Package ffx.openmm

Class MonteCarloFlexibleBarostat

java.lang.Object
ffx.openmm.Force
ffx.openmm.MonteCarloFlexibleBarostat
public class MonteCarloFlexibleBarostat extends Force
This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure. It assumes the simulation is running at constant temperature, and the box size is adjusted to maintain constant pressure. Unlike MonteCarloBarostat, this version allows flexible scaling of molecules, making it suitable for systems where molecular flexibility is important.

This class is most useful for simulating a system at constant pressure when flexible molecular scaling is desired, such as for systems with significant intramolecular flexibility or conformational changes.

  • Constructor Details

    • MonteCarloFlexibleBarostat

      public MonteCarloFlexibleBarostat(double defaultPressure, double defaultTemperature, int frequency, int scaleMoleculesAsRigid)
      Create a MonteCarloFlexibleBarostat.
      Parameters:
      defaultPressure - The default pressure acting on the system (in bar).
      defaultTemperature - The default temperature at which the system is being maintained (in Kelvin).
      frequency - The frequency at which Monte Carlo pressure changes should be attempted (in time steps).
      scaleMoleculesAsRigid - Whether to scale molecules as rigid bodies (1) or allow flexible scaling (0).

  • Method Details

    • computeCurrentPressure

      public void computeCurrentPressure(Context context, com.sun.jna.ptr.PointerByReference pressure)
      Compute the current pressure in the system.
      Parameters:
      context - The context for which to compute the pressure.
      pressure - The computed pressure (output).

    • destroy

      public void destroy()
      Destroy the force.
      Specified by:
      destroy in class Force

    • getDefaultPressure

      public double getDefaultPressure()
      Get the default pressure (in bar).
      Returns:
      The default pressure acting on the system.

    • getDefaultTemperature

      public double getDefaultTemperature()
      Get the default temperature at which the system is being maintained (in Kelvin).
      Returns:
      The default temperature.

    • getFrequency

      public int getFrequency()
      Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.
      Returns:
      The frequency of pressure change attempts.

    • getRandomNumberSeed

      public int getRandomNumberSeed()
      Get the random number seed. See setRandomNumberSeed() for details.
      Returns:
      The random number seed.

    • getScaleMoleculesAsRigid

      public int getScaleMoleculesAsRigid()
      Get whether molecules are scaled as rigid bodies.
      Returns:
      1 if molecules are scaled as rigid bodies, 0 if flexible scaling is used.

    • setDefaultPressure

      public void setDefaultPressure(double pressure)
      Set the default pressure acting on the system (in bar).
      Parameters:
      pressure - The default pressure acting on the system.

    • setDefaultTemperature

      public void setDefaultTemperature(double temperature)
      Set the default temperature at which the system is being maintained (in Kelvin).
      Parameters:
      temperature - The default temperature.

    • setFrequency

      public void setFrequency(int frequency)
      Set the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.
      Parameters:
      frequency - The frequency of pressure change attempts.

    • setRandomNumberSeed

      public void setRandomNumberSeed(int seed)
      Set the random number seed. The precise meaning of this parameter is undefined, and is left up to each Platform to interpret in an appropriate way. It is guaranteed that if two simulations are run with different random number seeds, the sequence of random numbers 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.

      Parameters:
      seed - The random number seed.

    • setScaleMoleculesAsRigid

      public void setScaleMoleculesAsRigid(int scaleMoleculesAsRigid)
      Set whether molecules should be scaled as rigid bodies.
      Parameters:
      scaleMoleculesAsRigid - 1 to scale molecules as rigid bodies, 0 for flexible scaling.

    • usesPeriodicBoundaryConditions

      public boolean usesPeriodicBoundaryConditions()
      Returns whether this force makes use of periodic boundary conditions.
      Overrides:
      usesPeriodicBoundaryConditions in class Force
      Returns:
      True if the force uses periodic boundary conditions.