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<div>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...</div>
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<div>Stephan</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Donnerstag, 26. Dezember 2013 um 14:04 Uhr<br/>
<b>Von:</b> "Justin Lemkul" <jalemkul@vt.edu><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> Re: [gmx-users] Potential energy calculations</div>
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On 12/26/13, 5:30 AM, lloyd riggs wrote:<br/>
> Zero it--> If you plot a potential energy value strait from the simulation it<br/>
> will be something like point a) -7000 point b) -7050 across a single<br/>
> simulation. Thus you have to find a beginning point and subtract it across the<br/>
> run. Additionally, fluctuations may dictate 10 or so runs to determine a good<br/>
> mean, as the drifet or error might be 20 kcal/mol in a system. As I read your<br/>
> other post, I would assume the experiment would be non random placement of DMSO<br/>
> in water (say a wall system), otherwise you would be looking at a single<br/>
> molecules energy dictated by conformational space over time...ie something like<br/>
> Justin's post...which you still may have to calculate a mean for, but I assume<br/>
> this is done through the -nmol option. You still also may have to "zero it",<br/>
> but I am not sure, direct use of g_energy gives abitrary starting points as<br/>
> above from my experience.<br/>
><br/>
<br/>
The values printed by g_energy are not arbitrary. They are the energy of a mole<br/>
of equivalent systems of a given configuration, hence their large magnitude.<br/>
<br/>
-Justin<br/>
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Justin A. Lemkul, Ph.D.<br/>
Postdoctoral Fellow<br/>
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Health Sciences Facility II, Room 601<br/>
University of Maryland, Baltimore<br/>
20 Penn St.<br/>
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jalemkul@outerbanks.umaryland.edu | (410) 706-7441<br/>
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