June 2019 Archives by thread

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Starting: Sat Jun 1 01:50:50 CEST 2019
Ending: Sun Jun 30 23:24:28 CEST 2019
Messages: 240

• [gmx-users] Chain ID   Nabil Abid
• [gmx-users] Trans-Gauche fraction for surfactant chain   anupama sharma
  • [gmx-users] Trans-Gauche fraction for surfactant chain   Dallas Warren
• [gmx-users] Coordinates of structures from a .trr file   Neena Susan Eappen
  • [gmx-users] Coordinates of structures from a .trr file   Nabil Abid
  • [gmx-users] Coordinates of structures from a .trr file   Justin Lemkul
• [gmx-users] protonation free energy: parameter setting   Udaya Dahal
• [gmx-users] List of H-bond donors and acceptors   Neena Susan Eappen
  • [gmx-users] List of H-bond donors and acceptors   Dallas Warren
• [gmx-users] FW: Free energy of solvation using the Bar method   Innocenti Malini, Riccardo
  • [gmx-users] FW: Free energy of solvation using the Bar method   Artem Shekhovtsov
    • [gmx-users] FW: Free energy of solvation using the Bar method   Innocenti Malini, Riccardo
• [gmx-users] oplsaa tooology for urea   Alex
  • [gmx-users] oplsaa tooology for urea   Dallas Warren
• [gmx-users] Rupture force definition   Rakesh Mishra
• [gmx-users] Error in generating a gromacs structure file for Arginine   Pandya, Akash
  • [gmx-users] Error in generating a gromacs structure file for Arginine   Dallas Warren
• [gmx-users] Question about center of mass definition in RDF tool (gromacs 5.11)   Sergio Garay
• [gmx-users] How to calculate angle between center of geometry of groups of atoms ?   Monia Kamly
  • [gmx-users] How to calculate angle between center of geometry of groups of atoms ?   Mark Abraham
    • [gmx-users] How to calculate angle between center of geometry of groups of atoms ?   Monia Kamly
• [gmx-users] Problem using RTX 2070   Armenio Barbosa
  • [gmx-users] Problem using RTX 2070   p buscemi
    • [gmx-users] Problem using RTX 2070   Armenio Barbosa
• [gmx-users] volume not shrinking when restrains present   p buscemi
  • [gmx-users] volume not shrinking when restrains present   p buscemi
• [gmx-users] ENERGY MINIMISATION   Dhrubajyoti Maji
  • [gmx-users] ENERGY MINIMISATION   Dallas Warren
  • [gmx-users] ENERGY MINIMISATION   spss4 at iacs.res.in
    • [gmx-users] ENERGY MINIMISATION   Dhrubajyoti Maji
• [gmx-users] wwtang at tju.edu.cn   汤伟伟
• [gmx-users] Density of ligand molecules around a particular residue   Pandya, Akash
  • [gmx-users] Density of ligand molecules around a particular residue   Smith, Micholas D.
• [gmx-users] Xeon W family vs scalable   강동우
  • [gmx-users] Xeon W family vs scalable   Kutzner, Carsten
    • [gmx-users] Xeon W family vs scalable   paul buscemi
• [gmx-users] There is no domain decomposition error   Dhrubajyoti Maji
  • [gmx-users] There is no domain decomposition error   Paul bauer
    • [gmx-users] There is no domain decomposition error   Dhrubajyoti Maji
• [gmx-users] force field for organometalic compound   antonia vyrkou
  • [gmx-users] force field for organometalic compound   Bratin Kumar Das
• [gmx-users] Water Density   Omkar Singh
  • [gmx-users] Water Density   Bratin Kumar Das
• [gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand   Prasanth G, Research Scholar
  • [gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand   Bratin Kumar Das
  • [gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand   Prasanth G, Research Scholar
    • [gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand   Mark Abraham
• [gmx-users] problem with topology   Maria Luisa
  • [gmx-users] problem with topology   Dallas Warren
    • [gmx-users] problem with topology   Maria Luisa
      • [gmx-users] problem with topology   Dallas Warren
• [gmx-users] (no subject)   Maria Luisa
• [gmx-users] Question about center of mass definition in RDF tool (gromacs 5.11)   Sergio Garay
• [gmx-users] dos command for extracting vibrational spectra for a particular bond   veerapandian
  • [gmx-users] dos command for extracting vibrational spectra for a particular bond   André Farias de Moura
• [gmx-users] trjconv -drop options   Gregory Man Kai Poon
• [gmx-users] Running gromacs analysis on a HPC   Pandya, Akash
  • [gmx-users] Running gromacs analysis on a HPC   John Whittaker
