From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Sat Aug 15 2009 - 15:55:35 CDT
Sorry for the delayed reply.
On Mon, Aug 10, 2009 at 1:33 PM, Hugh Martin<hughtendo_at_gmail.com> wrote:
> 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?
No, it should not occur. I would need more details to understand
what's happening. Incidentally, you seem to be using the NAMD 2.6
version of ABF, which is deprecated now. If you run into more
problems, you may consider switching to the new code. You will also
get better performance out of it.
> 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?
Yes, the ABF coordinate may always diffuse either way.
> Or will the ABF force
> be reapplied if the atom leaves the bin before sufficient sampling has
Sorry, you lost me there... If it moves to a bin where the sampling is
sufficient, then the bias will be applied.
> 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?
Yes, the force samples are measured at every step. This is a sensible
thing to do because the force fluctuations have a large, fast
oscillating component that averages out quickly if frequent samples
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