openmm-mdanalysis-reporter

import openmm.app as app import openmm as om from openmm_mdanalysis_reporter import MDAnalysisReporter import os # Create a simple system (e.g., single atom, just for demonstration) # In a real scenario, you'd load a PDB/GMX file with app.PDBFile, etc. system = om.System() system.addParticle(1.0) # mass in amu # Create an integrator integrator = om.VerletIntegrator(0.001) # 1 fs timestep # Create a simulation object # Use 'Reference' platform for broad compatibility without GPU platform = om.Platform.getPlatformByName('Reference') simulation = app.Simulation(system, integrator, platform) simulation.context.setPositions([[0, 0, 0]]) # Set initial position simulation.context.setVelocitiesToTemperature(300 * om.unit.kelvin) # Set initial velocities # Define output file path for the trajectory output_file = "trajectory.uaf" # UAF is recommended for MDAnalysisReporter # Add the MDAnalysisReporter # Report every 10 steps, enforce periodic box (set to False for this non-periodic system) # For periodic systems, ensure system.setDefaultPeriodicBoxVectors is called. reporter = MDAnalysisReporter(output_file, 10, enforcePeriodicBox=False) simulation.reporters.append(reporter) print(f"Running simulation and writing to {output_file}...") simulation.step(100) # Run for 100 steps print("Simulation finished.") # Optional: Load and inspect the generated trajectory with MDAnalysis try: import MDAnalysis as mda u = mda.Universe(output_file) print(f"Loaded trajectory with {u.trajectory.n_frames} frames.") # Clean up the generated file os.remove(output_file) print(f"Cleaned up {output_file}.") except ImportError: print("MDAnalysis not installed, skipping trajectory inspection and cleanup.") except Exception as e: print(f"Error loading trajectory with MDAnalysis: {e}. Attempting cleanup.") if os.path.exists(output_file): os.remove(output_file) # Still try to clean up