VMD-L Mailing List

From: Olaf Lenz (lenzo_at_mpip-mainz.mpg.de)
Date: Wed Aug 12 2009 - 10:56:53 CDT

Hi!

Liang, Linus H. wrote:
> I know it is possible to display periodic images, but is it possible to allow the periodic representations to interact with the original representation .

That depends on what you mean by that periodic images "interact". Do you
mean that you want to see bonds between atoms in periodic images?
As Axel already noted, the autobond feature does not allow for this.

However, if you have all the bonds between atoms already in the
trajectory file, it works. Usually, all bonds between atoms in the same
image are drawn. If you have wrapped atoms, then you have bonds that are
very long and stretch the whole image. To unwrap these, you can use "pbc
unwrap" in the console.

Olaf