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deepdrivewe

Implementation of WESTPA using Colmena.

Installation

To install the package, run the following command:

git clone [email protected]:braceal/deepdrivewe.git
cd deepdrivewe
pip install -e .

Full installation including dependencies:

git clone [email protected]:braceal/deepdrivewe.git
cd deepdrivewe
conda create -n deepdrivewe python=3.10 -y
conda install omnia::ambertools -y
conda install conda-forge::openmm==7.7 -y
pip install -e .

To use deep learning models, install the correct version of PyTorch for your system and drivers. To use mdlearn, you may need an earlier version of PyTorch:

pip install torch==1.12

Installation on VISTA

To install the package on VISTA, run the following commands:

ml gcc/14.2.0 cuda/12.5 hdf5

conda create -n deepdrivewe python=3.12 -y
conda activate deepdrivewe
conda install conda-forge::openmm -y
pip install torch --index-url https://download.pytorch.org/whl/cu124

git clone [email protected]:braceal/deepdrivewe.git
cd deepdrivewe
pip install -U pip setuptools wheel
pip install -e .

To run an example on VISTA, update the absolute paths in the submit script and the YAML config file, and then run the following command:

sbatch examples/openmm_ntl9_ddwe_vista/submit.sh

Usage

To run the example, run the following command:

python -m deepdrivewe.examples.amber_hk.main --config examples/amber_nacl_hk/config.yaml

To kill all the workers, run the following command:

ps -e | grep -E 'sander|python|process_worker|parsl' | awk '{print $1}' | xargs kill

To check if any errors occurred in simulations or inference:

cat runs/naive_resampler_test_v2/result/inference.json | grep '"success": false'
cat runs/naive_resampler_test_v2/result/simulation.json | grep '"success": false'

To check the number of iterations completed:

h5ls -d runs/naive_resampler_test_v2/west.h5/iterations

Running with SynD

To use the SynD simulation engine, install the following dependencies:

pip install git+https://github.com/jeremyleung521/SynD.git@rng-fix

To generate the basis state .npy files from a .txt file, run the following command:

python -m deepdrivewe.simulation.synd --basis-states examples/synd_ntl9/bstates.txt --output-dir examples/synd_ntl9/bstates

To run the example, run the following command:

nohup python -m deepdrivewe.examples.synd_ntl9.main --config examples/synd_ntl9/config.yaml &> nohup.log &

Running with OpenMM

To run the example, run the following command:

OPENMM_CPU_THREADS=1 nohup python -m deepdrivewe.examples.openmm_ntl9_hk.main --config examples/openmm_ntl9_hk/config.yaml &> nohup.log &

Note that we set OPENMM_CPU_THREADS=1 to restrict each OpenMM simulation to a single thread. This is necessary to prevent the simulations from using all available CPU resources. You can also run the simulations on a GPU by adjusting the Parsl configuration.

Contributing

For development, it is recommended to use a virtual environment. The following commands will create a virtual environment, install the package in editable mode, and install the pre-commit hooks.

python -m venv venv
source venv/bin/activate
pip install -U pip setuptools wheel
pip install -e '.[dev,docs]'
pre-commit install

To test the code, run the following command:

pre-commit run --all-files
tox -e py310