IMP::atom::MolecularDynamics Class Reference

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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).

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

See also:

VelocityScalingOptimizerState

LangevinThermostatOptimizerState

BerendsenThermostatOptimizerState

RemoveRigidMotionOptimizerState

Examples: dock with crosslinks

Inheritance diagram for IMP::atom::MolecularDynamics:

List of all members.

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.
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.

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Constructor & Destructor Documentation

IMP::atom::MolecularDynamics::MolecularDynamics

(

Model *

m = nullptr

)

Score based on the provided model

Reimplemented in IMP::isd::MolecularDynamics.

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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.

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()

virtual void IMP::atom::MolecularDynamics::propagate_coordinates	(	const ParticleIndexes &	ps,
		double	step_size
	)		[protected, virtual]

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
	)		[protected, virtual]

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.

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Member Data Documentation

int IMP::atom::MolecularDynamics::degrees_of_freedom_ [protected]

Number of degrees of freedom in the system.

Float IMP::atom::MolecularDynamics::velocity_cap_ [protected]

Maximum absolute value of a single velocity component.

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

Keys of the xyz velocities.

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

• atom/MolecularDynamics.h