comdist

  • Center of mass distance
  • Calculate the distance between the centers of mass of s1 and s2.

Example

  • The following example generates features about COM distance for MSM analysis

mdtraj

pacs genfeature comdist mdtraj -t 1 -tf prd.xtc -top inputs/example_gromacs/input.gro -s1 "residue 1" -s2 "residue 9"

Arguments

mdtraj

usage: pacs genfeature comdist mdtraj [-h] [-t] [-tf] [-top] [-od] [-p] [-s1] [-s2]
  • -t, --trial (int):
    • trial number without 0-fill
  • -tf, --trj-file (str):
    • trajectory file name (e.g. prd.xtc prd_rmmol.trr)
  • -top, --topology (str):
    • topology file path (e.g. .inputs/input.gro)
  • -od, --outdir (str):
    • output directory path
  • -p, --n_parallel (int):
    • number of parallel
  • -s1, --selection1 (str):
    • mdtraj selection1 for calculating distance
  • -s2, --selection1 (str):
    • mdtraj selection2 for calculating distance