gromacs.org_gmx-users

Messages by Date

2020/03/27 [gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites? Bjorn Wesen
2020/03/27 Re: [gmx-users] unexpecter rmsd Emran Heshmati
2020/03/27 Re: [gmx-users] unexpecter rmsd Justin Lemkul
2020/03/27 [gmx-users] unexpecter rmsd Emran Heshmati
2020/03/27 Re: [gmx-users] Inexpected rmsd Paul bauer
2020/03/27 Re: [gmx-users] Inexpected rmsd Jorden Cabal
2020/03/27 [gmx-users] Inexpected rmsd Emran Heshmati
2020/03/26 [gmx-users] interpolating frames between extremes Dave M
2020/03/26 Re: [gmx-users] compile with intel compiler Schulz, Roland
2020/03/26 Re: [gmx-users] Various questions related to Gromacs performance tuning Tobias Klöffel
2020/03/26 Re: [gmx-users] compilation error in multidimarray.h Herbert Fruchtl
2020/03/26 Re: [gmx-users] Force field for urea and urea-TMAO mixture Erik Marklund
2020/03/26 Re: [gmx-users] compilation error in multidimarray.h Mark Abraham
2020/03/26 [gmx-users] compilation error in multidimarray.h Herbert Fruchtl
2020/03/26 Re: [gmx-users] compile with intel compiler Harry Mark Greenblatt
2020/03/25 Re: [gmx-users] No default bond types Neena Susan Eappen
2020/03/25 Re: [gmx-users] No default bond types Justin Lemkul
2020/03/25 Re: [gmx-users] No default bond types Neena Susan Eappen
2020/03/25 Re: [gmx-users] No default bond types Justin Lemkul
2020/03/25 Re: [gmx-users] No default bond types Neena Susan Eappen
2020/03/25 Re: [gmx-users] No default bond types Justin Lemkul
2020/03/25 Re: [gmx-users] No default bond types Neena Susan Eappen
2020/03/25 Re: [gmx-users] compile with intel compiler Schulz, Roland
2020/03/25 Re: [gmx-users] No default bond types Justin Lemkul
2020/03/25 Re: [gmx-users] No default bond types Neena Susan Eappen
2020/03/25 Re: [gmx-users] gpu_id for more than 10 GPUs? Justin Lemkul
2020/03/25 Re: [gmx-users] compile with intel compiler Lyudmyla Dorosh
2020/03/25 Re: [gmx-users] How to reduce the penalty of small molecule from CGenFF Justin Lemkul
2020/03/25 [gmx-users] gpu_id for more than 10 GPUs? Leandro Bortot
2020/03/25 Re: [gmx-users] Extracting temperature of specific groups during the simulations Justin Lemkul
2020/03/25 [gmx-users] How to reduce the penalty of small molecule from CGenFF Rolly Ng
2020/03/25 Re: [gmx-users] Extracting temperature of specific groups during the simulations Mijiddorj B
2020/03/25 Re: [gmx-users] Calculate dihedrals Alessandra Villa
2020/03/25 Re: [gmx-users] Extracting temperature of specific groups during the simulations Justin Lemkul
2020/03/25 Re: [gmx-users] No default bond types Alessandra Villa
2020/03/25 Re: [gmx-users] Extracting temperature of specific groups during the simulations Alessandra Villa
2020/03/25 [gmx-users] Calculate dihedrals Marko Petrovic
2020/03/25 [gmx-users] compile with intel compiler Harry Mark Greenblatt
2020/03/25 [gmx-users] Extracting temperature of specific groups during the simulations Mijiddorj B
2020/03/24 [gmx-users] No default bond types Neena Susan Eappen
2020/03/24 [gmx-users] topology of co2 Afsane Farhadi
2020/03/24 [gmx-users] Drude polarization, practical matters Nicolás Marcelo Rozas Castro
2020/03/24 Re: [gmx-users] Various questions related to Gromacs performance tuning Mark Abraham
2020/03/24 Re: [gmx-users] Various questions related to Gromacs performance tuning Kutzner, Carsten
2020/03/24 Re: [gmx-users] Conversion of improper angles from amber object file to gromacs Justin Lemkul
2020/03/24 [gmx-users] Conversion of improper angles from amber object file to gromacs Daniel Bauer
2020/03/24 [gmx-users] GROMACS has switched to use Gitlab Paul bauer
2020/03/24 [gmx-users] Various questions related to Gromacs performance tuning Tobias Klöffel
2020/03/24 [gmx-users] Lincs warning in free energy calculation Sadaf Rani
