BioSimSpace.Metadynamics.Bound

class BioSimSpace.Metadynamics.Bound(value, force_constant=100.0, exponent=2.0, epsilon=1.0)[source]
__init__(value, force_constant=100.0, exponent=2.0, epsilon=1.0)[source]

Constructor.

Set a bound on the value of a collective variable along with the parameters used to define the bias potential.

The expression for the bias is:

\[k ((x - a)/s)^e\]
Parameters:

  • value (int, float, Type) – The value of the bound. Use ‘int’ or ‘float’ for dimensionless collective variables.

  • force_constant (float) – The force constant (k) for the bias potential. Note that the units of the force constant aren’t specified, i.e. the value takes the units of the collective variable to which it is later applied.

  • exponent (float) – The exponent (e) for the bias potential.

  • epsilon (float) – The rescaling factor (s) for the bias potential.

Methods

__init__(value[, force_constant, exponent, ...])

Constructor.

getEpsilon()

Get the rescaling factor (s) for the bias potential.

getExponent()

Get the exponent (e) for the bias potential.

getForceConstant()

Get the force constant (k) for the bias potential.

getValue()

Get the value of the bound.

setEpsilon(epsilon)

Set the rescaling factor (s) for the bias potential.

setExponent(exponent)

Set the exponent (e) for the bias potential.

setForceConstant(force_constant)

Set the force constant (k) for the bias potential.

setValue(value)

Set the value of the bound.
getEpsilon()[source]

Get the rescaling factor (s) for the bias potential.

Returns:

epsilon – The rescaling factor for the bias potential.

Return type:

float

getExponent()[source]

Get the exponent (e) for the bias potential.

Returns:

exponent – The exponent for the bias potential.

Return type:

float

getForceConstant()[source]

Get the force constant (k) for the bias potential.

Returns:

force_constant – The force constant for the bias potential.

Return type:

float

getValue()[source]

Get the value of the bound.

Returns:

value – The value of the bound.

Return type:

int, float, Type

setEpsilon(epsilon)[source]

Set the rescaling factor (s) for the bias potential.

Parameters:

epsilon (float) – The rescaling factor for the bias potential.

setExponent(exponent)[source]

Set the exponent (e) for the bias potential.

Parameters:

exponent (float) – The exponent for the bias potential.

setForceConstant(force_constant)[source]

Set the force constant (k) for the bias potential.

Parameters:

force_constant (float) – The force constant for the bias potential.

setValue(value)[source]

Set the value of the bound.

Parameters:

value (int, float, Type) – The value of the bound.