[gmx-users] Thermodynamic Integration

David spoel at xray.bmc.uu.se
Wed Jun 25 19:09:01 CEST 2003

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
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> David Bostick					Office: 262 Venable Hall
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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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