{"id":10013,"library":"openmm-mdanalysis-reporter","title":"OpenMM MDAnalysis Reporter","description":"The openmm-mdanalysis-reporter is a Python library that bridges OpenMM simulations with MDAnalysis. It allows users to create MDAnalysis Universe objects directly from OpenMM State objects and write trajectory data to any MDAnalysis-supported format, particularly the Universal Archive Format (UAF). The current version is 0.1, indicating an early development stage with an infrequent release cadence.","status":"active","version":"0.1","language":"en","source_language":"en","source_url":"https://github.com/MDAnalysis/openmm-mdanalysis-reporter","tags":["openmm","mdanalysis","molecular dynamics","simulation","reporter","trajectory"],"install":[{"cmd":"pip install openmm-mdanalysis-reporter","lang":"bash","label":"Install stable version"}],"dependencies":[{"reason":"Core molecular dynamics simulation engine.","package":"openmm","optional":false},{"reason":"Core library for molecular dynamics trajectory analysis.","package":"MDAnalysis","optional":false},{"reason":"Numerical operations, a transitive dependency via OpenMM and MDAnalysis.","package":"numpy","optional":false}],"imports":[{"symbol":"MDAnalysisReporter","correct":"from openmm_mdanalysis_reporter import MDAnalysisReporter"}],"quickstart":{"code":"import openmm.app as app\nimport openmm as om\nfrom openmm_mdanalysis_reporter import MDAnalysisReporter\nimport os\n\n# Create a simple system (e.g., single atom, just for demonstration)\n# In a real scenario, you'd load a PDB/GMX file with app.PDBFile, etc.\nsystem = om.System()\nsystem.addParticle(1.0) # mass in amu\n\n# Create an integrator\nintegrator = om.VerletIntegrator(0.001) # 1 fs timestep\n\n# Create a simulation object\n# Use 'Reference' platform for broad compatibility without GPU\nplatform = om.Platform.getPlatformByName('Reference') \nsimulation = app.Simulation(system, integrator, platform)\nsimulation.context.setPositions([[0, 0, 0]]) # Set initial position\nsimulation.context.setVelocitiesToTemperature(300 * om.unit.kelvin) # Set initial velocities\n\n# Define output file path for the trajectory\noutput_file = \"trajectory.uaf\" # UAF is recommended for MDAnalysisReporter\n\n# Add the MDAnalysisReporter\n# Report every 10 steps, enforce periodic box (set to False for this non-periodic system)\n# For periodic systems, ensure system.setDefaultPeriodicBoxVectors is called.\nreporter = MDAnalysisReporter(output_file, 10, enforcePeriodicBox=False)\nsimulation.reporters.append(reporter)\n\nprint(f\"Running simulation and writing to {output_file}...\")\nsimulation.step(100) # Run for 100 steps\nprint(\"Simulation finished.\")\n\n# Optional: Load and inspect the generated trajectory with MDAnalysis\ntry:\n    import MDAnalysis as mda\n    u = mda.Universe(output_file)\n    print(f\"Loaded trajectory with {u.trajectory.n_frames} frames.\")\n    # Clean up the generated file\n    os.remove(output_file)\n    print(f\"Cleaned up {output_file}.\")\nexcept ImportError:\n    print(\"MDAnalysis not installed, skipping trajectory inspection and cleanup.\")\nexcept Exception as e:\n    print(f\"Error loading trajectory with MDAnalysis: {e}. Attempting cleanup.\")\n    if os.path.exists(output_file):\n        os.remove(output_file) # Still try to clean up\n","lang":"python","description":"This quickstart demonstrates how to set up a minimal OpenMM simulation and attach the `MDAnalysisReporter` to write trajectory data. It uses a simple single-particle system for brevity. For real simulations, you would load a PDB, define forces, and set proper periodic boundary conditions. The example also shows how to optionally load the generated `.uaf` file using MDAnalysis for verification."},"warnings":[{"fix":"For non-periodic simulations, initialize the reporter with `enforcePeriodicBox=False`. For periodic simulations, ensure periodic box vectors are set on the `System` object (e.g., `system.setDefaultPeriodicBoxVectors(...)` or loaded from a PDB with CRYST1 records).","message":"The `enforcePeriodicBox` parameter requires the OpenMM `System` to have periodic box vectors defined. If `enforcePeriodicBox=True` is used for a non-periodic system (e.g., implicit solvent, gas phase without explicit box definition), the reporter will raise a `ValueError` during the report step.","severity":"gotcha","affected_versions":"0.1"},{"fix":"Prioritize using the `.uaf` extension for your trajectory output files. If another format is essential, thoroughly test its compatibility and data integrity with the reporter.","message":"The Universal Archive Format (`.uaf`) is the explicitly recommended output format for `MDAnalysisReporter`. While other MDAnalysis-supported formats might work, `.uaf` is designed for direct mapping from OpenMM states, offering better performance and reliability. Using other formats might lead to unexpected behavior, performance overheads, or data integrity issues.","severity":"gotcha","affected_versions":"0.1"},{"fix":"Consult the official GitHub repository for the latest documentation and potential updates. Exercise caution and thorough testing when relying on specific API behaviors or upgrading the library.","message":"As a `0.1` release, this library is in an early development stage. While functional, its API may not be entirely stable, and performance might not be fully optimized for all complex scenarios. Future minor or patch releases could introduce breaking changes or significant API adjustments.","severity":"gotcha","affected_versions":"0.1"}],"env_vars":null,"last_verified":"2026-04-17T00:00:00.000Z","next_check":"2026-07-16T00:00:00.000Z","problems":[{"fix":"Set `enforcePeriodicBox=False` when initializing the reporter for non-periodic systems, or ensure `system.setDefaultPeriodicBoxVectors` is explicitly called for periodic systems before running the simulation.","cause":"The `MDAnalysisReporter` was initialized with `enforcePeriodicBox=True`, but the OpenMM `System` does not have periodic box vectors set.","error":"ValueError: Cannot enforce periodic box for a system without periodic box vectors defined."},{"fix":"Verify that the simulation completed without errors and the output file exists at the specified path. Ensure the file is being written to the recommended `.uaf` format. Check MDAnalysis compatibility with the file version by trying to load it manually outside the reporter's context.","cause":"After simulation, MDAnalysis cannot open the generated trajectory file, possibly due to corruption, an incomplete write, or an unsupported format/version.","error":"MDAnalysis.exceptions.NoUniverseError: Unable to load topology or trajectory."},{"fix":"Always use `simulation.reporters.append(MDAnalysisReporter(...))` to add the reporter instance to the list of reporters, rather than trying to assign it directly or iterate over a single object.","cause":"This error or similar (e.g., `TypeError: 'MDAnalysisReporter' object is not iterable`) can occur if `simulation.reporters` is directly assigned a `MDAnalysisReporter` object instead of appending it.","error":"AttributeError: 'list' object has no attribute 'append'"}]}