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
--
========================================
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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