[gmx-users] Potential Energy

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 26 23:02:24 CET 2010

Yanmei Song wrote:
> Dear Users:
> I am in the process of setting up a new system.  I have a 8.0*8.0*8.0 
> nm3 system which include 27800 molecules. When the system approach 
> equilibrium, I found the potential energy is +3e5 (big positive number). 
> Is this normal? Since based on my experience, for systems in such size, 
> the potential energy is usually a big negative number? Does this mean 
> that my force field parameter or molecule structure have problems? 
> Thanks in advance!

A positive potential indicates repulsive interaction(s) is (are) present in your 
system, i.e. you have clashes or have faulty parameters.  Energy minimization 
should converge to a nice, negative number.


> -- 
> Yanmei Song
> Ph.D. Candidate
> Department of Chemical Engineering
> Arizona State University


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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