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We previously introduced a conformational sampling method, amulti-dimensional virtual-system coupled molecular dynamics (mD-VcMD), toenhance conformational sampling of a biomolecular system by computersimulations. Here, we present a new sampling method, subzone-based mD-VcMD, asan extension of mD-VcMD. Then, we further extend the subzone-based method usinggenetic algorithm (GA), and named it the GA-based mD-VcMD. Because theconformational space of the biomolecular system is vast, a single simulationcannot sample the conformational space throughout. Then, iterative simulationsare performed to increase the sampled region gradually. The new methods havethe following advantages: (1) The methods are free from a production run: I.e.,all snapshots from all iterations can be used for analyses. (2) The methods arefree from fine tuning of a weight function (probability distribution functionor potential of mean force). (3) A simple procedure is available to assign athermodynamic weight to snapshots sampled in spite that the weight function isnot used to proceed the iterative simulations. Thus, a canonical ensemble(i.e., a thermally equilibrated ensemble) is generated from the resultantsnapshots. (4) If a poorly-sampled region emerges in sampling, selectivesampling can be performed focusing on the poorly-sampled region withoutbreaking the proportion of the canonical ensemble. A free-energy landscape ofthe biomolecular system is obtainable from the canonical ensemble.

GA-guided mD-VcMD: A genetic-algorithm-based method for multi-dimensional virtual-system coupled molecular dynamics