Class Freefix


public class Freefix extends AlgorithmsCommand
The Freefix script calculates analytical free energy, entropy, and enthalpy corrections for flat-bottom harmonic restraints with inner and outer radii.
Usage:
ffxc test.Freefix [options] <filename>
  • Field Details

  • Constructor Details

    • Freefix

      public Freefix()
      Freefix Constructor.
    • Freefix

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

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

    • run

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

      public static double[] computeVolumeIntegrals(double innerRadius, double innerForce, double outerRadius, double outerForce, double temperature)
      Compute volume integrals and their temperature derivatives for restraint thermodynamics.
      Parameters:
      innerRadius - Inner flat-bottom radius
      innerForce - Inner force constant
      outerRadius - Outer flat-bottom radius
      outerForce - Outer force constant
      temperature - System temperature
      Returns:
      Array containing [volume, dvolume/dT]