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

From: Jerome Henin (
Date: Tue Nov 10 2009 - 10:52:34 CST


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.


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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