Re: Free energy of conformational change

From: Chris Harrison (
Date: Wed Mar 25 2009 - 17:51:17 CDT


Do you need an alchemical change that "causes" a conformational change, or just a conformational change evaluated? If just the free energy of a conformational change (and not the free energy of alchemical change) needs to be calculated I would suggest strongly that you download the new beta version of namd (namd2.7b1) and use either Adaptive Biasing Force or Metadynamics (both described in the new manual under the "Collective variables" section) to calculate the free energy change of your system. If there is also an alchemical change to be calculated, we can offer suggestions how you might best proceed, but your email sounds like you are interested in the conformational free energy change.


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                          Voice: 217-244-1733              Fax:   217-244-6078
Lixia Jin Day <> writes:
> Date: Wed, 25 Mar 2009 13:21:19 -0700
> From: Lixia Jin Day <>
> To:
> Subject: namd-l: Free energy of conformational change
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> In the FEP section of the user's guide, it says:" The system is efficient if
> only a few coordinates, either of individual atoms or centers of mass of
> groups of atoms, are needed."
> Here I have two conformations of a protein (about 300aa), can I calculate
> the free energy changes during the transition from one conformation to
> another?
> Thanks!
> Lixia

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