From: Mehdi Bagherpour (
Date: Fri Jul 10 2015 - 11:49:16 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*