Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein

From: Ajasja Ljubetič (
Date: Wed Jan 19 2011 - 10:01:42 CST

Thank you. For now I'll just take every 100 point from the running average.
(The file will be 100 times larger then necessary, but this is no problem).
A quick question on subdividing a PES into smaller parts (when doing ABF):
Should there be some overlap between the smaller regions in order to avoid
the effects of the artificial wall constraint? Can such
overlapping regions be put together using inputprefix?

Best regards,

On Wed, Jan 19, 2011 at 16:23, Jérôme Hénin <>wrote:

> On 19 January 2011 13:53, Ajasja Ljubetič <>
> wrote:
> > <write histogram or have a running average of a colvar not in abf>
> > I'm happy to report that having multiple histogram blocks in addition to
> > the ABF block works beautifully. At the same time it's also possible to
> run
> > the analysis.
> > One question regarding the runAveStride:
> > Is this the number of steps between two points inside the length window?
> so
> > if I have runAveStride 10 and runAveLength 100, then it will only average
> > ten points?
> > What I would really like is to output every 100th step the average for
> the
> > last 100 steps.
> This is not strictly speaking a running average, and not supported by
> the current code. Your best choice here is to save a colvar trajectory
> with sufficient time resolution.
> Cheers,
> Jerome

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