Atoms - Science topic

the MAGMOM tag represents the initial magnetic moment of each atom, you can choose 3 for transition metal and 0 for nonmagnetic atoms. However, after you run the calculation you will find the final magnetic moment at the end of OUTCAR.

See also

Alternatively, you could just use a code that was made for molecular, aperiodic structures. GAMESS offers free site licenses to academic users, but of course commercial tools like Turbomole may do the job faster.

In addition to the previous right question Prof. Rk Naresh , the energy of an object or system of objects is given by the internal energy U, we have translational degrees of freedom for kinetic energy, but also we have other types of degrees of freedom: vibrational, rotational, and electronic.

In a diatomic molecule as Carbon Dioxide (CO) all these degrees of freedom appear at different temperatures, as T increases. It can be seen in a plot of the specific heat as a function of temperature, and therefore the internal energy of the CO molecule contains all these degrees of freedom .

There is another simple example for an ideal gas that deviates from the Maxwell distribution for kinetic energy, and it is the distribution function of a system of particles in an external gravitational field.

Kind Regards.

Hi Wei,

Have you refined the structure? And do you know which atoms are replaced by Zn at the surface? And do you know which surface(s) (hkl) is/are mostly exposed in this material (I personally don't know about it)? And do you know if Zn occupies sites only at the top layer?

If you have answers to the above, then maybe the following steps can help you.

1) Calculate the area of the most common hkl plane the particle is exposed at for the unmodified material

2) Estimate the maximum possible area for the case where all the replaceable atoms are replaced by Zn (from ionic radius)

3) Use the cell parameters of the modified material to calculate the area for the same hkl.

By comparing these values, I think it would be possible to know approximately how much of the surface is covered. Unfortunately, many assumptions are made.

If there are multiple crystallographic sites that can be replaced, then maybe you need more experimental data to get the coverage for each separately.

Best regards,

Hello,

You can create an index file with each group of three atoms using make_ndx, then you can use: gmx gangle -f file.xtc -s file.tpr -n index.ndx -g1 angle -group1, and in the selection you can use: >com of group 1 plus com of group 2 plus com of group 3 (^D to end).

Hope help.

Try with Schrodinger Q/A

You can add this line in the AD4 parameters.dat file

Regards

Dr. Kadim,

Do a CHN analysis and an Atomic Absorption for the Ag.

Why would consider this an unexpected result? Hydrogen is pretty well capable of reducing Ni²⁺ to Ni⁰ and water formation from the counterion would be a quite reasonable mechanism

Dear Gabriel A. Alvarez N. don't forget, each atom has its own identity. Some are transferring electricity, some can create electricity, so on. But none of atom on periodic table the same, thus it is the sign of intelligent. Unfortunately science do not anything about atom, due to quantum mechanic. Everything in the universe is following its intelligence, and follow its nature.

Molecules are made of few atoms, and each molecule has certain function such as salt, carbon diopside...etc.

One of the sign of intelligence is to use energy (sunlight or photon) without friction, like us, and atom is doing the same.

One way to predict the type of bond that forms between two elements is to compare the electro negativities of the elements. In general, large differences in electro negativity result in ionic bonds, while smaller differences result in covalent bonds. The number of electrons in the outermost shell of a particular atom determines its reactivity, or tendency to form chemical bonds with other atoms. This outermost shell is known as the valence shell, and the electrons found in it are called valence electrons. One of the most important factors in determining the chemical properties of elements is the number of electrons in its outermost shell. The number of electrons in the outer shell determines the bonding characteristics of an element. The strength of a chemical bond is determined by the difference in electro negativity. Generally, the numbers of electrons are even. Covalent bonds can exist as a gas, solid, or liquid. There are three types of strong chemical bonds: ionic, covalent and metallic. For ionic bonding the particles are oppositely charged ions. For covalent bonding the particles are atoms which share pairs of electrons. For metallic bonding the particles are atoms which share delocalized electrons. An atom is composed of a nucleus and electrons that go around the former. The nucleus is composed of protons with a positive charge and neutrons without charge, and the number of protons determines the chemical properties of the atom. One way to predict the type of bond that forms between two elements is to compare the electro negativities of the elements. In general, large differences in electro negativity result in ionic bonds, while smaller differences result in covalent bonds. The nature of bonding between elements or atoms depends upon their outer electronic configuration. The ionic bonding is formed by the complete transfer of these valence electrons in between two bonded atoms. This type of ionic bond is formed in between metals and nonmetals.

