def gromacs_input_files():
"""Create gromacs .top and .gro files in the target directory."""
reference_system, topology = multistate_reporter_metadata(
app.ms_container, 'reference_state.system topography.topology'.split())
# create gromacs .top and .gro files in the target directory
generate_gromacs_input(target_container,
topology=topology,
system=reference_system,
split='.gro')
from mmdemux import extract_trajectory
from mmlite.gromacs import generate_gromacs_input
from mmlite.utils import multistate_reporter_metadata
burnin_iterations = 100 # number of burnin iterations (#iterations)
checkpoint_iterations = 10 # checkpoint_interval (#iterations)
ref_state_index = 0
ms_container = Path('frames/trj.nc') # trajectory filepath
target_container = Path('frames/trj.0.nc') # trajectory filepath
burnin_iterations += 1 # discard starting configuration from trajectory
start_frame = ceil(burnin_iterations / checkpoint_iterations)
reference_system, topology = multistate_reporter_metadata(
ms_container, 'reference_state.system topography.topology'.split())
# save the sampled configurations at the target thermodynamic state
trj = extract_trajectory(nc_path=ms_container,
to_file=target_container,
state_index=ref_state_index,
start_frame=start_frame)
# create gromacs .top and .gro files in the target directory
generate_gromacs_input(target_container,
topology=topology,
system=reference_system,
split='.gro')