Paper Citing NAMD - Abstract
Izaguirre, J.A.; Catarello, D.P.; Wozniak, J.M.; Skeel, R.D.
Langevin stabilization of molecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 114:2090-2098, FEB 1 2001
In this paper we show the possibility of using very mild stochastic damping to stabilize long time step 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 processes of interest, such as the velocity autocorrelation function. Two new multiple time stepping integrators, Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are introduced in this paper. Both use the mollified impulse method for the Newtonian term. LM uses a discretization of the Langevin equation that is exact for the constant force, and BBK-M uses the popular Brunger-Brooks-Karplus integrator (BBK). These integrators, along with an extrapolative method called LN, are evaluated across a wide range of damping coefficient values. When large damping coefficients are used, as one would for the implicit modeling of solvent molecules, the method LN is superior, with LM closely following. However, with mild damping of 0.2 ps(-1), LM produces the best results, allowing long time steps of 14 fs in simulations containing explicitly modeled flexible water. With BBK-M and the same damping coefficient, time steps of 12 fs are possible for the same system. Similar results are obtained for a solvated protein-DNA simulation of estrogen receptor ER with estrogen response element ERE. A parallel version of BBK-M runs nearly three times faster than the Verlet-I/r-RESPA (reversible reference system propagator algorithm) when using the largest stable time step on each one, and it also parallelizes well. The computation of diffusion coefficients for flexible water and ER/ERE shows that when mild damping of up to 0.2 ps-1 is used the dynamics are not significantly distorted. (C) 2001 American Institute of Physics.
