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

Karina van den Broek; Mirco Daniel; Matthias Epple; Jan-Mathis Hein; Hubert Kuhn; Stefan Neumann; Andreas Truszkowski; Achim Zielesny

doi:10.1186/s13321-020-00432-9

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

J Cheminform. 2020 May 1;12(1):29. doi: 10.1186/s13321-020-00432-9.

Authors

Karina van den Broek^{1

2}, Mirco Daniel², Matthias Epple¹, Jan-Mathis Hein², Hubert Kuhn³, Stefan Neumann⁴, Andreas Truszkowski⁵, Achim Zielesny⁶

Affiliations

¹ Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany.
² Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany.
³ CAM-D Technologies GmbH, Solingen, Germany.
⁴ GNWI - Gesellschaft für naturwissenschaftliche Informatik mbH, Dortmund, Germany.
⁵ Yara Deutschland, Dülmen, Germany.
⁶ Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany. achim.zielesny@w-hs.de.

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.

Keywords: DPD; Dissipative particle dynamics; GUI; Graphical user interface; MFD; MVC; Mesoscopic simulation; Model-view-controller; Molecular fragment dynamics; Molecular simulation; PDB parser; Pattern; Rich-client.