[gmx-developers] QMMM, exclusions and neighbor search

Pia Toelle pia.toelle at bccms.uni-bremen.de
Wed Jul 15 20:10:13 CEST 2009


(I am using Gromacs 4.0.5 (QM/MM))

I have a question about the exclusion of nonbonded (specially VdW)
interaction in QM/MM simulation. The coulomb and VdW interaction between
two QM Atoms should not be calculated by Gromacs as the QM-QM
interaction is done by the QM-program.
Where (and how) in the code is the VdW (and also coulomb) interaction
between two QM atoms excluded?

Please also comment on the following:

(topio.c called by grompp.c)
"generate_qmexcl" and "generate_qmexcl_moltype", here the exclusions for
the INTRA-molecular interaction are set. Is this right? What is about
the Interaction between different QM-Molecules?

In "search_neighbours" the "nsgrid_core" is called to set up the
neighbor lists (for all atoms QM and MM !?), then it is called to set up
the QM/MM neighbor list.

In "do_forces" the "do_force_lowlevel" is called, there the
QM-calculation and "do_nonbonded" takes place. The later does not
contain any information about the atom being QM or not, as far as I can
see. Therefore, I believe, that the decision to calculate VdW was made
by setting up the lists. Is this right???

Thanks in advance,
Pia Tölle

BCCMS, university of Bremen, Germany

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