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jSim for Gromacs is a Graphical User Interface for the MolecularDynamics Package Gromacs. It has a project style interface to organize your md simulations. It is also possible to start md simulations on remote computers with ssh.
Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)
Network monitoring and troubleshooting is hard. TotalView makes it easy.
This means every device on your network, and every interface on every device is automatically analyzed for performance, errors, QoS, and configuration.
Nanodesigner is a software platform for research on molecular nanotechnology. It has a plug-in architecture and will include tools for molecular visualization & modelling, design of complex new molecules, moleculardynamics,...