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首先，让高斯自动生成一个单体的自由度。
输入文件如下（直接从你给的输入文件里取出一个单体了）：
%chk=Monomer_1.chk
# opt pm6
Monomer 1
0 1
N -13.12265900 2.32453500 4.83503600
N -11.42495800 -3.34386700 -4.92760000
C -11.47230800 -1.91905300 -4.97797700
C -11.25892800 -4.12583700 -6.22176200
C -12.43836000 -3.83996100 -7.16885000
C -13.16968100 3.06622700 3.61661400
C -13.29029800 3.06172700 6.15276400
C -14.69821700 3.67793500 6.24625700
C -15.79227200 2.62263900 6.35931000
H -15.62625700 1.95354200 7.21240400
H -16.77584200 3.08761700 6.49123600
H -15.84512000 1.99627100 5.46139900
H -14.72917200 4.34802800 7.12956900
H -14.88719700 4.33721500 5.37226100
H -13.16959300 2.29290500 6.96779400
C -12.17584200 4.11735100 6.28264500
H -11.20221900 3.69397300 5.92638200
H -12.37564100 4.97287300 5.60315100
C -12.02375200 4.60022600 7.72007900
H -11.78401600 3.77815000 8.40464300
H -12.93770400 5.08137500 8.08809000
H -11.21456800 5.33676200 7.79777500
C -13.76194300 -4.37557200 -6.63524700
H -14.56981300 -4.22139600 -7.35969200
H -14.05756900 -3.87586300 -5.70573500
H -13.71018000 -5.45068100 -6.42383300
H -12.51528500 -2.75067100 -7.37066400
H -12.21598000 -4.30271000 -8.15242200
H -11.26595300 -5.21722400 -5.94013800
C -9.89572900 -3.77752000 -6.84856800
H -9.90085200 -2.73012200 -7.21544000
H -9.10506600 -3.82891600 -6.06584900
C -9.53014600 -4.72965600 -7.98186200
H -8.50528500 -4.52355400 -8.33608900
H -10.20416000 -4.62954900 -8.83919900
H -9.55148900 -5.77674900 -7.65702100
O -13.41716300 4.25681200 3.62099800
C -12.89722600 2.31494100 2.35493600
C -12.75376900 0.89444900 2.37839900
C -12.80476900 0.17576000 3.61157900
C -12.94985600 0.91107000 4.89977900
O -12.91230300 0.35165500 5.98091500
C -12.78748300 3.00685800 1.17172900
H -12.89819700 4.10269100 1.17462400
C -12.52861000 2.32896100 -0.06109300
C -12.35402000 3.06623100 -1.30488100
C -12.37377900 4.48630100 -1.32931100
H -12.51305500 5.04267900 -0.38900900
C -12.20272300 5.18101400 -2.50966500
H -12.21203400 6.27160300 -2.51621600
C -12.00475900 4.47904100 -3.72021600
H -11.87919000 5.03640000 -4.64817800
C -11.96962700 3.09899100 -3.71952100
H -11.80763700 2.55822400 -4.65585500
C -12.13563000 2.36366700 -2.51453200
C -12.06296200 0.90952000 -2.50507500
C -11.82877900 0.17381100 -3.70918800
H -11.71313000 0.71777400 -4.65861400
C -11.73616100 -1.19861100 -3.69869200
O -11.28993000 -1.32911600 -6.02663600
C -11.87686100 -1.92369500 -2.47675400
C -11.78108600 -3.34843900 -2.45886100
C -11.56892900 -4.10040200 -3.72700700
O -11.50391000 -5.31609900 -3.76373400
C -11.88671100 -4.04031500 -1.27457800
H -11.81011100 -5.13797900 -1.27789300
C -12.09250200 -3.35719900 -0.03512900
C -12.17261800 -4.08822500 1.22166700
C -12.02942300 -5.50176000 1.26061800
H -11.84964000 -6.04760000 0.32990300
C -12.10916100 -6.19083900 2.45419100
H -11.99817500 -7.27528400 2.47493000
C -12.33585300 -5.49094700 3.66094000
H -12.40445100 -6.04541500 4.59657700
C -12.46975300 -4.11697300 3.64778000
H -12.63986700 -3.57740700 4.58301700
C -12.38710900 -3.38582900 2.43166900
C -12.50983100 -1.93484000 2.41501500
C -12.69219900 -1.19480000 3.62590900
H -12.73153000 -1.73248400 4.58452900
C -12.42727400 -1.23890000 1.19918200
C -12.54463700 0.19402500 1.17178400
C -12.43233400 0.92858400 -0.05903200
C -12.20045800 0.20971100 -1.29645700
C -12.10164400 -1.22452800 -1.27200500
C -12.21047900 -1.95853200 -0.04062000
然后提交。优化了一步之后就可以杀掉了。在输出文件中可以看到如下内容：
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Initialization pass.
----------------------------
! Initial Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,6) 1.4272 estimate D2E/DX2 !
! R2 R(1,7) 1.5192 estimate D2E/DX2 !
! R3 R(1,41) 1.4255 estimate D2E/DX2 !
......
! D268 D(82,83,84,85) 0.6703 estimate D2E/DX2 !
! D269 D(56,84,85,61) -0.5604 estimate D2E/DX2 !
! D270 D(56,84,85,86) 178.6331 estimate D2E/DX2 !
! D271 D(83,84,85,61) 179.9578 estimate D2E/DX2 !
! D272 D(83,84,85,86) -0.8488 estimate D2E/DX2 !
! D273 D(61,85,86,67) 0.0929 estimate D2E/DX2 !
! D274 D(61,85,86,81) 179.3492 estimate D2E/DX2 !
! D275 D(84,85,86,67) -179.1008 estimate D2E/DX2 !
! D276 D(84,85,86,81) 0.1555 estimate D2E/DX2 !
--------------------------------------------------------------------------------
这些就是你要的自由度！之后把它们冻结即可。例如：
上面写的R(1,6)，你输入文件里冻结是这么写：B 1 6 F
上面写的D(84,85,86,81)，你输入文件里冻结是这么写：D 84 85 86 81 F
你可以写个脚本，或者用文本编辑器的替换功能，或者什么别的方法，批量替换一下。
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发表于 Post on 2021-2-3 17:50:09
楼主 Author