Hello Amber community,
I was wondering if cpptraj has a functionality for calculating
intermolecular contacts across periodic boundaries. I am doing simple
single-protein-in-a-water-box simulation and am curious if any of the
protein residues are influenced by residues *from the periodic images *(to
make sure the water box is large enough)*. *Such analysis is trivial enough
to do outside of AMBER for a rectangular box, but I am using a truncated
octahedron, and so was wondering if this functionality already existed?
Thank you,
Eugene Yedvabny
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Received on Wed May 21 2014 - 12:30:02 PDT
