Paper Citing NAMD - Abstract
Izaguirre, J.A.
Langevin stabilization of multiscale mollified molecular dynamics
MULTISCALE COMPUTATIONAL METHODS IN CHEMISTRY AND PHYSICS, 177:34-47, 2001
This paper shows the possibility of using very mild stochastic damping to stabilize long time steps integrators for Newtonian molecular dynamics. More specifically, stable and accurate integrations are obtained for damping coefficients that are only a few percent of the natural decay rate of the velocity autocorrelation function. Langevin Molly (LM) is introduced in this paper. It uses the mollified impulse method for the Newtonian term and the Langevin impulse method for the Langevin term. A parallel version of LM is available in the molecular dynamics program NAMD 2.1. LM and the Langevin integrators BBK and LN are evaluated across a wide range of damping coefficients values. Using LM and mild damping, time steps of up to 16 fs are possible even in the presence of explicitly modeled flexible water. When using mild damping, LM is superior to the other methods because it is symplectic in the zero damping limit, and it uses a better integration for the Langevin damping term. The second part of this paper compares several into grators (LM, BBK, and LN) for regular Langevin dynamics, a typical application of which is the implicit modeling of solvent molecules. In this case, the method called LN is superior, with LM closely following.
