The Molecular Mechanics Settings
================================================================================
.. currentmodule:: ost.mol.mm
The :class:`Settings` define all parameters to control the buildup of a
:class:`Topology` in the :class:`TopologyCreator` and the final setup
of the :class:`Simulation` object.
.. class:: Settings
.. attribute:: add_bonds
Flag, whether bonds should be parametrized
in :class:`TopologyCreator`. Default: True
.. attribute:: add_angles
Flag, whether angles should be parametrized
in :class:`TopologyCreator`. Default: True
.. attribute:: add_dihedrals
Flag, whether dihedrals should be parametrized
in :class:`TopologyCreator`. Default: True
.. attribute:: add_impropers
Flag, whether impropers should be parametrized
in :class:`TopologyCreator`. Default: True
.. attribute:: add_cmaps
Flag, whether cmaps should be parametrized
in :class:`TopologyCreator`. Default: True
.. attribute:: add_exclusions
Flag, whether exclusions should be parametrized
in :class:`TopologyCreator`. Default: True
.. attribute:: add_nonbonded
Flag, whether nonbonded interactions should be parametrized
in :class:`TopologyCreator`. Default: True
.. attribute:: add_gbsa
Flag, whether GBSA interactions should be parametrized
in :class:`TopologyCreator`. Default: False
.. attribute:: constrain_hbonds
Flag, whether bonds involving hydrogens should be constrained
in :class:`TopologyCreator`. Default: False
.. attribute:: constrain_bonds
Flag, whether all bonds should be constrained in
:class:`TopologyCreator`. Default: False
.. attribute:: rigid_water
Flag, whether water molecules should be made rigid in
:class:`TopologyCreator`. This is achieved by adding
a distance constraint on the O-H bonds and an additional
one between the two hydrogens. Default: False
.. attribute:: strict_interactions
Makes sure that an error is thrown when a particular interaction cannot
be parametrized with the given forcefield in the :class:`TopologyCreator`.
By setting it to False, these cases just get ignored. Default: True
.. attribute:: ideal_bond_length_constraints
Flag, whether the ideal bond length from the :class:`Forcefield` should be
taken for distance constraints in the :class:`TopologyCreator`. The actual
distances from the :class:`~ost.mol.EntityHandle` get taken otherwise.
Default: True
.. attribute:: fix_heavy_atoms
Flag, whether all heavy atom positions (non hydrogens) should be fixed in
space in the :class:`TopologyCreator`. Default: False
.. attribute:: kill_electrostatics
Flag, whether all charges should just be set to zero in the
:class:`TopologyCreator`. Default: False
.. attribute:: generate_disulfid_bonds
Flag, whether disulfid bonds based on a simple geometric criterion
(SG-SG dist < 2.5A) should be built in :class:`TopologyCreator`.
Default: True
.. attribute:: nonbonded_method
Nonbonded method set up at the creation of the :class:`Simulation`.
Must be one of mm.NoCutoff, mm.CutoffNonPeriodic, mm.CutoffPeriodic
mm.Ewald or mm.PME. Default: mm.NoCutoff
.. attribute:: nonbonded_cutoff
Nonbonded cutoff set when simulation is set up. Default: 10.0
.. attribute:: remove_cmm_motion
Whether a center of mass remover object should be attached to the
:class:`Simulation`. Default: True
.. attribute:: cmm_frequency
Frequency regarding simulation steps when the cmm remover should be applied.
Default: 1
.. attribute:: periodic_box_extent
:class:`ost.geom.Vec3` describing the X,Y and Z extents of the rectangular
simulation_box defined when setting up the :class:`Simulation`.
Default: (0,0,0)
.. attribute:: init_temperature
Initial simulation velocities get set according to a Boltzman distribution
controlled by init_temperature(Kelvin). Default: 0.0
.. attribute:: forcefield
:class:`Forcefield` that is used in :class:`TopologyCreator`. Default: None
.. attribute:: termini_exceptions
Use termini other than the defaults set in the :class:`Forcefield` when
using :class:`TopologyCreator`. Has to be a :class:`TerminiExceptions`
object. Default: None
.. attribute:: platform
Platform used by OpenMM to do the calculations. Must be one of mm.Reference,
mm.CPU, mm.CUDA or mm.OpenCL. If anything else than the reference platform
is used, the attribute openmm_plugin_directory has to be set accordingly.
