mythos.energy.martini.m2

Martini2 energy functions.

Submodules

Classes

`Angle`	Angle potential energy function for Martini 2.
`AngleConfiguration`	Configuration for Martini angle energy function.
`Bond`	Bond potential energy function for Martini 2.
`BondConfiguration`	Configuration for Martini bond energy function.
`LJ`	Lennard-Jones potential energy function for Martini 2.
`LJConfiguration`	"Configuration for Martini Lennard-Jones energy function.

Package Contents

class mythos.energy.martini.m2.Angle[source]

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[source]

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

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

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[source]: Hook for additional initialization in subclasses.

class mythos.energy.martini.m2.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.

class mythos.energy.martini.m2.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.

class mythos.energy.martini.m2.LJ[source]

Bases: mythos.energy.martini.base.MartiniEnergyFunction

Lennard-Jones potential energy function for Martini 2.

params: LJConfiguration

__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.

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

Bases: mythos.energy.martini.base.MartiniEnergyConfiguration

“Configuration for Martini Lennard-Jones energy function.

All parameters provided must be of the form “lj_sigma_A_B” or “lj_epsilon_A_B”, where A and B are bead types. Pair order is ignored unless both orderings are provided. It is required that sigma and epsilon parameters are provided for any bead type pairs present in the system.

Couplings are supported (see MartiniEnergyConfiguration for details).

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