Package ffx.openmm

Class CustomBondForce

java.lang.Object
ffx.openmm.Force
ffx.openmm.CustomBondForce
Direct Known Subclasses:
BondForce, RestrainDistanceForce
public class CustomBondForce extends Force
This class implements bonded interactions between pairs of particles. Unlike HarmonicBondForce, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions. It may depend on the distance between particles, as well as on arbitrary global and per-bond parameters.

To use this class, create a CustomBondForce object, passing an algebraic expression to the constructor that defines the interaction energy between each pair of bonded particles. The expression may depend on r, the distance between the particles, as well as on any parameters you choose. 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(). Finally, call addBond() once for each bond. 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 CustomBondForce that implements a harmonic potential:

<pre> CustomBondForce force = new CustomBondForce("0.5*k*(r-r0)^2"); </pre>

This force depends on two parameters: the spring constant k and equilibrium distance r0. The following code defines these parameters:

<pre> force.addPerBondParameter("k"); force.addPerBondParameter("r0"); </pre>

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 ^ (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.

  • Constructor Details

    • CustomBondForce

      public CustomBondForce(String energy)
      Create a CustomBondForce.
      Parameters:
      energy - an algebraic expression giving the interaction energy between two bonded particles as a function of r, the distance between them

  • Method Details

    • addBond

      public int addBond(int i1, int i2, DoubleArray parameters)
      Add a bond term to the force field.
      Parameters:
      i1 - the index of the first particle connected by the bond
      i2 - the index of the second particle connected by the bond
      parameters - the list of parameters for the new bond
      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. The parameter must have already been added with addGlobalParameter().
      Parameters:
      name - the name of the parameter

    • addGlobalParameter

      public int addGlobalParameter(String name, double value)
      Add a new global parameter that the interaction may depend on. The default value provided to this method is the initial value of the parameter in newly created Contexts. You can change the value at any time by calling setParameter() on the Context.
      Parameters:
      name - the name of the parameter
      value - the default value of the parameter
      Returns:
      the index of the parameter that was added

    • addPerBondParameter

      public int addPerBondParameter(String name)
      Add a new 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

    • destroy

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

    • getBondParameters

      public void getBondParameters(int index, IntBuffer i1, IntBuffer i2, DoubleArray parameters)
      Get the force field parameters for a bond term.
      Parameters:
      index - the index of the bond for which to get parameters
      i1 - the index of the first particle connected by the bond
      i2 - the index of the second particle connected by the bond
      parameters - the list of parameters for the bond

    • getBondParameters

      public void getBondParameters(int index, com.sun.jna.ptr.IntByReference i1, com.sun.jna.ptr.IntByReference i2, DoubleArray parameters)
      Get the force field parameters for a bond term.
      Parameters:
      index - the index of the bond for which to get parameters
      i1 - the index of the first particle connected by the bond
      i2 - the index of the second particle connected by the bond
      parameters - the list of parameters for the bond

    • getEnergyFunction

      public String getEnergyFunction()
      Get the algebraic expression that gives the interaction energy for each bond
      Returns:
      the energy function expression

    • getEnergyParameterDerivativeName

      public String getEnergyParameterDerivativeName(int index)
      Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.
      Parameters:
      index - the index of the parameter derivative, between 0 and getNumEnergyParameterDerivatives()
      Returns:
      the parameter name

    • 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 for which force field parameters have been defined.
      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.

    • getNumGlobalParameters

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

    • getNumPerBondParameters

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

    • 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.

    • setBondParameters

      public void setBondParameters(int index, int i1, int i2, DoubleArray parameters)
      Set the parameters for one bond in the OpenMM System.
      Parameters:
      index - The index of the bond.
      i1 - The index of the first atom.
      i2 - The index of the second atom.
      parameters - The bond parameters.

    • setEnergyFunction

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

    • setGlobalParameterDefaultValue

      public void setGlobalParameterDefaultValue(int index, double value)
      Set the default value of a global parameter.
      Parameters:
      index - The index of the parameter.
      value - 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 uses periodic boundary conditions.
      Parameters:
      periodic - If true, periodic boundary conditions will be used.

    • updateParametersInContext

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

    • 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.