VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 13 2006 - 00:09:46 CDT

Hi,
  Presently, VMD only calculates the intra-cell distance between
atoms, and will not return the (potentially many) other possible
inter-cell distances between two atoms. If you want to calculate
the distance between two periodic images, you'll have to calculate
and use the unit cell basis vectors to translate the atom coordinates
according to which periodic image instance you intend to measure against.
Does that make sense?

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 11, 2006 at 04:02:37PM -0400, dimka wrote:
> I can measure the distance between two atoms that are located in
> adjacent pbc images using mouse, but how do i do this through the
> command line?
>
> -dima 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078