mythos.energy.martini.m2.bond

Bond potential energy function for Martini 2.

Attributes

`BOND_K_PREFIX`
`BOND_R0_PREFIX`

Classes

`BondConfiguration`	Configuration for Martini bond energy function.
`Bond`	Bond potential energy function for Martini 2.

Functions

pair_bond(→ float)

Calculate bond energy for a given pair of particles.

Module Contents

mythos.energy.martini.m2.bond.BOND_K_PREFIX = 'bond_k_'

mythos.energy.martini.m2.bond.BOND_R0_PREFIX = 'bond_r0_'

class mythos.energy.martini.m2.bond.BondConfiguration(couplings: dict[str, list[str]] | None = None, **kwargs)[source]

Bases: mythos.energy.martini.base.MartiniEnergyConfiguration

Configuration for Martini bond energy function.

Bond params must be provided as “bond_k_NAME” and “bond_r0_NAME” in corresponding pairs for each bond name in the system. NAME should be in the format of “MOLTYPE_ATOMNAME1_ATOMNAME2”, e.g., “DMPC_NC3_PO4”.

__post_init__() → None[source]: Hook for additional initialization in subclasses.

mythos.energy.martini.m2.bond.pair_bond(centers: mythos.utils.types.Arr_States_3, pair: mythos.utils.types.Vector2D, k_bond: float, r0_bond: float, displacement_fn: callable) → float[source]: Calculate bond energy for a given pair of particles.

class mythos.energy.martini.m2.bond.Bond[source]

Bases: mythos.energy.martini.base.MartiniEnergyFunction

Bond potential energy function for Martini 2.

params: BondConfiguration

__post_init__(topology: None = None) → None[source]

compute_energy(trajectory: mythos.simulators.io.SimulatorTrajectory) → float[source]: Compute the energy of the system given the nucleotide.