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

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed Dec 12 13:46:36 CET 2012

How about it that I get a positive potential energy for a system of only protein and POPC? Makes sense?

Thanks for your explanation.


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, December 12, 2012 4:11 PM
Subject: Re: [gmx-users] Re: Poteintial energy of my system

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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