Upon request, Q-Chem will generate an input file for MolDen, a
freely-available molecular visualization
J. Comput.-Aided Mol. Design
(2000), 14, pp. 123. 13 J. Chem. Phys.
(1971), 55, pp. 4438. MolDen can be used to view ball-and-stick molecular models (including stepwise visualization of a geometry optimization), molecular orbitals, vibrational normal modes, and vibrational spectra. MolDen also contains a powerful Z-matrix editor. In conjunction with Q-Chem, orbital visualization via MolDen is currently supported for , , and functions (pure or Cartesian), as well as pure functions. Upon setting MOLDEN_FORMAT to TRUE, Q-Chem will append a MolDen-formatted input file to the end of the Q-Chem log file. As some versions of MolDen have difficulty parsing the Q-Chem log file itself, we recommend that the user cut and paste the MolDen-formatted part of the Q-Chem log file into a separate file to be read by MolDen.
MolDen-formatted files can also be read by MacMolPlt, another
freely-available visualization program.
J. Mol. Graphics Mod.
(1998), 16, pp. 133. 12 J. Chem. Phys.
(1961), 34, pp. 1476. MacMolPlt generates orbital iso-contour surfaces much more rapidly than MolDen, however, within MacMolPlt these surfaces are only available for Cartesian Gaussian basis functions, i.e., PURECART = 2222, which may not be the default.
$molecule 0 1 O H 1 0.95 H 1 0.95 2 104.5 $end $rem METHOD hf BASIS cc-pvtz PRINT_ORBITALS true (default is to print 5 virtual orbitals) MOLDEN_FORMAT true $end
For geometry optimizations and vibrational frequency calculations, one need only set MOLDEN_FORMAT to TRUE, and the relevant geometry or normal mode information will automatically appear in the MolDen section of the Q-Chem log file.
$molecule 0 1 O H 1 0.95 H 1 0.95 2 104.5 $end $rem JOBTYPE opt METHOD hf BASIS 6-31G* MOLDEN_FORMAT true $end