[gmx-users] Potential energy calculations

Justin Lemkul jalemkul at vt.edu
Thu Dec 26 14:06:30 CET 2013

On 12/26/13, 5:30 AM, lloyd riggs wrote:
> Zero it--> If you plot a potential energy value strait from the simulation it
> will be something like point a) -7000 point b) -7050 across a single
> simulation.  Thus you have to find a beginning point and subtract it across the
> run.  Additionally, fluctuations may dictate 10 or so runs to determine a good
> mean, as the drifet or error might be 20 kcal/mol in a system.  As I read your
> other post, I would assume the experiment would be non random placement of DMSO
> in water (say a wall system), otherwise you would be looking at a single
> molecules energy dictated by conformational space over time...ie something like
> Justin's post...which you still may have to calculate a mean for, but I assume
> this is done through the -nmol option.  You still also may have to "zero it",
> but I am not sure, direct use of g_energy gives abitrary starting points as
> above from my experience.

The values printed by g_energy are not arbitrary.  They are the energy of a mole 
of equivalent systems of a given configuration, hence their large magnitude.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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