Paper Citing NAMD - Abstract
Bajaj, Chandrajit; Zhao, Wenqi
FAST MOLECULAR SOLVATION ENERGETICS AND FORCES COMPUTATION
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 31:4524-4552, 2010
The total free energy of a molecule includes the classical molecular mechanical energy (which is understood as the free energy in vacuum) and the solvation energy, which is caused by the change of the environment of the molecule (solute) from vacuum to solvent. The solvation energy is important to the study of the intermolecular interactions. In this paper we develop a fast surface-based generalized Born method to compute the electrostatic solvation energy along with the energy derivatives for the solvation forces. The most time-consuming computation is the evaluation of the surface integrals over an algebraic spline molecular surface (ASMS), and the fast computation is achieved by the use of the nonequispaced fast Fourier transform (NFFT) algorithm. The main results of this paper involve (a) an efficient sampling of quadrature points over the molecular surface by using nonlinear patches, (b) fast linear time estimation of energy and intermolecular forces, (c) error analysis, and (d) efficient implementation combining fast pairwise summation and the continuum integration using nonlinear patches.
