DEMO: read and write forces

[hainm]

script

from __future__ import print_function
from parmed.utils.netcdf import netcdf_file
import pytraj as pt
import numpy as np

fh = netcdf_file('data/mdfrc', mmap=False) # change mdfrc to your force filename
forces = fh.variables['forces']

# do similar thing for velocities

top = pt.load_topology('data/mdfrc.prmtop') # change prmtop to your parm7 filename
traj = pt.Trajectory(xyz=np.ascontiguousarray(forces[:], dtype='f8'), top=top)
print('original trajectory', traj)

# strip atom atoms
# change ':1-100' to your mask (e.g ':WAT')
new_traj = pt.strip(':1-100', traj)
print('stripped trajectory', new_traj)

# write trajectory
new_traj.save('test.nc', overwrite=True)

[hainm]

expectation: