Run

AmberRunPrep()

Bases: SimulationRunPrep

Prepares files for Amber simulations

get_stage_input_lines(context)

Prepare input file lines for a single stage.

PARAMETER	DESCRIPTION
context	Specifies options and parameters. TYPE: dict[str, Any]

RETURNS	DESCRIPTION
list[str]	Input file lines for a single simulations. The lines do not end in \n.

get_stage_run_command(context)

Prepare bash command to run a single Amber simulation using pmemd.

PARAMETER	DESCRIPTION
context	Specifies options and parameters. TYPE: dict[str, Any]

RETURNS	DESCRIPTION
list[str]	Bash commands in a list to run one stage of a simulation.

Notes:

prepare_context should be ran before this.

Uses:

The following attributes are possibly used here and should be specified in simulation_context.

• stage_name: Unique label for this simulation stage. This will be used to build file paths.
• input_path: Path to input file for this Amber simulations.
• output_dir: Path to final output directory.
• scratch_dir: Path to scratch directory if desired. Will run the calculations here and then copy to output_dir.
• compute_platform: Computational platform to run the simulation on.
• cpu_cores: Number of cores to use for mpi simulations if requested.

prepare(simulation_context)

Run all steps to prepare simulations.

PARAMETER	DESCRIPTION
simulation_context	Context manager for simulations. TYPE: SimulationContextManager

prepare_context(simulation_context)

Preprocessing and validating of context for Amber simulations.

PARAMETER	DESCRIPTION
simulation_context	Context manager for simulations. TYPE: SimulationContextManager

prepare_stage(context, run_commands=None, write=True)

Write input files for a simulation stage and builds bash commands to run all splits.

PARAMETER	DESCRIPTION
context	Specifies options and parameters. TYPE: dict[str, Any]
run_commands	Cumulative run commands for all desired stages. TYPE: list[str] | None DEFAULT: None
write	Write input file to disk. TYPE: bool DEFAULT: True

RETURNS	DESCRIPTION
list[str]	Input file lines for this stage.
list[str]	Updated run_commands including this stage.

Notes:

prepare_context should be ran before this.