In collaboration with Prof. Vaidehi's group at City of Hope, the DARTS spacecraft multibody dynamics engine has been adapted to develop the Generalized Newton-Euler Inverse Mass Operator (GNEIMO) software for the molecular dynamics simulation of large-scale molecular systems. GNEIMO is in use for the simulation and analysis of protein folding, drug design, virus mechanisms and other applications. Other computational chemistry applications include the study of biomolecular processes and for the modeling and design of new materials including polymers and catalysts.

GNEIMO works with internal coordinates molecular models obtained by fixing the high frequency modes. The internal coordinates model reduces the number of degrees of freedom from 3N (where N is the number of atoms) to N (the number of dihedral degrees of freedom). The equations of motion for internal coordinates model are coupled and involve a dense mass matrix. The conventional algorithm for solving constrained equations involves inversion of the dense mass matrix M with computational cost scaling as the cubic power of N. The GNEIMO method provides a O(N) algorithm for solving the same equations of motion.

The development of the O(N) GNEIMO algorithm was motivated by the impracticality of useful long time molecular dynamics of macromolecules using conventional O(N3) algorithms for contrained molecular dynamics. The speed performance of the GNEIMO method has large implications on the ability to perform large scale molecular dynamics on biologically relevant molecules and materials. This has been demonstrated using GNEIMO. Mathematical techiniqes from JPL's Spatial Operator Algebra framework were used to analytically pose the constrained molecular dynamics problem, and to develop a the fast O(N) algorithms for their solution.

The GNEIMO software is available here.