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Review
. 2022 Jul 12;18(7):4047-4069.
doi: 10.1021/acs.jctc.1c01214. Epub 2022 Jun 16.

Accelerators for Classical Molecular Dynamics Simulations of Biomolecules

Derek Jones  1   2 , Jonathan E Allen  2 , Yue Yang  3 , William F Drew Bennett  3 , Maya Gokhale  4 , Niema Moshiri  1 , Tajana S Rosing  1
Affiliations
Review

Accelerators for Classical Molecular Dynamics Simulations of Biomolecules

Derek Jones et al. J Chem Theory Comput. .

Abstract

Atomistic Molecular Dynamics (MD) simulations provide researchers the ability to model biomolecular structures such as proteins and their interactions with drug-like small molecules with greater spatiotemporal resolution than is otherwise possible using experimental methods. MD simulations are notoriously expensive computational endeavors that have traditionally required massive investment in specialized hardware to access biologically relevant spatiotemporal scales. Our goal is to summarize the fundamental algorithms that are employed in the literature to then highlight the challenges that have affected accelerator implementations in practice. We consider three broad categories of accelerators: Graphics Processing Units (GPUs), Field-Programmable Gate Arrays (FPGAs), and Application Specific Integrated Circuits (ASICs). These categories are comparatively studied to facilitate discussion of their relative trade-offs and to gain context for the current state of the art. We conclude by providing insights into the potential of emerging hardware platforms and algorithms for MD.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

Figure 1
Figure 1
Representative time scales for protein motions.,−
Figure 2
Figure 2
Lennard-Jones potential as a function of interatomic distance for a diatomic system.
Figure 3
Figure 3
Description of an NVIDIA GPU architecture.
Figure 4
Figure 4
Description of an NVIDIA GPU Streaming Multiprocessor (SM) unit..
Figure 5
Figure 5
GPU price to performance comparison for Amber MD software for versions 2016 and 2018. The data are collected from the Amber Web site.
Figure 6
Figure 6
Description of an FPGA architecture.
See this image and copyright information in PMC

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