From: DimitryASuplatov (
Date: Sat May 23 2009 - 08:16:37 CDT


I am trying to write a tcl script to calculate rmsd of my MD simulation.
I`ve used the example from namd tutorial:

set outfile [open rmsd.dat w]
set nf [ molinfo top get numframes]
set frame0 [atomselect top "protein and backbone and noh" frame 0]
set sel [atomselect top "protein and backbine and noh"]
set sel [atomselect top "protein and backbone and noh"]
#rmsd calculation loop
for { set i 1 } { $i <= $nf } {incr i 1} {
$sel frame $i
$sel move [measure fit $sel $frame0 ]
puts $outfile "[measure rmsd $sel $frame0]"
close $outfile

The problem with it is that it shows only the rmsd for each frame - that
means no time present. This is sometimes a problem. What is the command
to take info (like current time of the frame) from a frame selection.

I guess it should be something like
set frame0time [get time frame0]
(this does not work unfortunately).

Thank you for your help.