Gaussian - Science topic

We are using gaussian G-16 to calculate molecular properties. When I specigy in the rout line def2qzvpp ( #P B3LYP/def2qzvpp opt output=pickett) with RU (Ruthenium atom in the atom list) -- Does the Gaussian do an ALL ELECTRON calculation -OR- use a core potential (ECP) for the Ru atom?

Hello,

I hope this message finds you well. I have just started to learn gaussian software. While running NLO calculations I used the keyword:

#p b3lyp/6-31g(d,p) geom=connectivity gfinput polar=(DCSHG, Cubic) CPHF=RdFreq 

Later I came to know the common keyword used for NLO is:

Which is the most apt set of keyowrds. And what is the difference between # and #p.

#rhf/3-21g pop=nboread RHF/3-21G for formamide (H2NCHO) 0 1   H  -1.908544      0.420906     0.000111   H  -1.188060     -1.161135     0.000063   N  -1.084526     -0.157315     0.000032   C    0.163001      0.386691    -0.000154   O   1.196265      -0.246372     0.000051   H    0.140159      1.492269     0.000126 $nbo nrt $end

I tried this example, but using gaussian the section with resonance weight is missing

I am optimizing a molecule in solvents where I am getting the following error:

"Inv3 failed in PCMMkU"

I have searched for the error and got some solutions like using "surface=sas" and "surface=ses", however, none of these solved the problem.

Can anyone suggest any other alternative solution?

Thanks in advance.

When I specify the number of processors = 4, my calculation works fine. But when I want to specify the number of processors more than four, the program gives: "Will use up to 8 processors via shared memory." and that's all. The calculation does not work. What should I do?

After installing gaussian 16 in windows version, i tried to run a molecule in it but it failed having empty output file. please suggest possible solutions.

Hi, I am new to gaussian and was wondering how to use KMLYP and BHHLYP in the gaussian input file

Hi all,

I seen CBM and VBM plots in articles plotted using VASP, i pasted a part of the sample picture.

I used to do with Gaussian, but can any one explain How exactly these could be plotted using VASP output?

Thank you.

Hi,

I have two rotamers from crystal structure data. I like to use the QST2 transition state search in Gaussian to investigate their interconversion barrier. Since they come from crystal structure data, the atom numbering/ordering of the two optimized rotamers is different. With around 100 atoms, I would really prefer not to try and renumber them by hand. Is there any automatic structure match and renumber routine out there, which would produce the two geometries with matching numbering?

Alternatively, if I have to go via the "traditional" TS search: is there any program which would allow to match/align two structures and to calculate an "averaged" structure from this? But I assume those would also require matching numbering...

Recently, I received a comment to report endogeneity for the structural model. Generally, endogeneity using Gaussian copula has single and combination tests. If I report a combination test (for example, double or triple tests for a big model), the table will be large. In this case, can I report only a single test?

in optimization process its showing for carbohydrates computational studies.

How to Solve Inaccurate quadrature in CalDSu. errors in Gaussian?

Log(output) file preview is as below:

Search did not lower the energy significantly.

No lower point found -- run aborted.

Error termination via Lnk1e in /opt/g16/l508.exe

Job cpu time: 0 days 14 hours 4 minutes 28.9 seconds.

Elapsed time: 0 days 2 hours 54 minutes 57.4 seconds.

File lengths (MBytes): RWF= 138 Int= 0 D2E= 0 Chk= 8 Scr= 1

If anyone know help me please.

Binding energy, spin polarization and gibbs free energy How i find in gaussian.because i not see these properties in frequency out put file

I want to do NBO analysis for a molecule in the excited state [the first singlet state]. I used the following command line,

#P td rb3lyp/ 6-311g Cis=(read, root= 1) pop=nboread

but the job crash with the following error

No CIS info on Chk file

How can I solve the error??

spin polarization (Hartree) (SP), molecular mass amount (MMA), enthalpy change kcal/mol (E nthal py C), Gibbs free energy change kcal/ mol (GFEC), binding energy kcal/mol (BE), entropy change kcal/mol.K ( E ntropy C), zero vibrational energy kcal/ mol (ZVE), octanol-water partition coefficients (XLogP3), covalently bonded unit count (CBUC), dipole moment (debye) (DM), and heavy atom count (HAC). I find these properties using dmol3 or gaussian software i do many try but i not get these properties.please tell me setting or basis set to help to me achieve these properties

or how can i draw it

I am working on the design of an image encryption algorithm. The algorithm has a sound score of entropy, low correlation, resistance to anti-cropping attacks, and resistance to salt and pepper noise. The only issue with the algorithm is its resistance to counter gaussian noise.

