Literature DB >> 32510225

Gaussian Mixture-Based Enhanced Sampling for Statics and Dynamics.

Jayashrita Debnath1,2, Michele Parrinello1,2,3.   

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.

Year:  2020        PMID: 32510225     DOI: 10.1021/acs.jpclett.0c01125

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  9 in total

1.  Deep learning the slow modes for rare events sampling.

Authors:  Luigi Bonati; GiovanniMaria Piccini; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2021-11-02       Impact factor: 11.205

2.  Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials.

Authors:  Benjamin Pampel; Omar Valsson
Journal:  J Chem Theory Comput       Date:  2022-06-28       Impact factor: 6.578

Review 3.  Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective.

Authors:  Katya Ahmad; Andrea Rizzi; Riccardo Capelli; Davide Mandelli; Wenping Lyu; Paolo Carloni
Journal:  Front Mol Biosci       Date:  2022-06-08

4.  Confronting pitfalls of AI-augmented molecular dynamics using statistical physics.

Authors:  Shashank Pant; Zachary Smith; Yihang Wang; Emad Tajkhorshid; Pratyush Tiwary
Journal:  J Chem Phys       Date:  2020-12-21       Impact factor: 3.488

5.  The role of water in host-guest interaction.

Authors:  Valerio Rizzi; Luigi Bonati; Narjes Ansari; Michele Parrinello
Journal:  Nat Commun       Date:  2021-01-04       Impact factor: 14.919

6.  Free Energy Surfaces and Barriers for Vacancy Diffusion on Al(100), Al(110), Al(111) Reconstructed Surfaces.

Authors:  Junais Habeeb Mokkath; Mufasila Mumthaz Muhammed; Ali J Chamkha
Journal:  Nanomaterials (Basel)       Date:  2021-12-28       Impact factor: 5.076

7.  Water regulates the residence time of Benzamidine in Trypsin.

Authors:  Narjes Ansari; Valerio Rizzi; Michele Parrinello
Journal:  Nat Commun       Date:  2022-09-16       Impact factor: 17.694

8.  Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems.

Authors:  John A Keith; Valentin Vassilev-Galindo; Bingqing Cheng; Stefan Chmiela; Michael Gastegger; Klaus-Robert Müller; Alexandre Tkatchenko
Journal:  Chem Rev       Date:  2021-07-07       Impact factor: 60.622

Review 9.  Collective variable-based enhanced sampling and machine learning.

Authors:  Ming Chen
Journal:  Eur Phys J B       Date:  2021-10-20       Impact factor: 1.500

  9 in total

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