[AMBER] Restraint-like bonds using ParmEd setBond?

From: Brian Radak <brian.radak.gmail.com>
Date: Mon, 1 Nov 2021 14:32:29 -0400

My understanding is that adding new bonds with ParmEd is akin to adding new
force field terms such that nonbonded exclusions are updated in the
topology. The only difference is that a bond does not necessitate angles
and dihedrals as in tleap (or a defined bond type). This seems to be
verified by "just doing it" and checking that the energy difference is not
in the BOND term only.

My question is - is there a way _not _ to update the exclusions so that the
new term is exactly like a harmonic restraint? This would trick the
bookkeeping in alchemical calculations, which apply a lambda factor to
nmropt terms.

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Received on Mon Nov 01 2021 - 12:00:02 PDT
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