VMD-L Mailing List

From: Robert Hoy (robhoy_at_pha.jhu.edu)
Date: Thu Sep 14 2006 - 16:10:52 CDT

Hi. I just started using VMD today, so apologies if I'm too green. I
am trying to use VMD to display configuration files from the LAMMPS
molecular dynamics package. I can easily convert the config files to
.xyz files, and view the atoms as points, so that's fine. The problem
comes in with displaying the bonds. I am displaying bulk linear
polymers, so each bead should have 2 bonds (or 1 if it's a chain end).
The .xyz file does not contain bond information, so it tries to infer
the bonds from a distance search. It gets the bonds all wrong - I get
error messages like

Info) Determining bond structure from distance search ...
ERROR) vmdgridsearch1: exceeded pairlist sanity check, aborted
ERROR) MolAtom 171297: Exceeded maximum number of bonds (8).
ERROR) MolAtom 171298: Exceeded maximum number of bonds (8).

So, I need a way to give VMD the bond topology. How can I do this most
simply?

Another thing I need to do is give different chains different colors.
I know Raster3D takes a RGB triplet for each plotted point. Is there
any way do input color information similarly in VMD?

Thanks,
Robert Hoy