Machine-Learned Coarse-Grained Models

The Journal of Physical Chemistry Letters
Karteek K BejagamSanket A Deshmukh

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.

References

May 18, 2000·Journal of Pharmaceutical and Biomedical Analysis·S Agatonovic-Kustrin, R Beresford
May 16, 2007·Physical Review Letters·Jörg Behler, Michele Parrinello
May 21, 2010·Physical Review Letters·Albert P BartókGábor Csányi
Jun 16, 2010·PLoS Computational Biology·Semen O YesylevskyySiewert J Marrink
Dec 20, 2011·Journal of Chemical Theory and Computation·James H McAliley, David A Bruce
Oct 1, 2013·Scientific Reports·Ghanshyam PilaniaRamamurthy Ramprasad
Jan 23, 2014·The Journal of Physical Chemistry. B·Shaorui YangJianmin Qu
Mar 26, 2014·The Journal of Physical Chemistry. B·Andrew W Long, Andrew L Ferguson
Nov 22, 2014·Journal of Computational Chemistry·Robin M Betz, Ross C Walker
Feb 5, 2015·The Journal of Physical Chemistry. a·Maxim V IvanovQadir K Timerghazin
Sep 5, 2015·Soft Matter·Andrew W LongAndrew L Ferguson
Aug 13, 2013·Journal of Chemical Theory and Computation·Katja HansenKlaus-Robert Müller
Nov 9, 2016·The Journal of Chemical Physics·Jörg Behler
May 17, 2017·Science Advances·Stefan ChmielaKlaus-Robert Müller
Aug 12, 2017·Journal of Chemical Theory and Computation·Ying LiBenoît Roux
Jan 21, 2013·Materials·Srikant Srinivasan, Krishna Rajan
Aug 19, 2017·Scientific Reports·Ivan KruglovArtem R Oganov
Oct 28, 2017·Physical Review Letters·Elia SchneiderMark E Tuckerman
Jan 23, 2018·The Journal of Physical Chemistry. B·Karteek K BejagamSanket A Deshmukh
Feb 9, 2018·Scientific Reports·Pascal FriederichWolfgang Wenzel

❮ Previous
Next ❯

Citations

Jul 16, 2020·Chemical Communications : Chem Comm·Yaxin An, Sanket A Deshmukh
Aug 3, 2019·The Journal of Chemical Physics·Feliks NüskeCecilia Clementi
Jan 30, 2021·Journal of Molecular Modeling·Lijuan LiaoChenguang Huang
Mar 2, 2019·The Journal of Physical Chemistry Letters·Alireza Moradzadeh, Narayana R Aluru
Jan 10, 2019·Chemical Reviews·Siewert J MarrinkMark S P Sansom
Jun 1, 2019·The Journal of Physical Chemistry. a·Samrendra K SinghSanket A Deshmukh
Oct 30, 2018·The Journal of Physical Chemistry Letters·Karteek K BejagamSanket A Deshmukh
Jan 5, 2019·The Journal of Physical Chemistry. B·Yaxin AnSanket A Deshmukh
May 30, 2019·ACS Central Science·Jiang WangCecilia Clementi

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.