[gmx-users] Positive Potential Energy after equilibration

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 11 12:45:15 CEST 2012

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.


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


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