MetaCVWriter

class cvpack.reporting.MetaCVWriter(metaCV, values=(), emasses=(), parameters=(), derivatives=(), allowReinitialization=False)

A custom writer for reporting meta-collective variable data.

Parameters:

• metaCV (MetaCollectiveVariable) – The meta-collective variable whose associated values will be reported.

• values (Sequence[str]) – The names of the inner variables whose values will be reported.

• emasses (Sequence[str]) – The names of the inner variables whose effective masses will be reported.

• parameters (Sequence[str]) – The names of the parameters whose values will be reported.

• derivatives (Sequence[str]) – The names of the parameters with respect to which the derivatives of the meta-collective variable will be reported.

• allowReinitialization (bool) – Whether to allow context reinitialization when the meta-collective variable shares its force group with other forces (needed for derivatives only).

Raises:

ValueError – If any name does not match an inner variable or a parameter

Examples

>>> import cvpack
>>> import openmm
>>> from math import pi
>>> from cvpack.reporting import StateDataReporter, MetaCVWriter
>>> from openmm import app, unit
>>> from sys import stdout
>>> from openmmtools import testsystems
>>> model = testsystems.AlanineDipeptideVacuum()
>>> phi = cvpack.Torsion(4, 6, 8, 14, name="phi")
>>> psi = cvpack.Torsion(6, 8, 14, 16, name="psi")
>>> umbrella = cvpack.MetaCollectiveVariable(
...     f"0.5*kappa*(min(dphi,{2*pi}-dphi)^2+min(dpsi,{2*pi}-dpsi)^2)"
...     "; dphi=abs(phi-phi0); dpsi=abs(psi-psi0)",
...     [phi, psi],
...     unit.kilojoules_per_mole,
...     name="umbrella",
...     kappa=100 * unit.kilojoules_per_mole/unit.radian**2,
...     phi0=5*pi/6 * unit.radian,
...     psi0=-5*pi/6 * unit.radian,
... )
>>> reporter = StateDataReporter(
...     stdout,
...     100,
...     writers=[
...         MetaCVWriter(
...             umbrella,
...             values=["phi", "psi"],
...             emasses=["phi", "psi"],
...             parameters=["phi0", "psi0"],
...             derivatives=["phi0", "psi0"],
...         ),
...     ],
...     step=True,
... )
>>> integrator = openmm.LangevinIntegrator(
...     300 * unit.kelvin,
...     1 / unit.picosecond,
...     2 * unit.femtosecond,
... )
>>> integrator.setRandomNumberSeed(1234)
>>> umbrella.addToSystem(model.system)
>>> simulation = app.Simulation(model.topology, model.system, integrator)
>>> simulation.context.setPositions(model.positions)
>>> simulation.context.setVelocitiesToTemperature(300 * unit.kelvin, 5678)
>>> simulation.reporters.append(reporter)
>>> simulation.step(1000)
#"Step","phi (rad)",...,"d[umbrella]/d[psi0] (kJ/(mol rad))"
100,2.6766...,-20.519...
200,2.3694...,0.7804...
300,3.1342...,49.272...
400,2.8179...,-10.012...
500,2.7565...,-8.9529...
600,2.6956...,23.049...
700,2.9331...,25.068...
800,2.6988...,-0.4481...
900,2.7477...,9.5528...
1000,2.7744...,21.986...

Methods

getHeaders()

Gets a list of strings containing the headers to be added to the report.

Return type:

list[str]

getValues(simulation)

Gets a list of floats containing the values to be added to the report.

Parameters:

simulation (Simulation) – The simulation object.

Return type:

list[float]