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

[mohsen ramezanpour]

Hi peter
I think the important is to don't couple small number of atoms(ligand
molecules or a few ions) separately to a reference tempreture!
It probably will result the same if you make two tcouple groups as below:
Protein-LIG   water-ions
or
Protein    water-ions-LIG

I think they will be equvalent( with a good approximation)!

On Mon, Apr 11, 2011 at 10:32 AM, Peter C. Lai <pcl at uab.edu> wrote:

> 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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