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

[Quyen V. Vu]

Hi,
you can think about employed multi-dimensional umbrella sampling and used
3D-WHAM to derived the PMF as professor Pander did in this paper: Petrone,
P. M., Snow, C. D., Lucent, D., & Pande, V. S. (2008). Side-chain
recognition and gating in the ribosome exit tunnel. *Proceedings of the
National Academy of Sciences of the United States of America*, *105*(43),
16549–16554. https://doi.org/10.1073/pnas.0801795105

I don't know whether he delivered the code for 3D-WHAM or not

Best,

On Thu, Feb 20, 2020 at 2:58 AM Qing Lv <lvqingjiejie at 163.com> 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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