From: Hugh Martin (hughtendo_at_gmail.com)
Date: Fri Nov 20 2009 - 09:10:08 CST
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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