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<p style="margin-bottom: 0in">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.</p>
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<p style="margin-bottom: 0in">Sincerely,</p>
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<p style="margin-bottom: 0in">Stephan Watkins</p>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Dienstag, 24. Dezember 2013 um 02:46 Uhr<br/>
<b>Von:</b> virk <virkblitz@yahoo.com><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> Re: [gmx-users] Potential energy calculations</div>
<div name="quoted-content">sorry, I didn't understand it what do you mean by zero it.....But I have<br/>
stabilised energy calculation for my simulation......I am thinking something<br/>
wrong with units or something with my simulation....<br/>
<br/>
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