Dynamic fragmentation with static fragments (DF/SF) algorithm designed for ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) simulations of polypeptides

Abstract

The ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) method was extended for simulation of solvated polypeptides by the introduction of an algorithm named dynamic fragmentation with static fragments (DF/SF). In FMO-MD, the force acting on each nucleus is calculated by the FMO method, which requires fragmentation of the simulated molecule. The fragmentation data must be redefined, depending on the time-dependent change of the molecular configuration, and the DF/SF algorithm governs this redefinition. In the DF/SF algorithm, some fragments are manually classified as static and unchanged, while others are considered dynamic and subject to change. Various options of the algorithm were implemented in the ABINIT-MP program. The options were tested and discussed as they applied to FMO-MD simulations of the solvated (Gly)2 dipeptide, in which the two amino acid residues of the peptide were regarded as static (invariable) while surrounding water molecules were regarded as dynamic (variable). Future prospects for the FMO-MD simulation of biopolymers are discussed based upon the tests of the DF/SF algorithm.