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# The Molecular Mechanics Settings¶

The Settings define all parameters to control the buildup of a Topology in the TopologyCreator and the final setup of the Simulation object.

class Settings
add_bonds

Flag, whether bonds should be parametrized in TopologyCreator. Default: True

add_angles

Flag, whether angles should be parametrized in TopologyCreator. Default: True

add_dihedrals

Flag, whether dihedrals should be parametrized in TopologyCreator. Default: True

add_impropers

Flag, whether impropers should be parametrized in TopologyCreator. Default: True

add_cmaps

Flag, whether cmaps should be parametrized in TopologyCreator. Default: True

add_exclusions

Flag, whether exclusions should be parametrized in TopologyCreator. Default: True

add_nonbonded

Flag, whether nonbonded interactions should be parametrized in TopologyCreator. Default: True

add_gbsa

Flag, whether GBSA interactions should be parametrized in TopologyCreator. Default: False

constrain_hbonds

Flag, whether bonds involving hydrogens should be constrained in TopologyCreator. Default: False

constrain_bonds

Flag, whether all bonds should be constrained in TopologyCreator. Default: False

rigid_water

Flag, whether water molecules should be made rigid in TopologyCreator. This is achieved by adding a distance constraint on the O-H bonds and an additional one between the two hydrogens. Default: False

strict_interactions

Makes sure that an error is thrown when a particular interaction cannot be parametrized with the given forcefield in the TopologyCreator. By setting it to False, these cases just get ignored. Default: True

ideal_bond_length_constraints

Flag, whether the ideal bond length from the Forcefield should be taken for distance constraints in the TopologyCreator. The actual distances from the EntityHandle get taken otherwise. Default: True

fix_heavy_atoms

Flag, whether all heavy atom positions (non hydrogens) should be fixed in space in the TopologyCreator. Default: False

kill_electrostatics

Flag, whether all charges should just be set to zero in the TopologyCreator. Default: False

generate_disulfid_bonds

Flag, whether disulfid bonds based on a simple geometric criterion (SG-SG dist < 2.5A) should be built in TopologyCreator. Default: True

nonbonded_method

Nonbonded method set up at the creation of the Simulation. Must be one of mm.NoCutoff, mm.CutoffNonPeriodic, mm.CutoffPeriodic mm.Ewald or mm.PME. Default: mm.NoCutoff

nonbonded_cutoff

Nonbonded cutoff set when simulation is set up. Default: 10.0

remove_cmm_motion

Whether a center of mass remover object should be attached to the Simulation. Default: True

cmm_frequency

Frequency regarding simulation steps when the cmm remover should be applied. Default: 1

periodic_box_extent

ost.geom.Vec3 describing the X,Y and Z extents of the rectangular simulation_box defined when setting up the Simulation. Default: (0,0,0)

init_temperature

Initial simulation velocities get set according to a Boltzman distribution controlled by init_temperature(Kelvin). Default: 0.0

forcefield

Forcefield that is used in TopologyCreator. Default: None

termini_exceptions

Use termini other than the defaults set in the Forcefield when using TopologyCreator. Has to be a TerminiExceptions object. Default: None

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

reference_properties

dict of OpenMM specific properties that can be set for the reference platform.

cpu_properties

dict of OpenMM specific properties that can be set for the cpu platform.

opencl_properties

dict of OpenMM specific properties that can be set for the opencl platform.

cuda_properties

dict of OpenMM specific properties that can be set for the cuda platform.

add_thermostat

Flag, whether an Andersen thermostat should be attached when settings up the Simulation. Default: False

thermostat_temperature

Temperature for the Andersen thermostat in K. Default: NaN

thermostat_collision_frequency

Collision frequency of the Andersen thermostat in 1/ps. Default: NaN

add_barostat

Flag, whether an MonteCarlo barostat should be attached when setting up the Simulation. Default: False

barostat_temperature

Temperature for the MonteCarlo Barostat in K. Default: NaN

barostat_pressure

Pressure for the MonteCarlo Barostat in bar. Default: NaN

barostat_frequency

Frequency of the MonteCarlo Barostat. Default: 25

integrator

Integrator to move the simulation forward in time. OpenMM offers following Integrators: VerletIntegrator, BrownianIntegrator, LangevinIntegrator, VariableVerletIntegrator and VariableLangevinIntegrator. Default: None

solvent_dielectric

Solvent dielectric constant. This is used for the GBSA force when the Simulation gets set up. Default: 78.3

solute_dielectric

Solute dielectric constant. This is used for the GBSA force when the Simulation gets set up. Default: 1.0

reaction_field_dielecric

Sets the reaction field dielectric for the Nonbonded Force when setting up the Simulation. Default: 78.3

use_dispersion_correction

Flag, whether the dispersion correction should be used when setting up the Nonbonded Force in the Simulation. Default: True

keep_ff_specific_naming

When running through the 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

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 configuring the compilation.

custom_plugin_directory

Path where custom plugins are searched for. Defaults to “share/openstructure/openmm_plugins” within the OST installation or to 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 Forcefield.

SetException(residue, exception_name)
Parameters: residue (ResidueHandle) – Residue for which the exception should be set. exception_name (str) – Name of the Blockmodifier in the forcefield that should be applied in case of a termini
HasException(residue)
Parameters: residue (ResidueHandle) – Residue that should be checked for exceptions bool True if residue has an exception
GetException(residue)
Parameters: residue (ResidueHandle) – Residue containing the exception RuntimeError if residue has no associated exception str describing the name of the Blockmodifier in the forcefield that should be applied in case of a terminal residue

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