June 2019 Archives by date

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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] 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] Trans-Gauche fraction for surfactant chain Dallas Warren
[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] oplsaa tooology for urea Alex
[gmx-users] oplsaa tooology for urea Dallas Warren
[gmx-users] FW: Free energy of solvation using the Bar method Innocenti Malini, Riccardo
[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] Problem using RTX 2070 Armenio Barbosa
[gmx-users] volume not shrinking when restrains present p buscemi
[gmx-users] Problem using RTX 2070 p buscemi
[gmx-users] Problem using RTX 2070 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] wwtang at tju.edu.cn 汤伟伟
[gmx-users] Problem using RTX 2070 Armenio Barbosa
[gmx-users] ENERGY MINIMISATION spss4 at iacs.res.in
[gmx-users] ENERGY MINIMISATION Dhrubajyoti Maji
[gmx-users] How to calculate angle between center of geometry of groups of atoms ? Mark Abraham
[gmx-users] Density of ligand molecules around a particular residue Pandya, Akash
[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] Density of ligand molecules around a particular residue Smith, Micholas D.
[gmx-users] force field for organometalic compound antonia vyrkou
[gmx-users] force field for organometalic compound Bratin Kumar Das
[gmx-users] There is no domain decomposition error Paul bauer
[gmx-users] There is no domain decomposition error Dhrubajyoti Maji
[gmx-users] There is no domain decomposition error Dhrubajyoti Maji
[gmx-users] Water Density Omkar Singh
[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] Water Density Bratin Kumar Das
[gmx-users] problem with topology Maria Luisa
[gmx-users] (no subject) Maria Luisa
[gmx-users] problem with topology Dallas Warren
[gmx-users] How to calculate angle between center of geometry of groups of atoms ? Monia Kamly
[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] problem with topology Maria Luisa
[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] problem with topology Dallas Warren
[gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand Prasanth G, Research Scholar
[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] Grompp not producing tpr files Israel Estrada
[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] correcting timesteps Leigh
[gmx-users] GPU issue - system that was stable on CPUs crashes Mark Abraham
[gmx-users] Grompp not producing tpr files Mark Abraham
[gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand Mark Abraham
[gmx-users] Some suggestions about the gmx current tool Mark Abraham
[gmx-users] Grompp not producing tpr files Bratin Kumar Das
[gmx-users] Details of g_rdf functions in version 4.6.5. Henry Vider
[gmx-users] Some suggestions about the gmx current tool Mahsa
[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] Grompp not producing tpr files Israel Estrada
[gmx-users] Grompp not producing tpr files Paul Bauer
[gmx-users] cmap error while making tpr file from dcd file Santanu Santra
[gmx-users] Grompp not producing tpr files Peter Stern
[gmx-users] GPU issue - system that was stable on CPUs crashes Hannah Baumann
[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] Details of g_rdf functions in version 4.6.5. Dallas Warren
[gmx-users] Improving the MD simulations. Ahmed
[gmx-users] How to measure distance and find salt bridges in GROMACS ? Dallas Warren
[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] Details of g_rdf functions in version 4.6.5. Henry Vider
[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] GROMACS 2019.3 patch release available Paul bauer
[gmx-users] MD Simulation Time Is Slow Ahmed
[gmx-users] Membrane protein simulation isotropic vs semiisotropic Prasanth G, Research Scholar
[gmx-users] Membrane protein simulation isotropic vs semiisotropic paul buscemi
[gmx-users] Spectrum from nmeig command up201406812
[gmx-users] Spectrum from nmeig command David van der Spoel
[gmx-users] Atomtype opls_116 not found when runnning GROMPP Justin Lemkul
[gmx-users] Cgenff generated force field problem Justin Lemkul
[gmx-users] Details of g_rdf functions in version 4.6.5. Justin Lemkul
[gmx-users] Membrane protein simulation isotropic vs semiisotropic Justin Lemkul
[gmx-users] Details of g_rdf functions in version 4.6.5. Henry Vider
[gmx-users] use of UFF m g
[gmx-users] Details of g_rdf functions in version 4.6.5. Justin Lemkul
[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] correcting timesteps Leigh
[gmx-users] Error in MD simulation Mark Abraham
[gmx-users] Grompp not producing tpr files Israel Estrada
[gmx-users] Grompp not producing tpr files Dallas Warren
[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] 2019.3 - Fixed Issue 2953: With DD, all intermolecular interactions were ignored? Mateusz Bieniek
