Average energy guided simulated tempering implemented into molecular dynamics algorithm for protein folding simulation

The performance of an average energy guided simulated tempering algorithm has been examined for a folding simulation of (Ala)16 system. The advantage of our method is that it can be easily implemented into molecular dynamics algorithm via a force scaling, and allows an automatic determination of the uniform sampling weight through an average energy guide. The simulation results demonstrate that our method is very effective to sample conformational spaces of biomolecules exhibiting complex potential energy landscape. Various thermodynamic quantities and free energy landscapes associated with a folding transition are obtained as a function of the temperature.