Google-Accelerated Biomolecular Simulations

  • Kai J. Kohlhoff
Part of the Methods in Molecular Biology book series (MIMB, volume 2022)


Biomolecular simulations rely heavily on the availability of suitable compute infrastructure for data-driven tasks like modeling, sampling, and analysis. These resources are typically available on a per-lab and per-facility basis, or through dedicated national supercomputing centers. In recent years, cloud computing has emerged as an alternative by offering an abundance of on-demand, specialist-maintained resources that enable efficiency and increased turnaround through rapid scaling.

Scientific computations that take the shape of parallel workloads using large datasets are commonplace, making them ideal candidates for distributed computing in the cloud. Recent developments have greatly simplified the task for the experimenter to configure the cloud for use and job submission. This chapter will show how to use Google’s Cloud Platform for biomolecular simulations by example of the molecular dynamics package GROningen MAchine for Chemical Simulations (GROMACS). The instructions readily transfer to a large variety of other tasks, allowing the reader to use the cloud for their specific purposes.

Importantly, by using Docker containers, a popular light-weight virtualization solution, and cloud storage, key issues in scientific research are addressed: reproducibility of results, record keeping, and the possibility for other researchers to obtain copies and directly build upon previous work for further experimentation and hypothesis testing.

Key words

Cloud computing Large-scale simulation Distributed computing 



This work was performed on Google infrastructure. The author thanks Jojo Dijamco for many detailed discussions and careful review of the manuscript, and members of the Google Accelerated Science team for helpful feedback.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Kai J. Kohlhoff
    • 1
  1. 1.ResearchGoogleMountain ViewUSA

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