How to do RMSD and RMSF

VMD

RMSD

set sel_ref0 [atomselect top "${SELREF[$ii]}" frame 0]
set sel_ref [atomselect top "${SELREF[$ii]}"]
set sel_rmsd0 [atomselect top "${SELRMSD[$ii]}" frame 0]
set sel_rmsd [atomselect top "${SELRMSD[$ii]}"]
set outfile [open "rmsd_${OUTPUT_NAME[$ii]}.dat" "w"]
for {set i 0} {\$i<\$num_frames} {incr i} {
   \$sel_all frame \$i
   \$sel_ref frame \$i
   \$sel_rmsd frame \$i
   \$sel_all move [measure fit \$sel_ref \$sel_ref0]
   set rmsd [measure rmsd \$sel_rmsd \$sel_rmsd0]
   puts \$outfile "\$i \t \$rmsd"
}
close \$outfile

RMSF

set outfile [open "rmsf_$OUTPUT_NAME.dat" "w"]
set seltext "protein and name CA"
set sel [atomselect top \$seltext]
set rmsf [measure rmsf \$sel first $start_frame last -1]
for {set i 0} {\$i <  [\$sel num] } {incr i} {
   puts \$outfile "[expr {\$i+1}] [lindex \$rmsf \$i]"
}
close \$outfile