February 2014 Archives by author

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Starting: Sat Feb 1 00:06:54 CET 2014
Ending: Fri Feb 28 22:37:26 CET 2014
Messages: 601

[gmx-users] Severe error with NPT sujithkakkat .
[gmx-users] Dubious results with NPT sujithkakkat .
[gmx-users] Different "optimal pme grid ... coulomb cutoff" values from identical input files yunshi11 .
[gmx-users] Since "nstlist has no effect on the accuracy" yunshi11 .
[gmx-users] z always small for domain decomposition grid? yunshi11 .
[gmx-users] Different "optimal pme grid ... coulomb cutoff" values from identical input files yunshi11 .
[gmx-users] Shifting in Verlet cut-off schemes? yunshi11 .
[gmx-users] Molecular volume from trajectory ABEL Stephane 175950
[gmx-users] conversion xtc to xyz format with openbabel ABEL Stephane 175950
[gmx-users] conversion xtc to xyz format with openbabel ABEL Stephane 175950
[gmx-users] Outputting Hessian related information Nik A
[gmx-users] peptide aggregation Shine A
[gmx-users] Combine parts Hassan Aaryapour
[gmx-users] Regarding DUM atom in Gromos force field Mark Abraham
[gmx-users] codes for non-bonded function selection (NBF) Mark Abraham
[gmx-users] Bond interaction exclusions Mark Abraham
[gmx-users] pbc problem Mark Abraham
[gmx-users] simulating multiple molecules in a box Mark Abraham
[gmx-users] Simulating spherocylinders Mark Abraham
[gmx-users] leapfrog does not yet support Nose-Hoover chains Mark Abraham
[gmx-users] multiple GPU on multiple nodes Mark Abraham
[gmx-users] multiple GPU on multiple nodes Mark Abraham
[gmx-users] question about gromacs Mark Abraham
[gmx-users] Old charmm force field Mark Abraham
[gmx-users] Custom urea topology Mark Abraham
[gmx-users] There is no domain decomposition for nodes that is compatible Mark Abraham
[gmx-users] Different "optimal pme grid ... coulomb cutoff" values from identical input files Mark Abraham
[gmx-users] Different "optimal pme grid ... coulomb cutoff" values from identical input files Mark Abraham
[gmx-users] Simulations with Nitroxide Spin Label Mark Abraham
[gmx-users] Dynamic selections Mark Abraham
[gmx-users] spliting trajectory g_hbond -contact Mark Abraham
[gmx-users] g_cluster Mark Abraham
[gmx-users] "Justifying" 4fs production runs after 1fs equilibrations? Mark Abraham
[gmx-users] .gro File manipulation Mark Abraham
[gmx-users] Water naming Mark Abraham
[gmx-users] PBC problem after MD Mark Abraham
[gmx-users] .gro File manipulation Mark Abraham
[gmx-users] gromacs 4.6.4 query Mark Abraham
[gmx-users] Bonds/constraits betweeen two moleculetypes? Mark Abraham
[gmx-users] Type of function for bond or bend in SPC/E or TIP3P model Mark Abraham
[gmx-users] Type of function for bond or bend in SPC/E or TIP3P model Mark Abraham
[gmx-users] parameters problem Mark Abraham
[gmx-users] Type of function for bond or bend in SPC/E or TIP3P model Mark Abraham
[gmx-users] Type of function for bond or bend in SPC/E or TIP3P model Mark Abraham
[gmx-users] g_cluster failing Mark Abraham
[gmx-users] g_principal -- bug or very bad choice of filenames Mark Abraham
[gmx-users] Fwd: Segmentation fault with mdrun Mark Abraham
[gmx-users] Is it possible to output the force/energy associated with each position restraint? Mark Abraham
[gmx-users] Add additional LJ to certain atom pair- experience and a funny result Mark Abraham
[gmx-users] Guidance on how to install Gromacs-5.0-beta2 Mark Abraham
[gmx-users] conversion xtc to xyz format with openbabel Mark Abraham
[gmx-users] Long trajectory split Mark Abraham
[gmx-users] conversion xtc to xyz format with openbabel Mark Abraham
[gmx-users] Long trajectory split Mark Abraham
[gmx-users] Temperature coupling Mark Abraham
[gmx-users] REMD slow's down drastically Mark Abraham
[gmx-users] Single or Double precision Mark Abraham
[gmx-users] gromacs5.0-beta2 version installing error Mark Abraham
[gmx-users] REMD slow's down drastically Mark Abraham
[gmx-users] REMD slow's down drastically Mark Abraham
[gmx-users] (Implicit Solvation) Effect of van der waal radii on dynamics of ion Mark Abraham
[gmx-users] Long trajectory split Mark Abraham
[gmx-users] PME Mark Abraham
[gmx-users] Martini Lo-phase seems gel-like David Ackerman
[gmx-users] Martini Lo-phase has gel-like properties David Ackerman
[gmx-users] Periodic Boundary removal in Coarse Grains Simulations Nikhil Agrawal
[gmx-users] intel GPU acceleration? Albert
[gmx-users] wall problem Albert
[gmx-users] wall problem Albert
[gmx-users] wall problem Albert
[gmx-users] wall problem Albert
[gmx-users] wall problem Albert
[gmx-users] lipids crashed Albert
[gmx-users] lipids crashed Albert
[gmx-users] GPU job often tailed Albert
