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)
# set velocities to temperature in integrator
