Chandrajit Bajaj



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, 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, Sept. 2010


Most MolEnergy functionality can be interfaces through TexMol.

Coming soon: stand alone, command-line interface to MolSurf package.

Software Usage

MolEnergy commands can be called through the Utilities menu of TexMol.