[gmx-users] GPU job often tailed Albert
[gmx-users] aMD for Gromacs? Albert
[gmx-users] aMD for Gromacs? Albert
[gmx-users] aMD for Gromacs? Albert
[gmx-users] Crashes when doing free energy due to pressure and LINCS warnings Matteo Aldeghi
[gmx-users] Problem with radius of gyration calculation Ali Alizadeh
[gmx-users] Problem with radius of gyration calculation Ali Alizadeh
[gmx-users] g_tcaf issue Jones de Andrade
[gmx-users] gromacs.org_gmx-users Digest, Vol 118, Issue 10 Rossen Apostolov
[gmx-users] g_principal -- bug or very bad choice of filenames Antonio Baptista
[gmx-users] g_principal -- bug or very bad choice of filenames Antonio Baptista
[gmx-users] g_principal -- bug or very bad choice of filenames Antonio Baptista
[gmx-users] Issues running Gromacs with MPI/OpenMP in cpu cluster Mousumi Bhattacharyya
[gmx-users] question about gromacs Andrew Bostick
[gmx-users] question about gromacs Andrew Bostick
[gmx-users] ref_t and gen_temp Turgay Cakmak
[gmx-users] Simulations in extreme conditions Dr. Vitaly Chaban
[gmx-users] Simulations in extreme conditions Dr. Vitaly Chaban
[gmx-users] Simulations in extreme conditions Dr. Vitaly Chaban
[gmx-users] Umbrella Sampling between Nanotubes Dr. Vitaly Chaban
[gmx-users] Bonds/constraits betweeen two moleculetypes? Dr. Vitaly Chaban
[gmx-users] protein-cnt Dr. Vitaly Chaban
[gmx-users] Periodic Boundary removal in Coarse Grains Simulations Dr. Vitaly Chaban
[gmx-users] Temperature coupling Dr. Vitaly Chaban
[gmx-users] conversion xtc to xyz format with openbabel Dr. Vitaly Chaban
[gmx-users] Temperature coupling Dr. Vitaly Chaban
[gmx-users] Interaction energy of system as a function of the interface area Dr. Vitaly Chaban
[gmx-users] Long trajectory split Dr. Vitaly Chaban
[gmx-users] Dubious results with NPT Dr. Vitaly Chaban
[gmx-users] Temperature coupling Dr. Vitaly Chaban
[gmx-users] Long trajectory split Dr. Vitaly Chaban
[gmx-users] REMD slow's down drastically Dr. Vitaly Chaban
[gmx-users] Dubious results with NPT Dr. Vitaly Chaban
[gmx-users] Dubious results with NPT Dr. Vitaly Chaban
[gmx-users] Dubious results with NPT Dr. Vitaly Chaban
[gmx-users] User-defined Potentials in Gromacs Dr. Vitaly Chaban
[gmx-users] please guide me through the confusing gromacs results!!! Dr. Vitaly Chaban
[gmx-users] how to increase vacuum thickness in a periodic system Dr. Vitaly Chaban
[gmx-users] difference in potenital energy on desktop and server run Dr. Vitaly Chaban
[gmx-users] Long trajectory split Dr. Vitaly Chaban
[gmx-users] gromacs 4.6.4 query Chaitali Chandratre
[gmx-users] gromacs 4.6.4 query Chaitali Chandratre
[gmx-users] gromacs 4.6.4 query Chaitali Chandratre
[gmx-users] Free energy calculation of multiple solutes Jeff Chen
[gmx-users] Free energy calculation of multiple solutes Jeff Chen
[gmx-users] Combine parts Chandan Choudhury
[gmx-users] Simulations in extreme conditions CipPruteanu
[gmx-users] Simulations in extreme conditions CipPruteanu
[gmx-users] Simulations in extreme conditions CipPruteanu
[gmx-users] Simulations in extreme conditions CipPruteanu
[gmx-users] Forcefield with halogen bonding treatments Dario Corrada
[gmx-users] Use g_wham on 2D PMF DAI, JIAN
[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995) João M. Damas
[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995) João M. Damas
[gmx-users] Dihedral force constants Dr. Ayan Datta
[gmx-users] Cationic Dummy atom method Williams Ernesto Miranda Delgado
[gmx-users] Cationic Dummy atom method Williams Ernesto Miranda Delgado
[gmx-users] Validation of molecular dynamic simulation results Marcelo Depólo
[gmx-users] Long trajectory split Marcelo Depólo
[gmx-users] Long trajectory split Marcelo Depólo
[gmx-users] Long trajectory split Marcelo Depólo
[gmx-users] Long trajectory split Marcelo Depólo
[gmx-users] Long trajectory split Marcelo Depólo
[gmx-users] Long trajectory split Marcelo Depólo
[gmx-users] Long trajectory split Marcelo Depólo
[gmx-users] Exclude Coulomb interactions among certain atoms in SWM4 water molecule Sandipan Dutta
[gmx-users] Exclude Coulomb interactions among certain atoms in SWM4 water molecule Sandipan Dutta
[gmx-users] Exclude Coulomb interactions among certain atoms in SWM4 water molecule Sandipan Dutta
[gmx-users] Exclude Coulomb interactions among certain atoms in SWM4 water molecule Sandipan Dutta
[gmx-users] leapfrog does not yet support Nose-Hoover chains Mahboobeh Eslami
[gmx-users] AMBER03 force field for protein-ligand complex Mahboobeh Eslami
[gmx-users] parameters of ligand for force field OPLS Mahboobeh Eslami
[gmx-users] Validation of molecular dynamic simulation results Amjad Farooq
