Re: [lammps-users] Jacobian terms in the COLVAR package

Hello Hadi, hideJacobian is generally off by default, and not implemented for use with writeTIPMF. It is only available as an option for ABF, but for historical reasons mostly. Here’s a relevant conversation that we had about it:

Because only ABF or other TI-based methods can actually compute the Jacobian term analytically, it makes more sense not to use it, because it would otherwise make comparisons between different methods extremely difficult. That also applies to extended-system ABF, which makes it even more confusing.

Calculating the Jacobian is a necessary step in the computation of total colvar forces, but hiding its contribution from the PMF is a matter of convention. Luckily, the only times when this may ever make sense is for distance- or distanceXY-based variables, when one wants to use the PMF between two particles to express the PMF between their species. Luckily, in those cases you have a simple expression to use (-2 kBT or -kBT respectively).