Fitting Protein Structures in VMD

# This script can be used to first load a reference structure and
# fit the second structure/trajectory to the reference.

mol new reference.pdb

mol new enzfibsol.psf
mol addfile md2.dcd type dcd first 0 last -1 step 1 waitfor all
mol addfile md3.dcd type dcd first 0 last -1 step 1 waitfor all
mol addfile md4.dcd type dcd first 0 last -1 step 1 waitfor all
mol addfile md5.dcd type dcd first 0 last -1 step 1 waitfor all

set backbone [atomselect 0 backbone]

for {set i 0} {$i < [molinfo 1 get numframes]} {incr i 1} {

set bk [atomselect 1 backbone frame $i]
set all [atomselect 1 all frame $i]
$all move [measure fit $bk $backbone]

}