FEP using separated topologies

From: David Huggins (djh210_at_cam.ac.uk)
Date: Thu Nov 12 2015 - 07:46:54 CST

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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