RedMD (Reduced Molecular Dynamics)

RedMD is an open source package for molecular dynamics simulations and normal mode analysis of coarse-grained models of proteins and nucleic acids. Force fields are based on one-bead elastic network models and their extensions.

NEW! version 2.0 is available since Nov 9, 2009

Surface Diver

Surface Diver allows describing, comparing, and classifying proteins according to their physicochemical properties without the need of prior 3D structural alignment.

PDC (Potential Derived Charges)

PDC (Potential Derived Charges) is a package to calculate effective charges for macromolecules so that they reproduce the molecular electrostatic potential calculated from the numerical solution of the Poisson-Boltzmann equation.