Package ffx.openmm.drude

Class DrudeLangevinIntegrator

java.lang.Object
ffx.openmm.Integrator
ffx.openmm.drude.DrudeIntegrator
ffx.openmm.drude.DrudeLangevinIntegrator
public class DrudeLangevinIntegrator extends DrudeIntegrator
This Integrator simulates systems that include Drude particles. It applies two different Langevin thermostats to different parts of the system. The first is applied to ordinary particles (ones that are not part of a Drude particle pair), as well as to the center of mass of each Drude particle pair. A second thermostat, typically with a much lower temperature, is applied to the relative internal displacement of each pair.

This integrator can optionally set an upper limit on how far any Drude particle is ever allowed to get from its parent particle. This can sometimes help to improve stability. The limit is enforced with a hard wall constraint. By default the limit is set to 0.02 nm.

This Integrator requires the System to include a DrudeForce, which it uses to identify the Drude particles.

  • Constructor Details

    • DrudeLangevinIntegrator

      public DrudeLangevinIntegrator(double stepSize, double temperature, double friction, double drudeTemperature, double drudeFriction)
      Create a DrudeLangevinIntegrator.
      Parameters:
      stepSize - the step size with which to integrator the system (in picoseconds)
      temperature - the temperature of the main heat bath (in Kelvin)
      friction - the friction coefficient which couples the system to the main heat bath (in inverse picoseconds)
      drudeTemperature - the temperature of the heat bath applied to internal coordinates of Drude particles (in Kelvin)
      drudeFriction - the friction coefficient which couples the system to the heat bath applied to internal coordinates of Drude particles (in inverse picoseconds)

  • Method Details

    • computeDrudeTemperature

      public double computeDrudeTemperature()
      Compute the instantaneous temperature of the Drude system, measured in Kelvin. This is calculated based on the kinetic energy of the internal motion of Drude pairs and should remain close to the prescribed Drude temperature.

    • computeSystemTemperature

      public double computeSystemTemperature()
      Compute the instantaneous temperature of the System, measured in Kelvin. This is calculated based on the kinetic energy of the ordinary particles (ones not attached to a Drude particle), as well as the center of mass motion of the Drude particle pairs. It does not include the internal motion of the pairs. On average, this should be approximately equal to the value returned by getTemperature().

    • destroy

      public void destroy()
      Destroy the integrator.

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

      Overrides:
      destroy in class DrudeIntegrator

    • getDrudeFriction

      public double getDrudeFriction()
      Get the friction coefficient which determines how strongly the internal coordinates of Drude particles are coupled to the heat bath (in inverse ps).
      Returns:
      the friction coefficient, measured in 1/ps

    • getFriction

      public double getFriction()
      Get the friction coefficient which determines how strongly the system is coupled to the main heat bath (in inverse ps).
      Returns:
      the friction coefficient, measured in 1/ps

    • getTemperature

      public double getTemperature()
      Get the temperature of the main heat bath (in Kelvin).
      Returns:
      the temperature of the heat bath, measured in Kelvin

    • setDrudeFriction

      public void setDrudeFriction(double friction)
      Set the friction coefficient which determines how strongly the internal coordinates of Drude particles are coupled to the heat bath (in inverse ps).
      Parameters:
      friction - the friction coefficient, measured in 1/ps

    • setFriction

      public void setFriction(double friction)
      Set the friction coefficient which determines how strongly the system is coupled to the main heat bath (in inverse ps).
      Parameters:
      friction - the friction coefficient, measured in 1/ps

    • setTemperature

      public void setTemperature(double temperature)
      Set the temperature of the main heat bath (in Kelvin).
      Parameters:
      temperature - the temperature of the heat bath, measured in Kelvin

    • step

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