FEP with ExtraBonds

From: Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (gareth.b.shannon_at_nasa.gov)
Date: Mon Jun 12 2017 - 15:30:59 CDT

Hi all,

I am performing FEP using the Extrabonds feature to restrain copies of the same atoms to each other to mimic a single-topology approach. This has been commented on in the forum previously (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2008-2009/1787.html).

What I am unsure of is whether the energies of the additional bonds are included in the free energy calculation i.e. do the free energies need to be adjusted to take the effect of these bonds into account?

Many thanks,


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