mod=viewthread&tid=29955&fromuid=9594(出处: 计算化学公社) GROMACS Tutorial 1-Lysozyme in Waterhttp://www.mdtutorials.com/gmx/lysozyme/index.html
nsteps=5000;Maximumnumber of(minimization)steps to perform nstenergy=1;Writeenergies to disk every nstenergy steps energygrps=System;Whichenergygroup(s)to write to disk;Parametersdescribing how to find the neighbors of each atom and how to calculate the interactions nstlist=1;Frequencyto update th...
Tutorial 1: Lysozyme in Water Tutorial 2: KALP15 in DPPC Tutorial 3: Umbrella Sampling Tutorial 4: Biphasic Systems Tutorial 5: Protein-Ligand Complex Tutorial 6: Free Energy of Solvation Tutorial 7: Virtual Sites These tutorials are designed as introductory material into using the GROMACS ...
因为自己在学习gromacs的时候是在油管上看的视频,但基本都是gromacs tutorial里的水中的溶菌酶这个第一个教程,所以想着把蛋白质配体复合物的模拟做个记录,可能会有不严谨或者错误的地方,多多包涵。如果能稍微帮到自学gromacs的人就太好了。知识 野生技能协会 蛋白质 分子动力学模拟 ...
gromacs tutorial gromacstutorial step one: prepare proteintopology we must download proteinstructure file we tutorial,we utilizet4 lysozyme l99a/m102q (pdb code 3htb). go rcsbwebsite pdbtext crystalstructure. once you have downloaded structure,you can visualize viewingprogram vmd,chimera, pymol, ...
GROMACS 教程 1 GROMACS Introductory Tutorial Gromacs ver 4.0 Author: John E. Kerrigan, Ph.D. Associate Director, Bioinformatics The Cancer Institute of NJ 195 Little Albany Street New Brunswick, NJ 08903 Phone: (732) 235-4473 Fax: (732) 235-6267 Email: kerrigje@umdnj.edu 翻译:梁(leunglm@...
GROMACS Tutorial Step One: Prepare the Protein Topology We must download the protein structure file we will be working with. For this tutorial, we will utilize T4 lysozyme L99A/M102Q (PDB code 3HTB). Go to theRCSBwebsite and download the PDB text for the crystal structure....
Umbrella Sampling:Also somewhat advanced, this tutorial is intended for users who wish to learn to use umbrella sampling to calculate the potential of mean force (PMF) along a single, linear degree of freedom. 雨伞取样: 也有些高级,这个教程是为用户那些希望学习使用雨伞取样,以计算单一的,线性的自...
Tutorial目的:分析Lysozyme 在水中的状态 模拟方法:分子动力学(Molecular Dynamics,MD) 模拟过程: 下载PDB文件并生成拓扑 构建模拟空间并溶剂化 加入离子 能量最小化 系综平衡(NVT,NPT) MD模拟 分析 1.下载PDB文件并生成拓扑: 1.1下载PDB文件 使用wget
1、准备模拟体系:你需要构建或获取模拟所需的分子结构文件,如PDB或GRO文件。 2、设置模拟参数:通过编辑MDP文件,你可以设置模拟的各种参数,如温度、压力、模拟时间等。 3、运行模拟:使用Gromacs命令行工具,你可以启动模拟并监控其进度。 4、分析模拟结果:模拟完成后,你可以使用Gromacs提供的工具对模拟结果进行分析,如...