April 2013 Archives by author

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Starting: Mon Apr 1 00:03:52 CEST 2013
Ending: Tue Apr 30 22:19:56 CEST 2013
Messages: 1014

[gmx-users] mdrun -rdd and -dds flag manara r. (rm16g09)
[gmx-users] Martini with PME, temp two low ABEL Stephane 175950
[gmx-users] RE : gmx-users Digest, Vol 108, Issue 154 ABEL Stephane 175950
[gmx-users] Martini with PME, temp two low ABEL Stephane 175950
[gmx-users] Martini with PME, temp two low ABEL Stephane 175950
[gmx-users] Re: Martini with PME, temp two low ABEL Stephane 175950
[gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950) ABEL Stephane 175950
[gmx-users] RE: Martini with PME, temp two low ABEL Stephane 175950
[gmx-users] RE: Martini with PME, temp two low ABEL Stephane 175950
[gmx-users] problem with REMD Shine A
[gmx-users] doubt in remd Shine A
[gmx-users] gromacs 4.6.1 on win7? Mark Abraham
[gmx-users] Re: gromacs 4.6.1 on win7? Mark Abraham
[gmx-users] Multiple runs with a single mdp file Mark Abraham
[gmx-users] replica exchange data in cpt file Mark Abraham
[gmx-users] H2U residue Mark Abraham
[gmx-users] Re: help with chromophore of a GFP Mark Abraham
[gmx-users] REMD temperature spacing formula Mark Abraham
[gmx-users] installating GROMACS on windows 7 64 bit system Mark Abraham
[gmx-users] New python package with gromacs support Mark Abraham
[gmx-users] replica exchange data in cpt file Mark Abraham
[gmx-users] nstxout, nstvout, . . . Mark Abraham
[gmx-users] RDF output has no data Mark Abraham
[gmx-users] nstxout, nstvout, . . . Mark Abraham
[gmx-users] amber99 with berger's lipids Mark Abraham
[gmx-users] Topology file-residue unknown Mark Abraham
[gmx-users] Simulating a large system Mark Abraham
[gmx-users] Re: Simulating a large system Mark Abraham
[gmx-users] Restarting a REMD simulation (error) Mark Abraham
[gmx-users] Improve performance Mark Abraham
[gmx-users] Restarting a REMD simulation (error) Mark Abraham
[gmx-users] Re: RDF output has no data Mark Abraham
[gmx-users] Maximum protein size for REMD? Mark Abraham
[gmx-users] Re: Re: Re: Re: help with chromophore of a GFP Mark Abraham
[gmx-users] doubt in remd Mark Abraham
[gmx-users] amber99 with berger's lipids Mark Abraham
[gmx-users] GPU performance Mark Abraham
[gmx-users] General conceptual question about advantage of GPUs Mark Abraham
[gmx-users] Re: Re: Re: help with a chromophore of GFP Mark Abraham
[gmx-users] Re: Re: Re: Re: help with a chromophore of GFP Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] Re: RDF output has no data Mark Abraham
[gmx-users] About gpu Mark Abraham
[gmx-users] Maximum protein size for REMD? Mark Abraham
[gmx-users] Re: Re: help: load imbalance Mark Abraham
[gmx-users] About parallelization Mark Abraham
[gmx-users] vdw-modifier in GROMACS 4.6.1. Mark Abraham
[gmx-users] gmx4.6.1 performance problem "CPU acceleration: NONE" Mark Abraham
[gmx-users] Memory requirement to store trajectories Mark Abraham
[gmx-users] fake atoms creation and causes a 1-4 interaction between atoms warning Mark Abraham
[gmx-users] Simulation of the HEM-containing proteins Mark Abraham
[gmx-users] updating amberff.03 files Mark Abraham
[gmx-users] updating amberff.03 files Mark Abraham
[gmx-users] gmx4.6.1 performance problem "CPU acceleration: NONE" Mark Abraham
[gmx-users] updating amberff.03 files Mark Abraham
[gmx-users] cygwin_mpi_gmx installation Mark Abraham
[gmx-users] Dihedral angle PCA Mark Abraham
[gmx-users] Fwd: [Fwd: QM MM modification] Mark Abraham
[gmx-users] install gromacs 4.6.1 on 64bit Windows 7 cygwin Mark Abraham
[gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093) Mark Abraham
[gmx-users] Building Single and Double Precision in 4.6.1? Mark Abraham
[gmx-users] trjcat set timestep/amb2gmx? Mark Abraham
[gmx-users] trjcat set timestep/amb2gmx? Mark Abraham
[gmx-users] new CHARMM-GUI output not supported? Mark Abraham
[gmx-users] ffnonbonded value of charmm to charmm27 ff Mark Abraham
[gmx-users] Autocorrelation of C-N Mark Abraham
[gmx-users] Running simulation over openmpi in rsh Mark Abraham
[gmx-users] Different energy using the identical tpr file Mark Abraham
[gmx-users] GROMACS 4.5.7 released Mark Abraham
[gmx-users] Re: Different energy using the identical tpr file Mark Abraham
[gmx-users] different checkpoint from remd after crash Mark Abraham
[gmx-users] Re: [gmx-announce] GROMACS 4.5.7 released Mark Abraham
[gmx-users] Re: [gmx-announce] GROMACS 4.5.7 released Mark Abraham
[gmx-users] gmx in parallel Mark Abraham
[gmx-users] Fwd: Selecting the temperature distribution Mark Abraham
[gmx-users] Problem with gromacs in Cluster Mark Abraham
[gmx-users] issue in replica exchange Mark Abraham
[gmx-users] Fwd: Selecting the temperature distribution Mark Abraham
[gmx-users] Fwd: amber03 force field Mark Abraham
[gmx-users] Manual installation of new analysis tool Mark Abraham
[gmx-users] issue in replica exchange Mark Abraham
[gmx-users] GPU efficiency question Mark Abraham
[gmx-users] Re: Genion cannot read from input Mark Abraham
[gmx-users] How to rescue trr trajectory when two or more corrupted frames exist Mark Abraham
[gmx-users] Using virtual site Mark Abraham
[gmx-users] Re: GROMACS 4.5.7 released Mark Abraham
Aw: [gmx-users] Order of atoms in topology Mark Abraham
Aw: [gmx-users] Order of atoms in topology Mark Abraham
[gmx-users] genion doesn't work in 4.6.1? Abhishek Acharya
[gmx-users] genion doesn't work in 4.6.1? Abhishek Acharya
[gmx-users] ATP/Mg+2 parameters Abhishek Acharya
[gmx-users] Applying periodic boundary conditions in energy minimization Abhinav Agrawal
[gmx-users] Using two integrators in energy minimization Abhinav Agrawal
[gmx-users] Re: Applying periodic boundary conditions in energy minimization Abhinav Agrawal
[gmx-users] Re:Applying periodic boundary conditions in energy minimization Abhinav Agrawal
[gmx-users] Re: Re: Re: Applying periodic boundary conditions in energy minimization Abhinav Agrawal
[gmx-users] Issuing multiple commands simultaneously Abhinav Agrawal
[gmx-users] 4.6.1 support double precision GPU now? Albert
[gmx-users] questions about umbrella sampling tutorial Albert
[gmx-users] Intel compiling failed Albert
[gmx-users] Intel compiling failed Albert
[gmx-users] Intel compiling failed Albert
[gmx-users] problem of umbrella sampling pulling code Albert
[gmx-users] genion doesn't work in 4.6.1? Albert
[gmx-users] genion doesn't work in 4.6.1? Albert
[gmx-users] where is gromos54a7_lipid FF? Albert
[gmx-users] amber99 with berger's lipids Albert
[gmx-users] fail to pull Albert
[gmx-users] fail to pull Albert
[gmx-users] fail to pull Albert
[gmx-users] fail to pull Albert
[gmx-users] can we use GPU from another machine for calculation? Albert
[gmx-users] how to extract last frame? Albert
[gmx-users] shall we add ions in FEP? Albert
[gmx-users] why no. of atoms doesn't match? Albert
[gmx-users] why no. of atoms doesn't match? Albert
[gmx-users] why no. of atoms doesn't match? Albert
[gmx-users] new CHARMM-GUI output not supported? Albert
[gmx-users] new CHARMM-GUI output not supported? Albert
[gmx-users] why minimization stop so fast Albert
[gmx-users] why minimization stop so fast Albert
[gmx-users] why minimization stop so fast Albert
[gmx-users] new CHARMM-GUI output not supported? Albert
[gmx-users] Re: why minimization stop so fast Albert
[gmx-users] how to direct log file correctly? Albert
[gmx-users] Announcement: new version of GridMAT-MD available Albert
