From: Hugh Martin (hughtendo_at_gmail.com)
Date: Wed Dec 09 2009 - 10:44:45 CST
Thanks for the response, it hasn't appeared to be necessary in my
simulations, I'm getting good results so far. I was just writing up about
the ABF method and was curious about the change.
2009/12/9 JÃ©rÃ´me HÃ©nin <jhenin_at_ifr88.cnrs-mrs.fr>
> Hi Hugh,
> Indeed, so far it has not seemed necessary to implement this in the
> new code. The benefits were dubious: the "deleterious effects" we
> mentioned at the time were mostly hypothetical, and since then we have
> found no clear evidence of them (our 2005 paper was not conclusive on
> this, apart from the expected result that too much smoothing is
> harmful). As a matter of fact, averaging of force data from
> neighbouring bins does effectively occur over time, as the coordinate
> diffuses across bin boundaries. We have not found short-timescale
> variations of the biasing force per se to cause numerical problems. At
> some point, we all but stopped using dSmooth.
> So for the new code, I decided to focus on basic functionality, and
> wait to see how much demand there would be for smoothing before I
> implemented it. There has not been any demand so far... Let me know if
> you have reasons to think it is needed.
> 2009/12/9 Hugh Martin <hughtendo_at_gmail.com>:
> > Hello,
> > In the NAMD2.7b1 implementation of ABF, I notice that neither the
> > option, nor an equivalent, is present. It is also not included in the
> > revised tutorial. It's purpose was initially:
> > "to alleviate the deleterious effects due to abrupt variations of the
> > the corresponding ï¬‚uctuations are smoothed out, using a weighted running
> > average over a present number of adjacent bins, in lieu of the average on
> > the current bin"
> > Does the new implementation avoid these effects without the 'dSmooth'
> > parameter?
> > Many thanks,
> > Hugh
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