This picture you saw on the frontpage shows two-body
interactions in water trimer.
It is obtained with
the FMO method for the quantum chemistry part and a
set of the FMOcube utilities (included in the tools set supplied with GAMESS).
More precisely, this is
the difference of the 2 and 1-body densities from a 2-body FMO-RHF calculation,
with the cutoff=0.0005 using Molekel
(a free graphics software). Negative areas are blue (that is where the electron
density decreases) and positive are grey (where the density increases).
Let us proceed in steps in
understanding what mysteries water encapsulates.
The picture above is the density difference of FMO1 (1-body FMO) and free
water molecules (i.e., each molecule separately). You can see polarisation of
hydrogens and oxygens.
This is the same picture from the front page (FMO2 and FMO1 density
difference). You can see hydrogen bond formation (grey sachets) between
If you have become very keen on water trimers,
here is another way of plotting this quantity.
This is the difference between FMO2 and free monomers. It shows the
sum of the previous two interactions, polarisation and two-body effects.
Note FMO2 is known to closely reproduce the full RHF density.
Hopefully this small graphical FMO tutorial made you interested in
using our method. You can plot the density for your
own very molecule using the tools we provide (for free, naturally, for love of
the game, so to speak).
The FMOcube utilities and the function to produce cube files are
released in FMO 2.0 and up. The option to produce free
monomer properties is included in FMO 3.0 and up.