Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics (MD) 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.
Cascade is a C++ library for efficient cycle-based simulation of hardware architectures.
TimeScapes is an analysis package that can be used to efficiently detect and characterize significant conformational changes in simulated biomolecular systems. It can be used with Desmond and other MD packages, as well as with Anton.
SNS-MP2 (spin-network-scaled MP2) is a semi-empirical quantum mechanical method for dimer interaction-energy calculations. An open-source Psi4 plugin for computing SNS-MP2 interaction energies and confidence intervals is available.