Two simple sets of preliminary calculations were performed in order to gain experience using the CASTEP code, and to ascertain the approximate accuracy of the structural results that can be obtained. The typical parameters for calculations of biological molecules were noted for later reference.
The first of these investigations was performed on thymine (See Figure 3.1), a nucleic acid. This is a typical simple biological molecule and hence is a suitable candidate for such a study. The convergence for a range of different cut off energies was investigated and the relaxed structure for LDA and GGA calculations were compared with that obtained by crystallographic analysis.
Figure 3.1: A
computer-generated image of the structure of thymine. (C=Grey, O=Red,
N=Blue, H=Yellow)
The second target chosen was the simple molecule 
. The
relaxed structure of this molecule was investigated and the results
compared with the known structure of this molecule. Particular
attention was paid to the relaxed bond angles and lengths and the
convergence of these values with both cut off energy and supercell
size.
The following sections detail the procedure followed and the results obtained for each of these investigations.