fit

  • This command is used after executing pacs mdrun
  • This command makes new trajectories that fit to the reference structure.
  • The newly created trajectories are placed in the same hierarchy as the original trajectories.

Caution

  • Fitting the molecules by using the script could take a long time (around 1 hour for 1 trial)

Example

  • In the following example, trajectories for all cycles and all replicas of trial1 are fitted with the protein, and then the output files are saved.

for single trajectory

pacs fit traj mdtraj -tf ./trial001/cycle001/replica001/prd.xtc -top ./inputs/input.gro -r ./inputs/input.gro -ts "backbone" -rs "backbone"

for single trial

pacs fit trial mdtraj -t 1 -s ./trial001/cycle001/replica001/prd.pdb -r ./trial001/cycle001/replica001/prd.pdb -ts "protein" -rs "protein" -tf prd.xtc -p 10

Arguments

for single trajectory

usage: pacs fit mdtraj [-h] [-tf] [-top] [-r] [-ts] [-rs] [-p] [-o]
  • -tf, --trj_file (str):
    • file name of the trajectory to be fitted (e.g. -tf prd.xtc)
  • -top, --topology (str):
    • topology file path for loading trajectory (e.g. -s trial001/cycle000/replica001/prd.pdb)
  • -r, --ref_structure (str):
    • reference structure file path for fitting reference (e.g. -r trial001/cycle000/replica001/prd.pdb)
  • -ts, --trj_selection (str):
    • atom selection for fitting trajectory (e.g. -ts "protein")
  • -rs, --ref_selection (str):
    • atom selection for fitting reference (e.g. -rs "protein")
  • -p, --parallel (int):
    • number of parallel processes (e.g. -p 10)
    • default: 1
  • -o, --out (str):
    • output file name (e.g. -o prd_fit.xtc)
    • default: {trj_file}_fit.{ext}

for single trial

usage: pacs fit trial mdtraj [-h] [-t] [-tf] [-top] [-r] [-ts] [-rs] [-p] [-o]
  • -t, --trial (int):
    • trial number (e.g. -t 1)
  • -tf, --trj_file (str):
    • file name of the trajectory to be fitted (e.g. -tf prd.xtc)
  • -top, --topology (str):
    • topology file path for loading trajectory (e.g. -s trial001/cycle000/replica001/prd.pdb)
  • -r, --ref_structure (str):
    • reference structure file path for fitting reference (e.g. -r trial001/cycle000/replica001/prd.pdb)
  • -ts, --trj_selection (str):
    • atom selection for fitting trajectory (e.g. -ts "protein")
  • -rs, --ref_selection (str):
    • atom selection for fitting reference (e.g. -rs "protein")
  • -p, --parallel (int):
    • number of parallel processes (e.g. -p 10)
    • default: 1
  • -o, --out (str):
    • output file name (e.g. -o prd_fit.xtc)
    • default: {trj_file}_fit.{ext}