[AMBER-Developers] Desmond SUX

From: Scott Le Grand <varelse2005.gmail.com>
Date: Thu, 13 May 2021 12:26:48 -0700

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 - 12:30:02 PDT
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