April 2020 Archives by thread

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Starting: Wed Apr 1 02:05:57 CEST 2020
Ending: Thu Apr 30 20:07:50 CEST 2020
Messages: 472

• [gmx-users] Effect of atomic charge on bonding parameters   Neena Susan Eappen
  • [gmx-users] Effect of atomic charge on bonding parameters   Justin Lemkul
  • [gmx-users] Effect of atomic charge on bonding parameters   Neena Susan Eappen
    • [gmx-users] Effect of atomic charge on bonding parameters   Justin Lemkul
• [gmx-users] How to reduce the penalty of small molecule from CGenFF   Justin Lemkul
• [gmx-users] Different force constants for different umbrella windows?   Justin Lemkul
• [gmx-users] 1-4 LJ interactions   Justin Lemkul
  • [gmx-users] 1-4 LJ interactions   Andrey Gurtovenko
    • [gmx-users] 1-4 LJ interactions   Justin Lemkul
• [gmx-users] PCA analysis with different atoms in -s and -f   ZHANG Cheng
  • [gmx-users] PCA analysis with different atoms in -s and -f   Eduardo Jardón
  • [gmx-users] PCA analysis with different atoms in -s and -f   ZHANG Cheng
• [gmx-users] gmx rms divergence from the starting structure   Wei-Ta Li
• [gmx-users] distance from geometrical center of protein to the surface   Wei-Ta Li
• [gmx-users] 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out   Seketoulie Keretsu
  • [gmx-users] 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out   Justin Lemkul
• [gmx-users] Optimising mdrun   Robert Cordina
  • [gmx-users] Optimising mdrun   Kevin Boyd
    • [gmx-users] Optimising mdrun   Robert Cordina
• [gmx-users] GROMACS mailing-list will move to a forum   Paul bauer
• [gmx-users] Problem with REST2   Joseph, Benjamin Philipp
  • [gmx-users] Problem with REST2   Daniel Burns
    • [gmx-users] Problem with REST2   Joseph, Benjamin Philipp
      • [gmx-users] Problem with REST2   Daniel Burns
      • [gmx-users] Problem with REST2   Joseph, Benjamin Philipp
• [gmx-users] Free energy of protonation   Gmx QA
  • [gmx-users] Free energy of protonation   Sotirios Dionysios I. Papadatos
• [gmx-users] Reviewing docking resluts   neelam wafa
• [gmx-users] Onsager coefficient   Sina Omrani
  • [gmx-users] Onsager coefficient   David van der Spoel
    • [gmx-users] Onsager coefficient   Sina Omrani
• [gmx-users] converting gromacs topology file to namd topology file   Hadi Rahmaninejad
  • [gmx-users] converting gromacs topology file to namd topology file   John Whittaker
• [gmx-users] Missing gromacs.lib when building Grmoacs 2020.1 in vs 2019   孙傲然
• [gmx-users] Issue with PMF   Alex
  • [gmx-users] Issue with PMF   Justin Lemkul
    • [gmx-users] Issue with PMF   Alex
      • [gmx-users] Issue with PMF   Justin Lemkul
      • [gmx-users] Issue with PMF   Quyen V. Vu
      • [gmx-users] Issue with PMF   Justin Lemkul
• [gmx-users] (no subject)   Feriel Terbeche
  • [gmx-users] (no subject)   Daniel Burns
• [gmx-users] Simulation of Protein-Protein Complex   Surya Sanjay
  • [gmx-users] Simulation of Protein-Protein Complex   Justin Lemkul
• [gmx-users] Fwd: geometry optimization of metalloenzyme   Nadia Elghobashi-Meinhardt
  • [gmx-users] Fwd: geometry optimization of metalloenzyme   Justin Lemkul
    • [gmx-users] Fwd: geometry optimization of metalloenzyme   Nadia Elghobashi-Meinhardt
      • [gmx-users] Fwd: Fwd: geometry optimization of metalloenzyme   Nadia Elghobashi-Meinhardt
      • [gmx-users] Fwd: geometry optimization of metalloenzyme   Justin Lemkul
• [gmx-users] Simulation of Protein-Protein Complex   Justin Lemkul
• [gmx-users] Fwd: no atom pairs for dispersion correction   Sadaf Rani
• [gmx-users] Scale Triclinic Box   Maryam Sadeghi
  • [gmx-users] Scale Triclinic Box   Salman Zarrini
    • [gmx-users] Scale Triclinic Box   Maryam Sadeghi
      • [gmx-users] Scale Triclinic Box   Justin Lemkul
      • [gmx-users] Scale Triclinic Box   Maryam Sadeghi
      • [gmx-users] Scale Triclinic Box   Justin Lemkul
• [gmx-users] change the top file of a homodimer protein   Qasim Pars
  • [gmx-users] change the top file of a homodimer protein   Justin Lemkul
• [gmx-users] How to parametrize a new molecule?   Herbert de Castro Georg
  • [gmx-users] How to parametrize a new molecule?   Justin Lemkul
    • [gmx-users] How to parametrize a new molecule?   Herbert de Castro Georg
      • [gmx-users] How to parametrize a new molecule?   Mahdi Bagherpoor
