[gmx-users] Positive Potential Energy

George Abadir georgea at ece.ubc.ca
Sat May 5 04:09:18 CEST 2007

     I am running a carbon nanotube in water simulation. I set the 
reaction field dielectric constant (epsilon_rf) to 80 (that of water) 
and the dielectric constant (epsilon_r)  to 1. The energy minimization 
(which ignores the temperature coupling) runs well and I get a negative 
potential energy. However, for the molecular dynamics simulation, I have 
a temperature coupling with reference temperature 300K. The final 
potential energy increases dramatically and it goes positive. Viewing 
the system with pymol, it didn't explode or anything. Is this positive 
potential energy normal; I think for the system to be stable it should 
be negative. What can be the reason of this problem?
   Thank you very much inadvance,

More information about the gromacs.org_gmx-users mailing list