Cloud-based molecular simulations for everyone
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. This repository is a supplementary material of the paper "Making it rain: Cloud-based molecular simulations for everyone" and we encourage you to read it before using this pipeline.
The main goal of this work is to demonstrate how to harness the power of cloud-computing to run microsecond-long MD simulations in a cheap and yet feasible fashion.
- AMBER
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Using AMBER to generate topology and to build the simulation box - CHARMM
Using inputs from CHARMM-GUI solution builder - AlphaFold2+MD
Using AlphaFold2_mmseqs2 to generate protein model + MD simulation using AMBER to generate topology and to build simulation box
- If you encounter any bugs, please report the issue to https://github.com/pablo-arantes/Making-it-rain/issues
- We would like to thank the OpenMM team for developing an excellent and open source engine.
- We would like to thank the AlphaFold team for developing an excellent model and open sourcing the software.
- Credit to Sergey Ovchinnikov (@sokrypton), Milot Mirdita (@milot_mirdita) and Martin Steinegger (@thesteinegger) for their fantastic ColabFold
- A Making it rain by Pablo R. Arantes (@pablitoarantes), Marcelo D. Polêto (@mdpoleto), Conrado Pedebos (@ConradoPedebos) and Rodrigo Ligabue-Braun (@ligabue_braun).
- Also, credit to David Koes for his awesome py3Dmol plugin.
Arantes P.R., Depólo Polêto M., Pedebos C., Ligabue-Braun R. Making it rain: cloud-based molecular simulations for everyone. ChemRxiv. doi: 10.33774/chemrxiv-2021-9f2m5 (2021).
