comvec

  • Center of mass vector
  • Calculate the vector between the centers of mass of s1 and s2
    • The vector is calculated as s1 - s2

Example

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

mdtraj

pacs genfeature comvec mdtraj -t 1 -tf prd.xtc -top inputs/input.gro -ref inputs/input.gro -ft "name CA" -fr "name CA" -s1 "resid 1" -s2 "resid 9"

Arguments

mdtraj

usage: pacs genfeature comvec mdtraj [-h] [-t] [-tf] [-top] [-od] [-p] [-ref] [-ft] [-fr] [-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
  • -ref, --reference (str):
    • reference file path for fitting
  • -ft, --fit-trj (str):
    • fitting selection for mdtraj in trajectory
  • -fr, --fit-ref (str):
    • fitting selection for mdtraj in reference
  • -s1, --selection1 (str):
    • mdtraj selection1 for calculating distance
  • -s2, --selection1 (str):
    • mdtraj selection2 for calculating distance