RegulatedNHLIntegrator

class openxps.integrators.RegulatedNHLIntegrator(temperature, timeConstant, stepSize, *, regulationParameter=1, forceFirst=False)

A Regulated Nosé-Hoover-Langevin (NHL) integrator [6].

The Regulated Nosé-Hoover-Langevin (NHL) integrator is effective at maintaining temperature control under steady-state conditions, such as in d-AFED/TAMD [3, 4] or UFED [5] simulations.

Note

The friction coefficient is initially set to the inverse of the time constant, but this value can be customized via setFrictionCoefficient().

Warning

This integrator is incompatible with systems subject to constraints.

Parameters:

• temperature (Quantity) – The temperature of the heat bath.

• timeConstant (Quantity) – The time constant (a.k.a. coupling/damping/relaxation time) of the thermostat.

• stepSize (Quantity) – The integration step size.

Keyword Arguments:

• regulationParameter – The regulation parameter (see [6] for details).

• forceFirst – If True, the integrator will apply a force-first scheme. Otherwise, it will apply a symmetric operator splitting scheme.

Example

>>> import openxps as xps
>>> from openmm import unit
>>> from openmmtools import testsystems

Symmetric scheme (default)

>>> integrator = xps.integrators.RegulatedNHLIntegrator(
...     temperature=300 * unit.kelvin,
...     timeConstant=100 * unit.femtoseconds,
...     stepSize=2 * unit.femtoseconds,
... )
>>> integrator
Per-dof variables:
  v1, active
Global variables:
  kT = 2.494...
  invQ = 40.090...
  a = 0.9801...
  b = 1.9801...
Computation steps:
   0: allow forces to update the context state
   1: v <- v + 0.5*dt*f/m
   2: x <- x + 0.5*dt*c*tanh(v/c); c=sqrt(1*kT/m)
   3: v1 <- active*(v1 + 0.5*dt*(m*v*c*tanh(v/c) - kT)*invQ); c=sqrt(1*kT/m)
   4: v <- v*exp(-0.5*dt*v1)
   5: v1 <- active*(a*v1 + b*gaussian)
   6: v <- v*exp(-0.5*dt*v1)
   7: v1 <- active*(v1 + 0.5*dt*(m*v*c*tanh(v/c) - kT)*invQ); c=sqrt(1*kT/m)
   8: x <- x + 0.5*dt*c*tanh(v/c); c=sqrt(1*kT/m)
   9: v <- v + 0.5*dt*f/m

Force-first scheme

>>> integrator_ff = xps.integrators.RegulatedNHLIntegrator(
...     temperature=300 * unit.kelvin,
...     timeConstant=100 * unit.femtoseconds,
...     stepSize=2 * unit.femtoseconds,
...     forceFirst=True
... )
>>> model = testsystems.AlanineDipeptideVacuum()
>>> try:
...     integrator_ff.registerWithSystem(model.system, False)
... except ValueError as e:
...     print(e)
Regulated NHL integrators do not support constraints.

Methods

getFrictionCoefficient()

Get the friction coefficient.

Returns:

The friction coefficient.

Return type:

openmm.unit.Quantity

getRegulationParameter()

Get the regulation parameter of the integrator.

Returns:

The regulation parameter.

Return type:

float

getTemperature()

Get the temperature.

Returns:

The temperature.

Return type:

openmm.unit.Quantity

getTimeConstant()

Get the time constant.

Returns:

The time constant.

Return type:

openmm.unit.Quantity

registerWithSystem(system, isExtension)

Register the integrator with the system.

setFrictionCoefficient(value)

Set the friction coefficient.

Parameters:

value (Quantity | float) – The friction coefficient.

setTemperature(value)

Set the temperature.

Parameters:

value (Quantity | float) – The temperature.

setTimeConstant(value)

Set the time constant.

Parameters:

value (Quantity | float) – The time constant.