pydft_qmmm.plugins.rigid package

Submodules

pydft_qmmm.plugins.rigid.rigid module

Plugins for implementing stationary or rigid-body residues.

class pydft_qmmm.plugins.rigid.rigid.RigidBody(query)

Bases: IntegratorPlugin

Apply rigid-body dynamics to select residues during integration.

Parameters:

query (str) – The VMD-like selection query which corresponds to residues that should be kept rigid during integration.

modify(integrator)

Modify the functionality of an integrator.

Parameters:

integrator (Integrator) – The integrator whose functionality will be modified by the plugin.

Return type:

None

class pydft_qmmm.plugins.rigid.rigid.Stationary(query)

Bases: IntegratorPlugin

Keep select residues stationary during integration.

Parameters:

query (str) – The VMD-like selection query which corresponds to residues that should be kept stationary during integration.

constrain_velocities(system)

Zero velocities for stationary residues.

Parameters:

system (System) – The system with stationary residues.

Returns:

New velocities which result from zeroing the system velocities of stationary residues.

Return type:

NDArray[np.float64]

modify(integrator)

Modify the functionality of an integrator.

Parameters:

integrator (Integrator) – The integrator whose functionality will be modified by the plugin.

Return type:

None

pydft_qmmm.plugins.rigid.rigid_utils module

Core functionality for performing rigid body dynamics.

Module contents

A sub-package for performing rigid body simulations.