Literature DB >> 31416918

Neural networks-based variationally enhanced sampling.

Luigi Bonati1,2,3, Yue-Yu Zhang2,4, Michele Parrinello5,3,4,6.   

Abstract

Sampling complex free-energy surfaces is one of the main challenges of modern atomistic simulation methods. The presence of kinetic bottlenecks in such surfaces often renders a direct approach useless. A popular strategy is to identify a small number of key collective variables and to introduce a bias potential that is able to favor their fluctuations in order to accelerate sampling. Here, we propose to use machine-learning techniques in conjunction with the recent variationally enhanced sampling method [O. Valsson, M. Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] in order to determine such potential. This is achieved by expressing the bias as a neural network. The parameters are determined in a variational learning scheme aimed at minimizing an appropriate functional. This required the development of a more efficient minimization technique. The expressivity of neural networks allows representing rapidly varying free-energy surfaces, removes boundary effects artifacts, and allows several collective variables to be handled.

Keywords:  deep learning; enhanced sampling; molecular dynamics

Year:  2019        PMID: 31416918      PMCID: PMC6731643          DOI: 10.1073/pnas.1907975116

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  34 in total

1.  Escaping free-energy minima.

Authors:  Alessandro Laio; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2002-09-23       Impact factor: 11.205

2.  Gaussian approximation potentials: the accuracy of quantum mechanics, without the electrons.

Authors:  Albert P Bartók; Mike C Payne; Risi Kondor; Gábor Csányi
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3.  Variationally Optimized Free-Energy Flooding for Rate Calculation.

Authors:  James McCarty; Omar Valsson; Pratyush Tiwary; Michele Parrinello
Journal:  Phys Rev Lett       Date:  2015-08-10       Impact factor: 9.161

4.  Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics.

Authors:  Jim Pfaendtner; Massimiliano Bonomi
Journal:  J Chem Theory Comput       Date:  2015-10-09       Impact factor: 6.006

5.  GROMACS: fast, flexible, and free.

Authors:  David Van Der Spoel; Erik Lindahl; Berk Hess; Gerrit Groenhof; Alan E Mark; Herman J C Berendsen
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

6.  Canonical sampling through velocity rescaling.

Authors:  Giovanni Bussi; Davide Donadio; Michele Parrinello
Journal:  J Chem Phys       Date:  2007-01-07       Impact factor: 3.488

7.  Comparison of multiple Amber force fields and development of improved protein backbone parameters.

Authors:  Viktor Hornak; Robert Abel; Asim Okur; Bentley Strockbine; Adrian Roitberg; Carlos Simmerling
Journal:  Proteins       Date:  2006-11-15

8.  Generalized neural-network representation of high-dimensional potential-energy surfaces.

Authors:  Jörg Behler; Michele Parrinello
Journal:  Phys Rev Lett       Date:  2007-04-02       Impact factor: 9.161

9.  Well-tempered metadynamics: a smoothly converging and tunable free-energy method.

Authors:  Alessandro Barducci; Giovanni Bussi; Michele Parrinello
Journal:  Phys Rev Lett       Date:  2008-01-18       Impact factor: 9.161

10.  Variational approach to enhanced sampling and free energy calculations.

Authors:  Omar Valsson; Michele Parrinello
Journal:  Phys Rev Lett       Date:  2014-08-27       Impact factor: 9.161

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  13 in total

1.  Variational embedding of protein folding simulations using Gaussian mixture variational autoencoders.

Authors:  Mahdi Ghorbani; Samarjeet Prasad; Jeffery B Klauda; Bernard R Brooks
Journal:  J Chem Phys       Date:  2021-11-21       Impact factor: 3.488

2.  Biomolecular modeling thrives in the age of technology.

Authors:  Tamar Schlick; Stephanie Portillo-Ledesma
Journal:  Nat Comput Sci       Date:  2021-05-20

3.  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

4.  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

5.  AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics.

Authors:  Lorenzo Casalino; Abigail Dommer; Zied Gaieb; Emilia P Barros; Terra Sztain; Surl-Hee Ahn; Anda Trifan; Alexander Brace; Anthony Bogetti; Heng Ma; Hyungro Lee; Matteo Turilli; Syma Khalid; Lillian Chong; Carlos Simmerling; David J Hardy; Julio D C Maia; James C Phillips; Thorsten Kurth; Abraham Stern; Lei Huang; John McCalpin; Mahidhar Tatineni; Tom Gibbs; John E Stone; Shantenu Jha; Arvind Ramanathan; Rommie E Amaro
Journal:  bioRxiv       Date:  2020-11-20

6.  Exact Topology of the Dynamic Probability Surface of an Activated Process by Persistent Homology.

Authors:  Farid Manuchehrfar; Huiyu Li; Wei Tian; Ao Ma; Jie Liang
Journal:  J Phys Chem B       Date:  2021-05-03       Impact factor: 2.991

7.  Unsupervised Learning Methods for Molecular Simulation Data.

Authors:  Aldo Glielmo; Brooke E Husic; Alex Rodriguez; Cecilia Clementi; Frank Noé; Alessandro Laio
Journal:  Chem Rev       Date:  2021-05-04       Impact factor: 60.622

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

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Journal:  Chem Rev       Date:  2021-07-07       Impact factor: 60.622

Review 9.  Synergistic Approach of Ultrafast Spectroscopy and Molecular Simulations in the Characterization of Intramolecular Charge Transfer in Push-Pull Molecules.

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Journal:  Molecules       Date:  2020-01-20       Impact factor: 4.411

Review 10.  Computational methods for exploring protein conformations.

Authors:  Jane R Allison
Journal:  Biochem Soc Trans       Date:  2020-08-28       Impact factor: 5.407

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