Class PhDynamics


public class PhDynamics extends AlgorithmsCommand
The PhDynamics command implements constant pH molecular dynamics.
Usage:
ffxc PhDynamics [options] <filename> [file2...]
  • Field Details

  • Constructor Details

    • PhDynamics

      public PhDynamics()
      PhDynamics Constructor.
    • PhDynamics

      public PhDynamics(FFXBinding binding)
      PhDynamics Constructor.
      Parameters:
      binding - The Binding to use.
    • PhDynamics

      public PhDynamics(String[] args)
      PhDynamics constructor that sets the command line arguments.
      Parameters:
      args - Command line arguments.
  • Method Details

    • getMolecularDynamics

      public MolecularDynamics getMolecularDynamics()
    • getPotentialObject

      public Potential getPotentialObject()
    • run

      public PhDynamics run()
      Execute this Command.
      Overrides:
      run in class FFXCommand
      Returns:
      The current FFXCommand.
    • getPotentials

      public List<Potential> getPotentials()
      Returns a List of all Potential objects associated with this script.
      Overrides:
      getPotentials in class AlgorithmsCommand
      Returns:
      All Potentials. Sometimes empty, never null.
    • sortMyArc

      public static void sortMyArc(File structureFile, int nReplicas, double pH, int myRank)
      Sort archive files by pH with string parsing