Re: ABF calculations: Jacobian term describing geometry entropy

From: Giacomo Fiorin (
Date: Mon Aug 23 2010 - 11:00:43 CDT

Hi Mary, that correction is only relevant when the density of states
strongly varies with the value of the variable. For instance, when you use
the isotropic distance, the density of states is proportional to the square
of the distance itself (that would be the surface of a sphere, where the
radius is the distance).

When you use the z-coordinate, the density of states is constant along it.
Hence, the Jacobian term in the derivatives is zero, and the hideJacobian
option doesn't change the results by any extent.


---- ----
  Dr. Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
---- ----

On Mon, Aug 23, 2010 at 9:13 AM, <> wrote:

> Hi all,
> "HideJacobian no" is a default implementation in the ABF calcultions.
> Does anybody knows the advantage to include this Jacobian term in the PMF
> calculations using ABF?
> For calculating a 1D PMF along the z-direction, is there any necessary to
> include this Jacobian term?
> Many thanks,
> Mary
> Department of chemistry
> University of Pittsburgh
> Pittsburgh, PA 15260

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