx-users] compile Gromacs using Cray compilers Mark Abraham
[gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial Mark Abraham
[gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial Mark Abraham
[gmx-users] is there extra parameters in .mdp file for running successful angle_restraints? Mark Abraham
[gmx-users] Distance restraints Mark Abraham
[gmx-users] How to get the density change along one direction? Mark Abraham
[gmx-users] Distance restraints Mark Abraham
[gmx-users] MSD and frequency of writing trajectories Mark Abraham
[gmx-users] error in running g_dist Mark Abraham
[gmx-users] C6 & C12 parameters for non-bonded interactions using tables Mark Abraham
[gmx-users] Re: MSD and frequency of writing trajectories Mark Abraham
[gmx-users] Re: MSD and frequency of writing trajectories Mark Abraham
[gmx-users] Effect of pressure coupling frequency on gpu simulations Mark Abraham
[gmx-users] Re: MSD and frequency of writing trajectories Mark Abraham
[gmx-users] Re: REMD analysis Mark Abraham
[gmx-users] Effect of pressure coupling frequency on gpu simulations Mark Abraham
[gmx-users] Re: REMD analysis Mark Abraham
[gmx-users] renumber residue number in file topology Mark Abraham
[gmx-users] Re: REMD analysis Mark Abraham
[gmx-users] Re: REMD analysis Mark Abraham
[gmx-users] Re: REMD analysis Mark Abraham
[gmx-users] mdrun generate a lot of files with # Mark Abraham
[gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme Mark Abraham
[gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme Mark Abraham
[gmx-users] file not found Mark Abraham
[gmx-users] Have your ever got a real NVE simulation (good energy conservation) in gromacs? Mark Abraham
[gmx-users] tpr of extend simulation Mark Abraham
[gmx-users] Re:The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme Mark Abraham
[gmx-users] Re: REMD analysis Mark Abraham
[gmx-users] Re: REMD analysis Mark Abraham
[gmx-users] REMD:subsystems are not compatible. Mark Abraham
[gmx-users] REMD:subsystems are not compatible. Mark Abraham
[gmx-users] grommp problem in gromacs 4.6.1 Mark Abraham
[gmx-users] mdrun outputs incorrect resnames Mark Abraham
[gmx-users] About Compilation error in gromacs 4.6 Mark Abraham
[gmx-users] About Compilation error in gromacs 4.6 Mark Abraham
[gmx-users] choice of forcefield Mark Abraham
[gmx-users] Extending simualtions Mark Abraham
[gmx-users] Vritual Sites and simulation time-step Mark Abraham
[gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field Mark Abraham
[gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field Mark Abraham
[gmx-users] GROMACS 4.6.2 released Mark Abraham
[gmx-users] GROMACS 4.6.2 released Mark Abraham
[gmx-users] Re: GROMACS 4.6.2 released Mark Abraham
[gmx-users] query on replica exchange Mark Abraham
[gmx-users] Increasing performance of siumulation in cluster Mark Abraham
[gmx-users] Increasing performance of siumulation in cluster Mark Abraham
[gmx-users] Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the box size (2.184750) Abhishek Acharya
[gmx-users] error after grompp Abhishek Acharya
[gmx-users] How to restrain dihedral angles to reserve the tacticity? Abhishek Acharya
[gmx-users] Re: How to restrain dihedral angles to reserve the tacticity? Abhishek Acharya
[gmx-users] Initial velocity Brighter Agyemang
[gmx-users] Initial velocity Brighter Agyemang
[gmx-users] MSD and frequency of writing trajectories Anna Akinshina
[gmx-users] About AMBER Force field SB 2012 (ff12SB), using ACPYPE Alan
[gmx-users] where can be obtain circled lipids bilayer? Albert
[gmx-users] GPU job often stopped Albert
[gmx-users] g_select question Albert
[gmx-users] how to distribute CPU in GPU workstation? Albert
[gmx-users] GROMACS 4.6.2 released Albert
R: [gmx-users] metadynamics Spitaleri Andrea
[gmx-users] trjcat: joining randomized PDB files Anirban
[gmx-users] trjcat: joining randomized PDB files Anirban
[gmx-users] mdp file help Muhammad Ayaz Anwar
[gmx-users] Wednesday, 15 May: upgrading redmine.gromacs.org Rossen Apostolov
[gmx-users] Re: [gmx-developers] Wednesday, 15 May: upgrading redmine.gromacs.org Rossen Apostolov
[gmx-users] If your mails are rejected from the list Rossen Apostolov
[gmx-users] compile Gromacs using Cray compilers Humayun Arafat
[gmx-users] compile Gromacs using Cray compilers Humayun Arafat
[gmx-users] compile Gromacs using Cray compilers Humayun Arafat
[gmx-users] compile Gromacs using Cray compilers Humayun Arafat
[gmx-users] compile Gromacs using Cray compilers Humayun Arafat
[gmx-users] compile Gromacs using Cray compilers Humayun Arafat
[gmx-users] file not found Humayun Arafat
[gmx-users] file not found Humayun Arafat
[gmx-users] RMSD Shima Arasteh
[gmx-users] unstable system Shima Arasteh
[gmx-users] unstable system Shima Arasteh
[gmx-users] unstable system Shima Arasteh
[gmx-users] US and SMD Shima Arasteh
[gmx-users] unstable system Shima Arasteh
[gmx-users] Running Pull Code Shima Arasteh
[gmx-users] puuling simulations Shima Arasteh
[gmx-users] Re: Running Pull Code Shima Arasteh
[gmx-users] Re: Running Pull Code Shima Arasteh
[gmx-users] Re: Running Pull Code Shima Arasteh
[gmx-users] visualizing the system Shima Arasteh
[gmx-users] Tryptophan rings are not connected in visualization Shima Arasteh
[gmx-users] Re: Running Pull Code Shima Arasteh
[gmx-users] Add CS ions to system Shima Arasteh
[gmx-users] numbering after 99999SOL Nuno Azoia
[gmx-users] numbering after 99999SOL Nuno Azoia
[gmx-users] Re: Have your ever got a real NVE simulation (good energy conservation) in gromacs? S. Alireza Bagherzadeh
[gmx-users] RNA MD Simulation using GROMACS Pruthvi Bejugam
[gmx-users] simulation single molecule in water Emanuel Birru
[gmx-users] position restrain dynamics error Subramaniam Boopathi
[gmx-users] gmx 4.6 does not detect GPUs, but 4.5 does Leandro Bortot
[gmx-users] Initial velocity Acoot Brett
[gmx-users] Re: Using virtual site Richard Broadbent
[gmx-users] Periodic Boundary Condition in evaporation of droplets Richard Broadbent
[gmx-users] Issue running gromacs in Cluster Broadbent, Richard
Aw: Re: [gmx-users] GPU-based workstation Broadbent, Richard
[gmx-users] issue in replica exchange Floris Buelens
