Re: Finer details of an ABF/colvar simulation

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Sun Nov 22 2009 - 13:37:32 CST

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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