VMD-L Mailing List

From: Sumit Kumar (sumit.iocl.chennai_at_gmail.com)
Date: Mon Aug 05 2013 - 19:00:03 CDT

Hello Experts,

I have my own coarse-grained code and I want to visualize polymer chains
(coarse-grained FENE model) using VMD. I actually want to create movies
using VMD. Currently, my code generates LAMMPS trajectory files which I use
for creating videos using videomach software. The bonds are connected
randomly and I have to remove all of them. Now what my video is left with
is the beads moving all around - I am using LEES-Edward BC in my code. The
beads representations don't seem good so I thought line representation will
look better than beads representation. Can I create animations using PBD
file alone. What else is required if I want to create animation using PDB
file? In PDB, there is a command 'CONECT' in which you can specify the
beads to be connected by bond but can I create animations using this PDB
file, how do I introduce frame?

If you have any better suggestions, and if any particular file format is
recommended, would you mind attaching those simple file formats so that I
could modify my code accordingly?

Thanks and Kind Regards
Sumit Latiyan