[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

More information about the gromacs.org_gmx-developers mailing list