CustomTorsionForce¶
-
class
OpenMM
::
CustomTorsionForce
¶ This class implements interactions between sets of four particles that depend on the torsion angle between them. Unlike
PeriodicTorsionForce
, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions. In addition to the angle formed by the particles, it may depend on arbitrary global and per-torsion parameters.To use this class, create a
CustomTorsionForce
object, passing an algebraic expression to the constructor that defines the interaction energy between each set of particles. The expression may depend on theta, the torsion angle formed by the particles, as well as on any parameters you choose. Then calladdPerTorsionParameter()
to define per-torsion parameters, andaddGlobalParameter()
to define global parameters. The values of per-torsion parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by callingContext::setParameter()
. Finally, calladdTorsion()
once for each torsion. After an torsion has been added, you can modify its parameters by callingsetTorsionParameters()
. This will have no effect on Contexts that already exist unless you callupdateParametersInContext()
. 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 periodic potential:CustomTorsionForce* force = new CustomTorsionForce("0.5*k*(1-cos(theta-theta0))");
This force depends on two parameters: the spring constant k and equilibrium angle theta0. The following code defines these parameters:
force->addPerTorsionParameter("k"); force->addPerTorsionParameter("theta0");
If a harmonic restraint is desired, it is important to be careful of the domain for theta, using an idiom like this:
CustomTorsionForce* force = new CustomTorsionForce("0.5*k*min(dtheta, 2*pi-dtheta)^2; dtheta = abs(theta-theta0); pi = 3.1415926535");
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 aContext
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.
Methods
Create a
CustomTorsionForce
.Get the number of torsions for which force field parameters have been defined.
Get the number of per-torsion parameters that the interaction depends on.
Get the number of global parameters that the interaction depends on.
Get the number of global parameters with respect to which the derivative of the energy should be computed.
Get the algebraic expression that gives the interaction energy for each torsion
Set the algebraic expression that gives the interaction energy for each torsion
Add a new per-torsion parameter that the interaction may depend on.
Get the name of a per-torsion parameter.
Set the name of a per-torsion parameter.
Add a new global parameter that the interaction may depend on.
Get the name of a global parameter.
Set the name of a global parameter.
Get the default value of a global parameter.
Set the default value of a global parameter.
Request that this
Force
compute the derivative of its energy with respect to a global parameter.Get the name of a global parameter with respect to which this
Force
should compute the derivative of the energy.Add a torsion term to the force field.
Get the force field parameters for a torsion term.
Set the force field parameters for a torsion term.
Update the per-torsion parameters in a
Context
to match those stored in thisForce
object.Set whether this force should apply periodic boundary conditions when calculating displacements.
Returns whether or not this force makes use of periodic boundary conditions.
-
CustomTorsionForce
(const std::string &energy)¶ Create a
CustomTorsionForce()
.- Parameters
energy – an algebraic expression giving the interaction energy between three particles as a function of theta, the torsion angle between them
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int
getNumTorsions
() const¶ Get the number of torsions for which force field parameters have been defined.
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int
getNumPerTorsionParameters
() const¶ Get the number of per-torsion parameters that the interaction depends on.
-
int
getNumGlobalParameters
() const¶ Get the number of global parameters that the interaction depends on.
-
int
getNumEnergyParameterDerivatives
() const¶ Get the number of global parameters with respect to which the derivative of the energy should be computed.
-
const std::string &
getEnergyFunction
() const¶ Get the algebraic expression that gives the interaction energy for each torsion
-
void
setEnergyFunction
(const std::string &energy)¶ Set the algebraic expression that gives the interaction energy for each torsion
-
int
addPerTorsionParameter
(const std::string &name)¶ Add a new per-torsion parameter that the interaction may depend on.
- Parameters
name – the name of the parameter
- Returns
the index of the parameter that was added
-
const std::string &
getPerTorsionParameterName
(int index) const¶ Get the name of a per-torsion parameter.
- Parameters
index – the index of the parameter for which to get the name
- Returns
the parameter name
-
void
setPerTorsionParameterName
(int index, const std::string &name)¶ Set the name of a per-torsion parameter.
- Parameters
index – the index of the parameter for which to set the name
name – the name of the parameter
-
int
addGlobalParameter
(const std::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
-
const std::string &
getGlobalParameterName
(int index) const¶ Get the name of a global parameter.
- Parameters
index – the index of the parameter for which to get the name
- Returns
the parameter name
-
void
setGlobalParameterName
(int index, const std::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
-
double
getGlobalParameterDefaultValue
(int index) const¶ 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
-
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
-
void
addEnergyParameterDerivative
(const std::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 withaddGlobalParameter()
.- Parameters
name – the name of the parameter
-
const std::string &
getEnergyParameterDerivativeName
(int index) const¶ 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
-
int
addTorsion
(int particle1, int particle2, int particle3, int particle4, const std::vector<double> ¶meters = std::vector<double>())¶ Add a torsion term to the force field.
- Parameters
particle1 – the index of the first particle connected by the torsion
particle2 – the index of the second particle connected by the torsion
particle3 – the index of the third particle connected by the torsion
particle4 – the index of the fourth particle connected by the torsion
parameters – the list of parameters for the new torsion
- Returns
the index of the torsion that was added
-
void
getTorsionParameters
(int index, int &particle1, int &particle2, int &particle3, int &particle4, std::vector<double> ¶meters) const¶ Get the force field parameters for a torsion term.
- Parameters
index – the index of the torsion for which to get parameters
particle1 – [out] the index of the first particle connected by the torsion
particle2 – [out] the index of the second particle connected by the torsion
particle3 – [out] the index of the third particle connected by the torsion
particle4 – [out] the index of the fourth particle connected by the torsion
parameters – [out] the list of parameters for the torsion
-
void
setTorsionParameters
(int index, int particle1, int particle2, int particle3, int particle4, const std::vector<double> ¶meters = std::vector<double>())¶ Set the force field parameters for a torsion term.
- Parameters
index – the index of the torsion for which to set parameters
particle1 – the index of the first particle connected by the torsion
particle2 – the index of the second particle connected by the torsion
particle3 – the index of the third particle connected by the torsion
particle4 – the index of the fourth particle connected by the torsion
parameters – the list of parameters for the torsion
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void
updateParametersInContext
(Context &context)¶ Update the per-torsion parameters in a
Context
to match those stored in thisForce
object. This method provides an efficient method to update certain parameters in an existingContext
without needing to reinitialize it. Simply callsetTorsionParameters()
to modify this object’s parameters, then callupdateParametersInContext()
to copy them over to theContext
.This method has several limitations. The only information it updates is the values of per-torsion parameters. All other aspects of the
Force
(such as the energy function) are unaffected and can only be changed by reinitializing theContext
. The set of particles involved in a torsion cannot be changed, nor can new torsions be added.
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void
setUsesPeriodicBoundaryConditions
(bool 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.
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bool
usesPeriodicBoundaryConditions
() const¶ Returns whether or not this force makes use of periodic boundary conditions.
- Returns
true if force uses PBC and false otherwise
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