Otsuka, T;
Taiji, M;
Bowler, DR;
Miyazaki, T;
(2016)
Linear-scaling first-principles molecular dynamics of complex biological systems with the CONQUEST code.
Japanese Journal of Applied Physics
, 55
(11)
, Article 1102B1. 10.7567/JJAP.55.1102B1.
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Abstract
The recent progress of linear-scaling or $\mathcal{O}(N)$ 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 $\mathcal{O}(N)$ 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.
| Type: | Article |
|---|---|
| Title: | Linear-scaling first-principles molecular dynamics of complex biological systems with the CONQUEST code |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.7567/JJAP.55.1102B1 |
| Publisher version: | http://iopscience.iop.org/article/10.7567/JJAP.55.... |
| Language: | English |
| Additional information: | Copyright © 2016 The Japan Society of Applied Physics. This is an author created, uncopyedited version of an article accepted for publication in the Japanese Journal of Applied Physics. The publisher is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at https://doi.org/10.7567/JJAP.55.1102B1 |
| Keywords: | Science & Technology, Physical Sciences, Physics, Applied, Physics, Electronic-structure Calculations, Multisite Local Orbitals, Recent Progress, Efficient, Model |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Physics and Astronomy |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1529627 |
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