Hello,

I am a grad student working on a project on the photisomerization of 2'-hydroxychalcone. I was instructed to create a PES surface for the triplet state. My first attempt did not produce accurate results by using the method of:

%chk=r66a20.chk

# opt=modredundant ub3lyp/6-311g(d,p) nosymm empiricaldispersion=gd3

H atom moved by 0.66 ratio and 200 degrees torsional rotation

0 3

C 4.40955200 -1.07991300 -0.54555900

C 3.26596800 -1.74755000 -0.09909700

C 2.01417800 -1.42748400 -0.63366800

C 1.89642800 -0.41766900 -1.60620700

C 3.05378000 0.22560800 -2.07096300

C 4.30412000 -0.09762500 -1.53408500

C 0.59255400 -0.09649200 -2.22324900

C -0.55116400 0.12512000 -1.55522300

C -0.64735300 0.50053500 -0.12258300

O 0.34423300 1.01373800 0.46366800

C -1.90915400 0.31643500 0.63358200

C -3.15247100 0.58942200 0.03132200

C -4.33985300 0.42672200 0.74976200

C -4.30311100 -0.00451700 2.07603100

C -3.07829900 -0.27235000 2.68958800

C -1.87966600 -0.11514800 1.97776200

O -0.66382100 -0.40167900 2.59940300

H 5.37814800 -1.33016300 -0.13247600

H 3.35032800 -2.51880500 0.65556100

H 1.14048600 -1.97116500 -0.29583500

H 2.98682100 0.98376600 -2.84181500

H 5.19191700 0.41070500 -1.88749300

H 0.55957000 -0.05444000 -3.30552000

H -1.46703200 0.04969000 -2.12553300

H -3.21091500 0.95579300 -0.98478200

H -5.29020100 0.64320200 0.27899600

H -5.22451200 -0.12796000 2.63040400

H -3.06071800 -0.60621700 3.71928400

H -0.26302800 0.16107800 1.75025600

B 10 29 F

B 17 29 F

D 9 8 7 4 F

and then I used TD-DFT:

%chk=TD_r66a20.chk

#p td=50-50 b3lyp/6-311g(d,p) guess=read geom=modredundant

empiricaldispersion=gd3

0 1

C 4.57698700 -1.53187000 -1.36424900

C 3.75481000 -1.51008200 -0.23758000

C 2.55798100 -0.80468800 -0.24377800

C 2.14632500 -0.10708600 -1.39547000

C 2.99699900 -0.13134300 -2.51984500

C 4.19414400 -0.83516100 -2.50858000

C 0.89159700 0.62999000 -1.55114300

C -0.27435800 0.70469200 -0.86532400

C -0.59792900 0.35067600 0.52831800

O 0.30513800 0.24919700 1.38241800

C -2.01433100 0.18454400 0.90698200

C -3.03855200 0.09651400 -0.06205900

C -4.36552400 -0.05278100 0.28825300

C -4.71245400 -0.11193000 1.64622500

C -3.74051600 -0.04526600 2.62493200

C -2.38264300 0.08394500 2.28222800

O -1.50585900 0.10857200 3.28772500

H 5.51156300 -2.08122700 -1.34739000

H 4.05390600 -2.04016600 0.65965800

H 1.94681000 -0.76569400 0.64361800

H 2.70339300 0.40370600 -3.41709000

H 4.82662300 -0.83984000 -3.38890700

H 0.83873200 1.11664200 -2.52366400

H -1.06583700 1.23983900 -1.37662000

H -2.77550200 0.12198400 -1.11161000

H -5.12838300 -0.12504600 -0.47694700

H -5.75246200 -0.22022600 1.93411400

H -3.98663500 -0.10382500 3.67800000

H -0.51723700 0.14856600 2.81931600

B 10 29 F

B 17 29 F

D 4 7 8 9 F

Using TD-DFT I got results that made chemical sense for a T1 state. Any help would be much appreciated

The image labeled T1 is from TD-DFT

It is possible to convert the Gaussian output file to CIF file format?

can anyone help me with this.

As per suggested i optimize molecule in semi emipirical Am1,pm3 set and reoptimize it in dft . And directly optimize from gaussian input file . But optimize geometrical parameter and mulliken charge were different for two cases.Is it okay to have different result?

Even fixing memory limit and processor unit does not work.

I am try to optimize molecule at 0 K using keyword "Temperature=0" but gaussian performs calculation at 298 K. How to get my required thermodynamic parameter at 0K

I'm trying to simulate the sulfate anion structure in Gaussian, but my double bonds disappeared after the calculations. I had the same problem when I was trying to simulate the acetate anion.

