MonteCarloMembraneBarostat Class Reference

This is a Monte Carlo barostat designed specifically for membrane simulations. More...

Inheritance diagram for MonteCarloMembraneBarostat:

Public Member Functions
def	Pressure
	Pressure() -> std::string const &. More...
def	SurfaceTension
	SurfaceTension() -> std::string const &. More...
def	getDefaultPressure
	getDefaultPressure(MonteCarloMembraneBarostat self) -> double More...
def	setDefaultPressure
	setDefaultPressure(MonteCarloMembraneBarostat self, double pressure) More...
def	getDefaultSurfaceTension
	getDefaultSurfaceTension(MonteCarloMembraneBarostat self) -> double More...
def	setDefaultSurfaceTension
	setDefaultSurfaceTension(MonteCarloMembraneBarostat self, double surfaceTension) More...
def	getFrequency
	getFrequency(MonteCarloMembraneBarostat self) -> int More...
def	setFrequency
	setFrequency(MonteCarloMembraneBarostat self, int freq) More...
def	getTemperature
	getTemperature(MonteCarloMembraneBarostat self) -> double More...
def	setTemperature
	setTemperature(MonteCarloMembraneBarostat self, double temp) More...
def	getXYMode
	getXYMode(MonteCarloMembraneBarostat self) -> OpenMM::MonteCarloMembraneBarostat::XYMode More...
def	setXYMode
	setXYMode(MonteCarloMembraneBarostat self, OpenMM::MonteCarloMembraneBarostat::XYMode mode) More...
def	getZMode
	getZMode(MonteCarloMembraneBarostat self) -> OpenMM::MonteCarloMembraneBarostat::ZMode More...
def	setZMode
	setZMode(MonteCarloMembraneBarostat self, OpenMM::MonteCarloMembraneBarostat::ZMode mode) More...
def	getRandomNumberSeed
	getRandomNumberSeed(MonteCarloMembraneBarostat self) -> int More...
def	setRandomNumberSeed
	setRandomNumberSeed(MonteCarloMembraneBarostat self, int seed) More...
def	__init__
	init(OpenMM::MonteCarloMembraneBarostat self, double defaultPressure, double defaultSurfaceTension, double temperature, OpenMM::MonteCarloMembraneBarostat::XYMode xymode, OpenMM::MonteCarloMembraneBarostat::ZMode zmode, int frequency=25) -> MonteCarloMembraneBarostat init(OpenMM::MonteCarloMembraneBarostat self, double defaultPressure, double defaultSurfaceTension, double temperature, OpenMM::MonteCarloMembraneBarostat::XYMode xymode, OpenMM::MonteCarloMembraneBarostat::ZMode zmode) -> MonteCarloMembraneBarostat init(OpenMM::MonteCarloMembraneBarostat self, MonteCarloMembraneBarostat other) -> MonteCarloMembraneBarostat More...
def	__del__
	del(OpenMM::MonteCarloMembraneBarostat self) More...
Public Member Functions inherited from Force
def	__init__
def	__del__
	del(OpenMM::Force self) More...
def	getForceGroup
	getForceGroup(Force self) -> int More...
def	setForceGroup
	setForceGroup(Force self, int group) More...
def	__copy__
def	__deepcopy__

Public Attributes
	this

Static Public Attributes
	XYIsotropic = _openmm.MonteCarloMembraneBarostat_XYIsotropic
	XYAnisotropic = _openmm.MonteCarloMembraneBarostat_XYAnisotropic
	ZFree = _openmm.MonteCarloMembraneBarostat_ZFree
	ZFixed = _openmm.MonteCarloMembraneBarostat_ZFixed
	ConstantVolume = _openmm.MonteCarloMembraneBarostat_ConstantVolume

Detailed Description

This is a Monte Carlo barostat designed specifically for membrane simulations.

It assumes the membrane lies in the XY plane. The Monte Carlo acceptance criterion includes a term to model isotropic pressure, which depends on the volume of the periodic box, and a second term to model surface tension, which depends on the cross sectional area of the box in the XY plane. Note that pressure and surface tension are defined with opposite senses: a larger pressure tends to make the box smaller, but a larger surface tension tends to make the box larger.

There are options for configuring exactly how the various box dimensions are allowed to change:

• The X and Y axes may be treated isotropically, in which case they always scale by the same amount and remain in proportion to each other; or they may be treated anisotropically, in which case they can vary independently of each other.

• The Z axis can be allowed to vary independently of the other axes; or held fixed; or constrained to vary in inverse proportion to the other two axes, so that the total box volume remains fixed.

This class assumes the simulation is also being run at constant temperature, and requires you to specify the system temperature (since it affects the acceptance probability for Monte Carlo moves). It does not actually perform temperature regulation, however. You must use another mechanism along with it to maintain the temperature, such as LangevinIntegrator or AndersenThermostat.

Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

init(OpenMM::MonteCarloMembraneBarostat self, double defaultPressure, double defaultSurfaceTension, double temperature, OpenMM::MonteCarloMembraneBarostat::XYMode xymode, OpenMM::MonteCarloMembraneBarostat::ZMode zmode, int frequency=25) -> MonteCarloMembraneBarostat init(OpenMM::MonteCarloMembraneBarostat self, double defaultPressure, double defaultSurfaceTension, double temperature, OpenMM::MonteCarloMembraneBarostat::XYMode xymode, OpenMM::MonteCarloMembraneBarostat::ZMode zmode) -> MonteCarloMembraneBarostat init(OpenMM::MonteCarloMembraneBarostat self, MonteCarloMembraneBarostat other) -> MonteCarloMembraneBarostat

Create a MonteCarloMembraneBarostat.

