meld.system.builders.amber.builder.AmberOptions

class meld.system.builders.amber.builder.AmberOptions(default_temperature=Quantity(value=300.0, unit=kelvin), forcefield='ff14sbside', solvation='implicit', gb_radii='mbondi3', implicit_solvent_model='gbNeck2', solute_dielectric=None, solvent_dielectric=None, implicit_solvent_salt_conc=None, solvent_forcefield='tip3p', solvent_distance=0.6, explicit_ions=False, p_ion='Na+', p_ioncount=0, n_ion='Cl-', n_ioncount=0, enable_pme=False, pme_tolerance=0.0005, enable_pressure_coupling=False, pressure=Quantity(value=1.01325, unit=bar), pressure_coupling_update_steps=25, cutoff=None, remove_com=True, use_big_timestep=False, use_bigger_timestep=False, enable_amap=False, amap_alpha_bias=1.0, amap_beta_bias=1.0)[source]

Bases: object

__init__(default_temperature=Quantity(value=300.0, unit=kelvin), forcefield='ff14sbside', solvation='implicit', gb_radii='mbondi3', implicit_solvent_model='gbNeck2', solute_dielectric=None, solvent_dielectric=None, implicit_solvent_salt_conc=None, solvent_forcefield='tip3p', solvent_distance=0.6, explicit_ions=False, p_ion='Na+', p_ioncount=0, n_ion='Cl-', n_ioncount=0, enable_pme=False, pme_tolerance=0.0005, enable_pressure_coupling=False, pressure=Quantity(value=1.01325, unit=bar), pressure_coupling_update_steps=25, cutoff=None, remove_com=True, use_big_timestep=False, use_bigger_timestep=False, enable_amap=False, amap_alpha_bias=1.0, amap_beta_bias=1.0)

Methods

__init__([default_temperature, forcefield, ...])

Attributes

`amap_alpha_bias`
`amap_beta_bias`
`cutoff`
`default_temperature`
`enable_amap`
`enable_pme`
`enable_pressure_coupling`
`explicit_ions`
`forcefield`
`gb_radii`
`implicit_solvent_model`
`implicit_solvent_salt_conc`
`n_ion`
`n_ioncount`
`p_ion`
`p_ioncount`
`pme_tolerance`
`pressure`
`pressure_coupling_update_steps`
`remove_com`
`solute_dielectric`
`solvation`
`solvent_dielectric`
`solvent_distance`
`solvent_forcefield`
`use_big_timestep`
`use_bigger_timestep`