CustomCVForce

class openmm.openmm.CustomCVForce(*args)

This class supports energy functions that depend on collective variables. To use it, you define a set of collective variables (scalar valued functions that depend on the particle positions), and an algebraic expression for the energy as a function of the collective variables. The expression also may involve tabulated functions, and may depend on arbitrary global parameters.

Each collective variable is defined by a Force object. The Force’s potential energy is computed, and that becomes the value of the variable. This provides enormous flexibility in defining collective variables, especially by using custom forces. Anything that can be computed as a potential function can also be used as a collective variable.

To use this class, create a CustomCVForce object, passing an algebraic expression to the constructor that defines the potential energy. Then call addCollectiveVariable() to define collective variables and addGlobalParameter() to define global parameters. The values of global parameters may be modified during a simulation by calling Context::setParameter().

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.

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.

__init__(self, energy)CustomCVForce
__init__(self, other)CustomCVForce

Create a CustomCVForce.

Parameters

energy (string) – an algebraic expression giving the energy of the system as a function of the collective variables and global parameters

Methods

__init__(-> CustomCVForce)

Create a CustomCVForce.

addCollectiveVariable(self, name, variable)

Add a collective variable that the force may depend on.

addEnergyParameterDerivative(self, name)

Request that this Force compute the derivative of its energy with respect to a global parameter.

addGlobalParameter(self, name, defaultValue)

Add a new global parameter that the interaction may depend on.

addTabulatedFunction(self, name, function)

Add a tabulated function that may appear in the energy expression.

getCollectiveVariable(-> Force)

Get a const reference to the Force object that computes a collective variable.

getCollectiveVariableName(self, index)

Get the name of a collective variable.

getCollectiveVariableValues(self, context)

Get the current values of the collective variables in a Context.

getEnergyFunction(self)

Get the algebraic expression that gives the energy of the system

getEnergyParameterDerivativeName(self, index)

Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.

getForceGroup(self)

Get the force group this Force belongs to.

getGlobalParameterDefaultValue(self, index)

Get the default value of a global parameter.

getGlobalParameterName(self, index)

Get the name of a global parameter.

getInnerContext(self, context)

Get the inner Context used for evaluating collective variables.

getName(self)

Get the name of this Force.

getNumCollectiveVariables(self)

Get the number of collective variables that the interaction depends on.

getNumEnergyParameterDerivatives(self)

Get the number of global parameters with respect to which the derivative of the energy should be computed.

getNumGlobalParameters(self)

Get the number of global parameters that the interaction depends on.

getNumTabulatedFunctions(self)

Get the number of tabulated functions that have been defined.

getTabulatedFunction(-> TabulatedFunction)

Get a reference to a tabulated function that may appear in the energy expression.

getTabulatedFunctionName(self, index)

Get the name of a tabulated function that may appear in the energy expression.

setEnergyFunction(self, energy)

Set the algebraic expression that gives the energy of the system

setForceGroup(self, group)

Set the force group this Force belongs to.

setGlobalParameterDefaultValue(self, index, …)

Set the default value of a global parameter.

setGlobalParameterName(self, index, name)

Set the name of a global parameter.

setName(self, name)

Set the name of this Force.

updateParametersInContext(self, context)

Update the tabulated function parameters in a Context to match those stored in this Force object.

usesPeriodicBoundaryConditions(self)

Returns whether or not this force makes use of periodic boundary conditions.

Attributes

thisown

The membership flag

property thisown

The membership flag

getNumCollectiveVariables(self)int

Get the number of collective variables that the interaction depends on.

getNumGlobalParameters(self)int

Get the number of global parameters that the interaction depends on.

getNumEnergyParameterDerivatives(self)int

Get the number of global parameters with respect to which the derivative of the energy should be computed.

getNumTabulatedFunctions(self)int

Get the number of tabulated functions that have been defined.

getEnergyFunction(self)std::string const &

Get the algebraic expression that gives the energy of the system

setEnergyFunction(self, energy)

Set the algebraic expression that gives the energy of the system

addCollectiveVariable(self, name, variable)int

Add a collective variable that the force may depend on. The collective variable is represented by a Force object, which should have been created on the heap with the “new” operator. The CustomCVForce takes over ownership of it, and deletes the Force when the CustomCVForce itself is deleted.

Parameters
  • name (string) – the name of the collective variable, as it will appear in the energy expression

  • variable (Force *) – the collective variable, represented by a Force object. The value of the variable is the energy computed by the Force.

