[gmx-users] energy comparison
jalemkul at vt.edu
Tue Oct 2 20:26:01 CEST 2012
On 10/2/12 12:49 PM, Edward Deira wrote:
> Dear all,
>>From the computational side of the question, can one compare the final
> energy values at the end of a simulation ? Are those energy values are
> meaningful ?
> Can I, with proper chemical judgement, say that a lower (more negative)
> value will correspond to a more "stable" system ?
I will make several assumptions about what you're dealing with to try to answer
this question. If I'm off-base, then please be (much) more specific about what
you're doing. For a "normal" case of some solute in water, the potential energy
is dominated by the water itself. The value of energy from a single snapshot
really doesn't mean much, and the only comparison you might be able to make
would be between identical systems, i.e. replicate simulations of the same
starting configuration. If the systems differ at all in their contents, you're
comparing apples and oranges since the potential energy is an extensive property.
There are considerably more robust approaches to real free energy analysis
coupled with conformational sampling that one can do. I would not be inclined
to believe a stability argument based on a statement like "the potential energy
of snapshot A was lower than that of snapshot B, so therefore configuration A is
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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