Hi,
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,
Regards,
George
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