Calculate grids for visualization in gOpenMol


The syntax and sub-options are exactly the same as for CUBE, except that the files produced are in a format that can be used directly in the gOpenMol visualization program. The following should be noted.

  • Only the base name (up to the last ’.’) in filename is used, and is appended by different suffices to create several different files:
    • .crd A CHARMm CRD-format file containing the coordinates is always produced, and may be used in the invocation of gOpenMol: rungOpenMol -ifilename.crd
    • _density.plt If DENSITY is given, then the file filename_density.plt is produced and contains the density grid in gOpenMol internal format.
    • _orbital_number.symmetry.plt If ORBITAL is given, then for each orbital number.symmetry specified, the file filename_orbital_number.symmetry.plt is produced and contains the orbital grid in gOpenMol internal format.
  • The default is not to produce any orbitals or densities, and so only the atomic coordinates are dumped.
  • The default is to use unformatted binary files, and this should not normally be changed.
  • The ORIGIN and AXIS commands should not be used.
  • If INTERACT is given in the input, when all the grids have been calculated, an attempt is made to start gOpenMol by executing the Unix command rungOpenMol. If rungOpenMol is not in $PATH, then nothing happens. Otherwise, gOpenMol should start and display the molecule. Any .plt files produced can be added to the display by following the Plot;Contour menu item. The name of the Unix command may be changed from the default rungOpenMol by specifying it as the first argument to the INTERACT directive. By default, gOpenMol is not started, and this is equivalent to giving the command BATCH.