Config

SimlifyConfig

Bases: BaseModel, YamlIO, Render

Contexts for setting up molecular simulations.

This class aggregates various configuration schemas required to define and execute molecular simulations using the Simlify workflow. It includes settings for job submission (Slurm), solution conditions, topology generation, runtime parameters, and the specific simulation engine to be used.

engine = None

Workflow schema for the molecular simulation engine (e.g., [Amber22Schema][simlify.schemas.amber.v22.Amber22Schema]). This attribute holds the specific engine configuration, allowing Simlify to interact with different simulation packages.

label = None

A descriptive label for this specific simulation configuration. This can be useful for identifying and organizing different simulation setups.

run = Field(default_factory=RunConfig)

Configuration schema for specifying parameters related to the simulation runtime environment. This includes working directories, input/output paths, and options for splitting the simulation into chunks.

slurm = Field(default_factory=SlurmSchema)

Configuration schema for submitting jobs to a Slurm workload manager. This includes parameters such as the number of nodes, tasks per node, partition, time limit, and other Slurm-specific settings.

solution = Field(default_factory=SolutionConfig)

Configuration schema for defining the solution environment of the molecular system. This includes parameters related to solvent, ions, and charge neutralization.

temp = Field(default={}, exclude=True)

A temporary dictionary for storing intermediate data during the workflow. This attribute is excluded from serialization and rendering.

topology = Field(default_factory=TopologyConfig)

Configuration schema for generating the topology and parameter files required for the molecular simulation. This can include options for appending extra lines to the topology file.