[gmx-users] Re: System equilibrium problems
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
> 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 ->
> 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 ->
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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