[gmx-users] Running simulation differences

[Justin Lemkul]

On Thu, Dec 20, 2018 at 1:01 PM Gonzalez Fernandez, Cristina <
cristina.gonzalezfdez at unican.es> wrote:

> 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?
>
>
As I said before, no, a massive difference like that, outside the error
bars, is not acceptable.

If you want more useful advice, you'll have to tell us exactly what you're
doing and trying to compare.

-Justin


>
> Thank you so much for all your help
>
> C.
>
> ________________________________
> 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
>
> --
>
> ==========================================
>
> 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
> http://www.thelemkullab.com
>
>
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-- 

==========================================

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
http://www.thelemkullab.com


==========================================