**From:** Jérôme Hénin (*jhenin_at_ifr88.cnrs-mrs.fr*)

**Date:** Mon Aug 23 2010 - 10:51:53 CDT

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Hi Mary,

*> Does anybody knows the advantage to include this Jacobian term in the PMF
*

*> calculations using ABF?
*

The choice is mostly a matter of convention. Still, it is only useful

in the case of distance coordinates (in 2d or 3d), if one wants to

plot a "traditional" PMF corresponding to a normalized radial

distribution function. It might make sense if the coordinate is a

radius of gyration, but then it is not customary.

*> For calculating a 1D PMF along the z-direction, is there any necessary to
*

*> include this Jacobian term?
*

In that case, it makes no difference, as the Jacobian term for such a

coordinate is zero.

Best,

Jerome

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