van den Broek Karina, Daniel Mirco, Epple Matthias, Hein Jan-Mathis, Kuhn Hubert, Neumann Stefan, Truszkowski Andreas, Zielesny Achim
Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany.
Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany.
J Cheminform. 2020 May 1;12(1):29. doi: 10.1186/s13321-020-00432-9.
MFsim is an open Java all-in-one rich-client computing environment for mesoscopic simulation with Jdpd as its default simulation kernel for Molecular Fragment (Dissipative Particle) Dynamics. The new environment comprises the complete preparation-simulation-evaluation triad of a mesoscopic simulation task and especially enables biomolecular simulation tasks with peptides and proteins. Productive highlights are a SPICES molecular structure editor, a PDB-to-SPICES parser for particle-based peptide/protein representations, a support of polymer definitions, a compartment editor for complex simulation box start configurations, interactive and flexible simulation box views including analytics, simulation movie generation or animated diagrams. As an open project, MFsim allows for customized extensions for different fields of research.
MFsim是一个开放的Java一体化富客户端计算环境，用于介观模拟，以Jdpd作为其分子片段（耗散粒子）动力学的默认模拟内核。这个新环境包含了介观模拟任务完整的准备-模拟-评估三元组，尤其适用于肽和蛋白质的生物分子模拟任务。其显著亮点包括一个SPICES分子结构编辑器、一个用于基于粒子的肽/蛋白质表示的PDB到SPICES解析器、对聚合物定义的支持、用于复杂模拟盒起始配置的隔室编辑器、包括分析、模拟电影生成或动画图表的交互式且灵活的模拟盒视图。作为一个开放项目，MFsim允许针对不同研究领域进行定制扩展。
