Contexts

Simulation contexts for Amber

AMBER_PROTEIN_STANDARD_CONTEXT = {'ff_protein': 'ff19SB', 'ff_water': 'opc3', 'cation_identity': 'Na+', 'anion_identity': 'Cl-', 'neutralize_charge': True, 'extra_cations': 0, 'extra_anions': 0, 'solvent_ionic_strength': 0.15, 'solvent_padding': 10.0} module-attribute

Reasonable values for explicitly solvated protein simulations in water.

The ff19SB protein force field offers improved protein backbone descriptions by incorporating the CMAP approach. OPC3 was found to provide best in-class accuracy and efficiency.

AmberContextValidator

Bases: ContextValidator

Validate Amber contexts.

compute_platform: Iterable[str] = ('mpi', 'cuda') class-attribute instance-attribute

Options for architecture to run simulations on.

ff_protein: Iterable[str] = ('ff19SB', 'ff14SB', 'ff99SB', 'ff15ipq', 'fb15', 'ff03ua') class-attribute instance-attribute

Options for protein force fields.

ff_water: Iterable[str] = ('tip4p', 'tip4pew', 'tip5p', 'spce', 'spceb', 'opc', 'opc3', 'opc3pol', 'opc3pol', 'pol3', 'tip3pfb', 'tip4pfb') class-attribute instance-attribute

Options for water force fields.

input_kwargs(value, context) staticmethod

Validate input parameters.

Enforces the following rules.

• Minimizations (e.g., imin = 1) cannot use GPUs. Sometimes when fewer bits are being used for float (i.e., float32 instead of float64), floating point errors can accumulate and make the force field calculations crash or very high forces. Thus, we do not allow compute_platform to be set to cuda during minimizations.

splits(value, context) staticmethod

Validate splits