Gaussian Mixture-Based Enhanced Sampling for Statics and Dynamics

The Journal of Physical Chemistry Letters
Jayashrita Debnath, Michele Parrinello

Abstract

We introduce an enhanced sampling method that is based on constructing a model probability density from which a bias potential is derived. The model relies on the fact that in a physical system most of the configurations visited can be grouped into isolated metastable islands. With each island we associate a distribution that is fitted to a Gaussian mixture. The different distributions are linearly combined together with coefficients that are computed self-consistently. This leads to an integrated procedure for discovering new metastable states, exploring reaction pathways, computing free energy differences, and estimating reaction rates.

References

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Sep 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Alessandro Laio, Michele Parrinello
Jun 23, 2005·Journal of the American Chemical Society·Davide BranduardiMichele Parrinello
Feb 20, 2008·The Journal of Chemical Physics·Yi Qin Gao
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Mar 17, 2009·The Journal of Physical Chemistry. B·Paul MaragakisMartin Karplus
Sep 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·Gareth A TribelloMichele Parrinello
Jan 31, 2014·Physical Review Letters·Pratyush Tiwary, Michele Parrinello
Jul 22, 2014·The Journal of Physical Chemistry. B·Pratyush Tiwary, Michele Parrinello
Sep 13, 2014·Physical Review Letters·Omar Valsson, Michele Parrinello
Sep 1, 2015·Physical Review Letters·James McCartyMichele Parrinello
Apr 8, 2014·Journal of Chemical Theory and Computation·Matteo SalvalaglioMichele Parrinello
Mar 2, 2016·Proceedings of the National Academy of Sciences of the United States of America·Pratyush Tiwary, B J Berne
Apr 7, 2017·Journal of Chemical Theory and Computation·Mohammad M Sultan, Vijay S Pande
Dec 3, 2017·The Journal of Chemical Physics·James McCarty, Michele Parrinello
May 8, 2018·The Journal of Physical Chemistry Letters·Dan MendelsMichele Parrinello
Aug 24, 2018·The Journal of Chemical Physics·João Marcelo Lamim RibeiroPratyush Tiwary
Sep 10, 2018·The Journal of Chemical Physics·Mohammad M Sultan, Vijay S Pande
Sep 18, 2018·Journal of Chemical Theory and Computation·GiovanniMaria PicciniMichele Parrinello
Oct 26, 2018·The Journal of Physical Chemistry Letters·Yi Isaac YangMichele Parrinello
Feb 20, 2019·Journal of Chemical Theory and Computation·Jayashrita DebnathMichele Parrinello
Mar 2, 2019·Journal of Chemical Theory and Computation·Michele Invernizzi, Michele Parrinello
Mar 20, 2020·The Journal of Physical Chemistry Letters·Michele Invernizzi, Michele Parrinello

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Citations

Jan 6, 2021·Nature Communications·Valerio RizziMichele Parrinello
Dec 24, 2020·The Journal of Chemical Physics·Shashank PantPratyush Tiwary
May 19, 2021·Journal of Chemical Theory and Computation·F GibertiM Ceriotti
Aug 23, 2021·The Journal of Chemical Physics·D Mandelli, M Parrinello
Sep 2, 2021·The Journal of Physical Chemistry Letters·Enrico Trizio, Michele Parrinello
Feb 5, 2022·The Journal of Physical Chemistry Letters·Umberto RaucciMichele Parrinello

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