Re: About RMSD based PMF's

From: Jérôme Hénin (
Date: Fri May 14 2010 - 06:05:28 CDT

Hi Felipe,

You've got it exactly right: the "RMSD = 0" state is extremely
unlikely, and more generally, the phase space volume corresponding to
a given RMSD value decreases very rapidly as RMSD approaches zero
(precisely as RMSD to the power 3N-4, where N is the number of atoms
involved), so does entropy. As a direct result, the PMF goes to
infinity there, even if the reference conformation is a very stable
one! In that case, the stable basin should be visible at small values
of the RMSD.


On 14 May 2010 06:03, Felipe Merino <> wrote:
> Hi,
> Maybe i am a little lost with this, but i have been performing some PMF
> calculations using RMSD as the order parameter. As the simulations
> approaches zero RMSD the free energy becomes very high i guess caused by a
> "conformational stretching".
> If we consider the number of microstates (really the volume of the phase
> space compatible with the E + dE energies given by the hamiltonian -
> including the harmonic RMSD constraint) that the system can show as a
> function of RMSD they seem to have an inverse relation, Indeed it is obvious
> when you consider that for the extreme case where RMSD is 0 there is just
> one microstate possible (considering only the constrained atoms). This
> should put an extra entropic component in the reconstructed PMF that i do
> not know if NAMD accounts for. I think that could explain some crazy things
> that i see on my PMF's.
> Any hints would be appreciated
> best
> Felipe
> Laboratorio de Bioquímica y Biología Molecular
> Facultad de Ciencias
> Universidad de Chile

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