[gmx-developers] Question about MM point charges in QM/MM calculation

Pia Toelle pia.toelle at bccms.uni-bremen.de
Fri Jan 30 18:09:03 CET 2009


I have got some questions concerning the MM-atom-list in a QM/MM

We do QM-MM calculations using the Gaussian interface (gromacs-3.3.3),
but modified the code to be able to use DFTB instead of Gaussian
Our (MM-)system is a SiO2-surface (with periodic boundary condition; full).
We use PME and DO NOT (!) define proper charge groups for the surface
structure, every atom forms its own charge group. Number of MM atoms ~1900.
(The proper definition of charge groups in our system is not obvious or
even impossible, as it is a solid and a periodic system)

We noticed, that the MM system considered in the QM calculation does not
consist of the entire MM system. The point charges
(mm->xMM[i][..],mm->MMcharges[i]) that are written to input.com (by
qm_gaussian.c) are only those of the MM atoms in the vicinity of the QM
atoms. The list of MM atoms in the vicinity of the QM-zone is set (as
far as we can see) using the neighbor-search algorithm depending also on
the charge groups (in ns5_core.c). Please correct me if I am wrong at
some point.
Is it right, that the cut-off for the QM/MM - neighbor search is set by
'rcoulomb' in the mdp-file? Or 'rlist'?

Anyhow, we would like to print out all (!) MM atoms (and their charges).
How to solve this problem?
Is there a simple way to put all MM atoms in the mm list? And please
tell me if a change of the (t_MMrec)-variable mm could cause problems
for the MM-part of the routine or is  the (t_MMrec)-variable mm only
used in the QM part.
Or would it be possible to print out all MM atoms + charges at an other
point in the program? Where?
I am grateful for any helpful information or idea.

Thanks in advance.

Pia Toelle

Uni Bremen
Am Fallturm 1
28359 Bremen

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