[gmx-users] Running simulation differences

[Gonzalez Fernandez, Cristina]

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

Thank you for all your help,
C. 

-----Mensaje original-----
De: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> En nombre de Gonzalez Fernandez, Cristina
Enviado el: lunes, 17 de diciembre de 2018 18:01
Para: gmx-users at gromacs.org
Asunto: Re: [gmx-users] Running simulation differences

Thank you  very much Justin for your suggestions.
C.

-----Mensaje original-----
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

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