More FEP using separated topologies

From: David Huggins (
Date: Fri May 27 2016 - 15:21:01 CDT

Dear 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".

I have used alchemify to switch off interactions between two ligands
in a protein binding site and the protocol requires me to run dynamics
where both ligands are fully coupled to the system (though not to each

However, the resulting simulations always exit early with a "Low
global exclusion count". I have tried gentle heating and reduced
timesteps but neither works.

Does anyone have any experience of running simulations where two fully
coupled species are overlapping and have no mutual interactions?

Best wishes,



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


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