Making-it-rain

Cloud-based molecular simulations for everyone

Hello there!

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.

1. AMBER - Using AMBER to generate topology and to build the simulation box
2. CHARMM - Using inputs from CHARMM-GUI solution builder
3. AlphaFold2+MD - Using AlphaFold2_mmseqs2 to generate protein model + MD simulation using AMBER to generate topology and to build simulation box

UPDATE (Oct 18 2021)

4. Protein-Ligand simulations - Using AMBER to generate topology and to build the simulation box and for the ligand using GAFF2 or OpenFF force fields
5. Using AMBER Inputs - Using inputs from AMBER suite of biomolecular simulation program
6. Using GROMACS Inputs - Using inputs from GROMACS biomolecular simulation package (AMBER, CHARMM and OPLS force fields are compatible)

Bugs

• If you encounter any bugs, please report the issue to https://github.com/pablo-arantes/Making-it-rain/issues

Acknowledgments

• 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.
• We would like to thank the ChemosimLab (@ChemosimLab) team for their incredible ProLIF (Protein-Ligand Interaction Fingerprints) tool.
• 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.
• Finally, we would like to thank Professor Giulia Palermo for her support and thoughtful comments in the development of the present work.

Do you want to cite this work?

Arantes P.R., Depólo Polêto M., Pedebos C., Ligabue-Braun R. Making it rain: cloud-based molecular simulations for everyone. Journal of Chemical Information and Modeling 2021. DOI: 10.1021/acs.jcim.1c00998.