August 2019 Archives by author

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Starting: Thu Aug 1 01:54:25 CEST 2019
Ending: Sat Aug 31 23:30:18 CEST 2019
Messages: 368

[gmx-users] Change forcefield directory Dhr. D.W. Sjoerdsma (d.w.sjoerdsma)
[gmx-users] Query regaring potential energy obtained using energy groups Nashit Jalal 17250017
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Mark Abraham
[gmx-users] best performance on GPU Mark Abraham
[gmx-users] best performance on GPU Mark Abraham
[gmx-users] inputfile character related issue Mark Abraham
[gmx-users] Gromacs 4.5.7 compatibility with Titan X GPU Mark Abraham
[gmx-users] Relation between tau_t and nstxout Mark Abraham
[gmx-users] Relation between tau_t and nstxout Mark Abraham
[gmx-users] Running on two nodes Mark Abraham
[gmx-users] Gromacs FEP tutorial Mark Abraham
[gmx-users] WARNING Mark Abraham
[gmx-users] typedefs.h in gromacs installation Mark Abraham
[gmx-users] Performance, gpu Mark Abraham
[gmx-users] Switching CPU to GPU in a simulation Mark Abraham
[gmx-users] Topology Mark Abraham
[gmx-users] Gromacs 2019.3 compilation with GPU support Mark Abraham
[gmx-users] CHOL still not recognised Mark Abraham
[gmx-users] HtoD cudaMemcpyAsync failed: invalid argument Mark Abraham
[gmx-users] HtoD cudaMemcpyAsync failed: invalid argument Mark Abraham
[gmx-users] Index file Mark Abraham
[gmx-users] Still "GB parameter(s) missing or negative for atom type 'C'" issue after 7 years Mark Abraham
[gmx-users] Performance, gpu Mark Abraham
[gmx-users] HtoD cudaMemcpyAsync failed: invalid argument Mark Abraham
[gmx-users] energy minimization Mark Abraham
[gmx-users] MDrun Slow! Mark Abraham
[gmx-users] Unreadable logfile after restart Gianfranco Abrusci
[gmx-users] Charmm36M neutral C-terminal Proline Akshay
[gmx-users] Switching CPU to GPU in a simulation Alex
[gmx-users] Performance, gpu Alex
[gmx-users] Performance, gpu Alex
[gmx-users] Webinar: "More bang for your buck: Improved use of GPU Nodes for GROMACS 2018" with Carsten Kutzner Rossen Apostolov
[gmx-users] No default G96Angle types Victor Barozi
[gmx-users] Error in calculating center of mass using distance command Sumedha Bhosale
[gmx-users] Building different size membranes using gromacs 5.1.4 Kevin Boyd
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Paul Buscemi
[gmx-users] best performance on GPU Paul Buscemi
[gmx-users] simulation on 2 gpus Paul Buscemi
[gmx-users] "comm-mode = Angular" gives error Jorden Cabal
[gmx-users] (no subject) Jorden Cabal
[gmx-users] "comm-mode = Angular" gives error Jorden Cabal
[gmx-users] Error in calculating center of mass using distance command Jorden Cabal
[gmx-users] "comm-mode = Angular" gives error Jorden Cabal
[gmx-users] Regarding too many LINCS warnings for bicarbonate ion Apramita Chand
[gmx-users] How to deal with "non-zero total charge" problem in gromacs? Bratin Kumar Das
[gmx-users] REMD Bratin Kumar Das
[gmx-users] Issue with protein-ligand simulation Bratin Kumar Das
[gmx-users] Continuation = yes keyword Bratin Kumar Das
[gmx-users] topology files for lipid bilayer Bratin Kumar Das
[gmx-users] How to create a group for a set of atoms with make_ndx Bratin Kumar Das
[gmx-users] Topolgen Bratin Kumar Das
[gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory? Bratin Kumar Das
[gmx-users] WARNING Bratin Kumar Das
[gmx-users] WARNING Bratin Kumar Das
[gmx-users] SASA calculation Bratin Kumar Das
[gmx-users] How to make all parts of a protein in the periodic box in when running "gmx editconf" command Bratin Kumar Das
[gmx-users] Average RDF Bratin Kumar Das
[gmx-users] Mutant_md_1ns.log, WT_md_1ns.log + 1 more item Lei Qian (via Google Drive)
[gmx-users] Mutant_md_1ns.log Lei Qian (via Google Drive)
[gmx-users] Running on two nodes Searle Duay
[gmx-users] Running on two nodes Searle Duay
[gmx-users] Still "GB parameter(s) missing or negative for atom type 'C'" issue after 7 years Vedat Durmaz
[gmx-users] Still "GB parameter(s) missing or negative for atom type 'C'" issue after 7 years Vedat Durmaz
