First-principle molecular dynamics with ultrasoft pseudopotentials: parallel implementation and application to extended bio-inorganic system

摘要

We present a plane-wave ultrasoft pseudopotential implementation offirst-principle molecular dynamics, which is well suited to model largemolecular systems containing transition metal centers. We describe an efficientstrategy for parallelization that includes special features to deal with theaugmented charge in the contest of Vanderbilt's ultrasoft pseudopotentials. Wealso discuss a simple approach to model molecular systems with a net chargeand/or large dipole/quadrupole moments. We present test applications tomanganese and iron porphyrins representative of a large class of biologicallyrelevant metallorganic systems. Our results show that accurateDensity-Functional Theory calculations on systems with several hundred atomsare feasible with access to moderate computational resources.