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

Mala L Radhakrishnan mradhakr at wellesley.edu
Fri Mar 22 18:15:32 CET 2019

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.


Mala L. Radhakrishnan
Whitehead Associate Professor of Critical Thought
Associate Professor of Chemistry
Wellesley College
106 Central Street
Wellesley, MA 02481

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