It depends on the trajectory file format of your data. In principle, you can use CHARMM to analyze your data (www.charmm.org) , GROMACS (http://manual.gromacs.org/programs/gmx-rmsf.html), but you may also use VMD which is a visual molecular dynamics (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/17320.html).

Don't expect meaningful answers to your very cryptic question.  I can suspect that RMSD = root mean square deviation, but I have no idea what RMSF might mean.  "100 ns simulation" suggests that you are working with differential equations of some kind, but what is "mutated model" under this circumstances?  Any relation  to genetic algorithms?  Sorry.

Hi, 

the following script will work on VMD, if you used NAMD, it can be used directly and if you used graomcs, Dr. Hiqmat already mentioned about it.

Suppose you have protein try the following script.

# rmsf.tcl

mol load psf yourfile.psf dcd yourfile.dcd

set outfile [open rmsf.dat w]

set sel [atomselect top "protein and alpha"]

set rmsf "[measure rmsf $sel first 0 last -1 step 1]"

for {set i 0} {$i < [$sel num]} {incr i} {

puts $outfile "[expr {$i+1}] [lindex $rmsf $i]"

}

close $outfile

mol delete all

thank you very much to all , finally i got