[gmx-users] Still "GB parameter(s) missing or negative for atom type 'C'" issue after 7 years Vedat Durmaz
[gmx-users] OPLS parameterization for a modified aminoacid Neena Susan Eappen
[gmx-users] OPLS parameterization for a modified aminoacid Neena Susan Eappen
[gmx-users] SIMD: SSE2 or AVX2_256? Neena Susan Eappen
[gmx-users] Relation between tau_t and nstxout Neena Susan Eappen
[gmx-users] Change forcefield directory Neena Susan Eappen
[gmx-users] Residue XXX not found in residue topology database Neena Susan Eappen
[gmx-users] gromacs is not recognising opls ff Ayesha Fatima
[gmx-users] CHOL still not recognised Ayesha Fatima
[gmx-users] Question about distance restraints Tanos Franca
[gmx-users] Problem to build an infinite DNA chain ... Sergio Garay
[gmx-users] inter-residue contact map Joe Greener
[gmx-users] GROMOS 54a7 mapping warning Gselman, Larissa
[gmx-users] simulation on 2 gpus Stefano Guglielmo
[gmx-users] simulation on 2 gpus Stefano Guglielmo
[gmx-users] simulation on 2 gpus Stefano Guglielmo
[gmx-users] simulation on 2 gpus Stefano Guglielmo
[gmx-users] continue run Mohammadreza Niknam Hamidabad
[gmx-users] continue run Mohammadreza Niknam Hamidabad
[gmx-users] [gmx-user] Parameter files for Lysozyme in water tutorial - Charmm36 Mohammadreza Niknam Hamidabad
[gmx-users] regarding changing the scale from ps to ns Mohammadreza Niknam Hamidabad
[gmx-users] typedefs.h in gromacs installation Johannes Hermann
[gmx-users] typedefs.h in gromacs installation Johannes Hermann
[gmx-users] Temperature intervals with simulated tempering Kenneth Huang
[gmx-users] wham analysis Jochen Hub
[gmx-users] Performance with Epyc Rome Jochen Hub
[gmx-users] Gromacs 4.5.7 compatibility with Titan X GPU Timothy Hurlburt
[gmx-users] Gromacs 4.5.7 compatibility with Titan X GPU Timothy Hurlburt
[gmx-users] inter-residue contact map SHAHEE ISLAM
[gmx-users] Steps to using Drude force field? James
[gmx-users] Potential Energy Distribution Plots in REMD Shan Jayasinghe
[gmx-users] Topology Shan Jayasinghe
[gmx-users] Gromacs-5.1.4 with CHARMM36 March 2019 RNA Residue Fatal Error Joseph,Newlyn
[gmx-users] Should Cation Ligand be removed before MD simulaiton Quin K
[gmx-users] [gmx-user] advantage of charmm force field over opls for protein md simulation and protein+Inhibitor md simulation Quin K
[gmx-users] [gmx-user] Parameter files for Lysozyme in water tutorial - Charmm36 Quin K
[gmx-users] [gmx-user] Parameter files for Lysozyme in water tutorial - Charmm36 Quin K
[gmx-users] [gmx-user] Parameter files for Lysozyme in water tutorial - Charmm36 Quin K
[gmx-users] MDrun Slow! Quin K
[gmx-users] ERROR: Failed to load the OptiX shared library. Iman Katouzian
[gmx-users] Topology for phosphorylated protein in gromacs using Amber Forcefield Seketoulie Keretsu
[gmx-users] simulation termination problem Prabir Khatua
[gmx-users] Equilibration Error, Skew Factor Hemant Khoba
[gmx-users] (no subject) Pradeepa Kumari
[gmx-users] Building different size membranes using gromacs 5.1.4 Pradeepa Kumari
[gmx-users] Building different size membranes using gromacs 5.1.4 Pradeepa Kumari
[gmx-users] Analysing multiple cavities in ion Channel through CompEl simulations Kutzner, Carsten
[gmx-users] GROMOS 54a7 mapping warning Justin Lemkul
[gmx-users] gromacs pullcode Justin Lemkul
[gmx-users] REMD Justin Lemkul
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Justin Lemkul
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Justin Lemkul
[gmx-users] Gromacs-5.1.4 with CHARMM36 March 2019 RNA Residue Fatal Error Justin Lemkul
[gmx-users] Purpose of repeated improper dihedrals Justin Lemkul
[gmx-users] Purpose of repeated improper dihedrals Justin Lemkul
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Justin Lemkul
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Justin Lemkul
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Justin Lemkul
[gmx-users] PRESS-XX, PRESS-YY, PRESS-ZZ in .edr file Justin Lemkul