For the sulfate, I put two double bounds in my structure and I decreased their length compared to the two remaining single length.

The following are my file details.

When I try to create a mapped surface in "surface and contours" the Gaussian gives the following error.. and the cube generation is getting failed

"String too long in BldStr.

Error termination via Lnk1e"

I'm trying to simulate the complex [V(H2O)6]³⁺ using Guassian, but the calculation does not converge.

I have recently gained access to a research cluster which has Gaussian 16. I am relatively new to both Gaussian and cluster computing. I am currently optimizing a combination of small first row metal-chalcogenide clusters with ligands using a TPSSh functional and a TZVP basis set. I currently have access to several nodes each with 48 cores and at least 8GB of ram per core.

In the .gjf file I have a bit of scratch memory, 32 cores, and 64GB of memory.

%LindaWorkers=str-c23

%NProcShared=32

%rwf=a1,20GB,a2,20GB

%NoSave

%nprocshared=32

%mem=64000MB

In the .slurm I have allocated 1 node, 32 cores, and 2GB of memory per core.

#SBATCH --nodes=1

#SBATCH --ntasks-per-node=32

#SBATCH --time=48:00:00

#SBATCH --mem-per-cpu=2GB

#SBATCH --output=%x_%j.out

Yet when running my optimizations I get dramatically different amounts of memory utilized.

For a run on a single ligand under these conditions it used 31.4 of the 64GB given.

For a larger ligand w/ same condtions used 20GB.

For the small ligand with a larger basis set (def2TZVP) it only used 12.7 GB.

For a metal cluster with 4 ligands (note: convergence failure) it used only 2-3GB.

Is there something I can do to better utilize the memory I have available?

Hello, Can anybody assist me in expanding the number of cores using gaussian 9.0 program. I have multiprocessor system with Intel® Core™ i5-1135G7 (up to 4.2 GHz with Intel® Turbo Boost Technology, 8 MB L3 cache, 4 cores) and 8GB RAM. I am using Avogadro and Gaussian, so kindly assist me where to put the commands?

I need a small workstation for gaussian package linux version to do some parallel processing. In this regard, what should be the configuration of a workstation?

Hello everybody,

The generic equation of an asymmetric Gaussian curve is :

y = k * exp[-{(x-x0)^2}/{2*sig^2}] * [1+erf({a*(x-x0)}/{sig*sqrt(2)})].

I need to know the coordinates ("x" and "y") of the top (assuming k>0) of such an asymmetric Gaussian curve, as a function of the asymmetry parameter "a". Does there exist an analytic function that gives this? At least, does there exist such a function for the more specific but also simpler "y = exp[-{x^2}/2] * [1+erf({a*x}/{sqrt(2)})]" (i.e. with k=1, sig=1, x0=0)? Then it would be easy to generalize for any k, sig and x0.

Thank you very much.

Hi!

I am working on a thesis project using Gaussian to model reactivtiy in compounds and I keep getting the error message " End of file reading connectivity." I have looked through Gaussian error messages and around on here and have not found anything. Find my output log attached.

Explain in detail.

I am trying to do a single-point polarizability calculation with TDDFT with input :

#p polar td=(nstates=8) M062X/6-31+g(d,p) geom=connectivity

I am getting an error like:

The selected state is a singlet.

CISGrX: IGrad=3 NXY=2 DFT=T

CISAX will form 3 AO SS matrices at one time.

Can anyone suggest any solution?

I have attached the output below.

<<The job is described in the followign code, where the gs.chk file is the result of a successful opt + freq calculation.>>

--link1--

%OldChk=8PhOPc_DMF_gs.chk

%Chk=8PhOPc_DMF_ex.chk

# td=(singlets,nstates=12) CAM-B3LYP TZVP Geom=check guess=read

scrf=(solvent=n,n-dimethylformamide) Int=(Ultrafine)

8-PhOPc TD 12 singly excited states: CAM-B3LYP/TZVP

0 1

<<This is the last few lines of output.>>

1 vectors produced by pass997 Test12= 5.85D-13 1.00D-09 XBig12= 5.26D-15 1.08D-09.

1 vectors produced by pass998 Test12= 5.85D-13 1.00D-09 XBig12= 5.35D-15 1.18D-09.

1 vectors produced by pass999 Test12= 5.85D-13 1.00D-09 XBig12= 5.23D-15 1.08D-09.

1 vectors produced by pass*** Test12= 5.85D-13 1.00D-09 XBig12= 5.29D-15 1.14D-09.

CPHF failed to converge in LinEq2.

Error termination via Lnk1e in /opt/apps/gaussian/16.c.01/g16/l1002.exe at Thu Jan 25 22:29:53 2024.

