OpenMM-MiMiC接口高效和灵活的多尺度模拟。

IF 5.3 2区 化学 Q1 CHEMISTRY, MEDICINAL
Andrea Levy, Andrej Antalík, Jógvan Magnus Haugaard Olsen and Ursula Rothlisberger*, 
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引用次数: 0

摘要

MiMiC是一个灵活有效的多尺度模拟框架,其中不同的子系统由单个客户程序处理。在这项工作中,我们提出了一个使用OpenMM作为MM客户端程序的新接口,并证明了它在QM/MM MD模拟中的效率。除了高性能(特别是在gpu上)和广泛的特性选择之外,OpenMM是一个高度灵活且易于扩展的程序,非常适合开发新的多尺度方法。由于MiMiC的开放式设计,OpenMM-MiMiC接口将自动支持任何新的QM客户端程序与MiMiC的QM/MM接口,并且只需进行最小的更改,就可以实现新的多尺度方法,开辟了超越静电嵌入QM/MM的新研究方向。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

OpenMM–MiMiC Interface for Efficient and Flexible Multiscale Simulations

OpenMM–MiMiC Interface for Efficient and Flexible Multiscale Simulations

MiMiC is a flexible and efficient framework for multiscale simulations in which different subsystems are treated by individual client programs. In this work, we present a new interface with OpenMM to be used as an MM client program and we demonstrate its efficiency for QM/MM MD simulations. Apart from its high performance, especially on GPUs, and a wide selection of features, OpenMM is a highly flexible and easily extensible program, ideal for the development of novel multiscale methods. Thanks to the open-ended design of MiMiC, the OpenMM–MiMiC interface will automatically support any new QM client program interfaced with MiMiC for QM/MM and, with minimal changes needed, new multiscale methods implemented, opening up new research directions beyond electrostatic embedding QM/MM.

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来源期刊
CiteScore
9.80
自引率
10.70%
发文量
529
审稿时长
1.4 months
期刊介绍: The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.
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