Achim Zielesny

• 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.