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. The new 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).
A more detailed description is provided in the scientific literature (see references below).
- MFSimVersionHistory.txt shows the version history of MFsim.
- The Installer for Windows OS folder provides a Windows OS installer executable for MFsim. Download this executable, start and follow the instructions to install MFsim. Note, that the installation includes a 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 8 gigabyte of RAM copy a shortcut to batch file Start_MFsim_64bit_8GB.bat which is located in the MFsim program folder C:\Program Files\GNWI\MFsim 2.2.4.0). To start MFsim double click the created shortcut. MFsim can be easily uninstalled by the provided Uninstall.exe executable in the MFsim program folder.
- The src folder contains all (Netbeans) source code packages including Unit tests.
- The lib folder comprises the open Java libraries used by MFsim (see MFSimVersionHistory.txt for details).
- The javadoc folder provides the source code Javadoc HTML documentations.
- The MFsim_Source folder 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 folder offers tutorial PDF documents which are also available in animated form (see corresponding README).
- The 2020 Cyclotide-membrane interaction study folder contains supplementary information for a cyclotide/membrane interaction study (see corresponding README).
MFsim is an integration project of the open molecular fragment cheminformatics roadmap
based on two already published 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 IO, Apache Commons Lang, Apache Commons RNG, BioJava, GraphStream, Java Matrix Package, JCommon, JDOM, JFreeChart, Jmol, PCG (pseudorandom generator implementation for Java), 3D Vector Math Package, FFmpeg (Static) Version
The support of CAM-D Technologies GmbH and GNWI - Gesellschaft für naturwissenschaftliche Informatik mbH is gratefully acknowledged.