[gmx-users] Since "nstlist has no effect on the accuracy" Ivan Gladich
[gmx-users] about normal mode analysis Gmail2
[gmx-users] .gro File manipulation Andres Ortega Guerrero
[gmx-users] Follow up (How to define pull-init for two pull groups) How to concatenate pullx.xvg files Rini Gupta
[gmx-users] Is cholesterol model available in Charmm36 ff? Davit Hakobyan
[gmx-users] Problem with radius of gyration calculation João Henriques
[gmx-users] g_cluster João Henriques
[gmx-users] g_cluster João Henriques
[gmx-users] TFE-water homogeneous system -NPT João Henriques
[gmx-users] Validation of molecular dynamic simulation results João Henriques
[gmx-users] Validation of molecular dynamic simulation results João Henriques
[gmx-users] Validation of molecular dynamic simulation results João Henriques
[gmx-users] intel GPU acceleration? Tamas Horvath
[gmx-users] Bond interaction exclusions Xu Dong Huang
[gmx-users] Bond interaction exclusions Xu Dong Huang
[gmx-users] coenzyme-protein complex Mostafa Javaheri
[gmx-users] Single or Double precision Mostafa Javaheri
[gmx-users] REMD slow's down drastically Francis Jing
[gmx-users] REMD slow's down drastically Francis Jing
[gmx-users] aMD for Gromacs? Francis Jing
[gmx-users] User-defined Potentials in Gromacs Francis Jing
[gmx-users] gromacs5.0-beta2 version installing error JuYeon
[gmx-users] Error in MD Simulation... Kalyanashis
[gmx-users] REMD slow's down drastically Singam Karthick
[gmx-users] gromacs.org_gmx-users Digest, Vol 118, Issue 104 Singam Karthick
[gmx-users] REMD slow's down drastically Singam Karthick
[gmx-users] DNA simulation with opls forcefield Gurunath Katagi
[gmx-users] position restraints Gurunath Katagi
[gmx-users] parameters problem Nidhi Katyal
[gmx-users] xpm2ps Nidhi Katyal
[gmx-users] (no subject) abhijit Kayal
[gmx-users] (no subject) abhijit Kayal
[gmx-users] mixing tabulated potential with force field for the AdResS Jakub Krajniak
[gmx-users] mixing tabulated potential with force field for the AdResS Jakub Krajniak
[gmx-users] Fwd: Segmentation fault with mdrun Pavan Kumar
[gmx-users] Segmentation Fault with mdrun_mpi Pavan Kumar
[gmx-users] Guidance on how to install Gromacs-5.0-beta2 Pavan Kumar
[gmx-users] Issues running Gromacs with MPI/OpenMP in cpu cluster Carsten Kutzner
[gmx-users] Custom urea topology Gabriele Lanaro
[gmx-users] Custom urea topology Gabriele Lanaro
[gmx-users] Error with g_bar Jong Wha Lee
[gmx-users] Umbrella Sampling Justin Lemkul
[gmx-users] coenzyme-protein complex Justin Lemkul
[gmx-users] about soft core potentials and very high VdW Justin Lemkul
[gmx-users] Error in minimisation Justin Lemkul
[gmx-users] pbc problem Justin Lemkul
[gmx-users] coenzyme-protein complex Justin Lemkul
[gmx-users] Bond interaction exclusions Justin Lemkul
[gmx-users] Spacing between adjacent umbrella sampling windows Justin Lemkul
[gmx-users] problem with tutorial KALP-15 in DPPC Justin Lemkul
[gmx-users] question Justin Lemkul
[gmx-users] question Justin Lemkul
[gmx-users] question Justin Lemkul
[gmx-users] intel GPU acceleration? Justin Lemkul
[gmx-users] Spacing between Umbrella sampling Justin Lemkul
[gmx-users] OPLS force field issue.... Justin Lemkul
[gmx-users] wall problem Justin Lemkul
[gmx-users] AMBER99sb-ILDN - protonated C-terminus Justin Lemkul
[gmx-users] question about gromacs Justin Lemkul
[gmx-users] wall problem Justin Lemkul
[gmx-users] wall problem Justin Lemkul
[gmx-users] DNA with charmm27 works fine but why Justin Lemkul
[gmx-users] DNA with charmm27 works fine but why Justin Lemkul
[gmx-users] DNA with charmm27 works fine but why Justin Lemkul
[gmx-users] [gmx-developers] bonding problem in simulating multiple objects in the same box Justin Lemkul
[gmx-users] Old charmm force field Justin Lemkul
[gmx-users] gdist: command not found Justin Lemkul
[gmx-users] Custom urea topology Justin Lemkul
[gmx-users] OPLS force field issue.... Justin Lemkul
[gmx-users] dna with charmm36 Justin Lemkul
[gmx-users] Custom urea topology Justin Lemkul
[gmx-users] lipids crashed Justin Lemkul
[gmx-users] There is no domain decomposition for nodes that is compatible Justin Lemkul
[gmx-users] lipids crashed Justin Lemkul
[gmx-users] There is no domain decomposition for nodes that is compatible Justin Lemkul
[gmx-users] There is no domain decomposition for nodes that is compatible Justin Lemkul
[gmx-users] center of mass Justin Lemkul
[gmx-users] Bond interaction exclusions Justin Lemkul
[gmx-users] solvent-exclusion model for implicit solvent Justin Lemkul
[gmx-users] Problem with radius of gyration calculation Justin Lemkul
[gmx-users] about normal mode analysis Justin Lemkul
