########################################################################### # # Handle user arguments # ########################################################################### start = time.time() parser = create_parser() args = parser.parse_args() nengines = args.nengines equil = args.equil stride = args.stride # Process args for MDI mdi.MDI_Init(args.mdi) snapshot_filename = args.snap probes = [int(x) for x in args.probes.split()] if args.byres and args.bymol: parser.error( "--byres and --bymol cannot be used together. Please only use one." ) if args.byres: residues = process_pdb(args.byres)[0] engine_comm = connect_to_engines(nengines) # Print the probe atoms
########################################################################### # # Handle user arguments # ########################################################################### start = time.time() parser = create_parser() args = parser.parse_args() nengines = args.nengines equil = args.equil stride = args.stride # Process args for MDI mdi.MDI_Init(args.mdi, mpi_world) if use_mpi4py: mpi_world = mdi.MDI_Get_Intra_Code_MPI_Comm() world_rank = mpi_world.Get_rank() snapshot_filename = args.snap probes = [int(x) for x in args.probes.split()] if args.byres and args.bymol: parser.error( "--byres and --bymol cannot be used together. Please only use one." ) if args.byres: residues = process_pdb(args.byres)[0]
arg = sys.argv[iarg] if arg == "-mdi": mdi_options = sys.argv[iarg + 1] iarg += 1 else: raise Exception("Unrecognized command-line option") iarg += 1 # Confirm that the MDI options were provided if mdi_options is None: raise Exception("-mdi command-line option was not provided") # Initialize the MDI Library mdi.MDI_Init(mdi_options, mpi_comm_world) # Get unit conversions colvar = distance.Distance(319, 320) kcalmol_to_atomic = mdi.MDI_Conversion_Factor("kilocalorie_per_mol", "atomic_unit_of_energy") angstrom_to_atomic = mdi.MDI_Conversion_Factor("angstrom", "atomic_unit_of_length") kcalmol_per_angstrom_to_atomic = kcalmol_to_atomic / angstrom_to_atomic # Input parameters width = 0.2 * angstrom_to_atomic # Gaussian width of first collective variable height = 0.1 * kcalmol_to_atomic # Gaussian height of first collective variable total_steps = 8000 # Number of MD iterations. Note timestep = 2fs tau_gaussian = 400 # Frequency of addition of Gaussians upper_restraint = 14.0 * angstrom_to_atomic