VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
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
have.

Best,
/A

On Wed, Dec 3, 2014 at 6:24 PM, Seera Suryanarayana <palusoori_at_gmail.com>
wrote:

> 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.
> 

-- 
Best,
/A