      • [gmx-users] How to parametrize a new molecule?   Herbert de Castro Georg
• [gmx-users] Calculate probability of presence of water around a residues   pooja kesari
• [gmx-users] How to use GROMACS license?   Nikhil Maroli
  • [gmx-users] How to use GROMACS license?   David van der Spoel
• [gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0   Wei-Tse Hsu
  • [gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0   Kevin Boyd
  • [gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0   Szilárd Páll
• [gmx-users] GROMACS 2020.1 failed to pass make check   Wei-Tse Hsu
  • [gmx-users] GROMACS 2020.1 failed to pass make check   Paul bauer
    • [gmx-users] GROMACS 2020.1 failed to pass make check   Wei-Tse Hsu
• [gmx-users] Fumbling in the dark with dihedral pulling   Marko Petrovic
  • [gmx-users] Fumbling in the dark with dihedral pulling   Justin Lemkul
    • [gmx-users] Fumbling in the dark with dihedral pulling   Marko Petrovic
      • [gmx-users] Fumbling in the dark with dihedral pulling   Justin Lemkul
      • [gmx-users] Fumbling in the dark with dihedral pulling   Marko Petrovic
      • [gmx-users] Fumbling in the dark with dihedral pulling   Justin Lemkul
• [gmx-users] Bonds definition in itp files   Sina Omrani
  • [gmx-users] Bonds definition in itp files   Justin Lemkul
    • [gmx-users] Bonds definition in itp files   Sina Omrani
      • [gmx-users] Bonds definition in itp files   Justin Lemkul
• [gmx-users] Protonation state of aminoacids from pdb and pdb2gmx   Javier Luque Di Salvo
  • [gmx-users] Protonation state of aminoacids from pdb and pdb2gmx   Justin Lemkul
• [gmx-users] NAG N-Acetylglucosamine force field parameters   Javier Luque Di Salvo
  • [gmx-users] NAG N-Acetylglucosamine force field parameters   Casalini Tommaso
  • [gmx-users] NAG N-Acetylglucosamine force field parameters   Kenny Goossens
• [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported"   Szilárd Páll
  • [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported"   Leandro Bortot
• [gmx-users] Anharmonic/Morse flexible water   Jacek Artur Kozuch
• [gmx-users] restarting a simulation   Sadaf Rani
  • [gmx-users] restarting a simulation   Quyen V. Vu
  • [gmx-users] restarting a simulation   Daniel Burns
    • [gmx-users] restarting a simulation   Justin Lemkul
• [gmx-users] Velocities from the .gro file   Mohamed Abdelaal
  • [gmx-users] Velocities from the .gro file   Justin Lemkul
    • [gmx-users] Velocities from the .gro file   Mohamed Abdelaal
      • [gmx-users] Velocities from the .gro file   Eric Smoll
      • [gmx-users] Velocities from the .gro file   Mohamed Abdelaal
      • [gmx-users] Velocities from the .gro file   Eric Smoll
      • [gmx-users] Velocities from the .gro file   Mohamed Abdelaal
      • [gmx-users] Velocities from the .gro file   Mohamed Abdelaal
      • [gmx-users] Velocities from the .gro file   Justin Lemkul
      • [gmx-users] Velocities from the .gro file   Mohamed Abdelaal
      • [gmx-users] Velocities from the .gro file   Eric Smoll
      • [gmx-users] Velocities from the .gro file   Mohamed Abdelaal
      • [gmx-users] Velocities from the .gro file   Eric Smoll
      • [gmx-users] Velocities from the .gro file   Mohamed Abdelaal
      • [gmx-users] Velocities from the .gro file   Eric Smoll
• [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units   ZHANG Cheng
  • [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units   André Farias de Moura
  • [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units   ZHANG Cheng
    • [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units   Justin Lemkul
      • [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units   André Farias de Moura
    • [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units   ZHANG Cheng
      • [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units   André Farias de Moura
      • [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units   ZHANG Cheng
      • [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units   Benson Muite
• [gmx-users] dt in mdp   Alex
  • [gmx-users] dt in mdp   Justin Lemkul
    • [gmx-users] dt in mdp   Alex
      • [gmx-users] dt in mdp   Alex
      • [gmx-users] dt in mdp   Justin Lemkul
      • [gmx-users] dt in mdp   Alex
      • [gmx-users] dt in mdp   Justin Lemkul
