VMD-L Mailing List

From: Nazanin Samadi (nsamadi_at_gmail.com)
Date: Thu Aug 14 2008 - 15:24:45 CDT

Hi there,
I hope I have understood your question properly, this is what I think:

in order ro see both the atoms and the bonds between atoms in VMD , two
different file formats are needed, 1:dcd format which exists in lammps code
 2: psf file format which needs to be created on your own.

fortunately you use Lammps and it has this ability to create a dcd file for
your dump file, about the psf file I should say that it shows the atoms
characteristics (excluding their coordinations) and also the bonds between
atoms.

therefore, by loading the files like example.psf and example.dcd together ,
you will be able to see the things you wanted to...
but one thing should be mentioned that after loading the files , you need to
use "Graphics" -> "Representations" -> "coloring methods: segname" ->
"drawing methods: points" to see all different atoms and bonds between
them.

I hope this was helpful enough for you.

Nazanin