[gmx-users] Continuation = yes keyword Justin Lemkul
[gmx-users] how can we include excluded atoms Justin Lemkul
[gmx-users] warning: Problem with chain definition Justin Lemkul
[gmx-users] Change forcefield directory Justin Lemkul
[gmx-users] Invalid particle type Justin Lemkul
[gmx-users] Printing energies at every step of energy minimization Justin Lemkul
[gmx-users] Cutoff Justin Lemkul
[gmx-users] Change forcefield directory Justin Lemkul
[gmx-users] Potential Energy Distribution Plots in REMD Justin Lemkul
[gmx-users] fatal error with grompp command Justin Lemkul
[gmx-users] Manual reparameterization for ligand topology Justin Lemkul
[gmx-users] Difference between residue (r) and residue index (ri) when selecting residue groups? Justin Lemkul
[gmx-users] continue run Justin Lemkul
[gmx-users] question on ffG43a1p force field Justin Lemkul
[gmx-users] question on ffG43a1p force field Justin Lemkul
[gmx-users] Wham analysis Justin Lemkul
[gmx-users] Topolgen Justin Lemkul
[gmx-users] Error Report Justin Lemkul
[gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory? Justin Lemkul
[gmx-users] "comm-mode = Angular" gives error Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory? Justin Lemkul
[gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory? Justin Lemkul
[gmx-users] question on ffG43a1p force field Justin Lemkul
[gmx-users] "comm-mode = Angular" gives error Justin Lemkul
[gmx-users] Tetrahedral order parameter Justin Lemkul
[gmx-users] typedefs.h in gromacs installation Justin Lemkul
[gmx-users] Charmm36M neutral C-terminal Proline Justin Lemkul
[gmx-users] Gromacs FEP tutorial Justin Lemkul
[gmx-users] Error when running pbs files using GROMACS on hpc cluster Justin Lemkul
[gmx-users] domain decomposition Justin Lemkul
[gmx-users] Incorrect SPC water density using oplsaa force field Justin Lemkul
[gmx-users] Error in calculating center of mass using distance command Justin Lemkul
[gmx-users] domain decomposition Justin Lemkul
[gmx-users] gromacs.org_gmx-users at maillist.sys.kth.se; jalemkul at vt.edu Justin Lemkul
[gmx-users] Steps to using Drude force field? Justin Lemkul
[gmx-users] "comm-mode = Angular" gives error Justin Lemkul
[gmx-users] question on ffG43a1p force field Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] Should Cation Ligand be removed before MD simulaiton Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] [gmx-user] advantage of charmm force field over opls for protein md simulation and protein+Inhibitor md simulation Justin Lemkul
[gmx-users] gromacs is not recognising opls ff Justin Lemkul
[gmx-users] How to restrain small molecules in a region where the small molecules can move freely? Justin Lemkul
[gmx-users] [HELP] Residue 'NI' not found in residue topology database Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] Residue XXX not found in residue topology database Justin Lemkul
[gmx-users] ADDITION OF COMPLEX IONS OUTSIDE BILAYER FOR TRANSPORTER PROTEIN SIMULATION Justin Lemkul
[gmx-users] Reparametrization of ligan topology Justin Lemkul
[gmx-users] [HELP] Residue 'NI' not found in residue topology database , Vol 184, Issue 67 Justin Lemkul
[gmx-users] question on ffG43a1p force field Justin Lemkul
[gmx-users] [gmx-user] Parameter files for Lysozyme in water tutorial - Charmm36 Justin Lemkul
[gmx-users] Mutant_md_1ns.log, WT_md_1ns.log + 1 more item Justin Lemkul
[gmx-users] [ERROR] NI+2 in gromacs simulations Justin Lemkul
[gmx-users] Fatal error: A coordinate in file box.gro does not contain a '.' Justin Lemkul
[gmx-users] simulation termination problem Justin Lemkul
[gmx-users] fails to minimization of ADP-protein Justin Lemkul
[gmx-users] Question about distance restraints Justin Lemkul
[gmx-users] How to make all parts of a protein in the periodic box in when running "gmx editconf" command Li, Shi
[gmx-users] Running on two nodes Dhaniram Mahato
[gmx-users] Difference between residue (r) and residue index (ri) when selecting residue groups? Dhaniram Mahato
