https://github.com/cole-group/coding-retreat2022
Progress from the OpenMM-MACE hackathon
Science Score: 23.0%
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Low similarity (9.3%) to scientific vocabulary
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Repository
Progress from the OpenMM-MACE hackathon
Basic Info
- Host: GitHub
- Owner: cole-group
- License: mit
- Language: Python
- Default Branch: main
- Size: 2.25 MB
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- Stars: 1
- Watchers: 2
- Forks: 3
- Open Issues: 1
- Releases: 0
Created over 3 years ago
· Last pushed over 3 years ago
https://github.com/cole-group/coding-retreat2022/blob/main/
# MACE-OpenMM Hackathon This repo contains work from the MACE-OpenMM hackathon hosted by the cole-group at the University of Newcastle 2022. This work builds upon the framework laid out by the Chodera lab in the [qmlify](https://github.com/choderalab/qmlify) package and accompanying [paper](https://www.biorxiv.org/content/10.1101/2020.07.29.227959v1). ## AIMS - :white_check_mark: Build an [openmm-ml](https://github.com/openmm/openmm-ml) interface for the [MACE](https://github.com/ACEsuit/mace). The interface can be found [here](https://github.com/davkovacs/mace/blob/4bf84df28cb87a6a9ef6d024bb5d0a3d0aabb7ba/mace/calculators/openmm.py#L161). - :white_check_mark: Run hybrid MM/ML simulations of ligands in [complex](https://twitter.com/ColeGroupNCL/status/1587449592949481474/photo/1) and solvent. - :white_check_mark: Develop a [general interface](https://github.com/jharrymoore/mace/blob/openmm-harry/mace/tools/mixed_system.py) built on OpenMM tools to calculate MM/ML free energy corrections starting from the output of MM relative binding calculations. - :white_check_mark: Implement a [QCEngine interface](scripts/mace_qcengine.py) to MACE allowing for single point calculations, geometry optimisations and torsiondrives. An example [notebook](examples/mace_qcengine.ipynb) using the interface to perform a geometry optimisation is also included.  A conda [environment](env.yaml) file is also supplied which was used to run the hybrid MM/ML simulations. This should be used to create the fresh environment using `conda env create -f env.yaml` this following packages should then be manually installed - openmm-ml - mace - openmmtools (Dominic's version) # Authors - Kovcs Dvid Pter - Finlay Clark - Harry Moore - Mateusz Bieniek - Josh Horton - Daniel Cole # Acknowledgements - Dominic Rufa - John Chodera
Owner
- Name: cole-group
- Login: cole-group
- Kind: organization
- Website: https://blogs.ncl.ac.uk/danielcole/
- Repositories: 3
- Profile: https://github.com/cole-group