VMD-L Mailing List

From: Ranyere Deyler (ranyere_at_gmail.com)
Date: Wed Mar 16 2011 - 14:12:45 CDT

Well, i just thought it was logical. But it seems not.
Does anyone have a script that calculates the MSD using VMD? I don't know
much about tcl to build one. If anyone knows about a script that does that i
would appreciate.
Thanks a lot.

Ranyere Deyler Trindade

On Wed, Mar 16, 2011 at 12:54 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>
> axel.
>
> >
> > Thanks a lot.
> >
> >
> > Ranyere Deyler Trindade
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>