Default: mm.Reference
.. attribute:: reference_properties
:class:`dict` of OpenMM specific properties that can be set for the
reference platform.
.. attribute:: cpu_properties
:class:`dict` of OpenMM specific properties that can be set for the
cpu platform.
.. attribute:: opencl_properties
:class:`dict` of OpenMM specific properties that can be set for the
opencl platform.
.. attribute:: cuda_properties
:class:`dict` of OpenMM specific properties that can be set for the
cuda platform.
.. attribute:: add_thermostat
Flag, whether an Andersen thermostat should be attached when settings up
the :class:`Simulation`. Default: False
.. attribute:: thermostat_temperature
Temperature for the Andersen thermostat in K. Default: NaN
.. attribute:: thermostat_collision_frequency
Collision frequency of the Andersen thermostat in 1/ps. Default: NaN
.. attribute:: add_barostat
Flag, whether an MonteCarlo barostat should be attached when setting up
the :class:`Simulation`. Default: False
.. attribute:: barostat_temperature
Temperature for the MonteCarlo Barostat in K. Default: NaN
.. attribute:: barostat_pressure
Pressure for the MonteCarlo Barostat in bar. Default: NaN
.. attribute:: barostat_frequency
Frequency of the MonteCarlo Barostat. Default: 25
.. attribute:: integrator
Integrator to move the simulation forward in time. OpenMM offers following
Integrators: :class:`VerletIntegrator`, :class:`BrownianIntegrator`,
:class:`LangevinIntegrator`, :class:`VariableVerletIntegrator` and
:class:`VariableLangevinIntegrator`. Default: None
.. attribute:: solvent_dielectric
Solvent dielectric constant. This is used for the GBSA force when the
:class:`Simulation` gets set up. Default: 78.3
.. attribute:: solute_dielectric
Solute dielectric constant. This is used for the GBSA force when the
:class:`Simulation` gets set up. Default: 1.0
.. attribute:: reaction_field_dielecric
Sets the reaction field dielectric for the Nonbonded Force when setting
up the :class:`Simulation`. Default: 78.3
.. attribute:: use_dispersion_correction
Flag, whether the dispersion correction should be used when setting
up the Nonbonded Force in the :class:`Simulation`. Default: True
.. attribute:: keep_ff_specific_naming
When running through the :class:`TopologyCreator`, the given entity gets
renamed to the forcefield specific naming. If set to true, the naming
stays like that, if not the entity gets renamed to PDB standard.
Default: True
.. attribute:: openmm_plugin_directory
Path where OpenMM specific plugins are searched. If you want
to use other platforms than Reference, this has to be set.
Defaults to *OPEN_MM_PLUGIN_DIR* which was set when
:ref:`configuring the compilation <cmake-flags>`.
.. attribute:: custom_plugin_directory
Path where custom plugins are searched for. Defaults to
"share/openstructure/openmm_plugins" within the OST installation or to
:attr:`openmm_plugin_directory` if the OST path could not be determined.
.. class:: TerminiExceptions
Can be used to define exceptions from the standard assignments
assigned in the :class:`Forcefield`.
.. method:: SetException(residue, exception_name)
:param residue: Residue for which the exception
should be set.
:param exception_name: Name of the
Blockmodifier in the forcefield that should be
applied in case of a termini
:type residue: :class:`ResidueHandle`
:type exception_name: :class:`str`
.. method:: HasException(residue)
:param residue: Residue that should be checked for
exceptions
:type residue: :class:`ResidueHandle`
:returns: :class:`bool` True if **residue** has an exception
.. method:: GetException(residue)
:param residue: Residue containing the exception
:type residue: :class:`ResidueHandle`
:raises: :class:`RuntimeError` if **residue** has no associated exception
:returns: :class:`str` describing the name of the Blockmodifier in
the forcefield that should be applied in case of a
terminal residue