Re: [AMBER] Constant pH MD + HMR

From: Jason Swails <>
Date: Sat, 3 Aug 2019 00:50:07 -0400

On Tue, Jul 9, 2019 at 7:41 AM Nikolay N. Kuzmich <>

> Hello Amber users,
> is it possible to employ hydrogen mass repartititioning scheme
> during the constant pH simulations?

It's certainly *possible* (the atomic masses are never used for anything
except integrating the classical equations of motion for standard MD). I
don't see any reason why it wouldn't "just work" out of the box (as there
have been studies that support the assertion that HMR does not
substantially affect the dynamical ensemble in many -- and possibly most --

We obviously don't model tunneling at all -- it's effect is accounted for
by the reference energy. Since you're not changing that reference energy,
there's no reason it should yield different protonation state ensembles.

That said, it couldn't hurt to do a quick experiment to verify that you get
the same result on a small-ish system with and without HMR.


Jason M. Swails
AMBER mailing list
Received on Fri Aug 02 2019 - 22:00:01 PDT
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