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

From: He, Amy via AMBER <amber.ambermd.org>
Date: Fri, 17 Feb 2023 17:36:39 +0000

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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Received on Fri Feb 17 2023 - 10:00:03 PST
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