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Dear Tian,
We know that the Interacting quantum atom (IQA) could be used to perform energy decomposition analysis (EDA). AIMAll software is a suitable choice to perform IQA calculations. In the AIMAll output, the sum of V_nn(A,B), V_en(A,B), V_ne(A,B), and V_ee_Coulomb(A,B) is related to the stabilizing electrostatic interaction, while V_ee_XC(A,B) represents the stabilizing orbital interaction. Could you please let me know how the destabilizing Pauli repulsion should be evaluated using AIMAll output? In other words, which term among the AIMAll outputs should be attributed to the Pauli repulsion?
Best regards,
Saeed
Dear Tian,
I tried to download DOI: 10.1002/anie.202504895 and DOI: 10.1016/B978-0-12-821978-2.00076-3, but unfortunately, our university does not support these publishers.
Could you please send me a copy of these articles through my Email or RG?
In advance, please accept my deepest gratitude, and excuse me for burdening you with such a request.
Best regards,
Saeed
Your kind attention, together with introducing highly valuable references, is deeply appreciated.
Saeed
Dear Tian,
It is well known that, in the some case of molecular systems, QTAIM is not able to correctly show the bond path and BCP regarding an interaction between two sites. That is, while there is an interaction between atoms A and B, QTAIM analysis does not show corresponding bond path and BCP between A and B. On the other hand, in such cases, IGM is nicely able to provide corresponding spike regarding interaction between A and B, resolving the QTAIM drawback.
Please, if possible, introduce me a decisive and valuable reference for such cases so that I can cite that in my manuscript (while I am sure such references are present on my PC, I could not find them!).
Best regards,
Saeed
Dear Tian,
OK. Many thanks for your comments, and please excuse me for taking up your valuable time.
Cheers,
Saeed
Dear Tian,
As you know better than me, when a metadynamic-based conformer sampling is performed by "CREST"; e.g. using:
crest input.xyz --nci --gfn 2 --uhf 0 --chrg 0 --mdlen 50 --tstep 1 --shake 2 --ewin 12 --alpb water
four different energetics files namely ensemble_energies.log, crest_conformers.xyz, crest_rotamers.xyz, and crest.energies are generated. Please let me know which of these files should be considered to extract the most accurate and reliable energy values. In other words, which of these files should be considered to perform subsequent DFT calculations on the most stable conformers?
For a given run, I have included the contents of these files:
File: crest.energies:
1 0.000
2 0.015
3 0.035
4 0.022
5 0.037
6 0.038
7 0.042
8 0.051
9 0.059
10 0.081
11 0.083
12 0.087
13 0.089
14 0.089
15 0.090
16 0.093
17 0.093
18 0.094
19 0.097
20 0.074
21 0.099
22 0.101
23 0.113
24 0.118
25 0.134
26 0.136
27 0.096
28 0.143
29 0.152
30 0.153
31 0.168
32 0.184
33 0.186
34 0.186
35 0.170
36 0.218
37 0.239
38 0.242
39 0.250
40 0.264
41 0.266
42 0.224
43 0.247
44 0.263
45 0.301
46 0.310
47 0.346
48 0.366
49 0.372
50 0.380
51 0.404
52 0.405
53 0.423
54 0.459
File: crest_conformers.xyz
15
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O 1.6600255851 1.9098464663 -0.1330027990
H 1.9782353726 1.0562772195 0.3432186382
H 2.3097028554 -2.2756032887 -1.2748485652
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H 2.4435010243 2.4746918661 -0.1252431801
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H 3.3081332310 0.8258495784 0.2192925030
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H 2.2054907806 -0.0217790098 -2.6572108642
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H 2.2718772486 -1.5126049123 2.1392584396
H -3.2963189235 2.0721624038 0.6313661464
15
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Rb -0.1199746197 -0.0030183789 -0.0839353174
O 2.2336011210 0.9107763382 0.5415086313
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O -2.5025881542 -1.9690474229 -0.3405960878
H -2.6672363328 -2.6965558420 0.2730305874
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H 1.8071002105 -0.4377395304 1.2203576651
H 2.5763314375 0.2061283543 -2.3813599886
O 1.7647800057 0.1044487884 -1.8674933446
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H 2.0354560223 0.4389907455 -0.9306238969
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H 2.0746577633 -1.6260337783 2.2009389495
H -2.0844024793 3.1988558573 0.5283173050
15
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Rb -0.1358796852 0.0388026492 -0.0518895432
O 2.2655233633 0.7944356232 0.6255520257
