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Item | Notes |
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Planning |
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Generic workflow | Step 1: Get a linux computer
# (if starting from docker) docker pull continuumio/miniconda docker run -it continuumio/miniconda # Inside the docker container groupadd -r app useradd -r -g app -d /home/app -s /bin/bash -c "Docker image user" app mkdir /home/app chown app /home/app su app cd wget "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" bash Miniconda3-latest-Linux-x86_64.sh -b -p miniconda3 . miniconda3/etc/profile.d/conda.sh conda activate base Step 2: Install the softwareOption A: Make a development build from master conda install -y anaconda-client -n base conda env create openforcefield/openff-benchmark-optimization conda activate openff-benchmark-optimization conda remove --force openff-benchmark git clone https://github.com/openforcefield/openff-benchmark.git cd openff-benchmark pip install -e . Option B: Make a production/stable build conda install -y anaconda-client -n base conda env create openforcefield/openff-benchmark-optimization conda activate openff-benchmark-optimization Option C: Using a single file installer # If using docker, either wget the installer, or move it in using docker cp bash openff-benchmark-2021.01.21.2-py37-Linux-x86_64.sh -b -p miniconda3 . miniconda3/etc/profile.d/conda.sh conda activate Step 3: Get some moleculesOption A: Make one from SMILES # To make a simple single-conf molecule from SMILES
python
from openforcefield.topology import Molecule
mol = Molecule.from_smiles('COCOCOCOCO')
mol.generate_conformers()
mol.to_file('input.sdf', file_format='sdf')
Step 4: Run the workflow# preprocess openff-benchmark preprocess validate -g BBB input.sdf openff-benchmark preprocess generate-conformers 1-validate_and_assign/ openff-benchmark preprocess coverage-report 2-generate_conformers openff_unconstrained-1.3.0.offxml # optimize ## qm calculations openff-benchmark optimize execute --season "1:1" -o 3-export-compute-qm 2-generate_conformers/ ## mm calculations openff-benchmark optimize execute --season "1:2" -o 3-export-compute-mm 3-export-compute-qm/b3lyp-d3bj/dzvp/ # analysis openff-benchmark report compare-forcefields --input-path 3-export-compute-mm/ --input-path 3-export-compute-qm/b3lyp-d3bj/dzvp/ --ref-method b3lyp-d3bj # plots openff-benchmark report plots --input-path 4-compare_conformers --ref-method b3lyp-d3bj |
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