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

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.

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

Thank you, Quyen. I will look into this paper. Qing At 2020-02-20 18:45:58, "Quyen V. Vu" 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., &

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

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

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

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