Contexts

RenderingConfig

Bases: BaseModel, YamlIO

Configuration for rendering files to write.

dir_input = '.'

Path to a directory relative to dir_work that will contain input files.

dir_output = '.'

Path to a directory relative to dir_work that the simulation will store output files.

dir_work = '.'

Working directory to write files.

RuntimeConfig

Bases: BaseModel, YamlIO

Configuration options during the simulation runtime.

dir_input = '.'

Path to a directory relative to dir_work that will contain input files.

dir_output = '.'

Path to a directory relative to dir_work that the simulation will store output files.

dir_run = '.'

Directory that calculations are performed in. This can be the same as dir_work or some scratch space like $SLURM_SCRATCH.

dir_work = '.'

Working directory during runtime. This can be the current work directory or a workload manager directory such as $SLURM_SUBMIT_DIR.

splits = 1

Split simulation stage into several chunks.

use_scratch = False

Treat dir_run as a scratch directory by copying input files to that location, running the simulation there, and then copying output files back.

SimlifyConfig

Bases: BaseModel, YamlIO

Contexts for setting up molecular simulations.

engine = None

Atomea workflow schema for the molecular simulation engine (e.g., Amber22Schema).

extra_lines_topo_gen = None

Extra lines to include when generating a topology.

label = None

Label for this specific simulation.

rendering = Field(default_factory=RenderingConfig)

runtime = Field(default_factory=RuntimeConfig)

slurm = Field(default_factory=SlurmSchema)

solution = Field(default_factory=SolutionConfig)

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

topology = Field(default_factory=TopologyConfig)

SolutionConfig

Bases: BaseModel, YamlIO

charge_anion_extra = 0

Number of extra anions of type charge_anion_identity to add to the system. This does not include any ions added if charge_neutralize is True.

charge_anion_identity = 'Cl-'

Many simulations include anions to either neutralize charge or prepare the solvent environment to have a specific ionic concentration. This specifies the anion to add to accomplish this.

charge_cation_extra = 0

Number of extra cations of type charge_cation_identity to add to the system. This does not include any ions added if charge_neutralize is True.

charge_cation_identity = 'Na+'

Many simulations include cations to either neutralize charge or prepare the solvent environment to have a specific ionic concentration. This specifies the cation to add to accomplish this.

charge_net = 0

Net charge of the molecular system before any preparation.

charge_neutralize = True

Flag to determine if system charge should be neutralized by placing additional ions of type charge_cation_identity or charge_anion_identity based on the value of charge_net.

solvent_ionic_strength = 0.15

Ionic strength of the solvent in mol/L.

solvent_padding = 10.0

Padding between solute and box edge to fill with solvent in Angstroms.

TopologyConfig

Bases: BaseModel, YamlIO

Topology configuration.

append_lines = []

Extra lines to include when generating a topology.