[gmx-users] demux.pl

Hi, I have 60 replicas simulated with REMD using gromacs. I demultiplex .xtc files with demux.pl script. I know we can generate a continue coordinate trajectory using "gmx trjcat" combined with "-demux replica_index.xvg" option. However I am confused with using the option "-demux

Re: [gmx-users] gromacs 2016 vs 5.1.4

Dear Nikhil, Use gmx2016. The 5.1.X versions only get bug fixes and a few backports now as far as I know. Kind regards, Erik > On 11 Oct 2016, at 07:19, Nikhil Maroli wrote: > > Dear all > > We have Workstation with GTX 1070 Cards, Which Gromacs I should install >

Re: [gmx-users] gromacs 2016 vs 5.1.4

Hi, As the release notes say, http://manual.gromacs.org/documentation/5.1.4/ReleaseNotes/index.html, we fixed bugs. Everybody needs to be able to feel confident that things are only likely to improve if they move up to a bug fix release, but acknowledge there will be bigger changes from 5.0, to

Re: [gmx-users] demux.pl

Hi, IIRC there's not intended to be any difference - you should be able to make idempotent round-trips by using two rounds of trjcat with the respective .xvg files. This is potentially useful for large simulation sets where you don't want to have to store the original trajectories (in case you

Re: [gmx-users] mdp file of membrane simulation

Hi, You need to find the resname/index name for the individual component,it depends on your system. add those names in energygps and do mdrerun You can find for PROT-LIPID PROT-MOLECULE PROT-REST/WATER LIPID-MOLECULE so on -- Gromacs Users mailing list * Please search the archive at

[gmx-users] PMF

Dear gromacs user, I am trying to simulate the PMF a small peptide adsorbed to a solid surface but no success unfurtunatly. For some force constant the peptide would not desorbed from the surface and for higher force constants what you can see in enclosed file will happen. Some question is: If it