[gmx-users] rationale behind tcoupling ligand with protein instead of with SOL

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 11 08:24:49 CEST 2011

> 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.


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