namd-L: tcl script for calculate RMS of MD calculation

Date: Thu Apr 15 2004 - 03:01:28 CDT

Dear sir,
  I want to calculate RMS for a MD calculation. I had downloaded one tcl
script as follows:
set outfile [open rmsd.dat w];
set nf [molinfo top get numframes]
set frame0 [atomselect top "protein and backbone and noh" frame 0]
# rmsd calculation loop
for {set i 1 } {$i < $nf } { incr i } {
    set sel [atomselect top "protein and backbone and noh" frame $i]
    $sel move [measure fit $sel $frame0]
    puts $outfile "[measure rmsd $sel $frame0]"
close $outfile
It seems this script takes the first time step of the simulation as a
reference. I want to get one script which use the average value as
reference. Would you like to give me the script for calculate RMS?

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