2020/03/24 Re: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities Justin Lemkul
2020/03/24 [gmx-users] Free energy change calculation Xiaotong Zhang
2020/03/24 Re: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities Wesley Michaels
2020/03/23 Re: [gmx-users] Error in free energy calculation (Chris Neale) Sadaf Rani
2020/03/23 Re: [gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ? Paul bauer
2020/03/23 Re: [gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ? Jochen Hub
2020/03/23 Re: [gmx-users] Replica exchange: Coordinates and simulation box size? Johannes Hermann
2020/03/23 Re: [gmx-users] Replica exchange: Coordinates and simulation box size? Justin Lemkul
2020/03/23 Re: [gmx-users] Replica exchange: Coordinates and simulation box size? Daniel Burns
2020/03/23 [gmx-users] Replica exchange: Coordinates and simulation box size? Johannes Hermann
2020/03/23 Re: [gmx-users] comm-grps Alex
2020/03/23 Re: [gmx-users] comm-grps Magnus Lundborg
2020/03/23 Re: [gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ? Magnus Lundborg
2020/03/23 [gmx-users] Gmx bundle regarding RAHUL SURESH
2020/03/23 Re: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities Alessandra Villa
2020/03/22 Re: [gmx-users] k-space settings in GROMACS Anh Vo
2020/03/21 [gmx-users] comm-grps Alex
2020/03/20 Re: [gmx-users] pdb2gmx command not found Dallas Warren
2020/03/20 [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities Wesley Michaels
2020/03/20 Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 yujie Liu
2020/03/20 Re: [gmx-users] Problem in protein ligand interaction Du, Yu
2020/03/20 Re: [gmx-users] ERROR 1 [file lig.itp, line 575]:: ; Duplicate atom index (19) in virtual_sites3 Justin Lemkul
2020/03/20 Re: [gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ? Justin Lemkul
2020/03/20 Re: [gmx-users] distance restraints between different chains Quyen V. Vu
2020/03/20 [gmx-users] distance restraints between different chains Oscar Hernandez Alba
2020/03/20 Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 Christian Blau
2020/03/20 Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 liuyujie714
2020/03/20 [gmx-users] Problem in protein ligand interaction Gonzalez Fernandez, Cristina
2020/03/19 [gmx-users] Error in free energy calculation Chris Neale
2020/03/19 [gmx-users] About peptide mutation with non-standard residue Chris Neale
2020/03/19 [gmx-users] pdb2gmx command not found Chris Neale
2020/03/19 [gmx-users] Non-linear slowdown in grompp with very many bonded interactions Chris Neale
2020/03/19 [gmx-users] pdb2gmx command not found Sutanu L'Étranger
2020/03/19 [gmx-users] ERROR 1 [file lig.itp, line 575]:: ; Duplicate atom index (19) in virtual_sites3 Adarsh V. K.
2020/03/19 [gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ? Jochen Hub
2020/03/19 [gmx-users] About peptide mutation with non-standard residue Vicente Domínguez
2020/03/19 Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 liuyujie714
2020/03/19 Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 liuyujie714
2020/03/19 Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 Christian Blau
2020/03/19 [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 liuyujie714
2020/03/19 Re: [gmx-users] alchemical free energy calculation with physical PBC Alessandra Villa
2020/03/19 [gmx-users] Error in free energy calculation Sadaf Rani
2020/03/18 Re: [gmx-users] About membrane leaflets and msd Kevin Boyd
2020/03/18 [gmx-users] alchemical free energy calculation with physical PBC Johannes Hermann
2020/03/18 Re: [gmx-users] How to find and open Gromacs after installation Benson Muite
2020/03/18 [gmx-users] How to find and open Gromacs after installation Sutanu L'Étranger
2020/03/18 Re: [gmx-users] lipid tail order parameter Piggot T .
