EDA with Multiwfn

jorgescf · 2024-02-05 20:35:14

I would like to perform an EDA for a cycloaddition reaction. Can anyone help me with instructions to perform it with Multiwfn? Thanks in advance.

sobereva · 2024-02-05 21:14:45

Multiwfn supports different forms of energy decomposition analysis, see Section 3.24 of latest version of Multiwfn for introductions, there are also examples in the manual.

If you need to obtain physical components of interaction energy between fragments at quantum chemistry level, the only method supported by Multiwfn is the sobEDA and sobEDAw recently proposed by me, note that this function not only needs Multiwfn but also requires Linux version of Gaussian 16. Please check original paper:

Tian Lu and Qinxue Chen, Simple, Efficient, and Universal Energy Decomposition Analysis Method Based on Dispersion-Corrected Density Functional Theory, J. Phys. Chem. A, 127, 7023?7035 (2023)
(There is a very detailed tutorial at http://www.shanxitv.org/soft/sobEDA_tutorial.zip)

patrashantigopal · 2024-08-25 02:29:59

I am trying sobEDA for an extensive system. But after 7 cycles, showing some error for the fragment and exiting.

"Error encountered; please check corresponding output file! Now script exits"

225
bcd_Ia_I
C 3.744953000 2.359613000 -3.861801000
H 4.434078000 3.193084000 -4.035237000
C 3.181732000 1.842082000 -5.194755000
H 4.027373000 1.647583000 -5.863755000
C 2.411842000 0.534788000 -4.989566000
H 1.532972000 0.725448000 -4.356694000
C 3.283977000 -0.499788000 -4.283410000
H 4.113793000 -0.782634000 -4.947573000
C 3.830509000 0.097772000 -2.970747000
H 2.996088000 0.273847000 -2.284940000
C 4.865297000 -0.793837000 -2.299428000
H 4.443256000 -1.787836000 -2.147808000
H 5.745481000 -0.888473000 -2.952743000
O 2.380122000 2.809834000 -5.855452000
H 1.734742000 3.179245000 -5.223482000
O 1.999664000 -0.006433000 -6.241137000
H 1.595859000 0.709967000 -6.753767000
O 2.460090000 -1.634947000 -4.021817000
O 4.510567000 1.357023000 -3.231459000
O 5.246060000 -0.311684000 -1.010951000
H 5.667641000 0.548917000 -1.134010000
C 2.926407000 -2.937985000 -4.334801000
H 3.844168000 -2.879799000 -4.929478000
C 1.827910000 -3.662756000 -5.131072000
H 2.230742000 -4.632395000 -5.447018000
C 0.607977000 -3.939805000 -4.238113000
H 0.132634000 -2.980554000 -3.978520000
C 1.054669000 -4.625332000 -2.937041000
H 1.391261000 -5.641248000 -3.175144000
C 2.191799000 -3.872632000 -2.231712000
H 1.817449000 -2.908827000 -1.862261000
C 2.817926000 -4.647102000 -1.074962000
H 3.568363000 -4.008164000 -0.587386000
H 2.047565000 -4.901335000 -0.344713000
O 1.529460000 -2.961628000 -6.317746000
H 1.453974000 -2.008938000 -6.131407000
O -0.286531000 -4.765477000 -4.957281000
H -1.030757000 -5.011709000 -4.378537000
O -0.090499000 -4.690441000 -2.063903000
O 3.276179000 -3.645625000 -3.161104000
O 3.397909000 -5.877376000 -1.492986000
H 4.044306000 -5.672158000 -2.183533000
C -0.509893000 -5.952289000 -1.597336000
H 0.039707000 -6.747429000 -2.109333000
C -2.019310000 -6.119292000 -1.815517000
H -2.273494000 -7.152630000 -1.539062000
C -2.818048000 -5.174569000 -0.924768000
H -2.592301000 -4.137855000 -1.212543000
C -2.413587000 -5.356371000 0.537995000
H -2.745350000 -6.338361000 0.895930000
C -0.887649000 -5.242960000 0.698731000
H -0.585666000 -4.205572000 0.499323000
C -0.392242000 -5.650548000 2.084354000
H 0.688820000 -5.462124000 2.143253000
