Trajectory file formats

gorder is highly optimized to read XTC files as quickly as possible. If you have an XTC file or can generate one, it is recommended to use it. However, gorder also supports various other trajectory file formats, namely TRR, GRO, PDB, Amber NetCDF, DCD, and LAMMPSTRJ. You can use any of these files instead of an XTC trajectory, and gorder will automatically recognize the format based on the file extension.

gorder identifies the file format based on the file extension: .xtc for XTC files, .trr for TRR files, .gro for GRO files, .pdb for PDB files, .nc for Amber NetCDF files, .dcd for DCD files, and .lammpstrj for LAMMPSTRJ files. Ensure that your trajectory file is named accordingly.

Note that some features of gorder are not available for certain trajectory file formats. Specifically, do not specify the analysis time range using begin and end if your trajectory file is a PDB file or an Amber NetCDF file. This will not work and will result in an error!

You can only use this feature with a GRO trajectory if the file contains simulation time and step information in the 'title' line, formatted as follows:

Some Arbitrarily Long Title (...) t= SIMULATION_TIME step= SIMULATION_STEP

For example:

System t= 100.00000 step= 5000

Additionally, note that gorder assumes that time information in DCD files is specified in ps.