Re: Free energy of conformational change

From: Lixia Jin Day (ljin12_at_asu.edu)
Date: Wed Mar 25 2009 - 18:04:37 CDT

Chris,
I want to calculate the conformational FE change. It looks that the new
version provides several methods to do it. I will look into it. Thank you
very much for the information.

Best,
Lixia

On Wed, Mar 25, 2009 at 3:51 PM, Chris Harrison <char_at_ks.uiuc.edu> wrote:

> Lixia,
>
> 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.
>
>
> C.
>
>
>
> --
> 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
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>
>
> Lixia Jin Day <ljin12_at_asu.edu> writes:
> > Date: Wed, 25 Mar 2009 13:21:19 -0700
> > From: Lixia Jin Day <ljin12_at_asu.edu>
> > To: namd-l_at_ks.uiuc.edu
> > Subject: namd-l: Free energy of conformational change
> > Return-Path: char_at_halifax.ks.uiuc.edu
> > Message-ID: <f7c18c850903251321o3312d82i119865796104e559_at_mail.gmail.com>
> > X-Spam-Status: No, score=-1.8 required=5.0 tests=BAYES_00,HTML_00_10,
> > HTML_MESSAGE autolearn=no version=3.1.7-0+tcb1
> >
> > 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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