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

From: Qinghua Liao <>
Date: Sat, 21 Nov 2020 21:32:04 +0100

Hello David,

Thanks a lot for your reply! I followed what you suggested.
I turned off plumed by setting plumed = 0, but I saw the same kind
of twisting of molecule during the simulation.

What possible problem could lead to such unphysical twisting?
Any other suggestions? Thanks so much!

All the best,

On 11/19/20 5:00 PM, David A Case wrote:
> 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.
> ....dac
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Received on Sat Nov 21 2020 - 13:00:03 PST
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