November 2019 Archives by author

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Starting: Fri Nov 1 05:03:06 CET 2019
Ending: Sat Nov 30 14:16:55 CET 2019
Messages: 325

[gmx-users] Slurm for GROMACS Mark Abraham
[gmx-users] slurm, gres:gpu, only 1 GPU out of 4 is detected Mark Abraham
[gmx-users] Segmentation fault using gmx solvent Mark Abraham
[gmx-users] Martini on GROMACS Shlomit Afgin
[gmx-users] gmx gangle in a for loop Alex
[gmx-users] droplet Alex
[gmx-users] Regarding silicon oxide parameter Mijiddorj B
[gmx-users] Regarding force field for silicon oxide Mijiddorj B
[gmx-users] Regarding force field for silicon oxide Mijiddorj B
[gmx-users] Polymer parameter preparation using CHARMM-GUI Mijiddorj B
[gmx-users] Polymer parameter preparation using CHARMM-GUI Mijiddorj B
[gmx-users] Regarding multiple ligands' topology Mijiddorj B
[gmx-users] polymer charmm27 parameter Mijiddorj B
[gmx-users] polymer charmm27 parameter Mijiddorj B
[gmx-users] polymer charmm27 parameter Mijiddorj B
[gmx-users] polymer charmm27 parameter Mijiddorj B
[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer Mijiddorj B
[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer Mijiddorj B
[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer Mijiddorj B
[gmx-users] multiple peptide simulation Mijiddorj B
[gmx-users] Regarding the atomic contact map in gromacs Mijiddorj B
[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer Mijiddorj B
[gmx-users] Regarding the atomic contact map in gromacs Dorj Bat
[gmx-users] issues by simulating adsorption of peptide on a polymer surface Baydan, Sezai-Raif
[gmx-users] polymer & peptide interaction pbc, visualization problem Sezai-Raif Baydan
[gmx-users] Ruuning MD simulation on laptop Swapnil Bhujbal
[gmx-users] (no subject) Christian Blau
[gmx-users] Simulated Annealing General Procedure Christian Blau
[gmx-users] Output from gmx h2order Christian Blau
[gmx-users] gmx gangle in a for loop Christian Blau
[gmx-users] Time step mismatch. Christian Blau
[gmx-users] Load Imbalance Christian Blau
[gmx-users] Stochastic Dynamics nsttcouple Christian Blau
[gmx-users] gmx trjorder Christian Blau
[gmx-users] (no subject) Christian Blau
[gmx-users] Script to merge protein and ligand topology for BAR calculation? Christian Blau
[gmx-users] eelctric field Christian Blau
[gmx-users] eelctric field Christian Blau
[gmx-users] applied electirc field with use potential Christian Blau
[gmx-users] Potential bug in IMD implementation (Interactive Molecular Dynamics) Christian Blau
[gmx-users] Regarding LSI calculation Christian Blau
[gmx-users] eelctric field Christian Blau
[gmx-users] droplet Christian Blau
[gmx-users] Superparamagnetism Christian Blau
[gmx-users] Magnetic effects in a classical force field Christian Blau
[gmx-users] the a.u. unit in the RMS distribution graph Christian Blau
[gmx-users] the a.u. unit in the RMS distribution graph Christian Blau
[gmx-users] Gromacs - Difference between target temperature and pressure in mdp and simulation Fabio Bologna
[gmx-users] Gromacs - Difference between target temperature and pressure in mdp and simulation Fabio Bologna
[gmx-users] emtol criterion Kevin Boyd
[gmx-users] Duplicated dihedral lines on .prm file Daniel Burns
[gmx-users] Duplicated dihedral lines on .prm file Daniel Burns
[gmx-users] Center of mass restraints Daniel Burns
[gmx-users] Center of mass restraints Daniel Burns
[gmx-users] Center of mass restraints Daniel Burns
[gmx-users] gmx rdf with surf option zeineb SI CHAIB
[gmx-users] pdb2gmx , or equivalent Ling Chan
