首先通过wget获取nvt.mdp参数文件 wget http://www.mdtutorials.com/gmx/lysozyme/Files/nvt.mdp 第二步通过grompp连接nvt.mdp, em.gro, topol.top并输出nvt.tpr文件 并通过mdrun 运行 gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr gmx mdrun -deffnm nvt -f 指定mdp参数...
本文翻译自CompChems的文章GROMACS Tutorial: Coarse-Grained Simulations with Martini 3 Force Field 粗粒化模拟与常规的全原子模拟没有本质的区别,(因此本文中一些Gromacs的基本知识会被省略,可以参考另一篇入门文章:GROMACS教程1:Lysozyme),唯一的不同点在于需要先将全原子模型转换成粗粒化模型, 通常的流程如下(下面...
Lysozyme in Water: The intent of this tutorial is to give new users a basic introduction into the tools used to prepare, run, and perform simple analysis on a "typical" system with GROMACS. KALP15 in DPPC: This tutorial is more advanced, and is designed for more experienced users who wan...
1、GROMACS TutorialLysozyme in WaterJusti n LemkulDepartme nt of Biochemistry, Virgi nia TechusingThis example will guide a new user through the process of sett ing up a simulatio n system containing a protein (lysozyme) in a box of water, with ions. Each step will contain an expla ...
GROMACS Tutorial Lysozyme in Water Justin Lemkul Department of Biochemistry, Virginia Tech This example will guide a new user through the process of setting up a simulation system containing a protein (lysozyme) in a box of water, with ions. Each step will contain an explanation of input and ...
GROMACS Introductory Tutorial 热度: GROMACS Tutorial Lysozyme in Water 热度: GROMACS用户手册 热度: GROMACSTutorial StepOne:PreparetheProteinTopology Wemustdownloadtheproteinstructurefilewewillbeworkingwith.Forthistutorial,wewillutilizeT4lysozymeL99A/M102Q(PDBcode3HTB).GototheRCSBwebsiteanddownloadthePDBtextfor...
进行蛋白质模拟的入门教程 PAGE 一个使用gromacs进行蛋白质模拟的入门教程 GROMACS Tutorial Lysozyme in Water Justin Lemkul Department of Biochemistry, Virginia Tech This example will guide a new user through the process of setting up a simulation system containing a protein (lysozyme) in a box of ...
This tutorial assumes you are using a GROMACS version in the series. GROMACS Tutorial Step One: Prepare the Topology We must download the protein structure file we will be working with. For this tutorial, we will utilize hen egg white lysozyme (PDB code 1AKI). Go to the RCSB website and...
Lysozyme in Water:The intent of this tutorial is to give new users a basic introduction into the tools used to prepare, run, and perform simple analysis on a "typical" system with GROMACS. 水中溶菌酶: 本教程的目的是向新用户介绍用于准备、运行和使用 GROMACS 对“经典的”系统进行简单分析的工具...
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....