[gmx-users] how to direct log file correctly? Albert
[gmx-users] GROMACS 4.6 with GPU acceleration (double Albert
[gmx-users] using CHARMM force field for organic molecule Albert
[gmx-users] compile error Albert
[gmx-users] compile error Albert
[gmx-users] GPU efficiency question Albert
[gmx-users] _gpu_id failed Albert
[gmx-users] can we use large timestep for membrane GPU simulation? Albert
[gmx-users] why files are so large? Albert
[gmx-users] why files are so large? Albert
[gmx-users] GPU job often stopped Albert
[gmx-users] GPU job often stopped Albert
[gmx-users] GPU job often stopped Albert
[gmx-users] GPU job often stopped Albert
[gmx-users] GPU job often stopped Albert
[gmx-users] Amber&Buckingham Ali Alizadeh
[gmx-users] Amber&Buckingham Ali Alizadeh
Fw: [gmx-users] water molecule can not be settled Anirban
[gmx-users] MD with Xenon Anirban
[gmx-users] Lipid membrane partially broken and create huge voids after NVT Anirban
[gmx-users] Block average RMSD using g_analyze Anirban
[gmx-users] port to Gromacs of recent CHARMM FF changes (C37) Guilherme Menegon Arantes
[gmx-users] water molecule can not be settled Shima Arasteh
Fw: [gmx-users] water molecule can not be settled Shima Arasteh
Fw: [gmx-users] water molecule can not be settled Shima Arasteh
Fw: [gmx-users] water molecule can not be settled Shima Arasteh
[gmx-users] unstable system Shima Arasteh
[gmx-users] unstable system Shima Arasteh
[gmx-users] unstable system Shima Arasteh
[gmx-users] unstable system Shima Arasteh
[gmx-users] unstable system Shima Arasteh
[gmx-users] unstable system Shima Arasteh
[gmx-users] unstable system Shima Arasteh
[gmx-users] unstable system Shima Arasteh
[gmx-users] unstable system Shima Arasteh
[gmx-users] renumtop script Shima Arasteh
[gmx-users] renumtop script Shima Arasteh
[gmx-users] umbrella sampling tutorial Shima Arasteh
[gmx-users] GROMACS 4.6v - Myrinet2000 Hrachya Astsatryan
[gmx-users] gmx 4.6 mpi installation through openmpi? Hrachya Astsatryan
[gmx-users] Different energy using the identical tpr file Fahimeh Baftizadeh
[gmx-users] Re: Different energy using the identical tpr file Fahimeh Baftizadeh
[gmx-users] Re: Different energy using the identical tpr file Fahimeh Baftizadeh
[gmx-users] Is it possible to pull 2 different groups with respect to a third group as reference? Saikat Banerjee
[gmx-users] vdw-modifier in GROMACS 4.6.1. Chrisostomos Batistakis
[gmx-users] vdw-modifier in GROMACS 4.6.1. Chrisostomos Batistakis
[gmx-users] How to rescue trr trajectory when two or more corrupted frames exist Ioannis Beis
[gmx-users] RE: How to rescue trr trajectory when two or more corrupted frames exist Ioannis Beis
[gmx-users] genbox box size problem Alexander Björling
[gmx-users] GPU performance Benjamin Bobay
[gmx-users] GPU performance Benjamin Bobay
[gmx-users] (4/7/2013 3:33:29 PM) Acoot Brett
[gmx-users] Setting virtual sites ? Broadbent, Richard
[gmx-users] mdrun -rdd and -dds flag Broadbent, Richard
[gmx-users] switching and shifting in GMX 4.6 on GPUs Broadbent, Richard
[gmx-users] Problem with gromacs in Cluster Richard Broadbent
[gmx-users] Doubt about the Gromacs versions Richard Broadbent
[gmx-users] Genion cannot read from input Nathan Bullock
[gmx-users] Re: Genion cannot read from input Nathan Bullock
[gmx-users] Re: Genion cannot read from input Nathan Bullock
[gmx-users] Re: Genion cannot read from input Nathan Bullock
[gmx-users] Gromacs Building Blocks Lara Bunte
[gmx-users] How to have two proteins randomly positioned and oriented in the box Zhikun Cai
[gmx-users] How to have two proteins randomly positioned and oriented in the box Zhikun Cai
[gmx-users] Inhomogeneity of water molecules insertion into the box Zhikun Cai
[gmx-users] gmx 4.6 mpi installation through openmpi? Zhikun Cai
[gmx-users] Viscosity calculation using cos_acceleration James Cannon
[gmx-users] Re: Viscosity calculation using cos_acceleration James Cannon
Fw: [gmx-users] water molecule can not be settled Luis Felipe Pineda de Castro
[gmx-users] genion doesn't work in 4.6.1? Luis Felipe Pineda de Castro
[gmx-users] Re: density profile Dr. Vitaly Chaban
[gmx-users] Re: density profile Dr. Vitaly Chaban
[gmx-users] Re: density profile Dr. Vitaly Chaban
[gmx-users] Re: density profile Dr. Vitaly Chaban
[gmx-users] Re: density profile Dr. Vitaly Chaban
[gmx-users] Re: density profile Dr. Vitaly Chaban
[gmx-users] Re: density profile Dr. Vitaly Chaban
[gmx-users] Re: g_density: Segmentation fault Dr. Vitaly Chaban
[gmx-users] Re: density profile Dr. Vitaly Chaban
[gmx-users] Re: surface tension-crash at step 0 Dr. Vitaly Chaban
[gmx-users] Re: surface tension-crash at step 0 Dr. Vitaly Chaban
[gmx-users] Re: surface tension-crash at step 0 Dr. Vitaly Chaban
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L Dr. Vitaly Chaban
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L Dr. Vitaly Chaban
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L Dr. Vitaly Chaban
[gmx-users] Re: Simulating a large system Dr. Vitaly Chaban
[gmx-users] Re: can we use GPU from another machine for calculation? Dr. Vitaly Chaban
[gmx-users] Re: Simulating a large system Dr. Vitaly Chaban
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L Dr. Vitaly Chaban
[gmx-users] Re: RDF output has no data Dr. Vitaly Chaban
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L Dr. Vitaly Chaban
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L Dr. Vitaly Chaban
[gmx-users] Re: RDF output has no data Dr. Vitaly Chaban
[gmx-users] Re: RDF output has no data Dr. Vitaly Chaban
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L Dr. Vitaly Chaban
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L Dr. Vitaly Chaban
[gmx-users] Re: Lipid membrane partially broken and create huge voids Dr. Vitaly Chaban
[gmx-users] Re: Viscosity calculation using cos_acceleration Dr. Vitaly Chaban
[gmx-users] Re: Water spreading on graphene! Dr. Vitaly Chaban
[gmx-users] using CHARMM force field for organic molecule Dr. Vitaly Chaban
[gmx-users] Martini with PME, temp two low Dr. Vitaly Chaban
[gmx-users] Problem with gromacs in Cluster Dr. Vitaly Chaban
[gmx-users] Martini with PME, temp two low Dr. Vitaly Chaban
[gmx-users] position restrained energy minimization Wu Chaofu
[gmx-users] Fwd: rmsd Preeti Choudhary
[gmx-users] Fwd: rmsd Preeti Choudhary
[gmx-users] nstxout, nstvout, . . . Chandan Choudhury
[gmx-users] 1-4 interactions Liron Cohen
[gmx-users] 1-4 interactions Liron Cohen
[gmx-users] (no subject) Liron Cohen
[gmx-users] 1-4 interactions warning Liron Cohen
[gmx-users] doubt in remd Simone Conti
[gmx-users] ATP/Mg+2 parameters João M. Damas
[gmx-users] General conceptual question about advantage of GPUs Andrew DeYoung
[gmx-users] Re: General conceptual question about advantage of GPUs Andrew DeYoung
[gmx-users] Including polarizability by a Drude oscillator or the shell model Andrew DeYoung
[gmx-users] Re: Only Ligand(Without Receptor) MD Simulation with solvent(other than water.) Baptiste Demoulin
[gmx-users] Re: Only Ligand(Without Receptor) MD Simulation with solvent(other than water.) Baptiste Demoulin
[gmx-users] Gromos 54A8 forcefield Rajat Desikan
[gmx-users] g_hbond Nilesh Dhumal
[gmx-users] g_hbond Nilesh Dhumal
[gmx-users] autocorrelation function of hydrogen bond : g_hbond Nilesh Dhumal
[gmx-users] autocorrelation function of hydrogen bond : g_hbond Nilesh Dhumal
[gmx-users] autocorrelation function of hydrogen bond : g_hbond Nilesh Dhumal
