Non-self-consistent Density-Functional Theory Exchange-Correlation Forces for GGA Functionals

J. Chem. Theory Comput.

Miyazaki

2014

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Multisite local orbitals, which are formed from linear combinations of pseudo-atomic orbitals from a target atom and its neighbor atoms, have been introduced in the large-scale density functional theory calculation code CONQUEST. Multisite local orbitals correspond to local molecular orbitals so that the number of required local orbitals can be minimal. The multisite support functions are determined by using the localized filter diagonalization (LFD) method [Phys. Rev. B 2009, 80, 205104]. Two new methods, the double cutoff method and the smoothing method, are introduced to the LFD method to improve efficiency and stability. TheHamiltonian and overlap matrices with multisite local orbitals are constructed by efficient sparse-matrix multiplications in CONQUEST. The investigation of the calculated energetic and geometrical properties and band structures of bulk Si, Al and DNA systems demonstrate the accuracy and the computational efficiency of the present method. The representability of both occupied and unoccupied band structures with the present method has been also confirmed.3

Section: Appendixmentioning

confidence: 97%

Efficient Calculations with Multisite Local Orbitals in a Large-Scale DFT Code CONQUEST

Nakata

J. Chem. Theory Comput.

Miyazaki

2014

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“…Using this ability of the code, the code has been used for structure relaxations of the nanoscale systems of semiconductor surfaces. 27,28) 2.2 Molecular dynamics with the CONQUEST code Even though we can now calculate the total energy and atomic forces 29,30) of very large systems using OðNÞ DFT method, this does not guarantee that stable, efficient, and accurate FPMD simulations are also practically possible. There are two methods widely used in conventional FPMD simulations: Car-Parrinello MD (CPMD) and Born-Oppenheimer MD (BOMD) methods.…”

Section: Introductionmentioning

confidence: 99%

Linear-scaling first-principles molecular dynamics of complex biological systems with the Conquest code

Otsuka¹,

Taiji²,

et al. 2016

Jpn. J. Appl. Phys.

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The recent progress of linear-scaling or OðNÞ methods in density functional theory (DFT) is remarkable. In this paper, we show that all-atom molecular dynamics simulations of complex biological systems based on DFT are now possible using our linear-scaling DFT code CONQUEST. We first overview the calculation methods used in CONQUEST and explain the method introduced recently to realise efficient and robust first-principles molecular dynamics (FPMD) with OðNÞ DFT. Then, we show that we can perform reliable all-atom FPMD simulations of a hydrated DNA model containing about 3400 atoms. We also report that the velocity scaling method is both reliable and useful for controlling the temperature of the FPMD simulation of this system. From these results, we conclude that reliable FPMD simulations of complex biological systems are now possible with CONQUEST.

“…Although the NSC method is less accurate than usual DFT calculations with the self-consistent field (SCF) method, it enables us to perform efficient structure optimization or MDs. Note that the code can calculate forces that are completely consistent with the NSC method [27,35]. This method may be useful for our future study on gA systems, and its accuracy is also checked in this paper.…”

Section: Introductionmentioning

confidence: 92%

Density-functional theory study of gramicidin A ion channel geometry and electronic properties

Todorović

Gillan

et al. 2013

J. R. Soc. Interface.

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Understanding the mechanisms underlying ion channel function from the atomic-scale requires accurate ab initio modelling as well as careful experiments.Here, we present a density functional theory (DFT) study of the ion channel gramicidin A (gA), whose inner pore conducts only monovalent cations and whose conductance has been shown to depend on the side chains of the amino acids in the channel. We investigate the ground state geometry and electronic properties of the channel in vacuum, focusing on their dependence on the side chains of the amino acids. We find that the side chains affect the ground state geometry, while the electrostatic potential of the pore is independent of the side chains. This study is also in preparation for a full, linear scaling DFT study of gA in a lipid bilayer with surrounding water. We demonstrate that linear scaling DFT methods can accurately model the system with reasonable computational cost. Linear scaling DFT allows ab initio calculations with 10 000-100 000 atoms and beyond, and will be an important new tool for biomolecular simulations.