**From:** Hugh Martin (*hughtendo_at_gmail.com*)

**Date:** Thu Nov 26 2009 - 09:30:21 CST

**Next message:**doty alexiou: "adding constraints"**Previous message:**Hugh Martin: "Re: Retrieving standard deviation values while using collective variables (ABF)"**In reply to:**Jerome Henin: "Re: Retrieving standard deviation values while using collective variables (ABF)"**Next in thread:**Dong Luo: "Is it possible to run replica exchange simulation on BlueGeneL?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*That's extremely helpful, as always, Dr. Hénin. I have a few ideas of how

to proceed now. Indeed my past experience has taught me to expect great

complexity/headaches when it comes to errors.

Many thanks,

Hugh*

2009/11/26 Jerome Henin <jhenin_at_cmm.chem.upenn.edu>

*> Yes, the system force is an instantaneous quantity, it is output as a
*

*> function of time. What you say is precisely what makes the error
*

*> analysis particularly complex. The data used to compute the estimate
*

*> in a given bin is a combination of multiple blocks of data, which were
*

*> collected each time the coordinate visited that particular bin. So the
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*> problem it to do a time correlation analysis on a time series that
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*> consists of little contiguous pieces with gaps inbetween (when the
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*> colvar was in other bins).
*

*>
*

*> One possibility is to merge all these little series into one, and
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*> analyze correlations within this large series. In practice, you'd do
*

*> that by matching the force trajectory and the colvar trajectory
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*> (that's the info you're missing, from what you wrote), and sorting the
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*> force data depending on what bin the colvar was visiting at the time
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*> it was collected.
*

*>
*

*> Otherwise, you'd have to formulate assumptions on the nature of
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*> correlations. It is tempting to assume that successive visits of the
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*> bin are decorrelated, but that's unlikely to be true.
*

*>
*

*> Yet another approach is to run a separate simulation for the sole
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*> purpose of studying time correlations. In that kind of simulation, the
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*> colvar can be confined to just one bin, so that a single, contiguous
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*> time-series is obtained.
*

*>
*

*> I warned you it was somewhat complex. The truth is, error analysis in
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*> biomolecular free energy calculations is never simple. When it is,
*

*> it's wrong.
*

*>
*

*> You should also look at this paper (if you haven't already):
*

*> http://link.aip.org/link/?JCPSA6/120/3563/1
*

*>
*

*> and our 2004 paper, which references it and adds some details.
*

*>
*

*> Best,
*

*> Jerome
*

*>
*

*>
*

*> 2009/11/26 Hugh Martin <hughtendo_at_gmail.com>:
*

*> > Thanks for the response, yes sorry I was referring the free energy
*

*> > derivative.
*

*> >
*

*> > I produced the system force from a simulation to see if I could reconcile
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*> > the data with the PMF output, but it seems that the outputSystemForce
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*> data
*

*> > correlates to the timestep rather than to the reaction coordinate (which
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*> the
*

*> > PMF corresponds to). Thus, given that the nature of ABF/colvar
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*> simulations
*

*> > means that the position of the pulling atom does not correlate to a
*

*> > particular timstep or timestep bin (compared to, say, constant
*

*> > velocity-SMD), I can't see a way to use the data to produce useful error
*

*> > bars on the free energy derivative output.
*

*> >
*

*> > I'm just wondering if I'm out of options here, and should maybe look to
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*> > other measures of error/deviation?
*

*> >
*

*> >
*

*> > Many thanks,
*

*> >
*

*> > Hugh
*

*> >
*

*> >
*

*> > 2009/11/10 Jerome Henin <jhenin_at_cmm.chem.upenn.edu>
*

*> >>
*

*> >> Hi,
*

*> >>
*

*> >> If you are talking about the standard deviation for the free energy
*

*> >> derivative, it is not available directly. The reason for that is, that
*

*> >> quantity is not useful on its own, but only within a somewhat complex
*

*> >> error analysis that should include time correlations. Hence, such an
*

*> >> analysis requires the time series of the system force (or
*

*> >> instantaneous colvar force, or whatever you call it). That quantity
*

*> >> will be output if you include the outputSystemForce keyword in your
*

*> >> colvar blocks.
*

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

*> >>
*

*> >> Best,
*

*> >> Jerome
*

*> >>
*

*> >>
*

*> >> 2009/11/10 Hugh Martin <hughtendo_at_gmail.com>:
*

*> >> > Hello,
*

*> >> >
*

*> >> > I'm using NAMD2.7b1 and the collective variables implementation in
*

*> order
*

*> >> > to
*

*> >> > perform ABF simulations. I was wondering if there is a way to output
*

*> the
*

*> >> > standard deviation of each point (bin). I see that there is an option
*

*> >> > for
*

*> >> > "runAve" which calculates the standard deviation of the running
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*> average,
*

*> >> > but
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*> >> > I don't see an option for the standard deviation of each point/bin. Is
*

*> >> > this
*

*> >> > possible?
*

*> >> >
*

*> >> > Many thanks,
*

*> >> >
*

*> >> > Hugh
*

*> >> >
*

*> >
*

*> >
*

*>
*

**Next message:**doty alexiou: "adding constraints"**Previous message:**Hugh Martin: "Re: Retrieving standard deviation values while using collective variables (ABF)"**In reply to:**Jerome Henin: "Re: Retrieving standard deviation values while using collective variables (ABF)"**Next in thread:**Dong Luo: "Is it possible to run replica exchange simulation on BlueGeneL?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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