janus.qmmm.AQMMM

class janus.qmmm.AQMMM(hl_wrapper, ll_wrapper, sys_info, sys_info_format, qmmm_param, class_type)

AQMMM super class for adaptive QMMM computations. Inherits from QMMM class.

Note

Since AQMMM is a super class and has abstract methods cannot actually instantiate AQMMM object, but only its child objects

__init__(hl_wrapper, ll_wrapper, sys_info, sys_info_format, qmmm_param, class_type)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(hl_wrapper, ll_wrapper, sys_info, …)	Initialize self.
compute_COM(atoms)	Computes the center of mass of a specified group
compute_gradients(system)	Computes the QM/MM gradients
compute_lamda_i(r_i)	Computes the switching function and the derivative of the switching function defined as a 5th order spline:
compute_zero_energy()	Compute the energy of the isolated groups at their minimum geometry
convert_input(fil, form)	Converts a set of input files into a MD trajectory
define_buffer_zone(qm_center)	Determines buffer group atoms.
AQMMM.edit_qm_atoms
electrostatic(system, main_info)	Gets energies of needed components and computes a QM/MM energy with a subtractive electrostatic embedding scheme
find_boundary_bonds([qm_atoms])	Identified any covalent bonds that the QM/MM boundary cuts across
find_buffer_atoms(qm_center)	Find the buffer groups whose COM falls in between Rmin and Rmax
get_Rmax()	Function to return self.Rmin
get_Rmin()	Function to return self.Rmin
AQMMM.get_buffer_info
get_external_charges(system)	Gets the point charges of atoms from secondary subsystem for electrostatic embedding
get_forces([run_ID])	Function to return qmmm forces
get_redistributed_positions(positions, bonds, mm)	Gets the positions for the redistributed point charges in the RC and RCD schemes
get_zero_energy()	Incorporates the zero energy of groups to the total qmmm energy
make_primary_subsys_trajectory([qm_atoms])	Creates a MDtraj trajectory object with just the primary subsystem, and adds in any link atoms
make_second_subsys_trajectory([qm_atoms])	Creates a MDtraj trajectory object with just the secondary subsystem
mechanical(system, main_info)	Gets energies of needed components and computes a QM/MM energy with a subtractive mechanical embedding scheme using the formula
partition(info)	Function implemented in individual child classes
prepare_link_atom()	Identifies where to put link atom.
run_aqmmm()	Function implemented in individual child classes
run_qmmm(main_info, wrapper_type)	Drives QM/MM computation.
set_Rmax(Rmax)	Function to set self.Rmax
set_Rmin(Rmin)	Function to set self.Rmin
update_traj(position, topology, wrapper_type)	Updates the positions and topology of self.traj, a MDtraj trajectory object

Attributes

nm_to_angstrom