From: Hugh Martin (hughtendo_at_gmail.com)
Date: Thu Nov 26 2009 - 09:30:21 CST
*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.
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
> problem it to do a time correlation analysis on a time series that
> consists of little contiguous pieces with gaps inbetween (when the
> colvar was in other bins).
> One possibility is to merge all these little series into one, and
> analyze correlations within this large series. In practice, you'd do
> that by matching the force trajectory and the colvar trajectory
> (that's the info you're missing, from what you wrote), and sorting the
> force data depending on what bin the colvar was visiting at the time
> it was collected.
> Otherwise, you'd have to formulate assumptions on the nature of
> correlations. It is tempting to assume that successive visits of the
> bin are decorrelated, but that's unlikely to be true.
> Yet another approach is to run a separate simulation for the sole
> purpose of studying time correlations. In that kind of simulation, the
> colvar can be confined to just one bin, so that a single, contiguous
> time-series is obtained.
> I warned you it was somewhat complex. The truth is, error analysis in
> 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):
> and our 2004 paper, which references it and adds some details.
> 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
> > the data with the PMF output, but it seems that the outputSystemForce
> > correlates to the timestep rather than to the reaction coordinate (which
> > PMF corresponds to). Thus, given that the nature of ABF/colvar
> > 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
> >> 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
> >> > to
> >> > perform ABF simulations. I was wondering if there is a way to output
> >> > standard deviation of each point (bin). I see that there is an option
> >> > for
> >> > "runAve" which calculates the standard deviation of the running
> >> > 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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