March 2019 Archives by date

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Starting: Fri Mar 1 01:14:01 CET 2019
Ending: Sat Mar 30 09:09:45 CET 2019
Messages: 330

[gmx-users] How to calculate double donor and double acceptors in gromacs? 이영규
[gmx-users] Fwd: Probability of number of atomic contacts Mark Abraham
[gmx-users] position restraints on backbone: index error morpheus
[gmx-users] position restraints on backbone: index error Quyen Vu
[gmx-users] position restraints on backbone: index error Quyen Vu
[gmx-users] Fwd: Probability of number of atomic contacts Mahsa
[gmx-users] Can I use RMSD increase to indicate the unfolding while the Rg remains unchanged? ZHANG Cheng
[gmx-users] Can I use RMSD increase to indicate the unfolding while the Rg remains unchanged? Justin Lemkul
[gmx-users] Pulling ion across the bilayer-choosing pull_coord1_geometry Justin Lemkul
[gmx-users] Output files RMSD (xvg). Convert Nanometer to Angstrom. Edjan Silva
[gmx-users] Output files RMSD (xvg). Convert Nanometer to Angstrom. Justin Lemkul
[gmx-users] edit dhdl.xvg file Qasim Pars
[gmx-users] edit dhdl.xvg file Justin Lemkul
[gmx-users] edit dhdl.xvg file Qasim Pars
[gmx-users] edit dhdl.xvg file Justin Lemkul
[gmx-users] [gmx-developers] GMX outputs GLY sidechain as Hydrogen L- or D- Justin Lemkul
[gmx-users] Handling terminal amino acids for Amber D. Yousefi
[gmx-users] How to calculate tetrahedral order parameter? 이영규
[gmx-users] can dynamic selection be used with gmx rdf? Cardenas, Alfredo E
[gmx-users] How to calculate tetrahedral order parameter? Dallas Warren
[gmx-users] Validation of forcefield for small molecules Hemalatha Jayabal
[gmx-users] edit dhdl.xvg file Berk Hess
[gmx-users] Force field error Swapnil Bhujbal
[gmx-users] Force field error Smith, Micholas D.
[gmx-users] Force field error Justin Lemkul
[gmx-users] Validation of forcefield for small molecules Justin Lemkul
[gmx-users] Error in NVT equilibration step banijamali_fs
[gmx-users] Error in NVT equilibration step John Whittaker
[gmx-users] Gromos54a7 FF Alex
[gmx-users] position restraints on backbone: index error morpheus
[gmx-users] position restraints on backbone: index error Justin Lemkul
[gmx-users] Gromos54a7 FF Justin Lemkul
[gmx-users] position restraints on backbone: index error Quyen Vu
[gmx-users] Gromos54a7 FF Ray, Bruce D
[gmx-users] In continuous I got another warning, could anyone help me? banijamali_fs
[gmx-users] Data collection xtc file Alex
[gmx-users] In continuous I got another warning, could anyone help me? Najamuddin Memon
[gmx-users] Are the D-CMAP terms present in the last release of CHARMM force field for GROMACS (charmm36-nov2018.ff.tgz)? ABEL Stephane
[gmx-users] Problems installing gromacs 2019.1 using bash (ubunto 18.04) on a win10 PC Fritjof Nilsson
[gmx-users] Are the D-CMAP terms present in the last release of CHARMM force field for GROMACS (charmm36-nov2018.ff.tgz)? Justin Lemkul
[gmx-users] In continuous I got another warning, could anyone help me? Najamuddin Memon
[gmx-users] Are the D-CMAP terms present in the last release of CHARMM force field for GROMACS ABEL Stephane
[gmx-users] In continuous I got another warning, could anyone help me? Justin Lemkul
[gmx-users] Fwd: Data collection xtc file Alex
[gmx-users] Defining a new molecule type Ali Khodayari
[gmx-users] Itp for a longer molecule out of a shorter one Alex
[gmx-users] Itp for a longer molecule out of a shorter one pbuscemi at q.com
[gmx-users] Itp for a longer molecule out of a shorter one Alex
