Force fields

AmberFF(
    ::AbstractAtomContainer{T},
    param_file::AbstractString = ball_data_path("forcefields/AMBER/amber96.ini")
)

Initializes an AMBER force field for the given atom container and the given parameter file (default: AMBER96).

Supported keyword arguments

• nonbonded_cutoff::T = 20
• vdw_cutoff::T = 15
• vdw_cuton::T = 13
• electrostatic_cutoff::T = 15
• electrostatic_cuton::T = 13
• scaling_vdw_1_4 = 2
• scaling_electrostatic_1_4::T = 1.2
• distance_dependent_dielectric::Bool = false
• assign_charges::Bool = true
• assign_typenames::Bool = true
• assign_types::Bool = true
• overwrite_nonzero_charges::Bool = true
• overwrite_typenames::Bool = false
• periodic_boundary_conditions::Bool = false
• periodic_box_width::T = 100
• periodic_box_height::T = 100
• periodic_box_depth::T = 100
• max_number_of_unassigned_atoms::Int = typemax(Int32)

optimize_hydrogen_positions!(ff::ForceField)

Variant of optimize_structure! that only optimizes hydrogen atom positions.

Supported keyword arguments

Same as optimize_structure!

optimize_structure!(ff::ForceField)

Attempts to solve the energy optimization problem represented by the given force field object.

Supported keyword arguments

This function passes all keyword arguments to Optimization.solve, with the following default values:

• alg = OptimizationLBFGSB.LBFGSB()

update!(ff::ForceField)

Update the internal data structures of the force field when the system changes (e.g., through coordinate updates).