[gmx-users] g_hbond : autocorrelation funciton Nilesh Dhumal
[gmx-users] g_hbond : autocorrelation funciton Nilesh Dhumal
[gmx-users] Cut off problem with protein in water-vacuum-water layers Nuria Cirauqui Diaz
[gmx-users] Problem with gromacs in Cluster Sainitin Donakonda
[gmx-users] Issue with RMSD profile Sainitin Donakonda
[gmx-users] pulling direction in Umbrella sampling Kshatresh Dutta Dubey
[gmx-users] Re: density profile Elisabeth
[gmx-users] Re: density profile Elisabeth
[gmx-users] g_density: Segmentation fault Elisabeth
[gmx-users] g_density: Segmentation fault Elisabeth
[gmx-users] surface tension Elisabeth
[gmx-users] surface tension Elisabeth
[gmx-users] surface tension-crash at step 0 Elisabeth
[gmx-users] Re: surface tension-crash at step 0 Elisabeth
[gmx-users] Re: surface tension-crash at step 0 Elisabeth
[gmx-users] speed of sound in liquid Elisabeth
[gmx-users] help with g_hydorder and g_polystat Emmanuel, Alaina
[gmx-users] Dihedral angle PCA Thomas Evangelidis
[gmx-users] Dihedral angle PCA Thomas Evangelidis
[gmx-users] gmx in parallel Ayesha Fatima
[gmx-users] Re: [gmx-developers] My system stops in the middle of a minimization Anton Feenstra
[gmx-users] how to use the trjconv -sep and -skip to get the individual file Francesco
[gmx-users] Problem with gromacs in Cluster Francesco
[gmx-users] amber03 force field Elisa Frezza
[gmx-users] Fwd: amber03 force field Elisa Frezza
[gmx-users] Fwd: amber03 force field Elisa Frezza
[gmx-users] genion doesn't work in 4.6.1? Warren Gallin
[gmx-users] pdb2gmx for small molecules? Warren Gallin
[gmx-users] Re: Genion cannot read from input Warren Gallin
[gmx-users] xpm2ps issue Neha Gandhi
[gmx-users] H2U residue Juan Antonio Raygoza Garay
[gmx-users] Restarting minimization Juan Antonio Raygoza Garay
[gmx-users] Simulating a large system Juan Antonio Raygoza Garay
[gmx-users] Re: Simulating a large system Juan Antonio Raygoza Garay
[gmx-users] FEP + Ham. REMD Yuri Garmay
[gmx-users] Re: FEP + Ham. REMD Yuri Garmay
[gmx-users] the value of pressure is negative Nur Syafiqah Abdul Ghani
[gmx-users] system explode when running in MD production Nur Syafiqah Abdul Ghani
[gmx-users] system explode when running in MD production Nur Syafiqah Abdul Ghani
[gmx-users] Membrane Simulation Giuseppe
[gmx-users] Re: Membrane Simulation Giuseppe
[gmx-users] Re: Membrane Simulation Giuseppe
[gmx-users] Gromacs 4.6 GPU on Nvidia 250 GTS? Hovakim Grabski
[gmx-users] request Group Gro
[gmx-users] Building Single and Double Precision in 4.6.1? Mike Hanby
[gmx-users] Building Single and Double Precision in 4.6.1? Mike Hanby
[gmx-users] Building Single and Double Precision in 4.6.1? Mike Hanby
[gmx-users] replica exchange data in cpt file João Henriques
[gmx-users] replica exchange data in cpt file João Henriques
[gmx-users] replica exchange data in cpt file João Henriques
[gmx-users] Restarting a REMD simulation (error) João Henriques
[gmx-users] Restarting a REMD simulation (error) João Henriques
[gmx-users] Differences between 4.5.5 and 4.6.2-dev? Berk Hess
[gmx-users] How to use multiple nodes, each with 2 CPUs and 3 GPUs Berk Hess
[gmx-users] Differences between 4.5.5 and 4.6.2-dev? Berk Hess
[gmx-users] 2d-pmf with plumed gromacs Yuan Hu
[gmx-users] Re: Viscosity calculation using cos_acceleration James
[gmx-users] Re: Manual installation of new analysis tool Christoph Junghans
[gmx-users] gmx 4.6.1, Expanded ensemble: weird balancing factors Joakim Jämbeck
[gmx-users] On initialization of the molecules Bao Kai
[gmx-users] On Decane coordinate file Bao Kai
[gmx-users] Differences between 4.5.5 and 4.6.2-dev? Stefan Kesselheim
[gmx-users] Differences between 4.5.5 and 4.6.2-dev? Stefan Kesselheim
[gmx-users] Differences between 4.5.5 and 4.6.2-dev? Stefan Kesselheim
[gmx-users] updating amberff.03 files Laura Kingsley
[gmx-users] updating amberff.03 files Laura Kingsley
[gmx-users] updating amberff.03 files Laura Kingsley
[gmx-users] 4.6.1 support double precision GPU now? Carsten Kutzner
[gmx-users] Intel compiling failed Carsten Kutzner
[gmx-users] Intel compiling failed Carsten Kutzner
[gmx-users] Intel compiling failed Carsten Kutzner
[gmx-users] Free Energy Calculations in Gromacs HANNIBAL LECTER
[gmx-users] Free Energy Calculations in Gromacs HANNIBAL LECTER
[gmx-users] New python package with gromacs support Gabriele Lanaro
[gmx-users] where is gromos54a7_lipid FF? Reid Van Lehn
[gmx-users] How to have two proteins randomly positioned and oriented in the box Justin Lemkul
[gmx-users] Fwd: clustering based on side-chain conformations Justin Lemkul
[gmx-users] Inhomogeneity of water molecules insertion into the box Justin Lemkul
[gmx-users] gromacs 4.6.1 on win7? Justin Lemkul
[gmx-users] Re: density profile Justin Lemkul
[gmx-users] About CNT-CYCLIC PETIDE constructio Justin Lemkul
[gmx-users] editconf- pdb to gro format Justin Lemkul
[gmx-users] editconf- pdb to gro format Justin Lemkul
[gmx-users] MD stop,systme not equilibrium Justin Lemkul
[gmx-users] Fwd: clustering based on side-chain conformations Justin Lemkul
[gmx-users] Maximum force on atom and unpacked lipids Justin Lemkul
[gmx-users] Position restraints Justin Lemkul
[gmx-users] REMD general protocol ... Justin Lemkul
[gmx-users] REMD general protocol ... Justin Lemkul
[gmx-users] REMD general protocol ... Justin Lemkul
[gmx-users] Re: Salt bridge Calculations Justin Lemkul
[gmx-users] g_density: Segmentation fault Justin Lemkul
[gmx-users] g_density: Segmentation fault Justin Lemkul
[gmx-users] Re: Salt bridge Calculations Justin Lemkul
[gmx-users] the value of pressure is negative Justin Lemkul
[gmx-users] RE: Position restraints Justin Lemkul
[gmx-users] water models tip3p.gro and spce.gro Justin Lemkul
[gmx-users] 1-4 interactions Justin Lemkul
[gmx-users] 1-4 interactions Justin Lemkul
[gmx-users] Simulation of the HEM-containing proteins Justin Lemkul
[gmx-users] Simulation of the HEM-containing proteins Justin Lemkul
[gmx-users] Applying periodic boundary conditions in energy minimization Justin Lemkul
[gmx-users] Using two integrators in energy minimization Justin Lemkul
[gmx-users] Salt bridge observation Justin Lemkul
[gmx-users] g_dipoles: "index group is not a set of the whole molecules" Justin Lemkul
[gmx-users] Re: cannot read frames out from trr files Justin Lemkul
[gmx-users] Re: Applying periodic boundary conditions in energy minimization Justin Lemkul
[gmx-users] Re: cannot read frames out from trr files Justin Lemkul
[gmx-users] Problem with generating topology file for OPLS force field for membrane protein simulation Justin Lemkul
[gmx-users] Salt bridge observation Justin Lemkul
[gmx-users] About Free energy surface .....g_sas Justin Lemkul
[gmx-users] Salt bridge observation Justin Lemkul
[gmx-users] Salt bridge observation Justin Lemkul
[gmx-users] About Free energy surface .....g_sas Justin Lemkul
[gmx-users] About Free energy surface .....g_sas Justin Lemkul
[gmx-users] Topology file-residue unknown Justin Lemkul
[gmx-users] Topology file-residue unknown Justin Lemkul
[gmx-users] Intel compiling failed Justin Lemkul
[gmx-users] questions about umbrella sampling tutorial Justin Lemkul
[gmx-users] HIS in charmm27.ff Justin Lemkul
[gmx-users] water molecule can not be settled Justin Lemkul
Fw: [gmx-users] water molecule can not be settled Justin Lemkul
Fw: [gmx-users] water molecule can not be settled Justin Lemkul
Fw: [gmx-users] water molecule can not be settled Justin Lemkul
