This Python script reads a trajectory in GROMACS' XTC format plus a
compatible PDB file describing the molecular system. It writes the
system and trajectory data to a netCDF file using MMTK conventions.
Usage: xtc2nc [options] pdb_file xtc_file nc_file
pdb_file and xtc_file must describe the same system. nc_file is the
name of the netCDF trajectory that is created.
Options:
--cell-shape
one of 'infinite', 'orthorhombic', or 'parallelepipedic'.
The default is 'parallelepipedic'. Note that the cell shape
information cannot be obtained from xtc_file nor from pdb_file.
It is, however, required for a correct interpretation of the
data. A wrong cell-shape leads to erroneous data in the
converted trajectory.
--block-size=number
specifies the block structure of the netCDF trajectory. The
default value of 1 optimizes the trajectory for step-by-step access
to conformations. Larger values favour atom-by-atom access to
one-particle trajectories for all times, which is required for the
calculation of dynamic quantities. The highest sensible value is
the number of steps in the trajectory.
Konrad Hinsen
Centre de Biophysique Moleculaire (CNRS Orléans)
and
Synchtron Soleil (Saint Aubin, France)
E-Mail: hinsen@cnrs.fr