Application of order-N first-principles DFT calculations with temperature controlled molecular dynamics to biomolecular system

Abstract

We have performed large-scale first-principle molecular dynamics (FPMD) calculations of the large-scale hydrated DNA system as an example of large-scale biomolecular system, using order-N density functional theory (DFT) code CONQUEST, which is based on the combined method with an order-N DFT method using the density matrix minimization scheme and the extended Lagrangian Born-Oppenheimer molecular dynamics (XL-BOMD) scheme. Our large-scale FPMD calculations by CONQUEST show stable FPMD simulation and good energy conservation in NVE ensemble. We also show temperature controlled MD simulations such as velocity scaling, stochastic velocity scaling, and Nosé-Hoover chain methods. Our protocols using velocity scaling, stochastic velocity rescaling, and Nosé-Hoover chain methods are very effective for temperature control in early stage of order-N FPMD simulations. Our order-N FPMD simulation would be able to realize the large-scale biomolecular simulations.