H -0.894349000 -5.047283000 2.843819000
O -2.317157000 -5.909600000 -3.192746000
H -3.282539000 -5.901369000 -3.278035000
O -4.188447000 -5.464032000 -1.158303000
H -4.743195000 -4.968382000 -0.523713000
O -3.053988000 -4.315697000 1.290586000
O -0.219037000 -6.131614000 -0.220322000
O -0.687798000 -7.008656000 2.385887000
H -0.253209000 -7.555207000 1.715613000
C -3.908233000 -4.662083000 2.357970000
H -4.031093000 -5.748088000 2.413106000
C -5.266326000 -3.971287000 2.178508000
H -5.924023000 -4.325204000 2.984451000
C -5.127287000 -2.458718000 2.291141000
H -4.506058000 -2.096674000 1.459244000
C -4.437344000 -2.084954000 3.601320000
H -5.108108000 -2.295542000 4.442629000
C -3.125299000 -2.867632000 3.790111000
H -2.392207000 -2.518162000 3.050487000
C -2.531541000 -2.731348000 5.190625000
H -1.583671000 -3.285745000 5.224678000
H -2.323046000 -1.681513000 5.409653000
O -5.823253000 -4.347292000 0.917784000
H -6.595381000 -3.779965000 0.769713000
O -6.439442000 -1.919782000 2.195014000
H -6.425212000 -0.979459000 2.458882000
O -4.170735000 -0.677857000 3.525198000
O -3.357512000 -4.282360000 3.605098000
O -3.425668000 -3.193024000 6.198601000
H -3.585196000 -4.133873000 6.039376000
C -4.525665000 0.148380000 4.613951000
H -5.036930000 -0.434587000 5.385700000
C -5.416026000 1.295372000 4.121259000
H -5.765070000 1.842284000 5.008115000
C -4.639435000 2.262051000 3.232411000
H -4.365115000 1.736460000 2.306291000
C -3.339564000 2.717215000 3.906808000
H -3.576035000 3.368276000 4.759483000
C -2.543827000 1.492429000 4.396121000
H -2.246888000 0.901518000 3.517575000
C -1.298168000 1.836563000 5.210105000
H -0.735586000 2.618131000 4.683783000
H -1.611878000 2.237038000 6.180217000
O -6.539197000 0.750789000 3.426194000
H -7.024398000 1.498845000 3.046153000
O -5.522404000 3.337488000 2.948425000
H -5.060121000 4.012072000 2.412923000
O -2.584985000 3.450439000 2.926381000
O -3.384020000 0.689977000 5.241540000
O -0.495298000 0.700239000 5.479089000
H -0.012506000 0.434954000 4.671436000
C -2.278594000 4.809192000 3.177641000
H -2.782660000 5.144129000 4.089666000
C -2.710395000 5.677924000 1.988857000
H -2.554907000 6.724711000 2.283938000
C -1.861730000 5.396330000 0.755835000
H -2.036351000 4.362445000 0.425012000
C -0.379232000 5.545497000 1.092785000
H -0.148131000 6.596931000 1.294395000
C -0.017441000 4.693992000 2.324321000
H -0.113634000 3.633772000 2.059304000
C 1.401732000 4.928133000 2.816225000
H 1.520894000 4.410700000 3.776850000
H 2.096410000 4.493116000 2.087035000
O -4.096478000 5.466506000 1.718499000
H -4.296997000 5.925239000 0.888266000
O -2.293300000 6.311146000 -0.242487000
H -1.690892000 6.264236000 -1.009067000
O 0.356406000 5.089270000 -0.054178000
O -0.903436000 5.004361000 3.420046000
O 1.627636000 6.331081000 2.955221000
H 2.502651000 6.474792000 3.335118000
C 1.304194000 5.931455000 -0.648942000
H 1.298084000 6.921838000 -0.183917000
C 1.015073000 6.030417000 -2.156383000
H 1.722930000 6.765862000 -2.571226000
C 1.232415000 4.679651000 -2.837116000
H 0.487463000 3.968976000 -2.468940000
C 2.627290000 4.121137000 -2.543815000
H 3.389815000 4.733738000 -3.047408000
C 2.892643000 4.134924000 -1.022573000
H 2.237346000 3.393833000 -0.550670000
C 4.345150000 3.830433000 -0.652899000
H 4.402687000 3.722924000 0.439084000
H 4.621019000 2.874050000 -1.099349000
O -0.317759000 6.496141000 -2.350989000
