VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Thu Aug 26 2021 - 10:18:17 CDT

Hi all,

I'm in the process of optimising the dihedral terms for a particularly
crowded molecule. The dihedrals in question are between two aryl groups
connected by a tertiary amide through -N- and I've trimmed excess
functional groups off to use the bare minimum model compound as a stand-in
for the full molecule.

Unfortunately, when analysing the scan outputs there are both major and
minor 'jumps' or discontinuities caused by sudden rotation of one of the
aryl groups into a more favourable conformation. I'm assuming the larger
jumps make the PES unsuitable for use, though perhaps those under ~+/- 1.5
kcal/mol are okay? Any ideas on how to resolve this? I was thinking of
constraining the aryl dihedral which causes the jumps to an intermediate
value, but will the resulting PES be valid for dihedral optimisation?

Any other suggestions are welcome.

Kind regards,

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326