From: Radak, Brian K (bradak_at_anl.gov)
Date: Mon Jun 12 2017 - 16:13:31 CDT
No. If the bonds are only between corresponding atoms in the different alchemical regions then the relative free energy is unaffected.
This is a fairly straightforward stat mech exercise, but you can also read the original paper by Axelsen and Li (although they do not appear to restrain hydrogens, which I do recommend):
Axelsen and Li, J Comput Chem 1998, 19, 1278-1283.
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From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] <gareth.b.shannon_at_nasa.gov>
Sent: Monday, June 12, 2017 3:30:59 PM
Subject: namd-l: FEP with ExtraBonds
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?
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