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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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