QM/MM proton transfer CV sampling

tarak karmakar tarak... at gmail.com
Fri Dec 18 04:32:11 UTC 2015

Dear All,
Kind of a query related to a CV (distance difference between donor and
acceptor) that samples protonation of an intermediate that gets generated
during the enzymatic reaction (QM/MM metadynamics simulations).

Once, the proton has been transferred from a proton donor (residue) to the
reaction intermediate two things are happening,
i) The residue moves away from its position (away from the reaction site).
ii) Once the intermediate gets the proton, it (the product) is moving
towards the other direction.

To report a converged free energy profile for this process I need to have
at least a couple of barrier recrossing.

Now, my questions are,
i) Could anyone report a free energy profile once the trajectory just comes
out of state A and enters state B?
ii) Can I keep constraints on the movement of the product and the proton
donor residue to facilitates resampling the states?

I appreciate any suggestions on this topic.

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