RPMDMonteCarloMembraneBarostat¶

class openmm.openmm.RPMDMonteCarloMembraneBarostat(*args)¶

This class is very similar to MonteCarloMembraneBarostat, but it is specifically designed for use with RPMDIntegrator. For each trial move, it scales all copies of the system by the same amount, then accepts or rejects the move based on the change to the total energy of the ring polymer (as returned by the integrator’s getTotalEnergy() method).

__init__(self, defaultPressure, defaultSurfaceTension, xymode, zmode, frequency=25, scaleMoleculesAsRigid=True) → RPMDMonteCarloMembraneBarostat¶

__init__(self, other) → RPMDMonteCarloMembraneBarostat

Create a RPMDMonteCarloMembraneBarostat.

Parameters:

defaultPressure (float) – the default pressure acting on the system (in bar)
defaultSurfaceTension (float) – the default surface tension acting on the system (in bar*nm)
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)
scaleMoleculesAsRigid (bool) – if true, coordinate scaling keeps molecules rigid, scaling only the center of mass of each one. If false, every atom is scaled independently.

Methods

`Pressure`()	This is the name of the parameter which stores the current pressure acting on the system (in bar).
`SurfaceTension`()	This is the name of the parameter which stores the current surface tension acting on the system (in bar*nm).
`__init__`(-> RPMDMonteCarloMembraneBarostat)	Create a RPMDMonteCarloMembraneBarostat.
`getDefaultPressure`(self)	Get the default pressure acting on the system (in bar).
`getDefaultSurfaceTension`(self)	Get the default surface tension acting on the system (in bar*nm).
`getForceGroup`(self)	Get the force group this Force belongs to.
`getFrequency`(self)	Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.
`getName`(self)	Get the name of this Force.
`getRandomNumberSeed`(self)	Get the random number seed.
`getScaleMoleculesAsRigid`(self)	Get whether scaling is applied to the centroid of each molecule while keeping the molecules rigid, or to each atom independently.
`getXYMode`(self)	Get the mode specifying the behavior of the X and Y axes.
`getZMode`(self)	Get the mode specifying the behavior of the Z axis.
`setDefaultPressure`(self, pressure)	Set the default pressure acting on the system.
`setDefaultSurfaceTension`(self, surfaceTension)	Set the default surface tension acting on the system.
`setForceGroup`(self, group)	Set the force group this Force belongs to.
`setFrequency`(self, freq)	Set the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.
`setName`(self, name)	Set the name of this Force.
`setRandomNumberSeed`(self, seed)	Set the random number seed.
`setScaleMoleculesAsRigid`(self, rigid)	Set whether scaling is applied to the centroid of each molecule while keeping the molecules rigid, or to each atom independently.
`setXYMode`(self, mode)	Set the mode specifying the behavior of the X and Y axes.
`setZMode`(self, mode)	Set the mode specifying the behavior of the Z axis.
`usesPeriodicBoundaryConditions`(self)	Returns whether or not this force makes use of periodic boundary conditions.

Attributes

`ConstantVolume`
`XYAnisotropic`
`XYIsotropic`
`ZFixed`
`ZFree`
`thisown`	The membership flag

property thisown¶: The membership flag

static Pressure() → str¶: This is the name of the parameter which stores the current pressure acting on the system (in bar).

static SurfaceTension() → str¶: This is the name of the parameter which stores the current surface tension acting on the system (in bar*nm).

getDefaultPressure(self) → float¶

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

Returns:: the default pressure acting on the system, measured in bar.
Return type:: float

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

getDefaultSurfaceTension(self) → float¶

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.
Return type:: float

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

getFrequency(self) → int¶: Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted. If this is set to 0, the barostat is disabled.

setFrequency(self, freq)¶: Set the frequency (in time steps) at which Monte Carlo pressure changes should be attempted. If this is set to 0, the barostat is disabled.

getXYMode(self) → OpenMM::RPMDMonteCarloMembraneBarostat::XYMode¶: Get the mode specifying the behavior of the X and Y axes.

setXYMode(self, mode)¶: Set the mode specifying the behavior of the X and Y axes.

getZMode(self) → OpenMM::RPMDMonteCarloMembraneBarostat::ZMode¶: Get the mode specifying the behavior of the Z axis.

setZMode(self, mode)¶: Set the mode specifying the behavior of the Z axis.

getRandomNumberSeed(self) → int¶: Get the random number seed. See setRandomNumberSeed() for details.

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.

usesPeriodicBoundaryConditions(self) → bool¶

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

Returns:: true if force uses PBC and false otherwise
Return type:: bool

getScaleMoleculesAsRigid(self) → bool¶

Get whether scaling is applied to the centroid of each molecule while keeping the molecules rigid, or to each atom independently.

Returns:: true if scaling is applied to molecule centroids, false if it is applied to each atom independently.
Return type:: bool

setScaleMoleculesAsRigid(self, rigid)¶: Set whether scaling is applied to the centroid of each molecule while keeping the molecules rigid, or to each atom independently.

getForceGroup(self) → int¶: Get the force group this Force belongs to.

getName(self) → str¶: Get the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.

setForceGroup(self, group)¶

Set the force group this Force belongs to.

Parameters:: group (int) – the group index. Legal values are between 0 and 31 (inclusive).

setName(self, name)¶: Set the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.