[gmx-users] Free energy calculation about ions (hope Justin A. Lemkul can give some suggestions )

[Justin A. Lemkul]

On 5/9/12 10:37 PM, DeChang Li wrote:
> Dear all,
>
>
>       I want to calculate the ion solvation free energy (e.g. an ion
> Na+ solvated in a water box) using Bennett Acceptance Ratio (BAR)
> method, following the tutorial by Justin A. Lemkul. However, if I turn
> off the Coulombic interaction, the total charge of my system would not
> neutral at all. Does this affact my calculation?
>

I would think so.  There have been numerous discussion on this topic over the 
years, so please consult the mailing list archive.  Among the more interesting 
posts you're likely to find:

http://lists.gromacs.org/pipermail/gmx-users/2006-September/023973.html
http://lists.gromacs.org/pipermail/gmx-users/2006-March/020677.html
http://lists.gromacs.org/pipermail/gmx-users/2008-February/032541.html

There is published literature on ion hydration free energies, so do some 
literature searching to see how others handle such situations.  Even a simple 
Google search turns up some useful information.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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