Long time step molecular dynamics using targeted Langevin stabilization

Authors:
Qun Ma;Jesús A. Izaguirre
Affiliations:
University of Notre Dame, Notre Dame, IN;University of Notre Dame, Notre Dame, IN
Venue:
Proceedings of the 2003 ACM symposium on Applied computing
Year:
2003

Citing 2
Cited 1

Dangers of multiple time step methods

Journal of Computational Physics
Long-Time-Step Methods for Oscillatory Differential Equations

SIAM Journal on Scientific Computing

ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics

ACM Transactions on Mathematical Software (TOMS)

Quantified Score

Hi-index	0.00

Visualization

Abstract

We introduce the B-spline Mollified Impulse (MOLLY) and the Targeted MOLLY (TM) for molecular dynamics (MD). TM uses targeted Langevin coupling to stabilize B-spline MOLLY. Results show that with a proper choice of parameters, the radial distribution function can be correctly recovered and the self-diffusion co-efficient can be correctly estimated from MD simulations of flexible waters using TM with outer time step of 16 fs, and a six-fold speedup is obtained. The basis of comparison is leapfrog with time step of 1 fs The overhead associated with mollification is low. Extention to handle larger molecules is discussed.