From: Ivan Degtyarenko (imd_at_fyslab.hut.fi)
Date: Fri Dec 08 2006 - 05:44:58 CST

On Fri, 8 Dec 2006, Nicolas Floquet wrote:

> does anyone knows about a script in tcl to compute the values of diffusion coefficient of one particular molecule in a system along a MD trajectory ?
>
> Thanks.
>
> Dr. Nicolas Floquet

What you need is the mean-square displacement (MSD). VMD has
implemented root mean-square displacement (RMSD) which is a square
root of MSD. See RMSD description in manual:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node183.html

see also
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/0628.html

YT, Ivan