Package ffx.openmm

Class CustomCentroidBondForce

java.lang.Object
ffx.openmm.Force
ffx.openmm.CustomCentroidBondForce
Direct Known Subclasses:
RestrainGroupsForce
public class CustomCentroidBondForce extends Force
This class is similar to CustomCompoundBondForce, but instead of applying forces between individual particles, it applies them between the centers of groups of particles. This is useful for a variety of purposes, such as restraints to keep two molecules from moving too far apart.

When using this class, you define groups of particles, and the center of each group is calculated as a weighted average of the particle positions. By default, the particle masses are used as weights, so the center position is the center of mass. You can optionally specify different weights to use. You then add bonds just as with CustomCompoundBondForce, but instead of specifying the particles that make up a bond, you specify the groups.

When creating a CustomCentroidBondForce, you specify the number of groups involved in a bond, and an expression for the energy of each bond. It may depend on the center positions of individual groups, the distances between the centers of pairs of groups, the angles formed by sets of three groups, and the dihedral angles formed by sets of four groups.

We refer to the groups in a bond as g1, g2, g3, etc. For each bond, CustomCentroidBondForce 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 centers of the groups. For example, x1 is the x coordinate of the center of group g1, and y3 is the y coordinate of the center of group g3.
  • distance(g1, g2): the distance between the centers of groups g1 and g2 (where "g1" and "g2" may be replaced by the names of whichever groups you want to calculate the distance between).
  • angle(g1, g2, g3): the angle formed by the centers of the three specified groups.
  • dihedral(g1, g2, g3, g4): the dihedral angle formed by the centers of the four specified groups.

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

To use this class, create a CustomCentroidBondForce 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 addGroup() to define the particle groups. Each group is specified by the particles it contains, and the weights to use when computing the center position.

Then 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 CustomCentroidBondForce that implements a harmonic force between the centers of mass of two groups of particles. 

   
    CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "0.5*k*distance(g1,g2)^2");
    force->addPerBondParameter("k");
    force->addGroup(particles1);
    force->addGroup(particles2);
    vector<int> bondGroups;
    bondGroups.push_back(0);
    bondGroups.push_back(1);
    vector<double> bondParameters;
    bondParameters.push_back(k);
    force->addBond(bondGroups, bondParameters);

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.

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 groups. This enables more flexible geometric calculations. For example, the following computes the distance from group g1 to the midpoint between groups g2 and g3. 

   
    CustomCentroidBondForce* force = new CustomCentroidBondForce(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

    • CustomCentroidBondForce

      public CustomCentroidBondForce(int numGroups, String energy)
      Create a CustomCentroidBondForce.
      Parameters:
      numGroups - the number of groups used to define each bond
      energy - an algebraic expression giving the interaction energy of each bond as a function of particle positions, inter-particle distances, angles, and dihedrals, and any global and per-bond parameters

  • Method Details

    • getNumGroupsPerBond

      public int getNumGroupsPerBond()
      Get the number of groups used to define each bond.

    • getNumGroups

      public int getNumGroups()
      Get the number of particle groups that have been defined.

    • getNumBonds

      public int getNumBonds()
      Get the number of bonds for which force field parameters have been defined.

    • getNumPerBondParameters

      public int getNumPerBondParameters()
      Get the number of per-bond parameters that the interaction depends on.

    • getNumGlobalParameters

      public int getNumGlobalParameters()
      Get the number of global parameters that the interaction depends on.

    • getNumEnergyParameterDerivatives

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

    • getNumTabulatedFunctions

      public int getNumTabulatedFunctions()
      Get the number of tabulated functions that have been defined.

    • getNumFunctions

      @Deprecated public int getNumFunctions()
      Deprecated.
      This method exists only for backward compatibility. Use getNumTabulatedFunctions() instead.
      Get the number of tabulated functions that have been defined.

    • getEnergyFunction

      public String getEnergyFunction()
      Get the algebraic expression that gives the interaction energy of each bond

    • setEnergyFunction

      public void setEnergyFunction(String energy)
      Set the algebraic expression that gives the interaction energy of each bond

    • 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

    • getPerBondParameterName

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

    • setPerBondParameterName

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

    • addGlobalParameter

      public int addGlobalParameter(String name, double defaultValue)
      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
      defaultValue - the default value of the parameter
      Returns:
      the index of the parameter that was added

    • getGlobalParameterName

      public String getGlobalParameterName(int index)
      Get the name of a global parameter.
      Parameters:
      index - the index of the parameter for which to get the name
      Returns:
      the parameter name

    • setGlobalParameterName

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

    • getGlobalParameterDefaultValue

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

    • setGlobalParameterDefaultValue

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

    • 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

    • 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

    • addGroup

      public int addGroup(IntArray particles, DoubleArray weights)
      Add a particle group.
      Parameters:
      particles - the indices of the particles to include in the group
      weights - the weight to use for each particle when computing the center position. If this is omitted, then particle masses will be used as weights.
      Returns:
      the index of the group that was added

    • getGroupParameters

      public void getGroupParameters(int index, IntArray particles, DoubleArray weights)
      Get the properties of a group.
      Parameters:
      index - the index of the group to get
      particles - the indices of the particles in the group
      weights - the weight used for each particle when computing the center position. If no weights were specified, this vector will be empty indicating that particle masses should be used as weights.

    • setGroupParameters

      public void setGroupParameters(int index, IntArray particles, DoubleArray weights)
      Set the properties of a group.
      Parameters:
      index - the index of the group to set
      particles - the indices of the particles in the group
      weights - the weight to use for each particle when computing the center position. If this is omitted, then particle masses will be used as weights.

    • addBond

      public int addBond(IntArray groups, DoubleArray parameters)
      Add a bond to the force
      Parameters:
      groups - the indices of the groups the bond depends on
      parameters - the list of per-bond parameter values for the new bond
      Returns:
      the index of the bond that was added

    • getBondParameters

      public void getBondParameters(int index, IntArray groups, DoubleArray parameters)
      Get the properties of a bond.
      Parameters:
      index - the index of the bond to get
      groups - the indices of the groups in the bond
      parameters - the list of per-bond parameter values for the bond

    • setBondParameters

      public void setBondParameters(int index, IntArray groups, DoubleArray parameters)
      Set the properties of a bond.
      Parameters:
      index - the index of the bond to set
      groups - the indices of the groups in the bond
      parameters - the list of per-bond parameter values for the bond

    • updateParametersInContext

      public void updateParametersInContext(Context context)
      Update the per-bond parameters and tabulated functions in a Context to match those stored in this Force object. This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setBondParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.

      This method has several limitations. The only information it updates is the values of per-bond parameters and tabulated functions. All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing the Context. Neither the definitions of groups nor the set of groups involved in a bond can be changed, nor can new bonds be added. Also, while the tabulated values of a function can change, everything else about it (its dimensions, the data range) must not be changed.

      Parameters:
      context - the OpenMM context.

    • setUsesPeriodicBoundaryConditions

      public void setUsesPeriodicBoundaryConditions(int periodic)
      Set whether this force should apply periodic boundary conditions when calculating displacements. Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
      Parameters:
      periodic - 1 if periodic boundary conditions should be used, 0 if not.

    • usesPeriodicBoundaryConditions

      public boolean usesPeriodicBoundaryConditions()
      Returns whether this force makes use of periodic boundary conditions.
      Overrides:
      usesPeriodicBoundaryConditions in class Force
      Returns:
      true if force uses PBC and false otherwise

    • destroy

      public void destroy()
      Destroy the OpenMM CustomCentroidBondForce.