Recipes

Quick start templates for real run folders

The README contains repeatable run-folder templates. The website version separates them into workstation, MPI/HPC, and analysis-only patterns.

Template A: local workstation

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mkdir -p RUNS/my_system
cd RUNS/my_system

cp ../../1_AutomateGromacs.py ../../2_AutomateGromacs.py ../../3A_AutomateGromacs.py ../../4PDF4MD.py .
cp -R ../../MDPs .
cp -R ../../charmm36.ff ../../charmm36_ljpme-jul2022.ff .
cp ../../my_input_structure.pdb .

conda activate cgenff
python 1_AutomateGromacs.py --pdb my_input_structure.pdb --ligand LIG

conda activate mdanalysis
python 2_AutomateGromacs.py --mode ligand --ligand LIG --ns 0.25 --compute auto
python 3A_AutomateGromacs.py --mode ligand --ligand LIG --headless
python 4PDF4MD.py

Template B: MPI or HPC folder

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mkdir -p RUNS/my_hpc_system
cd RUNS/my_hpc_system

cp ../../1_AutomateGromacs_MPI.py ../../2_AutomateGromacs_MPI.py ../../3A_AutomateGromacs_MPI.py .
cp -R ../../MDPs ../../charmm36.ff ../../charmm36_ljpme-jul2022.ff .
cp ../../my_input_structure.pdb .

conda activate cgenff
python 1_AutomateGromacs_MPI.py --pdb my_input_structure.pdb --ligand LIG --gmx-bin gmx_mpi

conda activate mdanalysis
python 2_AutomateGromacs_MPI.py --mode ligand --ligand LIG --gmx-bin gmx_mpi --ns 0.25
python 3A_AutomateGromacs_MPI.py --mode ligand --ligand LIG --headless

Template C: analysis-only

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conda activate mdanalysis
python 3A_AutomateGromacs.py --mode ligand --ligand LIG --headless
python 3B_NETWORX.py --ligand LIG
python 4PDF4MD.py