Cloud-based molecular simulations for everyone
+ 28Apr2023: We have updated all the notebooks to Python 3.10, everything is working fine
+ 01May2023: We have fixed the Amber, AlphaFol2+MD and Protei-Ligand notebooks.
+ 15Dec2023: We have corrected all the notebooks, and everything should be functioning properly now.
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.
Important: We've updated the notebooks to CondaColab. Now, all the dependencies will be installed faster than before (less than half of the previous time). You will see a CondaColab cell, just run and wait a few seconds, the session will restart and this is normal and expected. After that, you can continue running the cells like normal. Do not use the Run all
option. Run the condacolab
cell individually and wait for the kernel to restart. Only then, you can run all cells if you want. Thank you for your support.
Using AMBER to generate topology and to build the simulation box
Using inputs from CHARMM-GUI solution builder
Using AlphaFold2_mmseqs2 to generate protein model + MD simulation using AMBER to generate topology and to build simulation box
UPDATE (October 2021)
Using AMBER to generate topology and to build the simulation box and for the ligand using GAFF2 force field
Using inputs from AMBER suite of biomolecular simulation program
Using inputs from GROMACS biomolecular simulation package (AMBER, CHARMM and OPLS force fields are compatible)
UPDATE (March 2022)
Using a SMILES as input and outputs a mol2 file with RESP derived partial charges. Options for setting method (HF, B3LYP, ...), basis set (3-21G, 6-31G*) and singlepoint or geometry optimization are available
Using a SMILES as a input, geometry optimization with TorchANI and topology with AMBER (GAFF2 force field)
Using inputs from GLYCAM server
UPDATE (August 2022)
UPDATE (March 2024)
Using OpenFF to generate the topology and build the simulation box for protein-membrane systems with AMBER force fields.
Utilizing Vermouth, the Python library that powers Martinize2, to generate the topology and build the simulation box for protein systems using Martini force fields. Additionally, employing cg2at to predict all-atom trajectories from coarse-grained (CG) representations.
Performing mutations on protein/nucleic acid systems and utilizing AMBER to generate the topology and build the simulation box.
Tired to "just" run molecular simulations and want to try something new?
Gabriel Monteiro da Silva (@GMondaSilva) and I are thrilled to share a colab notebook for running the subsampled AlphaFold2 approach for predicting protein conformational ensembles. Check it out:
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.