QM_engines.amber_wrapper module

Description

This module defines the ParaMol.QM_engines.amber_wrapper.AmberWrapper class, which is a ParaMol implementation of a AMBER wrapper.

class ParaMol.QM_engines.amber_wrapper.AmberWrapper(system_name, interface, prmtop_file, inpcrd_file, cell, n_atoms, atom_list, atomic_number_list, sqm_params={'dftb_disper': '0', 'maxcyc': '0', 'pseudo_diag': '0', 'qm_charge': '0', 'qm_theory': 'AM1', 'scfconv': '1.0d-8', 'verbosity': '5'}, work_dir_prefix='AMBERWorkDir_', calc_file_prefix='sqm_')

Bases: object

ParaMol implementation of a AMBER SQM wrapper.

Parameters

  • system_name (str) – Name of the system to which this wrapper is associated.

  • interface (ParaMol.Utils.interface.ParaMolInterface) – ParaMol interface object instance.

  • prmtop_file (str) – Path to AMBER topology file.

  • inpcrd_file (str) – Path to AMBER coordinates file.

  • cell (list or np.array, shape=(3,3)) – Array with cell vectors

  • n_atoms (int) – Number of atoms.

  • atom_list (list of str) – List with atom symbols.

  • atomic_number_list (list of int) – List with atomic number of system’s atoms.

  • sqm_params (dict, default={"maxcyc": "0", "qm_theory": "AM1", "dftb_disper": "0", "qm_charge": "0", "scfconv": "1.0d-8", "pseudo_diag": "0", "verbosity": "5"}) – Keyword arguments used in the sqm input file.

  • work_dir (str, default="AMBERWorkDir") – Path to the working directory.

  • calc_file_prefix (str, default="sqm") – Prefix given to the sqm calculation file.

_check_cell_units()

Method that removes unit from the cell array.

Returns

cell (np.array(3,3)) – Array with cell vectors

run_calculation(coords, label)

Method that runs a calculation using AMBER’s quantum chemisty package sqm.

Parameters

  • coords (list or np.array) – (n_atoms,3) coordinates array

  • label (str) – Seed for the calculation

Returns

  • energy (float) – Energy is given in kJ/mol.

  • forces (float, np.array(n_atoms,3)) – Forces array in kJ/mol/nm.