I've run a series of simulations where, having found an opening, a metal and counter-ion is pulled from outside the Transferrin C-term binding pocket into where the metal binds to some residues, traversing about ~16A through a sort-of 'channel'. I've run these simulations for three metals (Fe, Eu and Cm) and varied the magnitude of the pulling force, with and without the counter-ion, etc.
There appears to be differences in the ease with which different metals traverse the channel. Eu and Cm are much bigger so, well, duh. Eu is a harder acid than Cm so you'd imagine there would be difference in binding to polar residues at the end of the trip but, in this case, I'm gathering that ionic radius is the bigger factor at play here.
What I'd like is to tie what I'm seeing to something measurable experimentally, ideally, but a meaningful quantity to make the metals comparable is the main goal. The channel is largely made up of apolar residues and you'd imagine the system would pass through a number of very similar microstates so I don't think a free energy calculation gets us there. I know CHARMM allows one to calculate a diffusion coefficient, which from what I can see is done via post-processing of the trajectory (true?). The latter would seem to most likely way forward.
For such a system, are other quantities CHARMM is able to calculate that might add something else? Doesn't have to be from post-processing, definitely not averse to setting up more simulations.