From: Josh Vermaas (
Date: Fri Jul 10 2015 - 14:23:56 CDT

Hi Mahdi,

Is there a specific reason you want the rmsd per atom? This is
equivalent to asking for the translation distance for each individual
atom from the reference state, which I've never seen measured before at
an atomic level. In principle, I don't see why your script wouldn't work
as written, but it'll generate an absolutely massive textfile (177*50000
lines = hard to parse later). Are you getting this textfile and see that
the RMSD isn't changing per frame, or is the textfile too short, and
something else is going on?

-Josh Vermaas

On 7/10/15 12:41 PM, Mehdi Bagherpour wrote:
> Dear VMD users,
> I want to find RMSD of first 176 atom that their index start from 0 to
> 176 during simulation (50000 frames).
> I have written below code but as I have seen for $selB it doesn't
> update frames.
> I will be appreciate If you could help me to find the bug of my script.
> set output [open "rmsd.dat" w]
> set mol [molinfo top]
> set nf [molinfo $mol get numframes]
> for {set x 0} {$x <= 176} {incr x} {
> set selA [atomselect $mol "index $x" frame 0]
> set selB [atomselect $mol "index $x"]
> set num_steps [molinfo $mol get numframes]
> for {set j 0} {$j < $nf} {incr j} {
> $selB frame $j
> set rmsd [measure rmsd $selB $selA]
> puts $output "$rmsd"
> }
> }
> close $output
> Best,
> Mahdi