Paper Citing NAMD - Abstract
Schafer, Nick; Negrut, Dan
A Quantitative Assessment of the Potential of Implicit Integration Methods for Molecular Dynamics Simulation
JOURNAL OF COMPUTATIONAL AND NONLINEAR DYNAMICS, 5 Art. No. 031012, JUL 2010
Implicit integration, unencumbered by numerical stability constraints, is attractive in molecular dynamics (MD) simulation due to its presumed ability to advance the simulation at large step sizes. It is not clear what step size values can be expected and if the larger step sizes will compensate for the computational overhead associated with an implicit integration method. The goal of this paper is to answer these questions and thereby assess quantitatively the potential of implicit integration in MD. Two implicit methods (midpoint and Hilber-Hughes-Taylor) are compared with the current standard for MD time integration (explicit velocity Verlet). The implicit algorithms were implemented in a research grade MD code, which used a first-principles interaction potential for biological molecules. The nonlinear systems of equations arising from the use of implicit methods were solved in a quasi-Newton framework. Aspects related to a Newton-Krylov type method are also briefly discussed. Although the energy conservation provided by the implicit methods was good, the integration step size lengths were limited by loss of convergence in the Newton iteration. Moreover, a spectral analysis of the dynamic response indicated that high frequencies present in the velocity and acceleration signals prevent a substantial increase in integration step size lengths. The overhead associated with implicit integration prevents this class of methods from having a decisive impact in MD simulation, a conclusion supported by a series of quantitative analyses summarized in the paper. [DOI: 10.1115/1.4001392]