[gmx-users] 'the reciprocal space calculation will not necessarily cancel' Floris Buelens
[gmx-users] Re: How to restrain dihedral angles to reserve the tacticity? Javier Cerezo
[gmx-users] g_msd for many molecules Dr. Vitaly Chaban
[gmx-users] where can be obtain circled lipids bilayer? Dr. Vitaly Chaban
[gmx-users] vacum simulation Dr. Vitaly Chaban
[gmx-users] Usage of g_spatial Dr. Vitaly Chaban
[gmx-users] simulation single molecule in water Dr. Vitaly Chaban
[gmx-users] Charmm27 potential energies. Dr. Vitaly Chaban
[gmx-users] DD fails Dr. Vitaly Chaban
[gmx-users] Re: DD fails Dr. Vitaly Chaban
[gmx-users] Why the shape of the molecules changed? Dr. Vitaly Chaban
[gmx-users] how to get the epsilon and sigma values of CO Dr. Vitaly Chaban
[gmx-users] Gromacs for Non biological systems Dr. Vitaly Chaban
[gmx-users] choice of forcefield Dr. Vitaly Chaban
[gmx-users] Re: choice of force field -reg Dr. Vitaly Chaban
[gmx-users] Continue simulation from the specific time Dr. Vitaly Chaban
[gmx-users] Continue simulation from the specific time Dr. Vitaly Chaban
[gmx-users] Re: choice of force field -reg Dr. Vitaly Chaban
[gmx-users] How to choose bd_fric value in brownian dynamics Dr. Vitaly Chaban
[gmx-users] How to choose bd_fric value in brownian dynamics Dr. Vitaly Chaban
[gmx-users] Extending simualtions Dr. Vitaly Chaban
[gmx-users] pulling simulations Dr. Vitaly Chaban
[gmx-users] Re: Extending simulations Dr. Vitaly Chaban
[gmx-users] Re: Extending simulations Dr. Vitaly Chaban
[gmx-users] .GRO Formatting Dr. Vitaly Chaban
[gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field Dr. Vitaly Chaban
[gmx-users] How to restrain dihedral angles to reserve the tacticity? Wu Chaofu
[gmx-users] random seed in molecular dynamics Preeti Choudhary
[gmx-users] random seed in molecular dynamics Preeti Choudhary
[gmx-users] g_cluster warning Preeti Choudhary
[gmx-users] g_cluster warning Preeti Choudhary
[gmx-users] do_dssp Preeti Choudhary
[gmx-users] Fwd: do_dssp Preeti Choudhary
[gmx-users] issue in replica exchange Simone Conti
[gmx-users] issue in replica exchange Simone Conti
[gmx-users] QM/MM simulations DavidPO
[gmx-users] Re: QM/MM simulations DavidPO
[gmx-users] Re: QM/MM simulations DavidPO
[gmx-users] Re: QM/MM simulations DavidPO
[gmx-users] Re: QM/MM simulations DavidPO
[gmx-users] Re: QM/MM simulations DavidPO
[gmx-users] Re: QM/MM simulations DavidPO
[gmx-users] mdrun-gpu error message on Gromacs 4.5.5 Andrew DeYoung
[gmx-users] Re: mdrun-gpu error message on Gromacs 4.5.5 Andrew DeYoung
[gmx-users] Conceptual question about the computational scaling of MD Andrew DeYoung
[gmx-users] About Warnings and Note in Production MD Baptiste Demoulin
[gmx-users] Parrinello-Rahman and Simulated Annealing Baptiste Demoulin
[gmx-users] Parrinello-Rahman and Simulated Annealing Baptiste Demoulin
[gmx-users] g_msd for many molecules Florian Dommert
[gmx-users] setting up a simulation of an ionic liquid Florian Dommert
[gmx-users] setting up a simulation of an ionic liquid Florian Dommert
[gmx-users] Problem with DSSP Sainitin Donakonda
[gmx-users] Issue running gromacs in Cluster Sainitin Donakonda
[gmx-users] Issue running gromacs in Cluster Sainitin Donakonda
[gmx-users] Increasing performance of siumulation in cluster Sainitin Donakonda
[gmx-users] Increasing performance of siumulation in cluster Sainitin Donakonda
[gmx-users] Increasing performance of siumulation in cluster Sainitin Donakonda
[gmx-users] Exdending Dubi
[gmx-users] help with g_hydorder and g_polystat Emmanuel, Alaina
[gmx-users] help with g_hydorder and g_polystat Emmanuel, Alaina
[gmx-users] help with g_hydorder and g_polystat Emmanuel, Alaina
[gmx-users] help with g_hydorder and g_polystat Emmanuel, Alaina
[gmx-users] doubt in mdrun Pablo Englebienne
[gmx-users] genion Ewaru
[gmx-users] Re: genion Ewaru
[gmx-users] Re: genion Ewaru
[gmx-users] proceed from output of MD Ewaru
[gmx-users] Re: proceed from output of MD Ewaru
[gmx-users] Re: gmx-users Digest, Vol 109, Issue 153 Ayesha Fatima
[gmx-users] installation Gromacs-Fedora18 Francesco
[gmx-users] equilibration of the simulated systems Francesco
[gmx-users] mdrun and simulation time Francesco
[gmx-users] mdrun and simulation time Francesco
[gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be Francesco
[gmx-users] mdp-settings for charmm36 and lipid apl values Patrick Fuchs
[gmx-users] subspace overlap Miguel Ángel Mompeán García
[gmx-users] Overlap between PC motions Miguel Ángel Mompeán García
[gmx-users] Overlap between PC motions Miguel Ángel Mompeán García
[gmx-users] Langevin thermostat implementation in GROMACS vs AMBER Julian Garrec
[gmx-users] Langevin thermostat implementation in GROMACS vs AMBER Julian Garrec
[gmx-users] Re: Langevin thermostat implementation in GROMACS vs AMBER Julian Garrec
[gmx-users] error after grompp Nur Syafiqah Abdul Ghani
[gmx-users] (no subject) Group Gro
[gmx-users] Viscosity calculation using cos_acceleration Berk Hess
[gmx-users] do_dssp Xu Dong Huang
[gmx-users] Lennard Jones parameters Ishwor
[gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial Vishal Kumar Jaiswal
[gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial Vishal Kumar Jaiswal
[gmx-users] How to visualize .gro file without .tpr file Vishal Kumar Jaiswal
[gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial Vishal Kumar Jaiswal
[gmx-users] Solvent molecules within a certain distance of solute Vishal Kumar Jaiswal
[gmx-users] Comparing Gromacs versions Djurre de Jong-Bruinink
[gmx-users] Comparing Gromacs versions Djurre de Jong-Bruinink
[gmx-users] Comparing Gromacs versions Djurre de Jong-Bruinink
[gmx-users] Re: installation Gromacs-Fedora18 Christoph Junghans
[gmx-users] Re: Langevin thermostat implementation in GROMACS vs AMBER Christoph Junghans
[gmx-users] How to visualize .gro file without .tpr file Bao Kai
[gmx-users] How to get the density change along one direction? Bao Kai
[gmx-users] On Decane coordinate file Bao Kai
[gmx-users] On Decane coordinate file Bao Kai
[gmx-users] Why the shape of the molecules changed? Bao Kai
[gmx-users] Why the shape of the molecules changed? Bao Kai
[gmx-users] On using CO2 as solvent Bao Kai
[gmx-users] On pressure controlling Bao Kai
