Re: Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances...

From: Giacomo Fiorin (
Date: Thu Apr 16 2020 - 13:05:59 CDT

Hi Zeynab, one small correction. I just noticed that you are using
distanceXY, i.e. the distance in cylindrical rather than polar
coordinates. The Jacobian term of the PMF in that case would be just -kB T


On Thu, Apr 16, 2020 at 10:13 AM Giacomo Fiorin <>

> Hi Zeynab, this is possibly due to the Jacobian term of the PMF, which
> comes from the geometric definition of the variable. See e.g. the
> appendices of the Colvars paper:
> For a distance "r" there are increasingly more microscopic states as you
> go to a larger r, because every spherical shell between r and (r + dr)
> carries a number of angular states proportional to 4 pi r^2. The Jacobian
> term for a distance can be calculated to be -kBT ln(r^2), or -2 kBT ln(r)--0000000000001ca53605a36c4bb0--

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