Dear Experts,
When doing alchemical free energy simulations, as I've read when starting state A completely overlaps final state B, this is the best scenario and simply using the phase space of A to directly sample B one can get a good free energy difference estimate (without need of intermediate states). But this is quite puzzling to me. To begin, I could not exactly think of a practical example of such a case. Would appreciate it if someone can provide a good example, where the phase space of A is much larger than B and completely overlapping B? Maybe that would alleviate my questions further down the line. Thanks so much.
Another parallel question would be that, it seems that when judging phase space overlap, people look at the potential energy distribution overlap. But that's also puzzling to me-what I imagine is that, 2 molecules can have hugely different potential energies, but sample overlapping phase space. Such example I could suppose, is A: a benzene ring with a long flexible carbon chain, and B: a simple benzene ring, both in water. Wouldn't A (alkylbenzene) cover all the phase space of B (benzene)? Or is this a wrong example of A being much larger than B in phase space and completely overlapping B. Thanks again.
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Received on Thu Oct 06 2022 - 22:00:03 PDT
