Hi, On Wed, Aug 2, 2017 at 11:22 AM ABEL Stephane <stephane.a...@cea.fr> 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 -multidir option needs a list of all your directories. The best way to do that is with shell (e.g. wildcard) expansion. Just using "md_" doesn't get expanded by anything. I recently observed someone suggest that "md_{0..75}" might do what you want, but I've never tried it. Anyway, md_* will expand them all, and IIRC mdrun will sort out the ordering from the values of the REMD control parameter. > 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) > Since there's only one directory named, because the shell couldn't expand anything for you, mdrun doesn't know how to proceed. Pro tip - get it working for a small number of replicas (e.g. 2) before worrying about using all 75. > 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 > Each simulation is independent and every e.g. mdp parameter is particular to it. So choose your number of steps in each mdp file to be the length of a single replica. Obviously nsteps * dt = time in the usual way, but since we don't know dt, you'll have to compute your nsteps ;-) Mark Could you help me ? > > Thanks for your help > > Stéphane > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.