[gmx-users] Running simulation differences
Gonzalez Fernandez, Cristina
cristina.gonzalezfdez at unican.es
Mon Dec 17 18:00:39 CET 2018
Thank you very much Justin for your suggestions.
De: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> En nombre de Justin Lemkul
Enviado el: lunes, 17 de diciembre de 2018 16:18
Para: Discussion list for GROMACS users <gmx-users at gromacs.org>
Asunto: Re: [gmx-users] Running simulation differences
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.
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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