Acceleration of the canonical molecular dynamics simulation by the particle mesh Ewald method combined with the multiple time-step integrator algorithm
نویسندگان
چکیده
Ž . The canonical molecular dynamics MD simulation was accelerated by the integrated method of the multiple time-step Ž . integrator algorithm combined with the particle mesh Ewald method PMEM applied not only to the calculation of the Coulomb interaction but also of the Van der Waals interaction. Although the previous integrated method, in which the PMEM was used in the calculation only for the Coulomb interaction, yielded a significant acceleration of the MD simulation, a further acceleration by a factor of about 2 in the entire MD simulation was obtained by extension of the integrated method to the Van der Waals interaction. q 1999 Elsevier Science B.V. All rights reserved.
منابع مشابه
Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems
The particle–particle particle–mesh ~P3M! method for calculating long-range electrostatic forces in molecular simulations is modified and combined with the reversible reference system propagator algorithm ~RESPA! for treating the multiple time scale problems in the molecular dynamics of complex systems with multiple time scales and long-range forces. The resulting particle–particle particle–mes...
متن کاملEfficient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations
We develop an efficient multiple-time-step force splitting scheme for particle-mesh-Ewald molecular dynamics simulations. Our method exploits smooth switch functions effectively to regulate direct and reciprocal space terms for the electrostatic interactions. The reciprocal term with the near field contributions removed is assigned to the slow class; the van der Waals and regulated particle-mes...
متن کاملOptimized particle-mesh EwaldÕmultiple-time step integration for molecular dynamics simulations
We develop an efficient multiple time step ~MTS! force splitting scheme for biological applications in the AMBER program in the context of the particle-mesh Ewald ~PME! algorithm. Our method applies a symmetric Trotter factorization of the Liouville operator based on the position-Verlet scheme to Newtonian and Langevin dynamics. Following a brief review of the MTS and PME algorithms, we discuss...
متن کاملLarge scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators
Large scale simulations of macromolecules in solution that do not suffer from artifacts arising from force truncations are becoming feasible. New force evaluation algorithms such as the fast multipole method ~FMM! and multiple time scale integration methods such as the reversible reference system propagator algorithm ~r-RESPA! have been combined and used to perform fast and stable simulations o...
متن کاملTargeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations
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 gr...
متن کامل