      • [gmx-users] dt in mdp   Alex
      • [gmx-users] dt in mdp   Justin Lemkul
• [gmx-users] Double-well potential for bonded interaction   Jacek Artur Kozuch
  • [gmx-users] Double-well potential for bonded interaction   John Whittaker
• [gmx-users] Dockerfile to use gromacs/gromacs in DockerHub?   fernando fuentes de la parra
• [gmx-users] Restarting a REST2 simulation   Joseph, Benjamin Philipp
  • [gmx-users] Restarting a REST2 simulation   Qinghua Liao
• [gmx-users] Concatenating trajectories   Pandya, Akash
  • [gmx-users] Concatenating trajectories   Qinghua Liao
    • [gmx-users] Concatenating trajectories   Mark Abraham
• [gmx-users] Converting a tpr file to an older version of gromacs   Mariem Ghoula
  • [gmx-users] Converting a tpr file to an older version of gromacs   Paul bauer
    • [gmx-users] Converting a tpr file to an older version of gromacs   Mariem Ghoula
• [gmx-users] How to extend the force field by polariation parameters   Zuzana Benkova
  • [gmx-users] How to extend the force field by polariation parameters   Justin Lemkul
    • [gmx-users] How to extend the force field by polariation parameters   Zuzana Benkova
      • [gmx-users] How to extend the force field by polariation parameters   Justin Lemkul
• [gmx-users] Buggy 2020?   Parvez Mh
  • [gmx-users] Buggy 2020?   Mark Abraham
    • [gmx-users] Buggy 2020?   Parvez Mh
• [gmx-users] treating trajectory for diffusion calculations   Dave M
  • [gmx-users] treating trajectory for diffusion calculations   Dave M
• [gmx-users] Regarding version of gromacs   Ashma Khan
  • [gmx-users] Regarding version of gromacs   FAISAL NABI
    • [gmx-users] Regarding version of gromacs   Justin Lemkul
• [gmx-users] GROMACS version issue   Yasaman KARAMI
  • [gmx-users] GROMACS version issue   Justin Lemkul
• [gmx-users] Problem with pdb2gmx   Elham Taghikhani
  • [gmx-users] Problem with pdb2gmx   Justin Lemkul
• [gmx-users] Protonated ligand free energy calculation in water   Rolly Ng
• [gmx-users] segmentation fault gmx do_dssp   Sadaf Rani
  • [gmx-users] segmentation fault gmx do_dssp   Qinghua Liao
  • [gmx-users] segmentation fault gmx do_dssp   Justin Lemkul
• [gmx-users] energy minimizing   Afsane Farhadi
• [gmx-users] segmentation fault gmx do_dssp   Sadaf Rani
  • [gmx-users] segmentation fault gmx do_dssp   Justin Lemkul
• [gmx-users] pdb2gmx: Selecting Force Field in first command   fernando at hypernetlabs.io
  • [gmx-users] pdb2gmx: Selecting Force Field in first command   Justin Lemkul
• [gmx-users] Regarding version of gromacs   Ashma Khan
  • [gmx-users] Regarding version of gromacs   Justin Lemkul
• [gmx-users] Cannot run short-ranged nonbonded interactions on a GPU because there is none detected.   Mahmood Naderan
• [gmx-users] Problem with pdb2gmx   Elham Taghikhani
  • [gmx-users] Problem with pdb2gmx   David van der Spoel
  • [gmx-users] Problem with pdb2gmx   Justin Lemkul
  • [gmx-users] Problem with pdb2gmx   Elham Taghikhani
    • [gmx-users] Problem with pdb2gmx   Justin Lemkul
    • [gmx-users] Problem with pdb2gmx   Elham Taghikhani
      • [gmx-users] Problem with pdb2gmx   Justin Lemkul
      • [gmx-users] Problem with pdb2gmx   Elham Taghikhani
      • [gmx-users] Problem with pdb2gmx   Justin Lemkul
• [gmx-users] Problem in energy minimization step   Xuan Zhang
• [gmx-users] Post processing REMD simulation   Mohammad Madani
  • [gmx-users] Post processing REMD simulation   David van der Spoel
    • [gmx-users] Post processing REMD simulation   Mohammad Madani
      • [gmx-users] Post processing REMD simulation   David van der Spoel
• [gmx-users] duplicate angle index- angle restraint   Sadaf Rani
  • [gmx-users] duplicate angle index- angle restraint   Justin Lemkul
• [gmx-users] duplicate angle index- angle restraint   Sadaf Rani
  • [gmx-users] duplicate angle index- angle restraint   Justin Lemkul
• [gmx-users] Electric field   Prithwish Nandi
  • [gmx-users] Electric field   Prithwish Nandi
• [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs   Lazaro Castanedo
• [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs   lazaro monteserin
  • [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs   John Whittaker
    • [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs   lazaro monteserin
• [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs   lazaro monteserin
