- 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.
- 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.
- The following example removes water molecules from the trajectory.
pacs rmmol mdtraj -t 1 -k "not water" -e .xtc -m trial001/cycle000/replica001/prd.gro
pacs rmmol gmx -t 1 -k "not_water" -e .xtc -n index.ndx -g gmx
pacs rmmol cpptraj -t 1 -k "not water" -e .nc -p trial001/cycle000/replica001/prd.parm7
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)
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)
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)