[gmx-users] Grompp not producing tpr files Israel Estrada
[gmx-users] XVG Plotting by Grace Mahmoud Mirzaei
[gmx-users] XVG Plotting by Grace Israel Estrada
[gmx-users] Hydrogen bond autocorrelation Gmx QA
[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] GROMACS Output Timestep Changes Over a Long, Check-pointed Simulation Eric R Beyerle
[gmx-users] XVG Plotting by Grace MOHD HOMAIDUR RAHMAN
[gmx-users] Hydrogen bond autocorrelation David van der Spoel
[gmx-users] Hydrogen bond autocorrelation Gmx QA
[gmx-users] Difference between NH2 in c-term and aminoacids Myunggi Yi
[gmx-users] Error in Solvation Box Mahmoud Mirzaei
[gmx-users] GROMACS Output Timestep Changes Over a Long, Check-pointed Simulation Mark Abraham
[gmx-users] correcting timesteps 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] Error in Solvation Box Dallas Warren
[gmx-users] OPLS-ff topology file for modified residue procedure? Neena Susan Eappen
[gmx-users] dragging gro files into VMD paul buscemi
[gmx-users] Cgenff generated force field problem Prabir Khatua
[gmx-users] Error in Solvation Box Bratin Kumar Das
[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] 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] Atomtype opls_116 not found when runnning GROMPP Fernando Nunes
[gmx-users] Difference between NH2 in c-term and aminoacids Justin Lemkul
[gmx-users] CHARMM36 in Gromacs :DNA terminus residues problem Justin Lemkul
[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] Error gmx pdb2gro Danilo Boskovic
[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] (-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] RNA molecule simulation Priyanka Singh
[gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs Bratin Kumar Das
[gmx-users] Check point file Mark Abraham
[gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs Dallas Warren
[gmx-users] Amber force field for metal Surface Kumari Shilpa
[gmx-users] Amber force field for metal Surface Alex
[gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs kalpana
[gmx-users] Check point file Alex
[gmx-users] Check point file Mark Abraham
[gmx-users] Error gmx pdb2gro Danilo Boskovic
[gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs Dallas Warren
[gmx-users] GROMOS FF conversion András Ferenc WACHA
[gmx-users] GROMOS FF conversion Piggot T.
[gmx-users] Kindly help kalpana
[gmx-users] Check point file Alex
[gmx-users] Minimization stops without reaching the requested precision Fmax < 1000 Mahdi Bagherpoor
[gmx-users] problem regarding gmx wham san kumar
[gmx-users] SMD Pull Direction Reza Esmaeeli
[gmx-users] Check point file Dallas Warren
[gmx-users] Kindly help Dallas Warren
[gmx-users] Minimization stops without reaching the requested precision Fmax < 1000 Dallas Warren
[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] Fetal error at grompp kalpana
[gmx-users] Fetal error at grompp Dallas Warren
[gmx-users] appropriate force fielf starlight
[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] Kindly help Abhishek Acharya
[gmx-users] appropriate force fielf Paul Buscemi
[gmx-users] Kindly help Bratin Kumar Das
[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] GROMOS FF conversion András Ferenc WACHA
[gmx-users] Visualizing hexamer with solvent Simone Orioli
[gmx-users] clustering of ions during NPT simulation Netaly Khazanov
[gmx-users] Implementing Drude Particles Finnigan, Sophie
[gmx-users] DGPU_DEPLOYMENT_KIT_ROOT_DIR anthonyliao_91
[gmx-users] clustering of ions during NPT simulation Paul Buscemi
[gmx-users] errors during installation kalpana
[gmx-users] errors during installation kalpana
[gmx-users] how to accelerate mdrun process kalpana
[gmx-users] Error gmx pdb2gro Justin Lemkul
[gmx-users] Implementing Drude Particles Justin Lemkul
[gmx-users] clustering of ions during NPT simulation Justin Lemkul
[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] interrupt of gmx mdrun Andrew Bostick
[gmx-users] Transference of dihedral potentials between united atom and all-atom force fields Pragati Sharma
[gmx-users] appropriate forcefield starlight
[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] Constraints Error; In Using Tetrahedral Zinc Dummy Model Mahdi Bagherpoor
[gmx-users] How to install gromacs on cpu cluster sunyeping
[gmx-users] How to install gromacs on cpu cluster Benson Muite
[gmx-users] clustering of ions during NPT simulation Netaly Khazanov
[gmx-users] How to install gromacs on cpu cluster Benson Muite
[gmx-users] errors during installation Mark Abraham
[gmx-users] how to accelerate mdrun process Mark Abraham
[gmx-users] How to define a user-defined potential Mark Abraham
[gmx-users] Fetal error at grompp Mark Abraham
[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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