Job cpu time: 45 days 22 hours 11 minutes 56.9 seconds.

Elapsed time: 1 days 3 hours 47 minutes 34.0 seconds.

File lengths (MBytes): RWF= 224288 Int= 0 D2E= 0 Chk= 337 Scr= 1

In Guassian, which convergence algorithm is best for working with transition metal interaction? It is taking a long time to even get the first block of coordinates, in the output file it said to use the steepest-descent method, but I think maybe this is not enough. I read that in Orca there is the KDIIS algorithm to enable faster convergence for transitional metals, is there something similar in Gaussian?

I tried scf=qc and scf=xqc and it does not work for the interaction between graphene and a transition metal cluster.

Hi, I was told that:

which means I should expect the CPU time to be less than the elapsed time by a factor of N, where N is the number of cores used.

However, in my Gaussian calculation, CPU time is equal to the elapsed time. My question is, was the job done on a single core? if it did, how do I enable it to run on multi-cores? I did my calculation on a Windows machine.

Thank you in advance.

Hi, I have been trying to obtain the checkpoint files from running gaussian jobs in OSC, but of no avail.

I have tried altering %chk=filename.chk to .fchk, used the utilities in gaussian to obtain the fch file using Formchk but it doesnt work. The formatted checkpoint files i generate always has the same error of "Incomplete data on line 2: JobType method basis", even though the log file has no errors.

Any help is appreciated.

I’m trying to submit another calculation now in B3LYP 6-31/G(d,p) and shown another two error messages:

error #2070 all processing of the last link ended abnormally, all process has been aborted

error #2061 can’t lock the block memory for the list job.

Can you help me with this problems?

thank

I was trying to build a g-C3N4 graphitic carbon nitride molecule using Gaussview; however, the file seemed to miss handle specific values representing certain atoms as "?s" and then specifying their coordinate values.

What do these "?s" represent, and how can I fix that?

Also, I wanted to ask how I can use the CIF file(from the materials project) directly for Gaussian calculations. As far as my knowledge goes, generally, the CIF files are built to work for vasp/qe software using plane-wave dft.

I also wanted to know if we can do a two or more layered structure analysis in Gaussian.

P.S. Pardon me for my silly and easy questions; I'm just an undergraduate curious to learn but stuck

I have three transition states corresponding to a catalytic cycle, and there are 3 non-bonding interactions involved in them. Are there any tools available in Gaussian 16 that could quantify the strength and nature of these interactions?

Also, can Wiberg Bond order index be used for determining the above?

Overall I would say no, because it can make big mistakes, but it seems to be able to somehow adapt to new knowledge, after processing its data exabytes. Let me give you a couple of examples.

- First, a basic mistake it made:

You

And mathematically, as functions on the real axis, is their behavior very different or similar? Are both peaked functions that tend to zero as the value of the variable increases or do their behaviors bear little similarity?

ChatGPT

Mathematically, both the sinc and Gaussian functions have similar behaviors in that they are both smooth functions that tend to zero as the independent variable moves infinitely further away on the real axis. However, there are differences in their specific forms and how quickly they tend to zero. Sinc Function: The sinc function has a bell shape and is defined as sinc(x)=sin(πx)/πx​. It vanishes for x=0 and has additional zeros at =±1,±2,…x=±1,±2,…. As ∣x∣ increases, the sinc function tends to zero, but its convergence is relatively slow, since the presence of zeros prevents a rapid decay

...

You

I think you are wrong. The sinc function that you have sent does not vanish at x=0 (its value at the origin is 1). On the other hand, the Gaussian always takes positive values ​​and decreases monotonically. For me it is a big difference. Don't you agree?

ChatGPT

My apologies for the confusion and thanks for pointing it out. You are correct in your observation. The sinc function, in fact, does not vanish at x=0 (its value is 1 at that point), and presents oscillations as ∣x∣ increases, which makes it not smooth in the sense of having continuous derivatives in all orders.

- Next, a situation in which it seems to be able to adapt to new knowledge:

You

But the Gaussian and Lorentzian representations do not need to be convolved with test functions in the Schwartz space (as distributions) to get the same result, they can be integrated together with any continuous function and produce the same result as they do with test functions. Only the sinc function or similarly problematic representations need to be restricted to the Schwartz space to become equal to the others. Did you know that? Do you think that this mathematical restriction is fair to the Gaussian and Lorentzian? In this sense, maybe we are talking about different categories of delta functions.

ChatGPT

Yes, you're correct in pointing out a subtle yet crucial distinction. The Gaussian and Lorentzian representations of the Dirac delta function indeed have a special property that allows them to be integrated with a broader class of functions, not necessarily limited to the Schwartz space, and still produce the same result. This property is a consequence of the fact that these representations are entire functions of t and have certain regularity properties.

