Re: followup question on error calculation in ABF

From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Wed Oct 07 2009 - 16:41:57 CDT

Sorry! Giovanni, but I cannot help you with this part of your query. From
what I understood from your previous query, I only thought you weren't able
to compute the factor (1+2k) as you did not know where to obtain the
instantaneous forces from.

I haven't performed an error analysis for ABF simulation myself but I am
sure Jerome or other ABF experts could best explain on how to
evaluate (1+2k)

best,
Ramya

On Wed, Oct 7, 2009 at 3:35 PM, Giovanni Bellesia
<gbellesia_at_chem.ucsb.edu>wrote:

> 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
> > 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
>> Phone: 805 893 2767
>> Web: http://www.chem.ucsb.edu/~gbellesia/>
>> ------------------------------------------
>>
>>
>
>
> --
> ------------------------------------------
> 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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