[gmx-users] about normal mode analysis Justin Lemkul
[gmx-users] error in g_wham Justin Lemkul
[gmx-users] Zero LJ energies during Free energy perturbation Justin Lemkul
[gmx-users] Reg No error in output Justin Lemkul
[gmx-users] error g_wham Justin Lemkul
[gmx-users] g_principal -- bug or very bad choice of filenames Justin Lemkul
[gmx-users] spliting trajectory g_hbond -contact Justin Lemkul
[gmx-users] Peptide orientation Justin Lemkul
[gmx-users] Trying to use user-defined potentials but getting out of range error Justin Lemkul
[gmx-users] Hydrogen bond with chlorine Justin Lemkul
[gmx-users] Fwd: Implicit solvent simulation Justin Lemkul
[gmx-users] Fwd: Implicit solvent simulation Justin Lemkul
[gmx-users] TFE-water homogeneous system -NPT Justin Lemkul
[gmx-users] free energy calculations for reference state for constant pH MD simulations... Justin Lemkul
[gmx-users] free energy calculations for reference state for constant pH MD simulations... Justin Lemkul
[gmx-users] g_enermat: group.dat file Justin Lemkul
[gmx-users] free energy calculations for reference state for constant pH MD simulations... Justin Lemkul
[gmx-users] g_enermat: group.dat file Justin Lemkul
[gmx-users] Validation of molecular dynamic simulation results Justin Lemkul
[gmx-users] peptide aggregation Justin Lemkul
[gmx-users] Protein - Ligand simulation Justin Lemkul
[gmx-users] Protein - Ligand simulation Justin Lemkul
[gmx-users] question Justin Lemkul
[gmx-users] question Justin Lemkul
[gmx-users] Exclude Coulomb interactions among certain atoms in SWM4 water molecule Justin Lemkul
[gmx-users] Number of coordinate in pr.top and solv.gro not matching Justin Lemkul
[gmx-users] g_rms -dist option Justin Lemkul
[gmx-users] question about g_density Justin Lemkul
[gmx-users] Simulations in extreme conditions Justin Lemkul
[gmx-users] Warning: atom is missing in residue Justin Lemkul
[gmx-users] order parameter Justin Lemkul
[gmx-users] Warning: atom is missing in residue Justin Lemkul
[gmx-users] order parameter Justin Lemkul
[gmx-users] RMSF per residue Justin Lemkul
[gmx-users] Error in MD Simulation... Justin Lemkul
[gmx-users] Simulations in extreme conditions Justin Lemkul
[gmx-users] parameters problem Justin Lemkul
[gmx-users] Nonsymetric molecule across pbc Justin Lemkul
[gmx-users] Nonsymetric molecule across pbc Justin Lemkul
[gmx-users] Nonsymetric molecule across pbc Justin Lemkul
[gmx-users] (Implicit solvation)Initial temperature changes to 0 K Justin Lemkul
[gmx-users] RMSD of a structure (was: gromacs.org_gmx-users Digest, Vol 118, Issue 73) Justin Lemkul
[gmx-users] position restraint during NVT equllibration Justin Lemkul
[gmx-users] Forcefield with halogen bonding treatments Justin Lemkul
[gmx-users] 答复： position restraint during NVT equllibration Justin Lemkul
[gmx-users] two ligand itp file from ACPYPE Justin Lemkul
[gmx-users] two ligand itp file from ACPYPE Justin Lemkul
[gmx-users] partial charge and LJ parameters for CH3 in gromos forcefields Justin Lemkul
[gmx-users] Cationic Dummy atom method Justin Lemkul
[gmx-users] Follow up (How to define pull-init for two pull groups) How to concatenate pullx.xvg files Justin Lemkul
[gmx-users] Is it possible to output the force/energy associated with each position restraint? Justin Lemkul
[gmx-users] Exclude Coulomb interactions among certain atoms in SWM4 water molecule Justin Lemkul
[gmx-users] Free energy calculation of multiple solutes Justin Lemkul
[gmx-users] Standard residue of C4S shown as missing in residue topology database Justin Lemkul
[gmx-users] Gromacs insatallation on centos 6 Justin Lemkul
[gmx-users] Free energy calculation of multiple solutes Justin Lemkul
[gmx-users] PMF plot against distance Justin Lemkul
[gmx-users] Is cholesterol model available in Charmm36 ff? Justin Lemkul
[gmx-users] Regarding error after equilibration of protein in membrane using g_membed Justin Lemkul
[gmx-users] Regarding error after equilibration of protein in membrane using g_membed Justin Lemkul
[gmx-users] Regarding error after equilibration of protein in membrane using g_membed Justin Lemkul
[gmx-users] Public server of gromacs to share my files Justin Lemkul
[gmx-users] Exclude Coulomb interactions among certain atoms in SWM4 water molecule Justin Lemkul
[gmx-users] Guidance on how to install Gromacs-5.0-beta2 Justin Lemkul
[gmx-users] Exclude Coulomb interactions among certain atoms in SWM4 water molecule Justin Lemkul
[gmx-users] protein-cnt Justin Lemkul
[gmx-users] Adding TPO and SEP to G53a6 Forcefield Justin Lemkul
[gmx-users] Periodic Boundary removal in Coarse Grains Simulations Justin Lemkul
