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

**Date:** Thu Nov 26 2009 - 07:38:13 CST

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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

the data with the PMF output, but it seems that the outputSystemForce data

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

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

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
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*> derivative, it is not available directly. The reason for that is, that
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*> quantity is not useful on its own, but only within a somewhat complex
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*> error analysis that should include time correlations. Hence, such an
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*> analysis requires the time series of the system force (or
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*> instantaneous colvar force, or whatever you call it). That quantity
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*> will be output if you include the outputSystemForce keyword in your
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*> colvar blocks.
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*> http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/node48.html
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*>
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*> Best,
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*> Jerome
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*>
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*>
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*> 2009/11/10 Hugh Martin <hughtendo_at_gmail.com>:
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*> > Hello,
*

*> >
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*> > I'm using NAMD2.7b1 and the collective variables implementation in order
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*> to
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*> > perform ABF simulations. I was wondering if there is a way to output the
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*> > standard deviation of each point (bin). I see that there is an option for
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*> > "runAve" which calculates the standard deviation of the running average,
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*> but
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*> > I don't see an option for the standard deviation of each point/bin. Is
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*> this
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*> > possible?
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*> >
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*> > Many thanks,
*

*> >
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*> > Hugh
*

*> >
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*>
*

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