Re: ABF for conformational analysis

From: Jérôme Hénin (
Date: Mon Nov 14 2005 - 03:34:21 CST

Dear Uma,

The key to answering your question is: can you define a nice, simple reaction
coordinate that describes the conformational change you're interested in? If
yes, ABF should be able to help. If in addition, that RC can be expressed
using one of the coordinates already implemented (see ABF in the NAMD user's
guide), then preparing the calculations should be fairly simple. If not, it
is possible to extend the current package by coding a new reaction
coordinate. It's just a matter of a short Tcl file.

Then, the success of the calculation will strongly depend on the various
intrinsic timescales of your system. ABF will try and overcome barriers along
the reaction coordinate, but other slow degrees of freedom, if they exist,
may be a serious obstacle. There is a J. Chem. Phys. paper currently in
press, that addresses the issue of necessary conditions for an efficient ABF
simulation (authors: Chipot and Henin). It should be available online

Feel free to ask more questions on this list as needed!

On Friday 11 November 2005 23:54, you wrote:
> Dear all,
> I am just trying to understand the new abf facility in NAMD and was
> wondering if abf can be used to do conformational analysis similar to
> the Free energy of conformational change method. If yes, does anyone
> have a sample script to do that?
> Thanks,
> Uma
> --
> Uma Mahankali,
> Graduate Student,
> Department of Chemistry,
> University of Cincinnati,
> Ohio-45219

Jérôme Hénin
Equipe de Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS
Tel : (33) 3 83 68 43 91        Fax : (33) 3 83 68 43 87

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