To make a density map from a 2D set of data, the first step is to compute values for the third dimension. (Gnuplot has no facilities for computing these values automatically.) The simplest way is to make a 2D histogram; the plot is divided in small 2D regions, and the z-values are proportional to the number of points inside these regions. The following Python script will make an histogram from a time series of two dihedral angles.
GAMESS-US is a full-featured electronic structure software package with MC-SCF, CC, DFT, and CI wave functions. QM/MM, FMO, solvation, and MD calculations are also possible.
NWChem is an electronic structure package that features MC-SCF, MPn, CC, CI, and DFT methods. Properties, solvation models, QM/MM, and MD simulations are also possible.
PyQuante is an open-source suite of programs for developing quantum chemistry methods. The program is written in the Python programming language, but has many "rate-determining" modules also written in C for speed.
The Computational Chemistry Comparison and Benchmark Database (CCCBDB) contains links to experimental and computational thermochemical data for a selected set of gas-phase atoms and molecules as well as tools for comparing experimental and computational ideal-gas thermochemical properties.
M. Ester, H. Kriegel, J. Sander, and X. Xu. Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD-96), page 226-231. AAAI Press, (1996)