Making it rain: cloud-based molecular simulations for everyone

Pablo Ricardo Arantes; Marcelo Depólo Polêto; Conrado Pedebos; Rodrigo  Ligabue-Braun

doi:10.26434/chemrxiv-2021-9f2m5

Theoretical and Computational Chemistry

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Making it rain: cloud-based molecular simulations for everyone

Working Paper

Pablo Ricardo Arantes Department of Bioengineering, University of California, Riverside, CA 92521, United States ,
Marcelo Depólo Polêto Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States ,
Conrado Pedebos School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, United Kingdom Present Address: Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom ,
Rodrigo Ligabue-Braun Department of Pharmacosciences, Federal University of Health Sciences of Proto ALegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil

Abstract

We present a user-friendly front-end for running molecular dynamics (MD) simulations using OpenMM toolkit on the Google Colab framework. Our goals are: 1) to highlight the usage of a cloud-computing scheme for educational purposes for a hands-on approach when learning MD simulations and 2) to exemplify how low-income research groups can perform MD simulations in the microsecond timescale. We hope this work facilitates teaching and learning of molecular simulation throughout the community.

Content

Supplementary weblinks

Making-it-rain - GitHub

https://github.com/pablo-arantes/Making-it-rain

This is a repository where you can find a Jupyter notebook scripts for running Molecular Dynamics (MD) simulations using OpenMM engine and AMBER and CHARMM force fields files on Google Colab.