[gmx-users] genion doesn't work in 4.6.1? Justin Lemkul
[gmx-users] genion doesn't work in 4.6.1? Justin Lemkul
[gmx-users] problem of umbrella sampling pulling code Justin Lemkul
[gmx-users] RDF output has no data Justin Lemkul
[gmx-users] genion doesn't work in 4.6.1? Justin Lemkul
[gmx-users] About PP/PME Justin Lemkul
[gmx-users] Fwd: Improve performance Justin Lemkul
[gmx-users] problem with REMD Justin Lemkul
[gmx-users] amber99 with berger's lipids Justin Lemkul
[gmx-users] amber99 with berger's lipids Justin Lemkul
[gmx-users] Restarting minimization Justin Lemkul
[gmx-users] fail to pull Justin Lemkul
[gmx-users] Adding second solvent Justin Lemkul
[gmx-users] Improve performance Justin Lemkul
[gmx-users] Gromacs 4.6 GPU on Nvidia 250 GTS? Justin Lemkul
[gmx-users] unstable system Justin Lemkul
[gmx-users] fail to pull Justin Lemkul
[gmx-users] fail to pull Justin Lemkul
[gmx-users] unstable system Justin Lemkul
[gmx-users] Simulating a large system Justin Lemkul
[gmx-users] GROMACS 4.6v - Myrinet2000 Justin Lemkul
[gmx-users] Re: Simulating a large system Justin Lemkul
[gmx-users] Calculation of Temperature of Cluster Justin Lemkul
[gmx-users] amber99 with berger's lipids Justin Lemkul
[gmx-users] Calculation of Temperature of Cluster Justin Lemkul
[gmx-users] Calculation of Temperature of Cluster Justin Lemkul
[gmx-users] Calculation of Temperature of Cluster Justin Lemkul
[gmx-users] Quadro FX 5800 incompatible? Justin Lemkul
[gmx-users] can I change atom position after x steps Justin Lemkul
[gmx-users] installing CGenFF in Gromacs Justin Lemkul
[gmx-users] About k20 Justin Lemkul
[gmx-users] a gro file at the end of simulation Justin Lemkul
[gmx-users] Obtain frames from every one ps Justin Lemkul
[gmx-users] how to split the disulfide bonds in CYSH? Justin Lemkul
[gmx-users] reading Hydrogens from an itp file Justin Lemkul
[gmx-users] Gromacs Building Blocks Justin Lemkul
[gmx-users] autocorrelation function of hydrogen bond : g_hbond Justin Lemkul
[gmx-users] General conceptual question about advantage of GPUs Justin Lemkul
[gmx-users] Re: General conceptual question about advantage of GPUs Justin Lemkul
[gmx-users] PTFE polymer chain Justin Lemkul
[gmx-users] PTFE polymer chain Justin Lemkul
[gmx-users] amber99 with berger's lipids Justin Lemkul
[gmx-users] About Topology construction for CNT wrapped by Cyclic peptide Justin Lemkul
[gmx-users] 1-4 interactions warning Justin Lemkul
[gmx-users] converting the normal hormonic potential bond to Fourth power potential bond? Justin Lemkul
[gmx-users] Fwd: rmsd Justin Lemkul
[gmx-users] help: load imbalance Justin Lemkul
[gmx-users] Re: Re: help: load imbalance (Justin Lemkul) Justin Lemkul
[gmx-users] tip5p water model:Atomtype LP1 not found Justin Lemkul
[gmx-users] Charges for calculation of Coulomb interaction Justin Lemkul
[gmx-users] mdrun -rdd and -dds flag Justin Lemkul
[gmx-users] tip5p water model:Atomtype LP1 not found Justin Lemkul
[gmx-users] tip5p water model:Atomtype LP1 not found Justin Lemkul
[gmx-users] tip5p water model:Atomtype LP1 not found Justin Lemkul
[gmx-users] tip5p water model:Atomtype LP1 not found Justin Lemkul
[gmx-users] pbc problem Justin Lemkul
[gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093) Justin Lemkul
[gmx-users] About Merging topologies Justin Lemkul
[gmx-users] On initialization of the molecules Justin Lemkul
[gmx-users] how to extract individual frames from trajectory Justin Lemkul
[gmx-users] pulling direction in Umbrella sampling Justin Lemkul
[gmx-users] Estimations of the drug's affinity Justin Lemkul
[gmx-users] Estimations of the drug's affinity Justin Lemkul
[gmx-users] binding energy calculation when appear this error: no distance restraints in topology Justin Lemkul
[gmx-users] binding energy calculation when appear this error: no distance restraints in topology Justin Lemkul
[gmx-users] g_hbond : autocorrelation funciton Justin Lemkul
[gmx-users] g_hbond : autocorrelation funciton Justin Lemkul
[gmx-users] pbc problem Justin Lemkul
[gmx-users] binding energy calculation when appear this error: no distance restraints in topology Justin Lemkul
[gmx-users] Issue with domain decomposition between v4.5.5 and 4.6.1 Justin Lemkul
[gmx-users] specbond detection Justin Lemkul
[gmx-users] Pulling along dihedral angle as the reaction coordinate Justin Lemkul
[gmx-users] g_covar with individual masses Justin Lemkul
[gmx-users] Fwd: Problem with generating topology file for OPLS force field for membrane protein simulation Justin Lemkul
[gmx-users] tip5p water model:Atomtype LP1 not found Justin Lemkul
[gmx-users] tip5p water model:Atomtype LP1 not found Justin Lemkul
[gmx-users] tip5p water model:Atomtype LP1 not found Justin Lemkul
[gmx-users] Peptide distance matrix Justin Lemkul
[gmx-users] Peptide distance matrix Justin Lemkul
[gmx-users] Peptide distance matrix Justin Lemkul
[gmx-users] Peptide distance matrix Justin Lemkul
[gmx-users] Peptide distance matrix Justin Lemkul
[gmx-users] trjcat set timestep/amb2gmx? Justin Lemkul
[gmx-users] mpi enabled gmx 4.5 Justin Lemkul
[gmx-users] why no. of atoms doesn't match? Justin Lemkul
Subject: Re: [gmx-users] Issue with domain decomposition between v4.5.5 and 4.6.1 Justin Lemkul
[gmx-users] trjcat set timestep/amb2gmx? Justin Lemkul
[gmx-users] On Decane coordinate file Justin Lemkul
[gmx-users] request Justin Lemkul
[gmx-users] Issuing multiple commands simultaneously Justin Lemkul
[gmx-users] why minimization stop so fast Justin Lemkul
[gmx-users] why minimization stop so fast Justin Lemkul
[gmx-users] why minimization stop so fast Justin Lemkul
[gmx-users] g_analyze error bar Justin Lemkul
[gmx-users] new CHARMM-GUI output not supported? Justin Lemkul
[gmx-users] g_analyze error bar Justin Lemkul
[gmx-users] how to simulate the transformation of loop Justin Lemkul
[gmx-users] Problem with OPLS parameters (too few parameters on line) Justin Lemkul
[gmx-users] position restrained energy minimization Justin Lemkul
[gmx-users] Simulations box type Justin Lemkul
[gmx-users] trjcat set timestep/amb2gmx? Justin Lemkul
[gmx-users] how to direct log file correctly? Justin Lemkul
[gmx-users] interaction energy Justin Lemkul
[gmx-users] installing gromacs-4.6.1 with CMake Justin Lemkul
[gmx-users] Regarding top2psf script Justin Lemkul
[gmx-users] Applying a Lennard-Jones Gauss potential function for TIP5P water Justin Lemkul
[gmx-users] Re: Applying a Lennard-Jones Gauss potential function for TIP5P water Justin Lemkul
[gmx-users] How to fix interfacial tension in NPT Justin Lemkul
[gmx-users] Membrane Simulation Justin Lemkul
[gmx-users] Free energy on GPU? Justin Lemkul
[gmx-users] pdb2gmx for small molecules? Justin Lemkul
[gmx-users] Announcement: new version of GridMAT-MD available Justin Lemkul
[gmx-users] A beginner's question ... Justin Lemkul
[gmx-users] specbonds not shwon Justin Lemkul
[gmx-users] Re: Membrane Simulation Justin Lemkul
[gmx-users] how to extract individual frames from trajectory Justin Lemkul
[gmx-users] specbonds are not taken by gromos force field? Justin Lemkul
[gmx-users] unstable system Justin Lemkul
[gmx-users] unstable system Justin Lemkul
[gmx-users] unstable system Justin Lemkul
[gmx-users] unstable system Justin Lemkul
[gmx-users] unstable system Justin Lemkul
[gmx-users] Cut off problem with protein in water-vacuum-water layers Justin Lemkul
[gmx-users] unstable system Justin Lemkul
[gmx-users] I can't figure out what is wrong with my .gro Justin Lemkul
