Dear Amber users,
Recently I came across a JCTC publication authored by Prof Jorgensen, which talks of creation of molecules rather than disappearing molecules in free energy calculations.
https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.9b00213
They use MC method and the paper claims that growing molecules in Absolute binding FE calculations is desirable as lesser lambda windows are needed for convergence as opposed to annihilation of molecules.
Has anyone in the mailing list used AMBER18 or AMBER20 for trying out this method?
I am understanding the theory of this process but finding it hard to execute it in AMBER.
Thanks everyone
Debarati
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Received on Thu Sep 03 2020 - 15:30:03 PDT
