Literature DB >> 30024761

Machine-Learned Coarse-Grained Models.

Karteek K Bejagam1, Samrendra Singh2, Yaxin An1, Sanket A Deshmukh1.   

Abstract

Optimizing force-field (FF) parameters to perform molecular dynamics (MD) simulations is a challenging and time-consuming process. We present a novel FF optimization framework that integrates MD simulations with particle swarm optimization (PSO) algorithm and artificial neural network (ANN). This new ANN-assisted PSO framework was used to develop transferable coarse-grained (CG) models for D2O and DMF as a proof of concept. The PSO algorithm was used to generate the set of input FF parameters for the MD simulations of the CG models of these solvents, which were optimized to reproduce their experimental properties. Herein, for the first time, a reverse approach was employed for on-the-fly training of the ANN model, where results (solvent properties) obtained from the MD simulations and their corresponding FF parameters were used as inputs and outputs, respectively. The ANN model was then required to predict a set of new FF parameters, which were tested for their ability to predict the desired experimental properties. This new framework can be extended to integrate any optimization algorithm with ANN and MD simulations to accelerate the FF development.

Entities:  

Year:  2018        PMID: 30024761     DOI: 10.1021/acs.jpclett.8b01416

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


  4 in total

1.  Effectiveness of coarse graining degree and speedup on the dynamic properties of homopolymer.

Authors:  Lijuan Liao; Changyu Meng; Chenguang Huang
Journal:  J Mol Model       Date:  2021-01-28       Impact factor: 1.810

Review 2.  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

Review 3.  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

4.  Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures.

Authors:  Vy T Duong; Elizabeth M Diessner; Gianmarc Grazioli; Rachel W Martin; Carter T Butts
Journal:  Biomolecules       Date:  2021-11-30
  4 in total

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