Yes I know what you mean, however when your looking over a unit cell and trying to define a single molecule in the solvent (even as represented by the entire solvent makup), does it properly alighn the energy based on the averidged "zero" point. I ask, not knowing, but playing with this (single small molecules), I found the systems standard error swamps the potential energy, and you then get a proper shaped graph, where the axis has to be corrected by an energy term (is what I meant by zeroing). I did this with just h2o playing around out of boardom at some point...as I had run across something showing perfect sinusoidal energy graphs of waters/solvent...but the trajectory used contained 5 ions and a single protein....DMSO is a tiny molecule...
Stephan
Gesendet: Donnerstag, 26. Dezember 2013 um 14:04 Uhr
Von: "Justin Lemkul" <[email protected]>
An: [email protected]
Betreff: Re: [gmx-users] Potential energy calculations
Von: "Justin Lemkul" <[email protected]>
An: [email protected]
Betreff: Re: [gmx-users] Potential energy calculations
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
--
==================================================
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
[email protected] | (410) 706-7441
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