From: Akash Banerjee (
Date: Thu Jan 07 2021 - 16:06:23 CST

Dear FFTK/VMD developers,

I am trying to optimize dihedrals of a polymer chain that has backbone and
side chain residues. I want to know what is the rule of thumb for
choosing an initial geometry for dihedral parameterization in FFTK :

1. Do I consider the entire polymer ? (making the QM simulations very
expensive and time consuming)
2. Just the 4 atoms that are a part of the dihedral? (very cheap QM
3. A fragment of the polymer that contains the 4 dihedral atoms and its
immediate neighbors.
4. Something else?

Thank you.

Kind regards,