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rmsd1.xvg:

...
60.0000000    0.1645018
80.0000000    0.1786710
100.0000000    0.2115960

rmsd2.xvg:

...
60.0000000    0.4645018
80.0000000    0.5786710
100.0000000    0.6115960

My code:

...
close($input_file1);
close($input_file2);
close($out_file);

Output file:

...
0.4645018
0.5786710
0.6115960

Requested:

...
60.0000000    0.1645018    0.4645018
80.0000000    0.1786710    0.5786710
100.0000000    0.2115960     0.6115960