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
khinsen/GromacsTrajectoryConverter
Converter from Gromacs' XTC trajectory file format to MMTK's netCDF format
PythonNOASSERTION