[gmx-users] pdb2gmx , or equivalent Ling Chan
[gmx-users] searching this mailing list Ling Chan
[gmx-users] GMXLIB for pdb2gmx Ling Chan
[gmx-users] atom indexing in top and gro files Ling Chan
[gmx-users] atom indexing in top and gro files Ling Chan
[gmx-users] multiple peptide simulation Apramita Chand
[gmx-users] GPU offload for reaction-field type dataset Jimmy Chen
[gmx-users] How to use gmx_mpi? ZHANG Cheng
[gmx-users] How to use gmx_mpi? ZHANG Cheng
[gmx-users] How to set more mpi for the REMD run? ZHANG Cheng
[gmx-users] How to set more mpi for the REMD run? ZHANG Cheng
[gmx-users] How to set more mpi for the REMD run? ZHANG Cheng
[gmx-users] Calculation of RMSF Nicolas Cheron
[gmx-users] Calculation of RMSF Nicolas Cheron
[gmx-users] Question about switching off non-bonded interactions between two molecules for MD simulation Soomin Choi
[gmx-users] pbc nojump with replica exchange behaves differently than with regular MD Ramon Crehuet
[gmx-users] pbc nojump with replica exchange behaves differently than with regular MD Ramon Crehuet
[gmx-users] pbc nojump with replica exchange behaves differently than with regular MD Ramon Crehuet
[gmx-users] Regarding free energy calculation Bratin Kumar Das
[gmx-users] (no subject) Bratin Kumar Das
[gmx-users] MMGBSA Bratin Kumar Das
[gmx-users] How to prepare protein-peptide/protein-ligand complex molecule in membrane environment Bratin Kumar Das
[gmx-users] (no subject) Bratin Kumar Das
[gmx-users] protein_ligand error NVT Bratin Kumar Das
[gmx-users] emtol criterion Christos Deligkaris
[gmx-users] How does the trjconv -fit rot+trans work? Nirali Desai
[gmx-users] Vibrational frequencies from gromacs trajectory Bakary N'tji Diallo
[gmx-users] Ruuning MD simulation on laptop Matthew Fisher
[gmx-users] gromos force field Patrick Fuchs
[gmx-users] How to run GROMACS in cluster Shradheya R.R. Gupta
[gmx-users] How to run GROMACS in cluster Shradheya R.R. Gupta
[gmx-users] Slurm for GROMACS Shradheya R.R. Gupta
[gmx-users] Slurm for GROMACS Shradheya R.R. Gupta
[gmx-users] Slurm for GROMACS Shradheya R.R. Gupta
[gmx-users] Load Imbalance Shradheya R.R. Gupta
[gmx-users] Load Imbalance Shradheya R.R. Gupta
[gmx-users] clustered structures Shradheya R.R. Gupta
[gmx-users] MMGBSA Shradheya R.R. Gupta
[gmx-users] MMGBSA Shradheya R.R. Gupta
[gmx-users] clustered structures Shradheya R.R. Gupta
[gmx-users] clustered structures Shradheya R.R. Gupta
[gmx-users] slurm, gres:gpu, only 1 GPU out of 4 is detected Tamas Hegedus
[gmx-users] slurm, gres:gpu, only 1 GPU out of 4 is detected Tamas Hegedus
[gmx-users] multidir, Segmentation fault Tamas Hegedus
[gmx-users] Help installing do_x3dna Salvador Herrera-Velarde
[gmx-users] calculation of cross sectional area of protein on lipid SHAHEE ISLAM
[gmx-users] calculation of cross sectional area of protein on lipid SHAHEE ISLAM
[gmx-users] Chain length of a polymer Shan Jayasinghe
[gmx-users] (no subject) Ayesha Kanwal
[gmx-users] Error in DNA.itp file Ayesha Kanwal
[gmx-users] protein_ligand error NVT Iman Katouzian
[gmx-users] Toluene .rtp Iman Katouzian
[gmx-users] 1 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. Farideh Badalkhani Khamseh
[gmx-users] Incompatible subsytems for REMD when running on multiple nodes Daniel Kozuch
[gmx-users] How to properly use tune_pme? Kutzner, Carsten
[gmx-users] Disulphide bonded cyclic peptides Sahil Lall
[gmx-users] Terminal dangling bond error despite pdb2gmx recognising specbond.dat for a cyclic peptide Sahil Lall
[gmx-users] Disulphide bonded cyclic peptides Sahil Lall
