comvec

• Center of mass vector

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