[gmx-users] Itp for a longer molecule out of a shorter one paul buscemi
[gmx-users] Itp for a longer molecule out of a shorter one paul buscemi
[gmx-users] v-rescale reproducible restart Sergio Perez
[gmx-users] script Amin Rouy
[gmx-users] question about the QM/MM calcuation in Gromacs/ORCA interface Mahnaz Tehrani
[gmx-users] script Quyen Vu
[gmx-users] script Justin Lemkul
[gmx-users] script Benson Muite
[gmx-users] script Amin Rouy
[gmx-users] script Quyen Vu
[gmx-users] User tabulated potential and VdW Modifier Kiesel, Matthias
[gmx-users] VMD visualization is failed mary ko
[gmx-users] script Amin Rouy
[gmx-users] script Quyen Vu
[gmx-users] script Pedro Deira
[gmx-users] script Amin Rouy
[gmx-users] (无主题) 吴修聪
[gmx-users] grompp is using a very large amount of memory on a modestly-sized system Sean Marks
[gmx-users] grompp is using a very large amount of memory on a modestly-sized system Justin Lemkul
[gmx-users] grompp is using a very large amount of memory on a modestly-sized system Sean Marks
[gmx-users] grompp is using a very large amount of memory on a modestly-sized system Sean Marks
[gmx-users] Calculating enthalpies of solvation. William Welch
[gmx-users] grompp is using a very large amount of memory on a modestly-sized system Mark Abraham
[gmx-users] gromacs performance Carlos Rivas
[gmx-users] gromacs performance Benson Muite
[gmx-users] gromacs performance Carlos Rivas
[gmx-users] gromacs performance Benson Muite
[gmx-users] gromacs performance Carlos Rivas
[gmx-users] gromacs performance Mark Abraham
[gmx-users] gmx distance marzieh gharouni
[gmx-users] Pairwise distances from COM of residues Pandya, Akash
[gmx-users] Pairwise distances from COM of residues Mark Abraham
[gmx-users] extra-bond Stefano Guglielmo
[gmx-users] Cys-Cys bonding alex rayevsky
[gmx-users] extra-bond Justin Lemkul
[gmx-users] Cys-Cys bonding Justin Lemkul
[gmx-users] info about gpus Stefano Guglielmo
[gmx-users] extra-bond Stefano Guglielmo
[gmx-users] hydrophobic interactions and electrostatic interactions between the protein chains Mahboobeh Eslami
[gmx-users] info about gpus paul buscemi
[gmx-users] extra-bond Mark Abraham
[gmx-users] gmx distance Dallas Warren
[gmx-users] Gomacs 2019 build on sles12 and centos Nelson Chris AWE
[gmx-users] pinoffset w LINCS error Tamas Hegedus
[gmx-users] Build a .top file monia kam
[gmx-users] Simulation crashed - Large VCM, Pressure scaling more than 1%, Bond length not finite zeineb SI CHAIB
[gmx-users] gmx analyze -av Amin Rouy
[gmx-users] gmx analyze -av Amin Rouy
[gmx-users] gmx analyze -av Justin Lemkul
[gmx-users] grompp is using a very large amount of memory on a modestly-sized system Sean Marks
[gmx-users] gromacs error in vacuum preparation simulation Mario Andres Rodriguez Pineda
[gmx-users] gromacs error in vacuum preparation simulation Justin Lemkul
[gmx-users] gromacs error in vacuum preparation simulation Mario Andres Rodriguez Pineda
[gmx-users] VMD movie making-remove water molecules from .trr after a simulation mary ko
[gmx-users] gromacs error in vacuum preparation simulation Justin Lemkul
[gmx-users] VMD movie making-remove water molecules from .trr after a simulation Justin Lemkul
[gmx-users] gmx trjconv trr xtc Alex
[gmx-users] gmx trjconv trr xtc Dallas Warren
[gmx-users] VMD movie making-remove water molecules from .trr after a simulation mary ko
[gmx-users] Hydrophobic interactions and electrostatic interactions between the protein chains Mahboobeh Eslami
