**Molecular Dynamics Theory and Development**

**1** 

*2Rikkyo University* 

*Japan* 

*4Ochanomizu University* 

*3National Institute of Health Sciences* 

**Recent Advances in Fragment** 

**Molecular Orbital-Based Molecular** 

Yuto Komeiji1, Yuji Mochizuki2, Tatsuya Nakano3 and Hirotoshi Mori4

Fragment molecular orbital (FMO)-based molecular dynamics simulation (MD), hereafter referred to as "FMO-MD," is an *ab initio* MD method (Komeiji *et al.*, 2003) based on FMO, a highly parallelizable *ab initio* molecular orbital (MO) method (Kitaura *et al.*, 1999). Like any *ab initio* MD method, FMO-MD can simulate molecular phenomena involving electronic structure changes such as polarization, electron transfer, and reaction. In addition, FMO's high parallelizability enables FMO-MD to handle large molecular systems. To date, FMO-MD has been successfully applied to ion-solvent interaction and chemical reactions of organic molecules. In the near future, FMO-MD will be used to handle the dynamics of

In this chapter, various aspects of FMO-MD are reviewed, including methods, applications, and future prospects. We have previously published two reviews of the method (Komeiji *et al.*, 2009b; chapter 6 of Fedorov & Kitaura, 2009), but this chapter includes the latest developments in FMO-MD and describes the most recent applications of this method.

FMO-MD is based on the Born-Oppenheimer approximation, in which the motion of the electrons and that of the nuclei are separated (Fig. 1). In FMO-MD, the electronic state is solved quantum mechanically by FMO using the instantaneous 3D coordinates of the nuclei (**r**) to obtain the energy (*E*) and force (**F**, minus the energy gradient) acting on each nucleus, which are then used to update **r** classical mechanically by MD. In the following subsections, software systems for FMO-MD are described, and then the FMO and MD aspects of the

FMO-MD can be implemented by using a combination of two independent programs, one for FMO and the other for MD. Most of the simulations presented in this article were

**1. Introduction** 

proteins and nucleic acids.

**2. Methodology of FMO-MD** 

**2.1 Software systems for FMO-MD** 

FMO-MD methodology are explained separately.

*1National Institute of Advanced Industrial Science and Technology (AIST)* 

**Dynamics (FMO-MD) Simulations** 
