Simplified method for calculating the energy of weakly interacting fragments

Harris, J.

doi:10.1103/physrevb.31.1770

Cited by 968 publications

(543 citation statements)

References 24 publications

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“…Figure 1 shows the R L dependence of the total energy for a DNA system, which is the target of the MD study shown in the next section. Here, the total energy using the Harris-Foulkes functional obtained by non-self-consistent (NSC) technique 23,24) is also presented together with the DFT total energy using the self-consistentfield (SCF) charge density. This graph shows that the total energy converges as the cutoff applied to the L matrix is increased, regardless of self-consistency.…”

Section: Introductionmentioning

confidence: 99%

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

Otsuka¹,

Taiji²,

Bowler

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.

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Section: Introductionmentioning

confidence: 99%

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

Otsuka¹,

Taiji²,

Bowler

et al. 2016

Jpn. J. Appl. Phys.

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“…11 The reaction energies, activation energies and ab initio molecular dynamics (MD) of the system were calculated in a 3D periodic model utilizing VASP. 12 In these calculations, the electronic energies were approximated using the projected augmented wave (PAW) 13 description of atomic cores and the functional of Perdew, Burke and Ernzerhof (PBE). 14 The plane wave cutoff energy was 400 eV.…”

Section: Computational Detailsmentioning

confidence: 99%

Multiple Proton Diffusion and Film Densification in Atomic Layer Deposition Modeled by Density Functional Theory

Shirazi

Elliott

2013

Chem. Mater.

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“…Fireball [1,15,16] is a first-principles TBMD simulation technique based on a selfconsistent version of the Harris-Foulkes [17,18] functional. The energy functional is written as:…”

Section: Ab Initio Tight Binding: Fireballmentioning

confidence: 99%

Multicenter approach to the exchange-correlation interactions inab initiotight-binding methods

et al. 2005

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A new approximate method to calculate exchange-correlation contributions in the framework of first-principles tight-binding molecular dynamics methods has been developed. In the proposed scheme on-site (off-site) exchange-correlation matrix elements are expressed as a one-center (twocenter) term plus a correction due to the rest of the atoms. The one-center (two-center) term is evaluated directly, while the correction is calculated using a variation of the Sankey-Niklewski[1] approach generalized for arbitrary atomic-like basis sets. The proposed scheme for exchangecorrelation part permits the accurate and computationally efficient calculation of corresponding tight-binding matrices and atomic forces for complex systems. We calculate bulk properties of selected transition (W,Pd), noble (Au) or simple (Al) metals, a semiconductor (Si) and the transition metal oxide TiO 2 with the new method to demonstrate its flexibility and good accuracy.

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Simplified method for calculating the energy of weakly interacting fragments

Cited by 968 publications

References 24 publications

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

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

Multiple Proton Diffusion and Film Densification in Atomic Layer Deposition Modeled by Density Functional Theory

Multicenter approach to the exchange-correlation interactions inab initiotight-binding methods

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