[gmx-users] How to create a group for a set of atoms with make_ndx Dhaniram Mahato
[gmx-users] gmx rdf Dhrubajyoti Maji
[gmx-users] continue run Dhrubajyoti Maji
[gmx-users] continue run Dhrubajyoti Maji
[gmx-users] domain decomposition Dhrubajyoti Maji
[gmx-users] domain decomposition Dhrubajyoti Maji
[gmx-users] domain decomposition Dhrubajyoti Maji
[gmx-users] energy minimization Dhrubajyoti Maji
[gmx-users] best performance on GPU Maryam
[gmx-users] best performance on GPU Maryam
[gmx-users] best performance on GPU Maryam
[gmx-users] Gromacs FEP tutorial Alex Mathew
[gmx-users] Gromacs FEP tutorial Alex Mathew
[gmx-users] Mailing list for Postdoctoral opportunities in Simulations Peter Mawanga
[gmx-users] Strange Behavior in gmx wham Moradzadeh, Alireza
[gmx-users] SIMD: SSE2 or AVX2_256? Benson Muite
[gmx-users] Gromacs-GPU help Benson Muite
[gmx-users] Gromacs-GPU help Benson Muite
[gmx-users] Why protein structure is outside of lipid environment after MD simulation using Gromacs? Muthusankar
[gmx-users] Gromacs 2019.3 compilation with GPU support Prithwish Nandi
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Carlos Navarro
[gmx-users] Analysing multiple cavities in ion Channel through CompEl simulations Carlos Navarro
[gmx-users] SASA calculation Pandya, Akash
[gmx-users] SASA calculation Pandya, Akash
[gmx-users] Obtaining AMBER parameter for Zwitterion Amino acids to use in Gromacs Pandya, Akash
[gmx-users] Wham analysis Negar Parvizi
[gmx-users] wham analysis Negar Parvizi
[gmx-users] how can we include excluded atoms Anjali Patel
[gmx-users] topology files for lipid bilayer Atila Petrosian
[gmx-users] Is it possible to control GPU utilizations when running two simulations in one workstation? Szilárd Páll
[gmx-users] Is it possible to control GPU utilizations when running two simulations in one workstation? Szilárd Páll
[gmx-users] best performance on GPU Szilárd Páll
[gmx-users] simulation on 2 gpus Szilárd Páll
[gmx-users] AVX_512 and GROMACS Szilárd Páll
[gmx-users] gpu usage Szilárd Páll
[gmx-users] simulation on 2 gpus Szilárd Páll
[gmx-users] question on ffG43a1p force field Lei Qian
[gmx-users] question on ffG43a1p force field Lei Qian
[gmx-users] question on ffG43a1p force field Lei Qian
[gmx-users] question on ffG43a1p force field Lei Qian
[gmx-users] question on ffG43a1p force field Lei Qian
[gmx-users] question on ffG43a1p force field Lei Qian
[gmx-users] Mutant_md_1ns.log, WT_md_1ns.log + 1 more item Lei Qian
[gmx-users] Error Report Dr Adekunle Rowaiye
[gmx-users] Error Report Dr Adekunle Rowaiye
[gmx-users] Issue with protein-ligand simulation GAYATHRI S
[gmx-users] Manual reparameterization for ligand topology DEEPANSHU SINGLA
[gmx-users] Reparametrization of ligan topology DEEPANSHU SINGLA
[gmx-users] gromacs.org_gmx-users at maillist.sys.kth.se; jalemkul at vt.edu Maryam Sadeghi
[gmx-users] Average RDF Maryam Sadeghi
[gmx-users] Average RDF Maryam Sadeghi
[gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure? Maryam Sadat Sadeghi
[gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure? Maryam Sadat Sadeghi
[gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure? Maryam Sadat Sadeghi
[gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure? Maryam Sadat Sadeghi
[gmx-users] Selection of Water Molecules for Individual Frames Soham Sarkar
[gmx-users] Selection of water molecules Soham Sarkar
[gmx-users] query: Yogesh Sharma
[gmx-users] ADDITION OF COMPLEX IONS OUTSIDE BILAYER FOR TRANSPORTER PROTEIN SIMULATION Yogesh Sharma
[gmx-users] Inconsistent shifts over periodic boundaries error. Artem Shekhovtsov
[gmx-users] [HELP] Residue 'NI' not found in residue topology database Edjan Silva
[gmx-users] [HELP] Residue 'NI' not found in residue topology database , Vol 184, Issue 67 Edjan Silva
[gmx-users] [ERROR] NI+2 in gromacs simulations Edjan Silva
[gmx-users] Fatal error: A coordinate in file box.gro does not contain a '.' Edjan Silva
[gmx-users] (no subject) Navneet Kumar Singh
[gmx-users] (no subject) Navneet Kumar Singh
