VMD-L Mailing List

From: Nguyen Hoang Phuong (phuong_at_theochem.uni-frankfurt.de)
Date: Wed Mar 03 2004 - 06:21:57 CST

> 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

That is possible. You just define the new atom types, e.g each bead has
name CA and also give him a residue name, e.g ALA, then write its
coordinates in the pdb format. You will get what you want.

Phuong