表面活性剂分子自组装体系中的分子动力学模拟_张鲁格研讨.pptxVIP

表面活性剂分子自组装体系中的分子动力学模拟 汇报人：张鲁格 2015年12月30日 优化后构型MS建模 2 加离子 4 加盒子并填充溶剂 3 提交分子PDB至ATB 1 一、构建模型上传至ATB Materials Studio GaussView 注册登录 关注FAQ 提交前可搜索一下这个分子存不存在，存在可直接下载pdb itp文件使用，搜索时有原子顺序要求，例如：CHNO CHON 提交注意电荷 先用MS摆出来一层 在某一个方向上加倍利用MS 可以利用命令 genconf 注意 By default the ATB only generates a complete topology for molecules containing 40 atoms. How can I generate a reliable topology for a larger molecule? By default the ATB only generates a complete topology (based on optimization at the B3LYP/6-31G* level of theory + Hessian) for molecules containing 40 atoms when submitted by an academic user. Molecules up to 50 atoms are optimization at the B3LYP/6-31G* level of theory but no Hessian is generated. The ATB will still generate an initial template for a larger molecules ( 500 atoms) based on semi-empirical methods. This template contains all atom-type information and bonded parameters. In some cases, initial estimates of the charges may also be given. Before use, these templates need to be examined and where necessary edited manually. In order to obtain more precise parameters, a larger molecule can be broken into smaller fragments and the parameters from these fragments can be used to complete the template of the larger molecule By default the ATB only generates a complete topology (based on optimization at the B3LYP/6-31G* level of theory + Hessian) for molecules containing 40 atoms when submitted by an academic user. Pdb文件分子含原子数 40，优化用B3LYP/6-31G*+Hessian矩阵 Molecules up to 50 atoms are optimization at the B3LYP/6-31G* level of theory but no Hessian is generated. Pdb文件分子含原子数 40 50，优化用B3LYP/6-31G* The ATB will still generate an initial template for a larger molecules ( 500 atoms) based on semi-empirical methods. This template contains all atom-type information and bonded parameters. In some cases, initial estimates of the charges may also be given. Before use, these templates need to be examined and where necessary edited manually. Pdb文件分子含原子数 50 500 时，用半经验方法，电荷