[gmx-users] Interaction energy of system as a function of the interface area Justin Lemkul
[gmx-users] Dubious results with NPT Justin Lemkul
[gmx-users] Long trajectory split Justin Lemkul
[gmx-users] Binding energy of membrane protein to the membrane lipids Justin Lemkul
[gmx-users] Long trajectory split Justin Lemkul
[gmx-users] Long trajectory split Justin Lemkul
[gmx-users] Binding energy of membrane protein to the membrane lipids Justin Lemkul
[gmx-users] Long trajectory split Justin Lemkul
[gmx-users] Dubious results with NPT Justin Lemkul
[gmx-users] Position restraints Justin Lemkul
[gmx-users] C-terminus residue name in Gromos43a1 Justin Lemkul
[gmx-users] interaction energy Justin Lemkul
[gmx-users] Binning of Free Energy landscapes Justin Lemkul
[gmx-users] Binning of Free Energy landscapes Justin Lemkul
[gmx-users] C-terminus residue name in Gromos43a1 Justin Lemkul
[gmx-users] aMD for Gromacs? Justin Lemkul
[gmx-users] C-terminus residue name in Gromos43a1 Justin Lemkul
[gmx-users] difference in potenital energy on desktop and server run Justin Lemkul
[gmx-users] please guide me through the confusing gromacs results!!! Justin Lemkul
[gmx-users] Adding TPO and SEP to G53a6 Forcefield Justin Lemkul
[gmx-users] difference in potenital energy on desktop and server run Justin Lemkul
[gmx-users] C-terminus residue name in Gromos43a1 Justin Lemkul
[gmx-users] difference in potenital energy on desktop and server run Justin Lemkul
[gmx-users] difference in potenital energy on desktop and server run Justin Lemkul
[gmx-users] C-terminus residue name in Gromos43a1 Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] ref_t and gen_temp Justin Lemkul
[gmx-users] Hydrogen bond with chlorine Jianguo Li
[gmx-users] Hydrogen bond with chlorine Jianguo Li
[gmx-users] Standard residue of C4S shown as missing in residue topology database Libin
[gmx-users] Is it possible to output the force/energy associated with each position restraint? Ling Liu
[gmx-users] spliting trajectory g_hbond -contact Kavyashree M
[gmx-users] spliting trajectory g_hbond -contact Kavyashree M
[gmx-users] Water naming Kavyashree M
[gmx-users] Water naming Kavyashree M
[gmx-users] Water naming Kavyashree M
[gmx-users] g_rms -dist option Kavyashree M
[gmx-users] g_rms -dist option Kavyashree M
[gmx-users] Water naming Kavyashree M
[gmx-users] Water naming Kavyashree M
[gmx-users] Simulating spherocylinders Sanku M
[gmx-users] Old charmm force field Sanku M
[gmx-users] counter ion and charged polymer in gas-phase Sanku M
[gmx-users] gdist: command not found Chetan Mahajan
[gmx-users] gdist: command not found Chetan Mahajan
[gmx-users] center of mass Chetan Mahajan
[gmx-users] Molecular volume from trajectory Erik Marklund
[gmx-users] Forcefield conversion script for POPC lipids Erik Marklund
[gmx-users] Forcefield conversion script for POPC lipids Erik Marklund
[gmx-users] Hydrogen bond with chlorine Erik Marklund
[gmx-users] Hydrogen bond with chlorine Erik Marklund
[gmx-users] Water naming Erik Marklund
[gmx-users] Water naming Erik Marklund
[gmx-users] A new script to read hbmap from g_hbond Erik Marklund
[gmx-users] Trying to use user-defined potentials but getting out of range error Davide Mercadante
[gmx-users] g_cluster failing Davide Mercadante
[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995) Teemu Murtola
[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995) Teemu Murtola
[gmx-users] Binning of Free Energy landscapes Ankita Naithani
[gmx-users] Binning of Free Energy landscapes Ankita Naithani
[gmx-users] REMD slow's down drastically Christopher Neale
[gmx-users] REMD slow's down drastically Christopher Neale
[gmx-users] TUBE - Lincs or bonds? Steven Neumann
[gmx-users] Rigid nanotube Steven Neumann
[gmx-users] There is no domain decomposition for nodes that is compatible Steven Neumann
[gmx-users] position restraints Steven Neumann
[gmx-users] There is no domain decomposition for nodes that is compatible Steven Neumann
[gmx-users] There is no domain decomposition for nodes that is compatible Steven Neumann
[gmx-users] There is no domain decomposition for nodes that is compatible Steven Neumann
[gmx-users] There is no domain decomposition for nodes that is compatible Steven Neumann
[gmx-users] There is no domain decomposition for nodes that is compatible Steven Neumann
[gmx-users] Umbrella Sampling between Nanotubes Steven Neumann
[gmx-users] Bonds/constraits betweeen two moleculetypes? Steven Neumann
[gmx-users] Bonds/constraits betweeen two moleculetypes? Steven Neumann
[gmx-users] Umbrella Sampling between Nanotubes Steven Neumann
[gmx-users] Nonsymetric molecule across pbc Steven Neumann
