From: Axel Kohlmeyer (
Date: Thu Sep 14 2006 - 16:39:36 CDT

On 9/14/06, Robert Hoy <> wrote:
> Hi. I just started using VMD today, so apologies if I'm too green. I

there is a _ton_ of tutorial material on the VMD homepage and
other pages it refers to. you should take the time and go through
some of it. it will automatically answer a lot of beginner's questions
before they even come up.

> 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

.xyz is about the worst file format to try.
since it provides no additional information.

> 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).

no surprise.

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

since your system is somewhat unusual, yet you should have the best
knowledge about it, writing a small program, that creates a .psf file, is
probably the best option. the .psf file can be very minimalistic an only
contain the information you want to feed into VMD.

> 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?

if you create a psf file, you can assign residue names, charges etc.
then you can use the various colorization schemes integrated in VMD.

have a look at the manual for details.


> Thanks,
> Robert Hoy

Axel Kohlmeyer
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.