diff --git a/README.md b/README.md index 7b40bd1..3321e5d 100644 --- a/README.md +++ b/README.md @@ -19,19 +19,25 @@ A Python package for running hybrid machine learning/molecular mechanics (ML/MM) ## Installation -First, create a conda environment with all of the required dependencies: +First, create a Conda environment with all required dependencies: ```bash conda env create -f environment.yaml conda activate fes-ml ``` -Finally, install `fes-ml` in interactive mode within the activated environment: +Next, install `fes-ml` in editable mode within the activated environment: ```bash pip install -e . ``` +For GPU functionality, you must have the appropriate CUDA drivers installed on your host system. On HPC login nodes without GPU drivers, set the `CONDA_OVERRIDE_CUDA` environment variable to the desired CUDA version before creating the Conda environment. For example: + +```bash +CONDA_OVERRIDE_CUDA=12.6 conda env create -f environment.yaml +``` + ## Alchemical Modifications The following alchemical transformations are supported in fes-ml: diff --git a/environment.yaml b/environment.yaml index 668af44..1a14ad7 100644 --- a/environment.yaml +++ b/environment.yaml @@ -1,30 +1,31 @@ -name: fes-ml-aev +name: fes-ml channels: - conda-forge - - openbiosim/label/emle + - openbiosim dependencies: - ambertools - compilers - - cudatoolkit=11.8 - eigen - loguru - - openmm>=8.1 + - openmm>=8.5 - openmm-torch - - openmm-ml + - openmm-ml>=1.7 - openmmforcefields - openff-toolkit - openff-interchange - nnpops - pip - pybind11 - - pytorch=*=*cuda* + - pytorch - python - pyyaml - sire - torchani - pygit2 + - setuptools<82.0 + - pymbar - pip: - git+https://github.com/chemle/emle-engine.git - coloredlogs