Re: followup question on error calculation in ABF

From: Giovanni Bellesia (gbellesia_at_chem.ucsb.edu)
Date: Wed Oct 07 2009 - 15:35:39 CDT

Hi Ramya,

the distFile is exactly what I'm using to calculate (for each bin) the
standard deviation via a Gaussian fit
of the distributions.
I was just wondering how I should calculate the factor (1+2k) which is
related to the correlation length of the instantaneous force.

Giovanni
> 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 profile
>
> 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.
>
>
> Ramya
>
> On Wed, Oct 7, 2009 at 1:50 PM, Giovanni Bellesia
> <gbellesia_at_chem.ucsb.edu <mailto:gbellesia_at_chem.ucsb.edu>> wrote:
>
> 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: gbellesia_at_chem.ucsb.edu <mailto:gbellesia_at_chem.ucsb.edu>
> Phone: 805 893 2767
> Web: http://www.chem.ucsb.edu/~gbellesia/
> <http://www.chem.ucsb.edu/%7Egbellesia/>
> ------------------------------------------
>
>

-- 
------------------------------------------
Giovanni Bellesia
Department of Chemistry and Biochemistry
University of California, Santa Barbara
Santa Barbara, California 93106-9510, USA.
Email: gbellesia_at_chem.ucsb.edu
Phone: 805 893 2767
Web: http://www.chem.ucsb.edu/~gbellesia/
------------------------------------------

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