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import MDAnalysis as mda
import numpy as np
def create_test_trj(uni, fname):
n_atoms = uni.atoms.n_atoms
pos = np.arange(3 * n_atoms).reshape(n_atoms, 3)
uni.trajectory.ts.dt = 1
orig_box = np.array([81.1, 82.2, 83.3, 75, 80, 85], dtype=np.float32)
uni.trajectory.ts.dimensions = orig_box
uni.trajectory.units = {
"time": "ps",
"length": "Angstrom",
"velocity": "Angstrom/ps",
"force": "kJ/(mol*Angstrom)",
}
print(uni.trajectory)
print(uni.trajectory.ts.__class__)
with mda.Writer(
fname,
n_atoms,
positions=True,
velocities=True,
forces=True,
convert_units=False,
) as w:
for i in range(5):
uni.atoms.positions = 2**i * pos
uni.trajectory.ts.time = i
uni.trajectory.ts.velocities = uni.atoms.positions / 10
uni.trajectory.ts.forces = uni.atoms.positions / 100
uni.trajectory.ts.frame = i
uni.trajectory.ts.dimensions[:3] = orig_box[:3] + i
uni.trajectory.ts.dimensions[3:] = orig_box[3:] + i * 0.1
print(uni.trajectory.ts.dimensions)
w.write(uni)
def main():
pdb = "test_topology.pdb"
u = mda.Universe(pdb)
create_test_trj(u, "test.h5md")
if __name__ == "__main__":
main()
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