[gmx-users] Re: Poteintial energy of my system
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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