What's wrong with sorting numerically?

#!/usr/bin/perl

use strict;
use warnings;

my @data = <DATA>;

{
    no warnings 'numeric';
    print sort { $a <=> $b } @data;
}

__DATA__
29.30.force.0.5.1LGY.pdb
30.31.force.0.5.1LGY.pdb
100.101.force.0.5.1LGY.pdb
9.10.force.0.5.1LGY.pdb
31.32.force.0.5.1LGY.pdb
200.201.force.0.5.1LGY.pdb
201.200.force.0.5.1LGY.pdb
101.102.force.0.5.1LGY.pdb
[download]

Output:

9.10.force.0.5.1LGY.pdb
29.30.force.0.5.1LGY.pdb
30.31.force.0.5.1LGY.pdb
31.32.force.0.5.1LGY.pdb
100.101.force.0.5.1LGY.pdb
101.102.force.0.5.1LGY.pdb
200.201.force.0.5.1LGY.pdb
201.200.force.0.5.1LGY.pdb
[download]

(if that's not the ordering you want, please post how exactly you want the sample list to be ordered)