[gmx-users] Simulation of Small Water Box Monoj Mon Kalita
[gmx-users] question about energygrps Hyunjin Kim
[gmx-users] question about energygrps Hyunjin Kim
[gmx-users] question about energygrps Hyunjin Kim
[gmx-users] question about energygrps Hyunjin Kim
[gmx-users] question about energygrps Hyunjin Kim
[gmx-users] question about energygrps Hyunjin Kim
[gmx-users] Distance restraints Rama Krishna Koppisetti
[gmx-users] Distance restraints Rama Krishna Koppisetti
[gmx-users] (no subject) Sathish Kumar
[gmx-users] (no subject) Sathish Kumar
[gmx-users] Thiolate cysteine Sathish Kumar
[gmx-users] Reax force field Sathish Kumar
[gmx-users] (no subject) Sathish Kumar
[gmx-users] puuling simulations Sathish Kumar
[gmx-users] Fwd: puuling simulations Sathish Kumar
[gmx-users] pulling simulations Sathish Kumar
[gmx-users] (no subject) Sathish Kumar
[gmx-users] metadynamics Sathish Kumar
[gmx-users] (no subject) Sathish Kumar
[gmx-users] pulling simulations Sathish Kumar
[gmx-users] Residue renaming during mdrun Laura Leay
[gmx-users] setting up a simulation of an ionic liquid Laura Leay
[gmx-users] setting up a simulation of an ionic liquid Laura Leay
[gmx-users] setting up a simulation of an ionic liquid Laura Leay
[gmx-users] mdrun outputs incorrect resnames Reid Van Lehn
[gmx-users] mdrun outputs incorrect resnames Reid Van Lehn
[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD Justin Lemkul
[gmx-users] local pressure Justin Lemkul
[gmx-users] stable branch using git Justin Lemkul
[gmx-users] stable branch using git Justin Lemkul
[gmx-users] help with g_hydorder and g_polystat Justin Lemkul
[gmx-users] input file for umbrella sampling Justin Lemkul
[gmx-users] local pressure Justin Lemkul
[gmx-users] help with g_hydorder and g_polystat Justin Lemkul
[gmx-users] g_msd for many molecules Justin Lemkul
[gmx-users] Gromacs mpi error while running REMD Justin Lemkul
[gmx-users] Temperature for individual amino acid residues Justin Lemkul
[gmx-users] surrounding a peptide by ions of magnesium Justin Lemkul
[gmx-users] surrounding a peptide by ions of magnesium Justin Lemkul
[gmx-users] vacum simulation Justin Lemkul
[gmx-users] vacum simulation Justin Lemkul
[gmx-users] Temperature for individual amino acid residues Justin Lemkul
[gmx-users] Temperature for individual amino acid residues Justin Lemkul
[gmx-users] Exdending Justin Lemkul
[gmx-users] where can be obtain circled lipids bilayer? Justin Lemkul
[gmx-users] installation Gromacs-Fedora18 Justin Lemkul
[gmx-users] Simulation of Small Water Box Justin Lemkul
[gmx-users] distance of pull group 1 is larger than the box size Justin Lemkul
[gmx-users] genion Justin Lemkul
[gmx-users] Re: rotation of a ligand Justin Lemkul
[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD Justin Lemkul
[gmx-users] Re: genion Justin Lemkul
[gmx-users] Umbrella sampling's equilibration runs Justin Lemkul
[gmx-users] including a new molecule to forcefield Justin Lemkul
[gmx-users] including a new molecule to forcefield Justin Lemkul
[gmx-users] epoxide group parameters Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] RMSD Justin Lemkul
[gmx-users] correct traj for water/ions density Justin Lemkul
[gmx-users] Reax force field Justin Lemkul
[gmx-users] Thiolate cysteine Justin Lemkul
[gmx-users] correct traj for water/ions density Justin Lemkul
[gmx-users] Tryptophan and tyrosine protonation Justin Lemkul
[gmx-users] Still having issues analyzing normal-mode hessian Justin Lemkul
[gmx-users] About Potential energy calculation Justin Lemkul
[gmx-users] mdrun-gpu error message on Gromacs 4.5.5 Justin Lemkul
[gmx-users] center of mass and box co-ordinates Justin Lemkul
[gmx-users] FW: Myristic Acid Simulations Justin Lemkul
[gmx-users] Atomtype C not found Justin Lemkul
[gmx-users] a program to calculate the adsorbed molecules Justin Lemkul
[gmx-users] unstable system Justin Lemkul
[gmx-users] error in running distances.pl Justin Lemkul
[gmx-users] position restrain dynamics error Justin Lemkul
[gmx-users] unstable system Justin Lemkul
[gmx-users] Problem with DSSP Justin Lemkul
[gmx-users] mdp-settings for charmm36 and lipid apl values Justin Lemkul
[gmx-users] mdp-settings for charmm36 and lipid apl values Justin Lemkul
[gmx-users] A problem with do_dssp command Justin Lemkul
[gmx-users] Re: A problem with do_dssp command Justin Lemkul
[gmx-users] Re: A problem with do_dssp command Justin Lemkul
[gmx-users] Re: A problem with do_dssp command Justin Lemkul
[gmx-users] Re: A problem with do_dssp command Justin Lemkul
[gmx-users] Re: A problem with do_dssp command Justin Lemkul
[gmx-users] Re: A problem with do_dssp command Justin Lemkul
[gmx-users] Re: A problem with do_dssp command Justin Lemkul
[gmx-users] trjcat: joining randomized PDB files Justin Lemkul
[gmx-users] trjcat: joining randomized PDB files Justin Lemkul
[gmx-users] Fw: probability from COM of micelle Justin Lemkul
[gmx-users] Charmm27 potential energies. Justin Lemkul
[gmx-users] groups selection make_ndx -f npt.gro Justin Lemkul
[gmx-users] US and SMD Justin Lemkul
[gmx-users] Difference between g_rms and g_rmsdist Justin Lemkul
[gmx-users] Problem importing PDB to Gromacs Justin Lemkul
[gmx-users] g_dist Justin Lemkul
[gmx-users] g_dist Justin Lemkul
[gmx-users] query respect to perl distances.pl Justin Lemkul
[gmx-users] unstable system Justin Lemkul
[gmx-users] Atomtype OW not found Justin Lemkul
[gmx-users] line wrapping on the gmx-users list Justin Lemkul
[gmx-users] question about energygrps Justin Lemkul
[gmx-users] system hangs while running perl distances.pl Justin Lemkul
[gmx-users] g_dist Justin Lemkul
[gmx-users] question about energygrps Justin Lemkul
[gmx-users] question about energygrps Justin Lemkul
[gmx-users] Inconsistent results in different clusters and cores Justin Lemkul
[gmx-users] Inconsistent results in different clusters and cores Justin Lemkul
[gmx-users] question about energygrps Justin Lemkul
[gmx-users] Inconsistent results in different clusters and cores Justin Lemkul
[gmx-users] question about energygrps Justin Lemkul
[gmx-users] Initial velocity Justin Lemkul
[gmx-users] Issue running gromacs in Cluster Justin Lemkul
