Re: Jarzinsky's equation

From: Fatemeh Khalili (
Date: Thu Dec 02 2010 - 13:54:33 CST

Hi Gianluca,

To use Jarzynski's equality you need to calculate the work done by the
external forces you apply to the system. The SMD forces (your external
force) are written in your log file. Proper distances (spring
extension/contraction) can also be extracted from the log file and your
trajectory. By knowing the expansion of the spring, you can calculate the
work applied to your system.


On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <> wrote:

> I would like to calculate the free energy of a protein-protein complex
> using the Jarzinsky's equation from already performed SMD simulations. I
> would be happy if somebody could point me out to some scripts which help me
> perform that.
> In a previous thread in response to somebody asking the same question
> (
> it was mentioned that NAMDenergy can calculate all sorts of energies.
> However, I cannot find any option for NAMDenergy which does that.
> Thanks!
> Gianluca
> -----------------------------------------------------
> Gianluca Interlandi, PhD
> +1 (206) 685 4435
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------

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