HYBRID MONTE-CARLO WITH ADAPTIVE TEMPERATURE IN MIXED-CANONICAL ENSEMBLE - EFFICIENT CONFORMATIONAL-ANALYSIS OF RNA

A hybrid Monte Carlo method with adaptive temperature choice is presen ted that exactly generates the distribution of a mixed-canonical ensem ble composed of two canonical ensembles at low and high temperature. T he analysis of resulting Markov chains with the reweighting technique shows an efficient sampling of the canonical distribution at low tempe rature whereas the high temperature component facilitates conformation al transitions, which allows shorter simulation times. The algorithm i s tested by comparing analytical and numerical results for the small n -butane molecule before simulations are performed for a triribonucleot ide. Sampling the complex multiminima energy landscape of this small R NA segment, we observe enforced crossing of energy barriers. (C) 1998 John Wiley & Sons, Inc.