[gmx-users] Center of Mass (COM) spacing between protein and ligand Justin Lemkul
[gmx-users] air-water-interface Justin Lemkul
[gmx-users] Residue renaming during mdrun Justin Lemkul
[gmx-users] mdrun and simulation time Justin Lemkul
[gmx-users] air-water-interface Justin Lemkul
[gmx-users] Initial velocity Justin Lemkul
[gmx-users] QM/MM simulations Justin Lemkul
[gmx-users] setting up a simulation of an ionic liquid Justin Lemkul
[gmx-users] Fwd: Rycaert-Bellemans function Justin Lemkul
[gmx-users] Charge groups Justin Lemkul
[gmx-users] Fwd: do_dssp Justin Lemkul
[gmx-users] do_dssp Justin Lemkul
[gmx-users] range angle calculated by g_sgangle Justin Lemkul
[gmx-users] lincs errors late in simulation Justin Lemkul
[gmx-users] Re: QM/MM simulations Justin Lemkul
[gmx-users] g_sgangle and P atoms on the DNA molecule. Justin Lemkul
[gmx-users] g_dist problem in Implicit solvent Justin Lemkul
[gmx-users] g_dist problem in Implicit solvent Justin Lemkul
R: Re: [gmx-users] range angle calculated by g_sgangle Justin Lemkul
[gmx-users] simulate a protein covalently binding with a organic molecule Justin Lemkul
[gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be Justin Lemkul
[gmx-users] g_dist problem in Implicit solvent Justin Lemkul
[gmx-users] changing protonation state of a residue during a simulation Justin Lemkul
[gmx-users] Problems installing 4.6.1 on Mac 10.8.3 Justin Lemkul
[gmx-users] coupling issue Justin Lemkul
[gmx-users] gmx 4.6 does not detect GPUs, but 4.5 does Justin Lemkul
[gmx-users] Inconsistent results in different clusters and cores Justin Lemkul
[gmx-users] Re: Running Pull Code Justin Lemkul
[gmx-users] Re: Running Pull Code Justin Lemkul
[gmx-users] Tryptophan rings are not connected in visualization Justin Lemkul
[gmx-users] charmm in gromacs cut-offs Justin Lemkul
[gmx-users] Re: Running Pull Code Justin Lemkul
[gmx-users] Add CS ions to system Justin Lemkul
[gmx-users] g_msd problem Justin Lemkul
[gmx-users] Expanding a .top file to have all connection information Justin Lemkul
[gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial Justin Lemkul
[gmx-users] About CNT cyclic PEptide Justin Lemkul
[gmx-users] About Production MD run error Justin Lemkul
[gmx-users] Re: QM/MM simulations Justin Lemkul
[gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial Justin Lemkul
[gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial Justin Lemkul
[gmx-users] Parrinello-Rahman and Simulated Annealing Justin Lemkul
[gmx-users] Distance restraints Justin Lemkul
[gmx-users] Mdrun_mip efficiency Justin Lemkul
[gmx-users] Mdrun_mip efficiency Justin Lemkul
[gmx-users] On Decane coordinate file Justin Lemkul
[gmx-users] residue labeling in g_rmsf Justin Lemkul
[gmx-users] the details about g_density Justin Lemkul
[gmx-users] the details about g_density Justin Lemkul
[gmx-users] Why the shape of the molecules changed? Justin Lemkul
[gmx-users] Why the shape of the molecules changed? Justin Lemkul
[gmx-users] mdrun generate a lot of files with # Justin Lemkul
[gmx-users] On using CO2 as solvent Justin Lemkul
[gmx-users] On pressure controlling Justin Lemkul
[gmx-users] Using many index file in one command line Justin Lemkul
[gmx-users] Re: FEP of ion binding protein Justin Lemkul
[gmx-users] Re: QM/MM simulations Justin Lemkul
[gmx-users] Lennard Jones parameters Justin Lemkul
[gmx-users] Re: QM/MM simulations Justin Lemkul
[gmx-users] About Warnings in Mdrun Justin Lemkul
[gmx-users] pulling simulations Justin Lemkul
[gmx-users] keeping water (entirely) out of the bilayer core Jianguo Li
[gmx-users] keeping water (entirely) out of the bilayer core Jianguo Li
[gmx-users] g_dist problem in Implicit solvent Tong Li
[gmx-users] Free energy calculation: merge the topology of 2 molecules Dejun Lin
[gmx-users] Free energy calculation: merge the topology of 2 molecules Dejun Lin
[gmx-users] Potential energy for partial system Po-Han Lin
[gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme Bin Liu
[gmx-users] Re:The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme Bin Liu
[gmx-users] query on replica exchange Sanku M
[gmx-users] Large number of solvent molecules Nikunj Maheshwari
[gmx-users] Large number of solvent molecules Nikunj Maheshwari
[gmx-users] How to visualize .gro file without .tpr file Nikunj Maheshwari
[gmx-users] vacum simulation Erik Marklund
[gmx-users] constant protonation state MD Erik Marklund
[gmx-users] random seed in molecular dynamics Erik Marklund
[gmx-users] constant protonation state MD Erik Marklund
[gmx-users] constant protonation state MD Erik Marklund
[gmx-users] (no subject) Erik Marklund
[gmx-users] Problem with DSSP Erik Marklund
[gmx-users] Large number of solvent molecules Erik Marklund
[gmx-users] Hydrogen Bond analysis using Gromacs Erik Marklund
[gmx-users] RNA MD Simulation using GROMACS Erik Marklund
[gmx-users] Solvent molecules within a certain distance of solute Erik Marklund
[gmx-users] MSD and frequency of writing trajectories Erik Marklund
[gmx-users] Have your ever got a real NVE simulation (good energy conservation) in gromacs? Erik Marklund
[gmx-users] g_hbond Erik Marklund
[gmx-users] the "-dist" flag of g_hbond tool Erik Marklund
[gmx-users] the "-dist" flag of g_hbond tool Erik Marklund
[gmx-users] the "-dist" flag of g_hbond tool Erik Marklund
[gmx-users] About Compiler Option Erik Marklund
[gmx-users] local pressure Sikandar Mashayak
[gmx-users] stable branch using git Sikandar Mashayak
[gmx-users] stable branch using git Sikandar Mashayak
[gmx-users] stable branch using git Sikandar Mashayak
[gmx-users] local pressure Sikandar Mashayak
[gmx-users] local pressure Sikandar Mashayak
[gmx-users] local pressure Sikandar Mashayak
[gmx-users] point in source code to access atom position Sikandar Mashayak
[gmx-users] Extending simualtions Fábio Filippi Matioli
[gmx-users] Difference between g_rms and g_rmsdist Nawel Mele
[gmx-users] umbrella sampling Nawel Mele
[gmx-users] Difference between g_rms and g_rmsdist Nawel Mele
[gmx-users] air-water-interface Nawel Mele
[gmx-users] air-water-interface Nawel Mele
[gmx-users] air-water-interface Nawel Mele
[gmx-users] Dihedral Autocorrelation Function with negative values Davide Mercadante
