VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 14 2014 - 09:47:50 CST

Hi,
  You will want to use the "pbctools" plugin to unwrap
your trajectory so that you don't get PBC unit cell boundary
crossings and you can then use the "measure" commands as one
would expected.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jan 04, 2014 at 11:03:43AM +0800, ?????? wrote:
> Hi.
> I tried to get value of bonds,angles using "measure".
> But it seems this command doesn't involve pbc box condition.
> sometimes I get unreal values.
> how can I overcome such problems?
>
>
> thx
> Kangjie lu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/