From: Jerome Henin (jhenin_at_vitae.cmm.upenn.edu)
Date: Thu Aug 03 2006 - 11:01:54 CDT
Sorry about that, I don't want errors to stay in the list archives forever.
> > Also, are within group
> > interactions scaled as well (ie, say you mutate an alanine to a lysine -
> > does the terminal amine group interact with lysine beta carbon at the
> > scaled level or normal level?)
> No, within-group interactions are preserved. The scaling only affects
> nonbonded interactions between one atom of the initial state and one atom
> of the final state.
What I wrote yesterday is plain wrong. In the NAMD implementation, nonbonded
interactions of perturbed groups are scaled, *including within-group
Note that bonded terms are not modified. Their contribution is expected to
cancel when a delta-delta-G is computed. I am still not convinced this is
perfectly accurate, though.
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