• [gmx-users] Analysis of water molecules   Soham Sarkar
• [gmx-users] Some suggestions about the gmx current tool   Mahsa
  • [gmx-users] Some suggestions about the gmx current tool   Mahsa
    • [gmx-users] Some suggestions about the gmx current tool   Mark Abraham
      • [gmx-users] Some suggestions about the gmx current tool   Mahsa
• [gmx-users] Grompp not producing tpr files   Israel Estrada
  • [gmx-users] Grompp not producing tpr files   Mark Abraham
    • [gmx-users] Grompp not producing tpr files   Bratin Kumar Das
      • [gmx-users] Grompp not producing tpr files   Israel Estrada
      • [gmx-users] Grompp not producing tpr files   Paul Bauer
      • [gmx-users] Grompp not producing tpr files   Israel Estrada
      • [gmx-users] Grompp not producing tpr files   Dallas Warren
      • [gmx-users] Grompp not producing tpr files   Israel Estrada
      • [gmx-users] Grompp not producing tpr files   Peter Stern
• [gmx-users] Atomtype opls_116 not found when runnning GROMPP   Fernando Nunes
  • [gmx-users] Atomtype opls_116 not found when runnning GROMPP   Justin Lemkul
    • [gmx-users] Atomtype opls_116 not found when runnning GROMPP   Fernando Nunes
• [gmx-users] Analysis the dynamics of water molecules   Soham Sarkar
• [gmx-users] GPU issue - system that was stable on CPUs crashes   Hannah Magdalena Baumann
  • [gmx-users] GPU issue - system that was stable on CPUs crashes   Mark Abraham
    • [gmx-users] GPU issue - system that was stable on CPUs crashes   Hannah Baumann
• [gmx-users] correcting timesteps   Leigh
• [gmx-users] Details of g_rdf functions in version 4.6.5.   Henry Vider
  • [gmx-users] Details of g_rdf functions in version 4.6.5.   Dallas Warren
    • [gmx-users] Details of g_rdf functions in version 4.6.5.   Henry Vider
      • [gmx-users] Details of g_rdf functions in version 4.6.5.   Justin Lemkul
      • [gmx-users] Details of g_rdf functions in version 4.6.5.   Henry Vider
      • [gmx-users] Details of g_rdf functions in version 4.6.5.   Justin Lemkul
• [gmx-users] simulation continuation - gen-vel = yes   John Whittaker
  • [gmx-users] simulation continuation - gen-vel = yes   Mark Abraham
    • [gmx-users] simulation continuation - gen-vel = yes   John Whittaker
• [gmx-users] cmap error while making tpr file from dcd file   Santanu Santra
  • [gmx-users] cmap error while making tpr file from dcd file   Mark Abraham
• [gmx-users] How to measure distance and find salt bridges in GROMACS ?   Vikram Dalal
  • [gmx-users] How to measure distance and find salt bridges in GROMACS ?   Dallas Warren
• [gmx-users] Improving the MD simulations.   Ahmed
• [gmx-users] Cgenff generated force field problem   Prabir Khatua
  • [gmx-users] Cgenff generated force field problem   Justin Lemkul
    • [gmx-users] Cgenff generated force field problem   Prabir Khatua
• [gmx-users] Cgenff generated force field issue   Prabir Khatua
• [gmx-users] cgenff generated force field problem   Prabir Khatua
• [gmx-users] Membrane protein simulation isotropic vs semiisotropic   Prasanth G, Research Scholar
  • [gmx-users] Membrane protein simulation isotropic vs semiisotropic   Bratin Kumar Das
  • [gmx-users] Membrane protein simulation isotropic vs semiisotropic   Prasanth G, Research Scholar
    • [gmx-users] Membrane protein simulation isotropic vs semiisotropic   paul buscemi
      • [gmx-users] Membrane protein simulation isotropic vs semiisotropic   Justin Lemkul
• [gmx-users] GROMACS 2019.3 patch release available   Paul bauer
• [gmx-users] MD Simulation Time Is Slow   Ahmed
• [gmx-users] Spectrum from nmeig command   up201406812
  • [gmx-users] Spectrum from nmeig command   David van der Spoel
• [gmx-users] use of UFF   m g
  • [gmx-users] use of UFF   Justin Lemkul
• [gmx-users] Water model choice   Pandya, Akash
  • [gmx-users] Water model choice   Justin Lemkul
• [gmx-users] water model in use of UFF   m g
• [gmx-users] Citrate topology in Charmm36 FF   Pandya, Akash
• [gmx-users] Error in MD simulation   Mahmoud Mirzaei
  • [gmx-users] Error in MD simulation   Mark Abraham
  • [gmx-users] XVG Plotting by Grace   Mahmoud Mirzaei
    • [gmx-users] XVG Plotting by Grace   Israel Estrada
    • [gmx-users] XVG Plotting by Grace   MOHD HOMAIDUR RAHMAN
