[gmx-users] FEP w/ monovalent ion
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:
> 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
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?
> David Bostick Office: 262 Venable Hall
> Dept. of Physics and Astronomy Phone: (919)962-0165
> Program in Molecular and Cellular Biophysics
> UNC-Chapel Hill
> CB #3255 Phillips Hall dbostick at physics.unc.edu
> Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
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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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