Class AnalyzeNEQ


public class AnalyzeNEQ extends AlgorithmsCommand
Performs analysis of Non-equilibrium work simulations. Takes directory paths to the forward and reverse work logs and uses them to create BAR files and calculate the BAR free energy difference.
Usage:
ffxc BAR [options] <structures1> <structures2>
  • Constructor Details

    • AnalyzeNEQ

      public AnalyzeNEQ()
      AnalyzeNEQ Constructor.
    • AnalyzeNEQ

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

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

    • run

      public AnalyzeNEQ 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.