mythos.energy.martini.m2.angle

Angle potential energy function for Martini 2.

Attributes

ANGLE_K_PREFIX
ANGLE_THETA0_PREFIX

Classes

AngleConfiguration	Configuration for Martini angle energy function.
Angle	Angle potential energy function for Martini 2.

Functions

compute_angle(→ float)	Compute the angle between three particles (angle at j).
triplet_angle(→ float)	Calculate angle energy for a given triplet of particles.

Module Contents

mythos.energy.martini.m2.angle.ANGLE_K_PREFIX = 'angle_k_'

mythos.energy.martini.m2.angle.ANGLE_THETA0_PREFIX = 'angle_theta0_'

class mythos.energy.martini.m2.angle.AngleConfiguration(couplings: dict[str, list[str]] | None = None, **kwargs)

Bases: mythos.energy.martini.base.MartiniEnergyConfiguration

Configuration for Martini angle energy function.

Angle params must be provided as “angle_k_I_J_K” and “angle_theta0_I_J_K” in corresponding pairs for each angle name in the system. NAME should be in the format of “MOLTYPE_ATOMNAME1_ATOMNAME2_ATOMNAME3”, e.g., “DMPC_NC3_PO4_GL1”.

__post_init__() → None

Hook for additional initialization in subclasses.

mythos.energy.martini.m2.angle.compute_angle(r_ij: mythos.utils.types.Vector3D, r_kj: mythos.utils.types.Vector3D) → float

Compute the angle between three particles (angle at j).

Parameters:

• r_ij – Displacement vector from j to i.

• r_kj – Displacement vector from j to k.

Returns:

The angle theta_ijk in radians.

mythos.energy.martini.m2.angle.triplet_angle(centers: mythos.utils.types.Arr_States_3, triplet: mythos.utils.types.Vector3D, k_angle: float, theta0_angle: float, displacement_fn: callable, use_G96: bool) → float

Calculate angle energy for a given triplet of particles.

Parameters:

• centers – Positions of all particles.

• triplet – Indices [i, j, k] of the three particles forming the angle.

• k_angle – Force constant for the angle.

• theta0_angle – Equilibrium angle in radians.

• displacement_fn – Function to compute displacement between particles.

• use_G96 – Whether to use Gromacs 1996 cosine-based angle potential (as in Martini 2) or standard harmonic angle potential.

Returns:

0.5 * k * (theta - theta0)^2

Return type:

Harmonic angle energy

class mythos.energy.martini.m2.angle.Angle

Bases: mythos.energy.martini.base.MartiniEnergyFunction

Angle potential energy function for Martini 2.

params: AngleConfiguration

use_G96: ClassVar[bool] = True

__post_init__(topology: None = None) → None

compute_energy(trajectory: mythos.simulators.io.SimulatorTrajectory) → float

Compute the energy of the system given the nucleotide.