Re: ABF error calculation

From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Fri Feb 29 2008 - 16:26:00 CST

Jiancong,

the answer to your question can essentially be found in two articles:

- Assessing the efficiency of free energy calculation methods.
   David Rodriguez-Gomez, Eric Darve and Andrew Pohorille
   J. Chem. Phys. 2004, 120, 3563-3578.

- Overcoming free energy barriers using unconstrained molecular
   dynamics simulations.
   Jerome Henin and Christophe Chipot
   J. Chem. Phys. 2004, 121, 2904-2914.

In a nutshell, you need to compute block averages of the instantaneous
force that acts along the reaction coordinate and estimate the variance
of the latter. Details of the calculations are spelled out in the above
papers.

Chris Chipot

Xu, Jiancong a écrit :
> Dear all NAMD users,
>
> I have one simple question regarding performing the error analysis
> from the ABF free energy calculations, and wondering how to use the
> distFile (the output file containg force distributions) to estimate
> the error bars. Thanks much!
>
> Jiancong

_______________________________________________________________________

Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Nancy Université Phone: +33 (0)3-83-68-40-97
B.P. 239 Fax: +33 (0)3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex

                             E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
                                            http://www.edam.uhp-nancy.fr

     Science without management is worse than management without science

                                                        N. G. van Kampen
_______________________________________________________________________

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