[gmx-users] energy group exclusions

Sikandar Mashayak symashayak at gmail.com
Mon Apr 18 05:38:29 CEST 2011


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?

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