Robert Johnson wrote:
Will function type 5 or 6 (for the harmonic bond) affect the
non-bonded exclusion list?
5 does, 6 doesn't. Have a look at table 5.4 and sections 4.3.4 and 5.3.5
in the manual for more info. Actually the manual contradicts my
suggestion of using distance restraints, but they do offer the advantage
of being able to have a flat region of zero potential at the bottom of
the well, so would be ideal for preserving a hydrogen bond over a range
of acceptable lengths, but only perturbing the potential when necessary.
Mark
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