[gmx-users] Atomtype C not found Sun Moon
[gmx-users] Atomtype OW not found Sun Moon
[gmx-users] g_select question Teemu Murtola
[gmx-users] bending angle between 2 vectors defined by cm of groups of atoms Teemu Murtola
[gmx-users] ionic liquids - viscosity via green kubo relation Krzysztof Murzyn
[gmx-users] Periodic Boundary Condition in evaporation of droplets Rasoul Nasiri
[gmx-users] Periodic Boundary Condition in evaporation of droplets Rasoul Nasiri
[gmx-users] Reduced Units Rasoul Nasiri
[gmx-users] Reduced Units Rasoul Nasiri
[gmx-users] keeping water (entirely) out of the bilayer core Christopher Neale
[gmx-users] keeping water (entirely) out of the bilayer core Christopher Neale
[gmx-users] keeping water (entirely) out of the bilayer core Christopher Neale
[gmx-users] Usage of g_spatial Christopher Neale
[gmx-users] Usage of g_spatial Christopher Neale
[gmx-users] mdp-settings for charmm36 and lipid apl values Christopher Neale
[gmx-users] keeping water (entirely) out of the bilayer core Christopher Neale
[gmx-users] line wrapping on the gmx-users list Christopher Neale
[gmx-users] line wrapping on the gmx-users list Christopher Neale
[gmx-users] Usage of g_spatial Christopher Neale
[gmx-users] RDF - water and protein Steven Neumann
[gmx-users] FEP of ion binding protein Steven Neumann
[gmx-users] renumber residue number in file topology Kieu Thu Nguyen
[gmx-users] Using many index file in one command line Kieu Thu Nguyen
[gmx-users] Using many index file in one command line Kieu Thu Nguyen
[gmx-users] ionic liquids - viscosity via green kubo relation Thomas P
[gmx-users] ionic liquids - viscosity via green kubo relation Thomas P
[gmx-users] g_hbond CHEN Pan
[gmx-users] the "-dist" flag of g_hbond tool CHEN Pan
[gmx-users] the "-dist" flag of g_hbond tool CHEN Pan
[gmx-users] the "-dist" flag of g_hbond tool CHEN Pan
[gmx-users] g_msd for many molecules George Patargias
[gmx-users] g_msd for many molecules George Patargias
[gmx-users] Different Cutoff Options PaulC
[gmx-users] fw: hey Wholly Peach
[gmx-users] RE : Hydrogen Bond analysis using Gromacs Keerthana S.P Periasamy
[gmx-users] local pressure XAvier Periole
[gmx-users] local pressure XAvier Periole
[gmx-users] issue in replica exchange XAvier Periole
[gmx-users] local pressure XAvier Periole
[gmx-users] issue in replica exchange XAvier Periole
[gmx-users] issue in replica exchange XAvier Periole
[gmx-users] issue in replica exchange XAvier Periole
[gmx-users] issue in replica exchange XAvier Periole
[gmx-users] issue in replica exchange XAvier Periole
[gmx-users] issue in replica exchange XAvier Periole
[gmx-users] issue in replica exchange XAvier Periole
[gmx-users] issue in replica exchange XAvier Periole
[gmx-users] keeping water (entirely) out of the bilayer core XAvier Periole
[gmx-users] issue in replica exchange XAvier Periole
[gmx-users] Re: REMD average acceptance ratio XAvier Periole
[gmx-users] REMD average acceptance ratio XAvier Periole
[gmx-users] REMD average acceptance ratio XAvier Periole
[gmx-users] REMD average acceptance ratio XAvier Periole
[gmx-users] Issue running gromacs in Cluster XAvier Periole
[gmx-users] issue in replica exchange XAvier Periole
[Spam:*****] [gmx-users] REMD analysis XAvier Periole
[gmx-users] Large number of solvent molecules XAvier Periole
[Spam:*****] [gmx-users] REMD analysis XAvier Periole
[Spam:*****] [gmx-users] REMD analysis XAvier Periole
[Spam:*****] [gmx-users] REMD analysis XAvier Periole
[gmx-users] REMD analysis XAvier Periole
[gmx-users] point in source code to access atom position XAvier Periole
[gmx-users] Re: REMD analysis XAvier Periole
[gmx-users] Re: REMD analysis XAvier Periole
[gmx-users] .GRO Formatting Phil
[gmx-users] changing protonation state of a residue during a simulation Payman Pirzadeh
[gmx-users] g_covar -ascii Payman Pirzadeh
[gmx-users] (no subject) Ishwor Poudyal
[gmx-users] how to get the epsilon and sigma values of CO Ishwor Poudyal
[gmx-users] a program to calculate the adsorbed molecules Za Pour
[gmx-users] equilibration of the simulated systems Za Pour
[gmx-users] cudaStreamSynchronize failed Szilárd Páll
[gmx-users] Performance (GMX4.6.1): MPI vs Threads Szilárd Páll
[gmx-users] Performance (GMX4.6.1): MPI vs Threads Szilárd Páll
[gmx-users] Comparing Gromacs versions Szilárd Páll
[gmx-users] Comparing Gromacs versions Szilárd Páll
[gmx-users] compile Gromacs using Cray compilers Szilárd Páll
[gmx-users] Re: Have your ever got a real NVE simulation (good energy conservation) in gromacs? Szilárd Páll
[gmx-users] About Compilation error in gromacs 4.6 Szilárd Páll
[gmx-users] GPU-based workstation Szilárd Páll
Aw: Re: [gmx-users] GPU-based workstation Szilárd Páll
[gmx-users] Re: GPU-based workstation Szilárd Páll
[gmx-users] mdp-settings for charmm36 and lipid apl values Gmx QA
[gmx-users] mdp-settings for charmm36 and lipid apl values Gmx QA
[gmx-users] Distance Restraints Rama
[gmx-users] Distance restraints Rama
[gmx-users] C6 & C12 parameters for non-bonded interactions using tables Andrish Reddy
[gmx-users] Re: error in running g_dist Andrish Reddy
Aw: [gmx-users] C6 & C12 parameters for non-bonded interactions using tables Andrish Reddy
[gmx-users] Usage of g_spatial Venkat Reddy
[gmx-users] Usage of g_spatial Venkat Reddy
[gmx-users] Usage of g_spatial Venkat Reddy
[gmx-users] Cholesteryl oleate parameters for CHARMM27 ff in Gromacs Venkat Reddy
[gmx-users] CHARMM lipid parameters Venkat Reddy
[gmx-users] residues interaction with ligand Venkat Reddy
[gmx-users] g_cluster warning Sabine Reisser
[gmx-users] g_cluster warning Sabine Reisser
[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD Reza
[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD Reza
[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD Reza
[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD Reza
[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD Reza
[gmx-users] Still having issues analyzing normal-mode hessian Bryan Roessler
[gmx-users] Expanding a .top file to have all connection information David Rosenman
[gmx-users] Expanding a .top file to have all connection information David Rosenman
