Re: Translocation problem while attempting to use ABF

From: Eric H. Lee (
Date: Mon Jul 06 2009 - 11:34:11 CDT

Two thoughts here:

1) The rapid movement of your polynucleotide away from its initial
position does suggest either that the system was setup incorrectly, or
you had failed to equilibrate the system long enough before starting
the ABF run.

2) In ABF simulations, what happens frequently is that the system may
get "stuck" along a poorly chosen reaction coordinate where the
movement you are sampling is coupled to slowly diffusing degrees of
freedom. Sometimes this is unavoidable without prior data to guide
the choice of a reaction coordinate (in your case, it looks like you
are choosing a straight line, which might already be the best choice)
- at that point all you can do is continue sampling to overcome that

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC

On Jul 6, 2009, at 10:39 AM, Hugh Martin wrote:

> Hello,
> I am attempting to use ABF to induce the translocation of a 20-base
> polynucleotide through a protein pore and am having some trouble
> getting the system to work in the way that I was expecting. I have
> tested the tutorial files with success but have not been able to
> apply the technique to my system.
> I realise that it is difficult for others to comment on using ABF in
> an unfamiliar system, so listed below is what I believe to be the
> key information for consideration:
> The alpha carbons of the protein pore are constrained to maintain
> their positions.
> One set of alpha carbons belonging to a protein pore residue is used
> as "abf1" for the reference point to "abf2"s translocation. Given
> that abf1's position is constrained (see above point), I presume
> that is will allow consistent translocation of abf2.
> The atom I wish to translocate is the leading atom of the
> polynucleotide (thus pulling the whole molecule with it).
> The precise z-axis separation of abf1 and abf2 begins as
> -34.4900016784 Angstroms.
> I wish to translocate the polynucleotide molecule from -34.5 to
> -42.5 separation.
> The problem is that no matter what alterations I seem to make to the
> input parameters, the abf2 atom simply moves very quickly from xiMin
> to the middle of xiMin and xiMax, and remains within roughly +/- 0.3
> Angstroms of the precise middle of those two values for the
> remainder of the simulation. If I have understood ABF correctly, I
> believe that the ABF scripts should sample the system while the abf2
> atom resides within each dxi bin starting from xiMin and ending with
> xiMax, and once each dxi bin has been sampled "abf fullSamples"
> number of times, the adaptive biasing force will allow abf2 to
> overcome energy barriers in order to move to the next dxi bin,
> though the movement is also dependent on the abf2 atom's self
> diffusion properties.
> The fact that it so quickly moves to the middle of xiMin and xiMax
> shows that I have either set up the simulation incorrectly, that I
> have misunderstood what is supposed to occur during the simulation,
> or that my system is not compatible with the ABF technique. Any
> clues as to which of these three may be the case would be greatly
> appreciated.
> Listed below is an example of my ABF input parameters in the conf
> file, though I have also run test simulations with altered
> parameters, in particular "abf xiMin", "abf xiMax", "abf dxi", "abf
> fullSamples", and "numsteps" in order to try and resolve the issue:
> source ../abf-1.8/abf.tcl
> abf coordinate zCoord-1atom
> # abf1 atoms are the CA atoms of protein resid 8, abf2 is the
> pulling atom
> abf abf1 {122863 95173 99788 104403 109018 113633 118248}
> abf abf2 262093
> # precise xiMin is -34.4900016784
> abf xiMin -34.5
> abf xiMax -42.5
> abf dxi 0.4
> abf fullSamples 100
> abf dSmooth 0.1
> abf forceConst 10.0
> abf writeXiFreq 200
> abf outFile abf_window1.abf
> numsteps 600000
> Many thanks,
> Hugh

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