H -0.558655000 6.327907000 -3.274909000
O 0.966495000 4.790109000 -4.246007000
H 1.613545000 5.389368000 -4.650562000
O 2.660279000 2.784338000 -3.047278000
O 2.625178000 5.446449000 -0.478697000
N 5.230835000 4.884771000 -1.127908000
H 4.921098000 5.830639000 -0.931376000
C 6.561494000 4.819646000 -1.467365000
C 7.224606000 3.456223000 -1.597521000
H 6.528001000 2.698961000 -1.975126000
H 8.014581000 3.577215000 -2.344340000
C 7.851891000 2.999631000 -0.262818000
H 8.494453000 3.806032000 0.111340000
H 7.065041000 2.854075000 0.490819000
C 8.674778000 1.711300000 -0.397412000
H 8.038280000 0.899941000 -0.780323000
C 9.319185000 1.262283000 0.920893000
H 9.958046000 2.070962000 1.303783000
H 8.533578000 1.110540000 1.675566000
C 10.149483000 -0.021560000 0.790191000
H 9.509501000 -0.829284000 0.406590000
H 10.934039000 0.130822000 0.034933000
C 10.796756000 -0.470449000 2.107064000
H 10.012403000 -0.621321000 2.863342000
H 11.436839000 0.337707000 2.489942000
C 11.626845000 -1.754523000 1.977706000
H 10.986544000 -2.562689000 1.595131000
H 12.410814000 -1.603863000 1.221337000
C 12.274831000 -2.203405000 3.294265000
H 11.490880000 -2.353312000 4.051074000
H 12.915694000 -1.395340000 3.676298000
C 13.104300000 -3.487830000 3.165646000
H 12.464028000 -4.296679000 2.783969000
H 13.888855000 -3.338892000 2.409242000
C 13.752680000 -3.937415000 4.481815000
H 12.969049000 -4.086696000 5.237694000
H 14.393163000 -3.129847000 4.862992000
C 14.578958000 -5.221345000 4.343863000
H 15.027075000 -5.514004000 5.299650000
H 13.958370000 -6.056535000 3.997797000
H 15.392860000 -5.092779000 3.620328000
O 7.199747000 5.855071000 -1.651764000
H 9.458843000 1.864576000 -1.152162000
C 2.463099000 -0.290493000 4.216705000
C 1.501739000 -0.505967000 2.135653000
C 2.731009000 -0.828123000 1.543180000
C 3.858643000 -0.853222000 2.357225000
C 3.729822000 -0.591851000 3.724854000
H 2.300936000 -0.075230000 5.269655000
H 2.799189000 -1.037573000 0.484697000
H 4.823578000 -1.083587000 1.916537000
H 4.584307000 -0.618623000 4.392207000
N 0.283373000 -0.506998000 1.398066000
H -0.487332000 -0.222084000 2.002491000
S 0.203556000 0.371894000 -0.081681000
C -1.493742000 0.097514000 -0.565988000
C -2.471283000 1.026745000 -0.184195000
C -1.797602000 -1.005957000 -1.367507000
C -3.781780000 0.843131000 -0.608445000
H -2.203587000 1.883549000 0.425099000
C -3.113098000 -1.177963000 -1.791716000
H -1.021998000 -1.703642000 -1.662994000
C -4.107179000 -0.261251000 -1.417440000
H -4.558773000 1.545539000 -0.331439000
H -3.388648000 -2.017103000 -2.421665000
N -5.408386000 -0.541439000 -1.911537000
N -6.285852000 0.302686000 -1.584634000
C -7.584226000 0.041445000 -2.059352000
C -8.558669000 0.970815000 -1.699227000
C -7.945540000 -1.075326000 -2.854286000
C -9.890469000 0.815507000 -2.112751000
H -8.274180000 1.821765000 -1.091135000
C -9.249489000 -1.243485000 -3.270788000
H -7.179838000 -1.791916000 -3.128950000
C -10.243349000 -0.307238000 -2.910530000
H -9.545347000 -2.090849000 -3.880040000
O -11.488475000 -0.524842000 -3.343878000
H -12.061715000 0.209148000 -3.011987000
C -10.935508000 1.777420000 -1.746351000
O -12.115146000 1.677139000 -2.090983000
O -10.517821000 2.808133000 -0.987792000
H -11.292210000 3.368960000 -0.811712000
O 1.097739000 -0.316295000 -1.019366000
O 0.398077000 1.808024000 0.175669000
N 1.368650000 -0.227175000 3.438147000

