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. © 2013 Wiley Periodicals, Inc.
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