The helix <-> random coil transition in alanine, valine, and leucine polypeptides consisting of 30 amino acids is studied in vacuo using the Langevin molecular dynamics approach. The influence of side chain radicals on internal energy and heat capacity of the polypeptides is discussed. The heat capacity of these polypeptides is calculated as a function of temperature using two different methods, namely, as the derivative of the energy with respect to temperature, and on the basis of energy fluctuations in the system. The convergence of the fluctuations based approach is analyzed as a function of simulation time. This study provides a comparison of methods for the description of structural transitions in polypeptides.
European Physical Journal D. Atomic, Molecular, Optical and Plasma Physics, 2009, Vol 51, p. 25-32