2
0 1
1-183
0 1
184-225

patrashantigopal · 2024-08-25 02:31:02

However, I could not find the error in the output file. Please help.

patrashantigopal · 2024-08-25 02:52:34

Running on HPC system.

sobereva · 2024-08-25 07:21:10

I don't know details of your HPC environment. Please carefully check all information printed by the sobEDA.sh shell script, everything is printed in detail for debugging, including which command is running, and file name of Gaussian input/output file.

patrashantigopal · 2024-09-17 11:31:28

The orbital contributions obtained from the EDA analysis and the NOCV method differ. There is some difference. How to report this in paper. In general orbital contribution coming from NOCV is 6-8 kcal/mol higher than the EDA analysis.

patrashantigopal · 2024-09-17 11:41:28

For NOCV, I am taking the fragments and final files obtained from the sobEDA calculations.

patrashantigopal · 2024-09-17 11:44:51

*************************
***** Final results *****
*************************

Total interaction energy: -29.49 kcal/mol

Physical components of interaction energy derived by sobEDA:
Electrostatic (E_els): -59.75 kcal/mol
Exchange (E_x): -60.62 kcal/mol
Pauli repulsion (E_rep): 194.48 kcal/mol
Exchange-repulsion (E_xrep = E_x + E_rep): 133.86 kcal/mol
Orbital (E_orb): -70.28 kcal/mol
DFT correlation (E_DFTc): -16.86 kcal/mol
Dispersion correction (E_dc): -16.46 kcal/mol
Coulomb correlation (E_c = E_DFTc + E_dc): -33.32 kcal/mol

--------------- Pair and NOCV orbital information --------------
There are totally 219 NOCV pairs and 438 NOCV orbitals
NOCV orbitals with absolute eigenvalues smaller than 1.0E-03 are not shown
Note: All energies are given in kcal/mol

Pair Energy | Orbital Eigenvalue Energy | Orbital Eigenvalue Energy
1 -44.19 1 0.80351 -121.50 438 -0.80351 -66.50
2 -31.83 2 0.65991 -121.30 437 -0.65991 -73.07
3 -0.96 3 0.09553 -108.74 436 -0.09553 -98.73
4 -1.59 4 0.08974 -58.59 435 -0.08974 -40.89
5 -0.75 5 0.07281 -68.29 434 -0.07281 -58.03
6 -0.75 6 0.07007 -58.85 433 -0.07007 -48.11
7 -0.70 7 0.05577 -6.06 432 -0.05577 6.57
8 -0.53 8 0.05334 -75.56 431 -0.05334 -65.58
9 -0.44 9 0.04884 -81.33 430 -0.04884 -72.30
10 -0.40 10 0.04721 -67.80 429 -0.04721 -59.29
11 -0.39 11 0.04350 -37.89 428 -0.04350 -28.86
12 -0.32 12 0.03404 20.83 427 -0.03404 30.26
13 -0.30 13 0.03079 -11.58 426 -0.03079 -1.88
14 -0.22 14 0.02948 -18.76 425 -0.02948 -11.23
15 -0.21 15 0.02723 -24.50 424 -0.02723 -16.96
16 -0.19 16 0.02532 -9.94 423 -0.02532 -2.55
17 -0.17 17 0.02376 23.83 422 -0.02376 31.18
18 -0.13 18 0.02108 -11.86 421 -0.02108 -5.56
19 -0.12 19 0.01954 -4.65 420 -0.01954 1.55
20 -0.11 20 0.01801 -23.29 419 -0.01801 -17.24
21 -0.11 21 0.01786 -6.10 418 -0.01786 -0.08
22 -0.07 22 0.01698 -23.22 417 -0.01698 -18.90
23 -0.10 23 0.01696 36.37 416 -0.01696 42.35
24 -0.07 24 0.01473 -0.09 415 -0.01473 4.79
25 -0.07 25 0.01384 11.39 414 -0.01384 16.18
26 -0.08 26 0.01371 -3.57 413 -0.01371 2.37
27 -0.06 27 0.01197 10.78 412 -0.01197 15.58
28 -0.06 28 0.01096 17.38 411 -0.01096 22.71
29 -0.06 29 0.01067 11.75 410 -0.01067 17.74
30 -0.04 30 0.01030 45.65 409 -0.01030 49.54
31 -0.02 31 0.00791 -26.25 408 -0.00791 -23.13
32 -0.03 32 0.00766 -88.50 407 -0.00766 -84.98
33 -0.04 33 0.00752 -129.67 406 -0.00752 -124.84
34 -0.02 34 0.00734 -35.26 405 -0.00734 -32.60
35 -0.01 35 0.00573 -39.90 404 -0.00573 -37.84
36 -0.01 36 0.00572 -1.86 403 -0.00572 0.36
37 -0.01 37 0.00560 -11.59 402 -0.00560 -8.99
38 -0.01 38 0.00501 -9.29 401 -0.00501 -7.34
39 -0.01 39 0.00495 -24.03 400 -0.00495 -22.34
40 -0.01 40 0.00451 -83.17 399 -0.00451 -80.91
41 -0.01 41 0.00438 -70.06 398 -0.00438 -68.22
42 -0.01 42 0.00421 -271.73 397 -0.00421 -268.95
43 -0.00 43 0.00406 -47.50 396 -0.00406 -46.30
44 -0.01 44 0.00401 -73.39 395 -0.00401 -71.69
45 -0.01 45 0.00381 -199.98 394 -0.00381 -197.49
46 -0.01 46 0.00373 -67.57 393 -0.00373 -66.15
47 -0.00 47 0.00360 -48.41 392 -0.00360 -47.27
48 -0.00 48 0.00346 -42.06 391 -0.00346 -40.76
49 -0.01 49 0.00325 -73.76 390 -0.00325 -72.18
50 -0.02 50 0.00307 -1534.97 389 -0.00307 -1528.03
51 -0.01 51 0.00277 -476.80 388 -0.00277 -474.01
52 -0.01 52 0.00213 -1563.57 387 -0.00213 -1558.78
53 -0.00 53 0.00195 -343.97 386 -0.00195 -342.27
54 -0.01 54 0.00176 -1087.31 385 -0.00176 -1084.24
55 -0.01 55 0.00161 -2531.08 384 -0.00161 -2525.21
56 -0.01 56 0.00121 -2409.17 383 -0.00121 -2404.98
57 -0.00 57 0.00114 -1034.03 382 -0.00114 -1032.05
Sum of NOCV eigenvalues: -0.00000
Sum of pair energies: -85.33 kcal/mol

