VMD-L Mailing List

From: Akash Banerjee (akashneon_at_gmail.com)
Date: Fri Jan 08 2021 - 07:30:11 CST

Thank you so much for your response. I will do that then.

Kind regards,
Akash

On Thu, Jan 7, 2021, 6:49 PM Gumbart, JC <gumbart_at_physics.gatech.edu> wrote:

> 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
>
>