[gmx-users] FEP w/ monovalent ion

David spoel at xray.bmc.uu.se
Sat Jun 11 09:43:58 CEST 2005

On Fri, 2005-06-10 at 20:15 -0400, David L. Bostick wrote:
> Hello,
> I wish to charge/discharge a monovalent ion in order to do a FEP study. I
> know that in the current CVS code, the ewald contribution to the free
> energy is now computed. However, are corrections to the net charge now
> implemented to remove the effect of the "neutralizing plasma" inherent to
> ewald, as I vary the rxn coordinate, lambda, from 0->1 in tinfoil boundary
> conditions?
I don't know about FEP, but the charge correction to the energy is very
small. You can try to run the src/contrib/pmetest program to see the
components of the energy.

> If it has been implemented, is there a publication that has been followed?
> I am aware of the work of, for example, Gerhard Hummer,
> and of Tom Darden.  There is also a paper by Stephen Bogusz, Thomas
> Cheatem, and Bernie Brooks (J. Phys. Chem. (1998) 108(17) p. 7070, that
> describes a charge correction method.  Is something like this employed?
> Thanks,
> David.
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> David Bostick					Office: 262 Venable Hall
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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