Creating a Workflow with Production MD

Here, we’ll look at a basic example of a custom workflow which uses pmemd.cuda to run some production MD. In reality, you would want to add some extra steps before or afterwards:

"""Run production Molecular Dynamics using PMEMD.CUDA through BioSimSpace."""

from pathlib import Path

from maize.core.workflow import Workflow
from maize.steps.exs.biosimspace import ProductionPmemdCuda
from maize.steps.io import LoadData, Return
from maize.utilities.execution import JobResourceConfig

# Build the graph
flow = Workflow(name="Prod_BSS_AMBER_Test", cleanup_temp=False, level="debug")

# Add the nodes
load_sys = flow.add(LoadData[list[Path]])
prod_pmemd = flow.add(
    ProductionPmemdCuda,
    name="Production_Amber",
    parameters={
        "runtime": 1.0, # ns
    },
)
retu = flow.add(Return[list[Path]])

# Set parameters
load_sys.data.set(
    [
        Path(
            "< path to complex.prm7>" # CHANGEME
        ),
        Path(
            "< path to complex.rst7>" # CHANGEME
        ),
    ]
)

# Connect the nodes
flow.connect(load_sys.out, prod_pmemd.inp)
flow.connect(prod_pmemd.out, retu.inp)

# Check and run!
flow.check()
flow.visualize()
flow.execute()

mols = retu.get()

# Load a BioSimSpace system from the returned paths
import BioSimSpace as BSS

sys = BSS.IO.readMolecules([str(mols[0]), str(mols[1])])
print(40 * "#")
print(sys)
# In reality, you would do something here...