On Fri, Nov 28, 2014, Aixiao Li wrote:
> I am currently running QM/MM ncsu_abmd for free energy calculation. It
> is just a simple proton transfer from water to O atom (of GTP).
Have you done a simple umbrella sampling calculation to get a rough free
energy surface, and hence to have confidence that your QM/MM model is a
reasonable one, and that your chosen progress variable(s) indeed span the
reaction? These are items that generally should come before running ABMD
calculations. Your ABMD results (you never get to small values of the proton
transfer coordinate) might be the result of a poorly-chosen Hamiltonian:
proton-transfer events can be very hard things to study.
...good luck....dac
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Received on Fri Nov 28 2014 - 09:30:03 PST