H -2.3022827859 -3.0118259902 0.0330863767
O -2.4101530734 -2.1039693233 -0.2777897741
H -3.2893606069 -2.0793561728 -0.6774215171
H 3.2258114745 0.8013180981 0.6961360236
O 1.6854262292 0.4431811191 -1.8659950179
H 2.0005571568 0.6003248731 -0.8967112392
H 2.1782311447 -2.0603352555 1.6695510939
O 1.4521189741 -1.5846827645 1.2462841341
H -2.1065055775 3.2019686539 0.6139049723
H 1.8577108408 -0.6663218025 1.0370528685
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H -3.2729010509 2.2074362120 0.6173143963
15
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Rb -0.1148320731 -0.0026904250 0.0320483334
O 2.2963260498 -0.3308246338 0.9620099221
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O -2.4756174656 -0.9093675134 1.9124311528
H -2.3993319962 -1.4687320453 2.6959000707
H 3.2587182571 -0.3570069811 0.9763405456
O 1.5937390938 1.9554357645 -0.0234391447
H 1.9574447777 1.0806969354 0.3756512847
H 2.2624578500 -2.2042015424 -1.4182054387
O 1.5272895158 -1.6513810519 -1.1235292674
H -2.8915030859 0.4257616844 -2.4864147149
H 1.9141588760 -1.1603708594 -0.3056865642
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H 2.3509999183 2.5533112561 0.0213463818
H -2.5999928987 1.8666592731 -2.0531752279
15
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Rb -0.1174061372 0.0178107721 0.0612573120
O 2.2837083654 -0.7665069114 0.6687741558
H -3.4158776699 -1.1352794454 1.6753155271
O -2.4621016022 -1.1899094696 1.8204934962
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15
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15
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15
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15
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H -3.1492612936 -2.1160300236 -0.7797764625
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H 1.9027685429 0.2306523489 -1.1721502103
H 2.3495016286 -1.1956870281 2.3131448152
O 1.6033522035 -0.9912600006 1.7348294131
H -3.2730202975 2.0392784107 0.6153608583
H 1.9676481955 -0.2288112429 1.1432251364
O -2.4130175053 1.8942412095 1.0314174987
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15
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H -2.3854340436 -0.7534255346 2.7943341098
15
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H -2.9016236253 1.7575019186 -1.7808661163
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H 2.2678593870 2.3830873628 1.0703201788
H -2.3327858869 0.7844972864 -2.8195690950
15
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H 1.9050690868 -0.7160474646 0.9521561947
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H 2.4298336967 1.9137040919 -1.5706604741
H -2.2315792099 3.0562739583 0.1542355905
15
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Rb -0.0616592386 -0.0091670407 -0.0490183885
O 2.2641734724 0.0624715671 1.0779147886
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O -2.4808326432 0.3837544049 1.9544929428
H -2.9105734360 1.2163146343 2.1887298065
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H 2.2907175176 -2.6466691512 -0.2782930954
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H -3.2251914329 -0.8981078670 -1.8940993794
H 1.9245621227 -1.2226330838 0.2565891790
O -2.7067206052 -0.1115022305 -1.6815836269
H 2.4965342698 2.2420817518 -1.0156637923
H -3.1869673821 0.6192967056 -2.0917386976
15
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Rb -0.1207504750 0.0912619309 0.0062589857
O 2.3350816983 0.8818055699 -0.2235835229
H -3.2991704781 -1.9985691495 0.3762062203
O -2.3468661961 -2.0505437267 0.2210782289
H -2.1642648085 -2.9918218410 0.1070268090
H 3.2975598245 0.8707416337 -0.2507675980
O 1.6078499101 -0.4245529001 1.8856275017
H 1.9821024443 0.0965785415 1.0813686888
H 2.2151616910 -1.3886934354 -2.2378783615
O 1.4768045305 -1.0527438160 -1.7135510489
H -2.6434589021 2.8042160137 -0.9448012376
H 1.9020117530 -0.2988650285 -1.1602911810
O -2.4616398375 2.2232897794 -0.1950211419
H 2.3849713656 -0.5617811657 2.4425079297
H -3.1382315196 2.4400843144 0.4598789217
15
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Rb -0.1300073199 0.0789655484 0.0133409763
O 2.3010524641 0.8552007619 -0.4298659245
H -3.1456169693 -2.0438693048 0.9007988033
O -2.3365303048 -2.0348256495 0.3724745559
H -2.2676785694 -2.9264798522 0.0073804419
H 3.2625968903 0.8535262546 -0.4820391359
O 1.6589336255 -0.0616794658 1.8986832583
H 1.9993300700 0.3117028999 1.0013172476
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File: crest_rotamers.xyz
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15
-25.226124689999999 1.6717750162755646E-002 !
