title: Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations.
abstract: Proper use of the adaptive biasing force (ABF) algorithm in free-energy calculations needs certain prerequisites to be met, namely, that the Jacobian for the metric transformation and its first derivative be available and the coarse variables be independent and fully decoupled from any holonomic constraint or geometric restraint, thereby limiting singularly the field of application of the approach. The extended ABF (eABF) algorithm circumvents these intrinsic limitations by applying the time-dependent bias onto a fictitious particle coupled to the coarse variable of interest by means of a stiff spring. However, with the current implementation of eABF in the popular molecular dynamics engine NAMD, a trajectory-based post-treatment is necessary to derive the underlying free-energy change. Usually, such a posthoc analysis leads to a decrease in the reliability of the free-energy estimates due to the inevitable loss of information, as well as to a drop in efficiency, which stems from substantial read-write accesses to file systems. We have developed a user-friendly, on-the-fly code for performing eABF simulations within NAMD. In the present contribution, this code is probed in eight illustrative examples. The performance of the algorithm is compared with traditional ABF, on the one hand, and the original eABF implementation combined with a posthoc analysis, on the other hand. Our results indicate that the on-the-fly eABF algorithm (i) supplies the correct free-energy landscape in those critical cases where the coarse variables at play are coupled to either each other or to geometric restraints or holonomic constraints, (ii) greatly improves the reliability of the free-energy change, compared to the outcome of a posthoc analysis, and (iii) represents a negligible additional computational effort compared to regular ABF. Moreover, in the proposed implementation, guidelines for choosing two parameters of the eABF algorithm, namely the stiffness of the spring and the mass of the fictitious particles, are proposed. The present on-the-fly eABF implementation can be viewed as the second generation of the ABF algorithm, expected to be widely utilized in the theoretical investigation of recognition and association phenomena relevant to physics, chemistry, and biology.
authors.forename: Haohao
authors.initials: H
authors.lastname: Fu
authors.affiliation: Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China.
authors.forename: Xueguang
authors.initials: X
authors.lastname: Shao
authors.affiliation: Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche No. 7565, Université de Lorraine , B.P. 70239, 54506 Vandœuvre-lès-Nancy cedex, France.|Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.|Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.
authors.forename: Christophe
authors.initials: C
authors.lastname: Chipot
authors.affiliation: Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China.
authors.forename: Wensheng
authors.initials: W
authors.lastname: Cai