Package ffx.openmm

Class CustomCompoundBondForce

java.lang.Object
ffx.openmm.Force
ffx.openmm.CustomCompoundBondForce
Direct Known Subclasses:
AngleTorsionForce, InPlaneAngleForce, OutOfPlaneBendForce, PiOrbitalTorsionForce, StretchBendForce, StretchTorsionForce
public class CustomCompoundBondForce extends Force
This class supports a wide variety of bonded interactions. It defines a "bond" as a single energy term that depends on the positions of a fixed set of particles. The number of particles involved in a bond, and how the energy depends on their positions, is configurable. It may depend on the positions of individual particles, the distances between pairs of particles, the angles formed by sets of three particles, and the dihedral angles formed by sets of four particles.

We refer to the particles in a bond as p1, p2, p3, etc. For each bond, CustomCompoundBondForce evaluates a user supplied algebraic expression to determine the interaction energy. The expression may depend on the following variables and functions:

  • x1, y1, z1, x2, y2, z2, etc.: The x, y, and z coordinates of the particle positions. For example, x1 is the x coordinate of particle p1, and y3 is the y coordinate of particle p3.
  • distance(p1, p2): the distance between particles p1 and p2 (where "p1" and "p2" may be replaced by the names of whichever particles you want to calculate the distance between).
  • angle(p1, p2, p3): the angle formed by the three specified particles.
  • dihedral(p1, p2, p3, p4): the dihedral angle formed by the four specified particles, guaranteed to be in the range [-pi,+pi].

The expression also may involve tabulated functions, and may depend on arbitrary global and per-bond parameters.

To use this class, create a CustomCompoundBondForce object, passing an algebraic expression to the constructor that defines the interaction energy of each bond. Then call addPerBondParameter() to define per-bond parameters and addGlobalParameter() to define global parameters. The values of per-bond parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter().

Next, call addBond() to define bonds and specify their parameter values. After a bond has been added, you can modify its parameters by calling setBondParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

As an example, the following code creates a CustomCompoundBondForce that implements a Urey-Bradley potential. This is an interaction between three particles that depends on the angle formed by p1-p2-p3, and on the distance between p1 and p3. 

   
    CustomCompoundBondForce* force = new CustomCompoundBondForce(3, "0.5*(kangle*(angle(p1,p2,p3)-theta0)^2+kbond*(distance(p1,p3)-r0)^2)");

This force depends on four parameters: kangle, kbond, theta0, and r0. The following code defines these as per-bond parameters: 

   
    force->addPerBondParameter("kangle");
    force->addPerBondParameter("kbond");
    force->addPerBondParameter("theta0");
    force->addPerBondParameter("r0");

This class also has the ability to compute derivatives of the potential energy with respect to global parameters. Call addEnergyParameterDerivative() to request that the derivative with respect to a particular parameter be computed. You can then query its value in a Context by calling getState() on it.

Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ˆ (power), and the following functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise. delta(x) = 1 if x is 0, 0 otherwise. select(x,y,z) = z if x = 0, y otherwise.

This class also supports the functions pointdistance(x1, y1, z1, x2, y2, z2), pointangle(x1, y1, z1, x2, y2, z2, x3, y3, z3), and pointdihedral(x1, y1, z1, x2, y2, z2, x3, y3, z3, x4, y4, z4). These functions are similar to distance(), angle(), and dihedral(), but the arguments are the coordinates of points to perform the calculation based on rather than the names of particles. This enables more flexible geometric calculations. For example, the following computes the distance from particle p1 to the midpoint between particles p2 and p3. 

   
    CustomCompoundBondForce* force = new CustomCompoundBondForce(3, "pointdistance(x1, y1, z1, (x2+x3)/2, (y2+y3)/2, (z2+z3)/2)");

In addition, you can call addTabulatedFunction() to define a new function based on tabulated values. You specify the function by creating a TabulatedFunction object. That function can then appear in the expression.