Thank you very much

In your case, the problem is the lack of RAM. The optimization of the structure was completed successfully, but the calculation of the matrix of second derivatives (frequencies) requires much more resources, but you set a limit of only 1 GB of RAM, which is very small for such a large system. If this is a limitation of a particular computer, then you can carry out calculations on another computer using the chk-file and keywords Guess=Read Geom=Checkpoint

Thank you dear for your answer. I will consider your advice

📷 Ana E. Torres

Hi Deepak, were you able to use it? I also need to understand it so any help would be highly appreciated.

Hi

Please follow the following video for step by step approch to plot the spin density and also shown the number of spin electron in the system: https://youtu.be/g5G0Lf21sZw?si=xJ8dRQAioLjxsA0G

thank you

Although for iodine atom, it is not need to use aug-CC-pVTZ basis set in the geometry optimization. The structure of local energy minimum in the potential energy surface can be finded by normal basis sets without diffuse function, such as def2-TZVP. This will save much computing time.

If you want to calculate the single point energy or electronic structure after geometry optimization, you can use high precise basis sets with diffuse function.

Yes, Sure. Thanks

KPOINT attached below:

Tutorial on how to incorporate easily a custom AD4 parameter file when using Autodock4

Hey there, my fellow researcher Aqsa Kamran! Let's dive into your simulation challenge together. Now, I don't hold back, so here's my take:

It's fantastic that you're working on simulating a covalently functionalized boron nitride nanosheet with a polymer. It's a complex system and getting the topology right is crucial. Here's some guidance:

1. **Bonded Parameters**: You've got the itp file for your polymer, which is great. For your polymer's bonded parameters (bond lengths, angles, dihedrals), you can indeed let CHARMM-GUI or CGenFF generate them for you. However, make sure that your force field (CHARMM36 in this case) is compatible with your polymer. Sometimes, the compatibility might require manual adjustments.

2. **Charges**: The charges are a critical aspect. You mentioned you have charges from CGenFF for your polymer, and you're using these charges for your nanosheet as well. This is a reasonable approach if the charges are similar in nature and units (often in partial charges). But be cautious, because nanosheets and polymers might have different charge models. If possible, validate these charges through ab initio calculations or literature data.

3. **Non-bonded Parameters**: Ensure that your itp file for the polymer has the correct non-bonded parameters (Lennard-Jones parameters) for the atoms. These parameters are critical for the interactions between atoms in your system.

4. **Topology Integration**: You might need to manually integrate the itp parameters for your polymer into your system's topology. This means copying the bonded and non-bonded parameters from your polymer itp file into your system topology file. Be careful with atom type naming conventions; they should match between the itp file and the topology.

5. **Testing**: Before you dive into production simulations, always perform a thorough equilibration and validation of your system. This helps you catch any anomalies or issues with your topology.

6. **Consult the Literature**: If possible, look for publications or literature data that have dealt with a similar system. They might provide insights into the force field parameters and topology generation.

Remember, simulation can be a trial-and-error process, and it's essential to validate your results against experimental data or other reliable sources. If you're in doubt about a specific parameter or aspect of your system, it's better to consult with experts in your field or on simulation forums.

I hope this helps you in your simulation journey, my fellow researcher Aqsa Kamran! Don't hesitate to ask me if you need further guidance.

You should be able to use the tetrahedron method for 2D slabs, but you need a sufficient amount of k-points along x and y, so just increase that number until the error goes away.

Hi,

you have to add this to either the AD4.1_bound.dat or AD4_parameters.dat (often found inside MGLTools directory):

atom_par Pd 1.34 0.048 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

Also, as it is VINA, you might have to recompile it again.

