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Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factorypattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The newdoi:10.1186/s13321-018-0278-7 pmid:29785513 pmcid:PMC5962482 fatcat:h7h6chnc6rhhdk4ynafoltmgcu