[gmx-users] regression tests 4.6.1 with intel 13.0.1 José Luis Gordillo Ruiz
[gmx-users] regression tests 4.6.1 with intel 13.0.1 José Luis Gordillo Ruiz
[gmx-users] vacum simulation Souilem Safa
[gmx-users] vacum simulation Souilem Safa
[gmx-users] vacum simulation Souilem Safa
[gmx-users] vacum simulation Souilem Safa
[gmx-users] installation Gromacs-Fedora18 Souilem Safa
[gmx-users] installation Gromacs-Fedora18 Souilem Safa
[gmx-users] simulation single molecule in water Souilem Safa
[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD Reza Salari
[gmx-users] parameter files for cholesteryl ester Revthi Sanker
[gmx-users] choice of forcefield Revthi Sanker
[gmx-users] choice of forcefield Revthi Sanker
[gmx-users] Re: choice of force field -reg Revthi Sanker
[gmx-users] Re: PMF calculation between protein and ligand Thomas Schlesier
[gmx-users] Re: umbrella sampling Thomas Schlesier
[gmx-users] Re: RDF - water and protein Thomas Schlesier
[gmx-users] Performance (GMX4.6.1): MPI vs Threads Thomas Schlesier
[gmx-users] Re: Running Pull Code Thomas Schlesier
[gmx-users] Re: umbrella sampling for two polymer interaction Thomas Schlesier
[gmx-users] Re: umbrella sampling for two polymer interaction Thomas Schlesier
[gmx-users] Re: GPU-based workstation Ehud Schreiber
[gmx-users] xtc2dcd conversion Roland Schulz
[gmx-users] compile Gromacs using Cray compilers Roland Schulz
[gmx-users] compile Gromacs using Cray compilers Roland Schulz
[gmx-users] Re: gmx-users Digest, Vol 109, Issue 2 Arunima Shilpi
[gmx-users] Re: gmx-users Digest, Vol 108, Issue 183 Arunima Shilpi
[gmx-users] PMF calculation between protein and ligand Arunima Shilpi
[gmx-users] distance of pull group 1 is larger than the box size Arunima Shilpi
[gmx-users] Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the box size (2.184750) Arunima Shilpi
[gmx-users] center of mass and box co-ordinates Arunima Shilpi
[gmx-users] error in running perl distance.pl Arunima Shilpi
[gmx-users] error in running distances.pl Arunima Shilpi
[gmx-users] groups selection make_ndx -f npt.gro Arunima Shilpi
[gmx-users] query respect to perl distances.pl Arunima Shilpi
[gmx-users] system hangs while running perl distances.pl Arunima Shilpi
[gmx-users] Center of Mass (COM) spacing between protein and ligand Arunima Shilpi
[gmx-users] Interaction spectra of inhibitor–residue pair in the protein–inhibitor complexes Arunima Shilpi
[gmx-users] residues interaction with ligand Arunima Shilpi
[gmx-users] error in running g_dist Arunima Shilpi
[gmx-users] residue labeling in g_rmsf Arunima Shilpi
[gmx-users] issue in replica exchange Michael Shirts
[gmx-users] issue in replica exchange Michael Shirts
[gmx-users] issue in replica exchange Michael Shirts
[gmx-users] issue in replica exchange Michael Shirts
[gmx-users] Fwd: Static compilation of gromacs Alexey Shvetsov
[gmx-users] Fwd: Static compilation of gromacs Alexey Shvetsov
[gmx-users] configuration/installation of gromacs-4.6.1 on heterogeneous cluster Martin Siegert
[gmx-users] configuration/installation of gromacs-4.6.1 on heterogeneous cluster Martin Siegert
[gmx-users] lincs errors late in simulation Joe Smerdon
[gmx-users] Re: where can be obtain circled lipids bilayer? (Björn Sommer) Björn Sommer
[gmx-users] Fw: probability from COM of micelle David van der Spoel
[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD David van der Spoel
[gmx-users] choice of forcefield David van der Spoel
[gmx-users] Re: choice of force field -reg David van der Spoel
[gmx-users] Dihedral Autocorrelation Function with negative values David van der Spoel
[gmx-users] Error after trjconf processing James Starlight
[gmx-users] Error after trjconf processing James Starlight
[gmx-users] Error after trjconf processing James Starlight
[gmx-users] Error after trjconf processing James Starlight
[gmx-users] Umbrella sampling's equilibration runs James Starlight
[gmx-users] Error after trjconf processing James Starlight
[gmx-users] xtc2dcd conversion James Starlight
[gmx-users] GPU-based workstation James Starlight
[gmx-users] Re: GPU-based workstation James Starlight
[gmx-users] GPU-based workstation James Starlight
Aw: Re: [gmx-users] GPU-based workstation James Starlight
[gmx-users] GPU-based workstation James Starlight
[gmx-users] Re: GPU-based workstation James Starlight
[gmx-users] GPU-based workstation James Starlight
[gmx-users] Vritual Sites and simulation time-step James Starlight
[gmx-users] Vritual Sites and simulation time-step James Starlight
[gmx-users] Vritual Sites and simulation time-step James Starlight
[gmx-users] namd2gmx topology conversion tool James Starlight
[gmx-users] Vritual Sites and simulation time-step James Starlight
[gmx-users] Nose-Hover chains for membrane protein simulation James Starlight
[gmx-users] FW: Myristic Acid Simulations Natalie Stephenson
[gmx-users] Charmm27 potential energies. Eric Stokes
[gmx-users] where can be obtain circled lipids bilayer? Jesper Sørensen
[gmx-users] where can be obtain circled lipids bilayer? Jesper Sørensen
[gmx-users] constant protonation state MD Jesper Sørensen
[gmx-users] constant protonation state MD Jesper Sørensen
[gmx-users] question about energygrps Jesper Sørensen
[gmx-users] Using many index file in one command line Terry
[gmx-users] Effect of pressure coupling frequency on gpu simulations Trayder Thomas
[gmx-users] Cut off setting Wende Tian
[gmx-users] Equilibrated system explodes after ~200ns? Trayder
[gmx-users] Effect of pressure coupling frequency on gpu simulations Trayder
[gmx-users] Re: Effect of pressure coupling frequency on gpu simulations Trayder
[gmx-users] On Decane coordinate file Naga Rajesh Tummala
[gmx-users] Re: initial temperature ridiculously high Valentina
[gmx-users] Re: g_x2top help Valentina
[gmx-users] Fwd: Rycaert-Bellemans function Marcelo Vanean
[gmx-users] Charge groups Marcelo Vanean
[gmx-users] cudaStreamSynchronize failed Cintia C. Vequi-Suplicy
[gmx-users] AMBER99 P450 heme topology Parker de Waal
[gmx-users] Domain Decomposition Error Parker de Waal
[gmx-users] where can be obtain circled lipids bilayer? Mirco Wahab
[gmx-users] Fwd: Static compilation of gromacs Mirco Wahab
[gmx-users] About Compilation error in gromacs 4.6 Mirco Wahab
