From: Axel Kohlmeyer (
Date: Wed Jun 10 2009 - 08:36:44 CDT

On Tue, 2009-06-09 at 13:08 -0500, Chetan Mahajan wrote:


please let me re-iterate. all your questions are pure VMD
questions and thus of little interest to the vast majority
of LAMMPS users. i'm thus removing the cc to the lammps list.

> So I tried with new 1.8.7 version.
> Firstly, the issue of parser bug is solved, as you said.

thanks. that is good to know.

> Secondly, I searched for topotools package so that I can test it, but no
> where did I find its tutorial or option in the menu. Could you direct me to
> it, please?

i don't know how you are searching for something, but i just
typed "topotools" into google and the third hit was the topotools
plugin documentation on the VMD homepage.

topotools is a pure script extension without a gui
(so is lmp2vmd), so it cannot show up in the extensions
menu. BTWL i had just recently before your question posted
an announcement about this package and the VMD beta
to the LAMMPS mailing list.

> Thirdly, now lmp2vmd script works, but I have little issues there:
> 1. I don't see any visible changes happening after I implement residue tool,
> in option b.

i am sorry, but you have to describe in detail what you did
and then i can comment on what went wrong or what is supposed
to happen. this statement tells me nothing an i don't want to
guess what you were doing.

as i stated before, my advice is to use the topotools package,
particularly using topo readlammpsdata should allow you to
read the lammps data file directly _including_ bonds in one go.

> 2. I can use coloring by atom name so that it gives different colors to
> different atoms. This is desirable for polymer molecule, but not for polymer
> and solvent molecules together if they have same atoms. So in addition, I
> want to assign different colors to different molecules, even though they
> carry same atoms, how to do that? that means I want to use atom name
> coloring selectively for polymer chain, but for different solvent molecules
> like water and methanol, I want to use different colors, even though same
> atoms are also there in polymer chain. IN my data file, I have different
> atom types for "such same" atoms, but belonging to different molecules, but
> I don't see that vmd is taking that information in, even though in lmptoname
> tool I use "H1 H2 H3 etc". I guess it assigns same color to same atom
> belonging to different molecules.

please don't guess, but read the VMD documentation. VMD is by design a
very simple minded program, it displays what you feed it in a simple
way. it cannot read your mind and figure out what you intend to show.
as for coloring by name, you have to keep in mind that VMD disregards
the number part of the atom name, as per convention for biomolecules.
however, you can use the color script command to adjust your colormap
or the color dialog in the VMD GUI.

> So with my limited knowledge, this can be solved by, (a)either assigning
> different colors to different atom "types as defined in my data file" (b)
> different colors to different molecules, in addition to atom color
> differentiation in polymer chain.
> How to do that??

write additional scripts. this is exactly _why_ VMD has an
embedded script interpreter. nobody can foresee all the potential
uses of VMD, and thus it is much simpler to augment the existing
features with a little scripting rather than trying to implement
it all into the GUI (well, even GUIs can be scripted).


> Thanks very much
> Regards
> Chetan

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.