[gmx-users] Nonsymetric molecule across pbc Steven Neumann
[gmx-users] Nonsymetric molecule across pbc Steven Neumann
[gmx-users] Nonsymetric molecule across pbc Steven Neumann
[gmx-users] Nonsymetric molecule across pbc Steven Neumann
[gmx-users] .gro File manipulation Andres Ortega
[gmx-users] g_cluster Mehmet Ozbil
[gmx-users] free energy calculations for reference state for constant pH MD simulations... Mehmet Ozbil
[gmx-users] free energy calculations for reference state for constant pH MD simulations... Mehmet Ozbil
[gmx-users] free energy calculations for reference state for constant pH MD simulations... Ozbil, Mehmet
[gmx-users] installation and fftw3.h Peter Palenchar
[gmx-users] Bond interaction exclusions XAvier Periole
[gmx-users] Use g_wham on 2D PMF XAvier Periole
[gmx-users] pbc problem Atila Petrosian
[gmx-users] question Thomas Piggot
[gmx-users] Forcefield conversion script for POPC lipids Thomas Piggot
[gmx-users] "Justifying" 4fs production runs after 1fs equilibrations? Thomas Piggot
[gmx-users] multiple GPU on multiple nodes Szilárd Páll
[gmx-users] intel GPU acceleration? Szilárd Páll
[gmx-users] multiple GPU on multiple nodes Szilárd Páll
[gmx-users] multiple GPU on multiple nodes Szilárd Páll
[gmx-users] multiple GPU on multiple nodes Szilárd Páll
[gmx-users] z always small for domain decomposition grid? Szilárd Páll
[gmx-users] Since "nstlist has no effect on the accuracy" Szilárd Páll
[gmx-users] Since "nstlist has no effect on the accuracy" Szilárd Páll
[gmx-users] Different "optimal pme grid ... coulomb cutoff" values from identical input files Szilárd Páll
[gmx-users] gromacs 4.6.4 query Szilárd Páll
[gmx-users] gromacs 4.6.4 query Szilárd Páll
[gmx-users] "Justifying" 4fs production runs after 1fs equilibrations? Szilárd Páll
[gmx-users] GPU job often tailed Szilárd Páll
[gmx-users] GPU job often tailed Szilárd Páll
[gmx-users] Issues running Gromacs with MPI/OpenMP in cpu cluster Szilárd Páll
[gmx-users] Issues running Gromacs with MPI/OpenMP in cpu cluster Szilárd Páll
[gmx-users] hybrid CPU/GPU nodes Szilárd Páll
[gmx-users] hybrid CPU/GPU nodes Szilárd Páll
[gmx-users] Can i use GPU for my desktop computer Szilárd Páll
[gmx-users] Guidance on how to install Gromacs-5.0-beta2 Yogendra Ramtirtha
[gmx-users] Guidance on how to install Gromacs-5.0-beta2 Yogendra Ramtirtha
[gmx-users] Guidance on how to install Gromacs-5.0-beta2 Yogendra Ramtirtha
[gmx-users] Guidance on how to install Gromacs-5.0-beta2 Yogendra Ramtirtha
[gmx-users] Guidance on how to install Gromacs-5.0-beta2 Yogendra Ramtirtha
[gmx-users] Regarding trjorder Venkat Reddy
[gmx-users] question about variables in calc_f_el() in sim_util.c Bernhard Reuter
[gmx-users] question about variables in calc_f_el() in sim_util.c Bernhard Reuter
[gmx-users] Warning: atom is missing in residue Ehsan Sadeghi
[gmx-users] hybrid CPU/GPU nodes Gloria Saracino
[gmx-users] hybrid CPU/GPU nodes Gloria Saracino
[gmx-users] gromacs.org_gmx-users Digest, Vol 118, Issue 73 Raghunath Satpathy
[gmx-users] Issues running Gromacs with MPI/OpenMP in cpu cluster Thomas Schlesier
[gmx-users] AMBER99sb-ILDN - protonated C-terminus Marieke Schor
[gmx-users] Protein - Ligand simulation Aldo Segura
[gmx-users] Hydrogen bond with chlorine Dhawal Shah
[gmx-users] Hydrogen bond with chlorine Dhawal Shah
[gmx-users] RMSF per residue Saman Shahriyari
[gmx-users] Spacing between adjacent umbrella sampling windows Arunima Shilpi
[gmx-users] Spacing between Umbrella sampling Arunima Shilpi
[gmx-users] error in g_wham Arunima Shilpi
[gmx-users] error g_wham Arunima Shilpi
[gmx-users] PMF plot against distance Arunima Shilpi
[gmx-users] Public server of gromacs to share my files Arunima Shilpi
[gmx-users] Annealing doesn't work with Andersen thermostat? Michael Shirts
[gmx-users] Free energy calculation problems (bug?) Michael Shirts
[gmx-users] Temperature coupling Michael Shirts
[gmx-users] Temperature coupling Michael Shirts
[gmx-users] Dubious results with NPT Michael Shirts
[gmx-users] Dubious results with NPT Michael Shirts
[gmx-users] aMD for Gromacs? Michael Shirts
[gmx-users] aMD for Gromacs? Michael Shirts
[gmx-users] g_hbond and index Ricardo O. S. Soares
[gmx-users] A new script to read hbmap from g_hbond Ricardo O. S. Soares
[gmx-users] TFE-water homogeneous system -NPT Archana Sonawani-Jagtap
[gmx-users] Gromacs insatallation on centos 6 Archana Sonawani-Jagtap
[gmx-users] Gromacs insatallation on centos 6 Archana Sonawani-Jagtap
[gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995) David van der Spoel
[gmx-users] xpm2ps David van der Spoel
[gmx-users] "Justifying" 4fs production runs after 1fs equilibrations? Piggot T.
