A platform for setting up high throughput polymer electrolyte MD simulations.
You can install HiTPoly directly from the source code:
# Clone the repository
git clone https://github.com/learningmatter-mit/HiTPoly.git
cd HiTPoly
# Install in editable mode
pip install -e .All required dependencies (including numpy, pandas, scipy, torch, rdkit, openmm, etc.) will be automatically installed.
The following main dependencies will be automatically installed:
- numpy
- pandas
- scipy
- PyTorch
- RDKit
- OpenMM
- matplotlib
- typing-extensions
- typed-argument-parser
To run HiTPoly, you need to:
- Download and install LigParGen locally on your machine following the tutorial here
- Install Packmol on your workstation, LINK
- Install OpenBabel on your workstation
conda install openbabel -c openbabel
HiTPoly can run simulations and interface either with Gromacs or OpenMM.
Gromacs can be installed via package managers or built from source. For optimal performance, we recommend building from source as described on the Gromacs website
Currently the simulation engine is programmed to be using CUDA. To install OpenMM with cuda run either:
conda install -c conda-forge openmm cuda-version=12
or
pip install openmm[cuda12]
To use HiTPoly with cpu compiled CUDA, platform name has to be adjusted in hitpoly/simulations/openmm_scripts.py
Full tutorial coming soon.
If you want to embedd your SMILES as descriped in the paper (PCA on long representation from MolFormer), run the script generate_embedding.py for your trianing and testing data and save it in a folder named batch0 which is a subfolder of where you want to save your batches. With the ht_script.sh script you can run the high throughput BO loop. This pipeline works based on a folder on your local machine that saves the files for each batch. You also need some method/file that keeps track of how many simulations have suceeded for that batch. We suggest a csv file that has the results from all previous simulations which also includes the polymers for which the simulations did not suceed with Nan values for the properties. The example code is written for a csv file that has the columns smiles and property. Further pointers are given in the ht_script.sh script.
Please cite:
This project is licensed under the MIT License.