Advanced tips and tricks¶

Enable PELE InterStepLogger¶

InterStepLogger functionality allows capturing structural and simulation data during different stages of a step. It is useful for debugging purposes.

To enable this option you need to set inter_step_logger parameter to true in your input.yaml:

inter_step_logger: true

The new report and trajectories files were saved in the subdirectory InterStepLogs, inside the PELE++ output folder.

Add custom simulation mode¶

If your simulation set up requires tweaking a lot of parameters, you can add a new feature to the platform.

1. Generate your own mode¶

Add a new feature with your own defaults under simulation_params key in pele_platform/features/adaptive.py, e.g.

"my_custom_induced_fit" : {"spawning_type": "independent", "bias_column": 5, "epsilon":0.25, "density": "null",
         "simulation_type": "pele", "iterations": 5, "pele_steps": 500,
         "cluster_values": "[1.75, 2.5, 4, 6]", "cluster_conditions": "[1, 0.6, 0.4, 0.0]",
         "steric_trials": 500, "overlap_factor": 0.65, "params": pcs.INDUCED_FIT,
         "box_radius": 6},

2. Include it in the pipeline¶

Assign the type of the simulation depending on the YAML arguments in pele_platform/features/adaptive.py, e.g.

elif args.my_custom_induced_fit:
    type_simulation = "my_custom_induced_fit"

3. Add an input option¶

A new input flag will not be recognised by the platform, unless you add it to:

_parse function in pele_platform/Utilities/Helpers/yaml_parser.py and set the default to None

VALID_FLAGS_PLATFORM dictionary in pele_platform/Checker/valid_flags.py

Example in yaml_parser.py:

self.induced_fit_fast = data.get(valid_flags["my_custom_induced_fit"], None)

4. Run your mode¶

To run your simulation mode in the input file, include the previously generated YAML flag, for example:

induced_fit_fast: true