Any rationale behind the thermostat coupling of a ligand with the protein
instead of the ligand with the solvent (as shown in Justin's T4 Lysozyme
binding example)? Especially with small drug-type molecules as generally the
ligand might/would take the usual place of solvent within a binding region
or other solvent accessible surface and it might be more realistic to
simulate the ligand as part of the solvent's ensemble (one might run two
simulations in order to compare the ligand-protein interaction to the
water-protein interaction at the interaction interface...)
Might depend how enclosed the binding pocket is, and whether things are
moving. The rate of inter-group heat flow (roughly) depends on the
surface area, and it's rational to group the ligand with the group that
has the larger relevant surface area in contact with the ligand.
Mark
--
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