Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS"

We develop an efficient technique for computing free energies corresponding to conformational transitions in complex systems by combining a Monte Carlo ensemble of trajectories generated by the shooting algorithm with umbrella sampling. Motivated by the transition path sampling method, our scheme "BOLAS" (named after a cowboy's lasso) preserves microscopic reversibility and leads to the correct equilibrium distribution. This makes possible computation of free energy profiles along complex reaction coordinates for biomolecular systems with a lower systematic error compared to traditional, force-biased umbrella sampling protocols. We demonstrate the validity of BOLAS for a bistable potential, and illustrate the method's scope with an application to the sugar repuckering transition in a solvated deoxyadenosine molecule. (C) 2004 American Institute of Physics.