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15
-25.226116590000000 1.6575068366582481E-002 !
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15
-25.226116099999999 1.6566476164941130E-002 !
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15
-25.226112059999998 1.6495803877511633E-002 !
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15
-25.226105879999999 1.6388279160577526E-002 !
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15
-25.226103320000000 1.6343943738853284E-002 !
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15
-25.226103110000000 1.6340312176219198E-002 !
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15
-25.226101910000001 1.6319575863980293E-002 !
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15
-25.226096450000000 1.6225557403975598E-002 !
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15
-25.226096179999999 1.6220922219845654E-002 !
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15
-25.226139190000001 1.6976242457908502E-002 !
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15
-25.226094780000000 1.6196909156907146E-002 !
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15
-25.226089699999999 1.6110074174908645E-002 !
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15
-25.226088390000001 1.6087757294157391E-002 !
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15
-25.226126950000001 1.6757778848007401E-002 !
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15
-25.226087610000000 1.6074484066920375E-002 !
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15
-25.226083509999999 1.6004894398789386E-002 !
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15
-25.226064770000001 1.5690634474285120E-002 !
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15
-25.226057359999999 1.5568081807529171E-002 !
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15
-25.226031750000001 1.5151846570857908E-002 !
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15
-25.226028920000001 1.5106539340668617E-002 !
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15
-25.226091669999999 1.6143692971188735E-002 !
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15
-25.226017779999999 1.4929504584613706E-002 !
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15
-25.226013479999999 1.4861726109270092E-002 !
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15
-25.226003570000000 1.4706689815592857E-002 !
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15
-25.226001119999999 1.4668610967018268E-002 !
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15
-25.225977400000001 1.4305005639850687E-002 !
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15
-25.225971829999999 1.4220937855773072E-002 !
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15
-25.225966490000001 1.4140805360553406E-002 !
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15
-25.225951989999999 1.3925487439522157E-002 !
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15
-25.225949300000000 1.3885904289420976E-002 !
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15
-25.225975049999999 1.4269476748533374E-002 !
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15
-25.225949079999999 1.3882671987370258E-002 !
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15
-25.225974579999999 1.4262381566340141E-002 !
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15
-25.225897560000000 1.3146075126610632E-002 !
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15
-25.225867269999998 1.2731389049822772E-002 !
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15
-25.225863850000000 1.2685397090550001E-002 !
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15
-25.225859700000001 1.2629811202533675E-002 !
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15
-25.225847040000001 1.2461741130826622E-002 !
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15
-25.225832369999999 1.2269782383339856E-002 !
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15
-25.225859199999999 1.2623130569480064E-002 !
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15
-25.225824570000000 1.2168925389406095E-002 !
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15
-25.225820530000000 1.2117012973979557E-002 !
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15
-25.225802630000000 1.1889656355541903E-002 !
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15
-25.225887910000001 1.3012516011282033E-002 !
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15
-25.225851370000001 1.2518971639601677E-002 !
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15
-25.225825820000001 1.2185032407381663E-002 !
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-25.225765780000000 1.1434948553225884E-002 !
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15
-25.225750420000001 1.1250588694017429E-002 !
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15
-25.225693750000001 1.0595745514287864E-002 !
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15
-25.225653430000001 1.0153171685071790E-002 !
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-25.225661440000000 1.0239597156399292E-002 !
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15
-25.225651769999999 1.0135352244197142E-002 !
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15
-25.225639210000001 1.0001535261068711E-002 !
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15
-25.225601470000001 9.6099818468944522E-003 !
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15
-25.225599089999999 9.5858095236420506E-003 !
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15
-25.225570619999999 9.3013264882947193E-003 !
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15
-25.225513119999999 8.7522500838560641E-003 !
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File: ensemble_energies.log
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-25.225601469951 -25.225601469951 0.10898E-03
In advance, too many thanks for your kind attention and highly valuable help.
Sincerely,
Saeed
OK and many thanks. Thus, Shermo is not able to automatically perform calculations and extract results as delta_values.
Sincerely,
Saeed
Dear Tian,
If possible, please let me ask a question about the "Shermo" ability to automatically compute the change in the thermochemical functions for a desirable reaction.