[gmx-users] Temperature coupling Marcelo Vanean
[gmx-users] Temperature coupling Marcelo Vanean
[gmx-users] Temperature coupling Marcelo Vanean
[gmx-users] Temperature coupling Marcelo Vanean
[gmx-users] Temperature coupling Marcelo Vanean
[gmx-users] Temperature coupling Marcelo Vanean
[gmx-users] C-terminus residue name in Gromos43a1 Francesca Vitalini
[gmx-users] C-terminus residue name in Gromos43a1 Francesca Vitalini
[gmx-users] C-terminus residue name in Gromos43a1 Francesca Vitalini
[gmx-users] C-terminus residue name in Gromos43a1 Francesca Vitalini
[gmx-users] C-terminus residue name in Gromos43a1 Francesca Vitalini
[gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7 Christian Wagner
[gmx-users] installation and fftw3.h Christian Wagner
[gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI Christian Wagner
[gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI Christian Wagner
[gmx-users] Gromacs insatallation on centos 6 Mirco Wahab
[gmx-users] difference in potenital energy on desktop and server run Mirco Wahab
[gmx-users] about soft core potentials and very high VdW Tsjerk Wassenaar
[gmx-users] g_cluster Tsjerk Wassenaar
[gmx-users] question about g_density Tsjerk Wassenaar
[gmx-users] Validation of molecular dynamic simulation results Tsjerk Wassenaar
[gmx-users] "Justifying" 4fs production runs after 1fs equilibrations? Tsjerk Wassenaar
[gmx-users] Annealing doesn't work with Andersen thermostat? William Welch
[gmx-users] gromacs.org_gmx-users Digest, Vol 118, Issue 10 William Welch
[gmx-users] OPLS force field issue.... Sidath Wijesinghe
[gmx-users] OPLS force field issue.... Sidath Wijesinghe
[gmx-users] codes for non-bonded function selection (NBF) Makoto Yoneya
[gmx-users] codes for non-bonded function selection (NBF) Makoto Yoneya
[gmx-users] Problem with radius of gyration calculation Jernej Zidar
[gmx-users] [SOLVED] Problem with radius of gyration calculation Jernej Zidar
[gmx-users] please guide me through the confusing gromacs results!!! delara aghaie
[gmx-users] Simulations with Nitroxide Spin Label akk5r
[gmx-users] Validation of molecular dynamic simulation results ananyachatterjee
[gmx-users] Validation of molecular dynamic simulation results ananyachatterjee
[gmx-users] Validation of molecular dynamic simulation results ananyachatterjee
[gmx-users] Cationic Dummy atom method andrea
[gmx-users] parameters of ligand for force field OPLS andrea
[gmx-users] parameters of ligand for force field OPLS andrea
[gmx-users] User-defined Potentials in Gromacs cchan2242-c
[gmx-users] multiple GPU on multiple nodes cyberjhon
[gmx-users] multiple GPU on multiple nodes cyberjhon
[gmx-users] multiple GPU on multiple nodes cyberjhon
[gmx-users] about soft core potentials and very high VdW cyberjhon
[gmx-users] multiple GPU on multiple nodes cyberjhon
[gmx-users] Position restraints davhak
[gmx-users] how to increase vacuum thickness in a periodic system decaiyu
[gmx-users] Molecular volume from trajectory rajat desikan
[gmx-users] g_helixorient help rajat desikan
[gmx-users] strange do_dssp error rajat desikan
[gmx-users] strange do_dssp error rajat desikan
[gmx-users] solvent-exclusion model for implicit solvent didymos
[gmx-users] about soft core potentials and very high VdW jhon michael espinosa duran
[gmx-users] Warning: atom is missing in residue ehs
[gmx-users] Warning: atom is missing in residue ehs
[gmx-users] C-terminus residue name in Gromos43a1 fra
[gmx-users] Replica Exchange MD bharat gupta
[gmx-users] Replica Exchange MD bharat gupta
[gmx-users] Replica Exchange Molecular Dynamics bharat gupta
[gmx-users] difference in potenital energy on desktop and server run gupta.rakesh082
[gmx-users] difference in potenital energy on desktop and server run gupta.rakesh082
[gmx-users] difference in potenital energy on desktop and server run gupta.rakesh082
[gmx-users] difference in potenital energy on desktop and server run gupta.rakesh082
[gmx-users] difference in potenital energy on desktop and server run gupta.rakesh082
[gmx-users] difference in potenital energy on desktop and server run gupta.rakesh082
[gmx-users] protein-cnt maryam haji
[gmx-users] Interaction energy of system as a function of the interface area maryam haji
[gmx-users] interaction energy maryam haji
[gmx-users] Error in minimisation hasthi
[gmx-users] Regarding error after equilibration of protein in membrane using g_membed shalini.s at iitg.ernet.in
[gmx-users] Regarding error after equilibration of protein in membrane using g_membed shalini.s at iitg.ernet.in
[gmx-users] Regarding error after equilibration of protein in membrane using g_membed shalini.s at iitg.ernet.in
[gmx-users] PBC problem after MD ipek
[gmx-users] two ligand itp file from ACPYPE ipek
[gmx-users] two ligand itp file from ACPYPE ipek
