I'm not a QM expert myself (Gerrit, comments?), but I'm pretty sure the
main reason is that you cannot either mutate atom types or decouple
interactions gradually in the QM part of the system. Once this is solved
for a pure QM system it should be straightforward to implement the QM/MM
interface of it.
One of the main things we plan to do with the free energy code (once I can
confirm I'm doing things right) is to modify the charge of the quantum
system for the lambda values, so atom types don't need to be modified for
this I believe, although I see how that could complicate other types of free
energy calculations. As for decoupling interactions I don't know what
impact that has for changing of charge.
For now, are there any major complications if all we want to do is modify
the charge from state A to state B (assuming the interaction problems you
mentioned aren't a problem)
fiske
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