How to do standard MD analysis

This is just how I do mine and I found it quite cost-effective and most importantly easy to trace. I am more happy to discuss on any better protocols. --Kevin (talk) 13:42, 3 October 2015 (CST)

• Cat trajectory to a protein/protein+membrane-only system
• Make a pdb out from the initial structure
• Calculate RMSD to see convergence of the simulation