parmed.openmm.reporters module

This module contains a handful of extra reporter classes for OpenMM simulations

class parmed.openmm.reporters.EnergyMinimizerReporter(f, volume=False, **kwargs)

Bases: parmed.openmm.reporters.StateDataReporter

This class acts as a simple energy reporter class for minimizations. This is not meant to be used as a reporter for OpenMM’s molecular dynamics routines, but instead passed a simulation object for printing out single-point energies.

Parameters

fstr or file-like

File name or object to write energies to

volumebool, optional

If True, write the system volume (default is False)

Methods

describeNextReport(*args, **kwargs)	Disable this reporter inside MD
finalize()	Closes any open file
report(simulation[, frame])	Print out the current energy

describeNextReport(*args, **kwargs)

Disable this reporter inside MD

finalize()

Closes any open file

report(simulation, frame=None)

Print out the current energy

class parmed.openmm.reporters.MdcrdReporter(**kwargs)

Bases: object

MdcrdReporter prints a trajectory in ASCII Amber format. This reporter will be significantly slower than binary file reporters (like DCDReporter or NetCDFReporter).

Parameters

filestr

Name of the file to write the trajectory to

reportIntervalint

Number of steps between writing trajectory frames

crdsbool=True

Write coordinates to this trajectory file?

velsbool=False

Write velocities to this trajectory file?

frcsbool=False

Write forces to this trajectory file?

Notes

You can only write one of coordinates, forces, or velocities to a mdcrd file.

Methods

describeNextReport(simulation)	Get information about the next report this object will generate.
finalize()	Closes any open file
report(simulation, state)	Generate a report.

describeNextReport(simulation)

Get information about the next report this object will generate.

Parameters

simulationapp.Simulation

The Simulation to generate a report for

Returns

nsteps, pos, vel, frc, eneint, bool, bool, bool, bool

nsteps is the number of steps until the next report pos, vel, frc, and ene are flags indicating whether positions, velocities, forces, and/or energies are needed from the Context

finalize()

Closes any open file

report(simulation, state)

Generate a report.

Parameters:

• simulation (Simulation) The Simulation to generate a report for

• state (State) The current state of the simulation

class parmed.openmm.reporters.NetCDFReporter(**kwargs)

Bases: object

NetCDFReporter prints a trajectory in NetCDF format

Methods

describeNextReport(simulation)	Get information about the next report this object will generate.
finalize()	Closes any open file
report(simulation, state)	Generate a report.

describeNextReport(simulation)

Get information about the next report this object will generate.

Parameters

simulationapp.Simulation

The Simulation to generate a report for

Returns

nsteps, pos, vel, frc, eneint, bool, bool, bool, bool

nsteps is the number of steps until the next report pos, vel, frc, and ene are flags indicating whether positions, velocities, forces, and/or energies are needed from the Context

finalize()

Closes any open file

report(simulation, state)

Generate a report.

Parameters

simulationapp.Simulation

The Simulation to generate a report for

statemm.State

The current state of the simulation

class parmed.openmm.reporters.ProgressReporter(**kwargs)

Bases: parmed.openmm.reporters.StateDataReporter

A class that prints out a progress report of how much MD (or minimization) has been done, how fast the simulation is running, and how much time is left (similar to the mdinfo file in Amber)

Parameters

fstr

The file name of the progress report file (overwritten each time)

reportIntervalint

The step interval between which to write frames

totalStepsint

The total number of steps that will be run in the simulation (used to estimate time remaining)

potentialEnergybool, optional

Whether to print the potential energy (default True)

kineticEnergybool, optional

Whether to print the kinetic energy (default True)

totalEnergybool, optional

Whether to print the total energy (default True)

temperaturebool, optional

Whether to print the system temperature (default True)

volumebool, optional

Whether to print the system volume (default False)

densitybool, optional

Whether to print the system density (default False)

systemMassfloat or unit.Quantity

The mass of the system used when reporting density (useful in instances where masses are set to 0 to constrain their positions)

Notes

In addition to the above, ProgressReporter also accepts arguments for StateDataReporter

Methods

describeNextReport(simulation)	Get information about the next report this object will generate.
finalize()	Closes any open file
report(simulation, state)	Generate a report and predict the time to completion (and current/overall MD performance)

describeNextReport(simulation)

Get information about the next report this object will generate.

