Re: ABF calculations: Jacobian term describing geometry entropy

From: Jérôme Hénin (
Date: Mon Aug 23 2010 - 10:51:53 CDT

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.


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:26 CST