[gmx-users] Pore size calculation RAHUL SURESH
[gmx-users] (no subject) Никита Шалин
[gmx-users] Video cards Benson Muite
[gmx-users] Videocard selection Никита Шалин
[gmx-users] Pore size calculation pbuscemi at q.com
[gmx-users] Videocard selection Никита Шалин
[gmx-users] Pore size calculation Никита Шалин
[gmx-users] Videocard selection Benson Muite
[gmx-users] Pore size calculation RAHUL SURESH
[gmx-users] Pore size calculation pbuscemi at q.com
[gmx-users] Videocard selection pbuscemi at q.com
[gmx-users] AWS Carlos Rivas
[gmx-users] Pore size calculation RAHUL SURESH
[gmx-users] AWS Никита Шалин
[gmx-users] AWS Justin Lemkul
[gmx-users] VMD movie making-remove water molecules from .trr after a simulation Justin Lemkul
[gmx-users] Research Programmer for VMD/NAMD at UIUC João Ribeiro
[gmx-users] Videocard selection Szilárd Páll
[gmx-users] gromacs error in vacuum preparation simulation Mario Andres Rodriguez Pineda
[gmx-users] Forcefield of coordinate bond between metal ion and residue 翻墙去上网
[gmx-users] Error in Gromacs msubrata
[gmx-users] Problem with cuda toolkit Shahrokh Nasseri (PhD)
[gmx-users] Steps for executing Markov state Modelling (MSM) analysis Soham Sarkar
[gmx-users] gmx trjconv trr xtc Mark Abraham
[gmx-users] Problem with cuda toolkit Mark Abraham
[gmx-users] Fwd: Probability of number of atomic contacts Mahsa
[gmx-users] Gomacs 2019 build on sles12 and centos Szilárd Páll
[gmx-users] Gomacs 2019 build on sles12 and centos Szilárd Páll
[gmx-users] gromacs performance Szilárd Páll
[gmx-users] gromacs performance Szilárd Páll
[gmx-users] Energy Conservation Conundrum Kruse, Luke E.(MU-Student)
[gmx-users] Principle component analysis data manipulation from gromacs SGR160055 Student
[gmx-users] [MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday Symposium: April 08-11, 2019 in Erlangen, Germany Harald Lanig
[gmx-users] gromacs performance Никита Шалин
[gmx-users] WG: WG: Issue with CUDA and gromacs Tafelmeier, Stefanie
[gmx-users] Dielectric constant Jianna Blocchi
[gmx-users] User tabulated potential and VdW Modifier Kiesel, Matthias
[gmx-users] Simulation is very slow 이영규
[gmx-users] Simulation is very slow Kevin Boyd
[gmx-users] Simulation is very slow Moir, Michael (MMoir)
[gmx-users] Simulation is very slow Benson Muite
[gmx-users] PDB file that can be read in Gromacs Phuong Chau
[gmx-users] PDB file that can be read in Gromacs Justin Lemkul
[gmx-users] PDB file that can be read in Gromacs RAHUL SURESH
[gmx-users] Steps for Markov State Modelling Soham Sarkar
[gmx-users] PDB file that can be read in Gromacs RAHUL SURESH
[gmx-users] Steps for Markov State Modelling Dallas Warren
[gmx-users] Steps for Markov State Modelling Justin Lemkul
[gmx-users] Free-energy on GMX-2019.1 ( lower performance on GPU) praveen kumar
[gmx-users] Free-energy on GMX-2019.1 ( lower performance on GPU) Mark Abraham
[gmx-users] generation of rtp and itp files Soham Sarkar
[gmx-users] generation of rtp and itp files RAHUL SURESH
[gmx-users] Free energy landscape RAHUL SURESH
[gmx-users] Free-energy on GMX-2019.1 ( lower performance on GPU) (Mark Abraham) praveen kumar
[gmx-users] generation of rtp and itp files Soham Sarkar
[gmx-users] PDB file that can be read in Gromacs paul buscemi
[gmx-users] Free-energy on GMX-2019.1 ( lower performance on GPU) (Mark Abraham) Mark Abraham
[gmx-users] WG: WG: Issue with CUDA and gromacs Szilárd Páll
[gmx-users] WG: WG: Issue with CUDA and gromacs Tafelmeier, Stefanie