• [gmx-users] Triclinic box is too skewed   Jun Zhou
• [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs   Neena Susan Eappen
  • [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs   lazaro monteserin
  • [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs   Neena Susan Eappen
    • [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs   lazaro monteserin
• [gmx-users] Parametrization POM molecule   Paolo Costa
• [gmx-users] vdW cut-off to LJPME: Simulation crashes immediately   Udaya Dahal
• [gmx-users] Same one lipid in bilayer causing LINCS crashing during minimization   Erik Henze
• [gmx-users] about simulation of small molecules in vacuum. link to dropbox   lazaro monteserin
• [gmx-users] vdW cut-off to LJPME: Simulation crashes immediately   Udaya Dahal
• [gmx-users] Error message   Prithwish Nandi
• [gmx-users] how to run equilibration when freezing part of an small molecule in vacuum and in water environment?   lazaro monteserin
  • [gmx-users] how to run equilibration when freezing part of an small molecule in vacuum and in water environment?   Justin Lemkul
    • [gmx-users] how to run equilibration when freezing part of an small molecule in vacuum and in water environment?   lazaro monteserin
• [gmx-users] energy minimization   Afsane Farhadi
  • [gmx-users] energy minimization   Dallas Warren
• [gmx-users] Polarization assistance request   Heroneme, Carl Joseph
• [gmx-users] Replica exchange probabilities beyond version 2016   Pritam Ganguly
  • [gmx-users] Replica exchange probabilities beyond version 2016   Gül Zerze
    • [gmx-users] Replica exchange probabilities beyond version 2016   Pritam Ganguly
• [gmx-users] Ways to calculate shear viscosity   Jun Zhou
• [gmx-users] Basic question about command line   Mohammad Madani
  • [gmx-users] Basic question about command line   Justin Lemkul
    • [gmx-users] Basic question about command line   shubhadip das
• [gmx-users] How to solve the "LINCS WARNING" problem   변진영
  • [gmx-users] How to solve the "LINCS WARNING" problem   Yu Du
    • [gmx-users] How to solve the "LINCS WARNING" problem   변진영
      • [gmx-users] How to solve the "LINCS WARNING" problem   Yu Du
      • [gmx-users] How to solve the "LINCS WARNING" problem   변진영
      • [gmx-users] How to solve the "LINCS WARNING" problem   Yu Du
      • [gmx-users] How to solve the "LINCS WARNING" problem   변진영
      • [gmx-users] How to solve the "LINCS WARNING" problem   Yu Du
• [gmx-users] Basic question about command line (Mohammad Madani)   Teslim Olayiwola
• [gmx-users] gromacs 2020, bug? high total energy   Tamas Hegedus
  • [gmx-users] gromacs 2020, bug? high total energy   Tamas Hegedus
• [gmx-users] How to prevent velocity generation for my position restrained molecules ?   Mohamed Abdelaal
  • [gmx-users] How to prevent velocity generation for my position restrained molecules ?   Justin Lemkul
• [gmx-users] semiisotropic pressure coupling.   Miro Astore
  • [gmx-users] semiisotropic pressure coupling.   Justin Lemkul
    • [gmx-users] semiisotropic pressure coupling.   Miro Astore
• [gmx-users] (NEW USER) Determining Complex Dielectric property of a solid state system   Tahsin Ashraf Khan
  • [gmx-users] (NEW USER) Determining Complex Dielectric property of a solid state system   David van der Spoel
• [gmx-users] Can we implement NMR restraint data in Gromacs?   Chaturvedi Navneet
  • [gmx-users] Can we implement NMR restraint data in Gromacs?   David van der Spoel
• [gmx-users] Error with Output from GMX cluster analysis   Teslim Olayiwola
• [gmx-users] Problem force constant bond stretc.   Paolo Costa
  • [gmx-users] Problem force constant bond stretc.   David van der Spoel
    • [gmx-users] Problem force constant bond stretc.   Paolo Costa
• [gmx-users] Trouble with restrained dihedrals   Marko Petrovic
  • [gmx-users] Trouble with restrained dihedrals   Marko Petrovic
  • [gmx-users] Trouble with restrained dihedrals   David van der Spoel
• [gmx-users] GROMACS PBS GPU JOB submission   Tuanan Lourenço
  • [gmx-users] GROMACS PBS GPU JOB submission   Yu Du
• [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported"   Alan Gray
  • [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported"   Leandro Bortot
• [gmx-users] WARNING 1 [file topol.top, line 60334] - How to manage? -maxwarn 1 or any other solution   Adarsh V. K.
