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. 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 > > 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.
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., & 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 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.
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 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 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.
[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 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.
