My code:

#!/usr/bin/perl 

use strict;
use warnings;

# Open file1 to read
open my $input_file1, '<', "rmsd1.xvg" or die qq{Failed to open "rmsd1.xvg" for writing: $!};

# Open file2 to read
open my $input_file2, '<', "rmsd2.xvg" or die qq{Failed to open "rmsd2.xvg" for writing: $!};

# Open new file to write
open my $out_file, '>', "out_file.xvg" or die qq{Failed to open "out_file.xvg" for writing: $!};


while(<$input_file1>)
{ 
 next if /(^\s*$)|(^#)|(^@)/;
 my @columns1 = split;
 print $out_file join("\t", $columns1[0],$columns1[1], "\n");
}

while(<$input_file2>)
{ 
 next if /(^\s*$)|(^#)|(^@)/;
 my @columns2 = split;
 print $out_file join("\t", $columns2[1]), "\n";
}
close($input_file1);
close($input_file2);
close($out_file);