Package ffx.algorithms.dynamics

Class NonEquilbriumDynamics

java.lang.Object
ffx.algorithms.dynamics.NonEquilbriumDynamics
public class NonEquilbriumDynamics extends Object
NonEquilbriumDynamics is a class that contains methods to control non-equilibrium molecular dynamics simulations.

  • Constructor Summary

    Constructors
    Constructor
    Description
    NonEquilbriumDynamics(int nonEquilibriumLambdaSteps, boolean reverseNEQ)
    Constructor for NonEquilbriumDynamics.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addWork(double work)
    Add a work contribution.
    int
    getCurrentLambdaBin(long step)
    Get the current lambda bin for a given MD step.
    double
    getInitialLambda()
    Get the initial lambda value.
    double
    getNextLambda(long step, double currentLambda)
    Get the non-equilibrium lambda value for a given MD step.
    int
    getNonEquilibriumLambdaSteps()
    Get the number of non-equilibrium lambda steps.
    double
    getWork()
    Get the total work for a given range of lambda bins.
    boolean
    isUpdateStep(long step)
    Check if the non-equilibrium lambda value should be updated at a given MD step.
    long
    setMDSteps(long nSteps)
    Configure increments of the non-equilibrium lambda values based on the total number of MD steps.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • NonEquilbriumDynamics

      public NonEquilbriumDynamics(int nonEquilibriumLambdaSteps, boolean reverseNEQ)
      Constructor for NonEquilbriumDynamics.
      Parameters:
      nonEquilibriumLambdaSteps - The number of non-equilibrium lambda steps.
      reverseNEQ - If true, lambda values should decrease from 1 to 0.

  • Method Details

    • getNonEquilibriumLambdaSteps

      public int getNonEquilibriumLambdaSteps()
      Get the number of non-equilibrium lambda steps.
      Returns:
      The number of non-equilibrium lambda steps.

    • getInitialLambda

      public double getInitialLambda()
      Get the initial lambda value.
      Returns:
      The initial lambda value.

    • setMDSteps

      public long setMDSteps(long nSteps)
      Configure increments of the non-equilibrium lambda values based on the total number of MD steps.
      Parameters:
      nSteps - The total number of MD steps.
      Returns:
      The total number of MD steps may be adjusted to be a multiple of the non-equilibrium lambda steps.

    • isUpdateStep

      public boolean isUpdateStep(long step)
      Check if the non-equilibrium lambda value should be updated at a given MD step.
      Parameters:
      step - The MD step number.
      Returns:
      True if the non-equilibrium lambda value should be updated.

    • addWork

      public void addWork(double work)
      Add a work contribution.
      Parameters:
      work - The work value.

    • getWork

      public double getWork()
      Get the total work for a given range of lambda bins.
      Returns:
      The total work.

    • getNextLambda

      public double getNextLambda(long step, double currentLambda)
      Get the non-equilibrium lambda value for a given MD step.
      Parameters:
      step - The MD step number.
      currentLambda - The current lambda value.
      Returns:
      The lambda value.

    • getCurrentLambdaBin

      public int getCurrentLambdaBin(long step)
      Get the current lambda bin for a given MD step.
      Parameters:
      step - The MD step number.
      Returns:
      The lambda bin.