###########################################################################
#
# 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