Re: acceptor

From: Giacomo Fiorin (
Date: Wed Jan 17 2018 - 10:20:34 CST

Do you mean the following donor and acceptor PSF fields? Those correspond
to very old terms of the CHARMM potential that are not used any more,
because the combination of partial charges and Lennard-Jones coefficients
allows to reproduce hydrogen bonds already. Without reading corresponding
terms in the parameter file, I believe that explicit donor-acceptor pairs
will be ignored. But you should definitely verify that by checking the
energy at the first timestep.

       0 !NDON: donors

       0 !NACC: acceptors

On Wed, Jan 17, 2018 at 1:02 AM, Suresh Ghimire <suresh.ghimire2049sg_at_gmail.
com> wrote:

> Dear namd user,
> I have prepared psf file for nanotube and water system. In my psf file
> there is zero accepter but there are non zero acceptors on psf file of the
> tutorial. Is it necessary to have non zero acceptors?
> --
> Regards
> Suresh Ghimire
> M Sc (Physics)
> Tribhuvan University, Patan Multiple Campus
> Lalitpur, Nepal

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:19:36 CST