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...)
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