proc rmsd_residue_over_time_igem {{mol top} res debut refer} {
    
# utilisé pour aligner les résidus avant rmsd
    set reference [atomselect $mol "backbone" frame $refer]
    # the frame being compared
    set compare [atomselect $mol "backbone"]

    #make a selection with all atoms
    set all [atomselect top all]

    #get the number of frames
    set num_steps [molinfo $mol get numframes]
    puts "Number of steps $num_steps ..."

    #open file for writing
    set fil [open data_rmsd.dat w]
    
    #init tableau rmsd
    for {set ff $debut} {$ff < $num_steps} {incr ff} {
         set rmsd($ff) 0
         }
    
    #loop over all frames in the trajectory
    for {set frame $debut} {$frame < $num_steps} {incr frame} {
	puts "Calculating rmsd for frame $frame ..."
	# get the correct frame
	$compare frame $frame
        $all frame $frame
	# compute the transformation
	set trans_mat [measure fit $compare $reference]
	# do the alignment
	$all move $trans_mat

	# compute the RMSD
	#loop through all residues
    set prev 0
	foreach r $res {
if { $prev != $r } {
	    set ref [atomselect $mol "resid $r and noh" frame $refer]
	    set comp [atomselect $mol "resid $r and noh" frame $frame]
	    #it could be interesting to test this, much faster and meaningfull
	    #set ref [atomselect $mol "resid $r and name CA" frame $refer]
	    #set comp [atomselect $mol "resid $r and name CA" frame $frame]

	    set rmsd($frame) [expr $rmsd($frame) + [measure rmsd $comp $ref]]
	    $comp delete
	    $ref delete
set prev  [ expr $r ]
}
	}
	
    }

set nbr_elem [llength $res]

for {set frame $debut} {$frame < $num_steps} {incr frame} {
set rmsd_temp [expr $rmsd($frame) / $nbr_elem]
puts $fil " $frame \t $rmsd_temp"
}
    close $fil
}