[gmx-users] Naming convention for Acetyl Terminal group Neena Susan Eappen
[gmx-users] WG: WG: Issue with CUDA and gromacs Szilárd Páll
[gmx-users] Naming convention for Acetyl Terminal group Mark Abraham
[gmx-users] WG: WG: Issue with CUDA and gromacs Tafelmeier, Stefanie
[gmx-users] WG: WG: Issue with CUDA and gromacs Szilárd Páll
[gmx-users] WG: WG: Issue with CUDA and gromacs Szilárd Páll
[gmx-users] DSSP regardin RAHUL SURESH
[gmx-users] coulombic color display all positive of the simulation model MD
[gmx-users] CU2+ nonbonded parameteres (sigma and epsilon) Mohsen Asadbegi
[gmx-users] protein-ligand analysis mary ko
[gmx-users] (no subject) shakira shukoor
[gmx-users] Replica exchange MD analysis Rituraj Purohit
[gmx-users] CU2+ nonbonded parameteres (sigma and epsilon) Paul Bauer
[gmx-users] CU2+ nonbonded parameteres (sigma and epsilon) Mohsen Asadbegi
[gmx-users] CU2+ nonbonded parameteres (sigma and epsilon) Justin Lemkul
[gmx-users] DSSP regardin Mateusz Bieniek
[gmx-users] DSSP regardin RAHUL SURESH
[gmx-users] WG: WG: Issue with CUDA and gromacs Tafelmeier, Stefanie
[gmx-users] Defining new atom in forcefield Hadi Rahmaninejad
[gmx-users] gmx do_dssp Eduardo Diniz
[gmx-users] gmx do_dssp John Whittaker
[gmx-users] gmx do_dssp João Henriques
[gmx-users] regarding solvating a molecule Ali Khodayari
[gmx-users] gmx do_dssp Bratin Kumar Das
[gmx-users] Chloroform simulation-Fatal error: Invalid angle type 1000 Lakshman Ji Verma
[gmx-users] Chloroform simulation-Fatal error: Invalid angle type 1000 Lakshman Ji Verma
[gmx-users] Chloroform simulation-Fatal error: Invalid angle type 1000 Dallas Warren
[gmx-users] Different models of TMAO Dilip.H.N
[gmx-users] V-rescale fatal error Adriana Garro
[gmx-users] V-rescale fatal error Justin Lemkul
[gmx-users] Replica exchange MD analysis Rituraj Purohit
[gmx-users] Coordinates mismatch between topol.top and solve.gro RAHUL SURESH
[gmx-users] Central atom for improper dihedral Tam, Benjamin
[gmx-users] Vanishing cofactors Erik Marklund
[gmx-users] Vanishing cofactors Erik Marklund
[gmx-users] Vanishing cofactors Erik Marklund
[gmx-users] gpu cpu use Mario Andres Rodriguez Pineda
[gmx-users] Different models of TMAO Dilip.H.N
[gmx-users] Freezing structure's atom Hadi Rahmaninejad
[gmx-users] NPT step after energy minimization Jianna Blocchi
[gmx-users] Freezing structure's atom Mateusz Bieniek
[gmx-users] NTMPI / NTOMP combination: 10 threads not "reasonable" for GROMACS? Stéphane Téletchéa
[gmx-users] Freezing structure's atom Hadi Rahmaninejad
[gmx-users] Freezing structure's atom Mateusz Bieniek
[gmx-users] Freezing structure's atom Hadi Rahmaninejad
[gmx-users] Freezing structure's atom Hadi Rahmaninejad
[gmx-users] Freezing structure's atom Mateusz Bieniek
[gmx-users] dssp error Mario Andres Rodriguez Pineda
[gmx-users] dssp error Qinghua Liao
[gmx-users] dssp error Mario Andres Rodriguez Pineda
[gmx-users] dssp error Qinghua Liao
[gmx-users] dssp error Mario Andres Rodriguez Pineda
[gmx-users] compatibility between ff14SB and GLYCAM_06j-1 force field Louise Lassalle
[gmx-users] Ris: compatibility between ff14SB and GLYCAM_06j-1 force field Casalini Tommaso
[gmx-users] dssp error Soham Sarkar
[gmx-users] cutoff for tabulated bonded interaction functions? Voronin, Arthur (SCC)
[gmx-users] nonstandard hydrogen names MD
[gmx-users] System Blowing up when more than one MPI thread is used Mayank Vats
[gmx-users] same initial velocities vs. -reprod Mala L Radhakrishnan
[gmx-users] same initial velocities vs. -reprod Mark Abraham
