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Thank you very much for the clarification. I have a follow-up question for just #4:
My situation is as following:
1) The ion-pairing is important in my molecule. I want to study the interaction between the cationic and anionic counterparts.
2) One atom is significantly negatively charged (calc. level: PBE0/ma-TZVP or def2-TZVP)
In the multiwfn manual on ETS-NOCV, it says “If there is no special reason, using diffuse functions is deprecated.” Does my situation fit into the “special reason”? Is ETS-NOCV absolutely meaningless when ma-TZVP is used?
Additional question: What if the ion-pairing is important, but there is no atom that is significantly negatively charged?
Dear Prof. Lu,
I’d be really grateful if I could get additional clarifications on dealing with diffuse functions (and some additional questions on ZPE correction)
1. If I use the complete set of ma-def2 series that you provided, how should I cite it when I publish?
2. If the net charge of my molecule is overall -1, but each atom is not significantly negatively charged (ADCH charge > -0.5), diffuse functions are not required. Correct?
3. In my reaction A + B -> [A-B], some atoms in the product [A-B] are significantly negatively charged, but not in the reactant forms (A and B). For the sake of reaction energy calculation, should these atoms be calculated using diffuse functions for both reactant (A and B) and product ([A-B]) calculations?
4. A molecule is overall neutral, and there is no atom with a significant negative charge. But it is a tight ion-pair, in which the cation and anion counterparts are electrostatically bound and deform each other's structure. The binding is strong, but it is still non-covalent. Should diffuse functions be widely used?
5. When using Shermo for a solute, the sophisticated way of input for Shermo setting is:
E = E(gas, high-level basis set) + [E(SMD, M05-2X/6-31G*) - E(gas, M05-2X/6-31G*)] + 1.89 kcal/mol.
Am I correct?
6. When I do opt-freq calculations using SCRF(IEFPCM), the ZPE values are, not surprisingly, different from the values from gas-phase optimization. This will be same for the molecules in F38/10 database used to obtain the scale factor. Then, shouldn't the ZPE scale factor become different?
7. For wavefunction analysis of a solute, it is recommended to calculate with high-level basis set & SMD. But at the same time, for the calculation of the solute's solvation energy, the same structure should be calculated with M05-2X/6-31G*. Am I correct?
1. What is the bar for significantly negatively charged atom? mulliken or nbo charge? For example, the atom with the most negative nbo charge in my molecule has nbo charge of -0.59.
2. Would it work to use def2-TZVPD for only the significantly negatively charged atom and def2-TZVP for the rest?
3. If the molecule is overall neutral, but contains an atom that is significantly negatively charged, should diffuse functions be used?
4. If I use def2-TZVPD for only one atom in a molecule with total 14 atoms, would the output be incompatible with wavefunction analysis?
Would you also agree with “it retains the merit of diffuse basis sets for calculation of, for example, anions”?
I see. Then, would it be correct to state that def2-TZVP can be used for Multiwfn functions that are incompatible with diffuse functions, but it retains the merit of diffuse basis sets for calculation of, for example, anions?
Dear Prof. Lu,
I know that many functions of Multiwfn are incompatible with diffuse functions. But I’m confused with the definition of diffuse functions.
What I attached here is the basis set information for the same atom (boron) in the same molecule, left one using 6-311+g** and right one using def2-TZVP.
Although 6-311+g** is said to have diffuse functions (and def2-TZVP does not), the def2-TXVP setting also contains a S-type function with an exponent smaller than 0.1 (the last S-type in the right figure, exponent=0.06056). Also, the def2-TZVP setting contains an additional D-type function (exponent=0.199) that is more “diffuse” than the sole D-type function in the 6-311+g** setting (exponent=0.401).
So, what is the exact standard for calling a basis set diffuse or not?
wham09 wrote:Dear Prof. Lu,
The Shermo code utilizes frequency scale factors for ZPE, U(T)-U(0), S, and CV. I can find the scale factors for ZPE in the literature, but the other three factors are rarely documented (especially, I could not find the factors for CV). So I'd like to ask if the following routine would work.
1. Fit the fundamental frequency factor for my functional/basis set using a database (F38/10 for example).
2. Run a opt-freq calculation for my molecule, and tabulate the computed harmonic frequencies.
3. Multiply the computed frequencies by the fitted fundamental frequency factor.
4. Put the results as the custom frequencies into a new freq calculation input with freq=(ReadFC, ReadIsotopes) keyword. (Or use scale keyword)
5. Use the output of the new freq calculation as the input file for Shermo, with the following settings:
5-1. sclZPE, sclheat, sclS, sclCV = 1.0
5-2. ilowfreq = 2 or 3Only ZPE scale factor is relatively important, you can simply set other factors to 1.