[gmx-users] (no subject) Navneet Kumar Singh
[gmx-users] (no subject) Navneet Kumar Singh
[gmx-users] HtoD cudaMemcpyAsync failed: invalid argument Navneet Kumar Singh
[gmx-users] (no subject) Navneet Kumar Singh
[gmx-users] HtoD cudaMemcpyAsync failed: invalid argument Navneet Kumar Singh
[gmx-users] HtoD cudaMemcpyAsync failed: invalid argument Navneet Kumar Singh
[gmx-users] (no subject) Navneet Kumar Singh
[gmx-users] HtoD cudaMemcpyAsync failed: invalid argument Navneet Kumar Singh
[gmx-users] Gromacs /MMPBSA Calculation Navneet Kumar Singh
[gmx-users] HtoD cudaMemcpyAsync failed: invalid argument Navneet Kumar Singh
[gmx-users] Tetrahedral order parameter Omkar Singh
[gmx-users] Regarding OH, HH vector distribution Omkar Singh
[gmx-users] MSD Omkar Singh
[gmx-users] Cutoff Omkar Singh
[gmx-users] Potential Energy Distribution Plots in REMD Omkar Singh
[gmx-users] Tetrahedral order parameter Omkar Singh
[gmx-users] Index file Omkar Singh
[gmx-users] Index file Omkar Singh
[gmx-users] (no subject) Priyanka Singh
[gmx-users] Turning off electrostatic between molecules Smith, Micholas D.
[gmx-users] Turning off electrostatic between molecules Smith, Micholas D.
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible Mohammed I Sorour
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Mohammed I Sorour
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Mohammed I Sorour
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Mohammed I Sorour
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Mohammed I Sorour
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Mohammed I Sorour
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Mohammed I Sorour
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Mohammed I Sorour
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Mohammed I Sorour
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Mohammed I Sorour
[gmx-users] PRESS-XX, PRESS-YY, PRESS-ZZ in .edr file David van der Spoel
[gmx-users] Regarding too many LINCS warnings for bicarbonate ion David van der Spoel
[gmx-users] Not all snapshots are written to trr during minimization David van der Spoel
[gmx-users] Question about Gromacs David van der Spoel
[gmx-users] Turning off electrostatic between molecules Tam, Benjamin
[gmx-users] Turning off electrostatic between molecules Tam, Benjamin
[gmx-users] The difference between selecting residue groups with r (residue) or ri (residue index) under gmx make_ndx Johnny Tam
[gmx-users] Difference between residue (r) and residue index (ri) when selecting residue groups? Johnny Tam
[gmx-users] Error with inflategro Meir Touitou
[gmx-users] Why partial charge on chlorine atom from GAFF is +ve? Lakshman Ji Verma
[gmx-users] Viscosity Calculation Visco, Daniele
[gmx-users] PRESS-XX, PRESS-YY, PRESS-ZZ in .edr file Anh Vo
[gmx-users] PRESS-XX, PRESS-YY, PRESS-ZZ in .edr file Anh Vo
[gmx-users] Error when running pbs files using GROMACS on hpc cluster Anh Vo
[gmx-users] Printing energies at every step of energy minimization Wahl, David M
[gmx-users] How to deal with "non-zero total charge" problem in gromacs? Dallas Warren
[gmx-users] How to deal with "non-zero total charge" problem in gromacs? Dallas Warren
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges Dallas Warren
[gmx-users] How to deal with "non-zero total charge" problem in gromacs? Dallas Warren
[gmx-users] Tetrahedral order parameter Dallas Warren
[gmx-users] structural clashes make the structure look like broken? Dallas Warren
[gmx-users] ERROR: Failed to load the OptiX shared library. Dallas Warren
[gmx-users] Is it possible to control GPU utilizations when running two simulations in one workstation? Dallas Warren
[gmx-users] Building different size membranes using gromacs 5.1.4 Dallas Warren
[gmx-users] How to create a group for a set of atoms with make_ndx Dallas Warren
[gmx-users] membrance Dallas Warren
[gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure? Dallas Warren
