On 4/18/2011 1:43 PM, Sikandar Mashayak wrote:
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?
The sets of atoms for energy groups and such exclusions are defined by
the index groups, not molecules. See manual 7.3 and wherever it talks
about groups in an early chapter.
On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak
<[email protected] <mailto:[email protected]>> 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?
Bonded interactions are unaffected, as you will see if you try it.
Mark
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