meld.system.restraints.RdcRestraint

class meld.system.restraints.RdcRestraint(system, scaler, ramp, atom1, atom2, kappa, d_obs, tolerance, force_const, quadratic_cut, weight, alignment_index)[source]

Bases: SelectableRestraint

Residual Dipolar Coupling Restraint

__init__(system, scaler, ramp, atom1, atom2, kappa, d_obs, tolerance, force_const, quadratic_cut, weight, alignment_index)[source]

Initialize an RdcRestraint

Parameters

  • system (ISystem) – the system this restraint belongs to

  • scaler (Optional[RestraintScaler]) – scale the force with alpha

  • ramp (Optional[TimeRamp]) – scale the force over time

  • atom1 (Union[AtomIndex, PeakMapping]) – the first atom in the RDC

  • atom2 (Union[AtomIndex, PeakMapping]) – the second atom in the RDC

  • kappa (Quantity) – prefactor for RDC calculation in \(Hz nm^3\)

  • d_obs (Quantity) – observed dipolar coupling in \(Hz\)

  • tolerance (Quantity) – calculed couplings within tolerance (in \(Hz\)) of d_obs will have zero energy and force

  • force_const (Quantity) – force constant in \(kJ/mol/Hz^2\)

  • quadratic_cut (Quantity) – force constant becomes linear beyond this deviation in \(s^-1\)

  • weight (float) – dimensionless weight to place on this restraint

  • alignment_index (int) – which alignment to use

Note

Typical values for kappa are:

  • 1H - 1H: \(-360.3 Hz nm^3\)

  • 13C - 1H: \(-90.6 Hz nm^3\)

  • 15N - 1H: \(36.5 Hz nm^3\)

Methods

__init__(system, scaler, ramp, atom1, atom2, ...)

Initialize an RdcRestraint

Attributes

atom_index_1

atom_index_2