Prep

simulation.amber.prep.AmberSimPrep()

Bases: SimPrep

Prepares files for Amber simulations

get_stage_input_lines(simlify_config) classmethod

Prepare input file lines for a single stage.

PARAMETER	DESCRIPTION
context	Specifies options and parameters.

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

get_stage_run_command(simlify_config) classmethod

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

PARAMETER	DESCRIPTION
context	Specifies options and parameters.

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

Notes:

[prepare_context][simulation.amber.prep.AmberSimPrep.prepare_context] should be ran before this.

Uses:

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

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

prepare(simlify_config) classmethod

Run all steps to prepare simulations.

PARAMETER	DESCRIPTION
simlify_config	Simlify configuration. TYPE: SimlifyConfig

prepare_sim_config(simlify_config) staticmethod

Preprocessing and validating of context for Amber simulations.

PARAMETER	DESCRIPTION
simlify_config	Simlify configuration. TYPE: SimlifyConfig

prepare_stage(simlify_config, run_commands=None, write=True) classmethod

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

PARAMETER	DESCRIPTION
context	Specifies options and parameters.
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][simulation.amber.prep.AmberSimPrep.prepare_context] should be ran before this.