Re: PMF from ABF simulation not plateauing

From: Aron Broom (
Date: Thu May 08 2014 - 13:56:37 CDT

in what way does it not plateau with the restraints? That is, does it keep
rising, or does it start to fall? And is the non-plateau nonetheless a
straight smooth line?

I suspect the Jacobian may be the issue. If I had to make a guess, I could
see it being the case that it's applying the jacobian correction in your
constrained case, in the same way it would for a full 3D distance, but
obviously you don't have the same amount of "geometric entropy" in the
constrained case, so you'll over-correct and get a positive slope instead
of a plateau.

So, if the above is true, then either the jacobian is only meant to be used
for a full 3D distance, or, it has been implemented generally, but you've
circumvented that with your choice of colvar. What I mean is, based on
your description it sounds like you are still using a regular distance
colvar, but just constraining your x and y, is that true? I suspect if you
want NAMD to handle it correctly, you'd want to use a DistanceZ colvar
instead. Or, the much better plan, would be to leave the hideJacobian
option as the default "no", and apply the appropriate correction for the
situation yourself afterwards.

But maybe I'm way off.


On Thu, May 8, 2014 at 1:08 PM, Riley Workman <> wrote:

> Hello all,
> I am trying to generate a PMF using ABF and am having trouble getting
> the PMF to plateau. I have hideJacobian set on.
> I use the selectConstraints x and y commands to restrict two water
> molecules to the z-coordinate. I am trying to generate a dimerization of
> the two water molecules from a specific conformation, thus the constraints.
> I am performing the ABF on a distance colvar between the oxygens of the two
> waters.
> When I run such a simulation without the constraints, I get a lovely
> smooth water-water PMF that plateaus at around 3.5 kcal/mol. Keep in mind I
> am setting hideJacobian to on, so the PMF *should *plateau. I have read
> the NAMD information on ABF and am aware that constraints on atoms involved
> in the distance coordinate can disrupt the accuracy of the PMF. My thought
> was that since the x and y constraints are orthogonal to the distance
> colvar, that might not happen.
> Can anyone with expertise in ABF lend any insight on why this happens
> and how I might circumvent the problem? I realize that I could use umbrella
> sampling or some other method of measuring the PMF, but I have performed
> some other related calculations with ABF and would like to use it with this
> one as well, if possible.
> Thanks for any and all suggestions.
> Riley Workman

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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