VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Thu Jan 07 2021 - 17:49:26 CST

I would choose #3.

Best,
JC

> On Jan 7, 2021, at 5:06 PM, Akash Banerjee <akashneon_at_gmail.com> wrote:
>
> 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 simulations)
> 3. A fragment of the polymer that contains the 4 dihedral atoms and its immediate neighbors.
> 4. Something else?
>
> Thank you.
>
> Kind regards,
> Akash
>
> --
> akash