Improved GROMACS algorithms using the MPI parallelization

摘要

Molecular dynamics (MD) studies the structure of molecular systems which are subject to certain constraints and forces. The simulation of particles is a tool for examining atomic systems during a period of nanoseconds in which the trajectory of atoms and the state of the system is analyzed. GROMACS is a package which supports molecular dynamics simulations and energy minimization, being started the University of Groningen. Usually molecular dynamics simulations are time consuming, sometimes taking weeks and even months. In order to obtain the output of the simulation in less time, parallelization is used through the use of MPI (Message Passing Interface). The article presents the MPI parallelization of a novel thermostat algorithm for molecular dynamics and experimental results.