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MSCALE: A General Utility for Multiscale Modeling
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DOI：10.1021/ct100738h.png)
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摘要
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The combination of theoretical models of macromolecules that exist at different spatial and temporal scales has become increasingly important for addressing complex biochemical problems. This work describes the extension of concurrent multiscale approaches, introduces a general framework for carrying out calculations, and describes its implementation into the CHARMM macromolecular modeling package. This functionality, termed MSCALE, generalizes both the additive and subtractive multiscale scheme [e.g., quantum mechanical/molecular mechanical (QM/MM) ONIOM-type] and extends its support to classical force fields, coarse grained modeling [e.g., elastic network model (ENM), Gaussian network model (GNM), etc.], and a mixture of them all. The MSC:ALE scheme is completely parallelized with each subsystem running as an independent but connected calculation. One of the most attractive features of MSCALE is the relative ease of implementation using the standard message passing interface communication protocol. This allows external access to the framework and facilitates the combination of functionality previously isolated in separate programs. This new facility is fully integrated with free energy perturbation methods, Hessian-based methods, and the use of periodicity and symmetry, which allows the calculation of accurate pressures. We demonstrate the utility of this new technique with four examples: (1) subtractive QM/MM and QM/QM calculations; (2) multiple force field alchemical free energy perturbation; (3) integration with the SANDER module of AMBER and the TINKER package to gain access to potentials not available in CHARMM; and (4) mixed resolution (i.e., coarse grain/all-atom) normal mode analysis. The potential of this new tool is clearly established, and in conclusion, an interesting mathematical problem is highlighted, and future improvements are proposed.
Keyword:
ELASTIC NETWORK MODELS
PROTEIN CONFORMATIONAL-CHANGES
FREE-ENERGY DIFFERENCES
MOLECULAR-DYNAMICS
SIMULATION
IMPLEMENTATION
STABILIZATION
OPTIMIZATION
MINIMIZATION
INTEGRATION
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期刊
IF:
5.5
论文数:
1.1W
被引数:
5.4W
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