    • [gmx-users] Error in Solvation Box   Mahmoud Mirzaei
      • [gmx-users] Error in Solvation Box   Dallas Warren
      • [gmx-users] Error in Solvation Box   Bratin Kumar Das
• [gmx-users] correcting timesteps   Leigh
  • [gmx-users] correcting timesteps   Mark Abraham
• [gmx-users] Water model for UFF   m g
• [gmx-users] membrane region fixed   Patricia Saenz Méndez
  • [gmx-users] membrane region fixed   Mark Abraham
• [gmx-users] Constraining a small molecule in a region   ehsan shahini
  • [gmx-users] Constraining a small molecule in a region   Mark Abraham
• [gmx-users] OPLS-ff topology file for modified residue procedure?   Neena Susan Eappen
  • [gmx-users] OPLS-ff topology file for modified residue procedure?   Neena Susan Eappen
• [gmx-users] 2019.3 - Fixed Issue 2953: With DD, all intermolecular interactions were ignored?   Mateusz Bieniek
  • [gmx-users] 2019.3 - Fixed Issue 2953: With DD, all intermolecular interactions were ignored?   Eiso AB
    • [gmx-users] 2019.3 - Fixed Issue 2953: With DD, all intermolecular interactions were ignored?   Mark Abraham
• [gmx-users] Hydrogen bond autocorrelation   Gmx QA
  • [gmx-users] Hydrogen bond autocorrelation   David van der Spoel
    • [gmx-users] Hydrogen bond autocorrelation   Gmx QA
• [gmx-users] GROMACS Output Timestep Changes Over a Long, Check-pointed Simulation   Eric R Beyerle
  • [gmx-users] GROMACS Output Timestep Changes Over a Long, Check-pointed Simulation   Mark Abraham
  • [gmx-users] GROMACS Output Timestep Changes Over a Long, Check-pointed Simulation   Eric R Beyerle
    • [gmx-users] GROMACS Output Timestep Changes Over a Long, Check-pointed Simulation   Mark Abraham
• [gmx-users] Difference between NH2 in c-term and aminoacids   Myunggi Yi
  • [gmx-users] Difference between NH2 in c-term and aminoacids   Justin Lemkul
• [gmx-users] dragging gro files into VMD   paul buscemi
• [gmx-users] Visualising RDF selections   Henry Vider
• [gmx-users] calculation of msd of water molecule   Soham Sarkar
• [gmx-users] CHARMM36 in Gromacs :DNA terminus residues   Mehdi Bagherpour
• [gmx-users] CHARMM36 in Gromacs :DNA terminus residues problem   Mahdi Bagherpoor
  • [gmx-users] CHARMM36 in Gromacs :DNA terminus residues problem   Justin Lemkul
• [gmx-users] Force field   Mijiddorj B
• [gmx-users] Error gmx pdb2gro   Danilo Boskovic
  • [gmx-users] Error gmx pdb2gro   Danilo Boskovic
    • [gmx-users] Error gmx pdb2gro   Danilo Boskovic
      • [gmx-users] Error gmx pdb2gro   Danilo Boskovic
  • [gmx-users] Error gmx pdb2gro   Justin Lemkul
    • [gmx-users] Error gmx pdb2gro   Danilo Boskovic
      • [gmx-users] Error gmx pdb2gro   Danilo Boskovic
      • [gmx-users] Error gmx pdb2gro   Justin Lemkul
• [gmx-users] aligning MD system to a reference (to use correlation driven MD with an EM map)   Cédric Leyrat
• [gmx-users] FEP in vacuum simulation - inconsistent results among FEP methods   Melania T
• [gmx-users] water model based on UFF   m g
• [gmx-users] aligning MD system to a reference (to use correlation driven MD with an EM map)   Cédric Leyrat
• [gmx-users] Check point file   Alex
  • [gmx-users] Check point file   Dallas Warren
  • [gmx-users] Check point file   Mark Abraham
    • [gmx-users] Check point file   Alex
      • [gmx-users] Check point file   Mark Abraham
      • [gmx-users] Check point file   Alex
      • [gmx-users] Check point file   Dallas Warren
• [gmx-users] (-13.000000 Total charge should normally be an integer)Facing problem while running gromacs   kalpana
• [gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs   kalpana
  • [gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs   Alex
    • [gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs   Bratin Kumar Das
      • [gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs   kalpana
      • [gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs   Dallas Warren
  • [gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs   Dallas Warren
• [gmx-users] RNA molecule simulation   Priyanka Singh
• [gmx-users] Amber force field for metal Surface   Kumari Shilpa
  • [gmx-users] Amber force field for metal Surface   Alex
• [gmx-users] GROMOS FF conversion   András Ferenc WACHA
  • [gmx-users] GROMOS FF conversion   Piggot T.
