XYZ

  • (x, y, z), 3 dimension coordinates

Example

  • The following example generates features about (x, y, z) for MSM analysis

mdtraj

pacs genfeature xyz mdtraj -t 1 -tf prd.xtc -top ./trial001/cycle000/replica001/input.gro -s "residue 1 to 5"

Arguments

mdtraj

usage: pacs genfeature xyz mdtraj [-h] [-t] [-tf] [-top] [-od OUTDIR] [-p N_PARALLEL] [-s]
  • -t, --trial (int):
    • trial number without 0-fill
  • -tf, --trj-file (str):
    • trajectory file name (ex. prd.xtc prd_rmmol.trr)
  • top, --topology (str):
    • topology file path (ex. .inputs/input.gro)
  • -od, --outdir (str):
    • output directory path
  • -p, --n_parallel (int):
    • number of parallel
  • -s, --selection (str):
    • mdtraj selection extracted in trajectory