  • [gmx-users] WARNING 1 [file topol.top, line 60334] - How to manage? -maxwarn 1 or any other solution   Justin Lemkul
• [gmx-users] about problem running script for Gibbs free energy simulation   lazaro monteserin
  • [gmx-users] about problem running script for Gibbs free energy simulation   Justin Lemkul
    • [gmx-users] about problem running script for Gibbs free energy simulation   lazaro monteserin
      • [gmx-users] about problem running script for Gibbs free energy simulation   Justin Lemkul
      • [gmx-users] about problem running script for Gibbs free energy simulation   lazaro monteserin
      • [gmx-users] about problem running script for Gibbs free energy simulation   Justin Lemkul
      • [gmx-users] about problem running script for Gibbs free energy simulation   lazaro monteserin
      • [gmx-users] about problem running script for Gibbs free energy simulation   lazaro monteserin
• [gmx-users] Measuring bond distances, angles and dihedrals   Robert Cordina
  • [gmx-users] Measuring bond distances, angles and dihedrals   Yu Du
    • [gmx-users] Measuring bond distances, angles and dihedrals   Robert Cordina
      • [gmx-users] Measuring bond distances, angles and dihedrals   Yu Du
      • [gmx-users] Measuring bond distances, angles and dihedrals   Smith, Micholas D.
      • [gmx-users] Measuring bond distances, angles and dihedrals   Justin Lemkul
      • [gmx-users] Measuring bond distances, angles and dihedrals   Robert Cordina
      • [gmx-users] [EXTERNAL] Re: Measuring bond distances, angles and dihedrals   Smith, Micholas D.
      • [gmx-users] [EXTERNAL] Re: Measuring bond distances, angles and dihedrals   Yu Du
• [gmx-users] Question on running gmx trjconv without 2 prompts   Lei Qian
  • [gmx-users] Question on running gmx trjconv without 2 prompts   Justin Lemkul
    • [gmx-users] Question on running gmx trjconv without 2 prompts   Lei Qian
• [gmx-users] Failed to find GROMACS magic number in trr frame header   Mijiddorj B
  • [gmx-users] Failed to find GROMACS magic number in trr frame header   Mijiddorj B
    • [gmx-users] Failed to find GROMACS magic number in trr frame header   Justin Lemkul
• [gmx-users] ' LONEPAIR LP1 ' gives error message in protein - ligand simulation   Adarsh V. K.
  • [gmx-users] ' LONEPAIR LP1 ' gives error message in protein - ligand simulation   Justin Lemkul
• [gmx-users] RIN (Residue interaction network) for protein ligand interactions   Prasanth G, Research Scholar
• [gmx-users] atomselection for index group of cyclic rings   Prasanth G, Research Scholar
  • [gmx-users] atomselection for index group of cyclic rings   Archana Sonawani-Jagtap
• [gmx-users] atomtype "OE" in charmm36   Schirra, Simone
  • [gmx-users] atomtype "OE" in charmm36   Justin Lemkul
    • [gmx-users] atomtype "OE" in charmm36   Schirra, Simone
• [gmx-users] Appending crashed Replica Exchange Simulations: init_step/-replex is not equal for all subsystems   Johannes Hermann
  • [gmx-users] Appending crashed Replica Exchange Simulations: init_step/-replex is not equal for all subsystems   Johannes Hermann
• [gmx-users] How to solve the "LINCS WARNING" problem (???)   Prasanth G, Research Scholar
  • [gmx-users] How to solve the "LINCS WARNING" problem (???)   변진영
    • [gmx-users] How to solve the "LINCS WARNING" problem (???)   Justin Lemkul
• [gmx-users] weird output from simultions of a protein between two sheets   Zuzana Benkova
  • [gmx-users] weird output from simultions of a protein between two sheets   Justin Lemkul
    • [gmx-users] weird output from simultions of a protein between two sheets   Zuzana Benkova
      • [gmx-users] weird output from simultions of a protein between two sheets   Justin Lemkul
      • [gmx-users] weird output from simultions of a protein between two sheets   Zuzana Benkova
      • [gmx-users] Spec'ing for new machines (again!)   Alex
      • [gmx-users] Spec'ing for new machines (again!)   FAISAL NABI
      • [gmx-users] Spec'ing for new machines (again!)   Kevin Boyd
      • [gmx-users] Spec'ing for new machines (again!)   Alex
      • [gmx-users] Spec'ing for new machines (again!)   Kevin Boyd
      • [gmx-users] Spec'ing for new machines (again!)   Alex
