Re: ABF question (free energy partition)

From: Chris Chipot (
Date: Sun Aug 09 2009 - 12:32:54 CDT

Dear Lei,

from a practical point of view, what you need to do is:

(1) loop over your trajectory and calculate the pair interactions
     that you are interested in, e.g. solute 1 and solute 2.

(2) collect the forces at play, van der Waals and electrostatics.

(3) project these forces onto your reaction coordinate, which for
     each configuration, should be determined independently.

(4) average the projected forces.

You now have components of the total average force, which you can
integrate to obtain the sought free-energy contributions.


Chris Chipot

Lei Shi a écrit :
> Dear NAMD users,
> I am a user of ABF and NAMD. I have a question about how to do the
> "partition of free energy" analysis from ABF simulations, similar as the
> one in Figure 3B JACS 2005, 127, 8478-8484 (also J. Phys. Chem. 2009,
> 113, 7836-7843 Figure 6). We have some initial simulation results from
> ABF calculation and are very interested to do free energy decomposition.
> We cannot find the solution in tutorials or manuals. Can anyone let me
> know how to perform this type of analysis?
> Thanks for your assistance.
> Lei
> -------------------------------------------------
> Lei Shi
> 207 Pleasant St SE, Mailbox L-15
> Department of Chemistry
> University of Minnesota, Twin Cities
> Minneapolis, MN 55455
> Phone: 612-625-0786 (o)


Chris Chipot, Ph.D.
on leave from Nancy Université, CNRS
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Phone: (217) 244-5711
Urbana, Illinois 61801 Fax: (217) 244-6078


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