From: Axel Kohlmeyer (
Date: Wed Mar 16 2011 - 10:54:41 CDT

On Wed, 2011-03-16 at 11:24 -0300, Ranyere Deyler wrote:
> Dear VMD users, i searched in the list for this question and i saw one
> or two reply but it's still not clear.
> What i want is to plot the MSD over time, so i can plot it and get
> some information over de diffusion, whether it is a superdiffusive or
> subdiffusive proccess.
> Well, namd has the "RMSD trajectory" plugin. So, theoretically i would
> have to get the square of the RMSD found on VMD plugin and then plot
> it.
> So i ask. Is that right? In this case, of vmd plugin, the square of
> the RMSD trajectory will give me the MSD?? Can i use it to look at the
> diffusion coefficient??

it is a _very_ bad idea to use acronyms as a base for science.
the RMSD that the plugin computes is something different from
the MSD that you compute for self-diffusion.


> Thanks a lot.
> Ranyere Deyler Trindade

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.