Hi,
When I read the colvar package manual, I do not find the manual so clear about the Jacobian terms in the potential of mean force (PMF) calculations. I am wondering if all methods have the Jacobian terms included in the PMF calculations as expected (see below).
In particular, in the context of harmonic restraints, if one calculates the PMFs using writeTIPMF does it include the Jacobian terms such as -2 kBT ln (r) for distances?
Unlike other methods, I noticed in the context of abf, the hideJacobain is available.
Thanks,
Hadi