2020/03/18 [gmx-users] (no subject) Sutanu L'Étranger
2020/03/18 Re: [gmx-users] About gmx msd and membrane leaflets Justin Lemkul
2020/03/18 Re: [gmx-users] NDG/BGLC Not Recognised In Force Fields Justin Lemkul
2020/03/18 Re: [gmx-users] NDG/BGLC Not Recognised In Force Fields McDonnell, Thomas
2020/03/18 [gmx-users] lipid tail order parameter Ipsita Basu
2020/03/18 Re: [gmx-users] About gmx msd and membrane leaflets Alessandra Villa
2020/03/18 Re: [gmx-users] k-space settings in GROMACS Anh Vo
2020/03/17 Re: [gmx-users] Failed HardwareTopologyTest on Install (GROMACS 2019.4) Mark Abraham
2020/03/17 Re: [gmx-users] Energy values for 1 step NVT/NVE simulation of 100 water molecules Mark Abraham
2020/03/17 Re: [gmx-users] k-space settings in GROMACS Mark Abraham
2020/03/17 [gmx-users] k-space settings in GROMACS Anh Vo
2020/03/17 [gmx-users] Energy values for 1 step NVT/NVE simulation of 100 water molecules Anh Vo
2020/03/17 [gmx-users] Viscosity of non-newtonian fluid Jun Zhou
2020/03/17 Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 191, Issue 42 McDonnell, Thomas
2020/03/17 Re: [gmx-users] GROMACS Quick and Dirty Installation Error Schulz, Roland
2020/03/17 [gmx-users] Failed HardwareTopologyTest on Install (GROMACS 2019.4) Adam Antoszewski
2020/03/17 [gmx-users] About gmx msd and membrane leaflets Poncho Arvayo Zatarain
2020/03/17 [gmx-users] About membrane leaflets and msd Poncho Arvayo Zatarain
2020/03/17 [gmx-users] Extraction of frames at different interval Farida Aziz
2020/03/17 Re: [gmx-users] Fwd: Reproducibility of a PMF plot André Farias de Moura
2020/03/17 [gmx-users] Fwd: Reproducibility of a PMF plot Alex
2020/03/17 [gmx-users] pdb2gmx - generating topology for helicase-DNA complex (3PJR) Max Winokan
2020/03/17 Re: [gmx-users] Gromax NDG/BGLC Force field Error Justin Lemkul
2020/03/17 Re: [gmx-users] pdb2gmx - generating topology for helicase-DNA complex (3PJR) Justin Lemkul
2020/03/17 [gmx-users] Gromax NDG/BGLC Force field Error McDonnell, Thomas
2020/03/17 [gmx-users] Problems with Non-equilibrium MD Jun Zhou
2020/03/17 Re: [gmx-users] makes sense for Ryckaert Bellemans dihs. only. Alessandra Villa
2020/03/16 [gmx-users] Quick and Dirty Installation Error Vinu Harihar
2020/03/16 [gmx-users] Electric field Mijiddorj B
2020/03/16 Re: [gmx-users] gmx msd unusual unit Joe Paul-Taylor
2020/03/16 [gmx-users] makes sense for Ryckaert Bellemans dihs. only. Sadaf Rani
2020/03/16 Re: [gmx-users] gmx msd unusual unit David van der Spoel
2020/03/16 Re: [gmx-users] energy minimization in vacuum Bratin Kumar Das
2020/03/16 [gmx-users] energy minimization in vacuum Deepanshi .
2020/03/16 [gmx-users] gmx msd unusual unit Joe Paul-Taylor
2020/03/16 Re: [gmx-users] gmx msd unusual unit Justin Lemkul
2020/03/16 Re: [gmx-users] Fatal error: Too many warnings (3) ; WARNING * [file lig.prm, line **] :: How to overcome this error -> simply delete the lines which give warnings? Justin Lemkul
2020/03/16 Re: [gmx-users] (no subject) Dallas Warren
2020/03/16 Re: [gmx-users] Can you help regarding this Dallas Warren
2020/03/16 Re: [gmx-users] Creating a simple water box Dallas Warren
2020/03/16 [gmx-users] Fwd: Problems with Non-equilibrium MD Jun Zhou
2020/03/16 Re: [gmx-users] Fwd: Problems with Non-equilibrium MD Benson Muite
2020/03/15 Re: [gmx-users] no subject Prasanth G, Research Scholar
2020/03/15 [gmx-users] Reproducibility of a PMF plot Alex
2020/03/15 Re: [gmx-users] positive potential energy David van der Spoel
2020/03/15 [gmx-users] positive potential energy Afsane Farhadi
2020/03/15 [gmx-users] Fatal error: Too many warnings (3) ; WARNING * [file lig.prm, line **] :: How to overcome this error -> simply delete the lines which give warnings? Adarsh V. K.
