title: On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics.
abstract: Mean-force dynamics (MFD), which is a fictitious dynamics for a set of collective variables on a potential of mean-force, is a powerful algorithm to efficiently explore free-energy landscapes. Recently, we have introduced logarithmic MFD (LogMFD) (Morishita et al., Phys. Rev. E 2012, 85, 066702) which overcomes difficulties encounterd in free-energy calculations using standard approaches such as thermodynamic integration. Here, we present a guide to implementing LogMFD calculations paying attention to the practical issues in choosing the parameters in LogMFD. A primary focus is given to the effect of the parameters on the accuracy of the reconstructed free-energy profiles. A recipe for reducing the errors due to energy dissipation is presented. We also demonstrate that multidimensional free-energy landscapes can be reconstructed on-the-fly using LogMFD, which cannot be accomplished using any other free-energy calculation techniques.
authors: Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.
authors: Tetsuya
authors: T
authors: Morishita
authors: Satoru G
authors: SG
authors: Itoh
authors: Hisashi
authors: H
authors: Okumura
authors: Masuhiro
authors: M
authors: Mikami
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics