Re: FullSamples variable in ABF

From: Christophe.Chipot_at_edam.uhp-nancy.fr
Date: Wed May 23 2007 - 02:04:37 CDT

Dear Alex,

the choice of FullSamples inherently depends on the nature of your system
and the choice of your reaction coordinate. If it is a slow degree of
freedom, then a large FullSamples might be required to ascertain that the
average force has converged towards the desired value. Excessively small
FullSamples would yield undesirable non-equilibrium effects and unphysical
biasing forces. You can monitor the convergence of the average force in
the force distribution histograms generated for every bins. This aspect of
ABF is documented in:

Exploring the free-energy landscape of a short peptide using an average
force. J. Chem. Phys. 2005, 123(24), 244906.

Chris Chipot

Selon alex digenova bravo <digenova_at_gmail.com>:

> hello everyone. I am interested in to find a good value of sampling
> for my ABF simulations (for example zcoord-1atom). How can I see that
> the force converge at given value of fullsamples variable?.
> Thank You very much.
> Alex Di Génova

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