[gmx-users] Charge transfer

David van der Spoel spoel at xray.bmc.uu.se
Fri Jul 11 11:38:33 CEST 2008

Alessandro.Maiorana at roma2.infn.it wrote:
> Hi,
> Can I modify Gromacs' kernel? I want to introduce a little program, that
> it calculate atoms' charges in operation of the interatomic distance. I
> want to modify the Potential energy function. The scope is to calculate
> the charge transferred by N(Hys) and/or Glu(O-) to Zn(2+). The charges on
> Zn and the N or  O atom coordinated to Zn are not fixed but change during
> the simulation, depending on the interatomic distance between Zn and the
> O/N  atom at time step t.  I assume a linear dependence of the amount of
> charge transfer on the distance (N/O - Zn). What does it ought to modify?
> Can you help me? I hope to have been clear. Thanks for the help you going
> to gave me.

Do you want to do this every step before computing the forces? In that 
case you could try to write a small routine in src/mdlib/sim_util.c that 
is called from do_force. However be aware that you are not certain to 
have the coordinates in a parallel run on all processors (and you only 
want to do it once).

An alternative would be to define the Zn-O interaction as a bonded 
interaction with a new functional form.

This is more a developers question by the way.

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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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