Re: [AMBER] molecule twisted in QM/MM simulation

From: David A Case <>
Date: Thu, 19 Nov 2020 11:00:25 -0500

On Thu, Nov 19, 2020, Qinghua Liao wrote:
>I used Amber/Orca/Plumed to do QM/MM metadynamics simulations to study
>a chemical reaction,
>but I found that the substrate, which was treated with QM method, was
>twisted unphysically, as attached.
>In the attached figure, the carboxylate and hydroxyl groups on the
>sugar ring are twisted, even the benzene ring are open.
>But none of the bond breaking is related to the chemical reaction.
>Similar problem was also observed when I used DFTB3 as QM method.

A simple test is whether you see the same thing without plumed, since
you state that the problem is unrelated to the chemical reaction.


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Received on Thu Nov 19 2020 - 08:30:02 PST
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