April 2020 Archives by author

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

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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