Re: Retrieving standard deviation values while using collective variables (ABF)

From: Hugh Martin (
Date: Thu Nov 26 2009 - 07:38:13 CST

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

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,


2009/11/10 Jerome Henin <>

> 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.
> Best,
> Jerome
> 2009/11/10 Hugh Martin <>:
> > 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 average,
> but
> > I don't see an option for the standard deviation of each point/bin. Is
> this
> > possible?
> >
> > Many thanks,
> >
> > Hugh
> >

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