**From:** Giacomo Fiorin (*giacomo.fiorin_at_gmail.com*)

**Date:** Thu Apr 16 2020 - 13:05:59 CDT

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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

ln(r).

Giacomo

On Thu, Apr 16, 2020 at 10:13 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>

wrote:

*> Hi Zeynab, this is possibly due to the Jacobian term of the PMF, which
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*> comes from the geometric definition of the variable. See e.g. the
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*> appendices of the Colvars paper:
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*> https://doi.org/10.1080/00268976.2013.813594
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*> For a distance "r" there are increasingly more microscopic states as you
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*> go to a larger r, because every spherical shell between r and (r + dr)
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*> carries a number of angular states proportional to 4 pi r^2. The Jacobian
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*> term for a distance can be calculated to be -kBT ln(r^2), or -2 kBT ln(r)--0000000000001ca53605a36c4bb0--
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