Large-Scale Molecular Dynamics Simulations of Cellular Compartments

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2021 Apr 20

PMID 33877636

Citations 2

Authors

Eric Wilson

John Vant

Jacob Layton

Ryan Boyd

Hyungro Lee

Matteo Turilli

Benjamin Hernandez

Sean Wilkinson

Shantenu Jha

Chitrak Gupta

Daipayan Sarkar

Abhishek Singharoy

Affiliations

Soon will be listed here.

Abstract

Molecular dynamics or MD simulation is gradually maturing into a tool for constructing in vivo models of living cells in atomistic details. The feasibility of such models is bolstered by integrating the simulations with data from microscopic, tomographic and spectroscopic experiments on exascale supercomputers, facilitated by the use of deep learning technologies. Over time, MD simulation has evolved from tens of thousands of atoms to over 100 million atoms comprising an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium. In this chapter, we present a step-by-step outline for preparing, executing and analyzing such large-scale MD simulations of biological systems that are essential to life processes. All scripts are provided via GitHub.

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