[gmx-users] Different models of TMAO Erik Marklund
[gmx-users] Question about gmx order ... Sergio Garay
[gmx-users] same initial velocities vs. -reprod Mala L Radhakrishnan
[gmx-users] same initial velocities vs. -reprod Benson Muite
[gmx-users] same initial velocities vs. -reprod Mala L Radhakrishnan
[gmx-users] Addition of custom restraints Pelin S Bulutoglu
[gmx-users] Cannot find position restraint file Neena Susan Eappen
[gmx-users] Cannot find position restraint file Hadi Rahmaninejad
[gmx-users] gromacs.org_gmx-users Digest, Vol 179, Issue 56 jonathanjanke at gmail.com
[gmx-users] Cannot find position restraint file Mateusz Bieniek
[gmx-users] Replica exchange MD analysis Rituraj Purohit
[gmx-users] Grompp error Hanin Omar
[gmx-users] Question about gmx order ... Dallas Warren
[gmx-users] Replica exchange MD analysis Dallas Warren
[gmx-users] applying surface tension to a membrane bilayer 凌未风
[gmx-users] GPU error RAHUL SURESH
[gmx-users] GPU error Mark Abraham
[gmx-users] Replica exchange MD analysis Mark Abraham
[gmx-users] (cross-)compiling mdrun independently from the rest of gromacs tools Vedat Durmaz
[gmx-users] energygrp_excl error in g_membed run Ava Xue
[gmx-users] Replica exchange MD analysis Rituraj Purohit
[gmx-users] Replica exchange MD analysis Justin Lemkul
[gmx-users] Replica exchange MD analysis Rituraj Purohit
[gmx-users] WG: WG: Issue with CUDA and gromacs Szilárd Páll
[gmx-users] GPU error RAHUL SURESH
[gmx-users] Help regarding clustering of conformations Sidhanta Swayam Prakash Das
[gmx-users] grompp error: Unknown bond_atomtype vicolls at fizyka.umk.pl
[gmx-users] Help regarding clustering of conformations Sidhanta Swayam Prakash Das
[gmx-users] grompp error: Unknown bond_atomtype RAHUL SURESH
[gmx-users] GPU error Justin Lemkul
[gmx-users] WG: WG: Issue with CUDA and gromacs Tafelmeier, Stefanie
[gmx-users] grompp error: Unknown bond_atomtype vicolls at fizyka.umk.pl
[gmx-users] grompp error: Unknown bond_atomtype RAHUL SURESH
[gmx-users] grompp error: Unknown bond_atomtype vicolls at fizyka.umk.pl
[gmx-users] grompp error: Unknown bond_atomtype RAHUL SURESH
[gmx-users] GPU error RAHUL SURESH
[gmx-users] extract chain information in xtc file tina-meryl.amans at ibcp.fr
[gmx-users] grompp error: Unknown bond_atomtype vicolls at fizyka.umk.pl
[gmx-users] grompp error: Unknown bond_atomtype vicolls at fizyka.umk.pl
[gmx-users] extract chain information in xtc file RAHUL SURESH
[gmx-users] extract chain information in xtc file RAHUL SURESH
[gmx-users] grompp error: Unknown bond_atomtype Justin Lemkul
[gmx-users] WG: WG: Issue with CUDA and gromacs Szilárd Páll
[gmx-users] NVT equilibration in vacuum Neena Susan Eappen
[gmx-users] NVT equilibration in vacuum Justin Lemkul
[gmx-users] NVT equilibration in vacuum Erik Marklund
[gmx-users] WG: WG: Issue with CUDA and gromacs Tafelmeier, Stefanie
[gmx-users] Zsh completion behaves differently from bash completion Lorenzo Gaifas
[gmx-users] Zsh completion behaves differently from bash completion Mark Abraham
[gmx-users] Zsh completion behaves differently from bash completion Mark Abraham
[gmx-users] (no subject) saranya
[gmx-users] WG: WG: Issue with CUDA and gromacs Szilárd Páll
[gmx-users] (no subject) Dallas Warren
[gmx-users] Mapping of the RMSF onto 3D structure James Starlight
[gmx-users] Berendsen Barostat for production runs Daniel Bauer
[gmx-users] Berendsen Barostat for production runs Mark Abraham
