OOPSE: An object‐oriented parallel simulation engine for molecular dynamics

Abstract

OOPSE is a new molecular dynamics simulation program that is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force-based decomposition method. Simulations are specified using a very simple C-based meta-data language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion-based schemes.

Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics

“…The SPME electrostatics were performed using the TINKER implementation of SPME, 54 while all other calculations were performed using the OOPSE molecular mechanics package. 53 All other portions of the energy calculation ͑i.e. Lennard-Jones interac-tions͒ were handled in exactly the same manner across all systems and configurations.…”

CO-Induced Restructuring on Stepped Pt Surfaces: A Molecular Dynamics Study

“…Simulations were performed using the open source molecular dynamics package, OpenMD. 75,76 Generalized coordination number For many catalytic reactions, only a subset of the atoms on a roughened surface or nanoparticle are catalytically active. While the coordination numbers of individual atoms can describe their binding strengths, Calle-Vallejo et al observed that including the first and second nearest neighbor counts allowed for a more complete description of an atom's local environment and its catalytic activity.…”

“…A portion of each step sunk into the surface allowing the two remaining plateaus to meet up to form a single step edge. 75.1 ns, (e) and 100 ns after exposure to CO. The step-edges indicated with a bracket in (a) approach each other while sinking into the surface.…”

Structures of small Pd–Pt bimetallic clusters by Monte Carlo simulation

“…Before starting the Monte Carlo runs, a relatively short steepest-descent minimization was performed to relax the lattice in the initial configuration, based on the embedded atom method (EAM) potential [20]. It is noticed that, in fact, the initial configuration can be generated in different ways without influencing the final configurations of the clusters of interest.…”