[gmx-users] About Warnings in Mdrun Mirco Wahab
[gmx-users] RE: keeping water (entirely) out of the bilayer core Dallas Warren
[gmx-users] equilibration of the simulated systems Dallas Warren
[gmx-users] Fwd: Rycaert-Bellemans function Dallas Warren
[gmx-users] Large number of solvent molecules Dallas Warren
[gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field Dallas Warren
[gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field Dallas Warren
[gmx-users] PCA_RMS fluctuation per residue? Tsjerk Wassenaar
[gmx-users] residue labeling in g_rmsf Tsjerk Wassenaar
[gmx-users] mdrun outputs incorrect resnames Tsjerk Wassenaar
[gmx-users] .GRO Formatting Tsjerk Wassenaar
[gmx-users] Overlap between PC motions Tsjerk Wassenaar
[gmx-users] Overlap between PC motions Tsjerk Wassenaar
[gmx-users] Can Gromacs do oscillatory shear? Yutian Yang
[gmx-users] RE: gmx-users Digest, Vol 109, Issue 112 Yutian Yang
[gmx-users] g_msd problem Yutian Yang
[gmx-users] Velocity autocorrelation problem Yutian Yang
[gmx-users] Re: MSD and frequency of writing trajectories Yutian Yang
[gmx-users] Entropy Yulian
[gmx-users] Problem importing PDB to Gromacs Jernej Zidar
[gmx-users] Compiling GROMACS w CUDA 5.0 problem Jernej Zidar
[gmx-users] Fw: probability from COM of micelle mohammad agha
[gmx-users] probability from COM of micelle mohammad agha
[gmx-users] probability from COM of micelle mohammad agha
[gmx-users] probability from COM of micelle mohammad agha
[gmx-users] g_dist mohammad agha
[gmx-users] g_dist mohammad agha
[gmx-users] g_dist mohammad agha
[gmx-users] g_dist mohammad agha
[gmx-users] Fw: probability from COM of micelle mohammad agha
[gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be aixintiankong
[gmx-users] simulate a protein covalently binding with a organic molecule aixintiankong
[gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be aixintiankong
[gmx-users] simulate a protein covalently binding with a organic molecule aixintiankong
[gmx-users] MODIFYING GROMACS' bondfree.c brighter
[gmx-users] Re: About Potential energy calculation cyberjhon
[gmx-users] Have your ever got a real NVE simulation (good energy conservation) in gromacs? cyberjhon
[gmx-users] Re: Have your ever got a real NVE simulation (good energy conservation) in gromacs? cyberjhon
[gmx-users] grommp problem in gromacs 4.6.1 cyberjhon
[gmx-users] arrange the atoms in sphere dariush
[gmx-users] oxidized lipid - Peroxidated lipid dariush
[gmx-users] Expanding a .top file to have all connection information davidjrosenman
[gmx-users] g_msd problem rajat desikan
[gmx-users] Re: MSD and frequency of writing trajectories rajat desikan
[gmx-users] Re: MSD and frequency of writing trajectories rajat desikan
[gmx-users] arrange the atoms in sphere rajat desikan
[gmx-users] GROMACS 4.6.2 released rajat desikan
[gmx-users] About Potential energy calculation jhon michael espinosa duran
[gmx-users] Gromacs mpi error while running REMD bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] Re: REMD average acceptance ratio bharat gupta
[gmx-users] Re: REMD average acceptance ratio bharat gupta
[gmx-users] REMD average acceptance ratio bharat gupta
[gmx-users] REMD average acceptance ratio bharat gupta
[gmx-users] REMD analysis bharat gupta
[Spam:*****] [gmx-users] REMD analysis bharat gupta
[Spam:*****] [gmx-users] REMD analysis bharat gupta
[Spam:*****] [gmx-users] REMD analysis bharat gupta
[Spam:*****] [gmx-users] REMD analysis bharat gupta
[gmx-users] REMD analysis bharat gupta
[Spam:*****] [gmx-users] REMD analysis bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] Re: REMD analysis bharat gupta
[gmx-users] GBSA problem susanta haldar
[gmx-users] constant protonation state MD baptista at itqb.unl.pt
[gmx-users] how to add angle_restraints and dihedral_restraints for atoms belonging to two different molecules jnsong
[gmx-users] is there extra parameters in .mdp file for running successful angle_restraints? jnsong
[gmx-users] Inconsistent results in different clusters and cores tarak karmakar
[gmx-users] Inconsistent results in different clusters and cores tarak karmakar
[gmx-users] Problem importing PDB to Gromacs tarak karmakar
[gmx-users] Inconsistent results in different clusters and cores tarak karmakar
[gmx-users] Inconsistent results in different clusters and cores tarak karmakar
[gmx-users] Fwd: electrostatic potential map tarak karmakar
[gmx-users] Fwd: electrostatic potential map tarak karmakar
[gmx-users] 1-4 scaling factor tarak karmakar
[gmx-users] Inconsistent results in different clusters and cores tarak karmakar
[gmx-users] Inconsistent results in different clusters and cores tarak karmakar
[gmx-users] charmm in gromacs cut-offs tarak karmakar
[gmx-users] charmm in gromacs cut-offs tarak karmakar
[gmx-users] charmm in gromacs cut-offs tarak karmakar
[gmx-users] charmm in gromacs cut-offs tarak karmakar
[gmx-users] charmm in gromacs cut-offs tarak karmakar
[gmx-users] charmm in gromacs cut-offs tarak karmakar
[gmx-users] cut-offs tarak karmakar
[gmx-users] Inconsistent results in different clusters and cores tarak karmakar
[gmx-users] Inconsistent results in different clusters and cores tarak karmakar
[gmx-users] Inconsistent results in different clusters and cores tarak karmakar
[gmx-users] Inconsistent results in different clusters and cores tarak karmakar
[gmx-users] charmm in gromacs cut-offs tarak karmakar
[gmx-users] OPLS-AA to CHARMM conversion in gromacs ffnonbonded.itp tarak karmakar
[gmx-users] Re: OPLS-AA to CHARMM conversion in gromacs ffnonbonded.itp tarak karmakar
[gmx-users] Problems installing 4.6.1 on Mac 10.8.3 khandelia
[gmx-users] g_sgangle and P atoms on the DNA molecule. anna_gromacs at libero.it
[gmx-users] g_sgangle and P atoms on the DNA molecule. anna_gromacs at libero.it
[gmx-users] range angle calculated by g_sgangle battistia at libero.it
R: Re: [gmx-users] range angle calculated by g_sgangle battistia at libero.it
[gmx-users] bending angle between 2 vectors defined by cm of groups of atoms battistia at libero.it
[gmx-users] Re: Free energy of solvation about peptide maggin
[gmx-users] Free energy of solvation's .mdp of peptide maggin
[gmx-users] NVT and NPT for small peptide maggin
