Clarification regarding some finer details in ABF simulations

From: Hugh Martin (hughtendo_at_gmail.com)
Date: Mon Aug 10 2009 - 12:33:47 CDT

Hello,

I was hoping someone could clarify a few minor points regarding ABF
simulations, after reading related papers and the documentation in detail
there are a couple of minor points still unclear to me:

1. The user guide states that parameter forceConst is applied at xiMin and
xiMax (the borders of the reaction coordinate) and not in between them. My
simulations show that this force is acting within the xiMin and xiMax
boundaries (along the whole reaction coordinate), this is not supposed to
occur, correct?

2. When the ABF force is applied, the moving atom makes its way to the next
reaction coordinate bin via diffusion, it moves mainly due to diffusion
because at this point the net force acting on the atom is roughly zero when
considering both the free energy landscape and the applied ABF force. Once
the atom is in the next bin, the applied ABF force is 'switched' off, does
this imply that the moving atom could then diffuse out of the bin in either
direction before sufficient sampling has taken place? Or will the ABF force
be reapplied if the atom leaves the bin before sufficient sampling has
occured?

3. As for the 'sampling' itself (abf fullSamples), I am unclear how the
scripts determine the frequency at which a 'sample' is taken? I was
expecting this to be a controllable parameter, but it appears that this is
not the case. I presume that a snapshot measurement of the force acting
along the reaction coordinate is taken, and I'm currently assuming that
these snapshots are taken at regular time intervals, is this the case?

Many thanks,

Hugh

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