This program can manupulate trajectory data. For example, during the MD simulations, water molecules spread out from  the unit cell, which can be wrapped into the unit cell by using crd_convert. In addition, the user can make a new trajectory file, where the focusing atoms are fitted to the initial structure, centered at the favorite position, and etc. Note that trajectory manipulation is done in the following order:

  1. Centering
  2. Wrapping
  3. Fitting To change this order, the users should modify the source codes in cc_convert.fpp in crd_convert by themselves.

This program can also convert the DCD format to PDB format. If the user specify split_trjpdb = YES, all snapshots in the trajectory files are split into individual PDB files.

Target protein is centered at the origin, and water and ions are wrapped into the unit cell 

[INPUT]
psffile        = ../BPTI_ionize.psf # protein structure file
reffile        = ../BPTI_ionize.pdb # PDB file

[OUTPUT]
trjfile        = output.dcd      # trajectory file
 
[TRAJECTORY]
trjfile1       = ../BPTI_run.dcd # trajectory file
md_step1       = 500000          # number of MD steps
mdout_period1  = 500             # MD output period
ana_period1    = 500             # analysis period
repeat1        = 1
trj_format     = DCD             # (PDB/DCD)
trj_type       = COOR+BOX        # (COOR/COOR+BOX)
trj_natom      = 0               # (0:uses reference PDB atom count)
 
[SELECTION]
group1         = all             # select all atoms
group2         = segid:BPTI      # select protein atoms
 
[FITTING]
fitting_method = NO              # [NO,TR,TR+ROT,TR+ZROT,XYTR,XYTR+ZROT]
 
[OPTION]
check_only     = NO
trjout_format  = DCD             # write DCD format
trjout_type    = COOR+BOX
trjout_atom    = 1               # output all atoms
split_trjpdb   = NO
centering      = YES             # protein is centered at the origin
centering_atom = 2
center_coord   = 0.0 0.0 0.0
pbc_correct    = MOLECULE        # molecules are wrapped into the unit cell

Make a new DCD file that contain only CA atoms of the protein (no fitting and no centering)

[SELECTION]
group1         = an:CA and segid:BPTI  # select protein CA atoms
 
[FITTING]
fitting_method = NO              # [NO,TR,TR+ROT,TR+ZROT,XYTR,XYTR+ZROT]
 
[OPTION]
check_only     = NO
trjout_format  = DCD             # write DCD format
trjout_type    = COOR+BOX
trjout_atom    = 1               # output all atoms
split_trjpdb   = NO
centering      = NO              # protein is centered at the origin
pbc_correct    = NO

Make a new DCD file that contain only protein CA atoms with fitting to the initial coordinates

[SELECTION]
group1         = an:CA and segid:BPTI  # select protein CA atoms
 
[FITTING]
fitting_method = TR+ROT                # [NO,TR,TR+ROT,TR+ZROT,XYTR,XYTR+ZROT]
fitting_atom   = 1 

[OPTION]
check_only     = NO
trjout_format  = DCD             # write DCD format
trjout_type    = COOR+BOX
trjout_atom    = 1               # output all atoms
split_trjpdb   = NO
centering      = NO              # protein is centered at the origin
pbc_correct    = NO

Combine several dcd files into one dcd file

[INPUT]
psffile        = ../BPTI_ionize.psf # protein structure file
reffile        = ../BPTI_ionize.pdb # PDB file

[OUTPUT]
trjfile        = output.dcd      # trajectory file
 
[TRAJECTORY]
trjfile1       = ../BPTI_run1.dcd # trajectory file
trjfile2       = ../BPTI_run2.dcd # trajectory file
trjfile3       = ../BPTI_run3.dcd # trajectory file
trjfile4       = ../BPTI_run4.dcd # trajectory file
trjfile5       = ../BPTI_run5.dcd # trajectory file
md_step1       = 500000          # number of MD steps
mdout_period1  = 500             # MD output period
ana_period1    = 500             # analysis period
repeat1        = 5
trj_format     = DCD             # (PDB/DCD)
trj_type       = COOR+BOX        # (COOR/COOR+BOX)
trj_natom      = 0               # (0:uses reference PDB atom count)
 
[SELECTION]
group1         = all             # select all atoms
 
[FITTING]
fitting_method = NO              # [NO,TR,TR+ROT,TR+ZROT,XYTR,XYTR+ZROT]
 
[OPTION]
check_only     = NO
trjout_format  = DCD             # write DCD format
trjout_type    = COOR+BOX
trjout_atom    = 1               # output all atoms

Split coordinates trajectory data into individual PDB file

[INPUT]
psffile        = ../BPTI_ionize.psf # protein structure file
reffile        = ../BPTI_ionize.pdb # PDB file

[OUTPUT]
trjfile        = output{}.pdb      # trajectory file
 
[TRAJECTORY]
trjfile1       = ../BPTI_run.dcd # trajectory file
md_step1       = 500000          # number of MD steps
mdout_period1  = 500             # MD output period
ana_period1    = 500             # analysis period
repeat1        = 1
trj_format     = DCD             # (PDB/DCD)
trj_type       = COOR+BOX        # (COOR/COOR+BOX)
trj_natom      = 0               # (0:uses reference PDB atom count)
 
[SELECTION]
group1         = all             # select all atoms
group2         = segid:BPTI      # select protein atoms
 
[FITTING]
fitting_method = NO              # [NO,TR,TR+ROT,TR+ZROT,XYTR,XYTR+ZROT]
 
[OPTION]
check_only     = NO
trjout_format  = PDB             # write PDB
trjout_type    = COOR+BOX
trjout_atom    = 1               # output all atoms
split_trjpdb   = YES
centering      = YES             # protein is centered at the origin
centering_atom = 2
center_coord   = 0.0 0.0 0.0
pbc_correct    = MOLECULE        # molecules are wrapped into the unit cell

Updated: