title: Efficient free energy calculations by combining two complementary tempering sampling methods.
abstract: Although energy barriers can be efficiently crossed in the reaction coordinate (RC) guided sampling, this type of method suffers from identification of the correct RCs or requirements of high dimensionality of the defined RCs for a given system. If only the approximate RCs with significant barriers are used in the simulations, hidden energy barriers with small to medium height would exist in other degrees of freedom (DOFs) relevant to the target process and consequently cause the problem of insufficient sampling. To address the sampling in this so-called hidden barrier situation, here we propose an effective approach to combine temperature accelerated molecular dynamics (TAMD), an efficient RC-guided sampling method, with the integrated tempering sampling (ITS), a generalized ensemble sampling method. In this combined ITS-TAMD method, the sampling along the major RCs with high energy barriers is guided by TAMD and the sampling of the rest of the DOFs with lower but not negligible barriers is enhanced by ITS. The performance of ITS-TAMD to three systems in the processes with hidden barriers has been examined. In comparison to the standalone TAMD or ITS approach, the present hybrid method shows three main improvements. (1) Sampling efficiency can be improved at least five times even if in the presence of hidden energy barriers. (2) The canonical distribution can be more accurately recovered, from which the thermodynamic properties along other collective variables can be computed correctly. (3) The robustness of the selection of major RCs suggests that the dimensionality of necessary RCs can be reduced. Our work shows more potential applications of the ITS-TAMD method as the efficient and powerful tool for the investigation of a broad range of interesting cases.
authors.affiliation: Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
authors.forename: Liangxu
authors.initials: L
authors.lastname: Xie
authors.affiliation: Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Shen
authors.affiliation: Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
authors.forename: Zhe-Ning
authors.initials: ZN
authors.lastname: Chen
authors.affiliation: Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
authors.forename: Mingjun
authors.initials: M
authors.lastname: Yang
mesh_terms: D004151:Dipeptides / Q000737:chemistry; D004735:Energy Transfer; D007536:Isomerism; D055641:Mathematical Concepts; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D004151:Dipeptides; D011506:Proteins; C002956:alanylalanine