[gmx-users] Re: System equilibrium problems

[Justin Lemkul]

On 6/14/13 10:45 AM, Parker de Waal wrote:
> HI Maggin,
>
> The Pressure came from NPT simulation, I apologize for the lack of
> annotation. Here are some of the outputs of your suggested checks of
> equilibrium
> https://docs.google.com/spreadsheet/ccc?key=0Ao2bINpUakZ-dHpiZG9SOXhkX0JGNXlqTHBfQ1kwbnc&usp=sharing
>
>
> I'm currently looking into the rvdw value as you suggested as well as the
> fourierspacing as Mark suggested.
>
> However to help with this problem I've uploaded all of .mdp files as well
> as my bash script here ->
> https://gist.github.com/ParkerdeWaal/8a7a73682e04a4878902
> Maybe there is a problem with my choice of box size? -bt cubic -d 1?
> Viewing the boxed and solvated system showed a distance of ~10A between the
> protein and the box which should be ample.
>
> Additionally a full output log of the run can be found here ->
> http://research.parkerdewaal.com/slurm-940372.out
> which seems to be error free until the final md run.
>

The cutoffs are wrong for 53A6.  Standard usage:

rcoulomb = 0.9
rlist = 0.9
rvdw = 1.4

The values of rcoulomb and rlist are fairly flexible when using PME.  The value 
of rvdw generally should not be toyed with.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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