Re: Regarding system forces in NAMD

From: Giacomo Fiorin (
Date: Thu Jan 07 2016 - 09:10:39 CST

Hi, a small addition about the comparison with the histogram. The Jacobian
force (which is very strong near zero for many distance-related variables
as Jérôme said) is only calculated explicitly for system forces, but is not
implemented for histograms.

You can either:
1) use the hideJacobian option of ABF (and you must use ABF with "applyBias
off" to calculate the system-force profile); or
2) add instead the Jacobian force to the derivative of the histogram, using
the formula for that specific colvar, as listed in the tables of our
reference paper.

Lastly, note that until full convergence is achieved, it is perfectly
normal to have different PMFs from the system force vs the histogram.


On Thu, Jan 7, 2016 at 9:37 AM, Jérôme Hénin <> wrote:

> Hi Sruthi,
> If you are looking at a radius of gyration, keep in mind that that
> coordinate experiences a strong Jacobian force especially at small values--001a113fe5b663becd0528bfe1d5--

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