) # Define the platform to use; CUDA, OpenCL, CPU, or Reference. Or do not specify # the platform to use the default (fastest) platform platform = mm.Platform.getPlatformByName('CUDA') prop = dict(CudaPrecision='mixed') # Use mixed single/double precision # Create the Simulation object sim = app.Simulation(ala5_gas.topology, system, integrator, platform, prop) # Set the particle positions sim.context.setPositions(ala5_gas.positions) # Minimize the energy print('Minimizing energy') sim.minimizeEnergy(maxIterations=500) # Set up the reporters to report energies and coordinates every 100 steps sim.reporters.append( AmberStateDataReporter(sys.stdout, 100, step=True, potentialEnergy=True, kineticEnergy=True, temperature=True) ) sim.reporters.append( NetCDFReporter('ala5_gb.nc', 100, atom=ala5_gas.ptr('natom'), uses_pbc=False, crds=True) ) # Run dynamics print('Running dynamics') sim.step(10000)
# Define the platform to use; CUDA, OpenCL, CPU, or Reference. Or do not specify # the platform to use the default (fastest) platform platform = mm.Platform.getPlatformByName('CUDA') prop = dict(CudaPrecision='mixed') # Use mixed single/double precision # Create the Simulation object sim = app.Simulation(ala2_solv.topology, system, integrator, platform, prop) # Set the particle positions sim.context.setPositions(ala2_solv.positions) # Minimize the energy print('Minimizing energy') sim.minimizeEnergy(maxIterations=500) # Set up the reporters to report energies and coordinates every 100 steps sim.reporters.append( AmberStateDataReporter(sys.stdout, 100, step=True, potentialEnergy=True, kineticEnergy=True, temperature=True, volume=True, density=True) ) sim.reporters.append( NetCDFReporter('ala2_solv.nc', 100, atom=ala2_solv.ptr('natom'), uses_pbc=True, crds=True) ) # Run dynamics print('Running dynamics') sim.step(10000)