Thank you, Quyen. I will look into this paper.
Qing At 2020-02-20 18:45:58, "Quyen V. Vu" <vuqv.p...@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 <lvqingjie...@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 >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.