def write(self, fname, universe, units=None):
universe.trajectory[-1]
universe.atoms.write(fname + '.gro')
trr = TRRWriter(fname + '.trr', universe.atoms.n_atoms)
if units:
trr.units = units
for ts in universe.trajectory:
trr.write(ts)
trr.close()
#
from MDAnalysis.analysis.rdf import InterRDF
charged = u.select_atoms("prop charge > 0")
rdf = InterRDF(charged, charged, nbins=7, range=(0, 10))
# This runs so far only over the single frame we have loaded.
# Multiframe averaging must be done by hand
rdf.run()
#
# ========================================================="
# Example #4: Saving frames to a GROMACS's TRR trajectory
# ========================================================="
#
from MDAnalysis.coordinates.TRR import TRRWriter
W = TRRWriter("traj.trr", n_atoms=len(system.part))
for i in range(100):
# integrate
system.integrator.run(1)
# replace last frame
# TODO loading new frames will be automated in future versions
u.load_new(eos.trajectory)
# append it to the .trr trajectory
W.write_next_timestep(u.trajectory.ts)
print("===> The trajectory has been saved in the traj.trr file")