显式溶剂化（SOLVATOR） #
隐式溶剂化模型是模拟溶剂化效应的一种有效方法。然而，若溶质与溶剂强烈相互作用或溶质作为反应物时，则需对溶剂分子进行显式处理。SOLVATOR 算法能够全自动地包含显式溶剂分子并生成溶剂化壳层。通过 %solvator 模块可轻松调用该算法。
! XTB ALPB(WATER)
%solvator
nsolv 30
end
* XYZFILE 0 1 solute.xyz
注
在没有任何进一步输入的情况下，SOLVATOR 可以使用 ALPB 提供的所有溶剂。然而，也可以通过输入定义自定义溶剂。
如果要添加大量溶剂分子，可以使用 SOLVATOR 中的随机模式，以牺牲准确性为代价大幅加快该过程。
! XTB ALPB(WATER)
%SOLVATOR
NSOLV 100
CLUSTERMODE STOCHASTIC
END
*XYZFILE 0 1 solute.xyz
示例 1：尿素的显式溶剂化 #
例如，我们将用 30 个水分子溶剂化一个尿素分子。为此，我们可以使用上面显示的输入，相应的输出将如下所示：
*****************
* ORCA Solvator *
*****************
Solvent chosen: WATER
Solvent radius: .... 1.69 Angs
Solvent max dimensions (x,y,z): .... 2.73, 2.32, 1.52 Angs
Number of solvent molecules to be added: .... 30 molecules
Method used to add the solvent: .... docking
Number of atoms of solvent molecule: .... 3 atoms
Coordinates of solvent in Angstroem:
O -0.000006 0.397814 -0.000000
H 0.763472 -0.198901 0.000000
H -0.763466 -0.198913 0.000000
Solute radius: .... 2.93 Angs
Ellipsoid potential radii: .... 6.33, 5.88, 4.58 Angs
Adding solvent molecules to the solute ....
Iter Energy Einter dE Time
(Eh) (kcal/mol) (kcal/mol) (min)
-------------------------------------------------------
1 -19.210306 -4.659502 -4.659502 0.21
2 -24.302552 -4.533387 0.126115 0.25
3 -29.394688 -4.464434 0.068952 0.29
[...]
24 -136.308378 -1.936280 4.656513 5.53
25 -141.398670 -3.272224 -1.335945 6.09
26 -146.487932 -2.627486 0.644738 6.47
Wall size increased by factor 1.05.
27 -151.580491 -4.663392 -2.035905 7.87
28 -156.682343 -4.840764 -0.177372 9.33
29 -161.768524 -0.720711 4.120053 8.96
30 -166.856255 -1.699958 -0.979247 10.30
Final radius after microsolvation: .... 5.55 Angs
Time needed for microsolvation : .... 5511.52 s
Final structured saved to : basename.solvator.xyz
****ORCA-SOLVATOR TERMINATED NORMALLY****
由此，我们可以观察到水分子的逐步添加、它们各自的相互作用能以及配位时的整体能量变化。溶剂化尿素分子的结构存储在 basename.solvator.xyz 文件中，团簇的生长过程如下所示：
结构示例 1 #
尿素
8
H 2.01822 0.20187 -0.06397
H 0.83499 1.40748 -0.41061
H -1.39434 0.89498 -0.21940
H -1.88388 -0.75647 -0.13275
O 0.40675 -1.67285 0.11342
C 0.11861 -0.48803 -0.06584
N 1.05605 0.49217 -0.06005
N -1.15640 -0.07915 -0.28146
示例 2：定制溶剂 - 氦液滴 #
SOLVATOR 不受限于预定义的溶剂。您可以通过 %SOLVATOR 块轻松定义任何自定义溶剂。在本例中，我们将使用 STOCHASTIC 和 DROPLET 模式，用 2000 个氦原子对倍半硅氧烷进行球形溶剂化。在这种情况下，我们的自定义溶剂是在 he.xyz 文件中定义的中性单重态氦原子。电荷和多重性通过 .xyz 文件中的第二行给出。
2
0 1
He 0 0 0
我们现在运行 SOLVATOR，并在我们的倍半硅氧烷分子周围获得一个球形氦液滴。
!XTB
%SOLVATOR
SOLVENTFILE "he.xyz"
NSOLV 2000
CLUSTERMODE STOCHASTIC
DROPLET true
END
* XYZFILE 0 1 solute.xyz
图：围绕一个倍半硅氧烷分子的 2000 个氦原子组成的球形氦液滴。#
结构示例 2 #
倍半硅氧烷
100
Si 2.30883927191187021677 -1.51404107261898013270 -0.06479458802821000396
Si 0.69844495028425856997 2.53054881818156962581 -0.57025875838537964935
Si 1.76968132551996903956 0.88645731306134989413 1.81815072089804852240
Si 1.24023679693334010210 0.12887051433739010742 -2.45462644723449940898
O 1.47797606920943969122 2.09710588445933909796 0.78327428664550924342
O 2.47037162112476949005 -0.36267740860083069743 1.06318958760345028125
O 2.14724279926403971430 -0.84019824205737059231 -1.52811718998416923299
O 1.17449611044826007777 1.61711183569708993879 -1.81868142591142012421
O 0.39950516912156014415 0.41014517960417962161 2.53909316241434979133
O 1.03577796006599931466 -2.45939073017393816656 0.26658822054469016871
