The crystal structure of acetylcholine chloride reported in
[16] omits the position of the three terminal hydrogen
atoms of the acetyl group. Some previous studies have defined the
positions of these atoms such that the dihedral angle
while others have defined
. These two possibilities were tested by
performing a simple total energy calculation for each
arrangement. This showed that the arrangement with
was energetically favourable and hence this was
used for the remaining calculations. The hydrogen atoms were arranged
relative to 
in the usual tetrahedral geometry for a methyl
group.
The convergence of the energy of the system with respect to supercell size was also investigated. The convergence had to be optimised subject to constraints on time and computing resources available. It was ascertained that absolute convergence of total energy was unobtainable, however the convergence of energy differences between different conformations was tested. It must be noted that acetylcholine has a net charge of +1 and hence the corrections described in Section 2.8 must be used when calculating the total energy and investigating its convergence.