I would be curious to know your opinion/experience, if only because AI will soon become widespread.

Processor: Intel(R) Xeon(R) CPU E5-1650 v2 @ 3.50GHz

Installed RAM: 32.0 GB

Cores: 6

Logical Processors: 12

Virtualization: Enabled

System type: 64-bit operating system, x64-based processor

With above configuration of workstation, how far can I increase the memory and no. of. processors in gaussian 09W to use the maximum resources and minimize the time of job?

Hello all, I hope someone here can help me with some TD-DFT calculations. I am trying to calculate the excited state optimised structures and energies of some Germanium compounds. Firstly, I run a TD calculation of the first 10 excited states, singlets and triplets, using: TDA=(Nstates=10,50-50) WB97XD/genecp From this output I see the first excites states energies and they look ok to me, such as:  Excited State   1:      Triplet-A      2.4156 eV  513.26 nm  f=0.0000  <S**2>=2.000      113 ->120        -0.18260      119 ->120         0.65189  This state for optimization and/or second-order correction.  Total Energy, E(CIS/TDA) =  -1629.19629051     Copying the excited state density for this state as the 1-particle RhoCI density.  Excited State   2:      Singlet-A      3.3296 eV  372.37 nm  f=0.0537  <S**2>=0.000      113 ->120        -0.18586      119 ->120         0.66543 I then try to optimise the first singlet and triplet as I want to see how the spin density looks like in those species. For the first triplet I just indicate multiplicity 3 in the gaussian input (0 3 right before the coordinates), and I get something that I think it makes sense, the molecule geometry changes and I get alpha and beta orbitals, one electron seems to be occupying a virtual orbital by himself.... etc The problem comes with the first singlet excited state, in order to calculate it I use: TD=(Nstates=6,50-50,root=2) WB97XD/genecp Based in the previously calculates excited states, in which the second state is the first singlet. However, after the calculation was done (it took quite a long time) I see an output with completely normal orbitals (not alpha and beta), a nice homo with two electrons and a empty LUMO, as in the molecule looks like a normal diamagnetic ground state molecule. Does someone see something weird in my procedures? If you need any more details please let me know. My apologies if I am making some very basic mistakes I am very new in TD-DFT. Thank you all in advance!

Recently, in a research paper, i found that the author had optimized the structures in an S1 excited state (S0 = G.S).

Hi all,

I have a project to calculate noncovalent bonding interaction. I want to identify if there are any INTRAmolecular interactions in my compound. I was using NCI from Multiwfn to perform it; however, I did not know how to separate the INTERmolecular and INTRAmolecular interactions from the result. Are there other methods to do this?

Thank you in advance.

How to solve the following error for tddft calculations with lc-wpbe functional in gaussian16?

MaxDer out of range in HSEd.

I want to convert the output files of .gjf format from Gaussian to smiles format.Is there any software or online server that accurately converts it.

Hi, everyone! when I scan the coordinate in Gussian software, The log file shows the following error:

New curvilinear step failed: FormB failed.

Error imposing constraints

Error termination via Lnk1e in /home/Gaussian/Gaussian/g09/l103.exe at Sun May 29 18:16:46 2022.

Has this ever happened to you?

Hello. Sorry for asking this question in poor English. I am a student studying organometallic chemistry. I am doing a TS calculation using gaussian16 to find a pathway for a catalytic reaction, but for some reason, it outputs a structure where the two molecules are far apart and not in a transition state. Each molecule has been structure-optimized with optfreq, and the scan calculation of each molecule is used as the initial structure for the TS calculation. I have done the same thing with the same keywords in the pre-reaction phase of the catalytic reaction, and it completes to TS without any problems. What seems to be the problem? I am currently trying to see if the "noeigentest" is not necessary. I used "noeigentest" in both failed and successful calculations, but I am not sure if "noeigentest" is appropriate for a calculation with 84 atoms.

I'm looking to calculate charges for my ligand and later run MD simulation on them. I ran into this error suddenly when it had worked in the past. I have Gaussian 16 installed.

Net charge: -1

Net charge: -1

Charge and Multiplicity [0,1]? Percent or Route card? Percent or Route card? Percent or Route card? Percent or Route card? Route card? Titles? Titles? Charge and Multiplicity? ../../simulation_OTP111_3One_0_Emin.sh: line 25: /programs/g16: Is a directory

Error termination in NtrErr:

ntran open failure returned to fopen.

