**From:** Giacomo Fiorin (*giacomo.fiorin_at_temple.edu*)

**Date:** Mon Aug 23 2010 - 11:00:43 CDT

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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.

Giacomo

---- ----

Dr. Giacomo Fiorin

ICMS - Institute for Computational Molecular Science - Temple University

1900 N 12 th Street, Philadelphia, PA 19122

giacomo.fiorin_at_temple.edu

---- ----

On Mon, Aug 23, 2010 at 9:13 AM, <chengh_at_ringo.chem.pitt.edu> 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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