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?
Nonbonded interactions are excluded between each defined pair. Therefore, with
energygrp_excl = Protein Protein SOL SOL
you are excluding all nonbonded interactions between protein atoms (Protein
Protein pair) and between solvent atoms (SOL SOL pair). Protein-solvent
interactions are calculated. The use of energygrp_excl (as documented)
indicates that only nonbonded interactions are affected. That is, bonded
energies should still be calculated for all groups.
-Justin
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?
thanks
sikandar
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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