Incremental update of electrostatic interactions in adaptively restrained particle simulations

• Published in: Journal of computational chemistry Vol. 39; no. 20; pp. 1455 - 1469
• Main Authors: Edorh, Semeho Prince A., Redon, Stéphane
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 30.07.2018; Wiley
• Subjects: adaptively restrained molecular dynamics; Algorithms; Computation; Computer Science; Computer simulation; electrostatics; Finite element method; LAMMPS; Modeling and Simulation; Molecular chains; Molecular dynamics; molecular simulations; multigrid; Multigrid methods; Simulation; LAMMPS; adaptively restrained molecular dynamics; electrostatics; molecular simulations; multigrid; Molecular Simulations; Multigrid; Electrostatics; Adaptively Restrained Molecular Dynamics
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.25215

The computation of long‐range potentials is one of the demanding tasks in Molecular Dynamics. During the last decades, an inventive panoply of methods was developed to reduce the CPU time of this task. In this work, we propose a fast method dedicated to the computation of the electrostatic potential in adaptively restrained systems. We exploit the fact that, in such systems, only some particles are allowed to move at each timestep. We developed an incremental algorithm derived from a multigrid‐based alternative to traditional Fourier‐based methods. Our algorithm was implemented inside LAMMPS, a popular molecular dynamics simulation package. We evaluated the method on different systems. We showed that the new algorithm's computational complexity scales with the number of active particles in the simulated system, and is able to outperform the well‐established Particle Particle Particle Mesh (P3M) for adaptively restrained simulations. © 2018 Wiley Periodicals, Inc. Adaptively restrained simulation of a nanopore system which contains a carbon (gray) graphene sheet, water molecules (oxygen red, hydrogen white), sodium (cyan) and chlorine (green). Particles are driven through the pore by an external electric field. The flux of sodium is restricted by positively charged particles (orange) located at the edge of the nanopore. Counterions (brown) ensure the neutrality of the system. The simulation is sped up by adaptively restraining the motion of water molecules.