C 3.86064736032040034530 -2.60084865441333024094 -0.09415481382276005839
C 1.14364000674242949351 4.33130288798302132136 -0.95831926241946008282
C 2.95427276296586960314 1.52116262557503967301 3.14908160016116855928
C 2.06043263801967002635 0.24730786165735027526 -4.15902291357893094670
C 3.90575117563901885731 -3.65841588533059125510 1.01113071648778030109
C 1.03633523105185809676 4.69271580225670970066 -2.44175622400742931006
C 2.42612388212526886022 2.75762877421782803822 3.87739875337951023226
C 2.76895479629271035193 -1.03630441656062011191 -4.59817790597404041364
C 3.99617575306170946803 -3.03554304523522056058 2.39737038341486030646
C -0.38978418583185003854 4.56868838311114000561 -2.95899800040501936849
C 3.40223083440897999807 3.25170654911326062475 4.93973454914741871846
C 1.79904320713196952397 -2.19849925304276050397 -4.75739565686958876256
Si -2.16923648489345977097 1.45426783117045044236 -0.01870960599793020790
Si -0.56318192368503949830 -2.58406051784629031687 0.49418191599628003008
Si -1.63152308951002988913 -0.93828528229811991590 -1.90091815923119988874
Si -1.09893107745471896308 -0.18602740921880953073 2.37739116950383966298
O -1.34685273353240986260 -2.13973745660979997041 -0.85332000914464001262
O -2.33456025887852014478 0.32000944971483041845 -1.16296686079512978651
O -2.00281184230103015409 0.77767883065566023593 1.44192675840557971156
O -1.03318807002326851219 -1.67816481400793904299 1.75111237908015970888
O -0.25591078342145984204 -0.47104763472030986016 -2.61742643815765951842
O -0.90165733572753015146 2.40762179951717092408 -0.34545383340373003733
C -3.73428050087115925848 2.51603829101419851355 -0.01815659898138005657
C -1.01235827566696867663 -4.38784603836863862369 0.86651868482533955795
C -2.80604844640132977673 -1.59380669992410939351 -3.23072457802342949407
C -1.92219349146365003911 -0.29101512884843022677 4.08107501501395031340
C -4.01896736325925019173 3.15358491116559047640 -1.37854494362718993372
C -0.96828017732090965186 -4.75078626933027869939 2.35290323022157021882
C -2.28944557534834869372 -2.86499709299084015512 -3.90555810015316007267
C -2.63016186476952018580 0.99701470478872022962 4.50870889568977872841
C -5.29465505813576875482 3.98863268133149162509 -1.36009570325191009310
C 0.43400029910372006636 -4.62639632611979045862 2.93113716048616979037
C -3.26303206554563995923 -3.38698577510639875499 -4.95678581013346875039
C -1.65879639885883878314 2.15844255245909044660 4.66558459805101932716
H 3.91951010594626980676 -3.10369193013083144450 -1.05973816979330970334
H 4.75013834211284891040 -1.97537461313113049677 -0.01669722396988995369
H 0.50054673213437972379 5.00161909257629133663 -0.38768802597859025605
H 2.16371909638209958260 4.52455437533658066940 -0.62639764452651036652
H 3.14542544271343915696 0.73649492147874962011 3.88167628963121913444
H 3.91736932797826975516 1.76343870330954977099 2.69946537333993008545
H 1.31470770815672022280 0.50997254094894017840 -4.90954460832408035031
H 2.78771120244437087266 1.05905880843276056780 -4.14858700990401718656
H 3.00534986598125808399 -4.26938181753094614379 0.94907211175572059325
H 4.76954135253091848767 -4.30990703001076802536 0.85218243687316996837
H 1.38666197667096047219 5.71820642646272947474 -2.58893781604851058731
