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教程(二十二)GaussView使用技巧-如何将指定区域原子进行固定

关键词:GaussView 如何将指定区域原子进行固定    发布时间:2020-04-09 00:16:14    点击数:2246

(一)引言:

➢ 在计算时,有时由于某些特殊原因,我们选择不进行全局优化,而选择固定某些原子进行局部优化。固定原子进行局部优化的方法有多种,比如前文介绍的在原子坐标前加“-1”进行固定(教程二十一),也可以通过关键词 opt=readopt 进行固定。但是,在体系较大时,如果想对某一个区域进行固定,上述两个方法就显得比较繁琐。本文将介绍GaussView对指定区域原子进行固定的方法。

(二)操作过程:

1. 复合物
█ 软件版本GaussView 6
█ 本文以掺C氮化硼为底物,二苯并噻吩为吸附物的体系为例(实际体系可能更大),介绍如何使用GaussView对掺C氮化硼进行固定(即固定侧视图中的下半部分)。



俯视图

侧视图



2. 用图标选中需要固定的区域




3. 打开Tools → Atom Groups 面板
█ 第1步:选择Atom Group Class中的Freeze功能;
█ 第2步:光标选择Group ID中的第二行(此时呈黄色);
█ 第3步:选择Group Actions中的Add Selected atoms to “Freeze(Yes)”选项。




█ 操作结束后,可以看到Atom Tags下,第二行就已经把选择的原子都冻结了。




4. 点击OK,然后保存为输入文件,然后查看输入文件内容:

%mem=16GB
%nprocshared=8
%chk=DBT-N-34543.chk
# opt b3lyp/6-31+g(d) guess=read empiricaldispersion=gd3

Title Card Required

0 1
 H               -1    1.84790600   -7.31236800   -0.35293500
 H               -1   -0.65330800   -7.25267200   -0.45615400
 H               -1   -2.91775500   -6.10200800   -0.59875600
 H               -1   -5.17444700   -4.93804400   -0.73778600
 H               -1   -6.68370000   -2.94587600   -0.88834900
 H               -1   -6.79952300   -0.43337600   -0.96923400
 H               -1   -6.93629800    2.07949300   -0.97982300
 H               -1   -5.63341600    4.21769100   -0.93698100
 H               -1   -3.50468900    5.60584500   -0.88543500
 H               -1   -1.36832300    6.98228400   -0.81587300
 H               -1    1.11378500    7.29656100   -0.70034900
 H               -1    3.34889500    6.14177600   -0.59137600
 H               -1    5.59161000    5.00420800   -0.47651200
 H               -1    6.79134200    2.80689700   -0.42105500
 H               -1    6.92792500    0.26867500   -0.39285300
 H               -1    7.04878400   -2.26992300   -0.32874900
 H               -1    6.07665800   -4.57778100   -0.29152400
 H               -1    3.95841400   -5.93800100   -0.33538100
 B               -1   -1.26936900   -0.15315200   -0.84621000
 N               -1    1.62077100   -0.00619300   -0.74762600
 N               -1   -0.60928200    1.13414200   -0.84986200
 B               -1   -1.14494800   -2.65289000   -0.74941200
 B               -1    3.06140400    0.06811100   -0.65853400
 B               -1   -3.37392800   -1.51245600   -0.86919700
 B               -1    3.31277200   -4.93760900   -0.42311000
 B               -1    5.41647800   -3.58547400   -0.37593400
 N               -1   -0.20640500   -6.34434000   -0.49090100
 N               -1    3.97377100   -3.65875400   -0.45824600
 N               -1    6.03844400   -2.30516600   -0.39163100
 N               -1   -2.45433300   -5.20180400   -0.63856100
 N               -1    3.84756300   -1.14872200   -0.58761500
 N               -1    5.91864500    0.21602700   -0.46546100
 N               -1   -4.69589300   -4.04603400   -0.77285500
 N               -1   -2.59058500   -2.72728300   -0.80258200
 N               -1    3.72064000    1.35937800   -0.63697000
 N               -1    5.78296400    2.73724000   -0.48640300
 B               -1    5.03466900    3.94804100   -0.52258500
 B               -1   -5.60687200   -0.37274000   -0.94868200
 B               -1    2.80652800    5.07922100   -0.64049300
 N               -1   -2.71476500   -0.22728900   -0.89857000
 N               -1    1.49269900    2.49935200   -0.75425100
 N               -1    3.59276400    3.87242300   -0.61116200
 N               -1   -4.95566100    0.91024500   -0.95289000
 N               -1   -2.84137800    2.27433200   -0.90850100
 N               -1    1.37139800    5.01004900   -0.72429200
 B               -1   -5.74206700    2.12316800   -0.95888000
 B               -1   -3.63046500    3.49107400   -0.91161200
 B               -1   -1.52241900    4.85744700   -0.85469800
 B               -1    0.58577400    6.22544900   -0.74365200
 N               -1   -5.06845700    3.37703900   -0.93097700
 N               -1   -2.95364800    4.75555900   -0.88708600
 N               -1   -0.83205000    6.12306100   -0.81150100
 C                0   -1.30421800   -0.34182500    2.48781100
 S                0   -0.73063300    2.24583200    2.55431500
 C                0    0.14597100   -0.25667000    2.53470000
 C                0    0.59941900    1.08319100    2.56537600
 C                0    1.96265400    1.39194100    2.58916800
 H                0    2.29880500    2.42503200    2.58881200
 C                0    2.88259300    0.34485500    2.59174500
 H                0    3.94609500    0.56713400    2.59016700
 C                0    2.44919100   -0.99148800    2.57044800
 C                0    1.09124000   -1.29391200    2.53961200
 H                0    3.18091700   -1.79416600    2.55416500
 H                0    0.76241000   -2.32901400    2.50172900
 C                0   -1.91301800    0.93547300    2.48888900
 C                0   -3.30233900    1.08182900    2.43236400
 H                0   -3.75746200    2.06802300    2.41390000
 C                0   -4.09054100   -0.06635300    2.37908600
 C                0   -3.50230800   -1.34243700    2.37987600
 C                0   -2.11899900   -1.48273900    2.43115600
 H                0   -4.13216600   -2.22529400    2.31837400
 H                0   -1.66821300   -2.47131100    2.41002800
 H                0   -5.17086700    0.02935000    2.31749000
 C               -1   -3.49922600    0.98636900   -0.91857000
 C               -1   -1.39442200    2.34953500   -0.87145300
 C               -1   -0.73501300    3.64017700   -0.85774400
 C               -1    0.70566900    3.71323000   -0.78073300
 C               -1    2.93429200    2.57198300   -0.67076300
 C               -1    5.16453500    1.43531800   -0.53265600
 C               -1    0.96075700   -1.29280000   -0.72901600
 C               -1   -0.48324400   -1.36840600   -0.78878200
 C               -1    0.83400300    1.20755400   -0.78443200
 C               -1    1.74615200   -2.51042800   -0.64791000
 C               -1    3.18809600   -2.43442400   -0.57006000
 C               -1    1.08518400   -3.79495700   -0.59670200
 C               -1    1.87618000   -5.01556000   -0.48722800
 C               -1    1.21569500   -6.30210700   -0.43824300
 C               -1   -1.02114400   -5.15869200   -0.59188600
 C               -1   -0.35892100   -3.86801200   -0.64292300
 C               -1   -3.25446100   -4.01429100   -0.74041700
 C               -1   -5.49142700   -2.86810000   -0.86174200
 C               -1   -4.83032200   -1.58375400   -0.90670200
 C               -1    5.29181800   -1.07452300   -0.48459200

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