[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:
> 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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