Thank you for the reply. As I said, I do understand that, but I just wanted to know if what I described would do the same thing as putting all scl values into Shermo?
Thank you for the clarification.
1. For sobEDAw, is it okay to use SDD (in combination with 6-31+G** or 6-311+G**)? I couldn't find any sobEDAw example in your paper and tutorial that deals with transition metals.
2. For both sobEDA and sobEDAw (actually, for any calculation), if I decided to use def2- family, would you recommend using a mixed basis set with SDD for TM-complex? Or use the def2- basis set solely?
3. If I want to do sobEDA or sobEDAw analysis using TPSSh/def2-TZVP, should I do the initial geometry optimization also using TPSSh/def2-family? I guess this question is also relevant to any calculation.
Additional questions:
1. I understand that unlike sclZPE, other scale factors are normally close to unity. But I still want to understand how they're derived. From what I read in Moran/Radom paper (doi/10.1021/jp073974n), sclheat and sclS cannot be obtained by simply fitting U_calc and U_exp (or S_calc and S_exp) linearly. Am I correct?
2. Can I get any reference where the scale factors for CV are derived? I could never find it.
3. I tried fitting the frequency scale factor myself. For some of the molecules in F38/10 set, the degenerate frequencies appeared to be different from each other. For example, the frequencies corresponding to the 3rd mode (pi_u symmetry) of CO2 are 646.6657 and 646.6429 in my calculation output. Did I do something wrong? Or should I just average them?
4. If what I want at the end is G(sol), should I put into Shermo the E value from SCRF calculation, rather than gas-phase single-point?
Dear Prof. Lu,
The Shermo code utilizes frequency scale factors for ZPE, U(T)-U(0), S, and CV. I can find the scale factors for ZPE in the literature, but the other three factors are rarely documented (especially, I could not find the factors for CV). So I'd like to ask if the following routine would work.
1. Fit the fundamental frequency factor for my functional/basis set using a database (F38/10 for example).
2. Run a opt-freq calculation for my molecule, and tabulate the computed harmonic frequencies.
3. Multiply the computed frequencies by the fitted fundamental frequency factor.
4. Put the results as the custom frequencies into a new freq calculation input with freq=(ReadFC, ReadIsotopes) keyword. (Or use scale keyword)
5. Use the output of the new freq calculation as the input file for Shermo, with the following settings:
5-1. sclZPE, sclheat, sclS, sclCV = 1.0
5-2. ilowfreq = 2 or 3
I'm a little confused because in the 5 template.gjf files,
The templates for b3lyp, blyp, TPSSTPSS: Do not contain the iop keyword.
The template for BHandHLYP contains: IOp(3/174=1000000,3/175=1035400,3/177=279300,3/178=4961500)
The template for TPSSh contains: IOp(3/174=1000000,3/175=2238200,3/177=452900,3/178=4655000)
So, are these options specific to each functional? or a combination of functional/basis set?
Just an additional technical question about sobEDA:
I noticed that among the sobEDA tutorials, the template gjf files for metal-containing systems (chromium alkylidene and copper/H2O) contain an additional keyword IOp(3/174=1000000,3/175=2238200,3/177=452900,3/178=4655000), which I believe is additional dispersion adjustment. Should this keyword (with these exact numbers) be applied to any organometallic species?
1. I looked into the sobEDA script file and concluded that the best option for me is using Multiwfn only to combine wavefunctions of fragments and generate promolecular & frozen input files, then run g16 jobs, and then tabulate the results in the l608 section myself. Could you confirm that this will work?
2. I now understand what you mean. Thank you very much!
Thank you for the reply.
1. I actually really wanted to try sobEDA, but I only have access to g16 in a remote server, where I'm not allowed to install Multiwfn. Is there a way to run sobEDA in this situation? If not, can I get any insight on how to interpret E_steric and E_quantum in the EDA-SBL framework?
2. I understand that EDA-SBL and ETS-NOCV are very different, but I thought that E_T, E_J, E_Nuc, E_V, E_xc, etc. are general terms in DFT. Then, shouldn't the NOCV stabilization energy have some correlation with a certain general energy component of the whole system?
Dear Prof. Lu,
I have two questions about interpreting EDA-SBL results.
1. Since my background is mostly synthetic organic, I have a difficulty understanding the chemical meaning of Weiszacker energy (E_steric). From what I read in the manual, E_quantum is basically a Pauli repulsion term, so to me, E_steric and E_quantum seem to be both steric hindrance terms. What is the difference of E_steric and E_quantum in terms of chemical meaning (structure and/or reactivity)?
2. From ETS-NOCV analysis, we can get stabilization energy of each NOCV pair. Can this stabilization energy be categorized as one of the EDA-SBL terms (E_steric, E_electrostatic, or E_quantum)?
