Paper Citing NAMD - Abstract
Ma, Q.; Izaguirre, J.A.
Targeted mollified impulse: A multiscale stochastic integrator for long molecular dynamics simulations
MULTISCALE MODELING & SIMULATION, 2:1-21, 2003
Molecular dynamics (MD) is widely used in simulations of biomolecular systems such as DNA and proteins, systems which are multiscale in nature. However, current time stepping integrators are not able to address the time scale problems. Multiscale integrators, in which the presence of "fast" modes does not affect the time integration of "slow" modes, are pressingly needed in light of the fast growing biological data generated from the many genome sequencing projects. In this paper, we present a new multiple time stepping (MTS) multiscale integrator with stochasticity built in for constant temperature molecular dynamics simulations, called the targeted mollified impulse method (TM). TM combines the mollified impulse method, which is a stabler version of Verlet-I/r-RESPA ( reversible REference System Propagator Algorithm), and a self-consistent dissipative leapfrog integrator commonly used in dissipative particle dynamics. TM introduces the Langevin coupling in a targeted manner to stabilize the MTS integrator such that the total linear momentum is conserved and less randomness in slower modes is imposed. Numerical experiments of simple model problems provide evidence that TM samples from the canonical ensemble. Possible applications include kinetics calculations such as conformational transition rates, computation of structural quantities from a canonical ensemble, and approximation of dynamical quantities from a canonical ensemble. We present results for the last two by showing that both the radial distribution functions and the self-diffusion coefficient are correctly computed from the simulations of flexible TIP3P waters using TM with outermost time step of 16 fs and innermost time step of 2 fs. Compared to leapfrog with time step of 1 fs, the implementation of TM achieves a six-fold computational speedup, whereas Verlet-I/r-RESPA with outer time step of 4 fs and inner time step of 1 fs achieves only a three-fold speedup. We also show how to generalize the method for the simulation of biological macromolecules.