Returns

the index within the Force of the variable that was added

Return type

int

getCollectiveVariableName(self, index)std::string const &

Get the name of a collective variable.

Parameters

index (int) – the index of the collective variable for which to get the name

Returns

the variable name

Return type

string

getCollectiveVariable(self, index)Force
getCollectiveVariable(self, index)Force

Get a const reference to the Force object that computes a collective variable.

Parameters

index (int) – the index of the collective variable to get

Returns

the Force object

Return type

Force

addGlobalParameter(self, name, defaultValue)int

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 (string) – the name of the parameter

  • defaultValue (double) – the default value of the parameter

Returns

the index of the parameter that was added

Return type

int

getGlobalParameterName(self, index)std::string const &

Get the name of a global parameter.

Parameters

index (int) – the index of the parameter for which to get the name

Returns

the parameter name

Return type

string

setGlobalParameterName(self, index, name)

Set the name of a global parameter.

Parameters
  • index (int) – the index of the parameter for which to set the name

  • name (string) – the name of the parameter

getGlobalParameterDefaultValue(self, index)double

Get the default value of a global parameter.

Parameters

index (int) – the index of the parameter for which to get the default value

Returns

the parameter default value

Return type

double

setGlobalParameterDefaultValue(self, index, defaultValue)

Set the default value of a global parameter.

Parameters
  • index (int) – the index of the parameter for which to set the default value

  • defaultValue (double) – the default value of the parameter

addEnergyParameterDerivative(self, 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 (string) – the name of the parameter

getEnergyParameterDerivativeName(self, index)std::string const &

Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.

Parameters

index (int) – the index of the parameter derivative, between 0 and getNumEnergyParameterDerivatives()

Returns

the parameter name

Return type

string

addTabulatedFunction(self, name, function)int

Add a tabulated function that may appear in the energy expression.

Parameters
  • name (string) – the name of the function as it appears in expressions

  • function (TabulatedFunction *) – a TabulatedFunction object defining the function. The TabulatedFunction should have been created on the heap with the “new” operator. The Force takes over ownership of it, and deletes it when the Force itself is deleted.

Returns

the index of the function that was added

Return type

int

getTabulatedFunction(self, index)TabulatedFunction
getTabulatedFunction(self, index)TabulatedFunction

Get a reference to a tabulated function that may appear in the energy expression.

Parameters

index (int) – the index of the function to get

Returns

the TabulatedFunction object defining the function

Return type

TabulatedFunction

getTabulatedFunctionName(self, index)std::string const &

Get the name of a tabulated function that may appear in the energy expression.

Parameters

index (int) – the index of the function to get

Returns

the name of the function as it appears in expressions

Return type

string

getCollectiveVariableValues(self, context)

Get the current values of the collective variables in a Context.

Parameters

context (Context) – the Context for which to get the values

Returns

values – the values of the collective variables are computed and stored into this

Return type

vector< double >

getInnerContext(self, context)Context

Get the inner Context used for evaluating collective variables.

When you create a Context for a System that contains a CustomCVForce, internally it creates a new System, adds the Forces that define the CVs to it, creates a new Context for that System, and uses it to evaluate the variables. In most cases you can ignore all of this. It is just an implementation detail. However, there are a few cases where you need to directly access that internal Context. For example, if you want to modify one of the Forces that defines a collective variable and call updateParametersInContext() on it, you need to pass that inner Context to it. This method returns a reference to it.

Parameters

context (Context) – the Context containing the CustomCVForce

Returns

the inner Context used to evaluate the collective variables

Return type

Context

updateParametersInContext(self, context)

Update the tabulated function parameters 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 getTabulatedFunction(index).setFunctionParameters() to modify this object’s parameters, then call updateParametersInContext() to copy them over to the Context.

This method is very limited. The only information it updates is the parameters of tabulated functions. All other aspects of the Force (the energy expression, the set of collective variables, etc.) are unaffected and can only be changed by reinitializing the Context.

usesPeriodicBoundaryConditions(self)bool

Returns whether or not this force makes use of periodic boundary conditions.

Returns

true if force uses PBC and false otherwise

Return type

bool

__copy__(self)Force
getForceGroup(self)int

Get the force group this Force belongs to.

getName(self)std::string const &

Get the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.

setForceGroup(self, group)

Set the force group this Force belongs to.

Parameters

group (int) – the group index. Legal values are between 0 and 31 (inclusive).

setName(self, name)

Set the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.