HiTPoly

A platform for setting up high throughput polymer electrolyte MD simulations.

Installation

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.

Dependencies

The following main dependencies will be automatically installed:

• numpy
• pandas
• scipy
• PyTorch
• RDKit
• OpenMM
• matplotlib
• typing-extensions
• typed-argument-parser

Requirements

To run HiTPoly, you need to:

1. Download and install LigParGen locally on your machine following the tutorial here
2. Install Packmol on your workstation, LINK
3. Install OpenBabel on your workstation conda install openbabel -c openbabel

HiTPoly can run simulations and interface either with Gromacs or OpenMM.

Installation of MD Engines

Gromacs Installation

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

OpenMM Installation

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

Usage

Full tutorial coming soon.

License

This project is licensed under the MIT License.