How can I compute the performance of an application software?

Question

[user366312]

I am working with protein PDB files.

Application 'A' generated 3884 PDB files from the protein's CA-trace. Application 'B' did the same.

So, I calculated the CRMSD values of each pair of files for both 'A' and 'B.' I.e., I have 3884 CRMSD valued for 'A' and another 3884 for 'B.'

Now, I want to find out which application is better.

How can I do that?