[gmx-users] Disulphide bonded cyclic peptides Sahil Lall
[gmx-users] Disulphide bonded cyclic peptides Sahil Lall
[gmx-users] Penetration of lipid bilayer by RNA-Au nanoparticle Dulari Hakamuwa Lekamlage
[gmx-users] How to run GROMACS in cluster Justin Lemkul
[gmx-users] How to build and simulate POPE/POPG bilayer with gromos54a7 force field Justin Lemkul
[gmx-users] ligand topology building. Justin Lemkul
[gmx-users] Umbrella Sampling on Lipid Bilayers, Pulling Issue and Umbrella Sampling Window Simulation Issues. Justin Lemkul
[gmx-users] Error in DNA.itp file Justin Lemkul
[gmx-users] defining parameters in a separate itp file Justin Lemkul
[gmx-users] calculation of cross sectional area of protein on lipid Justin Lemkul
[gmx-users] Polymer parameter preparation using CHARMM-GUI Justin Lemkul
[gmx-users] Stochastic Dynamics nsttcouple Justin Lemkul
[gmx-users] printing option Justin Lemkul
[gmx-users] Regarding multiple ligands' topology Justin Lemkul
[gmx-users] Problem running simulation on gromacs 2018.8 version Justin Lemkul
[gmx-users] How to use gmx_mpi? Justin Lemkul
[gmx-users] Duplicated dihedral lines on .prm file Justin Lemkul
[gmx-users] rdf Justin Lemkul
[gmx-users] Duplicated dihedral lines on .prm file Justin Lemkul
[gmx-users] rdf Justin Lemkul
[gmx-users] defining parameters in a separate itp file Justin Lemkul
[gmx-users] polymer charmm27 parameter Justin Lemkul
[gmx-users] Center of mass restraints Justin Lemkul
[gmx-users] polymer charmm27 parameter Justin Lemkul
[gmx-users] Center of mass restraints Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] Center of mass restraints Justin Lemkul
[gmx-users] segmentation fault core dumped Justin Lemkul
[gmx-users] How to produce "gro" format for calcite {1014} structure. Justin Lemkul
[gmx-users] defining parameters in a separate itp file Justin Lemkul
[gmx-users] pdb2gmx , or equivalent Justin Lemkul
[gmx-users] pdb2gmx , or equivalent Justin Lemkul
[gmx-users] polymer charmm27 parameter Justin Lemkul
[gmx-users] how to make index of a micelle Justin Lemkul
[gmx-users] how to make index of a micelle Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] protein_ligand error NVT Justin Lemkul
[gmx-users] GMXLIB for pdb2gmx Justin Lemkul
[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer Justin Lemkul
[gmx-users] How to prepare prm and itp files of ligands from gro and top files prepared with Gauss, ambertool and acpye for gromacs simulations Justin Lemkul
[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer Justin Lemkul
[gmx-users] anisotropic polarization Justin Lemkul
[gmx-users] Coulomb term calculation in gromacs Justin Lemkul
[gmx-users] Gromacs - Difference between target temperature and pressure in mdp and simulation Justin Lemkul
[gmx-users] Coulomb term calculation in gromacs Justin Lemkul
[gmx-users] Martini on GROMACS Justin Lemkul
[gmx-users] emtol criterion Justin Lemkul
[gmx-users] atom indexing in top and gro files Justin Lemkul
[gmx-users] pbc nojump with replica exchange behaves differently than with regular MD Justin Lemkul
[gmx-users] emtol criterion Justin Lemkul
[gmx-users] atom indexing in top and gro files Justin Lemkul
[gmx-users] pbc nojump with replica exchange behaves differently than with regular MD Justin Lemkul
[gmx-users] Calculation of RMSF Justin Lemkul
[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer Justin Lemkul
[gmx-users] Calculation of RMSF Justin Lemkul
[gmx-users] the a.u. unit in the RMS distribution graph Justin Lemkul
[gmx-users] Coulomb and vdW energies Justin Lemkul
