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.
Highlights
A molecular simulation workflow comprises three successive steps: The definition of a simulation job with all necessary input information, the approximate numerical integration of the equations of motion and the analysis of the simulation record with all calculated results
Molecular Fragment Dynamics (MFD) is a “bottom-up” Dissipative Particle Dynamics (DPD) variant which chooses the particles to be small “fragment molecules” of molar mass in the order of 100 Da where larger molecules are composed of adequate smaller “fragment molecule” particles that are bonded by harmonic springs to mimic covalent connectivities and spatial 3D conformations [5,6,7,8,9,10,11,12]
The Job Input features have to be defined in a top-down manner where a change in a higher-level feature leads to an immediate update of subordinate features in an adequate manner—e.g. a change in the number of particles via the Quantity feature automatically changes the subordinate Box size feature to be consistent with the new higher-level Quantity settings according to the even higher DPD density setting
Summary
A molecular simulation workflow comprises three successive steps: The definition of a simulation job with all necessary input information (preparation step), the approximate numerical integration of the equations of motion (the actual simulation step) and the analysis of the simulation record with all calculated results (evaluation step). The new MFsim project provides (to our knowledge) the first open Java all-in-one rich-client mesoscopic simulation environment and complements the few available commercial systems [13, 14] with specific support for biomolecular applications containing peptides and proteins.
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