From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Nov 12 2015 - 08:48:12 CST
You can do that using exclusion lists, which can be generated in a PSF file
using the Alchemify tool.
On 12 November 2015 at 14:46, David Huggins <djh210_at_cam.ac.uk> wrote:
> Hello all,
> I am trying to implement a NAMD version of the separated topologies
> method from "Separated topologies—A method for relative binding free
> energy calculations using orientational restraints" by Gabriel J.
> Rocklin, David L. Mobley, and Ken A. Dill.
> However, this requires coupling the VDW of a ligand (B) to a binding
> site where another ligand (A) is present and fully coupled throughout
> the process. To achieve this, interactions between A and B must be
> switched off, which can be achieved by setting 1 and -1 flags in the
> However, if this is the case then the calculation will couple B whilst
> uncoupling A, which is not what is needed. Is there a way to switch
> off interactions between A and B, whilst coupling (or decoupling) only
> one of them?
> Thanks very much,
> Dr David J. Huggins
> MRC New Investigator
> Theory of Condensed Matter Group
> Cavendish Laboratory
> JJ Thomson Avenue
> Cambridge, CB3 0HE
> United Kingdom
> Phone: +44 (0)1223 764164
> Fax: +44 (0)1223 337356
> Email: djh210_at_cam.ac.uk
> Web: http://www.tcm.phy.cam.ac.uk/~djh210/
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