Langevin Stabilization of Multiscale Molli ed Molecular Dynamics.pdfVIP

Langevin Stabilization of Multiscale Mollied Molecular Dynamics Jesus A. Izaguirre Department of Computer Science and Engineering University of Notre Dame, Notre Dame, IN 46556, USA Abstract. This pap er shows the p ossibility of using very mild sto chastic damping to stabilize long time steps integrators for Newtonian molec- ular dynamics. More sp ecically, stable and accurate integrations are obtained for damping co ecients that are only a few p ercent of the natural decay rate of the velo city auto correlation function. Langevin Molly (LM) is intro duced in this pap er. It uses the mollied impulse metho d for the Newtonian term and the Langevin impulse metho d 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 co ecients values. Using LM and mild damping, time steps of up to 16 fs are p ossible even in the presence of explicitly mo deled exible water. When using mild damping, LM is sup erior to the other metho ds b ecause it is symplectic in the zero damping limit, and it uses a b etter integration for the Langevin damping term. The second part of this pap er compares several inte- grators (LM, BBK, and LN) for regular Langevin dynamics, a typical application of which is the implicit mo deling of solvent molecules. In this case, the metho d called LN is sup erior, with LM closely following. 1 Intro duction This pap er shows the p ossibility of using very mild sto chastic damping