Error: segmentation violation

rax 0000000000000000, rbx 0000000005c10e60, rcx ffffffffffffffff

rdx 0000000000038f42, rsp 00007fffffa34778, rbp 00007fffffa347b0

rsi 000000000000000b, rdi 0000000000038f42, r8 00002aaaaaae8800

r9 00002aaaaaae8800, r10 00007fffffa33b60, r11 0000000000000206

r12 0000000000000000, r13 0000000005c04598, r14 00007fffffa39bd0

r15 00007fffffa39910

/lib64/libpthread.so.0(+0xf630) [0x2aaaab0ab630]

/lib64/libc.so.6(kill+0x7) [0x2aaaab5f0657]

/programs/g16/newzmat() [0x458fc5]

/programs/g16/newzmat() [0x49ccb9]

/programs/g16/newzmat() [0x4873f2]

/programs/g16/newzmat() [0x434284]

/programs/g16/newzmat() [0x411a36]

/programs/g16/newzmat() [0x4109a6]

/programs/g16/newzmat() [0x410864]

/lib64/libc.so.6(__libc_start_main+0xf5) [0x2aaaab5dc555]

/programs/g16/newzmat() [0x40afa9]

/scratch1/alex/glyco_project/glycomimetics/scripts/make_gaussian_input_file.sh: line 52: 233282 Aborted /programs/g16/newzmat -ichk -ozmat -prompt ${old_chk} ${gaussian_input} < newzmat_here_esp.txt

../../simulation_OTP111_3One_0_Emin.sh: line 31: /programs/g16: Is a directory

Num atoms : 19

Getting ESP charges on OTP111_3One_0_ligand_esp_g16.log

Running Resp

Error: No ESP fitting centers and fitting values exist, adding 'iop(6/33=2) iop(6/42=6)' to the key word list

/scratch1/alex/glyco_project/glycomimetics/scripts/Run.resp: line 42: /scratch2/alex/Set5/Trial_1/simulation/analog_OTP111_3One_0/1_leap/resp-2.2/resp: No such file or directory

Slurm script ends

I am trying to perform nbo calculations on an optimized structure using Gaussian software. I've included my input file as well as abbreviated NBO orbital interaction output. The separation of this molecule into unit 1 and unit 2 excludes orbital interactions of interest. Is there a way to force NBO calculations on a single molecular unit that includes all of the atoms in the structure?

%chk=popfull.chk

# pop=nbo def2tzvp m062x

Title Card Required

0 1

C 1.95142900 1.26670400 -0.64686300

C 1.49877700 1.25230100 0.81204400

C 0.68871800 -0.00064100 1.14730100

C 1.49928100 -1.25293900 0.81112200

C 1.95190300 -1.26607100 -0.64780600

C 2.73279200 0.00058800 -0.99641200

H 0.42464900 -0.00107800 2.20608600

H 2.39583300 1.26350300 1.44686400

H 0.94295000 2.16218600 1.04824300

H 1.07322900 1.34303900 -1.30171200

H 2.56075300 2.15028700 -0.84583400

H 2.39634600 -1.26420000 1.44592400

H 0.94384400 -2.16323700 1.04663700

H 2.56153300 -2.14928500 -0.84747900

H 1.07368200 -1.34221000 -1.30262700

H 3.67138100 0.00054400 -0.43267600

H 3.00144000 0.00105300 -2.05435600

F -2.91217100 0.00014000 -0.85547800

Cd -1.18278100 -0.00003100 0.09195700

-----------------------------------------------------------------------------------------

Donor NBO (i) Acceptor NBO (j) kcal/mol a.u. a.u.

===================================================================================================

within unit 1

1. BD ( 1) C 1 - C 2 /172. RY*( 1) C 6 0.62 2.04 0.032

from unit 1 to unit 2

10. BD ( 1) C 3 -Cd 19 /253. RY*( 1) F 18 1.42 1.98 0.048

from unit 2 to unit 1

25. CR ( 1) F 18 / 39. LP*( 6)Cd 19 2.78 25.22 0.239

within unit 2

33. LP ( 4) F 18 /257. RY*( 5) F 18 0.53 3.03 0.037

In NBO analysis by Gaussian I am getting BD(3) and BD(3)* . What do they mean?

How to interpret them

Dear community,

Is there any way to convert the .chk file to .fchk file WITHOUT using formchk tool of Gaussian software that strictly demand the compatibility of the Gaussian version?

I have generated the input file in Gaussian and given command pop=full. In the output file I am not able to figure out how can I obtain the density distribution directly. I need help regarding this.

I am uploading the input file.

I have used the hybrid function PBE0 and basis set as C,H,N,O=6-31G**, Co=def2-TZVP.

