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 <amber.ambermd.org> 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
> he.1768.osu.edu<mailto:he.1768.osu.edu>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Feb 17 2023 - 10:00:04 PST
