[gmx-users] Positive Potential Energy after equilibration

Satish Kamath satishs.kamath at gmail.com
Mon Jun 11 12:42:05 CEST 2012

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. 

Satish Kamath 
IISc Bangalore 

View this message in context: http://gromacs.5086.n6.nabble.com/Positive-Potential-Energy-after-equilibration-tp4998327.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list