[gmx-users] Thermodynamic Integration

[David L. Bostick]

Thank you David for responding,

On a less serious note, how should one choose the soft-core parameter
sc_alpha or are the calculations even all that sensitive to this
parameter?

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 25 Jun 2003, David wrote:

> On Wed, 2003-06-25 at 17:45, David L. Bostick wrote:
> > Hello all,
> >
> > I wish to calculate the free-energy of growing an ion in solvent, but I
> > have a question on how gmx deals with the ewald sum if I were to grow a
> > monovalent ion from an uncharged atom.  In other words, how do people
> > usually deal with a single charge in their system when using PME in gmx? Do
> > people usually rely on the inherent background charge from the ewald sum,
> > or is there a charge correction in gmx? If some correction is used, how
> > does it work and where can I find information on it?
>
> Actually I think this is an unsolved problem. I recall Berk saying that
> it could be implemented, but I don't know whether it has been. It would
> require two PME calculations for each time step I think...
>
> >
> > 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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> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
> 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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