Parameters

simulationapp.Simulation

The Simulation to generate a report for

Returns

nsteps, pos, vel, frc, eneint, bool, bool, bool, bool

nsteps is the number of steps until the next report pos, vel, frc, and ene are flags indicating whether positions, velocities, forces, and/or energies are needed from the Context

report(simulation, state)

Generate a report and predict the time to completion (and current/overall MD performance)

class parmed.openmm.reporters.RestartReporter(**kwargs)

Bases: object

Use a reporter to handle writing restarts at specified intervals.

Parameters

filestr

Name of the file to write the restart to.

reportIntervalint

Number of steps between writing restart files

write_multiplebool=False

Either write a separate restart each time (appending the step number in the format .# to the file name given above) if True, or overwrite the same file each time if False

netcdfbool=False

Use the Amber NetCDF restart file format

write_velocitiesbool=True

Write velocities to the restart file. You can turn this off for passing in, for instance, a minimized structure.

Methods

describeNextReport(simulation)	Get information about the next report this object will generate.
finalize()	No-op here
report(sim, state)	Generate a report.

describeNextReport(simulation)

Get information about the next report this object will generate.

Parameters

simulationapp.Simulation

The Simulation to generate a report for

Returns

nsteps, pos, vel, frc, eneint, bool, bool, bool, bool

nsteps is the number of steps until the next report pos, vel, frc, and ene are flags indicating whether positions, velocities, forces, and/or energies are needed from the Context

finalize()

No-op here

report(sim, state)

Generate a report.

Parameters

simapp.Simulation

The Simulation to generate a report for

statemm.State

The current state of the simulation

class parmed.openmm.reporters.StateDataReporter(**kwargs)

Bases: object

This class acts as a state data reporter for OpenMM simulations, but it is a little more generalized. Notable differences are:

• It allows the units of the output to be specified, with defaults being those used in Amber (e.g., kcal/mol, angstroms^3, etc.)

• It will write to any object containing a ‘write’ method; not just files. This allows, for instance, writing to a GUI window that implements the desired ‘write’ attribute.

Most of this code is copied from the OpenMM StateDataReporter class, with the above-mentioned changes made.

Parameters

fstr or file-like

Destination to write the state data (file name or file object)

reportIntervalint

Number of steps between state data reports

stepbool, optional

Print out the step number (Default True)

timebool, optional

Print out the simulation time (Defaults True)

potentialEnergybool, optional

Print out the potential energy of the structure (Default True)

kineticEnergybool, optional

Print out the kinetic energy of the structure (Default True)

totalEnergybool, optional

Print out the total energy of the system (Default True)

temperaturebool, optional

Print out the temperature of the system (Default True)

volumebool, optional

Print out the volume of the unit cell. If the system is not periodic, the value is meaningless (Default False)

densitybool, optional

Print out the density of the unit cell. If the system is not periodic, the value is meaningless (Default False)

separatorstr, optional

The string to separate data fields (Default ‘,’)

systemMassfloat, optional

If not None, the density will be computed from this mass, since setting a mass to 0 is used to constrain the position of that particle. (Default None)

energyUnitunit, optional

The units to print energies in (default unit.kilocalories_per_mole)

timeUnitunit, optional

The units to print time in (default unit.picoseconds)

volumeUnitunit, optional

The units print volume in (default unit.angstroms**3)

densityUnitunit, optional

The units to print density in (default unit.grams/unit.item/unit.milliliter)

Methods

describeNextReport(simulation)	Get information about the next report this object will generate.
finalize()	Closes any open file
report(simulation, state)	Generate a report.

describeNextReport(simulation)

Get information about the next report this object will generate.

Parameters

simulationapp.Simulation

The simulation to generate a report for

Returns

nsteps, pos, vel, frc, eneint, bool, bool, bool, bool

nsteps is the number of steps until the next report pos, vel, frc, and ene are flags indicating whether positions, velocities, forces, and/or energies are needed from the Context

finalize()

Closes any open file

report(simulation, state)

Generate a report.

Parameters

simulationapp.Simulation

The Simulation to generate a report for

statemm.State

The current state of the simulation