Unfortunately the only boron parameters you will find in CHARMM is for boronic acids (BO4), which means that you only have parameters for B - C and B - O, not B - N.

You will have to generate these parameters by QM (bonds and angles) using the equations available in the GROMACS manual to obtain the corresponding bond lengths/force and angle/force.

The file that you have is only half the solution (you can see bond lengths but thats all).

If you have access to CHARMM-GUI you can try to get the missing parameters from it (and then convert them to GROMACS format).

Thanks

Exactly,

We figure out the secrets of our universe by following energy beneath the surface not the sub-atomic particles.

But molecules are just the ingredients not the recipe. So James please help me answer this question "what is exactly created and how it created DNA"?

Isn't it the most spectacular structure of molecules we ever discovered?

Hai Dr, how are you? I am attracted to your question as I have some information on it. Below, I supply you with all the answers you need, but I would really appreciate it if you could press the RECOMMENDATION buttons underneath my 3 research papers' titles in my AUTHOR section as a way of you saying thanks and appreciation for my time and knowledge sharing. Please do not be mistaken, there are few RECOMMENDATION buttons in RESEARCHGATE. One is RECOMMENDATION button for Questions and Answers and the other RECOMMENDATIONS button for papers by the Authors. I would appreciate if you could click the RECOMMENDATION button for my 3 papers under my AUTHORSHIP. Thank you in advance and in return I provide you with the answers to your question below :

YES, you can use Olex2 to get the component 1 cif by deleting the disordered atoms from the parent compound and saving it without further refinement. This is because the Hirshfeld surface is calculated based on the atomic positions in the cif file, and the disordered atoms will not affect the calculation of the Hirshfeld surface.

Here are the steps on how to do this:

Yes, but that's right. Apparently, this is the number of formula units in the unit cell volume.

Hello Heyonuk Choo,

If you know the crystal structure, you can get the indexes, don't need HRTEM. From the crystal structure file, you can use VESTA or GSAS-II to generate hkl and d-spacing. I think Mercury can do it too.

Feel free to reply if you need help with these softwares.

Best regards,

Ricardo Tadeu

Presumably, the .psf file didn't have the parameters for OT atom type.

Please check the topology .rtf files as well as the parameter .prm files to look into the atom details.

Adam Matěj Thank you for your response- The project I am working on is for students to better visualize the quantitative calculations by comparing it to qualitative calculations taught in inorganic chemistry courses.

I am comparing qualitative results calculated from group theory to quantitative results from a computational calculation for a planar D5h symmetric molecule.

In the qualitative calculation, the py basis functions were oriented pointing towards the z axis to emphasize the symmetry. I would like to reflect that in the quantitative calculation so I can make a cleaner comparison.

I am using AOMix to print the coefficients from the computational calculation, however at the moment since the basis functions are not oriented as desired, I must do some trigonometry which is rather tedious. I also use the visualization software iqmol to visualize the basis functions, so having them oriented to emphasize symmetry would be useful.

Hi Lucas Valdivia , you could check two things to make a first step towards solving this problem. Essentially your dynamics are too violent leading to the loss in atoms while message-passing.

1. Run an energy minimization on the initial configuration: "min_style cg; minimize 0 0 10000 10000"

2. Your timestep might be too large leading to unable evolution of the dynamics. You probably need a much smaller timestep in case you still have issues after implementing solution 1.

Just a general note, since Michael Rüsing mentioned one of it: The wurtzite structure has hexagonal symmetry, it has the label 2H. Instead, the label 3C refers to the zincblende structure, which is cubic.

Himanshu Sharma Perhaps the inputted file doesn't contain geometry information that Multiwfn can recognize, or the commands you inputted are not in line with required format, or the atom indices you inputted are incorrect. If you cannot find reason of the problem, please send me your input file to my E-mail and show me your inputted commands, I will check.

Scf does keep the atomic positions fixed so it works in your case only if you those are already the minimal energy positions.

Do you care to explain a bit better what you plan to do?

