VariableVerletIntegrator

class openmm.openmm.VariableVerletIntegrator(*args)

This is an error controlled, variable time step Integrator that simulates a System using the leap-frog Verlet algorithm. It compares the result of the Verlet integrator to that of an explicit Euler integrator, takes the difference between the two as a measure of the integration error in each time step, and continuously adjusts the step size to keep the error below a specified tolerance. This both improves the stability of the integrator and allows it to take larger steps on average, while still maintaining comparable accuracy to a fixed step size integrator.

It is best not to think of the error tolerance as having any absolute meaning. It is just an adjustable parameter that affects the step size and integration accuracy. You should try different values to find the largest one that produces a trajectory sufficiently accurate for your purposes. 0.001 is often a good starting point.

Unlike a fixed step size Verlet integrator, variable step size Verlet is not symplectic. This means that at a given accuracy level, energy is not as precisely conserved over long time periods. This makes it most appropriate for constant temperate simulations. In constant energy simulations where precise energy conservation over long time periods is important, a fixed step size Verlet integrator may be more appropriate.

You can optionally set a maximum step size it will ever use. This is useful to prevent it from taking excessively large steps in usual situations, such as when the system is right at a local energy minimum.

__init__(self, errorTol) → VariableVerletIntegrator

__init__(self, other) → VariableVerletIntegrator

Create a VariableVerletIntegrator.

Parameters

errorTol (double) – the error tolerance

Methods

__init__(-> VariableVerletIntegrator)	Create a VariableVerletIntegrator.
getConstraintTolerance(self)	Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
getErrorTolerance(self)	Get the error tolerance.
getIntegrationForceGroups(self)	Get which force groups to use for integration.
getMaximumStepSize(self)	Get the maximum step size the integrator will ever use, in ps.
getStepSize(self)	Get the size of each time step, in picoseconds.
setConstraintTolerance(self, tol)	Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
setErrorTolerance(self, tol)	Set the error tolerance.
setIntegrationForceGroups(groups)	Set which force groups to use for integration.
setMaximumStepSize(self, size)	Set the maximum step size the integrator will ever use, in ps.
setStepSize(self, size)	Set the size of each time step, in picoseconds.
step(self, steps)	Advance a simulation through time by taking a series of time steps.
stepTo(self, time)	Advance a simulation through time by taking a series of steps until a specified time is reached.

Attributes

thisown

The membership flag

property thisown

The membership flag

getConstraintTolerance(self) → double

Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.

getIntegrationForceGroups(self) → int

Get which force groups to use for integration. By default, all force groups are included. This is interpreted as a set of bit flags: the forces from group i will be included if (groups&(1<<i)) != 0.

getStepSize(self) → double

Get the size of each time step, in picoseconds. If this integrator uses variable time steps, the size of the most recent step is returned.

Returns

the step size, measured in ps

Return type

double

setConstraintTolerance(self, tol)

Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.

setIntegrationForceGroups(groups)

Set which force groups to use for integration. By default, all force groups are included.

Parameters

groups (set or int) – a set of indices for which force groups to include when integrating the equations of motion. Alternatively, the groups can be passed as a single unsigned integer interpreted as a bitmask, in which case group i will be included if (groups&(1<<i)) != 0.

setStepSize(self, size)

Set the size of each time step, in picoseconds. If this integrator uses variable time steps, the effect of calling this method is undefined, and it may simply be ignored.

Parameters

size (double) – the step size, measured in ps

getErrorTolerance(self) → double

Get the error tolerance.

setErrorTolerance(self, tol)

Set the error tolerance.

getMaximumStepSize(self) → double

Get the maximum step size the integrator will ever use, in ps. If this is 0 (the default), no limit will be applied to step sizes.

setMaximumStepSize(self, size)

Set the maximum step size the integrator will ever use, in ps. If this is 0 (the default), no limit will be applied to step sizes.

step(self, steps)

Advance a simulation through time by taking a series of time steps.

Parameters

steps (int) – the number of time steps to take

stepTo(self, time)

Advance a simulation through time by taking a series of steps until a specified time is reached. When this method returns, the simulation time will exactly equal the time which was specified. If you call this method and specify a time that is earlier than the current time, it will return without doing anything.

Parameters

time (double) – the time to which the simulation should be advanced