A combined atomistic simulation involving static lattice and molecular dynamics simulation methods investigates the structure of poly(3-alkylthiophene)s in order to study their thermochromism. Taking the shortest alkyl chain (butyl) that makes the polymer thermochromic, conformational changes are monitored at different temperatures. The simulations demonstrate that there is a tendency for the side chain to twist between 40 and 70 o about the C-C bond linking it to the thiophene ring, although the carbon atoms in the side chain largely retain a trans conformation to above room temperature. These results, and the prediction of a non-zero setting angle, are qualitatively in accord with lattice powder diffraction structures. There is a step-like increase in the mean angle between the thiophene rings as a function of temperature at T=340K, suggesting the occurence of an abrupt reduction in the planarity of the conjugated chain at this temperature that should lead to an increased band width and thermochromism. This is shown to be concerted with similar changes in side chain torsions at the same temperature, on the basis of which a tentative mechanism for the thermochromism is proposed.