This command is used after executing PaCS-MD.
This command traces each cycle in reverse order, starting with the frame with the best CV in the last cycle, and generates one continuous trajectory file.
The generated file is named repr_complete and located in the genrepresent directory.
File extension is determined by the user.
This command operates on all of the trajectories in one trial at a time.
If you want to apply this for the multiplie trials, you could simply write an iteration shell script to achieve it.
The following example generates a trajectory file.
pacs genrepresent mdtraj -t 1 -trj prd.xtc -top ./inputs/input.gro
pacs genrepresent gmx -t 1 -trj prd.xtc -top ./inputs/input.gro -g gmx_mpi
pacs genrepresent cpptraj -t 1 -trj prd.nc -top inputs/input.prmtop
usage: pacs genrepresent mdtraj [-h] [-t] [-trj] [-top]
-t, --trial (int):
trial number without 0-fill when pacsmd was conducted (e.g. -t 1)
-trj, --trajectory (str):
trajectory file name (e.g. -trj prd.xtc)
-top, --topology (str):
topology file path (e.g. -m trial001/cycle000/replica001/prd.pdb)
usage: pacs genrepresent gmx [-h] [-t] [-trj] [-top] [-g]
-t, --trial (int):
trial number without 0-fill when pacsmd was conducted (e.g. -t 1)
-trj, --trajectory (str):
trajectory file name (e.g. -trj prd.xtc)
-top, --topology (str):
topology file path (e.g. -m trial001/cycle000/replica001/input.gro)
-g, --cmd_gmx (str):
gromacs command prefix (e.g. -g gmx_mpi)
usage: pacs genrepresent cpptraj [-h] [-t] [-trj] [-top]
-t, --trial (int):
trial number without 0-fill when pacsmd was conducted (e.g. -t 1)
-trj, --trajectory (str):
trajectory file name (e.g. -trj prd.nc)
-top, --topology (str):
topology file path (e.g. -m trial001/cycle000/replica001/input.parm7)