Hi, Lower performe especially with GPUs is not unexpected, but what you report is unusually large. I suggest you post your mdp and log file, perhaps there are some things to improve.
-- Szilárd On Wed, Jul 17, 2019 at 3:47 PM David de Sancho <david.desan...@ehu.eus> wrote: > Hi all > I have been doing some testing for Hamiltonian replica exchange using > Gromacs 2018.3 on a relatively simple system with 3000 atoms in a cubic > box. > For the modified hamiltonian I have simply modified the water interactions > by generating a typeB atom in the force field ffnonbonded.itp with > different parameters file and then creating a number of tpr files for > different lambda values as defined in the mdp files. The only difference > between mdp files for a simple NVT run and for the HREX runs are the > following lines: > > > ; H-REPLEX > > free-energy = yes > > init-lambda-state = 0 > > nstdhdl = 0 > > vdw_lambdas = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 > > I have tested for performance in the same machine and compared the standard > NVT run performance (~175 ns/day in 8 cores) with that for the free energy > tpr file (6.2 ns/day). > Is this performance loss what you would expect or are there any immediate > changes you can suggest to improve things? I have found a relatively old > post on this on Gromacs developers (https://redmine.gromacs.org/issues/742 > ), > but I am not sure whether it is the exact same problem. > Thanks, > > David > -- > 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.
