AMBER Archive (2008)

Subject: Re: AMBER: Steered MD and Jarzynski in pulling simulations

From: Gustavo Seabra (
Date: Sun Nov 09 2008 - 20:36:38 CST

On Wed, Nov 5, 2008 at 9:48 AM, Samuel Genheden wrote:
> I have to apply two restraints, one to the drug and one to the
> protein. The restraint of the drug should be time-dependent and it is
> pretty clear how to set this up by reading the Amber manual. However I
> also need to have a fixed restraint on the protein center-of-mass in
> order to prevent it from "going with" the ligand.

Are you sure this is really necessary? Why not just setting the
reaction coordinate to some distance between the protein and the

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