**From:** Giovanni Bellesia (*gbellesia_at_chem.ucsb.edu*)

**Date:** Wed Oct 07 2009 - 15:35:39 CDT

**Next message:**Ramya Gamini: "Re: followup question on error calculation in ABF"**Previous message:**Giovanni Bellesia: "followup question on error calculation in ABF"**In reply to:**Ramya Gamini: "Re: followup question on error calculation in ABF"**Next in thread:**Ramya Gamini: "Re: followup question on error calculation in ABF"**Reply:**Ramya Gamini: "Re: followup question on error calculation in ABF"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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 <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/ ------------------------------------------

**Next message:**Ramya Gamini: "Re: followup question on error calculation in ABF"**Previous message:**Giovanni Bellesia: "followup question on error calculation in ABF"**In reply to:**Ramya Gamini: "Re: followup question on error calculation in ABF"**Next in thread:**Ramya Gamini: "Re: followup question on error calculation in ABF"**Reply:**Ramya Gamini: "Re: followup question on error calculation in ABF"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:53:20 CST
*