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

From: Carlos Simmerling via AMBER <>
Date: Fri, 17 Feb 2023 12:51:46 -0500

Are you saying that you want to not use shake on some of the water? The
coomon water models are intended to be rigid, so you would need a good
reason for this, and understand that the models may not perform well. Also
they are likely to diffuse and it would be hard to turn on/off dynamically
(unless they are very buried).

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 - 10:00:04 PST
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