[gmx-users] number and size of NaCl crystals formed Maria Luisa
[gmx-users] defining parameters in a separate itp file Dave M
[gmx-users] defining parameters in a separate itp file Dave M
[gmx-users] defining parameters in a separate itp file Dave M
[gmx-users] defining parameters in a separate itp file Dave M
[gmx-users] GaMD in GROMACS Ram Mahato
[gmx-users] Measurement of tensile strength of a nanotube Nikhil Maroli
[gmx-users] Disulphide bonded cyclic peptides Nikhil Maroli
[gmx-users] Potential bug in IMD implementation (Interactive Molecular Dynamics) Xavier Martinez
[gmx-users] Time step mismatch. Maryam
[gmx-users] Error in DNA.itp file Najamuddin Memon
[gmx-users] Error in DNA.itp file Najamuddin Memon
[gmx-users] How to produce "gro" format for calcite {1014} structure. Najamuddin Memon
[gmx-users] segmentation fault core dumped Najamuddin Memon
[gmx-users] How to properly use tune_pme? Marcin Mielniczuk
[gmx-users] Regarding free energy calculation Rakesh Mishra
[gmx-users] Regarding free energy calculation Rakesh Mishra
[gmx-users] Some out of date GROMPP warnings Joshua Mitchell
[gmx-users] How to prepare protein-peptide/protein-ligand complex molecule in membrane environment Muthusankar
[gmx-users] cmake fails with custom gcc version Mahmood Naderan
[gmx-users] cmake fails with custom gcc version Mahmood Naderan
[gmx-users] Compile for sm_20 Mahmood Naderan
[gmx-users] C2075 not detected by gmx 2018.3 Mahmood Naderan
[gmx-users] c2075 is not detected by gmx Mahmood Naderan
[gmx-users] c2075 is not detected by gmx Mahmood Naderan
[gmx-users] c2075 is not detected by gmx Mahmood Naderan
[gmx-users] Segmentation fault using gmx solvent Anthony Nash
[gmx-users] the a.u. unit in the RMS distribution graph Lalehan Ozalp
[gmx-users] the a.u. unit in the RMS distribution graph Lalehan Ozalp
[gmx-users] the a.u. unit in the RMS distribution graph Lalehan Ozalp
[gmx-users] gmx trjorder Pandya, Akash
[gmx-users] SASA calculation in Gromacs Pandya, Akash
[gmx-users] printing option Patel, Lara Anne
[gmx-users] Umbrella Sampling on Lipid Bilayers, Pulling Issue and Umbrella Sampling Window Simulation Issues. Alexander Phillips
[gmx-users] Gromacs in cluster with CentOS 6 João Gabriel C. Poiani
[gmx-users] Calculation of RMSF Mala L Radhakrishnan
[gmx-users] printing option Hadi Rahmaninejad
[gmx-users] printing option Hadi Rahmaninejad
[gmx-users] Dummy atoms flopping everywhere Raphaël Robidas
[gmx-users] Dummy atoms flopping everywhere Raphaël Robidas
[gmx-users] eelctric field Amin Rouy
[gmx-users] eelctric field Amin Rouy
[gmx-users] eelctric field Amin Rouy
[gmx-users] eelctric field Amin Rouy
[gmx-users] applied electirc field with use potential Amin Rouy
[gmx-users] applied electirc field with use potential Amin Rouy
[gmx-users] eelctric field Amin Rouy
[gmx-users] eelctric field Amin Rouy
[gmx-users] anisotropic polarization Amin Rouy
[gmx-users] Superparamagnetism Amin Rouy
[gmx-users] Superparamagnetism Amin Rouy
[gmx-users] Iterative Boltzman Inversion Maryam Sadeghi
[gmx-users] replica exchange with GROMACS David de Sancho
[gmx-users] how to make index of a micelle Soham Sarkar
[gmx-users] Calculation of young's modulus from stress-strain plot Pragati Sharma
[gmx-users] ligand topology building Yogesh Sharma
[gmx-users] ligand topology building. Yogesh Sharma
[gmx-users] (no subject) Yogesh Sharma
[gmx-users] segmentation fault core dumped Yogesh Sharma
[gmx-users] Regarding LSI calculation Omkar Singh
[gmx-users] Fatal error during mdrun Samayaditya Singh
[gmx-users] [EXTERNAL] Iterative Boltzman Inversion Smith, Micholas D.
