[gmx-users] Some questions about free energy calculation

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 11 09:16:21 CET 2002

On Thu, 10 Jan 2002, David L. Bostick wrote:

>I have never done anything like that before, but if I were to try, I would
>first equilibrate a box of water, then place the ion wherever I saw fit
>into the resulting configuration.  I would then add the ion into the
>topology.  If the only parameters which involve interaction of Zinc with
>its environment are for LJ interaction and charge, then use slow growth to
>change the charge from 0 to +2 and the LJ constants from 0 to their desired
>values by specifying them as topologies A and B.  If the Zinc is in the box
>but doesn't interact with solvent until lambda is increased by its first
>step, DELTA(lambda), there is no need to do anything with dummy atoms... at
>least in principle, I guess.
Yes you will have to modify the Zn2+ into a dummy. Topology is not that 
difficult, check the manual.
You will also have to use soft-core interactions to prevent singularities 
in the potential. Finally you will have to compute an analytical cut-off 
correction (Born correction). As far as I know there is no ready tool to 
do this (please create one!). In this you have to correct for the ion 
itself and for the ordering of the water due to the ion. Non trivial 
stuff, check out older Straatsma and Berendsen stuff (J Chem Phys, IIRC).

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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