Biomedical Engineering Reference
In-Depth Information
9
Monte Carlo Simulations
When discussing QSAR in Chapter 6, I mentioned that the molecular volume was thought
to be a useful index and explained how it could be calculated within the framework of a
MM study.
To recap, Figure 9.1 shows a diatomic molecule, where the atomic radii are
R
A
and
R
B
.
The problem is to find the volume of the molecule AB. The volume of atomA is
3
π
R
A
and
the volume of atom B is
3
π
R
B
. The volume of AB is of course less than or equal to the sum
of these atomic volumes depending on the extent to which the atoms overlap. We have to
be careful not to count the shared volume X twice in the calculation.
A
X
B
Figure 9.1
A diatomic molecule AB
To expand on the discussion in Chapter 6, I suggest that the total can be calculated using
the following algorithm.