[gmx-users] Slurm for GROMACS Smith, Micholas D.
[gmx-users] helping increasing box Giuseppe R Del Sorbo
[gmx-users] how to make index of a micelle Giuseppe R Del Sorbo
[gmx-users] how to make index of a micelle Giuseppe R Del Sorbo
[gmx-users] how to make index of a micelle Giuseppe R Del Sorbo
[gmx-users] gmx rdf selrpos seltype Giuseppe R Del Sorbo
[gmx-users] Regarding force field for silicon oxide David van der Spoel
[gmx-users] cmake fails with custom gcc version David van der Spoel
[gmx-users] Regarding force field for silicon oxide David van der Spoel
[gmx-users] Vibrational frequencies from gromacs trajectory David van der Spoel
[gmx-users] anisotropic polarization David van der Spoel
[gmx-users] Toluene .rtp David van der Spoel
[gmx-users] single component temperature coupling Chong Teng
[gmx-users] Clarification on gpu acceleration for rf type dataset Vicky Tsang
[gmx-users] Slurm for GROMACS Alexander Tzanov
[gmx-users] mac OS Catalina segmentation fault Daskalakis Vangelis
[gmx-users] mac OS Catalina segmentation fault Daskalakis Vangelis
[gmx-users] How to produce "gro" format for calcite {1014} structure. Alessandra Villa
[gmx-users] Question about switching off non-bonded interactions between two molecules for MD simulation Alessandra Villa
[gmx-users] helping increasing box Alessandra Villa
[gmx-users] (no subject) Alessandra Villa
[gmx-users] Chain length of a polymer Alessandra Villa
[gmx-users] How does the trjconv -fit rot+trans work? Alessandra Villa
[gmx-users] Regarding free energy calculation Alessandra Villa
[gmx-users] Dummy atoms flopping everywhere Alessandra Villa
[gmx-users] Dummy atoms flopping everywhere Alessandra Villa
[gmx-users] Disulphide bonded cyclic peptides Alessandra Villa
[gmx-users] Terminal dangling bond error despite pdb2gmx recognising specbond.dat for a cyclic peptide Alessandra Villa
[gmx-users] Disulphide bonded cyclic peptides Alessandra Villa
[gmx-users] Calculation of young's modulus from stress-strain plot Alessandra Villa
[gmx-users] Disulphide bonded cyclic peptides Alessandra Villa
[gmx-users] clustered structures Quyen V. Vu
[gmx-users] searching this mailing list Quyen V. Vu
[gmx-users] single component temperature coupling Quyen V. Vu
[gmx-users] issues by simulating adsorption of peptide on a polymer surface Dallas Warren
[gmx-users] Automated Topology Builder changes randomly name of molecule submited Dallas Warren
[gmx-users] 1 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. Dallas Warren
[gmx-users] searching this mailing list Dallas Warren
[gmx-users] Gromacs - Difference between target temperature and pressure in mdp and simulation Dallas Warren
[gmx-users] Radial Density Profile Dallas Warren
[gmx-users] Fw: Radial Density Profile Dallas Warren
[gmx-users] Stochastic Dynamics nsttcouple John Whittaker
[gmx-users] Stochastic Dynamics nsttcouple John Whittaker
[gmx-users] Ruuning MD simulation on laptop Billy Williams-Noonan
