[gmx-users] Solvation Free Energy calculation (g_bar)

[Justin A. Lemkul]

On 6/18/12 10:41 AM, Daniel wrote:
> Hi everyone,
>
> I'm having problems when calculating Free energy through the g_bar tool. I'm
> trying to decouple separately the electrostatic and the Vdw terms. So, after
> performing the mdruns for all Coulombic processes (from 0 to 1, split in 0.1
> steps: 0.0-0.1-0.2...0.9-1.0) and the same for the LJ-terms, I'm applying
> the g_bar for all md*.xvg output files, from both decoupling steps, all
> together. I mean I join the md*.xvg files from the two decouplings and apply
> g_bar only once. As a result I'm getting a warning message informing that
> some results violate the Secong law of Thermodynamics and the error
> estimation is about 8 KJ/mol!
> On the other hand, when I apply the g_bar tool separately for the two
> decouplings I no longer "violate the Second Law" and the errors are more
> feasible (~0.3 KJ/mol), however I don't know how the join the two results in
> order to get the solvation Free energy of the whole process (considering
> that this is possible, I don't know this as well).
>

Since free energy is a state function, you simply take the sums of the two 
processes.

-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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