      • [gmx-users] Spec'ing for new machines (again!)   Szilárd Páll
      • [gmx-users] Spec'ing for new machines (again!)   Alex
• [gmx-users] position restrain of water   m g
  • [gmx-users] position restrain of water   Justin Lemkul
• [gmx-users] Disabling MKL   Mahmood Naderan
  • [gmx-users] Disabling MKL   Szilárd Páll
• [gmx-users] Dramatic decrease NVE production   Dorj Bat
  • [gmx-users] Dramatic decrease NVE production   Justin Lemkul
• [gmx-users] Does the energy minimization deals with velocity ?   Mohamed Abdelaal
  • [gmx-users] Does the energy minimization deals with velocity ?   Justin Lemkul
• [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6   Paolo Costa
  • [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6   Justin Lemkul
    • [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6   Paolo Costa
      • [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6   Justin Lemkul
      • [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6   Paolo Costa
      • [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6   Justin Lemkul
      • [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6   Paolo Costa
• [gmx-users] Installation on iPad?   Ali Khodayari
• [gmx-users] Regarding use of harmonic wall model   Shashank Ranjan Srivastava
  • [gmx-users] Regarding use of harmonic wall model   Justin Lemkul
• [gmx-users] Failed to find GROMACS magic number in trr frame header   Mijiddorj B
  • [gmx-users] Failed to find GROMACS magic number in trr frame header   Mark Abraham
  • [gmx-users] Failed to find GROMACS magic number in trr frame header   Justin Lemkul
• [gmx-users] Installation on iPad   Ali Khodayari
  • [gmx-users] Installation on iPad   Marko Petrovic
    • [gmx-users] Installation on iPad   Ali Khodayari
• [gmx-users] Artifact in pull-pbc-ref-prev-step-com   Alex
  • [gmx-users] Artifact in pull-pbc-ref-prev-step-com   Alex
  • [gmx-users] Artifact in pull-pbc-ref-prev-step-com   Magnus Lundborg
    • [gmx-users] Artifact in pull-pbc-ref-prev-step-com   Magnus Lundborg
      • [gmx-users] Artifact in pull-pbc-ref-prev-step-com   Alex
      • [gmx-users] Artifact in pull-pbc-ref-prev-step-com   Magnus Lundborg
      • [gmx-users] Artifact in pull-pbc-ref-prev-step-com   Alex
      • [gmx-users] Artifact in pull-pbc-ref-prev-step-com   Magnus Lundborg
      • [gmx-users] Artifact in pull-pbc-ref-prev-step-com   Alex
      • [gmx-users] Artifact in pull-pbc-ref-prev-step-com   Magnus Lundborg
• [gmx-users] Question about Mean Square Displacement (MSD)   Sina Omrani
  • [gmx-users] Question about Mean Square Displacement (MSD)   Arun Srikanth
    • [gmx-users] Question about Mean Square Displacement (MSD)   Sina Omrani
    • [gmx-users] Question about Mean Square Displacement (MSD)   Kevin Boyd
      • [gmx-users] Question about Mean Square Displacement (MSD)   Sina Omrani
      • [gmx-users] Question about Mean Square Displacement (MSD)   Kevin Boyd
      • [gmx-users] Question about Mean Square Displacement (MSD)   Sina Omrani
      • [gmx-users] Question about Mean Square Displacement (MSD)   Kevin Boyd
      • [gmx-users] Question about Mean Square Displacement (MSD)   Sina Omrani
      • [gmx-users] Question about Mean Square Displacement (MSD)   Kevin Boyd
• [gmx-users] about correct methodology to run MD of small molecule in gromacs   lazaro monteserin
  • [gmx-users] about correct methodology to run MD of small molecule in gromacs   Justin Lemkul
    • [gmx-users] about correct methodology to run MD of small molecule in gromacs   lazaro monteserin
      • [gmx-users] about correct methodology to run MD of small molecule in gromacs   Justin Lemkul
      • [gmx-users] about correct methodology to run MD of small molecule in gromacs   lazaro monteserin
      • [gmx-users] about correct methodology to run MD of small molecule in gromacs   Justin Lemkul
      • [gmx-users] about correct methodology to run MD of small molecule in gromacs   lazaro monteserin
• [gmx-users] Triclinic box is too skewed   Jun Zhou
• [gmx-users] error in pdb2gmx   Sadaf Rani
• [gmx-users] error in pdb2gmx   Sadaf Rani
• [gmx-users] Segmentation fault (core dumped) error during minimization   Elham Taghikhani
  • [gmx-users] Segmentation fault (core dumped) error during minimization   Justin Lemkul
