Large-Scale Molecular Dynamics Simulations of Cellular Compartments

Eric Wilson; John Vant; Jacob Layton; Ryan Boyd; Hyungro Lee; Matteo Turilli; Benjamín Hernández; Sean Wilkinson; Shantenu Jha; Chitrak Gupta; Daipayan Sarkar; Abhishek Singharoy

doi:10.1007/978-1-0716-1394-8_18

Large-Scale Molecular Dynamics Simulations of Cellular Compartments

Eric Wilson
, John Vant
, Jacob Layton
, Ryan Boyd
, Hyungro Lee
, Matteo Turilli
, Benjamín Hernández
, Sean Wilkinson
, Shantenu Jha
, Chitrak Gupta
, Daipayan Sarkar
, Abhishek Singharoy

Workflow and Ecosystem Services

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

6 Scopus citations

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.

Original language	English
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press Inc.
Pages	335-356
Number of pages	22
DOIs	https://doi.org/10.1007/978-1-0716-1394-8_18
State	Published - 2021

Publication series

Name	Methods in Molecular Biology
Volume	2302
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Funding

The authors acknowledge start-up funds from the School of Molecular Sciences and Center for Applied Structure Discovery at Arizona State University, and the resources of the OLCF at the Oak Ridge National Laboratory, which is supported by the Office of Science at DOE under Contract No. DEAC05-00OR22725, made available via the INCITE program. We also acknowledge NAMD and VMD developments supported by NIH (P41GM104601) and R01GM098243-02 for supporting our study of membrane proteins.

Keywords

Ensemble toolkit
High-performance computing
Molecular dynamics
Multiscale simulation
NAMD
Photosynthetic chromatophore
VMD

Access to Document

10.1007/978-1-0716-1394-8_18

Cite this

Wilson, E., Vant, J., Layton, J., Boyd, R., Lee, H., Turilli, M., Hernández, B., Wilkinson, S., Jha, S., Gupta, C., Sarkar, D., & Singharoy, A. (2021). Large-Scale Molecular Dynamics Simulations of Cellular Compartments. In Methods in Molecular Biology (pp. 335-356). (Methods in Molecular Biology; Vol. 2302). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-1394-8_18

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AU - Turilli, Matteo

AU - Hernández, Benjamín

AU - Wilkinson, Sean

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AU - Gupta, Chitrak

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Large-Scale Molecular Dynamics Simulations of Cellular Compartments

Abstract

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Keywords

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