[gmx-users] Re: System equilibrium problems

Justin Lemkul jalemkul at vt.edu
Fri Jun 14 18:04:37 CEST 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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