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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