    • [gmx-users] GROMOS FF conversion   András Ferenc WACHA
• [gmx-users] Kindly help   kalpana
  • [gmx-users] Kindly help   Dallas Warren
  • [gmx-users] Fetal error at grompp   kalpana
    • [gmx-users] Fetal error at grompp   Dallas Warren
    • [gmx-users] Fetal error at grompp   Mark Abraham
  • [gmx-users] Kindly help   Abhishek Acharya
    • [gmx-users] Kindly help   Bratin Kumar Das
• [gmx-users] Minimization stops without reaching the requested precision Fmax < 1000   Mahdi Bagherpoor
  • [gmx-users] Minimization stops without reaching the requested precision Fmax < 1000   Dallas Warren
• [gmx-users] problem regarding gmx wham   san kumar
• [gmx-users] SMD Pull Direction   Reza Esmaeeli
  • [gmx-users] SMD Pull Direction   Kevin Boyd
    • [gmx-users] SMD Pull Direction   Reza Esmaeeli
• [gmx-users] Error using gmx gangle   朱元昭
• [gmx-users] Difference between equilibration and production run   Neena Susan Eappen
  • [gmx-users] Difference between equilibration and production run   Bratin Kumar Das
• [gmx-users] appropriate force fielf   starlight
  • [gmx-users] appropriate force fielf   Paul Buscemi
• [gmx-users] Minimization stops without reaching the requested precision Fmax < 1000   Mahdi Bagherpoor
  • [gmx-users] Minimization stops without reaching the requested precision Fmax < 1000   Dallas Warren
• [gmx-users] from n2t to topology with similar groups   Claire M.
• [gmx-users] Generate OPLS Parameters for a modified residue   Neena Susan Eappen
• [gmx-users] Overall charge -0.0002   Bratin Kumar Das
• [gmx-users] Tool for two-dimensional cylindrical pair correlation function ?   Alessandro Triolo
• [gmx-users] Tool for two-dimensional cylindrical pair correlation function ?   Alessandro Triolo
• [gmx-users] Topology for CARG for Amber94 FF   Pandya, Akash
• [gmx-users] How to define a user-defined potential   Divya Rai
  • [gmx-users] How to define a user-defined potential   Mark Abraham
• [gmx-users] Visualizing hexamer with solvent   Simone Orioli
• [gmx-users] clustering of ions during NPT simulation   Netaly Khazanov
  • [gmx-users] clustering of ions during NPT simulation   Paul Buscemi
  • [gmx-users] clustering of ions during NPT simulation   Justin Lemkul
    • [gmx-users] clustering of ions during NPT simulation   Netaly Khazanov
• [gmx-users] Implementing Drude Particles   Finnigan, Sophie
  • [gmx-users] Implementing Drude Particles   Justin Lemkul
• [gmx-users] DGPU_DEPLOYMENT_KIT_ROOT_DIR   anthonyliao_91
• [gmx-users] errors during installation   kalpana
  • [gmx-users] errors during installation   kalpana
    • [gmx-users] errors during installation   Mark Abraham
• [gmx-users] how to accelerate mdrun process   kalpana
  • [gmx-users] how to accelerate mdrun process   Mark Abraham
• [gmx-users] How to install gromacs on cpu cluster   sunyeping
  • [gmx-users] How to install gromacs on cpu cluster   Benson Muite
    • [gmx-users] How to install gromacs on cpu cluster   sunyeping
      • [gmx-users] How to install gromacs on cpu cluster   Benson Muite
      • [gmx-users] How to install gromacs on cpu cluster   sunyeping
      • [gmx-users] How to install gromacs on cpu cluster   Benson Muite
      • [gmx-users] How to install gromacs on cpu cluster   Benson Muite
• [gmx-users] interrupt of gmx mdrun   Andrew Bostick
• [gmx-users] Transference of dihedral potentials between united atom and all-atom force fields   Pragati Sharma
  • [gmx-users] Transference of dihedral potentials between united atom and all-atom force fields   Peter Stern
    • [gmx-users] Transference of dihedral potentials between united atom and all-atom force fields   Justin Lemkul
• [gmx-users] appropriate forcefield   starlight
• [gmx-users] Constraints Error; In Using Tetrahedral Zinc Dummy Model   Mahdi Bagherpoor
• [gmx-users] Constraints Error; In Using Tetrahedral Zinc Dummy Model   Mahdi Bagherpoor
  • [gmx-users] Constraints Error; In Using Tetrahedral Zinc Dummy Model   Mark Abraham

Last message date: Sun Jun 30 23:24:28 CEST 2019
Archived on: Sun Jun 30 23:24:29 CEST 2019

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