今天的内容是：
GROMACS分子模拟基础实验教程第四篇-定义模拟体系的容器尺寸并加水
更多前序基础文章可以参考：
基础准备4-Ubuntu16版Linux下编译安装Gromacs2020
基础准备5-Linux7.6编译安装Gromacs2018版并行版
我们接着之前的实验文档：
GROMACS分子模拟基础实验教程(3)-检查和理解拓扑文件
4.1 晶胞容器说明
4.2、实操6-editconf定义容器大小
下面开始实际操作：
一、使用editconf模块定义晶胞容器的尺寸
执行：
gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic实操截图如下：
执行后，会把原先的拓扑文件做一个备份：/#topol.top.1
输出的关键文本信息如下：
GROMACS: gmx editconf, version 2020.7Executable: /apps/svr/gromacs/gmx2020/bin/gmxData prefix: /apps/svr/gromacs/gmx2020Working dir: /home/asp/mdtest/demo1Command line:gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubicNote that major changes are planned in future for editconf, to improve usability and utility.Read 1960 atomsVolume: 123.376 nm^3, corresponds to roughly 55500 electronsNo velocities foundsystem size : 3.817 4.234 3.454 (nm)diameter : 5.010 (nm)center : 2.781 2.488 0.017 (nm)box vectors : 5.906 6.845 3.052 (nm)box angles : 90.00 90.00 90.00 (degrees)box volume : 123.38 (nm^3)shift : 0.724 1.017 3.488 (nm)new center : 3.505 3.505 3.505 (nm)new box vectors : 7.010 7.010 7.010 (nm)new box angles : 90.00 90.00 90.00 (degrees)new box volume : 344.48 (nm^3)
4.3、实操7-solvate加入水溶剂
二、使用gmx调用溶剂模块向晶胞容器中填充水
Linux下执行：
gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top实操截图如下：
输出的关键文本信息如下：
GROMACS: gmx solvate, version 2020.7Executable: /apps/svr/gromacs/gmx2020/bin/gmxData prefix: /apps/svr/gromacs/gmx2020Working dir: /home/asp/mdtest/demo1Command line:gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.topReading solute configurationReading solvent configurationInitialising inter-atomic distances...WARNING: Masses and atomic (Van der Waals) radii will be guessedbased on residue and atom names, since they could not bedefinitively assigned from the information in your inputfiles. These guessed numbers might deviate from the massand radius of the atom type. Please check the outputfiles if necessary.NOTE: From version 5.0 gmx solvate uses the Van der Waals radiifrom the source below. This means the results may be differentcompared to previous GROMACS versions.++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++A. Bondivan der Waals Volumes and RadiiJ. Phys. Chem. 68 (1964) pp. 441-451-------- -------- --- Thank You --- -------- --------Generating solvent configurationWill generate new solvent configuration of 4x4x4 boxesSolvent box contains 39252 atoms in 13084 residuesRemoved 5451 solvent atoms due to solvent-solvent overlapRemoved 1869 solvent atoms due to solute-solvent overlapSorting configurationFound 1 molecule type:SOL ( 3 atoms): 10644 residuesGenerated solvent containing 31932 atoms in 10644 residuesWriting generated configuration to 1AKI_solv.groOutput configuration contains 33892 atoms in 10773 residuesVolume : 344.484 (nm^3)Density : 997.935 (g/l)Number of solvent molecules: 10644Processing topologyAdding line for 10644 solvent molecules with resname (SOL) to topology file (topol.top)Back Off! I just backed up topol.top to ./#topol.top.1#
注意新生成的topol.top中[ molecules ]的变化:
或者直接看最后几行的区别：右边新文件多了一行SOL溶剂水分子的数量
下一篇：GROMACS分子模拟基础实验教程(5)-为模拟体系添加离子
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