[gmx-users] tpr of extend simulation maggin
[gmx-users] g_hbond maggin
[gmx-users] Re: NVT and NPT for small peptide maggin
[gmx-users] Re: g_hbond maggin
[gmx-users] Re: residue labeling in g_rmsf maggin
[gmx-users] Re: g_hbond maggin
[gmx-users] Re: FEP of ion binding protein maggin
[gmx-users] REMD:subsystems are not compatible. suhani nagpal
[gmx-users] REMD:subsystems are not compatible. suhani nagpal
[gmx-users] constant protonation state MD shahid nayeem
[gmx-users] constant protonation state MD shahid nayeem
[gmx-users] constant protonation state MD shahid nayeem
[gmx-users] constant protonation state MD shahid nayeem
[gmx-users] constant protonation state MD shahid nayeem
[gmx-users] Re: local pressure ohsOllila
[gmx-users] Conceptual question about the computational scaling of MD francesco oteri
[gmx-users] Re: REMD analysis francesco oteri
[gmx-users] minimization of particular residue/atom gromacs query
[gmx-users] minimization of particular residue/atom gromacs query
[gmx-users] correct traj for water/ions density gromacs query
[gmx-users] Re: correct traj for water/ions density gromacs query
[gmx-users] correct traj for water/ions density gromacs query
[gmx-users] numbering after 99999SOL gromacs query
[gmx-users] numbering after 99999SOL gromacs query
[gmx-users] numbering after 99999SOL gromacs query
[gmx-users] coupling issue gromacs query
[gmx-users] umbrella sampling for two polymer interaction gromacs query
[gmx-users] umbrella sampling for two polymer interaction gromacs query
[gmx-users] Re: umbrella sampling for two polymer interaction gromacs query
[gmx-users] Re: umbrella sampling for two polymer interaction gromacs query
Aw: [gmx-users] Proteins with ADP & ATP cofactors lloyd riggs
Aw: Re: [gmx-users] Proteins with ADP & ATP cofactors lloyd riggs
Aw: Re: [gmx-users] PCA_RMS fluctuation per residue? lloyd riggs
Aw: Re: [gmx-users] air-water-interface lloyd riggs
Aw: Re: [gmx-users] Expanding a .top file to have all connection information lloyd riggs
Aw: [gmx-users] C6 & C12 parameters for non-bonded interactions using tables lloyd riggs
Aw: [gmx-users] GPU-based workstation lloyd riggs
Aw: Re: [gmx-users] the "-dist" flag of g_hbond tool lloyd riggs
Aw: [gmx-users] GPU-based workstation lloyd riggs
Aw: Re: [gmx-users] GPU-based workstation lloyd riggs
Aw: Re: Re: [gmx-users] GPU-based workstation lloyd riggs
Aw: Re: Re: [gmx-users] GPU-based workstation lloyd riggs
Aw: Re: Re: [gmx-users] GPU-based workstation lloyd riggs
Aw: [gmx-users] umbrella sampling for two polymer interaction lloyd riggs
Aw: [gmx-users] Free energy calculation: merge the topology of 2 molecules lloyd riggs
[gmx-users] Fwd: electrostatic potential map andrew ritchie
[gmx-users] AMBER99sb-ILDN charges for C-terminus GLY with COOH capping santanu roy
[gmx-users] Problem with Installing Gromacs 4.6.1 with GPU salehi
[gmx-users] choice of forcefield massimo sandal
[gmx-users] Re: choice of force field -reg massimo sandal
[gmx-users] About Warnings and Note in Production MD vidhya sankar
[gmx-users] Notes from Production MD vidhya sankar
[gmx-users] About CNT wrapped by Cyclic peptide vidhya sankar
[gmx-users] About CNT cyclic PEptide vidhya sankar
[gmx-users] About Production MD run error vidhya sankar
[gmx-users] About Compilation error in gromacs 4.6 vidhya sankar
[gmx-users] About Warnings in Mdrun vidhya sankar
[gmx-users] About Compiler Option vidhya sankar
[gmx-users] surrounding a peptide by ions of magnesium Mohan maruthi sena
[gmx-users] surrounding a peptide by ions of magnesium Mohan maruthi sena
[gmx-users] How to choose bd_fric value in brownian dynamics Mohan maruthi sena
[gmx-users] How to choose bd_fric value in brownian dynamics Mohan maruthi sena
[gmx-users] Re: NVT and NPT for small peptide shika
[gmx-users] Re: REMD analysis simula_460
[gmx-users] Re: REMD analysis simula_460
[gmx-users] Temperature for individual amino acid residues bipin singh
[gmx-users] Temperature for individual amino acid residues bipin singh
[gmx-users] Temperature for individual amino acid residues bipin singh
[gmx-users] Proteins with ADP & ATP cofactors micheal j twin
[gmx-users] Proteins with ADP & ATP cofactors micheal j twin
[gmx-users] Fwd: yakovenko_a at ukr.net
[gmx-users] FW: yakovenko_a at ukr.net
[gmx-users] FW: yakovenko_a at ukr.net
[gmx-users] COM coordinate fix L.Liu at utwente.nl
[gmx-users] the details about g_density vigaryang
[gmx-users] the details about g_density vigaryang
[gmx-users] Gromacs for Non biological systems Jeya vimalan
[gmx-users] mdrun generate a lot of files with # mu xiaojia
[gmx-users] Re: How to restrain dihedral angles to reserve the tacticity? xiaowu759
[gmx-users] Questions regarding REMD Statistics Kong xq
[gmx-users] REMD Statistics Kong xq
[gmx-users] REMD Statistics Kong xq
[gmx-users] rotation of a ligand Ahmet yıldırım
[gmx-users] Re: rotation of a ligand Ahmet yıldırım
[gmx-users] A problem with do_dssp command zugunder
[gmx-users] Re: A problem with do_dssp command zugunder
[gmx-users] Re: A problem with do_dssp command zugunder
[gmx-users] Re: A problem with do_dssp command zugunder
[gmx-users] Re: A problem with do_dssp command zugunder
[gmx-users] Re: A problem with do_dssp command zugunder
[gmx-users] Re: A problem with do_dssp command zugunder
[gmx-users] Re: A problem with do_dssp command zugunder
[gmx-users] Re: A problem with do_dssp command zugunder
[gmx-users] Re: A problem with do_dssp command zugunder
[gmx-users] ion mutation in FEP SEMRAN İPEK
[gmx-users] Fwd: Static compilation of gromacs Андрей Гончар
[gmx-users] Fwd: Static compilation of gromacs Андрей Гончар
[gmx-users] Mdrun_mip efficiency Андрей Гончар
[gmx-users] Mdrun_mip efficiency Андрей Гончар
[gmx-users] Continue simulation from the specific time Андрей Гончар
[gmx-users] Continue simulation from the specific time Андрей Гончар
[gmx-users] Re:Using virtual site 라지브간디
[gmx-users] Re: Using virtual site 라지브간디
[gmx-users] PCA_RMS fluctuation per residue? 라지브간디
[gmx-users] PCA_RMS fluctuation per residue? 라지브간디

Last message date: Fri May 31 23:59:01 CEST 2013
Archived on: Thu Nov 14 12:14:19 CET 2013

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