[gmx-users] Potential energy calculations

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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