mdsim is a codebase for training and running molecular dynamics simulation with machine learning force fields. This implementation was tested under Ubuntu 18.04, Python 3.9, PyTorch 1.11, and CUDA 11.3. Detailed versions of other packages are listed in the installiation guide. If you have any question, feel free to open an issue or reach out to xiangfu AT mit.edu.
if you find this code useful, please consider reference in your paper:
@article{
fu2023forces,
title={Forces are not Enough: Benchmark and Critical Evaluation for Machine Learning Force Fields with Molecular Simulations},
author={Xiang Fu and Zhenghao Wu and Wujie Wang and Tian Xie and Sinan Keten and Rafael Gomez-Bombarelli and Tommi S. Jaakkola},
journal={Transactions on Machine Learning Research},
issn={2835-8856},
year={2023},
url={https://openreview.net/forum?id=A8pqQipwkt},
note={Survey Certification}
}
deepmd-kit is required for training and simulating MD with DeepPot-SE (or other models from DeePMD-kit). We recommend installing it with conda while creating a conda environment (use Bash):
conda create -n mdsim python=3.9.11 deepmd-kit=2.1.0=*gpu libdeepmd=2.1.0=*gpu lammps cudatoolkit=11.3 horovod -c https://conda.deepmodeling.com -c defaults
Alternatively, install a conda environment without deepmd-kit:
conda create -n mdsim python=3.9.11
After installing the conda environment, activate by running:
conda activate mdsim
Then install other dependicies by running:
pip install --user lmdb==1.1.1
pip install --user numba==0.55.1
pip install --user numpy==1.21.2
pip install --user PyYAML==6.0
pip install --user ray==2.0.0
pip install --user rdkit==2022.3.5
pip install --user scikit_learn==1.1.2
pip install --user scipy==1.7.3
pip install --user setuptools==61.3.1
pip install --user submitit==1.4.5
pip install --user sympy==1.7.1
pip install --user tqdm==4.63.1
pip install --user wandb==0.12.17
pip install torch==1.11.0+cu113 torchvision==0.12.0+cu113 torchaudio==0.11.0 --extra-index-url https://download.pytorch.org/whl/cu113
pip install --user torch-scatter torch-sparse torch-cluster torch-spline-conv -f https://data.pyg.org/whl/torch-1.11.0+cu113.html
pip install --user pyg-nightly==2.0.5.dev20220418
pip install --user git+https://gitlab.com/ase/ase.git@master
pip install --user nequip==0.5.4
Then install mdsim as a package:
pip install -e ./
We use PLUMED for the MetaDynamics enhanced sampling of alanine dipeptide. We recommend installing it using conda:
conda install -c conda-forge py-plumed plumed
You may need to install libatlas-base-dev first:
sudo apt-get install libatlas-base-dev
PLUMED also needs ase nightly. If you have previously installed ase, update it to the latest version:
pip install --upgrade git+https://gitlab.com/ase/ase.git@master
Download all preprocessed data at Zenodo:
The default path is ./DATAPATH. Training should be immediately runnable if all preprocessed datasets are downloaded from Zenodo and the directory is properly renamed. Alternatively, the scripts for downloading and preprocessing each individual dataset are in preprocessing/. Specify data_path for the location of the saved source files, and specify db_path for the proprocessed files (Lmdb files for SchNet, DimeNet, etc. or npz files for NequIP). For example, download the MD17 aspirin dataset to DATAPATH and save processed files to DBPATH by running:
python preprocessing/md17.py --molecule aspirin --data_path DATAPATH --db_path DBPATH
Download the water dataset to DATAPATH and save processed files to DBPATH:
python preprocessing/water.py --data_path DATAPATH --db_path DBPATH
All datasets have unit eV for energy and ev/$\AA$ for forces. The mean and standard deviation of energy/forces are stored in metadata.npy.
All training configs are stored in configs/ except for DeepPot-SE. There are four datasets: ala, lips, md17, water. The implementations of SchNet, DimeNet, ForceNet, and GemNet are adapted from OCP are included in this repo. The training of NequIP directly calls the installed nequip package. Other models from OCP can be easily adapted to work with this repo.
We recommend logging with wandb and it is used by default. You need to have a wandb account and log in with wandb init. More details at https://wandb.ai/. You can use a different logger by changing logger in the base.yml config files.
Training is mostly through main.py. The training configs are included in configs/. You will need to modify dataset.src in base.yml for each dataset to the path where the processed data is saved. Run main.py to train a model while specifying the config. For example, train a SchNet on MD17 Aspirin with:
python main.py --mode train --config-yml configs/md17/schnet.yml --molecule aspirin
Or train a GemNet-T on water-1k with:
python main.py --mode train --config-yml configs/water/gemnet-T.yml --size 1k
main.py can also be used for training an NequIP model, with the --nequip flag. This is done by calling the built-in command of nequip. For example, train NequIP on MD17 Aspirin with:
python main.py --mode train --config-yml configs/md17/nequip/aspirin.yml --nequip
Or train a NequIP model on water-1k with:
python main.py --mode train --config-yml configs/water/nequip/nequip_1k.yml --nequip
Training DeepPot-SE models is done by calling the built-in command of deepmd-kit. All training configs for DeepPot-SE are stored in deeppot_se/. You need to modify the training.training_data.systems and training.validation_data.systems to the paths of the datasets. For training, go to the corresponding directory (e.g., deeppot_se/water1k for water-1k) and run:
dp train input.json
Configs for simulating MD are stored in configs/simulate/. For example, simulate a model with OCP implementation trained on the water dataset by running:
python simulate.py --config_yml configs/simulate/water.yml --model_dir MODELPATH
MODELPATH is the directory containing the training files/logs. We include an example trained model in this repo. If you have downloaded the data and renamed it to DATAPATH in the project home directory, You can try evaluation and simulating MD by running:
python simulate.py --config_yml configs/simulate/water.yml --model_dir example_model/water_1k_schnet
The --nequip flag and a nequip data config are needed for simulating with NequIP. The data configs are stored in configs/simulate/nequip_data_cfg. For example, simulate a NequIP model for water by running:
python simulate.py --config_yml configs/simulate/water.yml --model_dir MODELPATH --nequip
The --deepmd flag is needed for simulating with DeepPot-SE. For example, simulate a DeepPot-SE model for water by running:
python simulate.py --config_yml configs/simulate/water.yml --model_dir MODELPATH --deepmd
Use the argument --init_idx to select a specific initial configuration. This is useful for simulating alanine dipeptide.
Some example simulations from trained models are in example_sim/. observable.ipynb offers a guide on computing the observables reported in the paper.
Install the IPython kernel to use Jupyter notebook:
conda install ipykernel
python -m ipykernel install --user --name mdsim --display-name "mdsim"
nglview can be used to visualize MD simulations. We recommend installing it with conda:
pip install --user nglview
This codebase is built off the Open Catalyst Project codebase. A significant amount of code is borrowed from mdgrad and NeuralForceField. The MD simulation capabilities are built with ASE. The ML models are built with PyG. Simulation/training of NequIP and DeepMD-kit are built upon the original codebases.
