Re: How to deal with a long path in ABF simulation?

From: Chris Chipot (
Date: Wed Apr 26 2006 - 15:01:10 CDT


I would recommend to check first how your system diffuses along the
reaction coordinate. If diffusion is rapid, then a single, large
window is appropriate. If diffusion is hampered by orthogonal, slow
degrees of freedom, breaking the reaction coordinate into a number
of contiguous, non-overlapping windows is advisable to improve
sampling efficiency. Yet, you may want to ascertain that this form
of multistage sampling does not introduce non ergodicity at the
borders of the windows. If such were the case, turning to a single,
large window, using the biases inferred from the multistage free
energy calculation, is recommended.

Chris Chipot

Wenyu Zhong wrote:

> Dear Chipot,
> I want to calculate Free energy with ABF along a rather long reaction
> path. The only strategy is spliting the path into several parts?
> I think It is more convenient to complete them in a single simulation.
> Best regards
> Wenyu Zhong

Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1           Phone: (33) 3-83-68-40-97
B.P. 239                                      Fax:   (33) 3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex
     Science without management is worse than management without science
                                                        N. G. van Kampen

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