Simple molecular dynamics optimizer. More...

#include <IMP/atom/MolecularDynamics.h>

Inheritance diagram for IMP::atom::MolecularDynamics:

Public Member Functions
	MolecularDynamics (Model *m=nullptr)

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

virtual Float	get_kinetic_energy () const

Float	get_kinetic_temperature (Float ekinetic) const

void	set_velocity_cap (Float velocity_cap)
	Set maximum velocity in A/fs. More...

Public Member Functions inherited from IMP::atom::Simulator
	Simulator (Model *m, std::string name="Simulator %1%")
	Create the optimizer. More...

double	get_current_time () const

double	get_kt () const

ParticleIndexes	get_simulation_particle_indexes () const

ParticlesTemp	get_simulation_particles () const

double	get_temperature () const

	IMP_OPTIMIZER (Simulator)

void	set_temperature (double d)

double	simulate (double time_in_fs)
	Simulate until the given time in fs.

void	set_maximum_time_step (double ts)

double	get_maximum_time_step () const

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 ()

Particle *	get_particle (unsigned int i) const

Particles	get_particles () const

void	reserve_particles (unsigned int sz)

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

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

Model *	get_model () const
	Get the model being optimized.

ScoringFunction *	get_scoring_function () const
	Return the scoring function that is being used.

bool	get_stop_on_good_score () const

double	optimize (unsigned int max_steps)
	Optimize the model for up to max_steps iterations. More...

void	set_model (Model *m)
	Set the model being optimized. More...

virtual void	set_scoring_function (ScoringFunctionAdaptor sf)

void	set_stop_on_good_score (bool tf)

virtual void	show (std::ostream &out=std::cout) const
	Print info about the optimizer state. More...

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::base::Object
virtual void	clear_caches ()

virtual IMP::base::VersionInfo	get_version_info () const =0
	Get information about the module and version of the object.

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.

void	initialize ()

virtual void	propagate_coordinates (const ParticleIndexes &ps, double step_size)
	First part of velocity Verlet (update coordinates and half-step velocity)

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

virtual void	setup_degrees_of_freedom (const ParticleIndexes &ps)

Protected Attributes
int	degrees_of_freedom_
	Number of degrees of freedom in the system.

Float	velocity_cap_
	Maximum absolute value of a single velocity component.

FloatKey	vs_ [3]
	Keys of the xyz velocities.

Additional Inherited Members
Related Functions inherited from IMP::atom::Simulator
void	set_current_time (double ct)

typedef IMP::base::Vector < IMP::base::WeakPointer < Simulator > >	SimulatorsTemp

Detailed Description

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 34 of file atom/MolecularDynamics.h.

Constructor & Destructor Documentation

IMP::atom::MolecularDynamics::MolecularDynamics ( Model * m = nullptr )

Score based on the provided model

Member Function Documentation

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

virtual

Returns: 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

Returns: the current kinetic temperature of the system

Parameters

[in] ekinetic kinetic energy, e.g. from get_kinetic_energy()

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

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 58 of file atom/MolecularDynamics.h.

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

atom/MolecularDynamics.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation