Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu May 02 2019 - 12:10:41 CDT

So, I was just asked if it is possible to mix QM and MM with ABF. I know QMMM is possible with the string method and then using eABF. I am working on the tutorial for that. But this question was a bit different. Here is the example:

One of the windows has copper in the protein binding site. So, for that window, use QM. Then, in every other window along the protein reaction coordinate, treat the copper with MM parameters. Only do MM for the rest of the reaction coordinate. He was basically asking, can you tie in one window that is treated with QM, to all of the other windows treated with MM, and get a free energy profile? Or, as I move the copper along the reaction coordinate, do those windows need to be treated with QM so that all of the windows can be merged properly? He is worried that QMMM string method/eABF will take to long to get a free energy profile for our copper complexes in the protein. But, we can't completely trust any MM parameters that exist for copper...With MM ABF, I can get ~45 nanoseconds per day in each window. But with QM/MM, I can only get ~1.5-2 picoseconds per day with 4 GPUs using Terachem. Which is ~32x faster than ORCA without GPUs. But, how is it possible to get enough sampling for eABF in each window with QMMM?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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