[gmx-users] FEP w/ monovalent ion (addendum)

[David L. Bostick]

Hi Berk,

Pertaining to the PME inner loops for free energy ... Out of curiosity, why
was this feature removed from the code? Will it be re-integrated later?

Thanks,
David



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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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On Fri, 10 Jun 2005, David L. Bostick wrote:

>
> Also, this business of doing FEP with an ion is new to me.  If anyone can
> offer warnings/caveats for these types of (charged) simulations, or has
> done this in the past, I would appreciate any kind of advice.
>
> Thanks,
> David
>
>
>
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> 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
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>
> On Fri, 10 Jun 2005, 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?
> >
> > 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.
> >
> > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> > 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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