From: Hugh Martin (hughtendo_at_gmail.com)
Date: Mon Aug 31 2009 - 07:52:40 CDT
In case others experience this issue, it was indeed resolved by using the
implementation in NAMD2.7b1, using distancez colvar parameters.
Also just to note/contribute, in the current ABF tutorial files, I believe
the methane hydration example should read 'ref' and 'main' instead of
'group1' and 'group2' in the Transport-window1.in file.
Many thanks for all the help,
2009/8/5 Hugh Martin <hughtendo_at_gmail.com>
> Hi again,
> When I ran the simulation with a reduced force constant, the moving atom
> proceeded to translocate to the centre of xiMin and xiMax at a much slower
> rate, so it is indeed this parameter which is causing this. I find this
> confusing, as my understanding is that the force constant should only be
> active at the walls of xiMin and xiMax and not inbetween (according to the
> user guide and tutorial). So is it the NAMD2.6 PBC implementation that is
> causing the force constant to be applied where it shouldn't? I attempted to
> use NAMD2.7b1 and found that a similar phenomenon was occuring.
> Also, having read the following papers:
> *Calculating free energies using average force*<http://dx.doi.org/10.1063/1.1410978>,
> Eric Darve and Andrew Pohorille
> *Overcoming free energy barriers using unconstrained molecular dynamics
> simulations* <http://dx.doi.org/10.1063/1.1773132>, Jérôme Hénin and
> Christophe Chipot
> *Exploring the free-energy landscape of a short peptide using an average
> force* <http://dx.doi.org/10.1063/1.2138694>, Christophe Chipot and Jérôme
> I feel that I have a solid understanding of the theory behind ABF, however,
> I'm unsure of a couple of points: When the ABF force is applied, the moving
> atom is "allowed" to make its way to the next reaction coordinate bin via
> diffusion, 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 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
> As for the 'sampling' itself (abf fullSamples), I am unclear how the
> scripts determine the frequency that 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?
> Any clarification would be hugely appreciated,
> Many thanks in advance,
> 2009/7/6 Jerome Henin <jhenin_at_cmm.chem.upenn.edu>
> Hi Hugh,
>> You could be running into a problem with the way the abf code form
>> NAMD 2.6 handles PBC - that is, it mostly doesn't. One thing you can
>> look at is the role of the boundary potentials ("walls") on your
>> problem. Try setting forceConst to zero and see if the problem still
>> occurs. That's all I can say based on the info you provided.
>> Note that this code is currently being phased out, and replaced with
>> the version of ABF implemented in NAMD 2.7b1's module called
>> collective variable-based calculations:
>> On Mon, Jul 6, 2009 at 11:39 AM, Hugh Martin<hughtendo_at_gmail.com> 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
>> > system to work in the way that I was expecting. I have tested the
>> > 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
>> > 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
>> > parameters, the abf2 atom simply moves very quickly from xiMin to the
>> > 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--001517402a4287dc1304726f83be--
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