[gmx-users] question about g_density jhosamelly
[gmx-users] question about g_density jhosamelly
[gmx-users] Add additional LJ to certain atom pair- experience and a funny result jia jia
[gmx-users] Add additional LJ to certain atom pair- experience and a funny result jia jia
[gmx-users] Two-body Bonded Distance jolayfield
[gmx-users] pbc kannan
[gmx-users] PBC problem after MD kannan
[gmx-users] leapfrog does not yet support Nose-Hoover chains tarak karmakar
[gmx-users] question tarak karmakar
[gmx-users] problem with tutorial KALP-15 in DPPC tarak karmakar
[gmx-users] simulating multiple molecules in a box ibrahim khalil
[gmx-users] bonding problem in simulating multiple objects in the same box ibrahim khalil
[gmx-users] Dubious results with NPT sujith ks
[gmx-users] Fwd: Implicit solvent simulation prasun kumar
[gmx-users] Fwd: Implicit solvent simulation prasun kumar
[gmx-users] Fwd: Implicit solvent simulation prasun kumar
[gmx-users] Adding TPO and SEP to G53a6 Forcefield lalithkumar
[gmx-users] Adding TPO and SEP to G53a6 Forcefield lalithkumar
[gmx-users] Type of function for bond or bend in SPC/E or TIP3P model leila
[gmx-users] Protein - Ligand simulation lucaam86
[gmx-users] Protein - Ligand simulation lucaam86
[gmx-users] Number of coordinate in pr.top and solv.gro not matching mabbasi
[gmx-users] PME kiana moghaddam
[gmx-users] Opinions on Copernicus to streamline Gromacs workflows? ms
[gmx-users] Electrostatic Acting on a Residue mvcdelacerna
[gmx-users] question nafas
[gmx-users] (no subject) nafas
[gmx-users] (no subject) nafas
[gmx-users] question nafas
[gmx-users] g_enermat: group.dat file shivangi nangia
[gmx-users] g_enermat: group.dat file shivangi nangia
[gmx-users] Adding Born Radii for implicit solvent MD nichith
[gmx-users] (Implicit solvation)Initial temperature changes to 0 K nichith
[gmx-users] (Implicit Solvation) Effect of van der waal radii on dynamics of ion nichith
[gmx-users] Free energy calculation problems (bug?) asaffarhi at post.tau.ac.il
[gmx-users] Peptide orientation pratibha
[gmx-users] charges in vaccum simulations pratibha
[gmx-users] DNA with charmm27 works fine but why gromacs query
[gmx-users] DNA with charmm27 works fine but why gromacs query
[gmx-users] DNA with charmm27 works fine but why gromacs query
[gmx-users] dna with charmm36 gromacs query
[gmx-users] dna with charmm36 gromacs query
[gmx-users] order parameter rankinb
[gmx-users] order parameter rankinb
[gmx-users] MM-GB/SA analysis in Gromacs richa
[gmx-users] Type of function for bond or bend in SPC/E or TIP3P model leila salimi
[gmx-users] Type of function for bond or bend in SPC/E or TIP3P model leila salimi
[gmx-users] Type of function for bond or bend in SPC/E or TIP3P model leila salimi
[gmx-users] partial charge and LJ parameters for CH3 in gromos forcefields leila salimi
[gmx-users] Reg No error in output vidhya sankar
[gmx-users] problem with tutorial KALP-15 in DPPC serena
[gmx-users] Regarding DUM atom in Gromos force field bipin singh
[gmx-users] Regarding DUM atom in Gromos force field bipin singh
[gmx-users] Regarding Free energy perturbation bipin singh
[gmx-users] Zero LJ energies during Free energy perturbation bipin singh
[gmx-users] Zero LJ energies during Free energy perturbation bipin singh
[gmx-users] Dihedral force constants bipin singh
[gmx-users] Binding energy of membrane protein to the membrane lipids sojovictor
[gmx-users] Binding energy of membrane protein to the membrane lipids sojovictor
[gmx-users] Binding energy of membrane protein to the membrane lipids sojovictor
[gmx-users] Dubious results with NPT sujith
[gmx-users] position restraint during NVT equllibration sunyeping
[gmx-users] 答复： position restraint during NVT equllibration sunyeping
[gmx-users] "Justifying" 4fs production runs after 1fs equilibrations? unitALX
[gmx-users] "Justifying" 4fs production runs after 1fs equilibrations? unitALX
[gmx-users] "Justifying" 4fs production runs after 1fs equilibrations? unitALX
[gmx-users] kinetic energy distribution with and without constraints unitALX
[gmx-users] Can i use GPU for my desktop computer xiao
[gmx-users] about normal mode analysis Ahmet yıldırım
[gmx-users] PBC problem after MD SEMRAN İPEK
[gmx-users] PBC problem after MD SEMRAN İPEK
[gmx-users] two ligand itp file from ACPYPE SEMRAN İPEK
[gmx-users] Molecular volume from trajectory Андрей Гончар
[gmx-users] Molecular volume from trajectory Андрей Гончар
[gmx-users] Dynamic selections Андрей Гончар
[gmx-users] Free energy calculation problems (bug?) Олег Титов
[gmx-users] Free energy calculation problems (bug?) Олег Титов
[gmx-users] Free energy calculation problems (bug?) Олег Титов

Last message date: Fri Feb 28 22:37:26 CET 2014
Archived on: Fri Feb 28 22:37:27 CET 2014

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