[gmx-users] How to deal with unexpected reactions in umbrella sampling?

[Groenhof, Gerrit]

Hi,

There is not much information to go with, but I can give some general remarks.

Could this not suggest that either your reaction coordinate is not suited, driving the system into a region of very high potential energy, from where it can escape though the reaction you consider unreasonable. Before embarking on the QM/MM umbrella sampling, did you check whether the coordinate is suitable in isolation?

Alternatively, the QM description may fail to capture the electronic structure along your coordinate. Has your QM method been validated for the reaction you’re studying?

Best wishes & good luck with your simulations,

Gerrit
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> Dear Colleagues,
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> 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).
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> Thanks,
> Qing
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