RMSD

  • Root Mean Square Deviation
  • Calculate the RMSD relative to the structure specified in ref

Example

  • The following example generates features about RMSD for MSM analysis

mdtraj

pacs genfeature rmsd mdtraj -t 1 -tf prd.xtc -top ./inputs/input.gro -ref ./inputs/input.gro -ft "protein" -fr "protein" -ct "name CA" -cr "name CA"

Arguments

mdtraj

usage: pacs genfeature rmsd mdtraj [-h] [-tf] [-top] [-od] [-p] [-ref] [-ft] [-fr] [-ct] [-cr]
  • -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
  • -ref, --reference (str):
    • reference file path for fitting/RMSD calculation
  • -ft, --fit-trj (str):
    • mdtraj selection for fitting in trajectory
  • -fr, --fit-ref (str):
    • mdtraj selection for fitting in reference
  • -ct, --cal-trj (str):
    • mdtraj selection for calculating RMSD in trajectory
  • -cr, --cal-ref (str):
    • mdtraj selection for calculating RMSD in reference