genfeature
- This command should be executed after running
pacs mdrun. - It generates feature data in
.npyformat, which is cconvenient for MSM analysis in Python.- Feature data files (e.g.,
t001c002r010.npy) are stored in the directory specified with the-odoption. - Each
.npyfile has thenp.arryin the shape as described in the table below.
- Feature data files (e.g.,
- This command supports parallel processing.
Currently implemented analysis tools and the shape of the output data in .npy files.
| feature | mdtraj | gmx | cpptraj | shape of .npy |
|---|---|---|---|---|
| comdist | o | x | x | (n_frames,) |
| comvec | o | x | x | (n_frames, 3) |
| rmsd | o | x | x | (n_frames,) |
| xyz | o | x | x | (n_frames, n_atoms, 3) |