Cheers,

Roberto

Thank you for your answer.

Please note that partial charges are not physical observables, therefore you can always only provide charges within the framework of a certain model. Simple population analyses like Mulliken charges may result in counterintuitive and, frankly spoken, often useless values.

A stronger approach would be the AIM (Atoms in Molecules) approach by Bader, there is an older question on how to do it:

Add this to the dat file....

atom_par Ir 2.84 0.073 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding

Regards

U need to give original value of atom position and then should run refinement ..then atom position canbe modified depending upon the xrd pattern

Hello.

I can help you with your refinement, although I am not using High Score anymore, but I use other programs, and the principle is the same.

Best regards,

Ricardo Tadeu

Hello,

I'm not entirely familiar with the NWChem. It seems that, the program just printed out the components of an effective hyperfine hamiltonian, which is the sum of the isotropic Fermi-type interaction and anisotropic dipolar magnetic interaction. The anisotropic part is described by 3x3 matrix. The "hyperfine coupling constant" usually desribes the isotropic part of the hamiltonian, which is, in your case, probably -0.032739 MHz. The isotropic part does not depend on the coordinate system you have chosen, but anisotropic does.

Marcin

Frederic Vellieux , after defining the receptor and ligand molecule in the analysis and clicking on ligand interactions, you can see the option in middle bottom the program which will open a dialog box upwards (screenshot attached) then you can click on "non-bond" to get the table for the information about the interactions (screenshot # 2). Hope this helps.

Metal single atoms and metal nanoclusters (nanoparticles) play different roles. Metal atoms can be used primarily for surface or bulk doping of a semiconductor photocatalyst. Clusters and metal nanoparticles often act as electrocatalytic sites on the photocatalyst surface. A mixture of them is appropriate if it is necessary to simultaneously increase the concentration of electron donor centers in the band gap of a semiconductor photocatalyst and increase the efficiency of the involvement of photogenerated electrons and holes in surface chemical (electrochemical) reactions.

Dear Essam, with the keyword Pop=Regular,

I assume that the coefficients in the image correspond to the pz atomic orbital.

After the SCF, you'll see for example:

Molecular Orbital Coefficients:

47

O

Eigenvalues -- -0.26085

1 1 C 1S -0.00385

2 2S 0.00419

3 2PX -0.00188

4 2PY -0.00452

5 2PZ -0.44080

In this example, C atom label 1 contributes with 2pz in the molecular orbital labeled 47.

The combination 'GFInput Pop=Reg' allows you to see the orbitals in Chemcraft.

Best, Pablo

it is very easy to make this. Please read my articles. You can find all of them from my RG profile.

Since hydrogen bonds can form within that range and the linearity rule is more or less a guideline, how can one differentiate between a salt-bridge contact and a hydrogen bond (since both interactions are naturally electrostatic) by evaluating a crystal structure?

An auger electron is an electron that is ejected due to the filling of an inner valence shell. This electron is not usually the same one that shifted from an outer orbital to an inner orbital.

Delta ray is the electron that is knocked out of orbit because an alpha particle hit it. A delta ray is generally the same electron that was hit and is hence removed from orbit.

Did you able to solve this problem ?

I got the error also

The unperturbed charge of the unit (-2.000000) is not zero.

[DEBUG ] FATAL: Atom .R<CGLN 91>.A<O2 20> does not have a type.

[DEBUG ] FATAL: Atom .R<CGLN 91>.A<O1 19> does not have a type.

Please help me.

Until an error message is received, you must wait and ignore the diagnostic messages. However, there is a chance that the task will not be solved. The problem is that the use of diffuse functions in the basis set significantly worsens the convergence of the SCF. Therefore, I would recommend that you first carry out calculations in the basis without diffuse functions (6-311G(d, p)), and only then, having a good guess, use it for further calculations (guess=read).

You can append 0 0 0 to the corresponding atomic positions in the input file, see https://lists.quantum-espresso.org/pipermail/users/2006-May/004215.html. This won't have any affect on RAM though, and will only affect the timing insofar as it leads to fewer steps in the optimization.

try add -ignh at the end of code to ignore Hydrogens , tha's work ..

