[gmx-users] Re: Poteintial energy of my system

Justin Lemkul jalemkul at vt.edu
Wed Dec 12 13:41:55 CET 2012

On 12/12/12 5:16 AM, Shima Arasteh wrote:
> What are the possible solutions to solve the problem?
> My system is composed of protein, POPC, ions, and water. I follow the approached suggested in kalp15-DPPC tutorial.
> And I got such an incorrect potential for the first grompp.
> Would you please guide me?
> I would appreciate ur suggestions.

The outcome is rather puzzling.  Fmax indicates the system should be happy, but 
the potential is clearly not.  A positive potential indicates net repulsion 
and/or unsatisfied interactions, which should not happen for a condensed phase 
system.  In vacuo, positive potentials are more common (depending, of course, on 
what the system is).  Check for voids in the unit cell.  That's about the only 
thing I can think of.



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


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