qmmm_pme.plugins.pme package

Submodules

qmmm_pme.plugins.pme.pme module

A module defining the pluggable implementation of the SETTLE algorithm for the QM/MM/PME repository.

class qmmm_pme.plugins.pme.pme.PME[source]

Bases: QMMMCalculatorPlugin

A Plugin which implements the QM/MM/PME algorithm for energy and force calculations.

modify(calculator)[source]

Perform necessary modifications to the QMMMCalculator object.

Parameters:

calculator (QMMMCalculator) – The calculator to modify with the QM/MM/PME functionality.

Return type:

None

qmmm_pme.plugins.pme.pme_utils module

A module to define the PBCCalculator class.

qmmm_pme.plugins.pme.pme_utils.pme_components(system, quadrature, pme_potential, pme_gridnumber, pme_alpha)[source]
Parameters:

  • system (System) –

  • quadrature (NDArray[np.float64]) –

  • pme_potential (NDArray[np.float64]) –

  • pme_gridnumber (int) –

  • pme_alpha (float | int) –

Return type:

tuple[Any, …]

qmmm_pme.plugins.pme.pme_utils.project_to_grid(inverse_box, pme_gridnumber, points)[source]

Project points onto a PME grid in reciprocal space. This algorithm is identical to that used in method ‘pme_update_grid_index_and_fraction’ in OpenMM source code, ReferencePME.cpp.

Parameters:

  • points (NDArray[np.float64]) – The real-space points, in Bohr, to project onto the reciprocal-space PME grid.

  • inverse_box (NDArray[np.float64]) –

  • pme_gridnumber (int) –

Returns:

The projected points in reciprocal-space, in inverse Bohr.

Return type:

NDArray[np.float64]

Module contents

A sub-package for performing the QM/MM/PME algorithm during the energy and force calculation procedure.