Hi all, We set up replicate simulations (same starting mdp files and structures) that ran across GPUs WITHOUT using the -reprod flag, but we set gen-vel to no and used the same ld-seed value for both with the v-rescale thermostat. They also ran on the same machine -- so from a deterministic point of view, I would expect them to be "exactly" the same.
The simulations, while having similar average energetics throughout, sample different conformations and they start to differ pretty much right after the simulation starts. I understand that I could have gotten results to be more reproducible by using the -reprod flag, but in the case I describe (and I don't think I have any other stochastic things going on unless I'm not understanding ld-seed or gen-vel = no, or am forgetting something?), what is causing the difference? Online, I see something about domain decomposition and optimization, but I'd like to understand that better. My major question, though, is -- are the differences due to domain decomposition optimization enough to basically equal what you might get from "replicates" starting with different starting velocities, especially once equilibration (as measure by RMSD) is reached? That's what I'm seeing, so I wanted to make sure that these differences can actually be this big. Or is there some other source of stochasticity I'm forgetting? Thanks so much, and I hope my question makes sense. M -- Mala L. Radhakrishnan Whitehead Associate Professor of Critical Thought Associate Professor of Chemistry Wellesley College 106 Central Street Wellesley, MA 02481 (781)283-2981 -- 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.