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.

MDTRAJ                                            October 2020                                      MDCONVERT(1)