In using Opt TD=(nstates=n) in Gaussian, I get many data points for excited state energies of each state, i.e. the results for the TD calculation are repeated after each optimization. Should I just choose the last set? The energies are quite different for the same # excited state each time (~70nm difference for excited state 1 across the repeated results).

I have read some topic about counterpoise on RG. And I have 2 question

1. Is counterpoise with optimization actually meaningless since on Gaussian website has mentioned opt with counterpoise?

2. In Gaussian 16, the counterpoise output shows complexation energy (e.g AB) Do I need to perform opt A and B monomer separately?

Thanks in advance.

Dear,

I run the scf calculation for hexagonal BeO structure. And The c parameter was not optimized after calculation. I found this c parameter is differ from literature data. I added the optimization file code. Do you have any comment for this input file. Where could there be a mistake ?

&CONTROL

calculation = "vc-relax"

forc_conv_thr = 1.00000e-03

nstep = 100

prefix ="BeO_scf_cal"

verbosity ="high"

restart_mode = "from_scratch"

outdir = './outdir'

pseudo_dir = "C:/Users/LENOVO/Desktop/QE/deneme/BeO"

/

&SYSTEM

celldm(1) = 5.098

celldm(3) = 3.067

degauss = 0.01

ecutrho = 650.0

ecutwfc = 65.0

ibrav = 4

nat = 4

ntyp = 2

occupations = "smearing"

smearing = "gaussian"

/

&ELECTRONS

conv_thr = 1.00000e-8

electron_maxstep = 100

mixing_beta = 7.00000e-01

startingpot = "atomic"

startingwfc = "atomic+random"

/

&IONS

ion_dynamics = "bfgs"

/

&CELL

cell_dofree = "all"

cell_dynamics = "bfgs"

/

ATOMIC_SPECIES

Be 9.012 Be.pbe-n-rrkjus_psl.1.0.0.UPF

O 15.999 O.pbe-n-rrkjus_psl.1.0.0.UPF

ATOMIC_POSITIONS {crystal}

Be 0.0000 0.0000 0.0000

Be 0.3333 0.6666 0.5000

O 0.0000 0.0000 0.3780

O 0.3333 0.6666 0.8780

K_POINTS {automatic}

16 16 14 0 0 0

I am using Gaussian on a structure with Iodine. I use LanL2DZ for the Iodine atom and 6-31G for the other atoms. I cant seem to use Pop=MK. I get an error, "GetVDW: no radius for atom 12 atomic number 53." I need ESP information in the Gaussian output file for my next step using AmberMD. Any ideas?

# opt freq B3LYP/genecp Pop=mk iop(6/33=2,6/41=10,6/42=17)

remark line goes here

0 1

C 2.4590000000 -0.6850000000 -0.0220000000

C 2.4620000000 0.7060000000 0.0150000000

C 1.2490000000 1.3980000000 0.0240000000

C 0.0090000000 0.7110000000 -0.0090000000

C 0.0190000000 -0.6980000000 -0.0420000000

C 1.2430000000 -1.3660000000 -0.0440000000

C -1.2600000000 1.3330000000 -0.0130000000

C -2.4220000000 0.5700000000 -0.0520000000

C -2.2940000000 -0.8030000000 -0.0810000000

N -1.1060000000 -1.4440000000 -0.0740000000

O 1.2140000000 -2.7440000000 -0.0710000000

I 4.2920000000 -1.6840000000 -0.0470000000

Cl 1.3310000000 3.1280000000 0.0730000000

H 3.4000000000 1.2570000000 0.0350000000

H -1.3520000000 2.4160000000 0.0100000000

H -3.4000000000 1.0390000000 -0.0600000000

H -3.1700000000 -1.4460000000 -0.1120000000

H 0.2580000000 -2.9680000000 -0.0780000000

C H N O Cl 0

6-31g*

****

I 0

Lanl2dz

****

I 0

Lanl2dz

when we run our file with fchk additional keyword we get file with test.fchk name, how can we change test name?

Hello everyone, (Question about gaussian heat source)

It might be a very basic question but I am having a hard time imagining the Gaussian heat source. I want to apply the heat source through the node "deposited beam power". You can find this node under heat transfer module >Heat source> deposited beam power.

What I understood is, "O" is the origin of laser, not the point where we want to apply the heat source.

About "e" (laser beam's orientation), As you can see there are no units assigned to it. So, I think it must be a unit vector. I want to apply this heat source in my 2D ais symmetric model. So, I can only put the value in "z" column for "O" and "e". The coordinate where I want to apply the laser heat source is (0,-0.3), therefore:

O: (0,0,0)

e: (0,0,-0.3)

Is it okay ? I put my geometry in the negative z axis (-0.3) to put the negative sign in the "e" because of the direction of the laser. Please clear this.