sobereva · 2024-09-17 18:04:01

The sum of pair energies is not equal to the orbital component given by sobEDA, see red text in Section 3.26.2 of Multiwfn manual for the reason. The value given by sobEDA is exact. Anyway, the ETS-NOCV data is still very useful in understand relative importance of different types of interfragment interactions, and you may report percentage data in your paper.

patrashantigopal · 2024-09-18 03:40:40

Thanks for your reply. So, shall I mention this aspect in the paper? If the reviewer asks specific questions on why these are not the same, then what should be the possible answer?

sobereva · 2024-09-18 09:44:24

patrashantigopal wrote:

Thanks for your reply. So, shall I mention this aspect in the paper? If the reviewer asks specific questions on why these are not the same, then what should be the possible answer?

You can mention my above comment and the relevant information in Multiwfn manual. Alternatively, you can only report percentage contribution of different NOCV pairs

philbaran · 2024-12-28 15:33:20

I would like to perform EDA analysis for a system involving Be and He atoms. However, I encountered to the following caution:
"The index of the atom to be loaded exceeded actual number of atoms in the whole system."
Would you please guide me how should I solve it?

sobereva · 2024-12-29 02:33:39

philbaran wrote:

I would like to perform EDA analysis for a system involving Be and He atoms. However, I encountered to the following caution:
"The index of the atom to be loaded exceeded actual number of atoms in the whole system."
Would you please guide me how should I solve it?

Please check your fragment.txt, the atom indices should be wrongly defined.

Multiwfn forum

#1 2024-02-05 20:35:14

EDA with Multiwfn

#2 2024-02-05 21:14:45

Re: EDA with Multiwfn

#3 2024-08-25 02:29:59

Re: EDA with Multiwfn

#4 2024-08-25 02:31:02

Re: EDA with Multiwfn

#5 2024-08-25 02:52:34

Re: EDA with Multiwfn

#6 2024-08-25 07:21:10

Re: EDA with Multiwfn

#7 2024-09-17 11:31:28

Re: EDA with Multiwfn

#8 2024-09-17 11:41:28

Re: EDA with Multiwfn

#9 2024-09-17 11:44:51

Re: EDA with Multiwfn

#10 2024-09-17 18:04:01

Re: EDA with Multiwfn

#11 2024-09-18 03:40:40

Re: EDA with Multiwfn

#12 2024-09-18 09:44:24

Re: EDA with Multiwfn

#13 2024-12-28 15:33:20

Re: EDA with Multiwfn

#14 2024-12-29 02:33:39

Re: EDA with Multiwfn

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