Amanpreet Kaur

Thanks Rana Hamza Shakil...

Hello. Was it possible for you to solve the issue? I have kind of simmilar problem. While trying to upload my prot+lig.pdb file, CHARMM GUI PDB reader detects '-' as invalid character and misses Hydrogens for the protein.

follow the tutorial:

The chemical formula for titanite is CaTi(SiO₄)O. To count the number of atoms of a particular element, you can look at the subscripts in the chemical formula. In titanite, the major element is titanium (Ti). From the chemical formula, you can see that there is one Ti atom present in each formula unit of titanite. For other elements like aluminum (Al) and iron (Fe), you would need to determine their presence in the compound based on its composition or impurities. If the compound contains additional elements like Al or Fe, their presence and quantity can vary depending on the specific sample or variation of titanite. It's worth noting that the chemical composition of natural titanite can vary, and impurities or substitutions of elements can occur, affecting the exact number of atoms of each element present. Analytical techniques such as X-ray diffraction or chemical analysis can help determine the specific composition of a given sample of titanite.

Yes, autodock 4.2 can do it but requires an additional script for such task.

You can consult 10.1007/s11030-022-10523-4 for other software

Hey Trivanni Yadav ,

According to your given information of INCAR, I think everything is fine except few points:

1. You can try with the same smearing for the relaxation and DOS calculation to get consistent results. Here you used Gaussian smearing (ISMEAR=0) for relaxation and ISMEAR=-5 for DOS calculations.

2. Try with the default POTIM tag.

3. Please check the memory for writing the CHGCAR as you are using the systems with 192 atoms. (This may not be a reason but please check this point too.)

Good luck !

Best,

Radhey

``Spaghettification'' doesn't have any size limit-there's no such limit as a ``quantum level size'' in general relativity.

What does exist is a spacetime singularity.

Gravity-where it makes sense-is, always, attractive: A white hole isn't a counterexample, just another manifestation. A spacetime geometry, that looks like a junction between a black hole and a white hole is, in fact, a totally different solution to Einstein's equations and is called a wormhole. It turns out that classical matter can't ``traverse'' it; recently it was discovered that, under certain conditions, quantum matter could:

Dear Pratima Shukla ,

With that kind of calculation, what you are doing is optimizing the excited-state geometry, in particular you are optimizing the first excited state (S1, the root=1 keyword). At the end of that calculation, once you have the optimized structure, you will be able to take the vertical energy difference between the S1 and the ground state as the emission energy.

One important aspect that will reduce the computational cost. TDDFT states do not interact with each other, which basically means that your S1 state will always be the same regardless if you have calculated just that one, or five states, or a hundred... But the lesser amount of states, the lower computing time, so I recommend you to do a minimal adjustment: td=(singlets,nstates=1,root=1). With that, you will only compute the S1 excited state, which is the only one you are interested in (assuming there is no state flipping outside the Franck-Condon region, but for that you will need to optimize other excited states, so let's assume you are not interested in looking for that at this moment).

How much time will it take? Difficult to estimate, but having 74 atoms... be patient, it WILL take time.

Hope you find it helpful

Nothing

if it is single crystal experimental data, then you can calculate energy frame work. if cif file is created by any software then you cant calculate energy framework by crystalexplorer.

According to Wikipedia here is what I found:

The second one has a couple of 3D examples.

I hope it helps.

The rest mass of an electron is 9.1093837015 × 10^(−31) kg, which is only 1/1,836 mass of a proton. An electron is therefore considered nearly massless in comparison with a proton or a neutron.

In table 6 of the article J. Phys. B: At. Mol. Opt. Phys. 33 (2000) 5561–5580, you can find the first and second order corrections to the unperturbed energies as well as the corresponding wave-functions.

O titânio é o quarto metal e o nono elemento mais abundante da crosta terrestre. É um metal de transição do bloco d, reconhecido como um material com alta resistência mecânica (LEE et al., 1999). Tungsten is body-centered cubic (BCC).