title: Efficient Free Energy Calculation of Biomolecules from Diffusion-Biased Molecular Dynamics.
abstract: Recently proposed metadynamics techniques offer an effective means for improving sampling in simulations of complex systems, including polymers and biological macromolecules. One of the drawbacks of such methods has been the absence of well-defined or effective convergence criteria. A solution to this problem is considered here in which an optimal ensemble is introduced to minimize the travel time across the entire order parameter range of interest. The usefulness of the proposed approach is illustrated in the context of two systems consisting of biological molecules dissolved in water. The results presented in this work indicate that the proposed method is considerably faster than other existing algorithms for the study of these systems, and that the corresponding free energy that emerges from the simulations converges to the exact result.
authors.affiliation: Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
authors.forename: Sadanand
authors.initials: S
authors.lastname: Singh
authors.affiliation: Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
authors.forename: Chi-Cheng
authors.initials: CC
authors.lastname: Chiu
authors.affiliation: Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
authors.forename: Juan J
authors.initials: JJ
authors.lastname: de Pablo