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.

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

See Also: VelocityScalingOptimizerState; LangevinThermostatOptimizerState; BerendsenThermostatOptimizerState; RemoveRigidMotionOptimizerState

Definition at line 34 of file atom/MolecularDynamics.h.

Public Member Functions
	MolecularDynamics (kernel::Model *m)

virtual void	assign_velocities (Float temperature)
	Assign velocities representative of the given temperature. More...

virtual double	do_step (const kernel::ParticleIndexes &sc, double dt)
	Perform a single time step. More...

virtual bool	get_is_simulation_particle (kernel::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::base::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 kernel::ParticleIndexes &ps)

Public Member Functions inherited from IMP::atom::Simulator
	Simulator (kernel::Model *m, std::string name="Simulator %1%", double wave_factor=1.0)

double	get_current_time () const

double	get_kt () const

kernel::ParticleIndexes	get_simulation_particle_indexes () const

kernel::ParticlesTemp	get_simulation_particles () const
	Returns the set of particles used in the simulation. More...

double	get_temperature () const

void	set_current_time (double ct)
	Sets the current simulation time in femtoseconds to ct. More...

void	set_temperature (double d)

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

double	get_last_time_step () const

void	remove_particle (kernel::Particle *d)

void	remove_particles (const kernel::Particles &d)

void	set_particles (const kernel::Particles &ps)

void	set_particles_order (const kernel::Particles &objs)

unsigned int	add_particle (kernel::Particle *obj)

void	add_particles (const kernel::Particles &objs)

void	clear_particles ()

unsigned int	get_number_of_particles () const

bool	get_has_particles ()

kernel::Particle *	get_particle (unsigned int i) const

kernel::Particles	get_particles () const

void	reserve_particles (unsigned int sz)

Public Member Functions inherited from IMP::kernel::Optimizer
	Optimizer (kernel::Model *m, std::string name="Optimizer %1%")

double	get_last_score () const
	Return the score found in the last evaluate. More...

ScoringFunction *	get_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)

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 ()

OptimizerState *	get_optimizer_state (unsigned int i) const

OptimizerStates	get_optimizer_states () const

void	reserve_optimizer_states (unsigned int sz)

Public Member Functions inherited from IMP::kernel::ModelObject
	ModelObject (kernel::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...

Model *	get_model () const

ModelObjectsTemp	get_outputs () const

const ScoreStatesTemp &	get_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::base::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 kernel::ParticleIndexes &ps, double step_size)
	First part of velocity Verlet (update coordinates and half-step velocity) More...

virtual void	propagate_velocities (const kernel::ParticleIndexes &ps, double step_size)
	Second part of velocity Verlet (update velocity) More...

virtual void	setup_degrees_of_freedom (const kernel::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...

Protected Member Functions inherited from IMP::kernel::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::kernel::ModelObject
virtual ModelObjectsTemps	do_get_interactions () const

virtual void	handle_set_has_required_score_states (bool)

Protected Member Functions inherited from IMP::base::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...

FloatKey	vs_ [3]
	Keys of the xyz velocities. More...

Constructor & Destructor Documentation

IMP::atom::MolecularDynamics::MolecularDynamics ( kernel::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 83 of file atom/MolecularDynamics.h.

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

virtual

Perform a single time step.

Parameters

[in] dt maximum time step value

Returns: the amount that time should be advanced.

Implements IMP::atom::Simulator.

virtual bool IMP::atom::MolecularDynamics::get_is_simulation_particle ( kernel::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] ekinetic kinetic energy, e.g. from get_kinetic_energy()

virtual ::IMP::base::VersionInfo IMP::atom::MolecularDynamics::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 67 of file atom/MolecularDynamics.h.

virtual void IMP::atom::MolecularDynamics::propagate_coordinates	(	const kernel::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 kernel::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 57 of file atom/MolecularDynamics.h.

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

virtual

A Simulator class can perform setup operations before a series of simulation steps is taken.

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 95 of file atom/MolecularDynamics.h.

Float IMP::atom::MolecularDynamics::velocity_cap_

protected

Maximum absolute value of a single velocity component.

Definition at line 98 of file atom/MolecularDynamics.h.

FloatKey IMP::atom::MolecularDynamics::vs_[3]

protected

Keys of the xyz velocities.

Definition at line 92 of file atom/MolecularDynamics.h.

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

atom/MolecularDynamics.h

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation