Subject: Jarzynski's equality for free energy

From: Masakatsu Ito <m-ito=at=jp.fujitsu.com>
Date: Thu, 22 Apr 2004 14:19:16 +0900 (JST)

Hi CCLers,

I am looking for reviews and articles about the free energy
calculation of biomolecules. I have been impressed by Jarzynski's
equality (Phys.Rev.Lett. 78, 2690 (1997)) which enables one to
estimate free energy difference from an ensemble of short MD
simulations. This implies that the estimation can be drastically
accelerated by distributed computing.  But those MD simulations should
start from equilibrium, and I am wondering how such initial conditions
can be prepared for biomolecules. Because it is notoriously difficult
to get an equilibrium ensemble of biomolecular structures.

Thus I am very interested in the application of Jarzynski's equality
to biomolecular processes. Could someone please give me some advice or
point me to articles?

Thanks in advance for any help.  
Kind Regards,

Masakatsu Ito , Ph.D

Nanotechnology Research Center
FUJITSU LABORATORIES LTD.
10-1 Morinosato-Wakamiya, Atsugi 243-0197 Japan
Phone : +81-46-250-8234  Fax : +81-46-250-8844
E-mail m-ito=at=jp.fujitsu.com