use strict;
use warnings;

my @files = grep /^output\d+$/, <output*>;
foreach my $file ( @files ) {
  open (IN, "<$file") 
      or die "could not open $file: $!";
  print "$file\n";
  my ($total,$i) = (0,0); #initialize to zero for each file
  while ( my $input = <IN> ){
    #sine you don't seem to be using $x, $y, $z anyhow
    my $sum = (split /\s+/,$input)[3]; 
    $total += $sum;
    $i++;
    my $div = $total/$i;
    my $sqrt = sqrt($div);   
    print "$total\n";
    open (OUT2, ">RMSD$file") 
        or die "could not open RMSD$file: $!";    
    print OUT2 "$sqrt\n"
  }
}