MonteCarloMembraneBarostat

class OpenMM::MonteCarloMembraneBarostat

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.

Methods

MonteCarloMembraneBarostat	Create a MonteCarloMembraneBarostat.
getDefaultPressure	Get the default pressure acting on the system (in bar).
setDefaultPressure	Set the default pressure acting on the system.
getDefaultSurfaceTension	Get the default surface tension acting on the system (in bar*nm).
setDefaultSurfaceTension	Set the default surface tension acting on the system.
getFrequency	Get the frequency (in time steps) at which Monte Carlo volume changes should be attempted.
setFrequency	Set the frequency (in time steps) at which Monte Carlo volume changes should be attempted.
getDefaultTemperature	Get the default temperature at which the system is being maintained, measured in Kelvin.
setDefaultTemperature	Set the default temperature at which the system is being maintained.
getXYMode	Get the mode specifying the behavior of the X and Y axes.
setXYMode	Set the mode specifying the behavior of the X and Y axes.
getZMode	Get the mode specifying the behavior of the Z axis.
setZMode	Set the mode specifying the behavior of the Z axis.
getRandomNumberSeed	Get the random number seed.
setRandomNumberSeed	Set the random number seed.
usesPeriodicBoundaryConditions	Returns whether or not this force makes use of periodic boundary conditions.

Enum: XYMode

XYIsotropic	The X and Y axes are always scaled by the same amount, so the ratio of their lengths remains constant.
XYAnisotropic	The X and Y axes are allowed to vary independently of each other.

Enum: ZMode

ZFree	The Z axis is allowed to vary freely, independent of the other two axes.
ZFixed	The Z axis is held fixed and does not change.
ConstantVolume	The Z axis is always scaled in inverse proportion to the other two axes so the box volume remains fixed. Note that in this mode pressure has no effect on the system, only surface tension.

const std::string &Pressure()

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

const std::string &SurfaceTension()

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

const std::string &Temperature()

This is the name of the parameter which stores the current temperature at which the system is being maintained (in Kelvin)

MonteCarloMembraneBarostat(double defaultPressure, double defaultSurfaceTension, double defaultTemperature, XYMode xymode, ZMode zmode, int frequency = 25)

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)

• defaultTemperature – the default 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)

double getDefaultPressure() const

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

Returns

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

void setDefaultPressure(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.

double getDefaultSurfaceTension() const

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

Returns

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

void setDefaultSurfaceTension(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.

int getFrequency() const

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.

void setFrequency(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.

double getDefaultTemperature() const

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

void setDefaultTemperature(double temp)

Set the default temperature at which the system is being maintained. This will affect any new Contexts you create, but not ones that already exist.

Parameters

• temp – the system temperature, measured in Kelvin.

XYMode getXYMode() const

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

void setXYMode(XYMode mode)

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

ZMode getZMode() const

Get the mode specifying the behavior of the Z axis.

void setZMode(ZMode mode)

Set the mode specifying the behavior of the Z axis.

int getRandomNumberSeed() const

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

void setRandomNumberSeed(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.

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.

bool usesPeriodicBoundaryConditions() const

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

Returns

true if force uses PBC and false otherwise