[ MAIN | DARTS |DSHELL |ROAMS |DSENDS |SimScape |NEIMO | Dspace |YaM |]
The DARTS spacecraft multibody dynamics engine has been adapted to develop the Newton-Euler Inverse Mass Operator (NEIMO) software for the molecular dynamics simulation of large-scale molecular systems. NEIMO 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.
NEIMO 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 NEIMO method provides a O(N) algorithm for solving the same equations of motion.
The development of the O(N) NEIMO 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 NEIMO method has large implications on the ability to perform large scale molecular dynamics on biologically relevant molecules and materials. This has been demonstrated using NEIMO. 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.
For comments or questions, please e-mail Abhi.Jain@jpl.nasa.gov.