For instance, please assume a reaction as:
R1+2R2------->P
The geometry of the first reactant (R1), the second reactant (R2), and the only product (P) was fully optimized, followed by a frequency calculation using G16. Now, the R1.log, R2.log, and P.log output files are at hand.
I created a text file, namely "reaction.txt" with the following contents:
# Hydrogenation reaction: (s-trans)-CH2CHCHCH2 + 2H2 -> (trans)-C4H10
R1.log -1.0 # (s-trans)-CH2CHCHCH2 (reactant) with the stoichiometric coefficient of -1
R2.log -2.0 # H2 (reactant) with the stoichiometric coefficient of -2
P.log +1.0 # (trans)-C4H10 (product) with the stoichiometric coefficient of +1
Then, Shermo was ran as:
Shermo -r reaction.txt -T 298.15 -p 1 -unit kcal -o results.txt
The following error was displayed:
Shermo: A general code for calculating molecular thermochemistry properties
Version 2.6 Release date: 2024-Feb-11
Developer: Tian Lu (sobereva@sina.com)
Beijing Kein Research Center for Natural Sciences (http://www.keinsci.com)
Official website: http://sobereva.com/soft/shermo
**** If this code is utilized in your work, PLEASE CITE following paper ****
Tian Lu, Qinxue Chen, Shermo: A general code for calculating molecular thermodynamic properties, Comput. Theor. Chem., 1200, 113249 (2021) DOI: 10.1016/j.comptc.2021.113249
Loading running parameters from settings.ini...
Command of invoking Shermo:
Shermo -r reaction.txt -T 298.15 -p 1 -unit kcal -o results.txt
Note: One or more running parameters are overridden by arguments
Error: Unable to recognize argument reaction.txt
Could you please let me know the source of this error and, how should be resolved?
Thanking you in advance.
Best regards,
Saeed
Dear Tian,
Thank you very much for your highly valuable guidance.
Best regards,
Saeed
Thank you very much.
I do not know which of "Sobtop" or "Compliance" should be used. Indeed, I do not know what the difference is between the force constant estimated by your code and by the Compliance one. Could you please let me in more details?
Dear Tian,
As you know better than I, the bond stretching force constant (k) is one of the molecular properties with wide applications, and it is well correlated with many molecular characteristics.
If possible, please let me know how this quantity can be calculated through routine computational approaches.
I would be very grateful if your guidance includes detailed explanations, or please refer me to a detailed and comprehensive reference.
Please also let me know the address of ALL very informative and valuable posts/articles you have prepared about molecular dynamics or meta-dynamics using Orca/xtb/Gaussian. For instance, I found one very nice and informative of such articles (HTTP://sobereva.com/576) and I am extremely interested in all such articles.
Thanking you in advance.
With utmost regards,
Saeed
Many thanks.
Saeed
Dear Tian,
Please let me know how I can add the "GD3(BJ)" correction to the "wB97X" functional in G16 C02. Seemingly, only adding "em=gd3bj" keyword to "wB97X" functional is not enough, and G16 returns an error message indicating "Unable to choose the S8 parameter", and I think a specific IOP may be needed. However, please let me know if "wB97X-GD3(BJ)" is more accurate than "wB97X-D" when long-range interactions and non-covalent interactions play an important role.
Best regards,
Saeed
Thank you.
Thanks a lot.
Could you please make your meaning more evident?
For example, it is said that the surface charge density of atoms X in compound XY is "a" e/squar Angstrom. How is the value of "a" determined?
Saeed
Dear Tian,
Hi, I hope you are doing well.
Suppose I want to determine the surface charge density for the sodium atom in a compound like NaOH. In other words, I’d like to calculate the amount of electric charge per unit surface area on the sodium atom. Could you please let me know how this can be achieved using Multiwfn in a clear and step-by-step explanation?
Sincerely yours,
Saeed
Dear Tian,
Thank you very much.
Sincerely,
Saeed
Dear Tian,
Your very kind attention and highly informative comments are deeply appreciated.
In the "genmer.ini" there is an option namely "ngen" associated with the number of configurations expected to be generated. it seems a high number is better since when number is increased, the chance of finding most stable conformed is also increased. For instanse, suppose I want to put 4 molecules of water around one molecule of HCl. Then, I select 10 for "ngen" indicating that 10 times or ten configurations should randomly be constructed any of which includes one HCl and four H2O. Again, I select 50 for "ngen". This time, 50 configurations will be constructed and undoubtedly the chance of an arrangement corresponding to the most stable conformer increases. Do you agree with me?