[gmx-users] 2019.2 not using all available cores Dallas Warren
[gmx-users] Average RDF Dallas Warren
[gmx-users] Average RDF Dallas Warren
[gmx-users] Why protein structure is outside of lipid environment after MD simulation using Gromacs? Dallas Warren
[gmx-users] regarding changing the scale from ps to ns Dallas Warren
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges John Whittaker
[gmx-users] WARNING John Whittaker
[gmx-users] Fwd: Simulation blowing up in parallel (h-bonds constraints) John Whittaker
[gmx-users] wham analysis John Whittaker
[gmx-users] "comm-mode = Angular" gives error Billy Williams-Noonan
[gmx-users] Steps to using Drude force field? Billy Williams-Noonan
[gmx-users] How to create a group for a set of atoms with make_ndx Sun Yeping
[gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory? Sun Yeping
[gmx-users] Residence time Yildiz, Can Bora
[gmx-users] regarding changing the scale from ps to ns sudha bhagwati
[gmx-users] regarding changing the scale from ps to ns sudha bhagwati
[gmx-users] regarding changing the scale from ps to ns sudha bhagwati
[gmx-users] gpu usage p buscemi
[gmx-users] simulation on 2 gpus paul buscemi
[gmx-users] simulation on 2 gpus paul buscemi
[gmx-users] best performance on GPU paul buscemi
[gmx-users] inputfile character related issue asha choudhury
[gmx-users] Purpose of repeated improper dihedrals Dawid das
[gmx-users] Purpose of repeated improper dihedrals Dawid das
[gmx-users] Purpose of repeated improper dihedrals Dawid das
[gmx-users] Continuation = yes keyword Dawid das
[gmx-users] Continuation = yes keyword Dawid das
[gmx-users] Change forcefield directory Dawid das
[gmx-users] Change forcefield directory Dawid das
[gmx-users] Not all snapshots are written to trr during minimization Dawid das
[gmx-users] Incorrect SPC water density using oplsaa force field atb files
[gmx-users] Fwd: Simulation blowing up in parallel (h-bonds constraints) jan.joswig at fu-berlin.de
[gmx-users] Perturbation free energy m g
[gmx-users] Free energy m g
[gmx-users] membrance rabee khorram
[gmx-users] warning: Problem with chain definition afsaneh maleki
[gmx-users] Invalid particle type afsaneh maleki
[gmx-users] fatal error with grompp command afsaneh maleki
[gmx-users] Gromacs GPU tarzan p
[gmx-users] Gromacs-GPU help tarzan p
[gmx-users] AVX_512 and GROMACS tarzan p
[gmx-users] Topolgen rakesh parida
[gmx-users] Selection of Water Molecules for Individual Frames anupama sharma
[gmx-users] Selection of water molecules anupama sharma
[gmx-users] Mailing list for Postdoctoral opportunities in Simulations akhil srivastava
[gmx-users] How to deal with "non-zero total charge" problem in gromacs? sunyeping
[gmx-users] How to deal with "non-zero total charge" problem in gromacs? sunyeping
[gmx-users] How to deal with "non-zero total charge" problem in gromacs? sunyeping
[gmx-users] structural clashes make the structure look like broken? sunyeping
[gmx-users] Is it possible to control GPU utilizations when running two simulations in one workstation? sunyeping
[gmx-users] Is it possible to control GPU utilizations when running two simulations in one workstation? sunyeping
[gmx-users] How to create a group for a set of atoms with make_ndx sunyeping
[gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory? sunyeping
[gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory? sunyeping
[gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory? sunyeping
[gmx-users] How to make all parts of a protein in the periodic box in when running "gmx editconf" command sunyeping
[gmx-users] How to make all parts of a protein in the periodic box in when running "gmx editconf" command sunyeping
[gmx-users] fails to minimization of ADP-protein fatemeh.haghighi at univ-fcomte.fr
[gmx-users] How to restrain small molecules in a region where the small molecules can move freely? wtzou

Last message date: Sat Aug 31 23:30:18 CEST 2019
Archived on: Sat Aug 31 23:30:19 CEST 2019

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