Package ffx.openmm.drude

Class DrudeIntegrator

java.lang.Object
ffx.openmm.Integrator
ffx.openmm.drude.DrudeIntegrator
Direct Known Subclasses:
DrudeLangevinIntegrator, DrudeSCFIntegrator
public class DrudeIntegrator extends Integrator
A base class to encapsulate features common to Drude integrators.

  • Constructor Details

    • DrudeIntegrator

      public DrudeIntegrator(com.sun.jna.ptr.PointerByReference pointer)
      Create a DrudeIntegrator.
      Parameters:
      pointer - A pointer to the native OpenMM Drude integrator object.

    • DrudeIntegrator

      public DrudeIntegrator(double stepSize)
      Create a DrudeIntegrator.
      Parameters:
      stepSize - the step size with which to integrator the system (in picoseconds)

  • Method Details

    • destroy

      public void destroy()
      Destroy the integrator.

      This method releases the memory associated with the DrudeIntegrator object. After calling this method, the integrator should not be used.

      Specified by:
      destroy in class Integrator

    • getDrudeTemperature

      public double getDrudeTemperature()
      Get the temperature of the heat bath applied to internal coordinates of Drude particles (in Kelvin).
      Returns:
      the temperature of the heat bath, measured in Kelvin

    • getMaxDrudeDistance

      public double getMaxDrudeDistance()
      Get the maximum distance a Drude particle can ever move from its parent particle, measured in nm. This is implemented with a hard wall constraint. The default value is 0.02. If this distance is set to 0, the hard wall constraint is omitted.

    • getRandomNumberSeed

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

    • setDrudeTemperature

      public void setDrudeTemperature(double temperature)
      Set the temperature of the heat bath applied to internal coordinates of Drude particles (in Kelvin).
      Parameters:
      temperature - the temperature of the heat bath, measured in Kelvin

    • setMaxDrudeDistance

      public void setMaxDrudeDistance(double distance)
      Set the maximum distance a Drude particle can ever move from its parent particle, measured in nm. This is implemented with a hard wall constraint. The default value is 0.02. If this distance is set to 0, the hard wall constraint is omitted.

    • 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 forces 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.

    • step

      public void step(int steps)
      Advance a simulation through time by taking a series of time steps.
      Overrides:
      step in class Integrator
      Parameters:
      steps - the number of time steps to take