[gmx-users] trjconv center problem Justin Lemkul
[gmx-users] Re: trjconv center problem Justin Lemkul
[gmx-users] Re: trjconv center problem Justin Lemkul
[gmx-users] Re: trjconv center problem Justin Lemkul
[gmx-users] how to direct log file correctly? Justin Lemkul
[gmx-users] Only Ligand(Without Receptor) MD Simulation with solvent(other than water.) Justin Lemkul
[gmx-users] renumtop script Justin Lemkul
[gmx-users] align the 1000 frames from MD.xtc Justin Lemkul
[gmx-users] keeping the position and coordinates at the same when extarct frames Justin Lemkul
[gmx-users] extracting the multiple frames (pdb files) in align Justin Lemkul
[gmx-users] Re:gmx-users Digest, Vol 108, Issue 130 Justin Lemkul
[gmx-users] Re:Re:gmx-users Digest, Vol 108, Issue 130 Justin Lemkul
[gmx-users] Membrane simulations Justin Lemkul
[gmx-users] adjust charge Justin Lemkul
[gmx-users] Amber&Buckingham Justin Lemkul
[gmx-users] system explode when running in MD production Justin Lemkul
[gmx-users] system explode when running in MD production Justin Lemkul
[gmx-users] How to fix interfacial tension in NPT Justin Lemkul
[gmx-users] Re: Only Ligand(Without Receptor) MD Simulation with solvent(other than water.) Justin Lemkul
[gmx-users] How to fix interfacial tension in NPT Justin Lemkul
[gmx-users] using CHARMM force field for organic molecule Justin Lemkul
[gmx-users] using CHARMM force field for organic molecule Justin Lemkul
[gmx-users] using CHARMM force field for organic molecule Justin Lemkul
[gmx-users] Interaction across PBC Justin Lemkul
[gmx-users] Problem with the simulation of C2160 (fullerene) Justin Lemkul
[gmx-users] Interaction across PBC Justin Lemkul
[gmx-users] which tool returns vectors? Justin Lemkul
[gmx-users] specbonds are not taken by gromos force field? Justin Lemkul
[gmx-users] Re: protein-ligand interactions in charmm force field Justin Lemkul
[gmx-users] Fwd: Selecting the temperature distribution Justin Lemkul
[gmx-users] RMSD from the average structure Justin Lemkul
[gmx-users] Re: Membrane Simulation Justin Lemkul
[gmx-users] Re: protein-ligand interactions in charmm force field Justin Lemkul
[gmx-users] Problem with gromacs in Cluster Justin Lemkul
[gmx-users] Martini with PME, temp two low Justin Lemkul
[gmx-users] Doubt about the Gromacs versions Justin Lemkul
[gmx-users] How to fix interfacial tension in NPT Justin Lemkul
[gmx-users] g_rmsf Analysis. Justin Lemkul
[gmx-users] free energy of system Justin Lemkul
[gmx-users] xpm2ps issue Justin Lemkul
[gmx-users] Issue with RMSD profile Justin Lemkul
[gmx-users] mdrun on GPU Justin Lemkul
[gmx-users] _gpu_id failed Justin Lemkul
[gmx-users] Gromos 54A8 forcefield Justin Lemkul
[gmx-users] Calculation of helicity of alpha-helix which is parallel to X-axis Justin Lemkul
[gmx-users] Genion cannot read from input Justin Lemkul
[gmx-users] Genion cannot read from input Justin Lemkul
[gmx-users] Re: Genion cannot read from input Justin Lemkul
[gmx-users] about command do_dssp Justin Lemkul
[gmx-users] can we use large timestep for membrane GPU simulation? Justin Lemkul
[gmx-users] why files are so large? Justin Lemkul
[gmx-users] why files are so large? Justin Lemkul
[gmx-users] GPU job often stopped Justin Lemkul
[gmx-users] genbox box size problem Justin Lemkul
[gmx-users] umbrella sampling tutorial Justin Lemkul
Aw: [gmx-users] Order of atoms in topology Justin Lemkul
Aw: [gmx-users] Order of atoms in topology Justin Lemkul
Aw: [gmx-users] Order of atoms in topology Justin Lemkul
[gmx-users] Fatal error: Failed to lock: md.log. Function not implemented. Justin Lemkul
[gmx-users] Error in pdb2gmx Justin Lemkul
[gmx-users] no such moleculetype Justin Lemkul
[gmx-users] Error in pdb2gmx Justin Lemkul
[gmx-users] Umbrella sampling's equilibration runs Justin Lemkul
[gmx-users] help with g_hydorder and g_polystat Justin Lemkul
Aw: [gmx-users] Re: how is the pulling force measured Justin Lemkul
[gmx-users] Umbrella sampling's equilibration runs Justin Lemkul
[gmx-users] stable branch using git Justin Lemkul
[gmx-users] fail to pull Jianguo Li
[gmx-users] Re: Hamiltonian replica exchange umbrella sampling with gmx 4.6 Dejun Lin
[gmx-users] Re: Hamiltonian replica exchange umbrella sampling with gmx 4.6 Dejun Lin
[gmx-users] Free webinar on Gromacs-4.6 and GPUs together with Nvidia Erik Lindahl
[gmx-users] Lipids and virtual site in 4.6.1 Bastien Loubet
[gmx-users] Re: Lipids and virtual site in 4.6.1 Bastien Loubet
[gmx-users] install gromacs 4.6.1 on 64bit Windows 7 cygwin Hua Lu
[gmx-users] sc-coul and sc-r-power Magnus Lundborg
[gmx-users] Error in make install "no valid ELF RPATH". Cray XE6m Daniel Adriano Silva M
[gmx-users] Salt bridge Calculations Kavyashree M
[gmx-users] Re: Salt bridge Calculations Kavyashree M
[gmx-users] Re: Salt bridge Calculations Kavyashree M
[gmx-users] Re: Salt bridge Calculations Kavyashree M
[gmx-users] Re: Salt bridge Calculations Kavyashree M
[gmx-users] Salt bridge observation Kavyashree M
[gmx-users] Salt bridge observation Kavyashree M
[gmx-users] Salt bridge observation Kavyashree M
[gmx-users] Salt bridge observation Kavyashree M
[gmx-users] REMD temperature spacing formula Nikunj Maheshwari
[gmx-users] REMD temperature spacing formula Nikunj Maheshwari
[gmx-users] doubt in remd Nikunj Maheshwari
[gmx-users] Maximum protein size for REMD? Nikunj Maheshwari
[gmx-users] Maximum protein size for REMD? Nikunj Maheshwari
[gmx-users] Maximum protein size for REMD? Nikunj Maheshwari
[gmx-users] Maximum protein size for REMD? Nikunj Maheshwari
[gmx-users] Error in pdb2gmx Nikunj Maheshwari
[gmx-users] Error in pdb2gmx Nikunj Maheshwari
[gmx-users] Re: help with chromophore of a GFP Anna Marabotti
[gmx-users] Re: Re: Re: Re: help with chromophore of a GFP Anna Marabotti
[gmx-users] Re: Re: Re: help with a chromophore of GFP Anna Marabotti
[gmx-users] Re: Re: Re: Re: help with a chromophore of GFP Anna Marabotti
[gmx-users] REMD general protocol ... Erik Marklund
[gmx-users] g_hbond Erik Marklund
[gmx-users] COM restraint similar to distance restraints Erik Marklund
[gmx-users] -vsite in Umbrella sampling Erik Marklund
[gmx-users] doubt in remd Erik Marklund
[gmx-users] Maximum protein size for REMD? Erik Marklund
[gmx-users] Maximum protein size for REMD? Erik Marklund
[gmx-users] autocorrelation function of hydrogen bond : g_hbond Erik Marklund
[gmx-users] any other criteria for h-bond? Erik Marklund
[gmx-users] RMSD from the average structure Erik Marklund
[gmx-users] Memory requirement to store trajectories Sikandar Mashayak
[gmx-users] stable branch using git Sikandar Mashayak
[gmx-users] Compiling Gromacs Maciej Masłyk
[gmx-users] Funnel Metadynamics using PLUMED/Gromacs Davide Mercadante
[gmx-users] g_rmsf Analysis. Vivek Modi
[gmx-users] Membrane simulations Sun Moon
[gmx-users] Multiple runs with a single mdp file Tim Moore
[gmx-users] surface tension André Farias de Moura
[gmx-users] Re: SMD - reproducibility André Farias de Moura
[gmx-users] g_select: selection file problem Teemu Murtola
[gmx-users] Structure file for di atmoic molecule Juliette N.
[gmx-users] editconf- pdb to gro format Juliette N.
[gmx-users] editconf- pdb to gro format Juliette N.
[gmx-users] Topology file-residue unknown Juliette N.
[gmx-users] Topology file-residue unknown Juliette N.
[gmx-users] Topology file-residue unknown Juliette N.
[gmx-users] Adding second solvent Juliette N.
[gmx-users] mdrun on GPU Juliette N.
