Is there a way that I can view analyses of the quality of Desmond FEP calculations?

Yes. Multisim automatically produces an HTML document that graphically summarizes key quality features from a FEP calculation (both absolute and relative). These features can be used to troubleshoot FEP calculations or develop confidence that the sampling might be adequate. The document and supporting images are available in the last .tgz file for the FEP run, which you should extract to view the HTML document. The analysis includes energy distributions for the perturbations as well as the forward, backward, and running estimates for the dG values for the run as a whole and broken down by adjacent lamdba windows. The running estomates are not included if the calculation was too short to provide a meaningful plot (as is the case for the default 0.6 ns run time used in relative free energy calculations).

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