作为一种计算机模拟手段，分子动力学模拟研究物质之间的相互作用，它在微观尺度上对分子和原子细节进行动态追踪，展现比实验更加迷人的魅力，近年来受到广泛关注。根据研究对象的不同，模拟力场千差万别。在研究生物学现象时，为了让模拟体系更加可靠，不断接近实验体系，需要增大体系的时间尺度和空间尺度。为了满足这样的研究需求，模拟力场从全原子力场转变为粗粒化力场。粗粒化力场的核心思想是将若干个原子当作一个粒子，因而可以极大地减小体系的自由度。然而，使用传统的粗粒化力场仍然无法处理一些较大的体系，比如细胞膜变形的动态过程。一种可行的办法是在粗粒化力场的基础上进行隐式溶剂化处理，隐含体系中大量的水，从而进一步提升模拟速度。 在本论文的第一部分，介绍了我们发展的溶剂不显含的耗散粒子动力学（Im-DPD）力场。为了保证力场的可移植性，我们采用了Martini的四对一映射规则。除了传统的短程排斥力、随机力、耗散力，Im-DPD力场还包含一项长程憎水吸引力，该长程力中有三个待定参数。本文通过溶剂显含的耗散粒子动力学（Ex-DPD）的模拟可直接得到Im-DPD力场的两个参数，通过重现正确的磷脂囊泡结构和磷脂膜刚性来获得第三个参数。根据相似官能团参数接近的原则，我们将磷脂的Im-DPD参数分配给蛋白。通过和Ex-DPD的结果对比（三种典型磷脂膜的结构性质、弹性性质、磷脂翻转自由能、氨基酸侧链跨膜自由能和抗菌肽打孔）验证了这套力场的合理性。隐含体系中的水之后，模拟4000个磷脂的体系速度可以加快50倍左右。 在本论文的第二部分，我们使用隐式溶剂粗粒化方法模拟磷脂（L）和金纳米棒（G）的复合体系，并研究其形貌以及影响因素。通过控制L-G作用强度及L和G的摩尔比，我们得到组装形貌丰富的相图，包括球形囊泡封装金纳米棒、双凹囊泡封装金纳米棒、压扁囊泡封装金纳米棒、环、树枝、富余磷脂的环、富余磷脂的树枝、堆积和涡漩形貌。当L-G作用强度一定时，移除多余的磷脂会诱导复合体系的形貌从孤立的环或树枝状转变为聚集的涡漩或堆积状，反之亦然。随着复合体系从孤立相转变成聚集相，金纳米棒表面的磷脂结构也会从双层膜结构转变成非双层膜结构。

Molecular dynamics simulations employ computer simulation to study the interactions between materials. It can achieve dynamic tracking of microscale molecular or even atomistic details, showing more fascinating charm compared with experiments and thus having been extensively concerned. The force fields used in the simulations are varied according to the different needs of systems investigated. In the process of investigating biological phenomena, longer time scale and larger spatial scale are required, for the sake of more reliable simulation system approaching the experimental system. To cope with this research requirement, the simulated force fields have experienced a leap from the all atom force fields to the coarse-grained force fields. The basic idea of coarse-graining is to divide several atoms into one bead, thus greatly reducing the degrees of freedom of the system. However, for the dynamic process of many systems, such as the shape transition of phospholipid membranes, the coarse-grained method only provides unsatisfactory simulation speed. A solution is to average out the degrees of freedom of the solvent, which can provide a dramatically speedup in simulation efficiency. The first work of this thesis is to develop an implicit-solvent dissipative particle dynamics (Im-DPD) force fields. To guarantee high transplantability, Martini-like four-to-one mapping rule is adopted. Besides traditional short-range repulsive force, dissipative force, and random force, the implicit-solvent DPD forces include additional long-range hydrophobic attractive force with three undetermined parameters. In this work, two parameters are obtained directly from explicit-solvent DPD (Ex-DPD) simulations, whereas the third one is optimized by reproducing correct vesicle structure and membrane bending rigidity. These parameters were assigned to amino acid and polypeptide beads based on their hydrophilicity and hydrophobicity. The rationality of this force fields is demonstrated by comparing membrane's properties with Ex-DPD's results, such as strucure, elasticity, the free energy for phospholipid flip-floping, the free energy for peptide residue entering phospholipid membrane, and antibiotic peptide-induced membrane perforation. After the removal of the solvent for system containing 4000 lipids, a 50-fold increase of simulation speed is achieved. In the second part of this thesis, the assembly behaviors of phospholipids (L) and gold nanorods (G) are studied by using implicit-solvent coarse-grained method. By controlling the molar ratio of L versus G as well as the interaction strength between L and G, a rich phase diagram of assembled morphologies are obtained, it includes adhesion of gold nanorods onto surfaces of vesicular vesicles, gold nanorods encased in erythrocytic vesicles, gold nanorods wrapped by discoid vesicles, rings decorated by extra lipid vesicles, branch decorated by extra lipid vesicles, pure rings, pure branches, rigid stacks, and compact vortexes phases. At a certern L-G interaction strength, removal of excess lipid vesicles gives rise to a morphology transformation from the ring-like or branch-like structure to the vortex-like or stack-like structure and vice-versa. Along with the morphology transformation as well as aggregation of gold nanorods, the phospholipids absorpted by gold nanorods surface change from double-layer structure to single-layer structure.