  • [gmx-users] Segmentation fault (core dumped) error during minimization   Elham Taghikhani
    • [gmx-users] Segmentation fault (core dumped) error during minimization   Justin Lemkul
    • [gmx-users] Segmentation fault (core dumped) error during minimization   Elham Taghikhani
      • [gmx-users] Segmentation fault (core dumped) error during minimization   Justin Lemkul
• [gmx-users] Error in pdb2gmx   Sadaf Rani
• [gmx-users] Failed to find GROMACS magic number in trr frame header   Mijiddorj B
  • [gmx-users] Failed to find GROMACS magic number in trr frame header   Justin Lemkul
• [gmx-users] Problem with Potential Mean Force calculation   Rolly Ng
  • [gmx-users] Problem with Potential Mean Force calculation   Justin Lemkul
    • [gmx-users] 回复: Problem with Potential Mean Force calculation   Rolly Ng
      • [gmx-users] 回复: Problem with Potential Mean Force calculation   Justin Lemkul
      • [gmx-users] 回复: Problem with Potential Mean Force calculation   Quyen V. Vu
      • [gmx-users] 回复: 回复: Problem with Potential Mean Force calculation   Rolly Ng
      • [gmx-users] 回复: 回复: Problem with Potential Mean Force calculation   Rolly Ng
      • [gmx-users] 回复: 回复: Problem with Potential Mean Force calculation   Justin Lemkul
      • [gmx-users] 回复: 回复: 回复: Problem with Potential Mean Force calculation   Rolly Ng
• [gmx-users] Regarding use of harmonic wall model   Shashank Ranjan Srivastava
  • [gmx-users] Regarding use of harmonic wall model   Justin Lemkul
• [gmx-users] Dihedral Restraints   Jacek Artur Kozuch
• [gmx-users] How to report bugs or issues?   Subhamoy Mahajan
• [gmx-users] How to report bugs or issues?   Yu Du
• [gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion   ABEL Stephane
  • [gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion   Justin Lemkul
• [gmx-users] Problem C-H bonds of Benzene after minimization   Paolo Costa
  • [gmx-users] Problem C-H bonds of Benzene after minimization   Justin Lemkul
    • [gmx-users] Problem C-H bonds of Benzene after minimization   Paolo Costa
• [gmx-users] GROMACS performance issues on POWER9/V100 node   Jonathan D. Halverson
  • [gmx-users] GROMACS performance issues on POWER9/V100 node   Kevin Boyd
    • [gmx-users] GROMACS performance issues on POWER9/V100 node   Jonathan D. Halverson
      • [gmx-users] GROMACS performance issues on POWER9/V100 node   Kevin Boyd
      • [gmx-users] GROMACS performance issues on POWER9/V100 node   Alex
      • [gmx-users] GROMACS performance issues on POWER9/V100 node   Szilárd Páll
      • [gmx-users] GROMACS performance issues on POWER9/V100 node   Alex
      • [gmx-users] GROMACS performance issues on POWER9/V100 node   Szilárd Páll
      • [gmx-users] GROMACS performance issues on POWER9/V100 node   Jonathan D. Halverson
  • [gmx-users] GROMACS performance issues on POWER9/V100 node   Szilárd Páll
    • [gmx-users] GROMACS performance issues on POWER9/V100 node   Szilárd Páll
      • [gmx-users] GROMACS performance issues on POWER9/V100 node   Jonathan D. Halverson
• [gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion   ABEL Stephane
• [gmx-users] about error running temperature equilibration   lazaro monteserin
  • [gmx-users] about error running temperature equilibration   Justin Lemkul
• [gmx-users] Umbrella Sampling with 2 reaction coordinates   Ernesto Camparolla
• [gmx-users] COMPEL question: Channel filter outside membrane, how to orient compartment boundaries   Erik Henze
  • [gmx-users] COMPEL question: Channel filter outside membrane, how to orient compartment boundaries   Kutzner, Carsten
• [gmx-users] Periodic boundary conditions during the simulation   Mohamed Abdelaal
  • [gmx-users] Periodic boundary conditions during the simulation   Dallas Warren
• [gmx-users] Regarding use of harmonic wall model   Shashank Ranjan Srivastava
• [gmx-users] gromacs.org_gmx-users Digest, Vol 192, Issue 89   Jun Zhou
• [gmx-users] Why there is no phosphorous atom in the "DA5" residue in dna.rtp   Tingguang.S
  • [gmx-users] Why there is no phosphorous atom in the "DA5" residue in dna.rtp   Justin Lemkul
    • [gmx-users] Why there is no phosphorous atom in the "DA5" residue in dna.rtp   Tingguang.S
