MolEnergy is a library of routines for efficiently computing molecular free energies. The primary components are: Octree-based approximation algorithms for computing pairwise Lennard-Jones and Coulombic potentials, Born radii and generalized Born polarization energy, Nonuniform fast Fourier transform approach (using NFFT) to computing generalized Born polarization energy, and Kernel independent fast multipole-based boundary element solver for the Poisson-Boltmzann equation (using KIFMM3d and PETSc).