genfeature

  • This command should be executed after running pacs mdrun.
  • It generates feature data in .npy format, which is cconvenient for MSM analysis in Python.
    • Feature data files (e.g., t001c002r010.npy) are stored in the directory specified with the -od option.
    • Each .npy file has the np.arry in the shape as described in the table below.
  • This command supports parallel processing.

Currently implemented analysis tools and the shape of the output data in .npy files.

featuremdtrajgmxcpptrajshape of .npy
comdistoxx(n_frames,)
comvecoxx(n_frames, 3)
rmsdoxx(n_frames,)
xyzoxx(n_frames, n_atoms, 3)