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.
Sincerely,
Stephan Watkins
Von: virk <virkbl...@yahoo.com>
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] Potential energy calculations
stabilised energy calculation for my simulation......I am thinking something
wrong with units or something with my simulation....
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