VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 24 2009 - 15:34:05 CDT

Hi,
  I would suggest creating two atom selections (one each for the two
residues), and then use 'measure center' to get the centers of mass,
and so on, here's a hastily written prototype:
  set sel1 [atomselect top "residue 20"]
  set sel2 [atomselect top "residue 30"]

  set numframes [molinfo top get numframes]
  for {set frame 0} {$frame < $numframes} {incr frame} {
    $sel1 frame $frame
    $sel2 frame $frame
    set com1 [measure center $sel1 weight mass]
    set com2 [measure center $sel2 weight mass]
    
    set comdist [vecdist $com1 $com2]
    puts "COM distance for frame $frame: $comdist"
  }

  $sel1 delete
  $sel2 delete

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 24, 2009 at 03:59:14PM -0400, Naiyin Yu wrote:
> Hello,
>
> I would like to trace the distance between the center of mass of one residue on one chain and some element on the other chain. I have tried to use the "atomselect" but it failed. It seems we have to label residue instead of center of mass. Is there anyway to solve it?
>
> thanks,
> Evelyn 

-- 
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