Adaptive-partitioning

Heyden A, Lin H et al (2007) Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations. J Phys Chem B 111 2231... 

The WT has a variable partitioning ratio where the aspect ratio of the cells varies such that frequency resolution is proportional to centre frequency. WPT is the generalization of the WT method allows the best adapted analysis of the signal. WPT provides as adaptive partitioning - complete set of partitions are provided as alternatives, and the best for a given application is selected [19]. 

At present, in aU commonly used partitioning schemes, the partitions remain fixed over time, i.e., an MM atom cannot turn into a QM atom and vice versa. This can present a serious limitation, for instance, in the case of solvent diffusion through the chemically active region. A number of adaptive partitioning methods have been proposed to remedy this problem (Bulo et al. 2009 Heyden et al. 2007 Hofer et al. 2005 Kerdcharoen et al. 1996 Kerdcharoen and Morokuma 2002) however the computational overhead is enormous. 

Heyden, A., Lin, H., ScTruhlar, D. G. (2007). Adaptive partitioning in combined quantum mechanical... 

Recent Progress in Adaptive-Partitioning QM/MM Methods for Born-Oppenheimer Molecular Dynamics... 

There have been several excellent reviews on adaptive QM/MM methods in the literature [17, 36, 37]. In this contribution, we will provide a brief overview of the most recent progress in adaptive QM/MM algorithms, with the emphasis on the adaptive-partitioning (AP) QM/MM methods that have been developed by us and our collaborators. The scope of this review is limited to organic and biological systems, leaving out solid-state systems. At the end of this contribution, we will discuss a few key challenges in the future development of adaptive QM/MM methods. 

Pezeshki S, Lin H (2011) Adaptive-partitioning redistributed charge and dipole schemes for QM/MM dynamics simulations on-the-fly relocation of boundaries that pass through covalent bonds. J Chem Theory Comput 7 3625-3634... 

Pezeshki S, Davis C, Heyden A, Lin H (2014) Adaptive-partitioning QM/MM dynamics simulations 3. Solvent molecules entering and leaving protein binding sites. J Chem Theory Comput 10 4765 776... 

Pezeshki S, Lin H (2015) Adaptive-partitioning QM/MM fra- molecular dynamics simulations 4. Proton hopping in bulk water. J Chem Theory Comput 11 2398-2411... 

So far, we have reviewed approaches in which the QM/MM border is defined at the start and remain unchanged during the calculation, hi adaptive schemes, the size of the QM subsystem can adjust during the calculation so that atoms or charges can move between QM and MM subsystems. First approaches were presented by Rode and co-workers (hot spot method) [408-411], Other methods were proposed by Kerdcharoen and Morokuma (ONIOM-XS) [412-414] and by Zhang et al. (adaptive partitioning method) [338, 339, 415, 416]. A comparison of the various approaches was also provided by Zhang et al. [339]. For recent reviews about adaptive multiscale simulations we refer to the literature [417, 418]. 

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