[gmx-users] Calculation of Temperature of Cluster Rasoul Nasiri
[gmx-users] Calculation of Temperature of Cluster Rasoul Nasiri
[gmx-users] Calculation of Temperature of Cluster Rasoul Nasiri
[gmx-users] Calculation of Temperature of Cluster Rasoul Nasiri
[gmx-users] amber99 with berger's lipids Christopher Neale
[gmx-users] position restraint and umbrella potential contribution to the virial Christopher Neale
[gmx-users] How to use multiple nodes, each with 2 CPUs and 3 GPUs Christopher Neale
[gmx-users] How to use multiple nodes, each with 2 CPUs and 3 GPUs Christopher Neale
[gmx-users] Re: How to use multiple nodes, each with 2 CPUs and 3 GPUs Christopher Neale
[gmx-users] How to rescue trr trajectory when two or more corrupted frames exist Christopher Neale
[gmx-users] How to rescue trr trajectory when two or more corrupted frames exist Christopher Neale
[gmx-users] autocorrelation function of hydrogen bond : g_hbond Paulo Netz
[gmx-users] Peptide distance matrix Steven Neumann
[gmx-users] Peptide distance matrix Steven Neumann
[gmx-users] Peptide distance matrix Steven Neumann
[gmx-users] Peptide distance matrix Steven Neumann
[gmx-users] Peptide distance matrix Steven Neumann
[gmx-users] Peptide distance matrix Steven Neumann
[gmx-users] trjcat set timestep/amb2gmx? Steven Neumann
[gmx-users] trjcat set timestep/amb2gmx? Steven Neumann
[gmx-users] trjcat set timestep/amb2gmx? Steven Neumann
[gmx-users] run.mdp on 4.6-gpu Steven Neumann
[gmx-users] Autocorrelation of C-N Steven Neumann
[gmx-users] trjcat set timestep/amb2gmx? Steven Neumann
[gmx-users] trjcat set timestep/amb2gmx? Steven Neumann
[gmx-users] Interaction across PBC Steven Neumann
[gmx-users] Autocorrelation of C-N Steven Neumann
[gmx-users] Interaction across PBC Steven Neumann
[gmx-users] Interaction across PBC Steven Neumann
[gmx-users] which tool returns vectors? Steven Neumann
[gmx-users] Interaction across PBC Steven Neumann
[gmx-users] SMD - reproducibility Steven Neumann
[gmx-users] Re: SMD - reproducibility Steven Neumann
[gmx-users] Re: SMD - reproducibility Steven Neumann
[gmx-users] Illegal instruction (core dumped) - trjconv Steven Neumann
[gmx-users] Re: Illegal instruction (core dumped) - trjconv Steven Neumann
[gmx-users] pbc problem Kieu Thu Nguyen
[gmx-users] pbc problem Kieu Thu Nguyen
[gmx-users] Re: why minimization stop so fast Brad Van Oosten
[gmx-users] trjconv center problem Brad Van Oosten
[gmx-users] Re: trjconv center problem Brad Van Oosten
[gmx-users] Re: trjconv center problem Brad Van Oosten
[gmx-users] Re: trjconv center problem Brad Van Oosten
[gmx-users] Re: trjconv center problem Brad Van Oosten
[gmx-users] About the data loss due to Disk space problem PAVAN PAYGHAN
[gmx-users] ATP/Mg+2 parameters George Patargias
[gmx-users] ATP/Mg+2 parameters George Patargias
[gmx-users] FW: No subject Wholly Peach
[gmx-users] Re: [gmx-announce] GROMACS 4.5.7 released Luís Pereira
[gmx-users] issue in replica exchange XAvier Periole
[gmx-users] Martini with PME, temp two low XAvier Periole
[gmx-users] Martini with PME, temp two low XAvier Periole
[gmx-users] issue in replica exchange XAvier Periole
[gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950) XAvier Periole
[gmx-users] RE: Martini with PME, temp two low XAvier Periole
[gmx-users] Questions about the MFFA boundery implementation of Gromacs? XAvier Periole
[gmx-users] genbox box size problem XAvier Periole
[gmx-users] Re: genbox box size problem XAvier Periole
[gmx-users] (no subject) Za Pour
[gmx-users] a gro file at the end of simulation Za Pour
[gmx-users] gmx 4.6 mpi installation through openmpi? Szilárd Páll
[gmx-users] GROMACS 4.6v - Myrinet2000 Szilárd Páll
[gmx-users] GPU performance Szilárd Páll
[gmx-users] GPU performance Szilárd Páll
[gmx-users] General conceptual question about advantage of GPUs Szilárd Páll
[gmx-users] About 4.6.1 Szilárd Páll
[gmx-users] help: load imbalance Szilárd Páll
[gmx-users] General conceptual question about advantage of GPUs Szilárd Páll
[gmx-users] K20 test Szilárd Páll
[gmx-users] cygwin_mpi_gmx installation Szilárd Páll
[gmx-users] Re: cygwin_mpi_gmx installation Szilárd Páll
[gmx-users] Re: cygwin_mpi_gmx installation Szilárd Páll
[gmx-users] Re: cygwin_mpi_gmx installation Szilárd Páll
[gmx-users] Building Single and Double Precision in 4.6.1? Szilárd Páll
[gmx-users] Error in make install "no valid ELF RPATH". Cray XE6m Szilárd Páll
[gmx-users] GROMACS 4.6 with GPU acceleration (double presion) Szilárd Páll
[gmx-users] GROMACS 4.6 with GPU acceleration (double Szilárd Páll
[gmx-users] How to use multiple nodes, each with 2 CPUs and 3 GPUs Szilárd Páll
[gmx-users] compile error Szilárd Páll
[gmx-users] Re: Illegal instruction (core dumped) - trjconv Szilárd Páll
[gmx-users] GPU job often stopped Szilárd Páll
[gmx-users] GPU job often stopped Szilárd Páll
[gmx-users] GPU job often stopped Szilárd Páll
[gmx-users] GPU job often stopped Szilárd Páll
[gmx-users] Re: Glutamate to Alanine Mutation Sai Kumar Ramadugu
[gmx-users] Re: Glutamate to Alanine Mutation Sai Kumar Ramadugu
[gmx-users] A beginner's question ... Venkatesh Ramakrishnan
[gmx-users] Applying a Lennard-Jones Gauss potential function for TIP5P water Andrish Reddy
[gmx-users] Re: Applying a Lennard-Jones Gauss potential function for TIP5P water Andrish Reddy
[gmx-users] Re: Different energy using the identical tpr file Andrish Reddy
[gmx-users] Radial density calculation Venkat Reddy
[gmx-users] Radial density calculation Venkat Reddy
[gmx-users] RDF output has no data Venkat Reddy
[gmx-users] RDF output has no data Venkat Reddy
[gmx-users] RDF output has no data Venkat Reddy
[gmx-users] Re: RDF output has no data Venkat Reddy
[gmx-users] Re: RDF output has no data Venkat Reddy
[gmx-users] Re: RDF output has no data Venkat Reddy
[gmx-users] Re: RDF output has no data Venkat Reddy
[gmx-users] Plotting data from g_spatial Venkat Reddy
[gmx-users] Regarding top2psf script Venkat Reddy
[gmx-users] Manual installation of new analysis tool Venkat Reddy
[gmx-users] Re: Manual installation of new analysis tool Venkat Reddy
[gmx-users] Re: Manual installation of new analysis tool Venkat Reddy
[gmx-users] Normal Mode Analysis -- Expected Output Bryan Roessler
[gmx-users] Re: Bryan Roessler
[gmx-users] Normal Mode Analysis -- Expected Output Bryan Roessler
[gmx-users] How to fix interfacial tension in NPT Souilem Safa
[gmx-users] How to fix interfacial tension in NPT Souilem Safa
[gmx-users] How to fix interfacial tension in NPT Souilem Safa
[gmx-users] How to fix interfacial tension in NPT Souilem Safa
[gmx-users] How to fix interfacial tension in NPT Souilem Safa
[gmx-users] How to fix interfacial tension in NPT Souilem Safa
[gmx-users] interfacial-tension-interface simulation Souilem Safa
[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD Reza Salari
[gmx-users] Calculation of helicity of alpha-helix which is parallel to X-axis Sujit Sarkar
[gmx-users] Re: Water spreading on graphene! Sapna Sarupria
[gmx-users] Re: Water spreading on graphene! Sapna Sarupria
[gmx-users] Re: Water spreading on graphene! Sapna Sarupria
[gmx-users] Re: fail to pull Thomas Schlesier
[gmx-users] Re: Is it possible to pull 2 different groups with respect to a third group as reference? Thomas Schlesier
[gmx-users] Re: gmx-users Digest, Vol 108, Issue 165 Thomas Schlesier
[gmx-users] Re: SMD - reproducibility Thomas Schlesier
[gmx-users] Re: SMD - reproducibility Thomas Schlesier
[gmx-users] Re: how is the pulling force measured Thomas Schlesier
[gmx-users] gromacs 4.6.1 on win7? Roland Schulz
[gmx-users] adjust charge Arunima Shilpi
[gmx-users] Re: gmx-users Digest, Vol 108, Issue 140 Arunima Shilpi
[gmx-users] Re: Hamiltonian replica exchange umbrella sampling with gmx 4.6 Michael Shirts
[gmx-users] Free Energy Calculations in Gromacs Michael Shirts
[gmx-users] Lipids and virtual site in 4.6.1 David van der Spoel
[gmx-users] Lipids and virtual site in 4.6.1 David van der Spoel
[gmx-users] GROMACS 4.6 with GPU acceleration (double presion) David van der Spoel
[gmx-users] Dihedral angle PCA David van der Spoel
[gmx-users] Normal Mode Analysis -- Expected Output David van der Spoel
