Monte Carlo conformational sampling of the internal degrees of freedom of chain molecules

The challenge of controlled sampling of the conformations of internal secti ons of chain molecules, subject to constrained interatomic bond lengths and angles, is central to many areas of macromolecular science. A new method f or overcoming this challenge via an internal configuration bias (ICB) Monte Carlo algorithm is described. It is demonstrated that the algorithm obeys the detail balance (microscopic reversibility) criterion necessary for perf orming rigorous molecular simulations in equilibrium ensembles. The algorit hm is applied to a study of the molecular conformations of cyclic alkane mo lecules in a vacuum, where it is shown to be up to similar to 2 orders of m agnitude more efficient than standard molecular dynamics simulation techniq ues. Qualitative transitions between constrained ring and flexible chain be havior are observed between 16 and 30 backbone atoms for local structure (t orsion angle distribution) and between 30 and 50 backbone atoms for global ring dimensions.