Simultaneous escaping of explicit and hidden free energy barriers: application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling.

摘要: To overcome the pseudoergodicity problem, conformational sampling can be accelerated via generalized ensemble methods, e.g., through realization of random walks along prechosen collective variables, such as spatial order parameters, energy scaling or even system temperatures pressures, etc. As usually observed, in simulations, hidden barriers are likely to exist space perpendicular variable direction and these residual free could greatly abolish efficiency. This issue is particularly severe when defined a low-dimension subset target system; then "Hamiltonian lagging" which reveals fact that necessary structural relaxation falls behind move variable, may occur. this problem equilibrium sampling, we adopted orthogonal walk (OSRW) strategy, was originally developed context simulation [L. Zheng, M. Chen, W. Yang, Proc. Natl. Acad. Sci. U.S.A. 105, 20227 (2008)]. Thereby, simulations simultaneously escape both explicit strongly coupled with move. demonstrated our model studies, present OSRW based treatments show improved capability over corresponding classical treatments.