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OpenMM Reporters
================
MDTraj provides a few flexible reporters for use with the `OpenMM <https://simtk.org/home/openmm>`_ python app. OpenMM is a toolkit for molecular simulation using high performance GPU code. OpenMM itself ships with a `DCD reporter <https://simtk.org/api_docs/openmm/api5_0/python/classsimtk_1_1openmm_1_1app_1_1dcdreporter_1_1DCDReporter.html>`_, but it lacks the ability to, for instance, report on only a subset of the atoms, which might be desired to print only the protein coordinates and discard water during a simulation.
MDTraj currently provides three reporters, ``HDF5Reporter``, ``NetCDFReporter`` and ``DCDReporter``. Of these, ```HDF5Reporter`` is the most flexible, because the :ref:`HDF5 Format <HDF5FormatSpec>` is the most full-featured trajectory file format available.
Example Usage
-------------
.. code-block:: python
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
from mdtraj.reporters import NetCDFReporter # <-- new import from mdtraj
pdb = PDBFile("input.pdb")
forcefield = ForceField("amber99sb.xml", "tip3p.xml")
system = forcefield.createSystem(
pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1 * nanometer, constraints=HBonds
)
integrator = LangevinIntegrator(300 * kelvin, 1 / picosecond, 0.002 * picoseconds)
simulation = Simulation(pdb.topology, system, integrator)
simulation.context.setPositions(pdb.positions)
simulation.minimizeEnergy()
simulation.reporters.append(NetCDFReporter("output.nc", 1000)) # <-- AMBER compatible
simulation.step(10000)
.. currentmodule:: mdtraj.reporters
.. autosummary::
:toctree: generated/
HDF5Reporter
NetCDFReporter
DCDReporter
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