Thank you for the reply!
Dear Prof. Lu,
I have one question specific to animating electronic structures, and another question that is more general.
1. I read your article (http://sobereva.com/86) and am trying to do this myself on systems more complex than H2. I'd like to know how I can define the plane of interest, other than merely xy, yz, xz planes. For example, it would be useful if I can define a plane containing three atoms, just like some other functions of Multiwfn do.
2. Multiwfn functions mostly require wavefunction files that result from single-point calculations. I wonder if specifying a solvent (SCRF/SMD) for single-point calculation yields a wavefunction file that is more "real" than not specifying a solvent. Is there a general guideline for situations where specifying a solvent is recommended or not recommended?
I just sent you an email with the .out & .fch files attached.
Can you comment on the second input? I believe this one is exactly like the example in the manual. But the output from this input also caused the crash.
The output lines while Gaussian entered L608 typically look like below:
(Enter /****/g09/l608.exe)
A total of 0 models will be applied.
Results using SCF density:
FoFJK: IHMeth= 0 ICntrl= 500 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F
IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0.
FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0
NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T
wScrn= 0.000000 ICntrl= 500 IOpCl= 1 I1Cent= 0 NGrid= 0
NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
Symmetry not used in FoFCou.
ET= 632.554426 EV=-2900.409564 EJ= 1019.606524 EK= -79.090375 ENuc= 695.863243
Leave Link 608 at Thu Oct 9 21:43:40 2025, MaxMem= 2147483648 cpu: 24.8
I tried the following two input lines, and in both cases error termination happened.
[Input 1]
%nprocshared=2
%mem=16GB
%chk=filename.chk
#p scf=(maxcycle=300) sp pop=(nbo, full) M06/6-311+G** ExtraLinks=L608 nosym int=ultrafine
filename
charge multipl
coordinates
-54
[Input 2]
%nprocshared=1
%mem=16GB
%chk=filename.chk
# M06/6-311+G** ExtraLinks=L608
filename
charge multipl
coordinates
-54
Dear all,
I have two questions about EDA-FF analysis.
1. I'm having a trouble constructing molecule type files. For certain elements (in my case, boron, phosphorus, and palladium) I cannot find the corresponding AMBER or GAFF types. These only appear as "?" in gaussview.
2. For atomic charges, are there any selection criteria for CHELPG versus MK charges?
Thank you very much in advance.
Problem solved. Thank you!
Dear all,
I have a few questions regarding Multiwfn's bond order analysis.
1. From what I read in the manual, the Wiberg bond order analysis seems to work well with diffuse functions. Am I correct?
2. Is the Laplacian bond order analysis sensitive to diffuse functions?
3. Is the Laplacian bond order analysis appropriate for carbon-boron bonds, where the boron atom is tetracoordinate, anionic boron-ate? An example would be alkyl trifluoroborate salt.
4. Is the Laplacian bond order analysis appropriate for carbon-palladium bonds?
Thank you very much in advance.
Dear all,
I am trying to do TDDFT calculations to predict UV-Vis spectra of my compounds. I succeeded for an organic compound, but for an organometallic complex (palladium), the calculation ended with an error.
My input is as below:
%nprocshared=2
%mem=16GB
%chk=xxx.chk
#p scf=(maxcycle=300) pop=(nbo,full) scrf=(smd, solvent=dichloroethane)
M06/gen TD(NStates=30) guess=read nosym int=ultrafine
filename
charge/spin
coordinates
P C H F B 0
6-311+G**
****
Pd 0
SDD
****
The error message is as below:
Excessive mixing of frozen core and valence orbitals.
Error termination via Lnk1e in xxx/g09/g09/l801.exe
I normally put pseudo=read into my inputs, but here I didn't do it because I read somewhere that this is not compatible with TDDFT. The only difference from the input for the purely organic compound is that I used a mixed basis set. I tried M06/6-311+G**/SDD with no separate basis set block, but that also ended with another error.
Dear all,
I was trying to visualize the topology map of my molecule by VMD. I could follow the instructions (manual section 4.2.5) and currently can visualize the CPs and paths. Is it also possible to visualize the interbasin surfaces (together with CPs and paths) by VMD?
Thank you very much.
I see. Would you say it is currently not possible at all (using any software)?
Dear all,
What I want to do is as below:
Let's say there is a complex, consisting of 2 fragments (just like the situation of CDA analysis). There would be an NBO of a certain chemical bond of interest in the structure of the fragment A, whose electron density map would be reorganized in some extent when the fragment A and B form the whole complex. What I want to do is find out which NBO's in the structure of fragment B are responsible for this NBO reorganization (as well as the nature of the interactions and the % contributions).
Would this be possible by Multiwfn? Thank you very much in advance.
Thank you very much!