# Molecule alignment

I'd like to align ~2000 molecules consisting of 8 atoms of carbon and evaluate their similarity with RMSD (all vs all molecules).

What open software can do it in a day or less? I'd like it to work on Ubuntu, and if possible that it calculates the alignments in parallel.

My files are xyz: number of atoms, element+coordinates of each atom.

Thank you.

• A good idea to get this working in parallel would be to write a Python script that calls rmsd with multiprocessing, rather than using xargs or GNU parallel from the command line. – pentavalentcarbon May 14 '18 at 14:55