[gmx-users] -multidir option in REMD (GROMACS v2016.1)

Hermann, Johannes J.Hermann at lrz.tu-muenchen.de
Wed Aug 2 11:32:30 CEST 2017


On 02.08.2017 11:21, ABEL Stephane wrote:
> Dear all,
> I would like to do a REMD of a system with 75 replicas (with 75 directories named md_0,..., md_75) and I have two questions.
> 1) To launch the md calculation we should use the followng command :
> mpirun -np 4 mdrun_mpi -v -multidir sim[0123] -replex XXX
> My question is since I have 75 replicas (directories). How I should set the argument of -multidir ? Like this : -multidir md_[01234...75] or only "md_".
the .tpr file should be called same, e.g. md.tpr, then try:
-dffnm md - multidir YOURPATHBEFORE/md_*

The "*" fills all the available lambdas
> I have used the following command : mdrun_mpi -v -multidir ./"$Stage1_FileName"/md_ -replex 500, but the program stops with the following error : Need at least two replicas for replica exchange (option -multi)
> 2) Second question It is not clear to me how I should set the number of step in the mdp file of each replica use in the production runs.  For instance I want to do a simulation of 50 ns, should I set nsteps = 5000000/75
You set the steps for each replica in the mdp file. E.g.

nsteps = 5000000

Will simulate each replica for 50ns

> Could you help me ?
> Thanks for your help
> Stéphane

All the best

More information about the gromacs.org_gmx-users mailing list