Second, "d" (see the figure) is the distance between e and x. What is x here? How can I visualize it?

Your comments and suggestions are awaited.

Thank You.

Early assessment of biomarker variability in target populations is essential for the speedy validation and cost-efficient development of biomarkers.

Markers may increase and decrease to a different extent or remain unchanged in patients diagnosed with the same disease. (Cancer Res., 2019 Jul 1; 79(13):3492-3502)

Misclassification of samples on biomarkers may impact clinical trial patient recruitment and treatment outcomes.

We developed g3mclass, practical software that automates the Gaussian Mixture Model and Bayes classifier and augments conventional binary classification. (Sci Rep. 2022 Nov 5; 12(1):18742) https://www.nature.com/articles/s41598-022-23438-9

Are you interested in being an early software adopter? Don't hesitate to reach out to us!

Marina Guvakova, PhD

The g3mclass co-author and licensor

Respected Scientific Community,

I am facing an issue with reading data in .chk file that I have just transferred (using win-SCP) from Gaussian installed on supercomputer.

I have tried the tutorial available on Gaussian website (from Gaussian step > Utilities > Fchk using my window-based laptop (Gaussian 09)

It generated the .fchk file with 0 kb.

I would be highly obliged If any lead assist me in this regard?

Dear,

Greetings of the day,

I tried to convert .chk to .fchk format by formchk command and gaussian/utilities/formchk way, but it doesn't work.

Do you have any suggestions, please.

Thanking you​

Hi all,

I'm trying to run a single point calculation with swapped MO ( I used guess=Alter to swapped them.)

I checked that the MO order is swapped at the beginning of the SCF but it goes back to original ordering at the end of calculation. I want to just restrict the order not freeze MO.

Does anyone know the keyword to do this?

Thank you.

Hello everybody,

I analyzed a picture in ImageJ, but I encountered a problem with the threshold. I tried to count cells with analyzed particles. Before starting, I adjusted the picture by changing the contrast and applying a Gaussian filter. Until yesterday, I did it exactly as described, but today the program displayed a message: 'the threshold may not be correct (255-255).'

Can someone help me with this issue? Has anyone with the same problem been able to resolve it?

Hey all,

I am working with Gaussian 16 program package. For one of my geometry optimization calculations more than 100 geometry cycles runs are required. But even when I am including the tag "opt=(maxcycles=150)" in the input, it runs only up to 100 geometry cycles. So, please suggest the ways to increase the number of geometry cycle runs.

Your suggestions would be appreciated.

Thank You!

hello every body

Does anyone have any idea to solve error l801 in gaussian 09. here is the snapshot of the error. it is an mp2 optimizaion of guanine and Mg+2 cation. I would be very thankful.

I need optimization on Gaussian 16 using same xyz coordinates form ORCA output.

But in Gaussian i am not getting the same optimized geometry as in ORCA (structure changed). Which is reliable optimization? and how to fix Gaussian without error termination meggasge

currently, I am working on a computational method of drug delivery system using Gaussian 09. I want to study PET, PCT, and NCI analysis complex systems. let me know the protocol and procedure of this analysis and how to do it.

Thanks in advance

Gaussian noise refers to random variations that follow a normal distribution, also known as a Gaussian distribution. Fractals, on the other hand, are complex and self-repeating geometric patterns.

While noise in fractal patterns can be generated using various techniques, including random perturbations and iterative algorithms, adding Gaussian noise to a fractal can introduce additional random variations to its structure.

The process of adding Gaussian noise to a fractal involves applying random values from a Gaussian distribution to the fractal's existing structure. These random values can be used to modify the position, scale, or color of individual fractal elements, resulting in a distorted, yet still recognizable fractal pattern.

Brownian motion, also known as random walk, is a physical phenomenon where particles suspended in a fluid undergo random movements due to collisions with the fluid molecules. These movements appear to be erratic and unpredictable. Fractals, on the other hand, are mathematical objects that exhibit self-similarity at different scales. They are characterized by recursive patterns that repeat at smaller and smaller magnifications. When it comes to the relationship between Brownian motion and fractals, interesting connections can be drawn. One such connection is the concept of fractional Brownian motion (fBm), which is a generalization of classical Brownian motion to fractal dimensions. In classical Brownian motion, the increments of the random walk are independent of each other. In contrast, in fBm, the increments are correlated, giving rise to long-range dependence. This means that the behavior of the process at a given time is influenced by its past behavior over long periods. The fractal nature of fBm arises from the fact that its increments have a power-law autocovariance function, meaning that the correlation between increments decays as a power of the time lag. This power law behavior is similar to the self-similarity observed in fractals.