DrudeNoseHooverIntegrator

class OpenMM::DrudeNoseHooverIntegrator

This Integrator simulates systems that include Drude particles. It applies two different Nose-Hoover chain thermostats to the different parts of the system. The first is applied to ordinary particles (ones that are not part of a Drude particle pair), as well as to the center of mass of each Drude particle pair. A second thermostat, typically with a much lower temperature, is applied to the relative internal displacement of each pair.

This Integrator requires the System to include a DrudeForce, which it uses to identify the Drude particles.

Methods

DrudeNoseHooverIntegrator

Create a DrudeNoseHooverIntegrator.

~DrudeNoseHooverIntegrator

initialize

This will be called by the Context when it is created.

getMaxDrudeDistance

Get the maximum distance a Drude particle can ever move from its parent particle, measured in nm.

setMaxDrudeDistance

Set the maximum distance a Drude particle can ever move from its parent particle, measured in nm.

computeDrudeKineticEnergy

Compute the kinetic energy of the drude particles at the current time.

computeTotalKineticEnergy

Compute the kinetic energy of all (real and drude) particles at the current time.

getVelocitiesForTemperature

Return a list of velocities normally distributed around a target temperature, with the Drude temperatures assigned according to the Drude temperature assigned to the integrator.
DrudeNoseHooverIntegrator(double temperature, double collisionFrequency, double drudeTemperature, double drudeCollisionFrequency, double stepSize, int chainLength = 3, int numMTS = 3, int numYoshidaSuzuki = 7)

Create a DrudeNoseHooverIntegrator().

Parameters

  • temperature – the target temperature for the system (in Kelvin).

  • collisionFrequency – the frequency of the system’s interaction with the heat bath (in inverse picoseconds).

  • drudeTemperature – the target temperature for the Drude particles, relative to their parent atom (in Kelvin).

  • drudeCollisionFrequency – the frequency of the drude particles’ interaction with the heat bath (in inverse picoseconds).

  • stepSize – the step size with which to integrator the system (in picoseconds)

  • chainLength – the number of beads in the Nose-Hoover chain.

  • numMTS – the number of step in the multiple time step chain propagation algorithm.

  • numYoshidaSuzuki – the number of terms in the Yoshida-Suzuki multi time step decomposition used in the chain propagation algorithm (must be 1, 3, or 5).

~DrudeNoseHooverIntegrator()
void initialize(ContextImpl &context) override

This will be called by the Context when it is created. It informs the Integrator of what context it will be integrating, and gives it a chance to do any necessary initialization. It will also get called again if the application calls reinitialize() on the Context.

double getMaxDrudeDistance() const

Get the maximum distance a Drude particle can ever move from its parent particle, measured in nm. This is implemented with a hard wall constraint. If this distance is set to 0 (the default), the hard wall constraint is omitted.

void setMaxDrudeDistance(double distance)

Set the maximum distance a Drude particle can ever move from its parent particle, measured in nm. This is implemented with a hard wall constraint. If this distance is set to 0 (the default), the hard wall constraint is omitted.

double computeDrudeKineticEnergy()

Compute the kinetic energy of the drude particles at the current time.

double computeTotalKineticEnergy()

Compute the kinetic energy of all (real and drude) particles at the current time.

std::vector<Vec3> getVelocitiesForTemperature(const System &system, double temperature, int randomSeed) const override

Return a list of velocities normally distributed around a target temperature, with the Drude temperatures assigned according to the Drude temperature assigned to the integrator.

Parameters

  • system – the system whose velocities are to be initialized.

  • temperature – the target temperature in Kelvin.

  • randomSeed – the random number seed to use when selecting velocities