raise print('Done.') print('# platform used:', simulation.context.getPlatform().getName()) if args.verbose: print('# platforms available') for no_platform in range(Platform.getNumPlatforms()): # noinspection PyCallByClass,PyTypeChecker print('(%d) %s' % (no_platform, Platform.getPlatform(no_platform).getName())) print(os.environ) print(Platform.getPluginLoadFailures()) print(Platform.getDefaultPluginsDirectory()) if args.restart: arr = np.load(args.restart) simulation.context.setPositions(arr['positions'] * u.nanometers) simulation.context.setVelocities(arr['velocities'] * u.nanometers / u.picosecond) simulation.context.setPeriodicBoxVectors(*arr['box_vectors'] * u.nanometers) else: simulation.context.setPositions(pdb.positions) pbv = system.getDefaultPeriodicBoxVectors() simulation.context.setPeriodicBoxVectors(*pbv)