VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 03 2004 - 10:03:13 CST

Olaf,
  The difficulty involved in implementing coarse-grain visualization
in VMD would depend a lot on what you'd like to do. Do you want to be
able to display trajectories of these simulations? We've done a few
local hacks with scripts to load some coarse-grain models that were
done by another group as "atoms" of a sort. If you have your own file
format, then it'd probably be easy for you to write a plugin for it.
I'd recommend that you look at the XYZ plugin for starters, and once
you've got that working, look at one of the plugins that reads bond
information for guidance on how that's done. (assuming you want some
form of connectivity between the beads...)
Longer term there might be a need to teach VMD to deal with coarse-grain
models better, but until then, you can actually do a surprising amount
with what we already have.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 03, 2004 at 10:51:39AM +0100, Olaf Lenz wrote:
> Hello!
>
> I'd like to use VMD to visualize the results of my simulations.
> Unfortunately, I'm not doing simulations on the atomic scale, but I'm using
> a coarse-grained model (of a lipid bilayer), where each spheric bead
> represents about 2-3 carboxyl groups. Also, I have my own data format. It
> should be no problem, however, to convert this into any arbitrary format.
>
> Before I start trying this, I'd like to ask the experts on this list if they
>
> think it is possible and if I have the right idea of how to do it.
> What I'd try is to
> 1. write a file reader plugin for my data format and
> 2. define new "atom" types for the unified beads.
>
> I think 1. shouldn't be a problem (I know programming in C++ and Tcl/Tk),
> but I wondered if 2. is possible?
>
> Cheers
> Olaf
>
>
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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