Multi-level grid algorithms for faster molecular energetics

Bio-molecules reach their stable configuration in solvent which is primarily water with a small concentration of salt ions. One approximation of the total free energy of a bio-molecule includes the classical molecular mechanical energy EMM (which is understood as the self intra-molecular energy in vacuum) and the solvation energy Gsol which is caused by the change of the environment of the molecule from vacuum to solvent (and hence also known as the moleculesolvent interaction energy). This total free energy is used to model and study the stability of bio-molecules in isolation or in their interactions with drugs. In this paper we present fast O (N log N) multi-level grid based approximation algorithms (where N is the number of atoms) for efficiently estimating the compute-intensive terms of EMM and Gsol. The fast octree-based algorithm for Gsol is additionally dependent on an O (N) size computation of the biomolecular surface and its spatial derivatives (normals). We also provide sev...

• Type: Conference
• Year: 2010
• Where: SMA
• Authors: Rezaul Alam Chowdhury, Chandrajit L. Bajaj
• Keywords: Mechanical Energy Emm, SMA 2010, Solid Modeling, Solvation Energy Gsol, Total Free Energy