VMD-L Mailing List

From: Joshua D. Moore (joshuadmoore_at_gmail.com)
Date: Fri Sep 14 2012 - 13:36:44 CDT

If I understand correctly, maybe you are dumping wrapped coordinates,
so that VMD assigns the bonds based on the first frame, so when they
cross periodic boundaries it draws some huge bond.

I think there are several options, but maybe the easiest if you want a
CPK type look, you could have two representations, one with dynamic
bonds and the other with VDW but with small beads?

Or you could dump unwrapped coordinates, use CPK and use pbctools to
have VMD wrap in nicer way. Or maybe with your existing data, try
pbcunwrap, then a pbcwrap with possibly a pbcjoin.

On Thu, Sep 13, 2012 at 10:18 PM, luoyuan Q <luoyuan126_at_gmail.com> wrote:
> Hi,everyone.
> When i use VMD to visualize lammps dump files which contain many dump files
> , a animation appears in VMD display window, but there is a problem that if
> i chose CPK as drawing method ,no matter how far tow bonded atoms are, the
> bonds still exist for some atom type. Many atoms' bonds cover other
> atoms,as a result that i can't scan the process. The problem don't exists
> when i load only one file into VMD which shows a static picture of atoms
> distribution at that moment. How can i set to remove these bonds? Thank u
> for your time reading my mail and appreciate any suggestions. P.S. i don't
> know whether i have describe my problem clearly.
> Best wishes
> Yours sincerely
> Zongyang Qiu
> 13/09/2012