MonteCarloMembraneBarostat Class Reference

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

Inheritance diagram for MonteCarloMembraneBarostat:

List of all members.

Public Member Functions
def	Pressure
	Pressure() -> std::string const &.
def	SurfaceTension
	SurfaceTension() -> std::string const &.
def	getDefaultPressure
	getDefaultPressure(self) -> double
def	setDefaultPressure
	Set the default pressure acting on the system.
def	getDefaultSurfaceTension
	getDefaultSurfaceTension(self) -> double
def	setDefaultSurfaceTension
	Set the default surface tension acting on the system.
def	getFrequency
	getFrequency(self) -> int
def	setFrequency
	Set the frequency (in time steps) at which Monte Carlo volume changes should be attempted.
def	getTemperature
	getTemperature(self) -> double
def	setTemperature
	Set the temperature at which the system is being maintained.
def	getXYMode
	getXYMode(self) -> OpenMM::MonteCarloMembraneBarostat::XYMode
def	setXYMode
	Set the mode specifying the behavior of the X and Y axes.
def	getZMode
	getZMode(self) -> OpenMM::MonteCarloMembraneBarostat::ZMode
def	setZMode
	Set the mode specifying the behavior of the Z axis.
def	getRandomNumberSeed
	getRandomNumberSeed(self) -> int
def	setRandomNumberSeed
	Set the random number seed.
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(self) -> bool
def	__init__
	__init__(self, defaultPressure, defaultSurfaceTension, temperature, xymode, zmode, frequency=25) -> MonteCarloMembraneBarostat __init__(self, defaultPressure, defaultSurfaceTension, temperature, xymode, zmode) -> MonteCarloMembraneBarostat __init__(self, other) -> MonteCarloMembraneBarostat
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
tuple	Pressure = staticmethod(Pressure)
tuple	SurfaceTension = staticmethod(SurfaceTension)

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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.

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Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

__init__(self, defaultPressure, defaultSurfaceTension, temperature, xymode, zmode, frequency=25) -> MonteCarloMembraneBarostat __init__(self, defaultPressure, defaultSurfaceTension, temperature, xymode, zmode) -> MonteCarloMembraneBarostat __init__(self, other) -> MonteCarloMembraneBarostat

Create a MonteCarloMembraneBarostat.

Parameters:

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

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Member Function Documentation

def getDefaultPressure

(

self

)

getDefaultPressure(self) -> double

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

Returns:

(double) the default pressure acting on the system, measured in bar.

def getDefaultSurfaceTension

(

self

)

getDefaultSurfaceTension(self) -> double

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

Returns:

(double) the default surface tension acting on the system, measured in bar*nm.

def getFrequency

(

self

)

getFrequency(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.

def getRandomNumberSeed

(

self

)

getRandomNumberSeed(self) -> int

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

def getTemperature

(

self

)

getTemperature(self) -> double

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

def getXYMode

(

self

)

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

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

def getZMode

(

self

)

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

Get the mode specifying the behavior of the Z axis.

def Pressure

(

)

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

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

def setDefaultPressure	(		self,
			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

(double) the default pressure acting on the system, measured in bar.

def setDefaultSurfaceTension	(		self,
			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

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

def setFrequency	(		self,
			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.

def setRandomNumberSeed	(		self,
			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.

If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context is created from this Force. This is done to ensure that each Context receives unique random seeds without you needing to set them explicitly.

def setTemperature	(		self,
			temp
	)

Set the temperature at which the system is being maintained.

Parameters:

temp	(double) the system temperature, measured in Kelvin.

def setXYMode	(		self,
			mode
	)

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

def setZMode	(		self,
			mode
	)

Set the mode specifying the behavior of the Z axis.

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).

def usesPeriodicBoundaryConditions

(

self

)

usesPeriodicBoundaryConditions(self) -> bool

Returns whether or not this force makes use of periodic boundary conditions.

Returns:

(bool) true if force uses PBC and false otherwise

Reimplemented from Force.

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Member Data Documentation

ConstantVolume = _openmm.MonteCarloMembraneBarostat_ConstantVolume [static]

tuple Pressure = staticmethod(Pressure) [static]

tuple SurfaceTension = staticmethod(SurfaceTension) [static]

this

Reimplemented from Force.

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