[gmx-users] Thermodynamic Integration

[David]

On Wed, 2003-06-25 at 19:22, David L. Bostick wrote:
> 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?

Hm, isn't that in the manual? sc = 1.5 maybe? Otherwise you may want to
look at the original papers... (and also a recent Villa &  Mark, JCC
2001 IIRC).
> 
> 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 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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-- 
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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