2020/03/15 [gmx-users] "No atom pairs for dispersion correction" Warning from GROMACS 2020 mdrun Eric Legresley
2020/03/15 Re: [gmx-users] Regarding REMD using gromacs4.5.5 Mohammad Madani
2020/03/14 Re: [gmx-users] potential energy doesn't have negative value David van der Spoel
2020/03/14 Re: [gmx-users] potential energy doesn't have negative value Afsane Farhadi
2020/03/14 Re: [gmx-users] potential energy doesn't have negative value Afsane Farhadi
2020/03/14 Re: [gmx-users] potential energy doesn't have negative value Justin Lemkul
2020/03/14 Re: [gmx-users] potential energy doesn't have negative value Justin Lemkul
2020/03/14 Re: [gmx-users] Linking MYR residue to N-terminus using pdb2gmx Justin Lemkul
2020/03/14 Re: [gmx-users] Linking MYR residue to N-terminus using pdb2gmx Neena Susan Eappen
2020/03/14 [gmx-users] potential energy doesn't have negative value Afsane Farhadi
2020/03/14 [gmx-users] Request for Plumed sample scripts Peter Mawanga
2020/03/14 [gmx-users] Can you help regarding this Prasanth G, Research Scholar
2020/03/14 [gmx-users] (no subject) FAISAL NABI
2020/03/14 [gmx-users] Creating a simple water box dodia
2020/03/14 Re: [gmx-users] Gromacs Install problem Paul bauer
2020/03/13 [gmx-users] Linking MYR residue to N-terminus using pdb2gmx Billy Williams-Noonan
2020/03/13 [gmx-users] Can you help regarding this Kushal Roy
2020/03/13 Re: [gmx-users] Gromacs Install problem Alexander Tzanov
2020/03/13 Re: [gmx-users] Gromacs Install problem Alexander Tzanov
2020/03/13 Re: [gmx-users] Gromacs Install problem xuan Zhang
2020/03/13 Re: [gmx-users] checkpoint files with replica exchange/ -multidir Daniel Burns
2020/03/13 [gmx-users] Gromacs Install problem xuan Zhang
2020/03/13 [gmx-users] Regarding sg parameter Omkar Singh
2020/03/13 [gmx-users] Regarding parameters for Bromine ion in Charmm36 FF Dilip.H.N
2020/03/12 Re: [gmx-users] Setting a electric field in a simulation Mijiddorj B
2020/03/12 Re: [gmx-users] pressure fluctuation and actual density Dallas Warren
2020/03/12 Re: [gmx-users] checkpoint files with replica exchange/ -multidir Daniel Burns
2020/03/12 Re: [gmx-users] checkpoint files with replica exchange/ -multidir Mark Abraham
2020/03/12 [gmx-users] checkpoint files with replica exchange/ -multidir Daniel Burns
2020/03/12 Re: [gmx-users] Parametrization of Mn(ii) in charmm force field Justin Lemkul
2020/03/12 [gmx-users] pressure fluctuation and actual density Afsane Farhadi
2020/03/12 [gmx-users] (no subject) Afsane Farhadi
2020/03/12 Re: [gmx-users] GROMACS automation John Whittaker
2020/03/12 Re: [gmx-users] GROMACS automation Mohamed Abdelaal
2020/03/12 Re: [gmx-users] GROMACS automation John Whittaker
2020/03/12 Re: [gmx-users] slurm and gromacs John Whittaker
2020/03/12 [gmx-users] slurm and gromacs Atila Petrosian
2020/03/12 Re: [gmx-users] GROMACS automation Mohamed Abdelaal
2020/03/12 [gmx-users] Vacuum simulations with Gromacs 2018 Aishwary Shivgan
2020/03/12 Re: [gmx-users] Nose-Hoover vs Berendsen vs V-rescale Mark Abraham
2020/03/12 Re: [gmx-users] Parametrization of Mn(ii) in charmm force field Alessandra Villa
2020/03/11 [gmx-users] Nose-Hoover vs Berendsen vs V-rescale Hadi Rahmaninejad
2020/03/11 [gmx-users] Parametrization of Mn(ii) in charmm force field Pranav BVN
2020/03/11 Re: [gmx-users] query regarding running simulation using GPU Mark Abraham
2020/03/11 Re: [gmx-users] Chlorine atom displacement Justin Lemkul
2020/03/11 Re: [gmx-users] GROMACS automation Justin Lemkul
2020/03/11 [gmx-users] Chlorine atom displacement Samantha Rudinsky
2020/03/11 [gmx-users] gmx traj Alex
2020/03/11 [gmx-users] query regarding running simulation using GPU Snehasis Chatterjee
2020/03/11 Re: [gmx-users] GROMACS automation Mohamed Abdelaal
2020/03/11 Re: [gmx-users] GROMACS automation John Whittaker
2020/03/11 [gmx-users] GROMACS automation Mohamed Abdelaal
2020/03/11 Re: [gmx-users] NVT.mdp running in 4.6 version but failed in VERSION 5.1.2 Alessandra Villa
2020/03/10 [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells Cardenas, Alfredo E
2020/03/10 Re: [gmx-users] Script for looping n simulations Justin Lemkul
2020/03/10 Re: [gmx-users] Script for looping n simulations Neena Susan Eappen
2020/03/10 Re: [gmx-users] [gmx-developers] The setup of gpu_id has a bug? Szilárd Páll