MFsim—an open Java all-in-one rich-client simulation environment for mesoscopic simulation

Journal of Cheminformatics

Hubert Kuhn¹  Stefan Neumann²  Matthias Epple³  Karina van den Broek³  Mirco Daniel⁴  Jan-Mathis Hein⁴  Achim Zielesny⁴  Andreas Truszkowski⁵ 

[1]CAM-D Technologies GmbH

[2]GNWI – Gesellschaft für naturwissenschaftliche Informatik mbH

[3]Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen

[4]Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences

[5]Yara Deutschland

关键词: Molecular simulation;    Mesoscopic simulation;    Rich-client;    Model-view-controller;    MVC;    Pattern;   

DOI  :  10.1186/s13321-020-00432-9

来源: DOAJ

【 摘 要 】

Abstract 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.

【 授权许可】

Unknown