[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?


Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
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Received on Fri Feb 17 2023 - 10:00:03 PST
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