[gmx-users] Re: System equilibrium problems

[Parker de Waal]

Thanks Justin!

I've updated the values accordingly. However can I ask where you found
these? I'm curious if there is a site that I missed while searching.

Best,
Parker


On Fri, Jun 14, 2013 at 12:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ========================================
>
> 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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