Re: [AMBER-Developers] Desmond SUX

From: Michael R Shirts <Michael.Shirts.Colorado.EDU>
Date: Thu, 13 May 2021 20:39:15 +0000

> and they skipped calculating the Ewald Sum every other iteration (thanks Adrian!).

In their semi-defense, IIRC, their default on all DESMOND simulations for a while has been to do multiple timestepping of forces, including Ewald sum every other timestep. It's not entirely clear to me if this is sufficiently accurate, and they definitely should make that clearer that they are doing something different, but it's a valid approach (that more people should be investigating!) and it's not just a sales trick. Not that there aren't also sales tricks out there.

Michael Shirts
Associate Professor
Phone: (303) 735-7860
Office: JSCBB C123
Department of Chemical and Biological Engineering
University of Colorado Boulder

On 5/13/21, 1:27 PM, "Scott Le Grand" <> wrote:

    So, we're all getting our knickers in a bunch over an Apples to Oranges
    Desmond to AMBER performance comparison.

    Please don't...

    They cheated, because that's what they do to keep their investors happy.
    They used a 32^3 grid, and they skipped calculating the Ewald Sum every
    other iteration (thanks Adrian!). Rather than get upset here, point and
    laugh at DE Shaw et al. that they are afraid to go head to head with AMBER,
    and if they do (and they won't because they're chicken bawk bawk bawk), we
    have the people to address that as well.

    At our end, there's a ~50% or so performance deficit in AMBER 20 we need to
    fix. I've already fixed 2/3 of that building PMEMD 2.0 (770 ns/day DHFR 2
    fs already). Let them prance about with their greasy kids stuff desperate
    approximations and cheats, SPFP remains performance and accuracy with
    compromise and if they want to pick a fight with SPFP, make them do the
    work to demonstrate equivalent numerical stability (spoilers: they won't
    because they can't but oh the bellyacheing and handwaving they are willing
    to do, just watch).

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Received on Thu May 13 2021 - 14:00:03 PDT
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