Re: vmd-l: RMSD Question

From: Germain Salvato Vallverdu (
Date: Mon Nov 29 2010 - 02:56:05 CST


Can you say exactly why do you calculate a RMSD ?

You have to keep in mind that when you minimize the crystal structure
you compute forces and energy with a force field which is an
approximation of the correct forces and energy. Thus the minimized
structure might be different than the crystal one.

RMSD are often used (in MD) in order to control if the equilibrium
structure you find with your force field is not too far away the cristal
structure. That give you some garanties that your MD (and the force
field) is not bad. Thus you should not minimize your crystal structure.
But, again, it depends on what you are looking for with your RMSD.

1.4 A is not too bad. You can also look at only the backbone RMSD or
only the backbone RMSD of secondary structure part of your protein. A
good value for that RMSD is around 1 A.


-------- Message initial --------
De: snoze pa <>
Sujet: vmd-l: RMSD Question
Date: Sun, 28 Nov 2010 11:08:25 -0600

Dear NAMD/VMD Users,

 I am trying to calculate the RMSD between two proteins. One has
crystal structure and other is a model structure. I used modeller to
model the protein. When I calculate rmsd between model structure and
crystal structure then rmsd is fine, close to the rsolution of the
crystal structure. But When I minimize the structure using namd then
the rmsd increses up to 1.4 A.

So do you think I should also minimize the crystal structure also to
calculate the correct rmsd. Becuase in the minimzed model structure
the loop regions changes sometime, which may be true if we will
minimize the crystal structure.

Which is the correct way to calculate the RMSD? Please guide me.

Thank you for your help in advance.


Maître de Conférence
Université de Pau et des pays de l'Adour
05 59 40 78 51

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