Re: Question

From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu May 02 2019 - 13:59:15 CDT

Hi Kelly,

I recall seeing something like this (using umbrella sampling) proposed in
JCTC several years back - definitely not a standard kind of calculation.
There are intrinsic difficulties in "stitching together" QM and MM results
since the difference in zero of energy is often hard to define (and depends
on the method). Maybe the fact that ABF relies on force helps?

In short, you can probably run the simulations just fine but you might be
all alone in trying to figure out how to analyze the results.

HTH,
BKR

On Thu, May 2, 2019 at 1:12 PM McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> 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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