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

[Qing Lv]

Thank you, Quyen. I will look into this paper.


Qing





At 2020-02-20 18:45:58, "Quyen V. Vu" <vuqv.phys at gmail.com> wrote:
>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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