Question on making 'reversible' solvated simulation

From: Randy J. Zauhar (
Date: Sat Feb 10 2018 - 12:15:37 CST


I am running a ligand annihilation in a solvated system, and I would like to make it truly reversible if possible.

Issue is that a couple water molecules sneak into the active site when the ligand disappears. Then when I reverse and start creating the ligand, they are trapped.

A simple thing I will try is to constraint the water molecules close to the active site, hopefully creating a barrier to entrance.

However. this has to be a pretty common problem, is there a recommended approach to address it?


Randy J. Zauhar, PhD

Prof. of Biochemistry

Dept. of Chemistry & Biochemistry
University of the Sciences in Philadelphia
600 S. 43rd Street
Philadelphia, PA 19104

Phone: (215)596-8691
FAX: (215)596-8543

“Yeah the night is gonna fall, and the vultures will surround you /
And when you’re lookin’ in the mirror what you see is gon’ astound you"

  — Death Cab for Cutie, “Monday Morning"

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