On 6/11/12 6:42 AM, Satish Kamath wrote:
Hi gmx users,
I'm trying to create an equilibrated 2,3 dihydroxynaphthalene solvent box. I
used PRODRG2 server to create an itp file from the
downloaded pdb file. I used genbox to insert the solvent randomly into a 5
nm cubic box. Then I energy minimised it and did NVT and NPT equilibration
on the box. Both ran successfully but my system potential energy averages to
2.01e+4 after NPT. The temperature I used was 450 K which is well beyond its
melting point and pressure I used was 1 bar. The force field I used was
GROMOS53a6. Similar results were obtained when the above procedure was
applied on beta naphthol. Can someone help me find where exactly have I gone
wrong? Thank you for your help in advance.
Did you refine the PRODRG topologies by recalculating the charges suitably? If
not, you can expect bad results.
http://pubs.acs.org/doi/abs/10.1021/ci100335w
A positive potential indicates net repulsion in the system, so whatever cohesive
interactions your molecules should be feeling are going unsatisfied or being
outweighed by stronger repulsive interactions. Both of these factors suggest an
inadequate topology.
-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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