Projects

Deductive Multiscale Simulator (DMS): a C++ multiscale all-atom simulator that is based on the GROMACS molecular dynamics source code. DMS implements a multiscale factorization methodology to separate the atomistic from the coarse-grained phase. DMS can achieve a substantial speedup over traditional molecular dynamics when the size of the system is large enough, making it suitable for simulating virus-like particles large biomacromolecular systems. DMS is released under GPU v2.1.

ProtoMD: a prototyping toolkit for implementing coarse-grained and multiscale methods for molecular dynamics. ProtoMD is written in Python and released under GPU v3.

PyGran: a Python toolkit for running and analyzing discrete element method simulations. The emphasis is on granular (powder) systems. PyGran is released under GPU v2 and its source code is available from Github.