Re: [AMBER] Unexpected reaction occurred in QM/MM umbrella sampling

From: Goetz, Andreas <>
Date: Thu, 20 Feb 2020 02:41:06 +0000

Dear Qing,

If you observe what you describe as an unreasonable reaction, then most likely your biasing potential is not suitable. You may have to find a different reaction coordinate. Since your question is rather generic I am afraid it is not possible to give more specific advice.

All the best,

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

> On Feb 19, 2020, at 5:56 PM, Qing Lv <> wrote:
> Dear Colleagues,
> I am doing an umbrella sampling of an enzymatic reaction using QM/MM. However, as the reaction coordinate exceeds a certain value, an unexpected reaction, which is obviously unreasonable, often occurs during the umbrella sampling. So, how to deal with such problem? The only method I can think is to impose additional restraints to avoid this reaction, but the additional restraints will probably affect the umbrella sampling (although the additional restraints are not related to the reaction coordinate).
> Thanks,
> Qing
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Received on Wed Feb 19 2020 - 19:00:02 PST
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