VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 01 2012 - 23:14:38 CST

Joe,
  This could certainly be done. You would just need to measure
the RMSD values for each residue, and then store the results into
one of the available per-atom data fields for each atom in the residue
(e.g. use a "same residue as ...." type atom selection.)
Once the data has been stored, you can use the field you've loaded the
RMSD values into as the coloring method in VMD. For a time-varying property,
like RMSD or RMSF you'll want to use one of the four "user" fields, since
they are stored per-atom, for each frame.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 06, 2012 at 12:40:27PM -0500, Joseph Bylund wrote:
> I'm interested in coloring each residue in a trajectory by its RMSD to
> its initial location. Similar to here:
> http://www.ks.uiuc.edu/Training/Tutorials/science/aquaporin/tutorial_aqp-html/node5.html
> (except rmsd instead of qres), but using frames of a trajectory instead of
> aligned structures. Is there a way to do this?
> thanks for any help,
> -Joe 

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