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

Returns:

bool True if residue has an exception

GetException(residue)¶

Parameters:

residue (ResidueHandle) – Residue containing the exception

Raises:

RuntimeError if residue has no associated exception

Returns:

str describing the name of the Blockmodifier in the forcefield that should be applied in case of a terminal residue