From: Ranyere Deyler (
Date: Wed Mar 16 2011 - 09:24:54 CDT

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

Thanks a lot.

Ranyere Deyler Trindade