MFsim—an open Java all-in-one rich-client simulation environment for mesoscopic simulation View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2020-05-01

AUTHORS

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

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. More... »

PAGES

29

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13321-020-00432-9

DOI

http://dx.doi.org/10.1186/s13321-020-00432-9

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1127311418

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/33430951


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