VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 14 2005 - 18:45:30 CST

Hi,
  If I understand the definition of RMSF correctly, you're just wanting
to calculate the variance of the atom position over a trajectory
(which assumes a structure at equilibrium, otherwise the result
won't make any sense).
You can read through some of these other scripts to learn how to loop over
frames and so on. Basically you'll calculate the mean atom positions,
then use that to calculate the variance. Then set the per-atom "beta"
column with the results, use the "color by beta" setting and you'll
have a pretty structure. I don't have time to write this for you presently,
but I would think this could be done pretty quickly if you look at some
of the existing VMD scripts that process trajectories. I think you'll
find this script helpful as an example of how to average atom positions, etc:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/trajectory_smooth/

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Dec 15, 2005 at 07:10:28AM +0800, h9826299_at_hkusua.hku.hk wrote:
> Hi,
>
> Anybody know how to calculate rmsf (NOT rmsd) using tcl scripts in VMD? Or is
> there anyways to modify the commonly used rmsd scripts to calculate rmsf?
>
> for example, the rmsd_residue_over_time tcl script at
>
> http://www.ks.uiuc.edu/Training/Tutorials/vmd/vmd-tutorial-files/rmsd-fullthrottle.tcl
>
> Thank you very much!!!!
>
> cheers,
> 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