ALMOST (all atom molecular simulation toolkit) is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.
OpenMM Zephyr is a molecular simulation application for studying molecular dynamics of proteins, RNA, and other molecules. Zephyr guides the user through a work flow for setting up and running a specialized version of the molecular dynamics application gromacs. This version of gromacs uses the OpenMM API for GPU-accelerated molecular simulations.
PROTEAN is a set of Fortran subroutines for calculating the equations ofmotion in torsion space for polypeptides. Torsion space is the space of all rotatable bonds. Bond lengths and bond angles remain fixed at their ideal values in a torsion space simulation. Simulations in torsion space are at least ten times more efficient than simulations in Cartesian space.
YUP (Yammp Under Python), also known as Yammp 2, is a molecular modeling program. Although a general purpose tool, development is currently concentrated on molecular simulations (mechanics) and on reduced representation and multiscale modeling. YUP is based on an earlier program Yammp.