Hi peter<br>I think the important is to don't couple small number of atoms(ligand molecules or a few ions) separately to a reference tempreture!<br>It probably will result the same if you make two tcouple groups as below:<br>
Protein-LIG water-ions<br>or<br>Protein water-ions-LIG<br><br>I think they will be equvalent( with a good approximation)!<br><br><div class="gmail_quote">On Mon, Apr 11, 2011 at 10:32 AM, Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu">pcl@uab.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Any rationale behind the thermostat coupling of a ligand with the protein<br>
instead of the ligand with the solvent (as shown in Justin's T4 Lysozyme<br>
binding example)? Especially with small drug-type molecules as generally the<br>
ligand might/would take the usual place of solvent within a binding region<br>
or other solvent accessible surface and it might be more realistic to<br>
simulate the ligand as part of the solvent's ensemble (one might run two<br>
simulations in order to compare the ligand-protein interaction to the<br>
water-protein interaction at the interaction interface...)<br>
<br>
--<br>
===============================================================<br>
Peter C. Lai | University of Alabama-Birmingham<br>
Programmer/Analyst | BEC 257<br>
Genetics, Div. of Research | 1150 10th Avenue South<br>
<a href="mailto:pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>
(205) 690-0808 |<br>
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