From: Josh Vermaas (
Date: Mon May 02 2016 - 09:23:10 CDT

Hi Devanand,

This will require a script.

#Load in the two dcds. Look up how to do this in the userguide under the
"mol" command.
set refid [mol new ...]
set selid [mol new ...]
#Make two selections. Note that the selected number of atoms should match!
set ref [atomselect $refid "protein"]
set sel [atomselect $selid "protein"]
#The third selection is the one that gets moved to superimpose the
set all [atomselect $selid "all"]
if { [$ref num] != [$sel num] } {
     puts "unequal selection sizes. Fix you selections."
#Go through each frame, and align it
for { set f 0 } { $f < [molinfo $refid numframes] } { incr f } {
     $ref frame $f
     $sel frame $f
     $all frame $f
     $all move [measure fit $sel $ref]

However, I have a question. Why would you want to do this? Usually
trajectories diverge away from one another, and it makes just as much
sense to align everything to a single reference.


On 04/30/2016 04:29 PM, Devanand T wrote:
> Is it possible to superimpose 2 dcd files (with equal number of
> frames) frame by frame? If so, can someone help me on this?
> --
> regards,
> /Devanand T
> /