Welcome to PumMa!


Over the past five years the Molecular Dynamics Code PumMa has been developed by several people in the Computational Biology group of the Department of Biomedical Engineering at the Eindhoven University of Technology. The name of the program is short for Parallel Utility for Modeling of Molecular Aggregation, since its first design was aimed at micell forming in oil/water complexes.

Currently PumMa is being used by several groups at the Eindhoven University of Technology, as well as the City of Hope Research Center in Duarte, USA. Most of the simulations conducted with PumMa have applications in the field of biology, such as the forming of membranes, the fusion and fission of vesicles. Many of the biological simulations with PumMa are done with the coarse grained model. Together with the Department of Chemistry, simulations on dendrimers are performed, and with the Department of Mechanical Engineering on nanotube flow and heat exchange are investigated using PumMa attached to a Monte Carlo code. In collaboration with the City of Hope Research Center the coarse grained model is being developed further.

Along with PumMa also a toolkit has been developed, called PumMaTK. The aim of this toolkit is to simplify the construction or modification of systems under interest. Furthermore the toolkit provides analysis options, such as density profiles. The toolkit PumMaTK is written in Python with some routines in C.

Any questions with regard to PumMa, PumMaTK or this website can be directed to any of the development people.