[gmx-users] Memory requirement to store trajectories David van der Spoel
[gmx-users] Re: thermal conductivity,specific heat,enthalpy David van der Spoel
[gmx-users] pdb2gmx for small molecules? David van der Spoel
[gmx-users] Water spreading on graphene! David van der Spoel
[gmx-users] Re: Water spreading on graphene! David van der Spoel
[gmx-users] Re: Water spreading on graphene! David van der Spoel
[gmx-users] Including polarizability by a Drude oscillator or the shell model David van der Spoel
[gmx-users] Obtain frames from every one ps Ashalatha Sreshty
[gmx-users] Simulation of the HEM-containing proteins James Starlight
[gmx-users] Simulation of the HEM-containing proteins James Starlight
[gmx-users] Simulation of the HEM-containing proteins James Starlight
[gmx-users] Simulation of the HEM-containing proteins James Starlight
[gmx-users] Simulation of the HEM-containing proteins James Starlight
[gmx-users] amber99 with berger's lipids James Starlight
[gmx-users] amber99 with berger's lipids James Starlight
[gmx-users] amber99 with berger's lipids James Starlight
[gmx-users] amber99 with berger's lipids James Starlight
[gmx-users] amber99 with berger's lipids James Starlight
[gmx-users] Simulation of the HEM-containing proteins James Starlight
[gmx-users] Simulation of the HEM-containing proteins James Starlight
[gmx-users] Simulation of the HEM-containing proteins James Starlight
[gmx-users] Simulation of the HEM-containing proteins James Starlight
[gmx-users] Estimations of the drug's affinity James Starlight
[gmx-users] Estimations of the drug's affinity James Starlight
[gmx-users] Re: protein-ligand interactions in charmm force field James Starlight
[gmx-users] Re: protein-ligand interactions in charmm force field James Starlight
[gmx-users] Umbrella sampling's equilibration runs James Starlight
[gmx-users] Umbrella sampling's equilibration runs James Starlight
[gmx-users] GROMACS 4.6 with GPU acceleration (double presion) Mikhail Stukan
[gmx-users] GROMACS 4.6 with GPU acceleration (double Mikhail Stukan
[gmx-users] MD with Xenon Divya Sunil
[gmx-users] g_dipoles: "index group is not a set of the whole molecules" Oleksandr Sushko
[gmx-users] Re: g_dipoles: "index group is not a set of the whole molecules" Oleksandr Sushko
[gmx-users] g_select: selection file problem Oleksandr Sushko
[gmx-users] Re: g_select: selection file problem Oleksandr Sushko
[gmx-users] switching and shifting in GMX 4.6 on GPUs Jesper Sørensen
[gmx-users] switching and shifting in GMX 4.6 on GPUs Jesper Sørensen
[gmx-users] ATP/Mg+2 parameters Jesper Sørensen
[gmx-users] Linear Interaction Energy Method (LIE) Rajitha Tatikonda
[gmx-users] Issue with domain decomposition between v4.5.5 and 4.6.1 Stephanie Teich-McGoldrick
Subject: Re: [gmx-users] Issue with domain decomposition between v4.5.5 and 4.6.1 Stephanie Teich-McGoldrick
[gmx-users] Computer configuration Cintia C. Vequi-Suplicy
Good News for Cygwin users (was: Re: [gmx-users] gromacs 4.6.1 on win7?) Mirco Wahab
[gmx-users] Re: cygwin_mpi_gmx installation Mirco Wahab
[gmx-users] g_covar with individual masses Sebastian Waltz
[gmx-users] gmx4.6.1 performance problem "CPU acceleration: NONE" Yorquant Wang
[gmx-users] gmx4.6.1 performance problem "CPU acceleration: NONE" Yorquant Wang
[gmx-users] Radial density calculation Dallas Warren
[gmx-users] plots in gromacs Dallas Warren
[gmx-users] Applying periodic boundary conditions in energy minimization Tsjerk Wassenaar
[gmx-users] Re: Applying periodic boundary conditions in energy minimization Tsjerk Wassenaar
[gmx-users] Re: Re: Re: Applying periodic boundary conditions in energy minimization Tsjerk Wassenaar
[gmx-users] how to extract last frame? Tsjerk Wassenaar
[gmx-users] Peptide distance matrix Tsjerk Wassenaar
[gmx-users] Block average RMSD using g_analyze Tsjerk Wassenaar
[gmx-users] RMSD from the average structure Tsjerk Wassenaar
[gmx-users] gmx 4.6 mpi installation through openmpi? Zhikun
[gmx-users] g_enemat problem & suggestion Jernej Zidar
[gmx-users] g_enemat problem & suggestion Jernej Zidar
[gmx-users] MD stop,systme not equilibrium aixintiankong
[gmx-users] how to split the disulfide bonds in CYSH? aixintiankong
[gmx-users] how to extract individual frames from trajectory aixintiankong
[gmx-users] how to simulate the transformation of loop aixintiankong
[gmx-users] how to extract individual frames from trajectory aixintiankong
[gmx-users] how to use the trjconv -sep and -skip to get the individual file aixintiankong
[gmx-users] align the 1000 frames from MD.xtc aixintiankong
[gmx-users] keeping the position and coordinates at the same when extarct frames aixintiankong
[gmx-users] extracting the multiple frames (pdb files) in align aixintiankong
[gmx-users] Re:gmx-users Digest, Vol 108, Issue 130 aixintiankong
[gmx-users] Re:gmx-users Digest, Vol 108, Issue 130 aixintiankong
[gmx-users] Re:Re:gmx-users Digest, Vol 108, Issue 130 aixintiankong
[gmx-users] using CHARMM force field for organic molecule aixintiankong
[gmx-users] how to build the loop of protein model aixintiankong
[gmx-users] about command do_dssp aixintiankong
[gmx-users] Re: genbox box size problem alex.bjorling
[gmx-users] Re: how is the pulling force measured alex.bjorling
[gmx-users] Re: how is the pulling force measured alex.bjorling
[gmx-users] Energetics of ion and subatrate binding sites ram bio
[gmx-users] Quadro FX 5800 incompatible? bv07ay
[gmx-users] muliple GPU crash bv07ay
[gmx-users] Re: why no. of atoms doesn't match? bv07ay
[gmx-users] Fwd: clustering based on side-chain conformations anu chandra
[gmx-users] Fwd: clustering based on side-chain conformations anu chandra
[gmx-users] Dihedral angle PCA anu chandra
[gmx-users] Dihedral angle PCA anu chandra
[gmx-users] Tabulated non-bonded potentials - regd ramesh cheerla
[gmx-users] REMD general protocol ... rama david
[gmx-users] REMD general protocol ... rama david
[gmx-users] REMD general protocol ... rama david
[gmx-users] REMD general protocol ... rama david
[gmx-users] About Free energy surface .....g_sas rama david
[gmx-users] REMD temperature spacing formula rama david
[gmx-users] About Free energy surface .....g_sas rama david
[gmx-users] About Free energy surface .....g_sas rama david
[gmx-users] About Free energy surface .....g_sas rama david
[gmx-users] Problem with the simulation of C2160 (fullerene) jhon michael espinosa duran
[gmx-users] nstxout, nstvout, . . . dina dusti
[gmx-users] nstxout, nstvout, . . . dina dusti
[gmx-users] nstxout, nstvout, . . . dina dusti
[gmx-users] How to set the sigma and epsilon for Cu2+ in OPLS-AA/L force field fantasticqhl
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L fantasticqhl
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L fantasticqhl
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L fantasticqhl
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L fantasticqhl
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L fantasticqhl
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L fantasticqhl
[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L fantasticqhl
[gmx-users] Charges for calculation of Coulomb interaction fantasticqhl
[gmx-users] Re: dihre_fc option in new 4.6.1 version grant
[gmx-users] Re: Selecting the temperature distribution bharat gupta
[gmx-users] Fwd: Selecting the temperature distribution bharat gupta
[gmx-users] Fwd: Selecting the temperature distribution bharat gupta
[gmx-users] Fwd: Selecting the temperature distribution bharat gupta
[gmx-users] Fwd: Selecting the temperature distribution bharat gupta
[gmx-users] Fwd: Selecting the temperature distribution bharat gupta
[gmx-users] Fwd: Selecting the temperature distribution bharat gupta
[gmx-users] Fwd: Selecting the temperature distribution bharat gupta
[gmx-users] Fwd: Selecting the temperature distribution bharat gupta
[gmx-users] installating GROMACS on windows 7 64 bit system imsharmanitin
[gmx-users] Dihedral angle PCA baptista at itqb.unl.pt
[gmx-users] installing CGenFF in Gromacs jbermudez
[gmx-users] Re: installing CGenFF in Gromacs jbermudez
[gmx-users] free energy of system sarah k
[gmx-users] Re: free energy of system sarah k