• [gmx-users] lincs warning   Afsane Farhadi
  • [gmx-users] lincs warning   Yu Du
  • [gmx-users] lincs warning   Christian Blau
• [gmx-users] gromacs installation (2020&2019)   Netaly Khazanov
  • [gmx-users] gromacs installation (2020&2019)   Yu Du
    • [gmx-users] gromacs installation (2020&2019)   lazaro monteserin
      • [gmx-users] gromacs installation (2020&2019)   Netaly Khazanov
• [gmx-users] Fatal error pdb2gmx   Paolo Costa
  • [gmx-users] Fatal error pdb2gmx   Justin Lemkul
• [gmx-users] Error No default Proper Dih. types   Paolo Costa
  • [gmx-users] Error No default Proper Dih. types   Justin Lemkul
    • [gmx-users] Error No default Proper Dih. types   Paolo Costa
      • [gmx-users] Error No default Proper Dih. types   Justin Lemkul
      • [gmx-users] Error No default Proper Dih. types   Paolo Costa
      • [gmx-users] Error No default Proper Dih. types   Justin Lemkul
      • [gmx-users] Error No default Proper Dih. types   Paolo Costa
• [gmx-users] wham - Bootstraping   Alex
• [gmx-users] Atom CA used in that entry is not found in the input file   Daniel Burns
  • [gmx-users] Atom CA used in that entry is not found in the input file   Justin Lemkul
• [gmx-users] about how to create covar.ndx for dihedral Principal Component Analysis   lazaro monteserin
• [gmx-users] multiple nodes   Neha Gandhi
• [gmx-users] gmx sasa for protein-ligand complex(problem with command usage)   Archana Sonawani-Jagtap
• [gmx-users] lincs warning   Afsane Farhadi
• [gmx-users] Quick question: is TIP3P water model available in GROMOS54a7 force field?   Wei-Tse Hsu
  • [gmx-users] Quick question: is TIP3P water model available in GROMOS54a7 force field?   shakira shukoor
    • [gmx-users] Quick question: is TIP3P water model available in GROMOS54a7 force field?   Justin Lemkul
      • [gmx-users] Quick question: is TIP3P water model available in GROMOS54a7 force field?   Wei-Tse Hsu
• [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis   Neena Susan Eappen
  • [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis   Sahil Lall
  • [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis   Justin Lemkul
• [gmx-users] debugging   Miro Astore
  • [gmx-users] debugging   Christian Blau
• [gmx-users] Invalid atomtype format   Sadaf Rani
  • [gmx-users] Invalid atomtype format   Justin Lemkul
• [gmx-users] Atom positions change between topology generation and NVT mdrun   Max Winokan
• [gmx-users] Atom positions change between topology generation and NVT equilibration   Max Winokan
• [gmx-users] Atom positions change between topology generation and NVT equilibration   Max Winokan
  • [gmx-users] Atom positions change between topology generation and NVT equilibration   Christian Blau
  • [gmx-users] Atom positions change between topology generation and NVT equilibration   Justin Lemkul
• [gmx-users] POPC: Fatal error:   Dutta, Kunal
  • [gmx-users] POPC: Fatal error:   shakira shukoor
  • [gmx-users] POPC: Fatal error:   Justin Lemkul
• [gmx-users] about segmentation fault related with gmx trjconv   lazaro monteserin
• [gmx-users] GROMACS TUTOR WANTED   Joel Subach
• [gmx-users] about how to create angle.index with specific angles   lazaro monteserin
  • [gmx-users] about how to create angle.index with specific angles   Justin Lemkul
    • [gmx-users] about how to create angle.index with specific angles   lazaro monteserin
      • [gmx-users] about how to create angle.index with specific angles   Justin Lemkul
      • [gmx-users] about how to create angle.index with specific angles   lazaro monteserin
• [gmx-users] sadaf rani shared "Atom_type_error files.zip" with you   sadaf rani (via Dropbox)
• [gmx-users] Invalid atomtype format (Justin Lemkul)   Sadaf Rani
  • [gmx-users] Invalid atomtype format (Justin Lemkul)   Justin Lemkul
• [gmx-users] sadaf rani shared "atomtypes.atp" with you   sadaf rani (via Dropbox)
• [gmx-users] Invalid atomtype format (Justin Lemkul   Sadaf Rani
  • [gmx-users] Invalid atomtype format (Justin Lemkul   Justin Lemkul
• [gmx-users] GROMACS 2020.2 patch release available   Paul bauer

Last message date: Thu Apr 30 20:07:50 CEST 2020
Archived on: Thu Apr 30 20:07:52 CEST 2020

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