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  • BAR‐based optimum adaptive ...
    Wang, Xiaohui; Tu, Xingzhao; Deng, Boming; Zhang, John Z. H.; Sun, Zhaoxi

    Journal of computational chemistry, May 5, 2019, Volume: 40, Issue: 12
    Journal Article

    The equilibrium and nonequilibrium adaptive alchemical free energy simulation methods optimum Bennett's acceptance ratio and optimum crooks' equation (OCE), based on the statistically optimal bidirectional reweighting estimator named Bennett's Acceptance Ratio or Crooks' equation, perform initial sampling in the staging alchemical transformation and then determine the importance rank of different states via the time‐derivative of the variance. The method is proven to give speedups compared with the equal time rule. In the current work, we extend the time derivative of variance guided adaptive sampling method to the configurational space, falling in the term of steered MD (SMD). The SMD approach biasing physically meaningful collective variable (CV) such as one dihedral or one distance to pulling the system from one conformational state to another. By minimizing the variance of the free energy differences along the pathway in an optimized way, a new type of adaptive SMD (ASMD) is introduced. As exhibits in the alchemical case, this adaptive sampling method outperforms the traditional equal‐time SMD in nonequilibrium stratification. Also, the method gives much more efficient calculation of potential of mean force than the selection criterion‐based ASMD scheme, which is proven to be more efficient than traditional SMD. The OCE workflow is periodicity‐of‐CV dependent while ASMD is not. The performance is demonstrated in a dihedral flipping case and two distance pulling cases, accounting for periodic and nonperiodic CVs, respectively. © 2019 Wiley Periodicals, Inc. The adaptive nonequilibrium pulling scheme introduced in this work, the global optimum Crooks' equation (GOCE) method, is based on the statistically optimal and asymptotically unbiased estimator of Crooks' equation. GOCE achieves about an order of magnitude speedup in the construction of the free energy landscapes, compared with the previously proposed adaptive steered molecular dynamics method. The nonequal time rule used in GOCE leads to onefold speedup in minimizing the statistical uncertainty along the free energy profiles. As a result, the GOCE scheme is one of the fastest nonequilibrium pulling method for the construction of free energy landscapes. The approach is tested in three biologically relevant cases.