Package ffx.algorithms.dynamics

Class PhReplicaExchange

java.lang.Object
ffx.algorithms.dynamics.PhReplicaExchange
All Implemented Interfaces:
Terminatable
public class PhReplicaExchange extends Object implements Terminatable
The PhReplicaExchange implements pH replica exchange. Adapted from "ReplicaExchange.java" by Timothy D. Fenn and Michael J. Schnieders
Since:
1.0
Author:
Matthew Speranza and Andrew Thiel

  • Constructor Summary

    Constructors
    Constructor
    Description
    PhReplicaExchange(MolecularDynamics molecularDynamics, File structureFile, double pH, double[] pHLadder, double temp, ExtendedSystem extendedSystem, double[] x)
    pHReplicaExchange constructor.
    PhReplicaExchange(MolecularDynamics molecularDynamics, File structureFile, double pH, double[] pHLadder, double temp, ExtendedSystem extendedSystem, double[] x, MolecularDynamicsOpenMM molecularDynamicsOpenMM, Potential potential)
    OpenMM cycled pHReplicaExchange constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    sample(int cycles, long nSteps, double timeStep, double printInterval, double trajInterval, int initTitrDynamics)
    Sample.
    void
    sample(int cycles, long titrSteps, long confSteps, double timeStep, double printInterval, double trajInterval, int initDynamics)
     
    static double[]
    setEvenSpacePhLadder(double pHGap, double pH, int nReplicas)
    Sets an even pH ladder based on the pH gap.
    void
    terminate()
    This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • PhReplicaExchange

      public PhReplicaExchange(MolecularDynamics molecularDynamics, File structureFile, double pH, double[] pHLadder, double temp, ExtendedSystem extendedSystem, double[] x)
      pHReplicaExchange constructor.
      Parameters:
      molecularDynamics - a MolecularDynamics object.
      pH - pH = pKa will be changed from this initial value
      pHLadder - range of pH's that replicas are created for
      temp - temperature of replica
      extendedSystem - extended system attached to this process

    • PhReplicaExchange

      public PhReplicaExchange(MolecularDynamics molecularDynamics, File structureFile, double pH, double[] pHLadder, double temp, ExtendedSystem extendedSystem, @Nullable double[] x, @Nullable MolecularDynamicsOpenMM molecularDynamicsOpenMM, @Nullable Potential potential)
      OpenMM cycled pHReplicaExchange constructor.
      Parameters:
      molecularDynamics - a MolecularDynamics object.
      pH - pH = pKa will be changed from this initial value
      pHLadder - range of pH's that replicas are created for
      temp - temperature of replica
      extendedSystem - extended system attached to this process
      x - array of coordinates
      molecularDynamicsOpenMM - for running config steps on GPU

  • Method Details

    • sample

      public void sample(int cycles, long nSteps, double timeStep, double printInterval, double trajInterval, int initTitrDynamics)
      Sample. Restart file write-outs are entirely handled by this method based on how many steps are per cycle. User command input is ignored.
      Parameters:
      cycles - The number of cycles to run.
      nSteps - The number of steps per cycle.
      timeStep - The time step.
      printInterval - The print interval.

    • sample

      public void sample(int cycles, long titrSteps, long confSteps, double timeStep, double printInterval, double trajInterval, int initDynamics)

    • setEvenSpacePhLadder

      public static double[] setEvenSpacePhLadder(double pHGap, double pH, int nReplicas)
      Sets an even pH ladder based on the pH gap.

    • terminate

      public void terminate()
      This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point. For example, between minimize or molecular dynamics steps.

      This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point. For example, between minimize or molecular dynamics steps.

      Specified by:
      terminate in interface Terminatable