NAME

       mdconvert-mdtraj - use mdtraj to convert molecular dynamics trajectories between formats

DESCRIPTION

       usage: mdconvert-mdtraj [-h] -o OUTPUT [-c CHUNK] [-f] [-s STRIDE] [-i INDEX]

              [-a ATOM_INDICES] [-t TOPOLOGY] input [input ...]

       Convert  molecular  dynamics trajectories between formats. The DCD, XTC, TRR, PDB, binpos,
       NetCDF, binpos, LH5, and HDF5 formats are  supported  (.dcd,  .xtc,  .trr,  .binpos,  .nc,
       .netcdf, .h5, .lh5, .pdb)

   positional arguments:
       input  path  to  one or more trajectory files. Multiple trajectories, if supplied, will be
              concatenated together in the  output  file  in  the  order  supplied.  all  of  the
              trajectories should be in the same format. the format will be detected based on the
              file extension

   required arguments:
       -o OUTPUT, --output OUTPUT
              path to the save the output. the output  format  will  chosen  based  on  the  file
              extension (.dcd, .xtc, .trr, .binpos, .nc, .netcdf, .h5, .lh5, .pdb)

   optional arguments:
       -h, --help
              show this help message and exit

       -c CHUNK, --chunk CHUNK
              number  of  frames  to  read in at once. this determines the memory requirements of
              this code. default=1000

       -f, --force
              force overwrite if output already exsits

       -s STRIDE, --stride STRIDE
              load only every stride-th frame from the input file(s), to subsample.

       -i INDEX, --index INDEX
              load a *specific* set of frames. flexible, but inefficient for a large  trajectory.
              specify  your  selection  using (pythonic) "slice notation" e.g. '-i N' to load the
              the Nth frame, '-i -1' will load the last frame, '-i N:M to load  frames  N  to  M,
              etc. see http://bit.ly/143kloq for details on the notation

       -a ATOM_INDICES, --atom_indices ATOM_INDICES
              load only specific atoms from the input file(s).  provide a path to file containing
              a space, tab  or  newline  separated  list  of  the  (zero-based)  integer  indices
              corresponding to the atoms you wish to keep.

       -t TOPOLOGY, --topology TOPOLOGY
              path  to  a PDB/prmtop file. this will be used to parse the topology of the system.
              it's optional, but useful.  if specified, it enables you to output the  coordinates
              of your dcd/xtc/trr/netcdf/binpos as a PDB file. If you're converting *to* .h5, the
              topology will be stored inside the h5 file.