Parameters

defaultPressure	the default pressure acting on the system (in bar)
defaultSurfaceTension	the default surface tension acting on the system (in bar*nm)
temperature	the temperature at which the system is being maintained (in Kelvin)
xymode	the mode specifying the behavior of the X and Y axes
zmode	the mode specifying the behavior of the Z axis
frequency	the frequency at which Monte Carlo volume changes should be attempted (in time steps)

References simtk.openmm.openmm.stripUnits().

def __del__

(

self

)

del(OpenMM::MonteCarloMembraneBarostat self)

References simtk.openmm.openmm.stripUnits().

Member Function Documentation

def getDefaultPressure

(

self

)

getDefaultPressure(MonteCarloMembraneBarostat self) -> double

Get the default pressure acting on the system (in bar).

References simtk.openmm.openmm.stripUnits().

def getDefaultSurfaceTension

(

self

)

getDefaultSurfaceTension(MonteCarloMembraneBarostat self) -> double

Get the default surface tension acting on the system (in bar*nm).

References simtk.openmm.openmm.stripUnits().

def getFrequency

(

self

)

getFrequency(MonteCarloMembraneBarostat self) -> int

Get the frequency (in time steps) at which Monte Carlo volume changes should be attempted. If this is set to 0, the barostat is disabled.

References simtk.openmm.openmm.stripUnits().

def getRandomNumberSeed

(

self

)

getRandomNumberSeed(MonteCarloMembraneBarostat self) -> int

Get the random number seed. See setRandomNumberSeed() for details.

References simtk.openmm.openmm.stripUnits().

def getTemperature

(

self

)

getTemperature(MonteCarloMembraneBarostat self) -> double

Get the temperature at which the system is being maintained, measured in Kelvin.

References simtk.openmm.openmm.stripUnits().

def getXYMode

(

self

)

getXYMode(MonteCarloMembraneBarostat self) -> OpenMM::MonteCarloMembraneBarostat::XYMode

Get the mode specifying the behavior of the X and Y axes.

References simtk.openmm.openmm.stripUnits().

def getZMode

(

self

)

getZMode(MonteCarloMembraneBarostat self) -> OpenMM::MonteCarloMembraneBarostat::ZMode

Get the mode specifying the behavior of the Z axis.

References simtk.openmm.openmm.stripUnits().

def Pressure

(

)

Pressure() -> std::string const &.

This is the name of the parameter which stores the current pressure acting on the system (in bar).

References simtk.openmm.openmm.stripUnits().

def setDefaultPressure	(		self,
			args
	)

setDefaultPressure(MonteCarloMembraneBarostat self, double pressure)

Set the default pressure acting on the system. This will affect any new Contexts you create, but not ones that already exist.

Parameters

pressure

the default pressure acting on the system, measured in bar.

References simtk.openmm.openmm.stripUnits().

def setDefaultSurfaceTension	(		self,
			args
	)

setDefaultSurfaceTension(MonteCarloMembraneBarostat self, double surfaceTension)

Set the default surface tension acting on the system. This will affect any new Contexts you create, but not ones that already exist.

Parameters

surfaceTension

the default surface tension acting on the system, measured in bar.

References simtk.openmm.openmm.stripUnits().

def setFrequency	(		self,
			args
	)

setFrequency(MonteCarloMembraneBarostat self, int freq)

Set the frequency (in time steps) at which Monte Carlo volume changes should be attempted. If this is set to 0, the barostat is disabled.

References simtk.openmm.openmm.stripUnits().

def setRandomNumberSeed	(		self,
			args
	)

setRandomNumberSeed(MonteCarloMembraneBarostat self, int seed)

Set the random number seed. It is guaranteed that if two simulations are run with different random number seeds, the sequence of Monte Carlo steps will be different. On the other hand, no guarantees are made about the behavior of simulations that use the same seed. In particular, Platforms are permitted to use non-deterministic algorithms which produce different results on successive runs, even if those runs were initialized identically.

References simtk.openmm.openmm.stripUnits().

def setTemperature	(		self,
			args
	)

setTemperature(MonteCarloMembraneBarostat self, double temp)

Set the temperature at which the system is being maintained.

Parameters

temp	the system temperature, measured in Kelvin.

References simtk.openmm.openmm.stripUnits().

def setXYMode	(		self,
			args
	)

setXYMode(MonteCarloMembraneBarostat self, OpenMM::MonteCarloMembraneBarostat::XYMode mode)

Set the mode specifying the behavior of the X and Y axes.

References simtk.openmm.openmm.stripUnits().

def setZMode	(		self,
			args
	)

setZMode(MonteCarloMembraneBarostat self, OpenMM::MonteCarloMembraneBarostat::ZMode mode)

Set the mode specifying the behavior of the Z axis.

References simtk.openmm.openmm.stripUnits().

def SurfaceTension

(

)

SurfaceTension() -> std::string const &.

This is the name of the parameter which stores the current surface tension acting on the system (in bar*nm).

References simtk.openmm.openmm.stripUnits().

Member Data Documentation

ConstantVolume = _openmm.MonteCarloMembraneBarostat_ConstantVolume

static

this

XYAnisotropic = _openmm.MonteCarloMembraneBarostat_XYAnisotropic

static

XYIsotropic = _openmm.MonteCarloMembraneBarostat_XYIsotropic

static

ZFixed = _openmm.MonteCarloMembraneBarostat_ZFixed

static

ZFree = _openmm.MonteCarloMembraneBarostat_ZFree

static

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

• openmm.py