[gmx-users] Running simulation differences

Justin Lemkul jalemkul at vt.edu
Mon Dec 17 16:18:13 CET 2018

On Mon, Dec 17, 2018 at 10:15 AM Gonzalez Fernandez, Cristina <
cristina.gonzalezfdez at unican.es> wrote:

> Hi Kevin,
> Thank you very much for your answer. Do you know how I can set the "double
> precision"?
You would have to recompile and reinstall with the appropriate option given
to CMake. But I doubt that's necessary; most normal MD simulations are done
in mixed precision and are sufficiently accurate. What you're observing is
normal variability between MD simulations. This is why it is standard
practice to run several replicate simulations and pool or average over
those results. One trajectory is not necessarily more believable than
another. Recent literature suggests that at least 5 replicates, if not 10,
of any system should be simulated to get reasonable results.




Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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