MFsim

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

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 (DPD). The environment integrates and supports the complete preparation-simulation-evaluation triad of a mesoscopic simulation task. 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 enables customized extensions for different fields of research.

MFsim uses several open libraries (see MFSimVersionHistory.txt for details and references below) and is published as open source under the GNU General Public License version 3 (see LICENSE).

MFsim has been described in the scientific literature and used for DPD studies (see references below).

Content

• MFSimVersionHistory.txt shows the detailed version history of MFsim.
• The src subfolder contains all (Netbeans) source code packages.
• The test subfolder contains Unit tests.
• The lib subfolder comprises the open Java libraries used by MFsim (see MFSimVersionHistory.txt for details).
• The javadoc subfolder provides the source code Javadoc HTML documentations.
• The MFsim_Source subfolder is a complete MFsim installation with all Java bytecode libraries including MFsim.jar and splash image MFsimSplash.jpg (in subfolder lib), MFsim version history (in subfolder info), particle set files (in subfolder particles), tutorial PDF documents (in subfolder tutorials) and utility programs (in subfolder winUtils for Windows OS only). MFsim.jar may be started with an appropriate batch file of the operating system.
• The tutorials subfolder offers MFsim tutorials (see corresponding README).
• The subfolders 2020 Cyclotide-membrane interaction study, 2021 Cyclotide-membrane interaction study, 2022 C10E4-water bilayer formation study and 2022 Cyclotide-membrane electrostatics study contain supplementary information for specific studies performed with MFsim/Jdpd (see corresponding README files in each subfolder).

Installer for Windows OS

• A convenient Windows OS installer executable for MFsim is available. Download the installer executable (Version 2.6.4.0 via link), start and follow the instructions to install MFsim. Note, that the installation includes a full Java Runtime Environment (JRE). After installation, create a shortcut to an appropriate MFsim start batch file on your Windows desktop (e.g. for MFsim to use up to 16 gigabyte of RAM copy a shortcut to batch file Start_MFsim_64bit_16GB.bat which is located in the MFsim program folder C:\Program Files\GNWI\MFsim 2.6.4.0). To start MFsim double click the created shortcut. MFsim can be uninstalled by the provided Uninstall.exe executable in the MFsim program folder or standard Windows functions.

References

Software:

• K. van den Broek, M. Daniel, M. Epple, J.-M. Hein, H. Kuhn, S. Neumann, A. Truszkowski and A. Zielesny, MFsim - an open Java all-in-one rich-client simulation environment for mesoscopic simulation, Journal of Cheminformatics (2020), 12:29

Applications:

• F. Bänsch, C. Steinbeck and A. Zielesny, Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C10E4/water mixture with lamellar bilayer formation, Journal of Cheminformatics (2023), 15:23
• F. Bänsch, C. Steinbeck and A. Zielesny, Notes on the Treatment of Charged Particles for Studying Cyclotide/Membrane Interactions with Dissipative Particle Dynamics, Membranes (2022), 12(6):619
• K. van den Broek, M. Epple, L. S. Kersten, H. Kuhn and A. Zielesny, Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation, Journal of Chemical Information an Modeling (2021), 61, 3027-3040 (Link to ChemRxiv preprint)

MFsim is an integration project of the open molecular fragment cheminformatics roadmap

• A. Truszkowski, M. Daniel, H. Kuhn, S. Neumann, C. Steinbeck, A. Zielesny and M. Epple, A molecular fragment cheminformatics roadmap for mesoscopic simulation, Journal of Cheminformatics (2014), 6:45

based on two constructive projects along this road: The SPICES molecular structure line notation

• K. van den Broek, M. Daniel, M. Epple, H. Kuhn, J. Schaub and A. Zielesny, SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation, Journal of Cheminformatics (2018), 10:35
• SPICES repository on GitHub

and the Jdpd simulation kernel for Molecular Fragment (Dissipative Particle) Dynamics:

• K. van den Broek, H. Kuhn and A. Zielesny, Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics, Journal of Cheminformatics (2018), 10:25
• Jdpd repository on GitHub

Additionally used open projects:

• Apache Commons Lang, Apache Commons RNG, Apache Commons Math, BioJava, GraphStream, Java Matrix Package, JCommon, JDOM, JFreeChart, Jmol, 3D Vector Math Package, FFmpeg (Static) Version

Acknowledgements

The support of CAM-D Technologies GmbH and GNWI - Gesellschaft für naturwissenschaftliche Informatik mbH is gratefully acknowledged.