[gmx-users] Potential Energy

[Justin A. Lemkul]

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.

-Justin

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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