[gmx-users] energy comparison

[Justin Lemkul]

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 
more stable."

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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