VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 09 2006 - 11:34:46 CST

Hi,
  I haven't written the necessary code to do groups of atoms. You might
also have a look at the rmsf calculation tool that comes with Gromacs and see
if it does what you have in mind, it's more featureful than the routines
I wrote for VMD thus far. If there's enough interest in specific analysis
features of this sort, I can add them to the TODO list.

  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Dec 24, 2005 at 02:02:16AM +0800, h9826299_at_hkusua.hku.hk wrote:
> Hi,
>
> I using the measure rmsf command to calculate the rmsf value of selected atoms
> over a traj. However, this command on returns the indiviudal rmsf values but
> not the center of the grouped atoms, e.g. sidechain or backbone.
>
> Is there any way to calculate the gourped rmsf results? I've tried the measure
> center result as the input into the measure rmsf input as the selection but it
> doesn't work. Or do you think the average rmsf values of these atoms represents
> the center of the group though?
>
> thanks,
> Chung 

-- 
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