Re: followup question on error calculation in ABF

From: Ramya Gamini (
Date: Wed Oct 07 2009 - 15:26:15 CDT

Hi Giovanni,

As I understand .. .. ..the 'distFile' key word in the config file, will
allow you generate the '.dist' file that includes instantaneous components
of the force.
For each bin, the number of samples for instantaneous forces ranging from
-fMax to fMax will be generated. Default of fMax being 60 kcal/mol/A

Like these terms are defined in the namd -user guide under ABF section.
distFile Output file containing force distributions
Acceptable Values: Unix filename
Default Value: none
Description: Output file containing a distribution of the instantaneous
components of the force, , for every bin comprised between xiMin and xiMax.
This is useful for performing error analysis for the resulting free energy

fMax Half-width of the force histograms
Acceptable Values: positive decimal number, in kcal/mol/
Default Value: 60.0
Description: When force distributions are written in distFile, the histogram
collects values ranging from fMax to fMax.


On Wed, Oct 7, 2009 at 1:50 PM, Giovanni Bellesia

> Hi all,
> I am trying to use formula (22) in JCP 121(7), 2004 to calculate the error
> in my ABF data.
> From the simulations, I have the distributions of the instantaneous force
> for every bin.
> Therefore, I am calculating sigma(F_{e,i}) fitting these distributions with
> a Gaussian.
> My problem is: I understand the definition of "sampling ratio" (1+2k) but I
> don't know how to
> calculate it since I don't have the values of the instantaneous force.
> I think I'm missing something very simple here ... :o)
> Giovanni
> --
> ------------------------------------------
> Giovanni Bellesia
> Department of Chemistry and Biochemistry
> University of California, Santa Barbara
> Santa Barbara, California 93106-9510, USA.
> Email:
> Phone: 805 893 2767
> Web:>
> ------------------------------------------

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