OpenMM Reporters¶
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 HDF5 Format is the most full-featured trajectory file format available.
Example Usage¶
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)
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HDF5Reporter stores a molecular dynamics trajectory in the HDF5 format. |
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NetCDFReporter stores a molecular dynamics trajectory in the AMBER NetCDF format. |
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DCDReporter stores a molecular dynamics trajectory in the CHARMM / NAMD DCD Format |