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IMP Reference Guide  develop.97bab1d8fd,2021/09/21
The Integrative Modeling Platform
IMP::atom::MolecularDynamics Class Reference

Simple molecular dynamics optimizer. More...

#include <IMP/atom/MolecularDynamics.h>

+ Inheritance diagram for IMP::atom::MolecularDynamics:

Detailed Description

Simple molecular dynamics optimizer.

The particles to be optimized must have optimizable x,y,z attributes and a non-optimizable mass attribute; this optimizer assumes the score to be energy in kcal/mol, the xyz coordinates to be in angstroms, and the mass to be in AMU (g/mol).

Note
RigidBody particles are not handled properly.

Particles without optimized x,y,z and nonoptimized mass are skipped.

See Also
VelocityScalingOptimizerState
LangevinThermostatOptimizerState
BerendsenThermostatOptimizerState
RemoveRigidMotionOptimizerState

Definition at line 107 of file atom/MolecularDynamics.h.

Public Member Functions

 MolecularDynamics (Model *m)
 
virtual void assign_velocities (Float temperature)
 Assign velocities representative of the given temperature. More...
 
virtual double do_step (const ParticleIndexes &sc, double dt)
 Perform a single time step. More...
 
virtual bool get_is_simulation_particle (ParticleIndex p) const
 Return true if the passed particle is appropriate for the simulation. More...
 
virtual Float get_kinetic_energy () const
 Return the current kinetic energy of the system, in kcal/mol. More...
 
Float get_kinetic_temperature (Float ekinetic) const
 Return the current kinetic temperature of the system. More...
 
virtual std::string get_type_name () const
 
virtual ::IMP::VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
void set_velocity_cap (Float velocity_cap)
 Set maximum velocity in A/fs. More...
 
virtual void setup (const ParticleIndexes &ps)
 
- Public Member Functions inherited from IMP::atom::Simulator
 Simulator (Model *m, std::string name="Simulator %1%", double wave_factor=1.0)
 
double get_current_time () const
 
double get_kt () const
 
ParticleIndexes get_simulation_particle_indexes () const
 
ParticlesTemp get_simulation_particles () const
 Returns the set of particles used in the simulation. More...
 
double get_temperature () const
 Return the simulator temperature in kelvin. More...
 
void set_current_time (double ct)
 Sets the current simulation time in femtoseconds to ct. More...
 
void set_temperature (double d)
 Set the temperature of the simulator to d in kelvin units. More...
 
double simulate (double time_in_fs)
 Simulate for a given time in fs. More...
 
double simulate_wave (double time_in_fs, double max_time_step_factor=10.0, double base=1.5)
 
void set_maximum_time_step (double ts)
 
double get_maximum_time_step () const
 Get the maximum allowed time step in fs. More...
 
double get_last_time_step () const
 
void remove_particle (Particle *d)
 
void remove_particles (const Particles &d)
 
void set_particles (const Particles &ps)
 
void set_particles_order (const Particles &objs)
 
unsigned int add_particle (Particle *obj)
 
void add_particles (const Particles &objs)
 
void clear_particles ()
 
unsigned int get_number_of_particles () const
 
bool get_has_particles ()
 
Particleget_particle (unsigned int i) const
 
Particles get_particles () const
 
void reserve_particles (unsigned int sz)
 
- Public Member Functions inherited from IMP::Optimizer
 Optimizer (Model *m, std::string name="Optimizer %1%")
 
double get_last_score () const
 Return the score found in the last evaluate. More...
 
ScoringFunctionget_scoring_function () const
 Return the scoring function that is being used. More...
 
bool get_stop_on_good_score () const
 
double optimize (unsigned int max_steps)
 Optimize the model for up to max_steps iterations. More...
 
virtual void set_scoring_function (ScoringFunctionAdaptor sf)
 Set the scoring function to use. More...
 
void set_stop_on_good_score (bool tf)
 
void remove_optimizer_state (OptimizerState *d)
 
void remove_optimizer_states (const OptimizerStates &d)
 
void set_optimizer_states (const OptimizerStates &ps)
 
void set_optimizer_states_order (const OptimizerStates &objs)
 
unsigned int add_optimizer_state (OptimizerState *obj)
 
void add_optimizer_states (const OptimizerStates &objs)
 
void clear_optimizer_states ()
 
unsigned int get_number_of_optimizer_states () const
 
bool get_has_optimizer_states ()
 
OptimizerStateget_optimizer_state (unsigned int i) const
 
OptimizerStates get_optimizer_states () const
 
void reserve_optimizer_states (unsigned int sz)
 
- Public Member Functions inherited from IMP::ModelObject
 ModelObject (Model *m, std::string name)
 
bool get_has_dependencies () const
 Return whether this object has dependencies computed. More...
 
bool get_has_required_score_states () const
 Return whether score states are computed. More...
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 Get the interacting sets induced by this ModelObject. More...
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_required_score_states () const
 Get the score states that are ancestors of this in the dependency graph. More...
 
void set_has_dependencies (bool tf)
 Either invalidate the dependencies or ensure they are correct. More...
 
void set_has_required_score_states (bool tf)
 Compute the required score states. More...
 
