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

class meld.system.builders.amber.builder.AmberOptions(default_temperature=<factory>, 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=<factory>, 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, enable_gamd=False, boost_type_str='upper-total', conventional_md_prep=5, conventional_md=50, gamd_equilibration_prep=15, gamd_equilibration=150, total_simulation_length=1000, averaging_window_interval=2500, sigma0p=6.0, sigma0d=6.0, random_seed=0, friction_coefficient=1.0)[source]

Bases: object

__init__(default_temperature=<factory>, 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=<factory>, 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, enable_gamd=False, boost_type_str='upper-total', conventional_md_prep=5, conventional_md=50, gamd_equilibration_prep=15, gamd_equilibration=150, total_simulation_length=1000, averaging_window_interval=2500, sigma0p=6.0, sigma0d=6.0, random_seed=0, friction_coefficient=1.0)

Methods

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

Attributes

`amap_alpha_bias`
`amap_beta_bias`
`averaging_window_interval`
`boost_type_str`
`conventional_md`
`conventional_md_prep`
`cutoff`
`enable_amap`
`enable_gamd`
`enable_pme`
`enable_pressure_coupling`
`explicit_ions`
`forcefield`
`friction_coefficient`
`gamd_equilibration`
`gamd_equilibration_prep`
`gb_radii`
`implicit_solvent_model`
`implicit_solvent_salt_conc`
`n_ion`
`n_ioncount`
`p_ion`
`p_ioncount`
`pme_tolerance`
`pressure_coupling_update_steps`
`random_seed`
`remove_com`
`sigma0d`
`sigma0p`
`solute_dielectric`
`solvation`
`solvent_dielectric`
`solvent_distance`
`solvent_forcefield`
`total_simulation_length`
`use_big_timestep`
`use_bigger_timestep`
`default_temperature`
`pressure`