Re: [AMBER] Method (SHAKE/SETTLE, HMR) to conditionally constrain waters

From: Brian Radak via AMBER <>
Date: Fri, 17 Feb 2023 16:02:03 -0500

You might be able to escape SETTLE by renaming water residues. Sander/pmemd
are not actually that smart and just find water by being told that the
residue name is "WAT" (by default). If you have some other name you'll just
get regular SHAKE I think, or nothing at all with the right choice of

As Carlos said, the "floppy water" parameters are pretty much arbitrary and
not guaranteed to have any particularly nice properties other than to look
nice after minimization.


On Fri, Feb 17, 2023, 12:37 PM He, Amy via AMBER <> wrote:

> Dear Amber Community,
> I’m using sander in Amber20 for MD simulations. I just have a very very
> quick question about options to constrain explicit waters:
> With ntc = 2, SHAKE is applied to solutes and SETTLE for waters. Using
> option “no_shake” along with ntf = 1, we can conditionally SHAKE (or
> unshake) part of the system. So..
> Is there possibly a way to conditionally unshake, or repartition the mass
> of the waters in a distance-specified region?
> If I do a “conditional” SHAKE, am I essentially modifying the potential
> energy function of my system? Is the error (difference with respect to
> choices of unshaken atoms) estimatable?
> Bests,
> Amy
> --
> Amy He
> Chemistry Graduate Teaching Assistant
> Hadad Research Group
> Ohio State University
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Received on Fri Feb 17 2023 - 13:30:03 PST
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