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).


C. Bajaj, S.-C. Chen and A. Rand
An Efficient Higher-Order Fast Multipole Boundary Element Solution for Poisson-Boltzmann Based molecular Electrostatics
SIAM Journal on Scientific Computing, 33(2) 826-848, 2011, NIHMSID# 266230, PMCID: PMC3110014. (pdf)

C. Bajaj, W. Zhao
Fast Molecular Solvation Energetics and Force Computation
SIAM Journal on Scientific Computing, 31(6): 4524-4552, January 2010,, PMCID: PMC2830669

C. Bajaj and R. Chowdhury
Multi-level Grid Algorithms for Faster Molecular Energetics
Proceedings of the ACM Symposium on Solid and Physical Modeling, pp. 147-152, Sept. 2010


Most MolEnergy functionality can be interfaced through TexMol.

Binaries for the command line utility: linux (ubuntu), mac


  * Currently the source code is distributed only for academic use. Users interested in commercial licensing should contact Jitendra Jain.
  * Request academic license
  * Download source

Future Work

Software Usage

Software usage details and sample data to appear soon.