MDTraj provides a few flexible reporters for use with the OpenMM python app. OpenMM is a toolkit for molecular simulation using high performance GPU code. OpenMM itself ships with a DCD reporter, 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.
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