H 1.68322554092942966442 4.02803417397333074490 -3.01448664696216894754
H 2.24529627004391851841 3.54810008489985984070 3.14851734744065980820
H 1.47103305153703978192 2.51523697374575938568 4.34312230329484982860
H 3.28025904039187032879 -0.85902566957414994153 -5.54847977452326901471
H 3.52024789644420854628 -1.29657705457920746639 -3.85253639854650931085
H 3.14668902674270967168 -2.38151877517681098695 2.56756735695418880638
H 4.00711771561967999844 -3.80743850933508198864 3.16405351573453952341
H 4.90391151558519844400 -2.44338553454369744600 2.48795323727609973830
H -1.05324373529086856571 5.22214434287834716741 -2.39667419157567884724
H -0.44200202603668981016 4.84521860375389046283 -4.01000508779899966783
H -0.73701094612906004055 3.54566058125262006939 -2.84625863873755013955
H 4.35534625093372707028 3.51721477088752942919 4.48791970564398479127
H 3.00657477635410019801 4.12858427786754766942 5.44703648328616019114
H 3.58131708538499937688 2.47712734176321003332 5.68211170546796928704
H 1.03844542603209943898 -1.95635206821307017222 -5.49622938457011755986
H 2.32358818936812072664 -3.09454422193371092575 -5.08274073080039912043
H 1.30688236711312022464 -2.40240917758488015110 -3.81083588856759947205
H -4.59223453559549987801 1.90833280028286011998 0.27062566445760011247
H -3.64938883216220988359 3.30502599627088056167 0.72956950004708975843
H -2.01598654557988021807 -4.58643944548276127904 0.49028182462367042582
H -0.34183817421683959648 -5.05453229314074103939 0.32361826110324021233
H -3.78165341186373016313 -1.80188256932753954054 -2.79109577346592052649
H -2.96783654511175898350 -0.83203933706014954197 -3.99365066659321898968
H -2.65051356366059964742 -1.10204911215061041041 4.07548184529990020764
H -1.17845880359745991406 -0.54880046191694031865 4.83545608005379978778
H -3.17425636671041999648 3.78197656898877099252 -1.66011213965578030560
H -4.10692092972908895376 2.36599151951094821555 -2.12723450018604065548
H -1.63934897095727949434 -4.08680248081823105366 2.89789727201267988121
H -1.32445903563647049417 -5.77641257499842097900 2.48397765013837013015
H -1.32689939382206967267 -2.65448661718140055399 -4.37123161520532033109
H -2.12644275071908905872 -3.62858778509852974992 -3.14480528099144907017
H -3.37716247278667047738 1.25474422738565971613 3.75776950622156791226
H -3.14626184984560808289 0.82641495329852054930 5.45761245326638899655
H -5.21798740459044019246 4.78539784652138067145 -0.62389997330403046405
H -5.47423288763323778738 4.43751329567928198827 -2.33428761593805722541
H -6.15154417304282752355 3.36977611319346692653 -1.10419104363117792644
H 0.78936333102788935889 -3.60641984220516942372 2.82136714407547994909
H 0.43857927461324219820 -4.88989719753061091723 3.98666481754406865079
H 1.12048236632775966015 -5.28809174614212196275 2.40800635183417766072
H -3.42531384075182909754 -2.64005312060207009139 -5.73034451244428932881
H -2.87535577178886736505 -4.28811600615014931748 -5.42588319013786701817
H -4.22334594297450838241 -3.62187340364976950724 -4.50377181308966800799
H -1.16165677135020972699 2.35565262654516871521 3.72022806433342889676
H -2.18360718306651824250 3.05749725542114125787 4.98250872245835818575
H -0.90240043070232012212 1.92008284489281999541 5.41019438066246038943