[gmx-users] Script to merge protein and ligand topology for BAR calculation? Billy Williams-Noonan
[gmx-users] Script to merge protein and ligand topology for BAR calculation? Billy Williams-Noonan
[gmx-users] How to prepare prm and itp files of ligands from gro and top files prepared with Gauss, ambertool and acpye for gromacs simulations Sun Yeping
[gmx-users] Output from gmx h2order Decai Yu
[gmx-users] Output from gmx h2order Decai Yu
[gmx-users] How to produce "gro" format for calcite {1014} structure. Hamid Zaree
[gmx-users] Iterative Boltzman Inversion Salman Zarrini
[gmx-users] Radial Density Profile Salman Zarrini
[gmx-users] replica exchange with GROMACS hind ahmed
[gmx-users] gromacs.org_gmx-users Digest, Vol 187, Issue 49 hind ahmed
[gmx-users] Second beta release of GROMACS 2020 Paul bauer
[gmx-users] Error in DNA.itp file Paul bauer
[gmx-users] mac OS Catalina segmentation fault Paul bauer
[gmx-users] Webinar on mdp file settings Paul bauer
[gmx-users] How to set more mpi for the REMD run? Paul bauer
[gmx-users] How to set more mpi for the REMD run? Paul bauer
[gmx-users] (no subject) blau
[gmx-users] polymer & peptide interaction pbc, visualization problem p buscemi
[gmx-users] How to build and simulate POPE/POPG bilayer with gromos54a7 force field paul buscemi
[gmx-users] c2075 is not detected by gmx paul buscemi
[gmx-users] c2075 is not detected by gmx paul buscemi
[gmx-users] Automated Topology Builder changes randomly name of molecule submited daniel depope
[gmx-users] How to build and simulate POPE/POPG bilayer with gromos54a7 force field daniel depope
[gmx-users] regarding rmsd calculaton shakuntala dhurua
[gmx-users] regarding rmsd calculaton shakuntala dhurua
[gmx-users] (no subject) shakuntala dhurua
[gmx-users] (no subject) shakuntala dhurua
[gmx-users] rdf shakuntala dhurua
[gmx-users] rdf shakuntala dhurua
[gmx-users] rdf shakuntala dhurua
[gmx-users] (no subject) shakuntala dhurua
[gmx-users] (no subject) shakuntala dhurua
[gmx-users] (no subject) shakuntala dhurua
[gmx-users] Radial Density Profile elham
[gmx-users] Fw: Radial Density Profile elham
[gmx-users] Fw: Fw: Radial Density Profile elham
[gmx-users] Coulomb and vdW energies elham
[gmx-users] Fw: Radial Density Profile elham
[gmx-users] Magnetic effects in a classical force field atb files
[gmx-users] Problem running simulation on gromacs 2018.8 version pooja kesari
[gmx-users] gromacs.org_gmx-users Digest, Vol 187, Issue 21 pooja kesari
[gmx-users] (no subject) pooja kesari
[gmx-users] (no subject) saranya
[gmx-users] Coulomb term calculation in gromacs nikolaev at spbau.ru
[gmx-users] Coulomb term calculation in gromacs nikolaev at spbau.ru
[gmx-users] About errors displayed in regressiontests-2019.4 t0t0t0t0t0tttt at yahoo.co.jp
[gmx-users] Problems with installing GROMACS with MPI Дмитрий Дударев

Last message date: Sat Nov 30 14:16:55 CET 2019
Archived on: Sat Nov 30 14:16:56 CET 2019

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