VMD-L Mailing List

From: jiwu liu (liujiwu_at_msu.edu)
Date: Wed Oct 19 2005 - 18:04:31 CDT

Dear list:
   
    I ran a MD simulation of bead-string model with LAMMPS, and want to
visualize the structure with VMD. After reading previous mail from the list,
I added "dump_modify ID header xyz" into LAMMPS input script to ask it dump
a xyz file for visualization. Certainly, no bond is shown by VMD when I
loaded the xyz file, which, as I knew from that instructive mail, is because
xyz file doesn't have bonding information.
    So I think probably I can make a fake PDB file to tell the VMD about
bonding information and use the xyz file as trajectory data. I constructed
PDB file like below:

CONECT 1 2
CONECT 2 3
....
ATOM 1 B BEA 1 0.000 0.000 0.000 1.00 1.00 BE20
ATOM 2 B BEA 2 0.000 0.000 2.000 1.00 1.00 BE20
ATOM 3 B BEA 3 0.000 0.000 4.000 1.00 1.00 BE20
ATOM 4 B BEA 4 0.000 0.000 6.000 1.00 1.00 BE20
.......
END
 
    Again, VMD doesn't seem to understand this PDB file and draw a structure
without bond. I wonder what's wrong with this PDB file. Why can't it be
recagonized by VMD?

    Thanks!

-jiwu