**From:** Jérôme Hénin (*jhenin_at_ifr88.cnrs-mrs.fr*)

**Date:** Fri May 14 2010 - 06:05:28 CDT

**Next message:**muniyamuthu.raviprasad_at_ndsu.edu: "Re: error : atom moving too fast"**Previous message:**ipsita basu: "Re: error : atom moving too fast"**In reply to:**Felipe Merino: "About RMSD based PMF's"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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.

Cheers,

Jerome

On 14 May 2010 06:03, Felipe Merino <felmerino_at_uchile.cl> 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
*

*>
*

*>
*

**Next message:**muniyamuthu.raviprasad_at_ndsu.edu: "Re: error : atom moving too fast"**Previous message:**ipsita basu: "Re: error : atom moving too fast"**In reply to:**Felipe Merino: "About RMSD based PMF's"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:54:07 CST
*