[gmx-users] same initial velocities vs. -reprod

Mark Abraham mark.j.abraham at gmail.com
Fri Mar 22 18:21:37 CET 2019


The dynamic load balancing on by default for domain decomposition means
divergence happens by default. After a few ps it's logically equivalent to
starting from different velocities. See the GROMACS user guide for more
details on reproducibility questions!


On Fri., 22 Mar. 2019, 18:15 Mala L Radhakrishnan, <mradhakr at wellesley.edu>

> 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-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list