Literature DB >> 30037247

DeePCG: Constructing coarse-grained models via deep neural networks.

Linfeng Zhang1, Jiequn Han1, Han Wang2, Roberto Car3, Weinan E4.   

Abstract

We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called the Deep Coarse-Grained Potential (abbreviated DeePCG), exploits a carefully crafted neural network to construct a many-body coarse-grained potential. The network is trained with full atomistic data in a way that preserves the natural symmetries of the system. The resulting model is very accurate and can be used to sample the configurations of the coarse-grained variables in a much faster way than with the original atomistic model. As an application, we consider liquid water and use the oxygen coordinates as the coarse-grained variables, starting from a full atomistic simulation of this system at the ab initio molecular dynamics level. We find that the two-body, three-body, and higher-order oxygen correlation functions produced by the coarse-grained and full atomistic models agree very well with each other, illustrating the effectiveness of the DeePCG model on a rather challenging task.

Entities:  

Year:  2018        PMID: 30037247     DOI: 10.1063/1.5027645

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  15 in total

Review 1.  Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems.

Authors:  Paraskevi Gkeka; Gabriel Stoltz; Amir Barati Farimani; Zineb Belkacemi; Michele Ceriotti; John D Chodera; Aaron R Dinner; Andrew L Ferguson; Jean-Bernard Maillet; Hervé Minoux; Christine Peter; Fabio Pietrucci; Ana Silveira; Alexandre Tkatchenko; Zofia Trstanova; Rafal Wiewiora; Tony Lelièvre
Journal:  J Chem Theory Comput       Date:  2020-07-16       Impact factor: 6.006

2.  Computational methods and theory for ion channel research.

Authors:  C Guardiani; F Cecconi; L Chiodo; G Cottone; P Malgaretti; L Maragliano; M L Barabash; G Camisasca; M Ceccarelli; B Corry; R Roth; A Giacomello; B Roux
Journal:  Adv Phys X       Date:  2022

Review 3.  Protein Function Analysis through Machine Learning.

Authors:  Chris Avery; John Patterson; Tyler Grear; Theodore Frater; Donald J Jacobs
Journal:  Biomolecules       Date:  2022-09-06

Review 4.  Bottom-up Coarse-Graining: Principles and Perspectives.

Authors:  Jaehyeok Jin; Alexander J Pak; Aleksander E P Durumeric; Timothy D Loose; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2022-09-07       Impact factor: 6.578

Review 5.  Bottom-Up Coarse-Grained Modeling of DNA.

Authors:  Tiedong Sun; Vishal Minhas; Nikolay Korolev; Alexander Mirzoev; Alexander P Lyubartsev; Lars Nordenskiöld
Journal:  Front Mol Biosci       Date:  2021-03-17

Review 6.  Computational Modeling of Realistic Cell Membranes.

Authors:  Siewert J Marrink; Valentina Corradi; Paulo C T Souza; Helgi I Ingólfsson; D Peter Tieleman; Mark S P Sansom
Journal:  Chem Rev       Date:  2019-01-09       Impact factor: 72.087

7.  A deep learning approach to the structural analysis of proteins.

Authors:  Marco Giulini; Raffaello Potestio
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

Review 8.  Molecular Modeling Investigations of Sorption and Diffusion of Small Molecules in Glassy Polymers.

Authors:  Niki Vergadou; Doros N Theodorou
Journal:  Membranes (Basel)       Date:  2019-08-08

9.  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

10.  Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids.

Authors:  Christoph Scherer; René Scheid; Denis Andrienko; Tristan Bereau
Journal:  J Chem Theory Comput       Date:  2020-04-24       Impact factor: 6.006

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