IMP::atom::BerendsenThermostatOptimizerState Class Reference

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Detailed Description

Maintains temperature during molecular dynamics.

The thermostat scales velocities using the algorithm described in H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak "Molecular dynamics with coupling to an external bath", Journal of Chemical Physics 81 pp. 3684-3690 (1984).

At each update, velocities are rescaled by

where is the molecular dynamics timestep, is the coupling constant (in fs) of the thermostat, is the thermostat temperature, and is the instantaneous (kinetic) temperature of the dynamics. (This is equation 11 from the reference above.)

Inheritance diagram for IMP::atom::BerendsenThermostatOptimizerState:

List of all members.

Public Member Functions
	BerendsenThermostatOptimizerState (const Particles &pis, double temperature, double tau)
double	get_tau ()
double	get_temperature ()
void	rescale_velocities () const
	Rescale the velocities now.
void	set_particles (const Particles &pis)
	Set the particles to use.
void	set_tau (double tau)
void	set_temperature (double temperature)
virtual void	update ()
	Called when the Optimizer accepts a new conformation.
Public Member Functions inherited from IMP::OptimizerState
	OptimizerState (std::string name="OptimizerState %1%")
Optimizer *	get_optimizer () const
virtual void	set_is_optimizing (bool)
Public Member Functions inherited from IMP::base::Object
std::size_t	__hash__ () const
virtual std::string	get_type_name () const =0
	Return a string identifying the type of the object.
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.
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)

Static Public Member Functions
static BerendsenThermostatOptimizerState *	get_from (IMP::base::Object *o)

Additional Inherited Members
Protected Attributes inherited from IMP::OptimizerState
UncheckedWeakPointer< Optimizer >	optimizer_

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Member Function Documentation

void IMP::atom::BerendsenThermostatOptimizerState::rescale_velocities

(

)

const

Rescale the velocities now.

void IMP::atom::BerendsenThermostatOptimizerState::set_particles

(

const Particles &

pis

)

Set the particles to use.

virtual void IMP::atom::BerendsenThermostatOptimizerState::update ( )

virtual

Called when the Optimizer accepts a new conformation.

Implements IMP::OptimizerState.

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

• BerendsenThermostatOptimizerState.h