[gmx-users] Berendsen Barostat for production runs Justin Lemkul
[gmx-users] Help needed using gmx select of GROMACS Budheswar Dehury
[gmx-users] Help needed using gmx select of GROMACS Budheswar Dehury
[gmx-users] How to create top of small molecules with pdb2gmx Tingguang.S
[gmx-users] How to create top of small molecules with pdb2gmx Justin Lemkul
[gmx-users] AWH with multiple parallel simulations Piotr Setny
[gmx-users] Visualisation of free energy diagrams by gmx sham James Starlight
[gmx-users] How to create top of small molecules with pdb2gmx Tingguang.S
[gmx-users] How to create top of small molecules with pdb2gmx Justin Lemkul
[gmx-users] AWH with multiple parallel simulations Mark Abraham
[gmx-users] WG: WG: Issue with CUDA and gromacs Tafelmeier, Stefanie
[gmx-users] AWH with multiple parallel simulations Berk Hess
[gmx-users] AWH with multiple parallel simulations Piotr Setny
[gmx-users] Energy Conservation at the Beginning of a Production Run Kruse, Luke E.(MU-Student)
[gmx-users] Energy Conservation at the Beginning of a Production Run David van der Spoel
[gmx-users] Energy Conservation at the Beginning of a Production Run Kruse, Luke E.(MU-Student)
[gmx-users] extract chain information in xtc file Stéphane Téletchéa
[gmx-users] Energy Conservation at the Beginning of a Production Run David van der Spoel
[gmx-users] Energy Conservation at the Beginning of a Production Run Kruse, Luke E.(MU-Student)
[gmx-users] WG: WG: Issue with CUDA and gromacs Szilárd Páll
[gmx-users] How to create top of small molecules with pdb2gmx Tingguang.S
[gmx-users] Energy Conservation at the Beginning of a Production Run Justin Lemkul
[gmx-users] How to create top of small molecules with pdb2gmx Justin Lemkul
[gmx-users] How to create top of small molecules with pdb2gmx Tingguang.S
[gmx-users] How to create top of small molecules with pdb2gmx Justin Lemkul
[gmx-users] How to create top of small molecules with pdb2gmx Tingguang.S
[gmx-users] Coarse-grained Protein-ligand simulations Mac Kevin Braza
[gmx-users] Energy Conservation at the Beginning of a Production Run Mark Abraham
[gmx-users] PME constant shifts. Sergio Perez
[gmx-users] PME constant shifts. Berk Hess
[gmx-users] CG lipid diffusion coefficient Yasser Almeida Hernández
[gmx-users] PME constant shifts. (Sergio Perez) Groenhof, Gerrit
[gmx-users] Coarse-grained Protein-ligand simulations Justin Lemkul
[gmx-users] Energy Conservation at the Beginning of a Production Run Justin Lemkul
[gmx-users] Help needed in using gmx select Budheswar Dehury
[gmx-users] Help needed in using gmx select Budheswar Dehury
[gmx-users] Coarse-grained Protein-ligand simulations Mac Kevin Braza
[gmx-users] PME constant shifts. Sergio Perez
[gmx-users] PME constant shifts. Berk Hess
[gmx-users] PME constant shifts. Sergio Perez
[gmx-users] WG: WG: Issue with CUDA and gromacs Tafelmeier, Stefanie
[gmx-users] Energy Conservation at the Beginning of a Production Run Kruse, Luke E.(MU-Student)
[gmx-users] Energy Conservation at the Beginning of a Production Run Justin Lemkul
[gmx-users] Coarse-grained Protein-ligand simulations Justin Lemkul
[gmx-users] Trouble in generating gro file for GROMACS MD simulation. Aparna Chaturvedi
[gmx-users] Trouble in generating gro file for GROMACS MD simulation. RAHUL SURESH
[gmx-users] Trouble in generating gro file for GROMACS MD simulation. RAHUL SURESH

Last message date: Sat Mar 30 09:09:45 CET 2019
Archived on: Fri Apr 5 11:48:00 CEST 2019

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