Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters.
Random123 is a family of highly parallelizable counter-based random number generators (CBRNGs) that were originally developed for Anton but may be useful for a wide range of applications.
D. E. Shaw Research also develops trajectory analysis software that can be used with Desmond and other MD packages, as well as with Anton.
HiMach is a parallel analysis framework that allows users to write trajectory analysis programs sequentially and that carries out the parallel execution of the programs automatically.
TimeScapes is an analysis package that can be used to efficiently detect and characterize significant conformational changes in simulated biomolecular systems.