print(F'Bookkeeping:\t {elapsed}')
###########################################################################
#
# Send Probe Information to Tinker
#
###########################################################################
start = time.time()
# Inform Tinker of the probe atoms
for comm in engine_comm:
mdi.MDI_Send_Command(">NPROBES", comm)
mdi.MDI_Send(len(probes), 1, mdi.MDI_INT, comm)
mdi.MDI_Send_Command(">PROBES", comm)
mdi.MDI_Send(probe_pole_indices, len(probes), mdi.MDI_INT, comm)
angstrom_to_bohr = mdi.MDI_Conversion_Factor("angstrom",
"atomic_unit_of_length")
elapsed - time.time() - start
print(F'Sending info to tinker:\t {elapsed}')
###########################################################################
#
# Engine and Trajectory File Compatibility Check.
#
###########################################################################
# Check that engine and trajectory are compatible.
# Process first two lines of snapshot to get information.
with open(snapshot_filename, "r") as snapshot_file:
first_line = snapshot_file.readline()
natoms = int(first_line.split()[0])
second_line = snapshot_file.readline().split()
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
lower_restraint = 1.0 * angstrom_to_atomic
upper_window = 8.0 * angstrom_to_atomic
lower_window = 2.4 * angstrom_to_atomic
k_restraint = 10 * kcalmol_per_angstrom_to_atomic
verbose = False