[gmx-users] At what point is the random seed generated?
trayder.thomas at monash.edu
Wed Jan 29 04:47:00 CET 2014
Curses! Kinda seemed intuitive that way. I assume the philosophy being
worked towards is that every unique run should have a unique .tpr file that
it is reproducible from?
Curiously, I ran and checked a first batch on a different cluster and the
simulations rapidly diverged (even between simulations run one after the
other on the same node), while the second cluster managed to create 50
identical simulations across 50 different nodes. The most obvious
difference being that the diverging simulations used GPUs.
I suspect I never would have noticed if I had of stuck to the one cluster.
Might be worth stating explicitly in the manual for gen-seed, with
reproducibility being what it is.
Oh well, Thanks guys.
On Tue, Jan 28, 2014 at 10:55 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
> Indeed. grompp does report the seed it uses to stderr.
> On Tue, Jan 28, 2014 at 8:51 AM, David van der Spoel
> <spoel at xray.bmc.uu.se>wrote:
> > On 2014-01-28 08:37, Trayder Thomas wrote:
> >> Hi,
> >> When using 'gen-seed = -1' at what point is the random seed assigned?
> >> e.g. Does it use the process ID of grompp and embed the seed number in
> >> tpr file, or does it use the process ID of mdrun?
> >> I ask because I have 50 identical simulations started from the same tpr
> >> file :(
> >> Thanks,
> >> -Trayder
> >> I guess you found out. Sorry about that. It is done in grompp and same
> > tpr should give reproducible results. So you want to generate 50
> > tpr files.
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> > spoel at xray.bmc.uu.se http://folding.bmc.uu.se
> > --
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