Also, what about non-bonded interactions within the protein? Does exclusion group only exclude the non-bonded interactions between two different molecules and non-bonded interactions within the single molecule atoms are still computed?
On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak <symasha...@gmail.com>wrote: > Hi > > When we define energy group exclusions e.g. like in manual energygrp excl > = Protein Protein SOL SOL > and do md rerun, then only non-bonded interactions between Protein and SOL > are computed. I am wondering what happens to bonded interactions within the > protein, do they contribute to energies even though we have excluded > protein-protein interactions? > > thanks > sikandar >
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