Best regards,
Saeed
Dear Tian,
Thank you very very much.
Please, if possible, let me ask another question:
When the "isostat" is executed, a question "Input the geometry threshold for distinguishing different clusters e.g. 0.25 (in Angstrom)" is asked. Please let me know what is the exact meaning of this question. I always enter 999 for this question. Is it correct?
Please, also let me know if "isuffle=1" in genmer.ini is always better than "ishuffle=0" and, leads to much better results.
Sincerely,
Saeed
Dear Tian,
The below command is given in the settings.ini of Molclus:
xtb_arg= "--gfn 1 --chrg 0 --uhf 0" // Additional arguments for xtb, e.g. "vtight --gfn 1 --gbsa h2o --chrg 0" (don't write task keywords such as "--opt" here)
Please suppose one wants to use xtb and employs the gfn2 method, while the structure is also optimized and the implicit solvent such as water is also considered. Please let me know how the above line should be changes to satisfy these expectations.
My own changes:
I changed the "igprog" to 4 and change itask to 3 so that xtb is used as computational code and optimization together with frequency is employed along any xtb execution. In addition, I changed the above line to the: xtb_arg= "--alpb water --gfn 2 --chrg 0 --uhf 0" // Additional arguments for xtb, e.g. "vtight --gfn 1 --gbsa h2o --chrg 0" (don't write task keywords such as "--opt" here).
Please let me know if all these changes are in line with my goal.
Best regards,
Saeed
Dear Tian,
Thank you very much.
I will try to read your proposed examples and, if possible, I will again ask you provided that problems are encountered.
Sincerely,
Saeed
Dear Tian,
Your very nice and powerful code, Molclus, can be used to find conformers resulting from dihedral angle rotations. Can this code be used to optimize a cluster of water molecules, including 5,6,... molecules? If so, could you please let me know and provide more explanation?
Best regards,
Saeed
Dear Tian,
Thank you very much.
Best,
Saeed
Dear Tian,
If possible, please let me know how to compute the value of the dipole moment for a given specific bond in a molecular entity using Multiwfn.
Best regards,
Saeed
Dear Tian,
Many thanks for your very valuable guidance.
Best regards,
Saeed
Dear Tian,
A moment ago, I calculated the value of interaction energy (delta_E_int) for an A...B complex optimized at B3LYP-D3(BJ)/6-311+G(2d,p) level using G16. However, sobEDA was also used to recalculate the interaction energy exactly at the same level. Since both levels are quite the same, I expected to obtain quite identical values for delta_E_int. But, there is a somewhat difference; that is, delta_E_int from G16 is -9.29 kcal/mol while delta_E_int from sobEDA is -8.82 kcal/mol, rendering a difference by 0.47 kcal/mol in absolute. Could you please let me know the source of such a difference?
Sincerely,
Saeed
Dear Tian,
OK. I am so happy and honored you liked my suggestion; thank you very much.
Please, also, let me indicate that I found a very inappreciable problem in one of the written codes. I am working on that to resolve this problem. Once this problem was resolved, I will try to prepare a detailed instruction (which is so time-consuming since I should explain one-by-one five scripts) and, if you let me, I will send them to you through your email.
Best regards,
Saeed
Dear Tian,
If possible, and you kindly let me, I would like to respectfully inform you that I can finally prepare nice bash scripts to perform activation/strain as well as sobEDA analyses along the whole IRC profile in a completely automated manner. If you find it appropriate, I can send these scripts with detailed instructions so that you (probably after some personalization and improving user experience), include them in the next releases of Multiwfn.
Best regards,
Saeed
Dear Tian,
Many thanks for your nice and professional comments.
Best regards,
Saeed
Dear Tian,
Your highly kind attention to prompt reply with much valuable and informative comments is extremely appreciated. Thank you very very much for the valuable time you so kindly assigned to my post.
Given your comments, do you have any other solutions to analyze Pauli repulsion between fragments in a given TS structure?
In addition, you have mentioned option 4 of CDA can directly give the overlap matrix. Isn't it necessary to first find the fragments' orbitals participating in the Pauli repulsion? Indeed, we should first find which fragment orbitals and in which complex orbital repeal each other due to Pauli repulsion.
Please also let me state that you cod "GauIRC2xyz" immediately crashes if the IRC.log file includes a TS comprising of three fragments (diene+dienophile+catalyst). Could you please change your code to be appropriate for three fragments?
Sincerely yours,
Saeed