[gmx-users] GROMACS PBS GPU JOB submission

Hi everyone I am using GROMACS 2018 in a node with 80 core and 4 TESLA V1, the queue system is PBS. I am having some issues with the GPU selection, what I want is to use 1 GPU per job but GROMACS is always using all the four GPUs. My submission script is the following: #PBS -l select=1:ncpus=40:

[gmx-users] Gromacs compilation problem

Hi everyone, I am having some issues with the installation of Gromacs using the optimization flag -DGMX_SIMD=AVX_512. If I install without the optimization, everything goes ok and the software works fine. But, as recommended by Gromacs in the log file, I should compile using the optimization flag

[gmx-users] GMX CURRENT

6.0*V*k\sB\N*T / Sm^-1ps^-1. So the SIGMA value should be S/m??? If I try do the fitting by myself and multiple the value obtained by the Prefacactor E-H the value for the SIGMA is quite different from the gmx current message. Thank you very much. Cheers Tuanan Lo

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 177, Issue 12

On Mon, Jan 7, 2019 at 7:07 AM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.s

[gmx-users] Selections in gromacs

Hi everyone, I am trying to use the "gmx trjconv" to write a new trajectory from my "main trajecetory" that contains just two molecules then they are close to each other in a specific distance. The idea is to have a new trajectory that contains these molecules in this specific distance in each fra

[gmx-users] MSD close to a surface/layer

Hi everyone, I have a simulation with a metal slab and I would like to get the MSD of the molecules close to the slab. I have tried the gmx selection that works pretty well to structural analysis, but to the dynamical analysis such as msd or rotacf there are some issues. I have tried the dynan_mol_

[gmx-users] MSD close to a surface/slab

Hi everyone, I have a simulation with a metal slab and I would like to get the MSD of the molecules close to the slab. I have tried the gmx selection that works pretty well to structural analysis, but to the dynamical analysis such as msd or rotacf there are some issues. I have tried the dynan_mol_

[gmx-users] Gromacs MSD close to an slab/interface

Hi everyone, I have a simulation with a metal slab and I would like to get the MSD of the molecules close to the slab. I have tried the gmx selection that works pretty well to structural analysis, but to the dynamical analysis such as msd or rotacf there are some issues. I have tried the dynan_mol

[gmx-users] Viscosity by Gromacs

Hi everyone, I reading about the viscosity methods in the EMD by Gromacs and I have just a simple question. In the user manual in section 6.11 there is an explanation about the Einstein method used in the gmx energy -vis, however, in the section 8.6.5 there is another explanation about the Green K

[gmx-users] Ion pair

Hi everybody, I am working with electrolytes simulations using Gromacs, so I am trying to get the residence time (ion pair lifetime, ion cage lifetime) of the ions. I tried to use gmx hbond with the option -contat, but if try get the acf of the interaction the program always has a crash, I also ha

[gmx-users] PM3-AD ERROR GROMACS 5.1.1

Hi to all, I am trying to perform a simulation utilizing the PM3-AD method but I received this message of error: Fatal error: Unsupported electrostatic interaction: P3M-AD Can Anybody confirm to me, if this message is due to a bug in the GROMACS 5.1.1? ___

[gmx-users] Polarizable Li+ Drude Simulations

Hi, My name is Tuanan and I am a Ph.D Student from Brazil. I am trying simulate Li+ using the polarizable force field of Roux (J. Chem. Theor. Comput., (2010), 6, 774-786) but I don't understand how i create my Li+ structure PDB file. I must insert a Drude particle in Li+ PDB file??? Someone woul