From: Ashar Malik (
Date: Wed Dec 03 2014 - 00:27:32 CST

Hey Surya,

Yes, that should be fairly simple.

When you finish your minimization, you basically have a structure which has
an optimized geometry. This structure is what is used as a starting point
for the MD. Since you had a structure which you minimized, and a structure
after minimization, so in theory you should be able to get an RMSD.

As to your other question, there is no correct reference. Its your choice.
RMSD is just a measure to quantify the difference between two structure.
Its your choice what two structures you want to compare. One way would be
to use the crystal structure as a reference to see how much it changed as
it underwent minimization.

The exact commands on how to calculate the RMSD depend on what formats you


On Wed, Dec 3, 2014 at 6:24 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.