- Public Member Functions inherited from IMP::Object
virtual void clear_caches ()
 
CheckLevel get_check_level () const
 
LogLevel get_log_level () const
 
void set_check_level (CheckLevel l)
 
void set_log_level (LogLevel l)
 Set the logging level used in this object. More...
 
void set_was_used (bool tf) const
 
void show (std::ostream &out=std::cout) const
 
const std::string & get_name () const
 
void set_name (std::string name)
 

Protected Member Functions

void cap_velocity_component (Float &vel)
 Cap a velocity component to the maximum value. More...
 
void initialize ()
 
virtual void propagate_coordinates (const ParticleIndexes &ps, double step_size)
 First part of velocity Verlet (update coordinates and half-step velocity) More...
 
virtual void propagate_velocities (const ParticleIndexes &ps, double step_size)
 Second part of velocity Verlet (update velocity) More...
 
virtual void setup_degrees_of_freedom (const ParticleIndexes &ps)
 
- Protected Member Functions inherited from IMP::atom::Simulator
virtual Float do_optimize (unsigned int max_steps)
 override this function to do actual optimization More...
 
virtual double do_simulate (double time)
 
virtual double do_simulate_wave (double time_in_fs, double max_time_step_factor=10.0, double base=1.5)
 
- Protected Member Functions inherited from IMP::Optimizer
virtual ModelObjectsTemp do_get_inputs () const
 
virtual ModelObjectsTemp do_get_outputs () const
 don't return anything here to avoid pointless dependencies More...
 
ModelObjectsTemp get_optimizer_state_inputs () const
 
void update_states () const
 Update optimizer states, should be called at each successful step. More...
 
- Protected Member Functions inherited from IMP::ModelObject
virtual ModelObjectsTemps do_get_interactions () const
 
virtual void handle_set_has_required_score_states (bool)
 
- Protected Member Functions inherited from IMP::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
virtual void do_destroy ()
 

Protected Attributes

int degrees_of_freedom_
 Number of degrees of freedom in the system. More...
 
Float velocity_cap_
 Maximum absolute value of a single velocity component. More...
 

Constructor & Destructor Documentation

IMP::atom::MolecularDynamics::MolecularDynamics ( Model m)

Score based on the provided model

Member Function Documentation

virtual void IMP::atom::MolecularDynamics::assign_velocities ( Float  temperature)
virtual

Assign velocities representative of the given temperature.

Reimplemented in IMP::isd::MolecularDynamics.

void IMP::atom::MolecularDynamics::cap_velocity_component ( Float vel)
protected

Cap a velocity component to the maximum value.

Definition at line 156 of file atom/MolecularDynamics.h.

virtual double IMP::atom::MolecularDynamics::do_step ( const ParticleIndexes sc,
double  dt 
)
virtual

Perform a single time step.

Parameters
[in]scthe particles that should be moved
[in]dtmaximum time step value
Returns
the amount that time should be advanced.

Implements IMP::atom::Simulator.

virtual bool IMP::atom::MolecularDynamics::get_is_simulation_particle ( ParticleIndex  p) const
virtual

Return true if the passed particle is appropriate for the simulation.

Implements IMP::atom::Simulator.

Reimplemented in IMP::isd::MolecularDynamics.

virtual Float IMP::atom::MolecularDynamics::get_kinetic_energy ( ) const
virtual

Return the current kinetic energy of the system, in kcal/mol.

Reimplemented in IMP::isd::MolecularDynamics.

Float IMP::atom::MolecularDynamics::get_kinetic_temperature ( Float  ekinetic) const

Return the current kinetic temperature of the system.

Parameters
[in]ekinetickinetic energy, e.g. from get_kinetic_energy()
virtual ::IMP::VersionInfo IMP::atom::MolecularDynamics::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 140 of file atom/MolecularDynamics.h.

virtual void IMP::atom::MolecularDynamics::propagate_coordinates ( const ParticleIndexes ps,
double  step_size 
)
protectedvirtual

First part of velocity Verlet (update coordinates and half-step velocity)

Reimplemented in IMP::isd::MolecularDynamics.

virtual void IMP::atom::MolecularDynamics::propagate_velocities ( const ParticleIndexes ps,
double  step_size 
)
protectedvirtual

Second part of velocity Verlet (update velocity)

Reimplemented in IMP::isd::MolecularDynamics.

void IMP::atom::MolecularDynamics::set_velocity_cap ( Float  velocity_cap)

Set maximum velocity in A/fs.

At each dynamics time step, the absolute value of each velocity component is capped at this value. This prevents spurious strong forces (occasionally encountered with frustrated conformations) from causing large oscillations in the system. By default, velocities are not capped.

Note
The actual velocities that are capped are the half-step velocities in the velocity Verlet algorithm.

Definition at line 130 of file atom/MolecularDynamics.h.

virtual void IMP::atom::MolecularDynamics::setup ( const ParticleIndexes )
virtual

Perform any setup operations needed before running a series of simulation steps

Note
Called by do_simulate() or do_simulate_wave() before iterative calls to do_step()

Reimplemented from IMP::atom::Simulator.

Member Data Documentation

int IMP::atom::MolecularDynamics::degrees_of_freedom_
protected

Number of degrees of freedom in the system.

Definition at line 165 of file atom/MolecularDynamics.h.

Float IMP::atom::MolecularDynamics::velocity_cap_
protected

Maximum absolute value of a single velocity component.

Definition at line 168 of file atom/MolecularDynamics.h.


The documentation for this class was generated from the following file: