rmmol

  • This command is used after executing pacs mdrun.
  • This command removes unnecessary atoms from the trajectory created by running PaCS-MD.
  • This command reduces the file size and the burden on the computer capacity.

Caution

  • This command is not reversible.
  • This command operates on all trajectories of one trial at a time.
  • If you want to apply it to more than one trial, you could easily achieve it by writing an iteration shell script.

Example

  • The following example removes water molecules from the trajectory.

mdtraj

pacs rmmol mdtraj -t 1 -k "not water" -e .xtc -m trial001/cycle000/replica001/prd.gro

gromacs

pacs rmmol gmx -t 1 -k "not_water" -e .xtc -n index.ndx -g gmx --nojump

cpptraj

pacs rmmol cpptraj -t 1 -k "not water" -e .nc -p trial001/cycle000/replica001/prd.parm7

Arguments

mdtraj

usage: pacs rmmol mdtraj [-h] [-t] [-k] [-e] [-m]
  • -t, --trial (int):
    • trial number without 0-fill when pacsmd was conducted (e.g. -t 1)
  • -k, --keep_selection (str):
    • atom selection to be retained in trajectory (e.g. -k "not water")
  • -e, --trajectory_extension (str):
    • trajectory extension (e.g. -e .xtc)
  • -m, --top_mdtraj (str):
    • topology file path for mdtraj analysis (e.g. -m trial001/cycle000/replica001/prd.pdb)

gromacs

usage: pacs rmmol gmx [-h] [-t] [-k] [-n] [-g] [-e]
  • -t, --trial (int):
    • trial number without 0-fill when pacsmd was conducted (e.g. -t 1)
  • -k, --keep_selection (str):
    • index group to be retained in trajectory (e.g. -k "not_water")
  • -e, --trajectory_extension (str):
    • gromacs trajectory extension (e.g. -e .xtc)
  • -n, --index_file (str):
    • index file for gromacs (e.g. -n index.ndx)
  • -g, --cmd_gmx (str):
    • gromacs command prefix (e.g. -g gmx)
  • --nojump (bool):
    • whether to execute -pbc nojump treatment for the trajectory (e.g. --nojump)
    • If your PaCS-MD trajectory was generated with nojump=true, it is strongly strongly recommended to use this options as well
    • Also refer to the mdrun/inputfile page for more details.

cpptraj

usage: pacs rmmol cpptraj [-h] [-t] [-k] [-e] [-p]
  • -t, --trial (int):
    • trial number without 0-fill when pacsmd was conducted (e.g. -t 1)
  • -k, --keep_selection (str):
    • atom selection to be retained in trajectory (e.g. -k :!WAT)
  • -e, --trajectory_extension (str):
    • trajectory extension (e.g. -e .nc)
  • -p, --topology (str):
    • topology file path for cpptraj analysis (e.g. -p trial001/cycle000/replica001/prd.parm7)