Package ffx.algorithms.commands.test
Class Freefix
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.test.Freefix
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>
Usage:
ffxc test.Freefix [options] <filename>
-
Field Summary
FieldsFields inherited from class ffx.algorithms.cli.AlgorithmsCommand
activeAssembly, algorithmFunctions, algorithmListener, baseDir
Fields inherited from class ffx.utilities.FFXCommand
args, binding, color, help, logger, parseResult, version
-
Constructor Summary
ConstructorsConstructorDescriptionFreefix()
Freefix Constructor.Freefix
(FFXBinding binding) Freefix Constructor.Freefix constructor that sets the command line arguments. -
Method Summary
Modifier and TypeMethodDescriptionstatic double[]
computeVolumeIntegrals
(double innerRadius, double innerForce, double outerRadius, double outerForce, double temperature) Compute volume integrals and their temperature derivatives for restraint thermodynamics.run()
Execute this Command.Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand
destroyPotentials, getActiveAssemblies, getActiveAssembly, getPotentials, init, saveDirFile, setActiveAssembly, setBaseDir, updateTitle
Methods inherited from class ffx.utilities.FFXCommand
getCommand, helpString, listCommands, setBinding
-
Field Details
-
AVOGADRO
public static final double AVOGADRO- See Also:
-
STD_CONVERSION
public static final double STD_CONVERSION- See Also:
-
-
Constructor Details
-
Freefix
public Freefix()Freefix Constructor. -
Freefix
Freefix Constructor.- Parameters:
binding
- The Binding to use.
-
Freefix
Freefix constructor that sets the command line arguments.- Parameters:
args
- Command line arguments.
-
-
Method Details
-
run
Execute this Command.- Overrides:
run
in classFFXCommand
- 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 radiusinnerForce
- Inner force constantouterRadius
- Outer flat-bottom radiusouterForce
- Outer force constanttemperature
- System temperature- Returns:
- Array containing [volume, dvolume/dT]
-