Running workflows

Safeguards for first-time users

The installation guide provides a detailed explanation of the safeguards that are in place to prevent accidental data upload to NOMAD. Please make sure to read it before running Martignac for the first time. This assumes you've also made it through the Quick start.

Here's a list of workflows currently implemented in Martignac:

Workflow	Description	Class name
Solute generation	generate a solute in the gas phase	martignac.workflows.solute_generation
Solvent generation	generate a solvent: homogeneous liquid in a box	martignac.workflows.solvent_generation
Solute-in-solvent generation	generate a solute in a box of homogeneous liquid	martignac.workflows.solute_in_solvent_generation
Solute-in-solvent alchemical	alchemical transformation of a solute in a solvent	martignac.workflows.solute_in_solvent_alchemical
Bilayer generation	generate a bilayer	martignac.workflows.bilayer_generation
Solute-in-bilayer umbrella	umbrella sampling of a solute in a bilayer	martignac.workflows.solute_in_bilayer_umbrella

and a corresponding set of example init.py files to get started with screening each workflow:

Solute generation

specify the solute chemistry

import signac

from martignac.workflows.solute_generation import SoluteGenFlow

project = signac.init_project(path=SoluteGenFlow.workspace_path)

for solute_name in ["C4", "P6 C3, 0-1", "P6 C3 N1, 0_1 1_2 0-2"]:
    sp = {"type": "solute", "solute_name": solute_name}
    job = project.open_job(sp).init()

Solvent generation

specify the solvent chemistry

import signac

from martignac.workflows.solvent_generation import SolventGenFlow

project = signac.init_project(path=SolventGenFlow.workspace_path)

for solvent_name in ["HD"]:
    sp = {"type": "solvent", "solvent_name": solvent_name}
    job = project.open_job(sp).init()

Solute-in-solvent generation

specify the solute and solvent chemistry

import itertools
import signac

from martignac.workflows.solute_in_solvent_generation import SoluteInSolventGenFlow

project = signac.init_project(path=SoluteInSolventGenFlow.workspace_path)

solvent_names = ["HD"]
solute_names = ["P6"]

pairs = list(itertools.product(solute_names, solvent_names))

for solute_name, solvent_name in pairs:
    sp = {"type": "solute_solvation", "solvent_name": solvent_name, "solute_name": solute_name}
    job = project.open_job(sp).init()

Solute-in-solvent alchemical

specify the solute and solvent chemistry, and the lambda states for the alchemical transformation

import itertools
import signac

from martignac.workflows.solute_in_solvent_alchemical import SoluteInSolventAlchemicalFlow

project = signac.init_project(path=SoluteInSolventAlchemicalFlow.workspace_path)

solvent_names = ["W", "OCO"]
solute_names = ["P6"]
lambda_states = range(11)

triplets = list(itertools.product(solvent_names, solute_names, lambda_states))

for solvent_name, solute_name, lambda_state in triplets:
    sp = {
        "type": "alchemical_transformation",
        "solvent_name": solvent_name,
        "solute_name": solute_name,
        "lambda_state": lambda_state,
    }
    job = project.open_job(sp).init()

Bilayer generation

specify the phospholipid chemistry (solvent, e.g., water, is specific in the config.yaml file)

import signac

from martignac.liquid_models.mixtures import LiquidComponent, LiquidMixture
from martignac.workflows.bilayer_generation import BilayerGenFlow

project = signac.init_project(path=BilayerGenFlow.workspace_path)

for lipid_name in [LiquidMixture([LiquidComponent("M3.POPC", 1.0)])]:
    sp = {
        "type": "bilayer",
        "lipids": [{"name": c.name, "fraction": c.fraction} for c in lipid_name.components],
    }
    job = project.open_job(sp).init()

the "M3.POPC" follows the INSANE convention of specifying the Martini force field (version 3, here).

Solute-in-bilayer umbrella

specify the solute and bilayer chemistry, as well as the set of umbrella restraints

import itertools

import signac
import numpy as np

from martignac.liquid_models.mixtures import LiquidComponent, LiquidMixture
from martignac.workflows.solute_in_bilayer_umbrella import SoluteInBilayerUmbrellaFlow

project = signac.init_project(path=SoluteInBilayerUmbrellaFlow.workspace_path)

lipids = [LiquidMixture([LiquidComponent("M3.POPC", 1.0)])]
lipid_names = []
for lipid in lipids:
    lipid_names.append([{"name": c.name, "fraction": c.fraction} for c in lipid.components])
solute_names = ["C4"]
depths_from_bilayer_core = np.linspace(0.0, 4.0, 41)  # in nm

triplets = list(itertools.product(solute_names, lipid_names, depths_from_bilayer_core))

for solute, lipid, depth in triplets:
    sp = {
        "type": "solute_in_bilayer",
        "lipids": lipid,
        "solute_name": solute,
        "depth_from_bilayer_core": depth,
    }
    job = project.open_job(sp).init()