From: Vermaas, Joshua (
Date: Wed Apr 11 2018 - 11:07:32 CDT

Hi Jeams,

Its totally possible. If your trajectory is unwrapped, it is even what one might call easy, since you just need to select your atoms of interest, and compare their rmsd between the initial state and the state over time, and square it to get your msd.

set ref [atomselect top "noh and water" frame 0]
set sel [atomselect top "noh and water"]
for {set f 0 } { $f < [molinfo top get numframes] } { incr f } {
$sel frame $f
set rmsd [measure rmsd $sel $ref]
set msd [expr {$rmsd * $rmsd}]

If your trajectory is wrapped, unwrap it. You may find the pbctools documentation helpful (


On 2018-04-11 07:54:39-06:00 wrote:

Dear all
I am wondering is it possible to calculate MSD or diffusion coefficient in VMD??
Any suggestion will be very helpful
Thanks in advance