The Experiment Classes

ProteinExperiment

class amberpy.experiments.ProteinExperiment(protein_pdb, name=None, replica_name=None)

Bases: amberpy.experiments.Experiment

make_system(box_distance: float = 12.0, box_shape: str = 'box', ions: dict = {'Cl-': 0, 'Na+': 0}, hmr: bool = True, tleap_input: Optional[amberpy.md_setup.TleapInput] = None)

CosolventExperiment

class amberpy.experiments.CosolventExperiment(cosolvent, name=None, replica_name=None)

Bases: amberpy.experiments.Experiment

make_system(n_waters=None, n_cosolvents=100, box_size=[50, 50, 50], ions: dict = {'Cl-': 0, 'Na+': 0}, distance: float = 12.0, hmr: bool = True, packmol_input: Optional[amberpy.md_setup.PackmolInput] = None)

ProteinCosolventExperiment

class amberpy.experiments.ProteinCosolventExperiment(protein_pdb, cosolvent, name=None, replica_name=None)

Bases: amberpy.experiments.CosolventExperiment, amberpy.experiments.ProteinExperiment

Experiment

class amberpy.experiments.Experiment(name, replica_name=None, protein_pdb=None, cosolvent=None)

Bases: amberpy.md_setup.Setup, amberpy.simulation.Simulation

Base class for setting up and running an experiment. This class inherits from both the Simulation and Setup classes.

This class is intended to be inherited from by other classes that perform specific tasks e.g. ProteinExperient, CosolventExperiment, ProteinCosolventExperiment. If you want to make your own type of experiment then you should inherit from this class.

name

The name of the experiment.

Type

str

replica_name

The name of the replica (if this experiment is a replica).

Type

str

directory

The directory in which the experiment will take place.

Type

str

root_directory

The root directory containing all of the experiment directories if this experiment is a replica.

Type

str

property protein_termini

Terminal residues in tleap_pdb file associated with the experiment.

Type

tuple