Re: Finer details of an ABF/colvar simulation

From: Hugh Martin (hughtendo_at_gmail.com)
Date: Tue Nov 24 2009 - 10:07:46 CST

Thanks very much, all clear now.

Hugh

2009/11/22 Jerome Henin <jhenin_at_cmm.chem.upenn.edu>

> Hi Hugh,
> Your assumptions are correct. Basically, force samples are accrued at
> all times, whether or not the ABF bias is applied, but they do not
> include the contribution of the bias itself.
> Best,
> Jerome
>
> 2009/11/20 Hugh Martin <hughtendo_at_gmail.com>:
> > Hello,
> >
> > I was wondering if someone could clear up a small question I have about
> the
> > way an ABF/colvar simulation runs.
> >
> > In the case of a single atom being taken along a z-axis coordinate by the
> > adaptive biasing force, the force is not applied to the atom within a
> > particular bin until the fullSamples threshold has been reached. At this
> > point, the atom may translocate to the next bin via diffusion, but while
> the
> > atom is still in the previous bin (i.e. while it's still making its way
> > over), are force samples still being accrued? I presume it must do so, as
> > the sampling is always at least somewhat varied along a trajectory. And
> so
> > if force samples ARE being taken while atom remains in the bin where now
> the
> > force is being applied, then presumably the force measurement is
> corrected
> > corresponding to the applied force within that bin? I've tried studying
> the
> > ABF perl scripts to answer this question myself, but it still remains
> > unclear.
> >
> > Many thanks,
> >
> > Hugh
> >
>

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