[gmx-users] Running simulation differences

Gonzalez Fernandez, Cristina cristina.gonzalezfdez at unican.es
Thu Dec 20 19:01:32 CET 2018

Hi Justin,

Do you think that the difference between a value of -280 ± 37 kj/mol obtained by Gromacs and -367 kj/mol obtained by NAMD can be acceptable?

Thank you so much for all your help


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 <jalemkul at vt.edu>
Enviado: martes, 18 de diciembre de 2018 15:34:07
Para: Discussion list for GROMACS users
Asunto: Re: [gmx-users] Running simulation differences

On Tue, Dec 18, 2018 at 5:01 AM Gonzalez Fernandez, Cristina <
cristina.gonzalezfdez at unican.es> wrote:

> Hi again Justin,
> I've been thinking about the normal variability between MD simulations you
> commented. I am simulating the interaction of a lipid with water, but the
> van der waals energy value that I obtain (-257.25  ± 35.86 kj/mol) for me
> is considerably different from the published value (-361 kj/mol). However,
> according to your email maybe these values can be considered similar. Do
> you think my value and the published one are similar? How can I reduced the
> error of the results because my value correspond to a long

I would not call those values similar at all. The two quantities you posted
before were within error of one another; those are similar. A difference of
over 100 kJ/mol, outside error, is enormous. You need to evaluate what
you're doing because in that case, I suspect something is inconsistent
between what is published and what you're doing.

> simulation (60 ns)? Could you recommend me a paper where is stated the
> common deviations/errors that are acceptable to a simulation result?

There is none to my knowledge, and certainly can't be generalized.
Different quantities have different tolerances. Different software may
produce somewhat different results, as well.

Also I wouldn't consider 60 ns long, by any means :)




Justin A. Lemkul, Ph.D.

Assistant Professor

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