**From:** Ramya Gamini (*ramyabhargavi_at_gmail.com*)

**Date:** Wed Oct 07 2009 - 16:41:57 CDT

**Next message:**Jerome Henin: "Re: followup question on error calculation in ABF"**Previous message:**steve.kaminski_at_mail.tu-berlin.de: "NAMD CUDA release"**In reply to:**Giovanni Bellesia: "Re: followup question on error calculation in ABF"**Next in thread:**Jerome Henin: "Re: followup question on error calculation in ABF"**Reply:**Jerome Henin: "Re: followup question on error calculation in ABF"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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/Å
*

*> 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/ >
*

**Next message:**Jerome Henin: "Re: followup question on error calculation in ABF"**Previous message:**steve.kaminski_at_mail.tu-berlin.de: "NAMD CUDA release"**In reply to:**Giovanni Bellesia: "Re: followup question on error calculation in ABF"**Next in thread:**Jerome Henin: "Re: followup question on error calculation in ABF"**Reply:**Jerome Henin: "Re: followup question on error calculation in ABF"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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