Subject: CHARMM dummy atoms

From: Rick Venable <rvenable$at$pollux.cber.nih.gov>
Date: Thu, 1 Apr 2004 23:37:25 -0500

An aside: those with CHARMM related questions may wish to try the web
based bulletin board system at www.charmm.org   A number of developers
and advanced users participate regularly.

On Thu, 1 Apr 2004 martin$at$yangtze.hku.hk wrote:
> I would like to consult about how to add two or more dummy atoms in
> Charmm?

Dummy atoms are used for a variety of purpose, and can be assigned
arbitrary properties by editing RTF and PARAM files if needed.  It
really depends on how you want to use these dummy atoms.  There is an
existing DUM atom type in several of the distributed RTF/PARAM file
pairs.

> Actually, I am calculating a system with 2 segments. I would like
> to introduce constant velocity to 1 segment (all the atoms in segment
> move in one direction with same spped).
>
> How can I do so?

Modify the velocities in a dynamics restart file; they are listed for
each atom in PSF order, which is the same ordering as that in the
corresponding CHARMM .crd file.

=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   Rick_Venable$at$nih.gov
ALT email:  rvenable$at$speakeasy.org
-------------------------------------
"Don't blame me, I voted for Kang."
                         Homer
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=