Trajectory File Commands


These commands control the reading and writing of trajectory files. There are three trajectory types in cpptraj: input, output, and reference. In cpptraj, trajectories are always associated with a topology file. If a topology file is not specified, a trajectory file will be associated with the first topology file loaded by default (this is true for both input and output trajectories.

Cpptraj currently understands the following trajectory file formats:

Format Keyword(s) Extension Notes
Amber Trajectory crd .crd Default format if keywords/extensions not recognized
Amber NetCDF cdf, netcdf .nc No compression.
Amber Restart restart .rst7
Amber NetCDF Restart ncrestart, restartnc .ncrst
Charmm DCD dcd, charmm .dcd
Charmm COR cor .cor Read Only
PDB pdb .pdb
Mol2 mol2 .mol2
Scripps Binpos binpos .binpos
Gromacs TRR trr .trr
Gromacs GRO gro .gro Read Only
Gromacs XTC xtc .xtc
CIF cif .cif Read Only
Tinker ARC arc .arc Read Only
SQM Input sqm .sqm Write Only
SDF sdf .sdf Read Only
LMOD Conflib conflib .conflib Read Only, Detection by extension

The following trajectory-related commands are available:

Command Description
ensemble Set up a trajectory ensemble for reading during a run.
ensemblesize (MPI only) specify number of members expected in subsequent ensemble commands.
reference Read in a reference structure.
trajin Set up a trajectory for reading during a Run.
trajout Set up an output trajectory or ensemble for writing during a Run.