[gmx-users] energy comparison

[Justin Lemkul]

On 10/2/12 2:45 PM, Edward Deira wrote:
> not that off-base, actually. one of my aims is to compare two different
> proteins with the same ligand and try to figure out which system is
> energetically more favourable without having to go through qm/mm. so i
> suppose the proper way would be estimating the "absolute" free energy of
> the system.
>
> can i do that with gromacs ? i know that computing deltaG is ***trivial***
> (not the best word,i know), but what about "absolute" values?

I have never attempted to calculate the absolute free energy of a given 
configuration, but again I suspect that you will fall victim to the same 
problems I have already described.  Energy differences in these systems will be 
dominated by the solvent, which comprises somewhere between 75%-90% of the atoms 
in any system (unless it's implicit, of course).  Small differences like 
different ligands (which may also induce protein conformational changes and thus 
differences in solute-solvent interactions, i.e. entropic changes in the 
solvent) will make your headaches worse.

I suspect there's no "trivial" way to do this, as all of the quick-and-dirty 
approaches probably create more questions than they answer.

Perhaps someone else who has actually attempted this can comment.  I'm sure I've 
seen similar inquiries posted to the list before, so there may be something 
useful in the archive, as well.

-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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