* 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.
* 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. An expression may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.
* select(x,y,z) = z if x = 0, y otherwise. An expression may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.
*
* 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 expressions.
* part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter().
* part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter().
* Finally, call addTorsion() once for each torsion. After an torsion has been added, you can modify its parameters by calling setTorsionParameters().
* Finally, call addTorsion() once for each torsion. After an torsion has been added, you can modify its parameters by calling setTorsionParameters().
* This will have no effect on Contexts that already exist unless you call updateParametersInContext().
* This will have no effect on Contexts that already exist unless you call updateParametersInContext().
* theta is guaranteed to be in the range [-pi,+pi]
* Note that theta is guaranteed to be in the range [-pi,+pi], which may cause issues with force discontinuities if the energy function does not respect this domain.
*
*
* As an example, the following code creates a CustomTorsionForce that implements a harmonic potential:
* As an example, the following code creates a CustomTorsionForce that implements a periodic potential:
*
*
* <tt>CustomTorsionForce* force = new CustomTorsionForce("0.5*k*(theta-theta0)^2");</tt>
* <tt>CustomTorsionForce* force = new CustomTorsionForce("0.5*k*(1-cos(theta-theta0))");</tt>
*
*
* This force depends on two parameters: the spring constant k and equilibrium angle theta0. The following code defines these parameters:
* This force depends on two parameters: the spring constant k and equilibrium angle theta0. The following code defines these parameters:
*
*
...
@@ -65,6 +65,10 @@ namespace OpenMM {
...
@@ -65,6 +65,10 @@ namespace OpenMM {
* force->addPerTorsionParameter("theta0");
* force->addPerTorsionParameter("theta0");
* </pre></tt>
* </pre></tt>
*
*
* If a harmonic restraint is desired, it is important to be careful of the domain for theta, using an idiom like this:
*
* <tt>CustomTorsionForce* force = new CustomTorsionForce("0.5*k*min(dtheta, 2*pi-dtheta)^2; dtheta = abs(theta-theta0); pi = 3.1415926535");</tt>
*
* This class also has the ability to compute derivatives of the potential energy with respect to global parameters.
* 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
* 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.
* computed. You can then query its value in a Context by calling getState() on it.
