From: Mehdi Bagherpour (
Date: Fri Jul 10 2015 - 12:41:25 CDT

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
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