Jarzinsky's equation

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Dec 01 2010 - 01:54:57 CST

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
(http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2719.html)
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 gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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