[gmx-users] lysine side chain shrinking tarak karmakar
[gmx-users] how to build the loop of protein model tarak karmakar
[gmx-users] plots in gromacs tarak karmakar
[gmx-users] any other criteria for h-bond? kim2811
[gmx-users] how is the pulling force measured kim2811
[gmx-users] Re: how is the pulling force measured kim2811
[gmx-users] Re: SMD - reproducibility rajendra kumar
[gmx-users] plots in gromacs pragna lakshmi
[gmx-users] Re: plots in gromacs pragna lakshmi
[gmx-users] PTFE polymer chain luanadelorenzo at libero.it
R: Re: Re: [gmx-users] PTFE polymer chain luanadelorenzo at libero.it
[gmx-users] dummy atom fep topology chris liopiri
[gmx-users] Fatal error: Failed to lock: md.log. Function not implemented. maggin
[gmx-users] Re: Fatal error: Failed to lock: md.log. Function not implemented. maggin
[gmx-users] g_cluster nan/segmentation fault error mahealey
[gmx-users] COM restraint similar to distance restraints nahren manuel
[gmx-users] COM restraint similar to distance restraints nahren manuel
[gmx-users] fake atoms creation and causes a 1-4 interaction between atoms warning aviv naftaly
[gmx-users] replica exchange data in cpt file francesco oteri
[gmx-users] replica exchange data in cpt file francesco oteri
[gmx-users] trjcat set timestep/amb2gmx? francesco oteri
[gmx-users] g_potential ansuman at physics.iisc.ernet.in
[gmx-users] reading Hydrogens from an itp file gromacs query
[gmx-users] can I change atom position after x steps fatemeh ramezani
[gmx-users] binding energy calculation when appear this error: no distance restraints in topology fatemeh ramezani
[gmx-users] binding energy calculation when appear this error: no distance restraints in topology fatemeh ramezani
[gmx-users] binding energy calculation when appear this error: no distance restraints in topology fatemeh ramezani
[gmx-users] interaction energy fatemeh ramezani
[gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093) swati rana
[gmx-users] Lipid membrane partially broken and create huge voids after NVT swati rana
[gmx-users] Position restraints alex rayevsky
[gmx-users] RE: Position restraints alex rayevsky
Fw: Aw: Re: [gmx-users] Re: density profile lloyd riggs
Aw: [gmx-users] Re:Concept lloyd riggs
Aw: [gmx-users] Re: Simulating a large system lloyd riggs
Aw: Re: [gmx-users] MD publications lloyd riggs
Aw: Re: [gmx-users] Estimations of the drug's affinity lloyd riggs
Aw: [gmx-users] Re: how is the pulling force measured lloyd riggs
Aw: [gmx-users] Re: how is the pulling force measured lloyd riggs
[gmx-users] REMD general protocol ... massimo sandal
[gmx-users] Fwd: Selecting the temperature distribution massimo sandal
[gmx-users] Fwd: Selecting the temperature distribution massimo sandal
[gmx-users] Fwd: Selecting the temperature distribution massimo sandal
[gmx-users] Fwd: Selecting the temperature distribution massimo sandal
[gmx-users] Fwd: Selecting the temperature distribution massimo sandal
[gmx-users] Fwd: Selecting the temperature distribution massimo sandal
[gmx-users] Fwd: Selecting the temperature distribution massimo sandal
[gmx-users] Fwd: Selecting the temperature distribution massimo sandal
[gmx-users] Fwd: Selecting the temperature distribution massimo sandal
[gmx-users] Fwd: Selecting the temperature distribution massimo sandal
[gmx-users] About CNT-CYCLIC PETIDE constructio vidhya sankar
[gmx-users] About Topology construction for CNT wrapped by Cyclic peptide vidhya sankar
[gmx-users] About Merging topologies vidhya sankar
[gmx-users] Water spreading on graphene! sarupria
[gmx-users] Maximum force on atom and unpacked lipids sdshine
[gmx-users] Lipid membrane partially broken and create huge voids after NVT sdshine
[gmx-users] Pulling along dihedral angle as the reaction coordinate neeru sharma
[gmx-users] Pulling along dihedral angle as the reaction coordinate neeru sharma
[gmx-users] Re: Salt bridge Calculations bipin singh
[gmx-users] RMSD from the average structure bipin singh
[gmx-users] Doubt about the Gromacs versions bipin singh
[gmx-users] RMSD from the average structure bipin singh
[gmx-users] Doubt about the Gromacs versions bipin singh
[gmx-users] Doubt about the Gromacs versions bipin singh
[gmx-users] RMSD from the average structure bipin singh
[gmx-users] -vsite in Umbrella sampling raghav singh
[gmx-users] Simulations box type raghav singh
[gmx-users] install gromacs 4.5.5 on cluster song.yongshun
[gmx-users] Applying periodic boundary conditions in energy minimization song.yongshun
[gmx-users] Questions about the MFFA boundery implementation of Gromacs? song.yongshun
[gmx-users] Questions about the MFFA boundary implementation of Gromacs? song.yongshun
[gmx-users] different checkpoint from remd after crash andrea spitaleri
[gmx-users] different checkpoint from remd after crash andrea spitaleri
[gmx-users] Problem with generating topology file for OPLS force field for membrane protein simulation Parul tew
[gmx-users] Fwd: Problem with generating topology file for OPLS force field for membrane protein simulation Parul tew
[gmx-users] Problem with OPLS parameters (too few parameters on line) Parul tew
[gmx-users] g_dipoles -g molecular center of mass issue traviskemper
[gmx-users] plots in gromacs vansh
[gmx-users] Re: plots in gromacs vansh
[gmx-users] Re: plots in gromacs vansh
[gmx-users] cannot read frames out from trr files mu xiaojia
[gmx-users] Re: cannot read frames out from trr files mu xiaojia
[gmx-users] Re: cannot read frames out from trr files mu xiaojia
[gmx-users] water models tip3p.gro and spce.gro Ahmet yıldırım
[gmx-users] tip5p water model:Atomtype LP1 not found Ahmet yıldırım
[gmx-users] thermal conductivity,specific heat,enthalpy Ahmet yıldırım
[gmx-users] tip5p water model:Atomtype LP1 not found Ahmet yıldırım
[gmx-users] tip5p water model:Atomtype LP1 not found Ahmet yıldırım
[gmx-users] tip5p water model:Atomtype LP1 not found Ahmet yıldırım
[gmx-users] tip5p water model:Atomtype LP1 not found Ahmet yıldırım
[gmx-users] Re: thermal conductivity,specific heat,enthalpy Ahmet yıldırım
[gmx-users] tip5p water model:Atomtype LP1 not found Ahmet yıldırım
[gmx-users] tip5p water model:Atomtype LP1 not found Ahmet yıldırım
[gmx-users] tip5p water model:Atomtype LP1 not found Ahmet yıldırım
[gmx-users] Re: thermal conductivity,specific heat,enthalpy Ahmet yıldırım
[gmx-users] g_analyze error bar Ahmet yıldırım
[gmx-users] g_analyze error bar Ahmet yıldırım
[gmx-users] Only Ligand(Without Receptor) MD Simulation with solvent(other than water.) zyduscadila
[gmx-users] Re: Only Ligand(Without Receptor) MD Simulation with solvent(other than water.) zyduscadila
[gmx-users] Free energy on GPU? Олег Титов
[gmx-users] installing gromacs-4.6.1 with CMake 中野佑香
[gmx-users] installing gromacs-4.6.1 with CMake 中野佑香
[gmx-users] help: load imbalance 申昊
[gmx-users] Re: Re: help: load imbalance 申昊
[gmx-users] Re: Re: help: load imbalance (Justin Lemkul) 申昊
[gmx-users] About PP/PME 陈照云
[gmx-users] Fwd: Improve performance 陈照云
[gmx-users] Improve performance 陈照云
[gmx-users] About k20 陈照云
[gmx-users] About 4.6.1 陈照云
[gmx-users] About gpu 陈照云
[gmx-users] About parallelization 陈照云
[gmx-users] K20 test 陈照云
[gmx-users] gromacs 4.6.1 on win7? 라지브간디
[gmx-users] Re: gromacs 4.6.1 on win7? 라지브간디
[gmx-users] Setting virtual sites ? 라지브간디
[gmx-users] HIS in charmm27.ff 라지브간디
[gmx-users] gmx 4.6 mpi installation through openmpi? 라지브간디
[gmx-users] converting the normal hormonic potential bond to Fourth power potential bond? 라지브간디
[gmx-users] cygwin_mpi_gmx installation 라지브간디
[gmx-users] Re: cygwin_mpi_gmx installation 라지브간디
[gmx-users] specbond detection 라지브간디
[gmx-users] mpi enabled gmx 4.5 라지브간디
[gmx-users] Running simulation over openmpi in rsh 라지브간디
[gmx-users] ffnonbonded value of charmm to charmm27 ff 라지브간디
[gmx-users] specbonds not shwon 라지브간디
[gmx-users] virtual site cause energy minimization error? 라지브간디
[gmx-users] specbonds are not taken by gromos force field? 라지브간디
[gmx-users] specbonds are not taken by gromos force field? 라지브간디
[gmx-users] Using virtual site 라지브간디

Last message date: Tue Apr 30 22:19:56 CEST 2013
Archived on: Thu Nov 14 12:14:08 CET 2013

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