First-principle molecular dynamics with ultrasoft pseudopotentials: parallel implementation and application to extended bioinorganic systems

J Chem Phys. 2004 Apr 1;120(13):5903-15. doi: 10.1063/1.1652017.

Abstract

We present a plane-wave ultrasoft pseudopotential implementation of first-principle molecular dynamics, which is well suited to model large molecular systems containing transition metal centers. We describe an efficient strategy for parallelization that includes special features to deal with the augmented charge in the contest of Vanderbilt's ultrasoft pseudopotentials. We also discuss a simple approach to model molecular systems with a net charge and/or large dipole/quadrupole moments. We present test applications to manganese and iron porphyrins representative of a large class of biologically relevant metalorganic systems. Our results show that accurate density-functional theory calculations on systems with several hundred atoms are feasible with access to moderate computational resources.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • Computational Biology*
  • Iron / chemistry
  • Manganese / chemistry
  • Metalloporphyrins / chemistry*
  • Molecular Conformation
  • Myoglobin / chemistry
  • Myoglobin / metabolism
  • Thermodynamics

Substances

  • Metalloporphyrins
  • Myoglobin
  • Manganese
  • Iron