  • Constructor Details

    • CustomCompoundBondForce

      public CustomCompoundBondForce(int numParticles, String energy)
      Create a CustomCompoundBondForce.
      Parameters:
      numParticles - The number of particles per bond.
      energy - The energy expression for the force.

  • Method Details

    • addBond

      public int addBond(IntArray particles, DoubleArray parameters)
      Add a bond to the force.
      Parameters:
      particles - The indices of the particles in the bond.
      parameters - The bond parameters.
      Returns:
      The index of the bond that was added.

    • addEnergyParameterDerivative

      public void addEnergyParameterDerivative(String name)
      Request that this Force compute the derivative of its energy with respect to a global parameter.
      Parameters:
      name - The name of the parameter to compute the derivative of the energy with respect to.

    • addFunction

      @Deprecated public int addFunction(String name, com.sun.jna.ptr.PointerByReference values, double min, double max)
      Deprecated.
      This method exists only for backward compatibility. Use addTabulatedFunction() instead.
      Add a tabulated function that may appear in the energy expression.
      Parameters:
      name - The name of the function as it appears in expressions.
      values - The tabulated values of the function.
      min - The minimum value of the independent variable for which the function is defined.
      max - The maximum value of the independent variable for which the function is defined.
      Returns:
      The index of the function that was added.

    • addGlobalParameter

      public int addGlobalParameter(String name, double defaultValue)
      Add a global parameter that the interaction may depend on.
      Parameters:
      name - The name of the parameter.
      defaultValue - The default value of the parameter.
      Returns:
      The index of the parameter that was added.

    • addPerBondParameter

      public int addPerBondParameter(String name)
      Add a per-bond parameter that the interaction may depend on.
      Parameters:
      name - The name of the parameter.
      Returns:
      The index of the parameter that was added.

    • addTabulatedFunction

      public int addTabulatedFunction(String name, com.sun.jna.ptr.PointerByReference function)
      Add a tabulated function that may appear in the energy expression.
      Parameters:
      name - The name of the function as it appears in expressions.
      function - A TabulatedFunction object defining the function.
      Returns:
      The index of the function that was added.

    • destroy

      public void destroy()
      Destroy the force.
      Specified by:
      destroy in class Force

    • getBondParameters

      public void getBondParameters(int index, IntArray particles, DoubleArray parameters)
      Get the parameters for a bond.
      Parameters:
      index - The index of the bond.
      particles - The indices of the particles in the bond.
      parameters - The bond parameters.

    • getEnergyFunction

      public String getEnergyFunction()
      Get the energy expression for the force.
      Returns:
      The energy expression for the force.

    • getEnergyParameterDerivativeName

      public String getEnergyParameterDerivativeName(int index)
      Get the name of a parameter with respect to which the derivative of the energy should be computed.
      Parameters:
      index - The index of the parameter derivative.
      Returns:
      The name of the parameter.

    • getFunctionParameters

      public void getFunctionParameters(int index, com.sun.jna.ptr.PointerByReference name, com.sun.jna.ptr.PointerByReference values, DoubleBuffer min, DoubleBuffer max)
      Get the parameters for a tabulated function.
      Parameters:
      index - The index of the function.
      name - The name of the function.
      values - The tabulated values.
      min - The minimum value of the independent variable.
      max - The maximum value of the independent variable.

    • getFunctionParameters

      public void getFunctionParameters(int index, com.sun.jna.ptr.PointerByReference name, com.sun.jna.ptr.PointerByReference values, com.sun.jna.ptr.DoubleByReference min, com.sun.jna.ptr.DoubleByReference max)
      Get the parameters for a tabulated function.
      Parameters:
      index - The index of the function.
      name - The name of the function.
      values - The tabulated values.
      min - The minimum value of the independent variable.
      max - The maximum value of the independent variable.

    • getGlobalParameterDefaultValue

      public double getGlobalParameterDefaultValue(int index)
      Get the default value of a global parameter.
      Parameters:
      index - The index of the parameter.
      Returns:
      The default value of the parameter.

