VMD-L Mailing List

From: Luca UvA (lghiring_at_science.uva.nl)
Date: Tue Feb 04 2003 - 04:50:40 CST

Hi,
    I have the following problem. I'd like to visualize a trajectory of a liquid sample, in which, in every frame, atoms should have different colors related to certain properties. For example, as simplest thing, even having a sample of P atoms, I'd like to have, e.g., red the 4-fold coordinated, green the 3-fold, and so on. Normally I can generate a multi frame pdb file, I tried to simply change the name of the atom in different frame, but the kind of atom it is given on the first frame then it is preserved. I tried generating an xyz file, but I cannot find the way to load multiframes.
Is there a file format supported that allow this or a script that can do that after a, say, pdb is loaded on VMD?
Furthemore, it is essential that I can load in parallel the same trajectory twice since I need both the dynamic bonds feature and the VDW, to have balls marking non bonded atoms: this is possible with a pdf file, but it seems not for xyz (I use both Win and Linux version).

Thanking for any advice,
Luca Ghiringhelli