[gmx-developers] Exclude specific nonbonded interactions during md rerun for Verlet

Bernd Doser bernd.doser at h-its.org
Fri Sep 12 15:56:32 CEST 2014

Dear GROMACS developers,

As the energy group exclusions are not implemented for the Verlet cutoff
scheme, I am search for a alternative possibility to exclude specific
nonbonded interactions during an md rerun.

One idea is to use the topology exclusion list. The top->excl arrays
could be modified for example at the beginning of do_force() in
sim_util.c. I have tested it for a small protein and a water dimer and
it works. Is there any problem doing this for more complex structures or
have anyone a better idea to exclude nonbonded interactions to reduce
computation time?

Thank you very much in advance!

Best regards,
Bernd Doser

Dr. Bernd Doser
Software Developer

Schloss-Wolfsbrunnenweg 35
69118 Heidelberg

Phone: +49 6221 533 249
Fax: +49 6221 533 298
E-Mail: bernd.doser at h-its.org
Online: www.h-its.org

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