    • getGlobalParameterName

      public String getGlobalParameterName(int index)
      Get the name of a global parameter.
      Parameters:
      index - The index of the parameter.
      Returns:
      The name of the parameter.

    • getNumBonds

      public int getNumBonds()
      Get the number of bonds.
      Returns:
      The number of bonds.

    • getNumEnergyParameterDerivatives

      public int getNumEnergyParameterDerivatives()
      Get the number of parameters with respect to which the derivative of the energy should be computed.
      Returns:
      The number of parameters.

    • getNumFunctions

      @Deprecated public int getNumFunctions()
      Deprecated.
      This method exists only for backward compatibility. Use getNumTabulatedFunctions() instead.
      Get the number of tabulated functions.
      Returns:
      The number of tabulated functions.

    • getNumGlobalParameters

      public int getNumGlobalParameters()
      Get the number of global parameters.
      Returns:
      The number of global parameters.

    • getNumParticlesPerBond

      public int getNumParticlesPerBond()
      Get the number of particles per bond.
      Returns:
      The number of particles per bond.

    • getNumPerBondParameters

      public int getNumPerBondParameters()
      Get the number of per-bond parameters.
      Returns:
      The number of per-bond parameters.

    • getNumTabulatedFunctions

      public int getNumTabulatedFunctions()
      Get the number of tabulated functions.
      Returns:
      The number of tabulated functions.

    • getPerBondParameterName

      public String getPerBondParameterName(int index)
      Get the name of a per-bond parameter.
      Parameters:
      index - The index of the parameter.
      Returns:
      The name of the parameter.

    • getTabulatedFunction

      public com.sun.jna.ptr.PointerByReference getTabulatedFunction(int index)
      Get a reference to a tabulated function.
      Parameters:
      index - The index of the function.
      Returns:
      A reference to the function.

    • getTabulatedFunctionName

      public String getTabulatedFunctionName(int index)
      Get the name of a tabulated function.
      Parameters:
      index - The index of the function.
      Returns:
      The name of the function.

    • setBondParameters

      public void setBondParameters(int index, IntArray particles, DoubleArray parameters)
      Set the parameters for a bond.
      Parameters:
      index - The index of the bond.
      particles - The indices of the particles in the bond.
      parameters - The bond parameters.

    • setEnergyFunction

      public void setEnergyFunction(String energy)
      Set the energy expression for the force.
      Parameters:
      energy - The energy expression for the force.

    • setFunctionParameters

      public void setFunctionParameters(int index, String name, com.sun.jna.ptr.PointerByReference values, double min, double max)
      Set the parameters for a tabulated function.
      Parameters:
      index - The index of the function.
      name - The name of the function.
      values - The tabulated values.
      min - The minimum value of the independent variable.
      max - The maximum value of the independent variable.

    • setGlobalParameterDefaultValue

      public void setGlobalParameterDefaultValue(int index, double defaultValue)
      Set the default value of a global parameter.
      Parameters:
      index - The index of the parameter.
      defaultValue - The default value of the parameter.

    • setGlobalParameterName

      public void setGlobalParameterName(int index, String name)
      Set the name of a global parameter.
      Parameters:
      index - The index of the parameter.
      name - The name of the parameter.

    • setPerBondParameterName

      public void setPerBondParameterName(int index, String name)
      Set the name of a per-bond parameter.
      Parameters:
      index - The index of the parameter.
      name - The name of the parameter.

    • setUsesPeriodicBoundaryConditions

      public void setUsesPeriodicBoundaryConditions(boolean periodic)
      Set whether this force should apply periodic boundary conditions when calculating displacements.
      Parameters:
      periodic - If true, periodic boundary conditions will be used.

    • updateParametersInContext

      public void updateParametersInContext(Context context)
      Update the parameters in the context.
      Parameters:
      context - The context to update.

    • usesPeriodicBoundaryConditions

      public boolean usesPeriodicBoundaryConditions()
      Check if the force uses periodic boundary conditions.
      Overrides:
      usesPeriodicBoundaryConditions in class Force
      Returns:
      True if the force uses periodic boundary conditions.