Multiscaling algorithms for molecular dynamics simulations with GROMACS

Abstract

This article presents the parallel implementation of a new multiscale model that is currently developed in the Molecular Dynamics Group from the University of Groningen. Multiscale methods combine the advantages of two levels of simulation, an atomistic and a coarse-grain one, with a small loss of performance. We designed a parallel implementation of this multiscale approach based on the improved parallel algorithms from the GROMACS MD simulator. The properties of the simulated systems were undisturbed and the errors were kept to a minimum. By having a parallel multiscale simulation, one can take advantage of a reduced simulation time by running it on multiple processors, and in the same time, access to both atomistic and macroscopic details is offered for a better understanding of the desired phenomenon.