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 theTopologyCreator
. The actual distances from theEntityHandle
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 theSimulation
. 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 inTopologyCreator
. Default: None
- termini_exceptions¶
Use termini other than the defaults set in the
Forcefield
when usingTopologyCreator
. Has to be aTerminiExceptions
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
andVariableLangevinIntegrator
. 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