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

From: Goetz, Andreas <>
Date: Sat, 21 Nov 2020 20:49:42 +0000

> On Nov 21, 2020, at 3:32 PM, Qinghua Liao <> wrote:
> 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?

What you observe could be due to a bad starting structure or a system that was not minimized / equilibrated, thus resulting in unphysically large forces that break the molecule.

How did you prepare the system before switching to QM/MM?
How does your starting structure look like?

All the best,

Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771

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Received on Sat Nov 21 2020 - 13:00:03 PST
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