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<div>I got boared at one point and indexed everything, and was looking at total energy, but found if you look at any parameter (LJSR, etc...) for solvent they appear like sinusoidal...but was jsut in my brain equating these to potential energy, and assumed the OP was trying to look at only the DMSO not the system, thus trying to make a stab at it. Couldn't figure out how to deliniate the two, as the error estimates would overlap to the point of making either non-significant, without a perterbation, and you cant direct plot potential for an indexed molecule (summed other energies), but the potential for a whole simple system has a very large standard error and drift, which overlaps the small molecules potential energies, in any case, I let it rest now happy hollidays...</div>
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<div>Sincerely,</div>
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<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Samstag, 28. Dezember 2013 um 00:52 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, 4:52 PM, lloyd riggs wrote:<br/>
> Yes I know what you mean, however when your looking over a unit cell and trying<br/>
> to define a single molecule in the solvent (even as represented by the entire<br/>
> solvent makup), does it properly alighn the energy based on the averidged "zero"<br/>
> point. I ask, not knowing, but playing with this (single small molecules), I<br/>
> found the systems standard error swamps the potential energy, and you then get a<br/>
> proper shaped graph, where the axis has to be corrected by an energy term (is<br/>
> what I meant by zeroing). I did this with just h2o playing around out of<br/>
> boardom at some point...as I had run across something showing perfect sinusoidal<br/>
> energy graphs of waters/solvent...but the trajectory used contained 5 ions and a<br/>
> single protein....DMSO is a tiny molecule...<br/>
<br/>
We're not dealing with a single molecule, at least assuming I understand what<br/>
the OP is discussing. One has a homogeneous box of solvent, such that the<br/>
potential energy of the system can be divided evenly between equivalent<br/>
molecules and averaged over time. The literature often reports the<br/>
"configurational energy" of such a liquid.<br/>
<br/>
I'm not entirely sure what it is that you were playing around with, but such<br/>
decompositions as these are not suited for heterogeneous systems, and what<br/>
you've come up with really just sounds like a way of looking at the<br/>
interconversion of kinetic and potential energy.<br/>
<br/>
-Justin<br/>
<br/>
> Stephan<br/>
> *Gesendet:* Donnerstag, 26. Dezember 2013 um 14:04 Uhr<br/>
> *Von:* "Justin Lemkul" <jalemkul@vt.edu><br/>
> *An:* gmx-users@gromacs.org<br/>
> *Betreff:* Re: [gmx-users] Potential energy calculations<br/>
><br/>
><br/>
> 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/>
><br/>
> --<br/>
> ==================================================<br/>
><br/>
> Justin A. Lemkul, Ph.D.<br/>
> Postdoctoral Fellow<br/>
><br/>
> Department of Pharmaceutical Sciences<br/>
> School of Pharmacy<br/>
> Health Sciences Facility II, Room 601<br/>
> University of Maryland, Baltimore<br/>
> 20 Penn St.<br/>
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><br/>
> jalemkul@outerbanks.umaryland.edu | (410) 706-7441<br/>
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==================================================<br/>
<br/>
Justin A. Lemkul, Ph.D.<br/>
Postdoctoral Fellow<br/>
<br/>
Department of Pharmaceutical Sciences<br/>
School of Pharmacy<br/>
Health Sciences Facility II, Room 601<br/>
University of Maryland, Baltimore<br/>
20 Penn St.<br/>
Baltimore, MD 21201<br/>
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