**From:** Jerome Henin (*jhenin_at_cmm.chem.upenn.edu*)

**Date:** Thu Oct 08 2009 - 04:04:51 CDT

**Next message:**namd_chcwaaa_at_yahoo.com.cn: "about restart"**Previous message:**Ramya Gamini: "Re: followup question on error calculation in ABF"**In reply to:**Ramya Gamini: "Re: followup question on error calculation in ABF"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi everyone,

To evaluate the correlation length, you need the time series of F_xi

(and some skill, and possibly some luck).

In the old implementation (NAMD 2.6), the time series is obtained

using the keyword writeFxiFreq, which I realize is undocumented, as

discussed a couple of years ago on this list:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6712.html

(and then the code was obsoleted, so I never got around to fixing the

documentation)

In NAMD 2.7b1, that's done at the colvar level; the keyword is

outputSystemForce, and the data ends up in the colvar trajectory file.

http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/node48.html

Cheers,

Jerome

2009/10/7 Ramya Gamini <ramyabhargavi_at_gmail.com>:

*>
*

*> 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/
*

*>>> ------------------------------------------
*

*>>>
*

*>>
*

*>>
*

*>>
*

*>> --
*

*>> ------------------------------------------
*

*>> 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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