From: Abhijit Muley (
Date: Wed Dec 03 2014 - 00:10:12 CST

You can calculate RMSD as long as you have a reference structure and a
second structure. The reference structure in your case could be the
original crystal structure of the protein


On Wed, Dec 3, 2014 at 2:24 PM, Seera Suryanarayana <>

> Dear VMD users
> Is it possible to calculate the rmsd value for a protein after energy
> minimization?
> If yes, please tell me how calculate rmsd value for the energy minimized
> protein and what structure can I give as reference structure. I have done
> md simulation by gromacs and I have to calculate the energy minimized
> protein em.gro.
> Thanks in advance
> Surya
> Graduate student
> India.