Re: Clarification regarding some finer details in ABF simulations

From: Hugh Martin (hughtendo_at_gmail.com)
Date: Tue Aug 18 2009 - 10:01:08 CDT

Thanks indeed, a small follow up question: Once the reaction coordinate is
sufficiently sampled (according to the parameter 'abf fullSamples'), and the
simulation is still running (due to a high 'numsteps' parameter), will the
system then attempt to evenly add further samples? From my simulations this
appears to be the case, but I wanted to be sure. This then appears to be a
trivial way of sampling the reaction coordinate further, rather than
drastically increasing the 'abf fullSamples' parameter, which the paper
"exploring the free-energy landscape of a short peptide using an average
force" indicates can be problematic, if I've understood correctly.

Many thanks,

Hugh

2009/8/15 Jerome Henin <jhenin_at_cmm.chem.upenn.edu>

> Hugh,
> Sorry for the delayed reply.
>
> On Mon, Aug 10, 2009 at 1:33 PM, Hugh Martin<hughtendo_at_gmail.com> wrote:
> > 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?
>
> 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
> > occured?
>
> 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
> are taken.
>
> Best,
> Jerome
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:20 CST