From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri May 27 2016 - 23:00:20 CDT
I was reminded today that explicitly excluded atoms are expected to lie
within the cutoff distance. Those exclusions are not required (anymore) in
standard FEP runs because those atoms belong to separate partitions. That
might be the way to go for your needs.
On 27 May 2016 at 22:21, David Huggins <djh210_at_cam.ac.uk> wrote:
> 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
> Email: djh210_at_cam.ac.uk
> Web: http://www.tcm.phy.cam.ac.uk/~djh210/
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