[gmx-developers] Non-periodic interaction in a periodic box
David van der Spoel
spoel at xray.bmc.uu.se
Wed Aug 20 17:31:11 CEST 2014
I wonder whether it is possible to define special interactions, say
between all atom-pairs in a protein, not considering PBC. That is, to
have a box which is slightly larger than the protein but not twice as
large in all dimensions, and define these special interactions without
considering PBC. This then assumes that the molecule is non-periodic
Previously this would have been possible using the graph mechanism, but
with domain decomposition molecules are split into atoms when they move
over the box boundary, right?
An ugly way could be to restrain the protein in the center of the box
and ignoring PBC for the special interactions, but this would not
conserve energy, and be dependent on the location of the protein which
one can not be sure of when computing the interaction.
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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