Published August 13, 2021
| Version v1.01
Software
Open
Making-it-rain
- 1. Department of Bioengineering, University of California, Riverside, CA 92521, United States
- 2. Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
- 3. 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
- 4. Department of Pharmacosciences, Federal University of Health Sciences of Proto ALegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil
Description
Making-it-rain
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.
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.
- Credit to Sergey Ovchinnikov (@sokrypton), Milot Mirdita (@milot_mirdita) and Martin Steinegger (@thesteinegger) for their fantastic ColabFold
- A 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.
Files
Making_it_Rain.pdf
Files
(36.2 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:3f8ea410a1a644548f9de6a9dbb030fe
|
7.5 MB | Preview Download |
|
md5:85fb661775a1591e11fd43484d22b548
|
28.7 MB | Preview Download |
Additional details
Related works
- Is supplement to
- https://github.com/pablo-arantes/Making-it-rain/tree/v1.01 (URL)