xianghong qi wrote:
Thanks, Mark. That means I can set energygrp_excl = Protein Protein,
then I can get rid of those parameter which are related to
electrostatics, Vdw( like rcoulomb, vdw-type, rvdw, rvdw-switch, etc).
Am I right?
No. Section 7.3.19 indicates how this should be done. I think you want
energygrp_excl = Methane1 Methane2
so you will need to use make_ndx suitably to create these groups.
If "Protein" includes only your pair of methanes, then
energygrp_excl = Protein Protein
will have the same effect, only because there are no intramolecular
nonbonded interactions in methane. It's thus not a generalizable solution...
Mark
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